cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28724608.v1
title: Comprehensive characterization of the molecular feature of T cells in laryngeal cancer: evidence from integrated single-cell and bulk RNA sequencing data using multiple machine learning approaches

description: The clinical relevance of T cell-related molecules at single-cell resolution in laryngeal cancer (LC) has not been clarified. Three LC tissues and matching adjoining normal tissues from the hospital were used to perform 10X single-cell RNA sequencing. Hub T cell-related genes (TCRGs) were detected by applying ten machine learning (ML) techniques based TCGA and GEO databases, which were also utilized to create a prediction model (TCRG classifier) and a multicenter validation model. Lastly, we conducted a comprehensive analysis of the TCRG’s correlation with immunological properties. The analysis of single-cell RNA-seq data revealed that T cells are the primary components of the tumor microenvironment (TME), are significantly involved in cell differentiation pathways, and play a considerable role in intercellular communication. Based on 10 ML approaches, TCRG classifier were identified to develop and validate. The TCRG classifier exhibited excellent prognostic values with a mean C-index of 0.66 in six cohorts, serving as an independent risk factor (<i>p</i> &lt; 0.01). Additionally, the TCRG exhibited a significant relationship with immune score, immune cell infiltration, immune-associated pathways, immune checkpoint inhibitors, human leukocyte antigen, and immunogenicity. Lastly, IPS, TCIC, TIDE, and IMvigor210 cohort analysis illustrated that the immunotherapy response may be accurately predicted using TCRG. A TCRG classifier is an excellent resource for predicting a patient’s prognosis, potentially guiding the preservation of laryngeal function, and identifying patients who may have a positive response to immunotherapy, which might have profound effects on therapeutic practice.
DOI: 10.6084/m9.figshare.29246820
title: Prognostic value of baseline and absolute change of inflammatory markers in patients with thymic epithelial tumors

description: This study aims to investigate the prognostic value of baseline and absolute changes of inflammatory markers in thymic epithelial tumors (TETs). This real-world study enrolled 147 patients. Inflammatory markers, including baseline and absolute changes of platelet-to-lymphocyte (PLR), platelet-to-monocyte (PMR), lymphocyte-to-monocyte (LMR), and neutrophil-to-lymphocyte ratio (NLR), were retrospectively collected. Survival analysis was conducted using Kaplan–Meier analysis. Lasso and multivariate Cox regression were conducted to assess the relationship between disease-free survival (DFS), overall survival (OS) and inflammatory markers. Predictive nomograms were constructed by variables identified in Cox regression. Higher baseline NLR and PLR, lower baseline LMR and PMR, a greater change in PLR and smaller changes in LMR, PMR, and PNR related to inferior DFS and OS. Multivariate Cox regression identified higher baseline PLR and advanced Masaoka Stage were risk, while higher baseline PMR was protective OS factors. Age, higher baseline PLR, and advanced Masaoka Stage were risk DFS factors. A greater absolute PLR change and metastasis were risk, while a lower absolute PMR change was protective OS factors. Age and a greater absolute PLR change were risk, while a greater absolute LMR change was favorable DFS factors. The present study is the first to reveal the prognostic role of the baseline and absolute changes of inflammatory markers in TETs. The prognostic models based on these inflammatory markers offer promising tools for predicting the prognosis of TET patients.
DOI: 10.6084/m9.figshare.29246820.v1
title: Prognostic value of baseline and absolute change of inflammatory markers in patients with thymic epithelial tumors

description: This study aims to investigate the prognostic value of baseline and absolute changes of inflammatory markers in thymic epithelial tumors (TETs). This real-world study enrolled 147 patients. Inflammatory markers, including baseline and absolute changes of platelet-to-lymphocyte (PLR), platelet-to-monocyte (PMR), lymphocyte-to-monocyte (LMR), and neutrophil-to-lymphocyte ratio (NLR), were retrospectively collected. Survival analysis was conducted using Kaplan–Meier analysis. Lasso and multivariate Cox regression were conducted to assess the relationship between disease-free survival (DFS), overall survival (OS) and inflammatory markers. Predictive nomograms were constructed by variables identified in Cox regression. Higher baseline NLR and PLR, lower baseline LMR and PMR, a greater change in PLR and smaller changes in LMR, PMR, and PNR related to inferior DFS and OS. Multivariate Cox regression identified higher baseline PLR and advanced Masaoka Stage were risk, while higher baseline PMR was protective OS factors. Age, higher baseline PLR, and advanced Masaoka Stage were risk DFS factors. A greater absolute PLR change and metastasis were risk, while a lower absolute PMR change was protective OS factors. Age and a greater absolute PLR change were risk, while a greater absolute LMR change was favorable DFS factors. The present study is the first to reveal the prognostic role of the baseline and absolute changes of inflammatory markers in TETs. The prognostic models based on these inflammatory markers offer promising tools for predicting the prognosis of TET patients.
DOI: 10.6084/m9.figshare.29940048
title: Incidence, mortality, and DALYs of global pharyngeal cancer: systematic analysis and projections Based on global burden of disease study 2021

