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58 protocols using origin 2015

1

Sensory Transduction Biophysical Analysis

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Data were analyzed with Clampfit and ORIGIN 2015 (OriginLab) and are
presented as means ± SEM as noted in the text and figure legends. Number
(n) of hair cells recorded is indicated for each mean value
given in the text and figures legends. Number of mice used is indicated in the
figures legends. One-way analysis of variance (ANOVA) or Student’s t test
was used to compare biophysical properties of sensory transduction currents
using the statistical function in ORIGIN 2015 (OriginLab). Statistical
significance is indicated as p values.
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2

Collision-Induced Unfolding of PvDBP-Antibody Complex

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PvDBP Region II and monoclonal antibodies were purified as described [29 (link)] and buffer exchanged into PBS. Stock antigen and antibodies solutions in PBS buffer were exchanged into 200 mM ammonium acetate solution (pH = 6.5–7). Before each experiment, the antigen and antibody were mixed and diluted to 5 μM and 6 μM, respectively. The sample solution was incubated at 25 ºC for 30 min before MS analysis.
Samples were analyzed using a quadrupole ion-mobility time-of-flight mass spectrometer (Synapt G2 HDMS, Waters, Milford, MA). Protein and complex ions were generated in a nESI source in the positive-ion mode. The source parameters were optimized to provide gentle ESI conditions. The traveling-wave IM separator was operated at a N2 pressure of ~1.5 mbar; the IMS wave velocity was 650 m/s; and the IMS wave height 40 V. The ToF-MS was operated over a m/z range of 100–15,000. For a CIU experiment, the trap-collision voltage applied to the ions in the traveling-wave-based ion trap situated prior to the IM separator was increased from 10 to 200 V in 10 V increments, and ion-mobility mass spectra were acquired at each increment.
Mass spectra were processed with Masslynx V4.1 software (Waters). Arrival time distributions at each collision voltage were extracted in the Drift Scope (Waters) and plotted as a 2D contour plot using Origin 2015 (OriginLab, Northampton, MA).
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3

Non-parametric Statistical Analysis of Data

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Curve fitting and statistical analysis were performed using GraphPad Prism v7.05 (GraphPad Software, San Diego, CA). Data were tested with a D’Agostino and Pearson normality test. Since at least one experimental group in each condition significantly deviated from a Gaussian distribution, we chose non-parametric tests for statistical analysis. We selected a Mann-Whitney test for unpaired comparisons between two groups; whereas a Kruskal-Wallis test with a Dunn’s post hoc test was used for multiple comparisons. For comparing paired data in more than two conditions, we selected a Friedman test with a Dunn’s post hoc test for multiple comparisons. No power analysis was conducted a priori. Graphics were constructed using Origin 2015 (OriginLab, Northampton, MA). Descriptive statistics are specified in the figure legends.
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4

Cadmium Exposure Effects Analysis

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Tests for normality and two- and three-way ANOVA were performed in SIGMAPLOT 12 (Systat Software Inc., San Jose, CA, USA) at a significance level of P<0.05 for Cd concentration and weeks of exposure for the w5 and w10 measured data, and Cd concentration, tissue, and individual experiment for the data obtained from the harvested material. In the case of significant effects, the Holm–Sidak method was used for an all-pairwise post-hoc multiple comparison. Tests for linear trends were done as linear regression in Origin 2015 (OriginLab Corporation, Northampton, MA, USA). The probability that the slope is zero is given as ‘Prob>F’ and Pearsson’s correlation coefficient as R2.
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5

Optogenetic Modulation of Neural Circuits

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All statistical tests were run in “Origin 2015” (Origin Lab). The individual tests we used are given in the figure legends and the details are supplied in Supplementary Table 1. All data are given as mean ± SEM unless otherwise stated in the figure legends. No statistical methods were used to pre-determine sample sizes but our sample sizes are similar to those reported in previous publications21 (link),44 (link). The data met the assumptions of the statistical tests used. Before using any given statistical test we formally tested for normality and equal variances. When we found the data were non-normal we used non-parametric tests (details in the relevant figure legends and in in Supplementary Table 1). All t-tests were two-sided.
We excluded mice where it was subsequently found that the placement of the opto-fibers was misplaced or that there was no AAV transgene expression or when this expression was in the wrong place. Mice were assigned randomly to the experimental and control groups. When possible, experimental treatments were also randomized. When mice were given drugs verses saline, for example, they received the drug or saline in random order. All experimental data analysis was blinded, including cFOS counting, the analysis of EEG data and animal behaviour that was scored from videos.
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6

Prognostic Value of Circulating Tumor Cells

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Overall survival (OS) and progression-free survival (PFS) were chosen as the endpoints to evaluate the prognostic value of CTC counts. The survival time was estimated using the Kaplan-Meier method, and the difference in survival between groups was assessed using a log-rank test. The SPSS 22.0 for Windows software was used for statistical analyses. To confirm the correlation between the CTC count change ratio; where CTCi is the CTC count at time point i and CTC0 is the baseline CTC count and imaging response results, a two-tailed Student's t-test with a 95% confidence interval was performed using Origin 2015 (OriginLab Corp.). P-values < 0.05 were considered statistically significant.
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7

Statistical Analysis of Experimental Data

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Statistical Analysis was performed using Origin 2015 (OriginLab, Northampton, MA, USA). Significance analysis was determined using two-sample t-test including a check of standard distribution. If the sample showed no standard distribution, the Mann–Whitney U test was used.
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8

Contractile Myocyte Mechanics Analysis

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Results are expressed as mean ± SEM values, n denotes the number of myocytes or multicellular preparations studied. Statistical significance of differences was evaluated using one-way ANOVA followed by Student's t-test for paired or unpaired data as pertinent. Differences were considered significant when p was less than 0.05. Data were processed, analyzed and figures were created in Excel (Microsoft Corp., Redmond, WA, USA), and Origin 2015 (Originlab Corp., Northampton, MA, USA).
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9

Image Processing and Data Visualization

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The gray scale images were processed and analyzed using ImageJ (NIH) and MATLAB (Mathworks). The plots were prepared using Origin 2015 (OriginLab Corp) and Datagraph 4.0 (Visual Data Tools, Inc.).
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10

Comprehensive Data Analysis Workflow

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Flow cytometry data were analysed in FlowJo (versions 9 and 10; FlowJo) and Prism (version 7; GraphPad). Structural figures were generated in PyMOL (version 2.0.7; Schrodinger). For SPR and ITC, data were analysed in BIAevaluation (GE Healthcare) and Origin 2015 (OriginLab).
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