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1

Longitudinal Brain Function Changes in Abstinence

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Statistical analysis was performed using SPSS 24.0 (SPSS, Inc, Chicago, IL, USA) and MATLAB, and the threshold of significance was P < 0.05.
The statistical analysis process for the short‐term and long‐term abstinent groups was as follows: normally distributed data were expressed as the mean ± standard deviation. Significant differences in BIS‐11 data, ALFF values, and ReHo values between the short‐term and long‐term abstinent groups were evaluated using the paired sample t‐test based on SPSS and MATLAB code, respectively, and the ALFF and ReHo results were corrected for multiple comparisons by false discovery rate (FDR) correction.
The statistical analysis process of the three groups that experienced long‐term abstinence was as follows: sex, smoking, and drinking using chi‐square tests. Afterward, one‐way ANOVA was used to calculate the demographic characteristics and statistical differences in the brain region of ALFF and ReHo from paired sample t‐tests.
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2

Statistical Analysis in Biological Research

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The Mann-Whitney U-test or Wilcoxon signed-rank test was used to evaluate differences between unpaired or paired data from two groups, respectively. When data from three groups were compared, Tukey-Kramer test was used as a post hoc test after ANOVA. The correlation coefficients and the P values were calculated using Spearman rank correlation test. When the difference between two slopes was evaluated, the slope test was performed. The χ2 test was used to evaluate the difference between two percentages. These tests were performed using SPSS (IBM, Tokyo, Japan) or MATLAB software. All of the data in the text and graphs are presented as means ± SE.
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3

Multivariate Statistical Analyses of Photometry and Behavior

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Photometry recordings and behavioral experiments were statistically analyzed using MATLAB and SPSS version 24 (IBM, USA). Normality and equal variances were formally tested. Two-sample comparisons were performed by two-sided unpaired t test or two-way repeated-measures ANOVA followed by post hoc Bonferroni correction. If the data were not normally distributed, we performed with the nonparametric two-sided Wilcoxon signed-rank test. Multiple group comparisons were performed by Mann–Whitney U-test and the significance was set at a familywise false discovery rate (FDR) adjusted p value of 0.05. k-means clustering was done using the MATLAB function kmeans. Data distribution was analyzed by Spearman’s rank correlation test. Sample sizes were not predetermined, but our sample sizes are similar to (n animals) or higher than (n traces) those generally employed in the field [20 (link), 35 (link)]. All tests used are specified in the supplementary table.
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4

Multivariate Analysis of Biological Data

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Data is presented as mean ± SD. Statistical analysis was performed in SPSS Statistics (IBM version 23) and MATLAB. Group comparison was done using the Kruskal-Wallis H test, with post-hoc pairwise comparison of statistically significant results using Dunn's procedure with a Bonferroni correction for multiple comparisons. Correlation was done using Spearman Rank Correlation as the test for normality was not fulfilled. Statistical significance was set at 95%.
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5

Optimizing Soil Hydraulic Properties with γ-PGA

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The data are processed by MS Excel, Origin 8.0, MATLAB, and IBM SPSS 25.0. Multiple comparisons are performed with the LSD method. The equations of retention curves of the γ-PGA-treated soil are fitted by RETC code. Both the retention curves and the measured amount of cumulative infiltration are entered into the HYDRUS-1D model. The inversed solution in HYDRUS-1D and the Levenberg–Marquardt optimization method are used to optimize the soil hydraulic parameters. The corresponding soil hydraulic parameters of the soil mixed with different γ-PGA content are presented in Table 3. The objective function is defined as the sum of squared residuals (SSQ). The correspondence between simulated and observed data are evaluated by correlation coefficient (R2) at p = 0.05, and the root mean square error (RMSE).
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6

Data Analysis and Visualization Techniques

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Data analysis was conducted using Matlab and SPSS (IBM Corporation). Data visualisation was done using Python using Jupyter notebooks in conjunction with a number of libraries including numpy, scipy, matplotlib, seaborn, and pandas.
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7

Statistical Analysis of miRNA in NEN

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Statistical analyses of clinical parameters were performed using SPSS Statistics (IBM, Armonk, NY, USA, version 25) and MATLAB. Differences in miRNA content and normalized miRNA expression were evaluated between NEN and non-NEN samples, and within NEN pathological types using the non-parametric Kruskal–Wallis (K–W) test (21 ); a two-sided P-value of <0.05 was considered significant. Similarities in miRNA expression between samples were determined using Spearman’s correlation (22 ).
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8

Stay-Switch Analysis of Two-Step Task Behavior

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The one-trial-back stay-switch analysis is the most widely used method for characterizing behavior on the two-step task (Daw et al., 2011 (link); Akam, Costa, & Dayan, 2015 (link); Wunderlich et al., 2012 (link)). This method quantifies the tendency of a participant to repeat the choice made on the last trial or switch to the other choice, as a function of the outcome and transition on the previous trial. We considered four possible outcomes: Common-Rewarded (CR), Rare-Rewarded (RR), Common-Unrewarded (CU), and Rare-Unrewarded (RU). Model-based and model-free indices were computed from the stay probabilities following each outcome according to:
MF=(P(stay|CR)+P(stay|RR))(P(stay|CU)+P(stay|RU)), MB=(P(stay|CR)+P(stay|RU))(P(stay|CU)+P(stay|RR)).
We also examined whether hunger modulated other measures of simple reinforcement learning. We found no effect of hunger on changes in model-free control for second-stage choices or for action-specific, stimulus-irrelevant choices at the first-stage (Fig. S1).
Statistical analyses were implemented in MATLAB and SPSS (IBM Corp. Released 2019. IBM SPSS statistics for Windows, Version 26.0. Armonk, NY: IBM Corp.). We report the effect size with Cohen’s d and ηp2 and report the 95% confidence interval (CI) of the difference between groups.
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9

Evaluating Anesthesia Depth Monitoring

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Statistical analysis was performed using SPSS (IBM v22, North Castle, NY, USA) and MATLAB. To evaluate the ANN effect, the performance of the original SDI was compared with the one random ANN regression–derived SDI. The Pearson correlation coefficient, mean absolute error (MAE), and area under the curve (AUC) for the EACL were computed and considered the gold standard. The receiver operating characteristic (ROC) curve was calculated to obtain the AUC, which is often used in medical fields during diagnosis of disease. The binary threshold used to distinguish between anaesthesia and consciousness was set to 65 (Johansen & Sebel, 2000 ). The parametric paired Student’s t-test was then used to assess the statistical significance. To prove the capability of the EANN-derived SDI to measure DoA, its relationship with EACL was analysed. Furthermore, the commonly used BIS was used as a reference. The same significance test was also undertaken between the two indices, thus demonstrating a solid and convincing result.
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10

Measuring Corneal Topography Reproducibility

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The distribution of differences in the agreement and reproducibility experiments followed a normal distribution with the presence of some outliers. The outliers were not removed from the sample to remark these particular cases that are outside the limits of agreement (LoAs) and that are critical for computing the PCS. The agreement between manual and automated methods for measuring WTW with the Orbscan and Keratograph systems was represented by the mean differences with their corresponding LoAs (1.96 × standard deviation).[12 (link)] The reproducibility (SR) was calculated with one-way analysis of variance (ANOVA) and the reproducibility limit (R) was equal to .[13 (link)] The sample size used was considered enough to achieve 10% of confidence in the estimate as it has been previously reported.[13 (link)] The statistical analyses were performed using the SigmaPlot™ software (version 12, Systat Software, Inc.), Matlab, and IBM SPSS 20.0 for Windows (SPSS, Chicago, IL).
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