Additional file 1 of COSMIC-based mutation database enhances identification efficiency of HLA-I immunopeptidome

Additional file 1: Figure S1. A Whole picture of HLA-A/B western blot. B. Scatter plot experimental RT and predicted RT for PSM from 3 biological replicates of HepG2 cell line. C. Overlap of 9 a.a identified peptides for three biological replicates from HepG2 cells using Uniprot Human database. Figure S2. A Log2 intensity for binding peptides predicted by NetMHCpan, ranked by peptide length. B HLA-I immunopeptides main binding motifs by Gibbs cluster, when cluster number = 1. C HLA-I immunopeptides main binding motifs by Gibbs cluster, when cluster number = 3. D Scatter plot shows the proportion of P2 and P3 amino acids in the Gibbs clustered peptides and NetMHCpan HLA-A0201 data set. E Scatter plot shows the proportion of P2 and P3 amino acids in the Gibbs clustered peptides and NetMHCpan HLA-A2402 data set. Figure S3. A Tumor tissue distribution of COSMIC-reported somatic mutations in the identified mutant peptides using COSMIC-based database. B The proportion of equal weight peptides to unique peptides HepG2 WES-based or COSMIC-based database. Figure S4. A MS2 spectrum of identified binder mutant peptides using COSMIC-based database. B MS2 spectrum of identified non-binder mutant peptides using COSMIC-based database. Table S1. HLA-I peptidome identification from UniProt Human databas

Diversity and species concept of the Vischeria/Eustigmatos complex (Eustigmatophyceae)

Vischeria and Eustigmatos are closely related genera occurring in terrestrial habitats. These genera were distinguished by the differences in the features of the cell wall (projections and ridges of different form, smooth surface respectively). Up to date three species of the genus Eustigmatos and twelve species of the genus Vischeria have been described, but nine of the Vischeria species have been rarely, if ever, observed since the original description. This work is focused on evaluating molecular variability, diversity, and taxonomy of the Vischeria/Eustigmatos complex. Ninety seven strains, obtained from public algal collections or newly isolated from localities from all over the world, were studied, including the type strains of two Eustigmatos species and three Vischeria species. Phylogenetic analyses of the ITS2 rDNA and rbcL sequences showed that these genera are not genetically separated. The five types strains each represented a separate evolutionary lineage. Some of the additional lineages included strains morphologically corresponding to the species Eustigmatos magnus. Some of the newly isolated strains are according to the markers examined genetically indistinguishable from known strains from public algal collections. However, some of them are new lineages. Only one of the phylogenetic..

Forest plot of the comparison between SSYX combined with anti-arrhythmia drugs plus routine treatment and anti-arrhythmia drugs plus routine treatment for the outcome Maintenance of Sinus Rhythm.

<p>Forest plot of the comparison between SSYX combined with anti-arrhythmia drugs plus routine treatment and anti-arrhythmia drugs plus routine treatment for the outcome Maintenance of Sinus Rhythm.</p

Shensongyangxin Capsules for Paroxysmal Atrial Fibrillation: A Systematic Review of Randomized Clinical Trials

<div><p>Objective</p><p>To evaluate the evidence for the effectiveness and safety of Shensongyangxin Capsules (SSYX) for treating paroxysmal atrial fibrillation (PAF).</p><p>Methods</p><p>We searched for randomized clinical trials for SSYX in PAF up to June 2015. The Cochrane risk of bias tool was used to assess the methodological quality. RevMan 5.3 was used to synthesize the results.</p><p>Results</p><p>We included 22 trials involving 2,347 PAF patients. The quality of the included studies was generally poor. The results of the meta-analysis showed that SSYX plus routine treatment was more effective at improving P-wave dispersion (Pwd) and the frequency of PAF attacks compared with routine treatment alone. The results from the included trials that compared SSYX plus routine treatment and arrhythmic drugs plus routine treatment were inconsistent. Trials reported on Pwd, quality of life, frequency of PAF attacks or maintenance rate of sinus rhythm and found that SSYX combined with anti-arrhythmic drugs plus routine treatment was more effective than anti-arrhythmic drugs plus routine treatment. Four of the trials reported adverse events, indicating that SSYX was potentially safer than anti-arrhythmic drugs.</p><p>Conclusions</p><p>There appears to be some benefit from the use of SSYX. However, due to poor methodological quality, we could not draw confirmative conclusions regarding the beneficial effect of using SSYX.</p></div

The selection process of this systematic review.

<p>The selection process of this systematic review.</p

Forest plot of the comparison between SSYX plus routine treatment and routine treatment for the outcome frequency of PAF attack.

<p>Forest plot of the comparison between SSYX plus routine treatment and routine treatment for the outcome frequency of PAF attack.</p

Characteristics of patients, interventions, and outcomes that were compared in the studies included in this systematic review.