description: Compared to other head and neck cancers, pharyngeal cancer (PC) has poorer survival, representing a significant health burden. This study aimed to assess the burden and trends of PC at global, regional, and national levels and analyze mortality-related factors. Data on PC, including incidence, mortality, disability-adjusted life-years (DALYs), and death-related risk factors from 1990 to 2021, were obtained from the Global Burden of Disease Study 2021. Estimated annual percentage changes (EAPCs) were calculated to assess trends. In 2021, PC incidence was 169,820, with 98,435 deaths and 2,843,781 DALYs. Age-standardized rates for incidence, death, and DALYs were 1.93, 1.13, and 32.30 per 100,000, respectively. South Asia had the highest death and DALYs rates (3.23 and 93.00). Low-middle socio-demographic index (SDI) regions showed the highest death rate (2.19) and the greatest EAPC for death rates (0.684%). A positive correlation between SDI and death rates was observed globally (<i>R</i> = 0.26, <i>p</i> &lt; 0.05), particularly in males (<i>R</i> = 0.3, <i>p</i> &lt; 0.05), but not in females. Males exhibited a trend toward younger ages at death by aclohol, peaking in the 35–39-year group. In 2021, global PC incidence, deaths, and DALYs increased significantly, with notable regional disparities, especially in low-middle SDI regions. Alcohol-related mortality disproportionately affected younger males. Strengthening oral health resources, controlling alcohol and tobacco use are essential to reducing the global PC burden.
DOI: 10.6084/m9.figshare.29940048.v1
title: Incidence, mortality, and DALYs of global pharyngeal cancer: systematic analysis and projections Based on global burden of disease study 2021

description: Compared to other head and neck cancers, pharyngeal cancer (PC) has poorer survival, representing a significant health burden. This study aimed to assess the burden and trends of PC at global, regional, and national levels and analyze mortality-related factors. Data on PC, including incidence, mortality, disability-adjusted life-years (DALYs), and death-related risk factors from 1990 to 2021, were obtained from the Global Burden of Disease Study 2021. Estimated annual percentage changes (EAPCs) were calculated to assess trends. In 2021, PC incidence was 169,820, with 98,435 deaths and 2,843,781 DALYs. Age-standardized rates for incidence, death, and DALYs were 1.93, 1.13, and 32.30 per 100,000, respectively. South Asia had the highest death and DALYs rates (3.23 and 93.00). Low-middle socio-demographic index (SDI) regions showed the highest death rate (2.19) and the greatest EAPC for death rates (0.684%). A positive correlation between SDI and death rates was observed globally (<i>R</i> = 0.26, <i>p</i> &lt; 0.05), particularly in males (<i>R</i> = 0.3, <i>p</i> &lt; 0.05), but not in females. Males exhibited a trend toward younger ages at death by aclohol, peaking in the 35–39-year group. In 2021, global PC incidence, deaths, and DALYs increased significantly, with notable regional disparities, especially in low-middle SDI regions. Alcohol-related mortality disproportionately affected younger males. Strengthening oral health resources, controlling alcohol and tobacco use are essential to reducing the global PC burden.
DOI: 10.6084/m9.figshare.29320820
title: Anoikis classification of lung squamous cell carcinoma reveals correlation with clinical prognosis and immune characteristics

