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1

Microbial Diversity and Antimicrobial Resistance

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The difference in relative abundance among the top 30 genera was assessed using STAMP software v2.1.3. The physicochemical properties, TC content and alpha diversity indices were analyzed by performing a one-way ANOVA followed by Duncan’s multiple-range test using SPSS 21.0 software (IBM Co., Armonk, NY, United States). Correlation analysis among bacterial populations, physicochemical properties, and ARGs was also performed with the Spearman method using SPSS 21.0 software (IBM Co., Armonk, NY, United States).
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2

Statistical Analysis of Experimental Data

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The data of the present study were analyzed using the SPSS 21.0 software (IBM, Armonk, NY, USA). Statistical analysis was performed using the SPSS 21.0 software (IBM, Armonk, NY, USA). The data were analyzed with Mann Whitney U, Wilcoxon signed-rank test, paired t-test, and Independent-T test. The testing was performed at α = 0.05.
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3

HCV Genotype Analysis and Viral Load Assessment

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The data were analyzed using IBM SPSS 21.0 software (IBM Corp., Armonk, NY) and presented as mean ± standard error of the mean, unless otherwise stated. The HCV prevalence rate and significant differences between HCV genotypes were performed using IBM SPSS 21.0 based on a chi-squared or Fisher exact test with Crosstabs in IBM SPSS. One-way analysis of variance and the least significant difference were used to analyze all experimental data of HCV viral load. Differences between the means of 2 groups were analyzed using an independent samples Student t test. P < .05 was considered to indicate a statistically significant difference.
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4

Yak Calf Rumen Microbiome Analysis

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All the data (except the sequencing data of experiment 2) were statistically analyzed using ANOVA followed with Duncan's multiple comparison test using SPSS 21.0 (IBM Corp., Armonk, NY). Correlation was assessed using Spearman's correlation test in SPSS 21.0. Difference was considered to be statistically significant at P < 0.05.
For the RNA sequencing data of experiment 2, based on negative binomial distribution, DEG were identified based on the expected read counts from RSEM by using DESeq with an adjusted P < 0.05 and fold change >2 or <0.5 (Li and Dewey, 2011) (link). For 16S rRNA gene sequencing data, α diversity measurements were analyzed using ANOVA in SPSS 21.0 (IBM Corp., Armonk, NY). The principal coordinates analysis was further assessed using analysis of similarities to compare the rumen microbiota among the treatment groups. The linear discriminant analysis effect size analysis (Paulson et al., 2013) (link) was performed to estimate the effect size of species that contributed to the differences between the treatments. The threshold of the linear discriminant analysis score was set at a default value of 2.0. The correlation between the identified genera and significantly altered performance of yak calves was assessed using Spearman's rank correlation coefficient.
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5

Comparative Analysis of Microbial Communities

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The difference of top 30 genera between two groups was assessed using the STAMP software v2.1.3. The student t test was conducted to compare the growth properties, physicochemical properties, and alpha diversity indices between two groups using the software SPSS 21.0 (IBM Co., Armonk, NY, USA). Correlation analysis between physicochemical properties and bacterial populations were also analyzed with the Spearman method using the software SPSS 21.0 (IBM Co., Armonk, NY, USA). The principal coordinate analysis (pCoA) and the dissimilarity tests (MRPP, Adonis, and ANOSIM) were used to demonstrate the bacterial community differences among the five groups (Anderson 2010 (link); Caporaso et al. 2010 (link)). Canonical correspondence analysis (CCA) was used to measure the correlation between the bacterial community and different environmental factors. FAPROTAX was used to establish Functional Annotation of Prokaryotic Taxa (Louca et al. 2016 (link)).
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6

IBS Neuroendocrine Response to Distention

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The sample size in this study was calculated based on the sample size determination theory of statistics. Sample size was calculated using an effect size of 0.75, beta value of 0.2, and alpha value of 0.05. Demographic data were analyzed using SPSS 21.0 (IBM Corporation; Armonk, NY, USA). All data are presented as mean ± SD. The significance level threshold was set to P < 0.05. The data were analyzed using the non-parametric Student’s t-test and the Spearman rank correlation coefficient to account for non-normal distributions of some variables. An overall generalized estimating equation (GEE) analysis [29 (link)] (SPSS 21.0, IBM Corp.) was performed during the random distention. The fixed main effects included those of group (IBS or HC), drug (CRH or saline), condition (no distention, 20 mmHg distention, or 40 mmHg distention), and sex (female or male), as well as their potential interactions with the dependent variables of interest. Network analyses within the neuroendocrine system were conducted using structural equation modeling in Amos 22.0 (IBM Corp.). The strengths of relationships between two factors are indicated as standardized beta weights using an arrow path. A satisfactory model usually has a comparative fit index ≥ 0.95 and a root mean square error of approximation < 0.05. The significance level threshold was set to P < .0125.
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7

