cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28524541.v1
title: Sodium butyrate alleviates DSS-induced inflammatory bowel disease by inhibiting ferroptosis and modulating ERK/STAT3 signaling and intestinal flora

description: Inflammatory bowel disease (IBD), encompassing Crohn’s disease (CD) and ulcerative colitis (UC), can seriously impact patients’ quality of life. Sodium butyrate (NaB), a product of dietary fiber fermentation, has been shown to alleviate IBD symptoms. Some studies have shown that it is related to ferroptosis. However, the precise mechanism linking NaB, IBD, and ferroptosis is not clear. This study aimed to demonstrate that NaB suppresses ferroptosis, thereby alleviating inflammatory bowel disease (IBD) through modulation of the extracellular regulated protein kinases/signal transducer and activator of transcription 3 (ERK/STAT3) signaling pathway and intestinal flora. An IBD model was established using 2.5% (<i>w/v</i>) dextran sulfate sodium (DSS). Mice were orally administered low-dose NaB, high-dose NaB , or 5-aminosalicylic acid (5-ASA). Ferroptosis-related molecules were measured using specific kits, and western blotting (WB) and real-time polymerase chain reaction (RT-qPCR) were used to determine the levels of the target molecules. NaB alleviated symptoms in IBD mice, including reduced weight loss, prolonged colon length, reduced disease activity index (DAI), and reduced spleen index and mRNA expression of inflammatory factors. Additionally, NaB reduced the content of Fe<sup>2+</sup> and myeloperoxidase (MPO) and increased the content of GSH and the activity of superoxide dismutase (SOD), which reflected NaB-inhibited ferroptosis. Moreover, western blotting showed that NaB enhanced STAT3 and ERK phosphorylation. In addition, NaB regulates the composition and functions of flora related to IBD. NaB alleviates IBD by inhibiting ferroptosis and modulating ERK/STAT3 signaling and the intestinal flora. Sodium butyrate; IBD; ferroptosis; STAT3; ERK; gut microbiota
DOI: 10.6084/m9.figshare.28613672
title: Visualized hysteroscopic artificial intelligence fertility assessment system for endometrial injury: an image-deep-learning study

description: Asherman’s syndrome (AS) is a significant cause of subfertility in women from developing countries. Over 80% of AS cases in these regions are linked to dilation and curettage (D&C) procedures following pregnancy. The incidence of AS in patients with infertility and recurrent miscarriage can be as high as 10%, while the pregnancy rate in cases of moderate to severe adhesions can be as low as 34%. We aimed to establish a hysteroscopic artificial intelligence system using image-deep-learning algorithms for fertility assessment. This diagnostic study included 555 cases with 4922 hysteroscopic images from a Chinese intrauterine adhesions cohort clinical database (NCT05381376). The study evaluated two image-deep-learning algorithms’ effectiveness in predicting pregnancy within one year, using AUCs and decision curve analysis. The models’ performance was evaluated for two-year prediction <i>via</i> concordance index and cumulative time-dependent ROC. A quantifiable visualization panel of the system was established. The proportional hazard CNN system accurately predicted conception, with AUCs of 0.982, 0.992, and 0.990 in three randomly assigned datasets, superior to the InceptionV3 framework, and achieved a net benefit of 69.4% for subfertility assessment. The system fitted well with c-indexes of 0.920–0.940 and was time-stable. The quantifiable visualization panel displayed four intrauterine pathologies intuitively. The performance was comparable to senior hysteroscopists, with a kappa value of 0.84–0.89. The CNN based on the proportional hazard approach accurately assesses fertility postoperatively. The quantifiable visualization panel could assist in intrauterine pathologies assessment, optimize treatment strategies, and achieve individualized and cost-efficient practices.
DOI: 10.6084/m9.figshare.28613672.v1
title: Visualized hysteroscopic artificial intelligence fertility assessment system for endometrial injury: an image-deep-learning study

description: Asherman’s syndrome (AS) is a significant cause of subfertility in women from developing countries. Over 80% of AS cases in these regions are linked to dilation and curettage (D&C) procedures following pregnancy. The incidence of AS in patients with infertility and recurrent miscarriage can be as high as 10%, while the pregnancy rate in cases of moderate to severe adhesions can be as low as 34%. We aimed to establish a hysteroscopic artificial intelligence system using image-deep-learning algorithms for fertility assessment. This diagnostic study included 555 cases with 4922 hysteroscopic images from a Chinese intrauterine adhesions cohort clinical database (NCT05381376). The study evaluated two image-deep-learning algorithms’ effectiveness in predicting pregnancy within one year, using AUCs and decision curve analysis. The models’ performance was evaluated for two-year prediction <i>via</i> concordance index and cumulative time-dependent ROC. A quantifiable visualization panel of the system was established. The proportional hazard CNN system accurately predicted conception, with AUCs of 0.982, 0.992, and 0.990 in three randomly assigned datasets, superior to the InceptionV3 framework, and achieved a net benefit of 69.4% for subfertility assessment. The system fitted well with c-indexes of 0.920–0.940 and was time-stable. The quantifiable visualization panel displayed four intrauterine pathologies intuitively. The performance was comparable to senior hysteroscopists, with a kappa value of 0.84–0.89. The CNN based on the proportional hazard approach accurately assesses fertility postoperatively. The quantifiable visualization panel could assist in intrauterine pathologies assessment, optimize treatment strategies, and achieve individualized and cost-efficient practices.
DOI: 10.18112/openneuro.ds007212.v1.0.0
title: Chronic Brain Lesion MRI with Manual Lesion Segmentations (CCNRP, Cambridge)
DOI: 10.6084/m9.figshare.29956307
title: Exosomal miR-216a-5p targeting TLR-4 alleviates liver ischemia-reperfusion injury by regulating M2 macrophage polarization and neutrophil inflammation