description: Anoikis is a new mode of cell death that has been shown to correlate significantly with tumors. However, the clinical prognostic significance of anoikis in lung squamous cell carcinoma (LUSC) remains poorly studied. The differentially expressed ARGs and candidate genes were selected by the differential analysis to construct a predictive model. Independent prognostic gene was determined by Cox and LASSO analysis and we used the HCC95 and NCI H520 cell line to verify the gene function. We used the data from TCGA, GEO, GeneCards, and Harmonizome databases to analyze the immune microenvironment, functional enrichment, and drug sensitivity analysis. We identified 717 differentially expressed and selected 3 ARGs (FADD, SNAI1, and BAG4) to construct a predictive model. We found that SNAI1 is an independent prognostic gene and confirmed that knocking out the SNAI1 inhibited the HCC95<b>/</b>NCI H520 cell proliferation. We used single-sample gene-set enrichment analysis (ssGSEA) to evaluate the immune infiltration based on the 3 ARG expression levels. We constructed a risk score and provided a visual representation of the prophetic implications of the ARGs-based signature through a nomogram. We found 15 susceptible drugs in the high-risk group and 15 sensitive drugs in the low-risk group by the drug sensitivity analysis. We used ARGs to construct a prognosis model for LUSC that can accurately predict the prognosis of LUSC patients. ARGs, especially SNAI1, play an essential role in developing LUSC. These findings could provide individualized treatment plans and new research ideas for LUSC patients.
DOI: 10.6084/m9.figshare.29320820.v1
title: Anoikis classification of lung squamous cell carcinoma reveals correlation with clinical prognosis and immune characteristics

description: Anoikis is a new mode of cell death that has been shown to correlate significantly with tumors. However, the clinical prognostic significance of anoikis in lung squamous cell carcinoma (LUSC) remains poorly studied. The differentially expressed ARGs and candidate genes were selected by the differential analysis to construct a predictive model. Independent prognostic gene was determined by Cox and LASSO analysis and we used the HCC95 and NCI H520 cell line to verify the gene function. We used the data from TCGA, GEO, GeneCards, and Harmonizome databases to analyze the immune microenvironment, functional enrichment, and drug sensitivity analysis. We identified 717 differentially expressed and selected 3 ARGs (FADD, SNAI1, and BAG4) to construct a predictive model. We found that SNAI1 is an independent prognostic gene and confirmed that knocking out the SNAI1 inhibited the HCC95<b>/</b>NCI H520 cell proliferation. We used single-sample gene-set enrichment analysis (ssGSEA) to evaluate the immune infiltration based on the 3 ARG expression levels. We constructed a risk score and provided a visual representation of the prophetic implications of the ARGs-based signature through a nomogram. We found 15 susceptible drugs in the high-risk group and 15 sensitive drugs in the low-risk group by the drug sensitivity analysis. We used ARGs to construct a prognosis model for LUSC that can accurately predict the prognosis of LUSC patients. ARGs, especially SNAI1, play an essential role in developing LUSC. These findings could provide individualized treatment plans and new research ideas for LUSC patients.
DOI: 10.6084/m9.figshare.30529117
title: Qing-Re-Xiao-Zheng-yi-qi formula protects renal function by stabilizing lysosomal membranes and inhibiting NLRP3-inflammasome-mediated pyroptosis in diabetic kidney disease

description: Qing-Re-Xiao-Zheng-Yi-Qi formula (QRXZYQF), based on the "Shen-Luo-Zheng-Jia" principles of traditional Chinese medicine, has been reported to reduce 24-hour urinary total protein in diabetic kidney disease (DKD) patients, slow disease progression, and improve podocyte injury. This study aims to explore the mechanisms of QRXZYQF in improving podocyte injury. Diabetes was induced in male C57BL/6J mice by intraperitoneal injection of streptozotocin (STZ). After 12 weeks of QRXZYQF, blood glucose, blood urea nitrogen, serum creatinine, microalbumin, and the urinary albumin-to-creatinine ratio (UACR) were monitored. Renal pathological changes were evaluated using hematoxylin and eosin (H&E), Masson, and periodic acid–Schiff (PAS) staining. RNA sequencing (RNA-Seq) was performed to identify differences in renal mRNA expression and enrichment pathways. The involvement of autophagy–lysosomal and NOD-like receptor pathways was examined by western blotting and immunofluorescence in renal tissues and cultured podocytes. Following 12 weeks of QRXZYQF, renal function improved and ECM accumulation and glomerulosclerosis were markedly reduced. Subsequently, RNA-Seq analysis showed that the autophagy–lysosomal and NOD-like receptor signaling pathways were the potential pathways involved in the mechanism of QRXZYQF. Moreover, QRXZYQF reduced the levels of NLRP3, apoptosis-associated speck-like protein (ASC), as well as Caspase-1 in vitro. Furthermore, we performed interventions using the lysosomal membrane-permeabilizing agent (L-leucyl-L-leucine-O-methylester) and found that QRXZYQF inhibits NLRP3 overexpression by protecting lysosomal membranes and preventing the leakage of Cathepsin B (CB) into the cytoplasm. QRXZYQF inhibits NLRP3-mediated podocyte pyroptosis by stabilizing lysosomal membranes, providing insights into its protective mechanism and potential therapeutic targets for DKD.
DOI: 10.6084/m9.figshare.30529117.v1
title: Qing-Re-Xiao-Zheng-yi-qi formula protects renal function by stabilizing lysosomal membranes and inhibiting NLRP3-inflammasome-mediated pyroptosis in diabetic kidney disease

