Additional file 2 of Neural network-based prognostic predictive tool for gastric cardiac cancer: the worldwide retrospective study

Additional file 2: Supplement File 1. The Neural network-based prognostic predictive tool for GCC patients

Additional file 4 of Neural network-based prognostic predictive tool for gastric cardiac cancer: the worldwide retrospective study

Additional file 4: Supplement Table 1. The mean and standard deviation of numerical clinical features in train cohort

Additional file 3 of Neural network-based prognostic predictive tool for gastric cardiac cancer: the worldwide retrospective study

Additional file 3: Supplement File 2. The raw data of this study

Additional file 5 of Neural network-based prognostic predictive tool for gastric cardiac cancer: the worldwide retrospective study

Additional file 5: Supplement Table 2. The models’ performance of previous research in overall survival

Additional file 1 of Neural network-based prognostic predictive tool for gastric cardiac cancer: the worldwide retrospective study

Additional file 1: Supplement Figure 1. The training curves of neural network-based prognostic predictive model for GCC

Bak expression is increased and correlates with CD4+ T cell counts and CD95-induced apoptosis in HIV-1-infected individuals.

<p>(A) Mean fluorescence intensity (MFI) of Bak, Bax and Bim expression <i>ex vivo</i> shown in CD4+ T cells and CD8+ T cells from HIV-1+ patients and healthy controls. Each dot depicts a donor, the lines indicate 10% and 90% and the boxes depict 25%, median and 75% quantiles. The P values were calculated by using the nonparametric Wilcoxon signed rank test for unpaired samples. (B) Spearman's rho correlation shown between <i>ex vivo</i> Bak (n = 25), Bax (n = 24) and Bim (n = 19) expression in CD4+ T cells and CD4+ T counts in HIV-1-infected individuals. (C) Spearman's rho or Pearson's r correlations shown between <i>ex vivo</i> Bak expression and the percentage of spontaneous apoptosis, AICD and CD95/Fas-mediate apoptosis in CD4+ and CD8+ T cells from HIV-1-infected individuals (n = 10).</p

Bak silencing markedly reduces the sensitivity of T cells in chronic HIV-1 infection to CD95/Fas-induced apoptosis.

<p>(A) Efficiency of siRNA uptake in T cells transfected with a pool of siRNAs and siGlo fluorescent oligonucleotides (to monitor transfection) compared to an electroporated negative control (no RNA or siGlo). Silencing of (B) Bak and (C) Bax (off-target control) by siRNA sequences targeting Bak in primary PBMC from a representative HIV+ patient measured by quantitative PCR. Expression (mean, SEM) normalized to 18S rRNA is presented as fold change relative to non-targeting control siRNA. (D) CD95/Fas-specific apoptosis of CD4+ T cells and CD8+ T cells in chronic HIV-1 infection following transfection with a pool of siRNAs directed against Bak, relative to a pool of non-targeting siRNAs (negative control). (E) Percent inhibition of CD95/Fas-specific cell death in T cells from chronically HIV-1-infected individuals following transfection with a Bak siRNA pool. Results were obtained from 3 independent experiments with 3 different HIV-1-infected patients.</p

IFNα-induced gene expression is increased in HIV-1 infection and correlates with Bak expression, CD95/Fas-induced T cell apoptosis and CD4+ T cell loss.

<p>(A) <i>Ex vivo IFI6-16</i> and (B) <i>ISG56</i> levels as measured by real-time RT PCR are significantly increased in HIV-1-infected patients (n = 7–14) compared to healthy donors (n = 6–8). P values were calculated by using the Wilcoxon signed rank test for unpaired samples. Spearman's rho correlations shown between <i>IFI6-16</i> expression in PBMC and (C) <i>ex vivo</i> T cell Bak expression (n = 11), (D) <i>ex vivo</i> T cell Bax expression (n = 11) (E) <i>ex vivo</i> T cell Bim expression (n = 7) (F) <i>ex vivo</i> CD95/Fas-mediated T cell apoptosis sensitivity (n = 12) and (G) CD4+ T cell counts (n = 10) in ART-naive HIV-1-infected individuals. Correlations are shown for ART-naïve HIV-1-infected patients (n = 7) between plasma viral load and (H) IFI6-16 mRNA levels, (I) ISG56 mRNA levels. Spearman's rho correlations depicted between CD95/Fas-specific apoptosis of CD4+ T cells and (J) <i>ISG56</i> expression, (K) <i>IFI6-16</i> expression and (L) plasma viral load in ART-naïve HIV-1 patients.</p

Type I IFN increases the sensitivity of T cells from HIV-1-infected individuals to CD95/Fas-induced death, but not TRAIL- and TNFα-mediated apoptosis.

<p>(A) Treatment-specific apoptosis shown for CD4+ T cells (n = 10) and CD8+ (n = 10) T cells pre-treated with IFNα (1000 U/ml) for 72 hours prior to a 14 hour stimulation with plate-bound anti-CD95/Fas antibody, TRAIL (10 ng/ml) or TNFα (10 ng/ml). n.s. = not significant. (B) Representative flow cytometry (left panel) and pooled data (right panel) showing apoptosis sensitivity of HIV-specific CD8+ T cells (n = 7) and CMV/EBV-specific CD8+ T cells (n = 5) after pre-incubation of PBMC with IFNα or IFNβ (1000 U/ml) for 72 hours and subsequent stimulation with plate-bound anti-CD95/Fas antibody for 14 hours. Bars in graphs indicate mean ± standard error. P values shown in graphs were calculated by using the parametric Student's t-test or nonparametric Wilcoxon signed rank test for paired samples.</p

<i>Ex vivo</i> pro- and anti-apoptotic molecule expression in HIV-1-infected patient T cells.

∧<p>ΔMFI ± standard error.</p>*<p>P<0.05,</p>**<p>P<0.02,</p>***<p>P<0.005 compared to healthy controls.</p