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578 protocols using jmp pro 15

1

Comprehensive Chemical and Antioxidant Analysis

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Statistical analysis of the chemical composition and antioxidant measurements was performed by using Microsoft Excel 2013 (Microsoft Inc., Redmond, WA, USA) and JMP pro15 (SAS Institute Inc., Cary, NC, USA). Averages and standard deviation (SD) were calculated in Microsoft Excel. One way analysis of variance (ANOVA) and Tukey’s honest significant difference test were performed in the JMP pro15 software (SAS, Cary, NC, USA) for each sample of each group. For all samples, statistical significance was set to p ˂ 0.05. Principal components analysis (PCA) was performed in JMP pro15 to evaluate the relationship between TPC and antioxidant activity of the extracts where a correlation probability test (Pearson product-moment correlation) was used to determine the correlation between variables.
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2

Microbiome Changes in Silage Ensiling

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The numbers of culturable microorganisms were expressed as log 10 values. Data were analyzed using the Fit Model procedure of JMP Pro 15 (SAS Institute Inc.). Data on fresh forage (5 replicates per treatment) at d 0 were analyzed as a completely randomized design and data on the silages (5 replicates per treatment) from each opening day were analyzed separately as a completely randomized design with a 3-by-2 factorial arrangement of treatments with the main factors being the effect of DM content (LDM, MDM, and HDM) and additive treatment (CTR and INO) and their interaction. If significance was detected for a specific effect or interaction (P ≤ 0.05), Tukey's test (Snedecor and Cochran, 1980) was then performed. Bivariate analysis of aerobic stability by DM content was done on JMP Pro 15 (SAS Institute Inc.) using linear regression.
The output of the distance matrices of the β-diversity analysis were analyzed statistically using permutational multivariate ANOVA (PERMANOVA) and analysis of multivariate homogeneity of group dispersions (PERM-DISP) on Qiime 2 version 2020.6 (Bolyen et al., 2019) (link).
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3

Comparative Transcriptomics Analysis of Fetal Development

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Proportional-area Venn diagrams based on the Euler method [52 (link)] were generated to identify shared and unique DEG between various contrast groups using JMP Pro 15.0.0 (SAS Institute). PCA was used to understand the clustering relationship between fetal groups within tissue using JMP software. Using the individual groups vs CTRL (i.e., UNINF, PLCO-VIA, PLCO-MEC, LVL-VIA, LVL-MEC, HVL-VIA, and HVL-MEC) log2FC results from all 286 genes within tissue was used as input into the PCA with default parameters. The top positively and negatively loaded genes placed onto component 1 and 2 within tissue were plotted to investigate informative expression patterns across fetal groups to reveal factors contributing to the separation of the principle components.
Heatmaps were generated to visualize and identify informative expression patterns using hierarchical clustering with default parameters in JMP Pro 15.0.0 (SAS Institute). Input data was based on the unique and shared pathways in the placenta and thymus in the V + F based on the Venn Diagram result in Fig. 2c. Data on the log2FC of all 286 genes for every contrast group to CTRL were clustered.
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4

Dietary Intervention Taxa Analysis

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Taxonomic comparisons and bar plots visualizing the average relative abundance of classified taxa were generated using JMP Pro 15.0.0 (SAS Institute, 2019). To determine if there were differences in the most prominent phyla (Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria) after dietary intervention, changes in taxonomic counts from baseline were calculated for each diet. Normality was assessed and non-normal variables were log-transformed. Differences were calculated with JMP Pro 15.0.0 (SAS Institute, 2019) using a mixed model with diet as a fixed effect and participant ID considered a random effect. Tukey’s HSD was utilized to correct for multiple comparisons. To identify enriched taxa, linear discriminant analysis effect size was used to compare the change in relative abundance from the initial baseline to post-intervention as well as between diets at post-intervention.
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5

