cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27826742
title: Identification of copper metabolism-related markers in Parkinson’s disease

description: This study aimed to identify key genes related to copper metabolism in Parkinson’s disease (PD), providing insight into their roles in disease progression. Using bioinformatic analyses, the study identified hub genes related to copper metabolism in PD patients. Differentially expressed genes (DEGs) were identified using the limma package, and copper-metabolism-related genes (CMRGs) were sourced from the Genecard database. Immune cell-related genes were derived through immune infiltration and Weighted Gene Co-expression Network Analysis (WGCNA). Hub genes were pinpointed by integrating DEGs, CMRGs, and immune cell-related genes. Functional analyses included Receiver Operating Characteristic (ROC) analysis, Ingenuity Pathway Analysis (IPA), and networks for miRNA-mRNA-transcription factor (TF), Competitive Endogenous RNA (ceRNA), and hub gene-drug interactions. Validation was performed in cerebrospinal fluid (CSF) samples from PD patients, while in vitro experiments utilized GBE1- overexpressing SH-SY5Y cells to examine cell proliferation, migration, and viability. Nine hub genes (HPRT1, GLS, SNCA, MDH1, GBE1, DDC, STXBP1, ACHE, and AGTR1) were identified from 753 CMRGs, 416 DEGs, and 951 immune cell-related genes. ROC analysis showed high predictive accuracy for PD, and principal component analysis (PCA) effectively distinguished PD patients from controls. IPA identified 20 significant pathways, and various networks highlighted miRNA, TF, and drug interactions with the hub genes. Hub gene expression was validated in PD CSF samples. GBE1-overexpressing cells displayed enhanced proliferation, migration, and viability. The study identified nine copper metabolism-related genes as potential therapeutic targets in PD, highlighting their relevance in PD pathology and possible treatment pathways.
DOI: 10.6084/m9.figshare.27826742.v1
title: Identification of copper metabolism-related markers in Parkinson’s disease

description: This study aimed to identify key genes related to copper metabolism in Parkinson’s disease (PD), providing insight into their roles in disease progression. Using bioinformatic analyses, the study identified hub genes related to copper metabolism in PD patients. Differentially expressed genes (DEGs) were identified using the limma package, and copper-metabolism-related genes (CMRGs) were sourced from the Genecard database. Immune cell-related genes were derived through immune infiltration and Weighted Gene Co-expression Network Analysis (WGCNA). Hub genes were pinpointed by integrating DEGs, CMRGs, and immune cell-related genes. Functional analyses included Receiver Operating Characteristic (ROC) analysis, Ingenuity Pathway Analysis (IPA), and networks for miRNA-mRNA-transcription factor (TF), Competitive Endogenous RNA (ceRNA), and hub gene-drug interactions. Validation was performed in cerebrospinal fluid (CSF) samples from PD patients, while in vitro experiments utilized GBE1- overexpressing SH-SY5Y cells to examine cell proliferation, migration, and viability. Nine hub genes (HPRT1, GLS, SNCA, MDH1, GBE1, DDC, STXBP1, ACHE, and AGTR1) were identified from 753 CMRGs, 416 DEGs, and 951 immune cell-related genes. ROC analysis showed high predictive accuracy for PD, and principal component analysis (PCA) effectively distinguished PD patients from controls. IPA identified 20 significant pathways, and various networks highlighted miRNA, TF, and drug interactions with the hub genes. Hub gene expression was validated in PD CSF samples. GBE1-overexpressing cells displayed enhanced proliferation, migration, and viability. The study identified nine copper metabolism-related genes as potential therapeutic targets in PD, highlighting their relevance in PD pathology and possible treatment pathways.
DOI: 10.6084/m9.figshare.26968781
title: Chromosomal instability is associated with prognosis and efficacy of bevacizumab after resection of colorectal cancer liver metastasis