<p>NR, not reported; t, treatment group; c, control group; HBP, high blood pressure; CHD, coronary heart disease; DCM, dilated cardiomyopathy; RHD, rheumatic heart disease; DM, diabetes mellitus; HF, heart failure; LAD, left atrium canon; LVEF, left ventricular ejection fraction; CRP, C-reactive protein; IL, interleukin.</p

Image_2_Comprehensive analysis and immune landscape of chemokines- and chemokine receptors-based signature in hepatocellular carcinoma.tif

BackgroundDespite encouraging results from immunotherapy combined with targeted therapy for hepatocellular carcinoma (HCC), the prognosis remains poor. Chemokines and their receptors are an essential component in the development of HCC, but their significance in HCC have not yet been fully elucidated. We aimed to establish chemokine-related prognostic signature and investigate the association between the genes and tumor immune microenvironment (TIME).Methods342 HCC patients have screened from the TCGA cohort. A prognostic signature was developed using least absolute shrinkage and selection operator regression and Cox proportional risk regression analysis. External validation was performed using the LIHC-JP cohort deployed from the ICGC database. Single-cell RNA sequencing (scRNA-seq) data from the GEO database. Two nomograms were developed to estimate the outcome of HCC patients. RT-qPCR was used to validate the differences in the expression of genes contained in the signature.ResultsThe prognostic signature containing two chemokines-(CCL14, CCL20) and one chemokine receptor-(CCR3) was successfully established. The HCC patients were stratified into high- and low-risk groups according to their median risk scores. We found that patients in the low-risk group had better outcomes than those in the high-risk group. The results of univariate and multivariate Cox regression analyses suggested that this prognostic signature could be considered an independent risk factor for the outcome of HCC patients. We discovered significant differences in the infiltration of various immune cell subtypes, tumor mutation burden, biological pathways, the expression of immune activation or suppression genes, and the sensitivity of different groups to chemotherapy agents and small molecule-targeted drugs in the high- and low-risk groups. Subsequently, single-cell analysis results showed that the higher expression of CCL20 was associated with HCC metastasis. The RT-qPCR results demonstrated remarkable discrepancies in the expression of CCL14, CCL20, and CCR3 between HCC and its paired adjacent non-tumor tissues.ConclusionIn this study, a novel prognostic biomarker explored in depth the association between the prognostic model and TIME was developed and verified. These results may be applied in the future to improve the efficacy of immunotherapy or targeted therapy for HCC.</p

Image_6_Comprehensive analysis and immune landscape of chemokines- and chemokine receptors-based signature in hepatocellular carcinoma.tif

BackgroundDespite encouraging results from immunotherapy combined with targeted therapy for hepatocellular carcinoma (HCC), the prognosis remains poor. Chemokines and their receptors are an essential component in the development of HCC, but their significance in HCC have not yet been fully elucidated. We aimed to establish chemokine-related prognostic signature and investigate the association between the genes and tumor immune microenvironment (TIME).Methods342 HCC patients have screened from the TCGA cohort. A prognostic signature was developed using least absolute shrinkage and selection operator regression and Cox proportional risk regression analysis. External validation was performed using the LIHC-JP cohort deployed from the ICGC database. Single-cell RNA sequencing (scRNA-seq) data from the GEO database. Two nomograms were developed to estimate the outcome of HCC patients. RT-qPCR was used to validate the differences in the expression of genes contained in the signature.ResultsThe prognostic signature containing two chemokines-(CCL14, CCL20) and one chemokine receptor-(CCR3) was successfully established. The HCC patients were stratified into high- and low-risk groups according to their median risk scores. We found that patients in the low-risk group had better outcomes than those in the high-risk group. The results of univariate and multivariate Cox regression analyses suggested that this prognostic signature could be considered an independent risk factor for the outcome of HCC patients. We discovered significant differences in the infiltration of various immune cell subtypes, tumor mutation burden, biological pathways, the expression of immune activation or suppression genes, and the sensitivity of different groups to chemotherapy agents and small molecule-targeted drugs in the high- and low-risk groups. Subsequently, single-cell analysis results showed that the higher expression of CCL20 was associated with HCC metastasis. The RT-qPCR results demonstrated remarkable discrepancies in the expression of CCL14, CCL20, and CCR3 between HCC and its paired adjacent non-tumor tissues.ConclusionIn this study, a novel prognostic biomarker explored in depth the association between the prognostic model and TIME was developed and verified. These results may be applied in the future to improve the efficacy of immunotherapy or targeted therapy for HCC.</p

Risk of bias summary: review of the authors’ judgments regarding the risk of bias for each item for the included studies.

<p>Risk of bias summary: review of the authors’ judgments regarding the risk of bias for each item for the included studies.</p