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22 protocols using originpro version 9

1

Phospholipid Monolayer Compression Isotherms

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The phospholipid mono-layer was compressed from 2 sides with a total speed of 10 mm/min (5 mm/min from opposite sides, Figure 2A) using a Kibron pTroughXS equipped with a Teflon ribbon (polytetrafluoroethylene, hydrophobic barrier). The temperature was maintained at 25 °C using an external water bath. The surface tension of the subphase during each compression was monitored using a wire probe as a Wilhemy plate. The surface pressure was calculated from the surface tension using equation 1 where π is the surface pressure, y0 is the surface tension of water (72.8 mN/m), and γ is the surface tension at a given area per phospholipid after the film has been applied.
Each compression isotherm experiment consisted of at least 3 replicates and the averages with standard deviations of the area per phospholipid at every 5 mN/m was calculated using Microsoft Excel. The worked-up data were transferred to OriginPro Version 9.1 to be graphed. From the averages of the compression isotherms, the percent difference from the control of each sample at 5mN/m, 30 mN/m, and 35 mN/m were calculated. The compression moduli were calculated using OriginPro Version 9.1 from the compression isotherm average results using equation 2, where Cs1 is the compression modulus, A is the surface area, and π is the surface pressure.
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2

Quantification of Extracellular Hsp70 in Plasma

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Blood samples were collected by venepuncture of a large antecubital vein after overnight fasting from 7 a.m. to 9 a.m. into tubes with anticoagulant tripotassium ethylenediaminetetraacetic acid (K3 EDTA) (Greiner Bio-One, GmbH, Kremsmünster, Austria). After centrifugation at 1000× g for 15 min at 4 °C, plasma was separated and stored at -80 °C until eHsp70 determination. The AMP'D HSP70 high-sensitivity ELISA kit (Enzo Life Science, Farmingdale, NY, USA) was used for the eHsp70 concentration measurement, and the manufacturer's protocol was followed. As recommended, EDTA plasma samples were minimally diluted in a 1:4 ratio with assay buffer to remove matrix interference. The concentration of eHsp70 was determined at 495 nm using the SpectraMax i3x multi-mode microplate reader (Molecular Devices, San Jose, CA, USA). The eHsp70 concentration in the samples was calculated using a fourparameter logistic curve fit in OriginPro version 9.0 software (OriginLab Corporation, Northampton, MA, USA).
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3

Quantitative IL-1β ELISA Assay

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IL-1β concentrations were measured in EDTA plasma using the Quantikine HS ELISA human IL-1β/IL-1F2 immunoassay (R&D Systems, Minneapolis, MN, USA), according to the manufacturer's protocol. The concentration of IL-1β was measured at 450 nm using the SpectraMax i3x multi-mode microplate reader (Molecular Devices, San Jose, CA, USA). IL-1β concentration was calculated by a four-parameter logistic curve fit in OriginPro version 9.0 software (OriginLab Corporation, Northampton, MA, USA).
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4

Microplastics Abundance Analysis in Environmental Samples

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The statistical analyses were performed using OriginPro version 9.1 software (Origin Lab Corp., Northampton, MA, USA) and R Software (R development team, Version 1.4.1). The abundance of microplastics was evaluated using Kruskal–Wallis (post hoc: Bonferonni correction) subjected to a non-parametric dataset for various types and colors between the station and period of the study. The significance level was set at p < 0.05. The results obtained are presented in the form of a dendrogram graph, with 3 clusters of color following the number of the collected color sample within the sampling time. Box plot analysis was used to compare the shape distribution of the samples.
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5

Brain Activity Changes in Pyramidotomy

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A group-level linear mixed-effect model was performed with the 3dLME program in AFNI to evaluate the differences between baseline (PL−1), PL4, and PL7 images for the sham-operated and pyramidotomy groups. Statistical maps were corrected and thresholded at the significance level (p < 0.001, FDR q < 0.05), and then overlaid on the MRI template to show the areas with significant changes in brain activity.
Data analyses were performed with statistical analysis software (OriginPro version 9.1, OriginLab, Northampton, MA, USA). Behavioral data were analyzed with a one-way analysis of variance on the effect of groups and times (p < 0.05, Bonferroni corrected for multiple comparisons). All data are represented as the mean ± standard error of the mean (SEM). p values < 0.05 were considered significant.
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6

Mass Spectrometry Data Processing and Analysis Protocol

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An R-based in-house software tool, IsoMS [14 (link)], was used to process the raw data generated from the multiple LC-MS runs. A zero-fill program [15 (link)] was used to replace a few intensity values that were missing in the LC-MS runs due to low MS sensitivity. Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were used for multivariate statistical analyses. Volcano plots were prepared using OriginPro version 9.1 (OriginLab, Wellesley Hills, MA, USA). Hierarchical clustering and heat map generation were performed using R version 3.1 (http://www.r-project.org). The metabolites were identified based on retention time and accurate mass matching to a dansyl standard library or accurate mass matching to the human metabolome database (HMDB). The MyCompoundID program (http://www.mycompoundid.org) was used to search for accurate mass matches within the HMDB. The mass accuracy tolerance window was set at 10 ppm for the database search. Metabolite set enrichment analysis and pathway analysis were based on MetaboAnalyst (http://www.metaboanalyst.ca). The Homo sapiens pathway library was used. Cytoscape 3.4.0 on MetScape (http://www.cytoscape.org) was used for large-scale network analysis and the visualization of the integrated metabolism pathways [16 (link)].
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7

Comparative Data Analysis Methods

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Data are expressed as mean ± SEM. Statistical data analyses were performed using Origin Pro Version 9.1 (Origin Lab Corp., Northampton, USA). All data came from at least three replicates of the experiment. The data between the two groups were analyzed by t‐test. The data among multiple groups were compared by Turkey‐Kramer post hoc descriptive test and one‐way analysis of variance. A p‐value less than .05 was considered statistically significant (p < .05).
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8

Comparative Statistical Analysis of Protein Sequences

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For comparisons between two groups, the Mann–Whitney test was performed to determine whether differences between groups were significant. A p value of less than 0.05 was considered statistically significant. To estimate the relationship between two dependent variables, simple linear regression analysis was performed. OriginPro, version 9.1 (OriginLab Corp. Northampton, MA, USA) was used for these analyses. We eliminated TK-III-57 for these analyses because its length is three amino acids shorter than others.
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9

Spectroscopic Analysis of DeltaNaR Cation Binding

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UV–Vis spectra were recorded using a Varian CARY 4000 spectrophotometer equipped with an integrating sphere. Changes in the UV–Vis spectrum of DeNaR upon addition of K+, Na+, NMG+, or Mg2+ to cation-free samples were monitored from 300 to 850 nm. Flash-induced absorption changes in samples containing spin-labeled single- and double-cysteine mutant DeNaR to be used for the EPR measurements were acquired with a laboratory-constructed cross-beam laser flash photolysis system as described previously24 (link) but with a GaGe Octopus digitizer board (model CS8327, DynamicSignals LLC, Lockport, IL) at a sampling rate of up to 40 ns/point. All comparative UV–Vis and flash photolysis data were collected from the same initial batch of salt-free protein with cations added prior to data collection to avoid sample variation. Data analysis was performed with OriginPro version 9.1 (OriginLab, Northampton, MA).
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10

Parametric Statistical Analysis Protocol

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Statistical analyses were conducted using Originpro version 9.1 (OriginLab). All of the results conformed to a normal distribution and are expressed as the mean ± SEM. The t-test was used to compare two groups. P<0.05 was considered to indicate a statistically significant difference.
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