description: Individualized treatment of colorectal cancer liver metastases (CRLM) remains challenging due to differences in the severity of metastatic disease and tumour biology. Exploring specific prognostic risk subgroups is urgently needed. The current study aimed to investigate the prognostic value of chromosomal instability (CIN) in patients with initially resectable CRLM and the predictive value of CIN for the efficacy of bevacizumab. Ninety-one consecutive patients with initially resectable CRLM who underwent curative liver resection from 2006 to 2018 at Sun Yat-sen University Cancer Center were selected for analysis. CIN was evaluated by automated digital imaging systems. Immunohistochemistry (IHC) was performed to detect interleukin-6 (IL-6), vascular endothelial growth factor A (VEGFA) and CD31 expression in paraffin-embedded specimens. Recurrence-free survival (RFS) and overall survival (OS) were analysed using the Kaplan–Meier method and Cox regression models. Patients with high chromosomal instability (CIN-H) had a worse 3-year RFS rate (HR, 1.953; 95% CI, 1.001–3.810; <i>p</i> = 0.049) and a worse 3-year OS rate (HR, 2.449; 95% CI, 1.150–5.213; <i>p</i> = 0.016) than those with low chromosomal instability (CIN-L). CIN-H was identified as an independent prognostic factor for RFS (HR, 2.569; 95% CI, 1.078–6.121; <i>p</i> = 0.033) and OS (HR, 3.852; 95% CI, 1.173–12.645; <i>p</i> = 0.026) in the multivariate analysis. The protein levels of IL-6, VEGFA and CD31 were upregulated in patients in the CIN-H group compared to those in the CIN-L group in both primary tumour and liver metastases tissues. Among them, 22 patients with recurrent tumours were treated with first-line bevacizumab treatment and based on the clinical response assessment, disease control rates were adversely associated with chromosomal instability (<i>p</i> = 0.043). Our study showed that high chromosomal instability is a negative prognostic factor for patients with initially resectable CRLM after liver resection. CIN may have positive correlations with angiogenesis through expression of IL-6–VEGFA axis and be used as a potential predictor of efficacy of bevacizumab.
DOI: 10.6084/m9.figshare.26968781.v1
title: Chromosomal instability is associated with prognosis and efficacy of bevacizumab after resection of colorectal cancer liver metastasis

description: Individualized treatment of colorectal cancer liver metastases (CRLM) remains challenging due to differences in the severity of metastatic disease and tumour biology. Exploring specific prognostic risk subgroups is urgently needed. The current study aimed to investigate the prognostic value of chromosomal instability (CIN) in patients with initially resectable CRLM and the predictive value of CIN for the efficacy of bevacizumab. Ninety-one consecutive patients with initially resectable CRLM who underwent curative liver resection from 2006 to 2018 at Sun Yat-sen University Cancer Center were selected for analysis. CIN was evaluated by automated digital imaging systems. Immunohistochemistry (IHC) was performed to detect interleukin-6 (IL-6), vascular endothelial growth factor A (VEGFA) and CD31 expression in paraffin-embedded specimens. Recurrence-free survival (RFS) and overall survival (OS) were analysed using the Kaplan–Meier method and Cox regression models. Patients with high chromosomal instability (CIN-H) had a worse 3-year RFS rate (HR, 1.953; 95% CI, 1.001–3.810; <i>p</i> = 0.049) and a worse 3-year OS rate (HR, 2.449; 95% CI, 1.150–5.213; <i>p</i> = 0.016) than those with low chromosomal instability (CIN-L). CIN-H was identified as an independent prognostic factor for RFS (HR, 2.569; 95% CI, 1.078–6.121; <i>p</i> = 0.033) and OS (HR, 3.852; 95% CI, 1.173–12.645; <i>p</i> = 0.026) in the multivariate analysis. The protein levels of IL-6, VEGFA and CD31 were upregulated in patients in the CIN-H group compared to those in the CIN-L group in both primary tumour and liver metastases tissues. Among them, 22 patients with recurrent tumours were treated with first-line bevacizumab treatment and based on the clinical response assessment, disease control rates were adversely associated with chromosomal instability (<i>p</i> = 0.043). Our study showed that high chromosomal instability is a negative prognostic factor for patients with initially resectable CRLM after liver resection. CIN may have positive correlations with angiogenesis through expression of IL-6–VEGFA axis and be used as a potential predictor of efficacy of bevacizumab.
DOI: 10.6084/m9.figshare.27641685
title: Enamel matrix derivative in the treatment of tooth replantation: from a biological basis to clinical application