Statistical Analysis of Canine Elbow Outcomes

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Data analyses were performed using JMP Pro 15.0 (SAS Institute Inc., Cary, NC). All continuous parameters were presented as mean ±SD and assessed with a repeated measure ANOVA with a mixed effect model was used with time as the fixed effect and each dog as the random effects with the variance compounds covariance structure within each dose group and within treated or untreated elbow. Kenward-Roger approximation was used to determine the degrees of freedom in the model. A contrast hypothesis was performed at each time point against baseline. Assumptions of these models (linearity, normality of residuals, and homoscedasticity of residuals) and influential data points were assessed by examining standardized residual and quantile plots, and the normality of residual was confirmed with the Shapiro–Wilk test. Ordinal subjective variables at each time point were presented as median (range). Due to small sample size, the data was combined and compared with baseline and untreated elbow using a Wilcoxon signed-rank test. The outcomes of positive response among 3 groups were evaluated with Fisher’s exact test. Significance was set at P <0.05.
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6

Hospital Revisits and Risk Factors

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We compared demographic and clinical characteristics of index hospitalizations that resulted in a 30-day revisit to those that did not result in a 30-day revisit, as well as between preventable and nonpreventable revisits. We used the Fisher's exact test to compare dichotomous variables, the chi-square test for multicategory variables, and the Wilcoxon rank sum test for continuous variables, as not all data were normally distributed. For all analyses, statistical significance was set at p < 0.05. JMP Pro 15.0 was used for statistical analysis (SAS Institute Inc., Cary, North Carolina).
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7

Factors Influencing Afatinib Response

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Associations between clinical characteristics and the treatment response to afatinib were analyzed using Fisher's exact test or the chi-square test. Survival analysis was performed using Kaplan–Meier estimation to assess differences between the groups. Statistical significance was set at P ≤ 0.05. All statistical analyses were performed using JMP Pro 15.0 (SAS Institute Inc.).
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8

Statistical Analyses of Biological Data

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Statistical analyses were performed using Student's t‐test, the chi‐square test, or Fisher's exact test for categorical data, and the Mann–Whitney U‐test for nonparametric data. Correlations were assessed by calculating the Pearson's correlation coefficient. p < 0.05 was considered statistically significant. Patient survival was examined with the Kaplan–Meier method, and the log‐rank test was used to determine significance. Data are shown as the mean ± SD of the indicated number of experiments. Statistical analyses were performed using JMP Pro 15.0 (SAS Institute Inc.).
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9

Multivariate Analysis of Cognitive-Neural Relationships

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JMP Pro 15.0 (SAS) was used to process participant behavioral data. To reduce the dimensionality of our statistical model and address collinearity among model predictors (i.e., mitigate the effect of reduced statistical significance due to collinearity between skill retention and visuospatial test scores), principal component analysis (PC) was used to create a ‘composite score’ that represented the shared variance of skill retention and Delayed Recall score for each participant. Since our previous work has shown a relationship between these two variables [11 (link), 28 (link)], the PC analysis allowed for consideration of only the shared variance between them as an independent variable. Only PCs with an eigenvalue greater than one were carried forward in subsequent analyses.
Using MATLAB 2020 (MathWorks, Inc.), significant PCs and age (a covariate of noninterest) were entered into a general linear model that was applied at each voxel for each diffusion map and an FDR-correction was applied to account for multiple statistical tests. Clusters were defined as at least 100 contiguous voxels where the FDR corrected p-value was < 0.01; clusters were transformed from template space to MNI using antsApplyTransforms (ANTs) and the Johns Hopkins University JHU atlas [38 (link), 39 (link)] was used to identify the neuroanatomical location of each cluster.
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10

Determinants of Significant Tricuspid Regurgitation

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Continuous data (variables) were expressed as mean ± standard deviation (SD) or median (interquartile range). Categorical variables were presented as number of patients (percentage). Differences between patients with and without significant TR were compared with Student’s t-test or the Wilcoxon rank-sum test as appropriate. For categorical variables, Pearson’s chi-square test was performed. Univariable and multivariable logistic regression analyses were used to identify the determinants of significant TR, and odds ratios (ORs) along with 95% confidence intervals (CI) reported. Those with a p-value < 0.05 on univariable analysis were selected as independent variables for multivariable analysis. To clarify the best indexation of TV parameters for significant atrial FTR, receiver operating characteristic (ROC) curves were constructed to evaluate and compare the area under the curve (AUC). Two-sided p-values < 0.05 were considered to indicate statistical significance. JMP Pro 15.0 (SAS Institute, NC, USA) was used for all statistical analyses.
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