SPSS (IBM Corp. version 25.0) and PAST 3 [36 ] software packages were used for descriptive and inferential statistics. Group differences between continuous variables were tested using the Mann–Whitney U test, and categorical variables were tested using the chi-squared test. All tests were two-sided, and correction for multiple comparisons was conducted using the Benjamini–Hochberg false discovery rate (FDR). p-values were considered significant at FDR <0.05. Orthogonal partial least square discriminant analysis (OPLS-DA) (SIMCA 15; Sartorius Stedim Data Analytics AB, Malmö, Sweden) was used to search for differences in oral microbiota between the cases and controls. Clustering of subjects by bacterial taxa in the saliva microbiota was performed by agglomerative hierarchical cluster analysis using Ward’s method, and the linear discriminant analysis (LDA) effect size (LEfSe) method was used for high-dimensional class comparisons [37 (link)]. Potential molecular functions of the saliva microbiota were predicted using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) plugin for QIIME2 and converted to functions via the Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology database (https://www.genome.jp/kegg/ko , accessed 1 September 2020) [38 (link)].
Past 3
Manufactured by IBM
Sourced in United States
The PAST 3 is a laboratory equipment product designed for general scientific applications. It functions as a programmable automated sample treatment device, capable of performing various sample preparation tasks. The core purpose of the PAST 3 is to automate and streamline sample handling processes in a controlled and consistent manner.
Automatically generated - may contain errors
Lab products found in correlation
3 protocols using past 3
1
Comparative Analysis of Oral Microbiome
2
Bacterial Diversity Analysis in IBS
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Diversity measures and statistics of the bacterial populations were analyzed using R, PAST3, and SPSS 26.0 (IBM Corporation, Armonk, NY, USA). All data are presented as mean ± SD. Alpha-diversities of bacterial compositions, as indicated by Shannon indices, were estimated using PAST. The fecal amplicon sequencing analysis was performed using taxa detected in 50% of the subjects. Data were analyzed using the unpaired t-test/Mann–Whitney U-test for comparison between HC and IBS patients due to normal/non-normal distributions of some/other variables. Wilcoxon signed-rank test was applied for changes from IBS-n to IBS-s. The significance level threshold was set as P < 0.05. Graphs were plotted using the R ggplot2 package.
3
Agreement between PSG and ACT Sleep Stages
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In order to determine the degree of agreement between the two recording techniques (PSG and ACT, where Wake was considered equivalent to Active, and non-REM sleep plus REM sleep was considered equivalent to Inactive) we used Cohen’s Kappa (κ), the variable of interest is categorical, which is a statistical method designed to take into account chance agreement (Watson and Petrie, 2010 (link)). When Cohen’s kappa equals 1, there is complete agreement between the two techniques, while a kappa value equal to zero suggests that the agreement is no better than that which would be obtained by chance alone (Watson and Petrie, 2010 (link)). According to Watson and Petrie (2010) (link) (adapted from Landis and Koch, 1977 (link)) there is no formal scale for Cohen’s kappa, but suggest the following levels of agreement: Poor if κ < 0.00, Slight if 0.00 ≤ κ ≤ 0.20, Fair if 0.21 ≤ κ ≤ 0.40, Moderate if 0.41 ≤ κ ≤ 0.60, Substantial if 0.61 ≤ κ ≤ 0.80 and Almost perfect if κ > 0.80. All statistical analyses, where possible, were conducted using IBM SPSS Statistics software version 23 and PAST 3 (Hammer et al., 2001 ).
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