description: Qing-Re-Xiao-Zheng-Yi-Qi formula (QRXZYQF), based on the "Shen-Luo-Zheng-Jia" principles of traditional Chinese medicine, has been reported to reduce 24-hour urinary total protein in diabetic kidney disease (DKD) patients, slow disease progression, and improve podocyte injury. This study aims to explore the mechanisms of QRXZYQF in improving podocyte injury. Diabetes was induced in male C57BL/6J mice by intraperitoneal injection of streptozotocin (STZ). After 12 weeks of QRXZYQF, blood glucose, blood urea nitrogen, serum creatinine, microalbumin, and the urinary albumin-to-creatinine ratio (UACR) were monitored. Renal pathological changes were evaluated using hematoxylin and eosin (H&E), Masson, and periodic acid–Schiff (PAS) staining. RNA sequencing (RNA-Seq) was performed to identify differences in renal mRNA expression and enrichment pathways. The involvement of autophagy–lysosomal and NOD-like receptor pathways was examined by western blotting and immunofluorescence in renal tissues and cultured podocytes. Following 12 weeks of QRXZYQF, renal function improved and ECM accumulation and glomerulosclerosis were markedly reduced. Subsequently, RNA-Seq analysis showed that the autophagy–lysosomal and NOD-like receptor signaling pathways were the potential pathways involved in the mechanism of QRXZYQF. Moreover, QRXZYQF reduced the levels of NLRP3, apoptosis-associated speck-like protein (ASC), as well as Caspase-1 in vitro. Furthermore, we performed interventions using the lysosomal membrane-permeabilizing agent (L-leucyl-L-leucine-O-methylester) and found that QRXZYQF inhibits NLRP3 overexpression by protecting lysosomal membranes and preventing the leakage of Cathepsin B (CB) into the cytoplasm. QRXZYQF inhibits NLRP3-mediated podocyte pyroptosis by stabilizing lysosomal membranes, providing insights into its protective mechanism and potential therapeutic targets for DKD.
DOI: 10.6084/m9.figshare.29430515
title: LncRNA <i>C5orf64</i> polymorphisms (rs12518552 and rs2950218) decreases pulmonary tuberculosis susceptibility

description: Pulmonary tuberculosis (PTB) remains a significant global health issue, with genetic factors playing a crucial role in susceptibility. Long noncoding RNA (lncRNA) <i>C5orf64</i> has been implicated in immune responses and cancer, but its association with PTB risk has not been fully explored. Genomic DNA was extracted from peripheral blood samples of 955 participants (474 PTB cases and 481 controls). Rs12518552 and rs2950218 in <i>C5orf64</i> were genotyped using the Agena MassARRAY system. Logistic regression analysis was performed to assess the association between these polymorphisms and PTB risk. Stratified analysis was conducted to evaluate the influence of age, gender, and smoking status. Rs12518552-G (OR = 0.82, <i>p</i> = 0.034) and rs2950218-T (OR = 0.77, <i>p</i> = 0.012) were associated with a reduced PTB risk. Stratified analysis revealed that rs12518552 was associated with a protective effect against PTB in individuals over 40 years old (OR = 0.73, <i>p</i> = 0.024), females (OR = 0.77, <i>p</i> = 0.034), and non-smokers (OR = 0.78, <i>p</i> = 0.040), and rs2950218 was also associated with a reduced PTB risk in individuals over 40 years old (OR = 0.73, <i>p</i> = 0.040), females (OR = 0.72, <i>p</i> = 0.046), and non-smokers (OR = 0.72, <i>p</i> = 0.011). <i>C5orf64</i> polymorphisms, particularly rs12518552 and rs2950218, are associated with a reduced risk of PTB. These findings suggest that C5orf64 polymorphisms contribute to genetic susceptibility to PTB, with implications for PTB targeted screening and personalized therapeutic strategies.
DOI: 10.6084/m9.figshare.29430515.v1
title: LncRNA <i>C5orf64</i> polymorphisms (rs12518552 and rs2950218) decreases pulmonary tuberculosis susceptibility