Mating Effects on Reproductive Traits

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The raw data for copulation duration, number of eggs, and longevity of the F0, F1, and F2 generation individuals were analyzed using SPSS 21 (SPSS 21.0, IBM). All data were tested for normality using the Kolmogorov–Smirnov test and met the assumption of ANOVA. The number of eggs’ data was transformed into a logarithmic transformation to approximate a normal distribution. The number of eggs and longevity were subsequently analyzed by one‐way analysis of variance (ANOVA) followed by Tukey's HSD test (p < .05). The distribution of the copulation duration data was skewed and was analyzed by nonparametric Kruskal–Wallis analysis of variance. All data are presented as the mean ± standard error (SE). Survival curve analysis was evaluated by log‐rank test for the different mating treatments. The parameters of intrinsic rates of increase, finite rate of increase, net reproductive rates, and mean generation time were calculated using the bootstrap method included in the computer program TIMING–MSChart (Chi, 2020 ). Because bootstrap analysis uses random resampling, a small number of replications will generate variable means and standard errors. To generate fewer variable results, 100,000 replications were used in this study.
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8

Statistical Analysis of circRNA Profiles

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Statistical analysis was performed with SPSS 21.0 (IBM, Inc., USA). First, adjustment to normal distribution was tested for all continuous variables as per one-sample Kolgomorov-Smirnov test and the normal quantil-quantil (QQ) plots. Data represents the mean ± standard deviation (SD) or the median (interquartile range). In the discovery cohort, univariate analysis of demographic and clinical characteristics was performed by ANOVA or Kruskall-Wallis test along with Chi square test. In the validation cohort, univariate analysis of demographic and clinical characteristics was performed by Student t-test or U Mann–Whitney test along with Chi square test. circRNA expression differences between two groups was estimated by Mann–Whitney U test. For all the comparisons, significance level was set at p-value < 0.05. SPSS 21.0 (IBM, Inc., USA) was used to draw graphs.
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9

COVID-19 Transmission Simulation and Analysis

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The imported cases were simulated as transmission sources and the secondary cases were employed for the curve fitting. Berkeley Madonna 8.3.18 (developed by Robert Macey and George Oster of the University of California at Berkeley. Copyright ©1993–2001 Robert I. Macey & George F. Oster, CA, USA) was employed to perform the procedures of curve fitting and the simulation. The simulation methods (Runge–Kutta method of order four with tolerance set at 0.001) were the same as the previously published researches11 (link),12 (link),14 (link)–16 (link),18 (link). The goodness of fit was judged by Chi-square (χ2) value calculated by SPSS 21.0 (IBM Corp, Armonk, NY, USA). Epidemiological characteristics analysis was also performed by SPSS 21.0 (IBM Corp, Armonk, NY, USA). Differences in epidemiological characteristics of COVID-19 were analyzed by two side way tests.
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10

Dietary Iron Optimization for Ducks

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All data were analyzed using one-way analysis of variance (ANOVA) and protected Least Significant Difference Test (SPSS 21.0, IBM Corp., Armonk, NY, USA). Data were expressed as the mean, with P < 0.05 considered statistically significant. Estimation of maximum responses to additive dietary iron was done using a quadratic polynomial (QP) regression model for ducks of different ages according to Taschetto et al. (2017) (link). The QP model (Y=β1+β2×Fe+β3×(Fe)2) had Y as the dependent variable as a function of dietary level of iron, β1 as the intercept, β2 as the linear coefficient and β3 as the quadratic coefficient. The maximum response to iron was defined as Iron=β2/2β3 . 120 mg/kg as Fe-Gly group and 120 mg/kg as FeSO4 group were subjected to analysis by T-test. R software was used to perform Metastat analysis to determine the differences in the relative abundance of fecal microbiomes. Pearson correlation analysis (SPSS 21.0, IBM Corp., Armonk, NY, USA) was used to analyze the strength and significance of relationships between cecal microbiota and the tested trait (White et al., 2009 ).
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