description: An efficient therapeutic strategy for patients with replanted teeth has been extremely challenging because complete displacement of the teeth is inevitably accompanied by severe damage to periodontal tissue. Enamel matrix derivative (EMD) shows promise for periodontal regeneration, but its effects on replanted teeth remain unknown. This study systematically summarized the biological basis of EMD in replantation dental therapy and assessed its effect on clinical prognosis. Potential studies were searched <i>via</i> the Cochrane Library, Web of Science and PubMed databases from inception to November 23, 2023. A total of 329 patients with 375 replanted teeth met the inclusion criteria. Our pooling results indicated that EMD did not provide a numerical advantage for restoring normal PDL healing in replanted teeth (RR=0.38, <i>P</i>=0.161). A significantly lower extraction risk was observed in EMD-treated group than non-EMD-treated group (RR=0.47, <i>P</i>=0.001). Moreover, the survival rate of replanted teeth with root resorption was significantly increased by the application of EMD (RR=2.21, <i>P</i>=0.017). Although the pooled outcomes suggested increased incidence of surface resorption (RR=1.19, <i>P</i>=0.730) and decreased risk of inflammation resorption (RR=0.68, <i>P</i>=0.560) among replanted teeth with resorption in the EMD-treated group, neither difference was statistically significant. For patients with replanted teeth, EMD treatment may not result in a numerical increase in normal PDL healing. However, as a biological regulator, EMD may arrest the progression of resorption, thus reducing the risk of extraction in the early stage. Well-designed randomized trials are required to validate these results due to the poor quality of evidence.
DOI: 10.6084/m9.figshare.27641685.v1
title: Enamel matrix derivative in the treatment of tooth replantation: from a biological basis to clinical application

description: An efficient therapeutic strategy for patients with replanted teeth has been extremely challenging because complete displacement of the teeth is inevitably accompanied by severe damage to periodontal tissue. Enamel matrix derivative (EMD) shows promise for periodontal regeneration, but its effects on replanted teeth remain unknown. This study systematically summarized the biological basis of EMD in replantation dental therapy and assessed its effect on clinical prognosis. Potential studies were searched <i>via</i> the Cochrane Library, Web of Science and PubMed databases from inception to November 23, 2023. A total of 329 patients with 375 replanted teeth met the inclusion criteria. Our pooling results indicated that EMD did not provide a numerical advantage for restoring normal PDL healing in replanted teeth (RR=0.38, <i>P</i>=0.161). A significantly lower extraction risk was observed in EMD-treated group than non-EMD-treated group (RR=0.47, <i>P</i>=0.001). Moreover, the survival rate of replanted teeth with root resorption was significantly increased by the application of EMD (RR=2.21, <i>P</i>=0.017). Although the pooled outcomes suggested increased incidence of surface resorption (RR=1.19, <i>P</i>=0.730) and decreased risk of inflammation resorption (RR=0.68, <i>P</i>=0.560) among replanted teeth with resorption in the EMD-treated group, neither difference was statistically significant. For patients with replanted teeth, EMD treatment may not result in a numerical increase in normal PDL healing. However, as a biological regulator, EMD may arrest the progression of resorption, thus reducing the risk of extraction in the early stage. Well-designed randomized trials are required to validate these results due to the poor quality of evidence.
DOI: 10.6084/m9.figshare.27143681
title: Development and validation of a model for early survival prediction following liver transplantation based on donor and recipient characteristics

description: Circulating cytokine levels not only correlate with the progression of liver disease but also serve as indicators for the infection status of the body. Growing evidence points to the connection between donor cytokines and graft function following transplantation. This study set out to explore the clinical significance of donor cytokines in predicting liver transplantation prognosis. Data from 172 deceased donor liver transplantations conducted between 2017 and 2022, with available donor serum cytokine information, were collected. The subjects were randomly divided into estimation (<i>n</i> = 120) and validation (<i>n</i> = 52) groups to establish and validate the model. The newly developed SA10 score was compared against established models EAD, MEAF, L-GrAFT7, and L-GrAFT10. Donor IL-10, along with donor age and recipient AST peak value within the first 7 days post-operation, was identified as an independent factor associated with recipient survival and was incorporated into the SA10 score. SA10 exhibited robust predictive capability, particularly for 1-month survival (AUC = 0.90, 95% CI = 0.84–0.96), outperforming EAD (AUC = 0.75, 95% CI = 0.60–0.90, <i>p</i> = 0.04) and L-GrAFT7 (AUC = 0.65, 95% CI = 0.49–0.81, <i>p</i> &lt; 0.01). Comparable performance was observed between SA10, MEAF, and L-GrAFT10. Donor IL-10 independently influences recipient survival, with the SA10 score demonstrating comparable and even superior predictive ability compared to existing models.
DOI: 10.6084/m9.figshare.27143681.v1
title: Development and validation of a model for early survival prediction following liver transplantation based on donor and recipient characteristics