description: Pulmonary tuberculosis (PTB) remains a significant global health issue, with genetic factors playing a crucial role in susceptibility. Long noncoding RNA (lncRNA) <i>C5orf64</i> has been implicated in immune responses and cancer, but its association with PTB risk has not been fully explored. Genomic DNA was extracted from peripheral blood samples of 955 participants (474 PTB cases and 481 controls). Rs12518552 and rs2950218 in <i>C5orf64</i> were genotyped using the Agena MassARRAY system. Logistic regression analysis was performed to assess the association between these polymorphisms and PTB risk. Stratified analysis was conducted to evaluate the influence of age, gender, and smoking status. Rs12518552-G (OR = 0.82, <i>p</i> = 0.034) and rs2950218-T (OR = 0.77, <i>p</i> = 0.012) were associated with a reduced PTB risk. Stratified analysis revealed that rs12518552 was associated with a protective effect against PTB in individuals over 40 years old (OR = 0.73, <i>p</i> = 0.024), females (OR = 0.77, <i>p</i> = 0.034), and non-smokers (OR = 0.78, <i>p</i> = 0.040), and rs2950218 was also associated with a reduced PTB risk in individuals over 40 years old (OR = 0.73, <i>p</i> = 0.040), females (OR = 0.72, <i>p</i> = 0.046), and non-smokers (OR = 0.72, <i>p</i> = 0.011). <i>C5orf64</i> polymorphisms, particularly rs12518552 and rs2950218, are associated with a reduced risk of PTB. These findings suggest that C5orf64 polymorphisms contribute to genetic susceptibility to PTB, with implications for PTB targeted screening and personalized therapeutic strategies.
DOI: 10.6084/m9.figshare.29950543
title: Association of lactate-albumin ratio with native liver survival in paediatric acute liver failure: a 10-year retrospective study

description: Paediatric acute liver failure (PALF) is a severe life-threatening condition with complex aetiologies and high mortality rates. Prognostic research, particularly in the Chinese paediatric population, is limited. The lactate-albumin ratio (LAR) is a potential prognostic indicator for adverse outcomes in critical illness, and its correlation with survival with the native liver (SNL) in PALF patients requires further study. LAR was calculated as follows: [lactate (mmol/L)/serum albumin (g/L)×100%]. This study utilized early LAR, defined as the initial measurement of lactate and albumin levels conducted within the first 24h following hospital admission, to investigate the correlation between LAR and SNL in PALF. This retrospective cohort study included 77 patients with PALF. The data collected included demographic information, etiologies, complications, laboratory findings, and the Liver Injury Unit score. Logistic regression, smooth curve fitting, generalized additive models, and interaction effects analysis were used for statistical analysis. Among 77 patients, 46.8% (36 cases) had SNL, with 14.3% (11 cases) requiring transplantation. A significant decrease in SNL was associated with higher LAR (<i>p</i> = 0.005), with a 4% decline in SNL for each 1% increase in LAR. When the LAR≥ 10.5%, the odds ratios(ORs) for SNL in Models I, II, and III were 0.259 (95% confidence interval(CI) 0.101-0.668), 0.213 (95% CI 0.076-0.6), and 0.053 (95% CI 0.007-0.378), respectively. Smooth curve fitting confirmed a linear relationship (<i>p</i> for nonlinearity = 0.531). The subgroup analysis showed an association between LAR and SNL in non-shocked patients (OR 0.1121, 95% CI 0.0153-0.8206) and significant interactions in patients with higher-grade hepatic encephalopathy (<i>p</i> &lt; 0.001). No significant differences in clinical outcomes were observed regardless of etiology. Our findings suggest a significant correlation between LAR and SNL in patients with PALF from Northeast China. Elevated LAR is predictive of a reduced probability of surviving PALF without the need for liver transplantation, highlighting its potential as a prognostic marker in PALF.