description: Circulating cytokine levels not only correlate with the progression of liver disease but also serve as indicators for the infection status of the body. Growing evidence points to the connection between donor cytokines and graft function following transplantation. This study set out to explore the clinical significance of donor cytokines in predicting liver transplantation prognosis. Data from 172 deceased donor liver transplantations conducted between 2017 and 2022, with available donor serum cytokine information, were collected. The subjects were randomly divided into estimation (<i>n</i> = 120) and validation (<i>n</i> = 52) groups to establish and validate the model. The newly developed SA10 score was compared against established models EAD, MEAF, L-GrAFT7, and L-GrAFT10. Donor IL-10, along with donor age and recipient AST peak value within the first 7 days post-operation, was identified as an independent factor associated with recipient survival and was incorporated into the SA10 score. SA10 exhibited robust predictive capability, particularly for 1-month survival (AUC = 0.90, 95% CI = 0.84–0.96), outperforming EAD (AUC = 0.75, 95% CI = 0.60–0.90, <i>p</i> = 0.04) and L-GrAFT7 (AUC = 0.65, 95% CI = 0.49–0.81, <i>p</i> &lt; 0.01). Comparable performance was observed between SA10, MEAF, and L-GrAFT10. Donor IL-10 independently influences recipient survival, with the SA10 score demonstrating comparable and even superior predictive ability compared to existing models.
DOI: 10.6084/m9.figshare.27275800
title: Construction of circRNA–miRNA–mRNA ceRNA regulatory network and screening of diagnostic targets for tuberculosis

description: Tuberculosis (TB) is a chronic infectious disease caused by <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>), which threatens human health and safety all over the world. Hundreds of thousands of people die from TB every year. Timely early diagnosis and treatment of patients is the most important measure to control the source of infection and curb the epidemic of tuberculosis. The existing diagnostic methods have the disadvantages of poor sensitivity and long culture time. Competitive endogenous RNAs (ceRNAs) can regulate the expression of corresponding target genes by competing for the same microRNA (miRNA) response elements (MREs) as mRNA. Recent studies have found that circRNA has the advantages of long half-life, good stability and tissue specificity, and can be used as a biomarker for predicting, diagnosing and treating various diseases, and is an ideal candidate for biomarkers in body fluid biopsy. In this study, transcriptome sequencing was performed on whole blood samples to screen out TB-related mirna and mRNA differential expression, and to construct the ceRNA regulatory network. Through the analysis of ceRNA regulatory network, it was found that circRNA could competitively bind has-miR-607 and induce down-regulation of has-miR-607, thereby inhibiting the expression of IFNG. The hsa_circ_0000566, hsa_circ_0001844, hsa_circ_0005408, hsa_circ_0007587, hsa_circ_0086710, IFNG and has-miR-607 couble be used as new diagnostic targets for TB. The results of this study not only provide a new perspective for studying the potential role of ceRNA regulatory network in tuberculosis, but also provide a new target and method for the diagnosis of tuberculosis.
DOI: 10.6084/m9.figshare.27275800.v1
title: Construction of circRNA–miRNA–mRNA ceRNA regulatory network and screening of diagnostic targets for tuberculosis

description: Tuberculosis (TB) is a chronic infectious disease caused by <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>), which threatens human health and safety all over the world. Hundreds of thousands of people die from TB every year. Timely early diagnosis and treatment of patients is the most important measure to control the source of infection and curb the epidemic of tuberculosis. The existing diagnostic methods have the disadvantages of poor sensitivity and long culture time. Competitive endogenous RNAs (ceRNAs) can regulate the expression of corresponding target genes by competing for the same microRNA (miRNA) response elements (MREs) as mRNA. Recent studies have found that circRNA has the advantages of long half-life, good stability and tissue specificity, and can be used as a biomarker for predicting, diagnosing and treating various diseases, and is an ideal candidate for biomarkers in body fluid biopsy. In this study, transcriptome sequencing was performed on whole blood samples to screen out TB-related mirna and mRNA differential expression, and to construct the ceRNA regulatory network. Through the analysis of ceRNA regulatory network, it was found that circRNA could competitively bind has-miR-607 and induce down-regulation of has-miR-607, thereby inhibiting the expression of IFNG. The hsa_circ_0000566, hsa_circ_0001844, hsa_circ_0005408, hsa_circ_0007587, hsa_circ_0086710, IFNG and has-miR-607 couble be used as new diagnostic targets for TB. The results of this study not only provide a new perspective for studying the potential role of ceRNA regulatory network in tuberculosis, but also provide a new target and method for the diagnosis of tuberculosis.
DOI: 10.6084/m9.figshare.27937559
title: Association between renal function trajectories and risk of cardiovascular disease: a prospective cohort study

description: It is unclear whether changing trajectories of renal function will increase the risk prediction information of cardiovascular disease (CVD). This study aimed to evaluate the trajectory patterns of estimated glomerular filtration rate (eGFR) and the association between eGFR trajectories and CVD risk. A total of 4742 participants were included in the cohort from the 51st Regiment of Xinjiang Production and Construction Corps. The study endpoint was the occurrence of CVD events. eGFR trajectories were identified using a linear mixed-effects model in four distinct patterns. Multivariate Cox proportional hazards models analysed the correlations between eGFR trajectories and CVD. During a median follow-up period of 5.7 years, a total of 559 (11.8%) CVD, 404 (8.5%) myocardial infarction (MI), 244 (5.2%) ischemic stroke (IS), and 62 (1.3%) heart failure (HF) incidents occurred. After multivariable adjustment, gradual decline trajectory increased the risk of CVD (<i>HR</i> 1.42, 95% <i>CI</i> 1.16–1.74), MI (<i>HR</i> 1.41, 95% <i>CI</i> 1.11–1.79), and IS (<i>HR</i> 1.41, 95% <i>CI</i> 1.04–1.92); gradual increase trajectory reduced the risk of CVD (<i>HR</i> 0.40, 95% <i>CI</i> 0.25–0.64) and MI (<i>HR</i> 0.49, 95% <i>CI</i> 0.29–0.81). Consistent results were obtained in sensitivity and subgroup analyses. Decline and increase of renal function were related to the risk of CVD, MI, and IS in the rural areas of Xinjiang. Monitoring eGFR changing trajectory is of great significance in improving the risk of CVD.
DOI: 10.6084/m9.figshare.27937559.v1
title: Association between renal function trajectories and risk of cardiovascular disease: a prospective cohort study

description: It is unclear whether changing trajectories of renal function will increase the risk prediction information of cardiovascular disease (CVD). This study aimed to evaluate the trajectory patterns of estimated glomerular filtration rate (eGFR) and the association between eGFR trajectories and CVD risk. A total of 4742 participants were included in the cohort from the 51st Regiment of Xinjiang Production and Construction Corps. The study endpoint was the occurrence of CVD events. eGFR trajectories were identified using a linear mixed-effects model in four distinct patterns. Multivariate Cox proportional hazards models analysed the correlations between eGFR trajectories and CVD. During a median follow-up period of 5.7 years, a total of 559 (11.8%) CVD, 404 (8.5%) myocardial infarction (MI), 244 (5.2%) ischemic stroke (IS), and 62 (1.3%) heart failure (HF) incidents occurred. After multivariable adjustment, gradual decline trajectory increased the risk of CVD (<i>HR</i> 1.42, 95% <i>CI</i> 1.16–1.74), MI (<i>HR</i> 1.41, 95% <i>CI</i> 1.11–1.79), and IS (<i>HR</i> 1.41, 95% <i>CI</i> 1.04–1.92); gradual increase trajectory reduced the risk of CVD (<i>HR</i> 0.40, 95% <i>CI</i> 0.25–0.64) and MI (<i>HR</i> 0.49, 95% <i>CI</i> 0.29–0.81). Consistent results were obtained in sensitivity and subgroup analyses. Decline and increase of renal function were related to the risk of CVD, MI, and IS in the rural areas of Xinjiang. Monitoring eGFR changing trajectory is of great significance in improving the risk of CVD.