description: Macrophages and neutrophil play a key role in the initiation and recovery of liver ischemia reperfusion injury (IRI) through transitions in the phenotype and induces inflammation, However, the mechanisms governing these damages have yet to be fully elucidated. Exosomes have emerged as an important mediator of cellular crosstalk in various physiological and pathological processes. This study explored the role of exosomal miRNA in macrophage polarization and liver IRI. Through high-throughput sequencing of small RNAs in exosomes, we identified the negative regulator miR-216a-5p in liver IRI. Mechanistically, miR-216a-5p skewed M2 macrophage polarization and inhibited neutrophil infiltration by targeting TLR4. In conclusion, we demonstrated that exosome-derived miR-216a-5p favors an anti-inflammatory environment by promoting the M2 polarization of macrophages and inhibiting the neutrophil inflammatory response by targeting the TLR4/NF-κB and PI3K/AKT signaling pathways, revealing the endogenous protective mechanism in liver IRI.
DOI: 10.6084/m9.figshare.29956307.v1
title: Exosomal miR-216a-5p targeting TLR-4 alleviates liver ischemia-reperfusion injury by regulating M2 macrophage polarization and neutrophil inflammation

description: Macrophages and neutrophil play a key role in the initiation and recovery of liver ischemia reperfusion injury (IRI) through transitions in the phenotype and induces inflammation, However, the mechanisms governing these damages have yet to be fully elucidated. Exosomes have emerged as an important mediator of cellular crosstalk in various physiological and pathological processes. This study explored the role of exosomal miRNA in macrophage polarization and liver IRI. Through high-throughput sequencing of small RNAs in exosomes, we identified the negative regulator miR-216a-5p in liver IRI. Mechanistically, miR-216a-5p skewed M2 macrophage polarization and inhibited neutrophil infiltration by targeting TLR4. In conclusion, we demonstrated that exosome-derived miR-216a-5p favors an anti-inflammatory environment by promoting the M2 polarization of macrophages and inhibiting the neutrophil inflammatory response by targeting the TLR4/NF-κB and PI3K/AKT signaling pathways, revealing the endogenous protective mechanism in liver IRI.
DOI: 10.6084/m9.figshare.29967032
title: Comprehensive analysis of the leukocyte immunoglobulin-like receptor family in clear cell renal cell carcinoma

description: Renal cell carcinoma (RCC) is a malignant tumor originating from the renal tubular epithelium and is the 14th most common cancer worldwide, causing around 180,000 deaths annually. Clear cell renal cell carcinoma (ccRCC) is the predominant subtype, accounting for 70–80% of cases. The potential of the leukocyte immunoglobulin-like receptor (LILR) family members in tumor progression and immune evasion has garnered significant attention. To construct a prognosis signature based on the LILR family in ccRCC patients, and explore its relationship with clinical pathological features, immune microenvironment, and drug sensitivity. We analyzed the expression and prognostic value of the LILR family in ccRCC, developed a risk scoring model, and examined its correlation with clinical features, immune infiltration, and treatment efficacy. The study also explored the expression and impact of the core gene LILRB3 on ccRCC. Our findings indicate that the aberrant expression of LILR family members in ccRCC is associated with tumorigenesis and inhibition of anti-tumor immunity. The risk model enhances long-term survival predictions and supports personalized therapies. These insights establish a foundation for further research into their potential as targets for cancer immunotherapy, improving predictive capabilities and the development of personalized treatments.
DOI: 10.6084/m9.figshare.29967032.v3
title: Comprehensive analysis of the leukocyte immunoglobulin-like receptor family in clear cell renal cell carcinoma

description: Renal cell carcinoma (RCC) is a malignant tumor originating from the renal tubular epithelium and is the 14th most common cancer worldwide, causing around 180,000 deaths annually. Clear cell renal cell carcinoma (ccRCC) is the predominant subtype, accounting for 70–80% of cases. The potential of the leukocyte immunoglobulin-like receptor (LILR) family members in tumor progression and immune evasion has garnered significant attention. To construct a prognosis signature based on the LILR family in ccRCC patients, and explore its relationship with clinical pathological features, immune microenvironment, and drug sensitivity. We analyzed the expression and prognostic value of the LILR family in ccRCC, developed a risk scoring model, and examined its correlation with clinical features, immune infiltration, and treatment efficacy. The study also explored the expression and impact of the core gene LILRB3 on ccRCC. Our findings indicate that the aberrant expression of LILR family members in ccRCC is associated with tumorigenesis and inhibition of anti-tumor immunity. The risk model enhances long-term survival predictions and supports personalized therapies. These insights establish a foundation for further research into their potential as targets for cancer immunotherapy, improving predictive capabilities and the development of personalized treatments.
DOI: 10.6084/m9.figshare.29967032.v2
title: Comprehensive analysis of the leukocyte immunoglobulin-like receptor family in clear cell renal cell carcinoma

description: Renal cell carcinoma (RCC) is a malignant tumor originating from the renal tubular epithelium and is the 14th most common cancer worldwide, causing around 180,000 deaths annually. Clear cell renal cell carcinoma (ccRCC) is the predominant subtype, accounting for 70–80% of cases. The potential of the leukocyte immunoglobulin-like receptor (LILR) family members in tumor progression and immune evasion has garnered significant attention. To construct a prognosis signature based on the LILR family in ccRCC patients, and explore its relationship with clinical pathological features, immune microenvironment, and drug sensitivity. We analyzed the expression and prognostic value of the LILR family in ccRCC, developed a risk scoring model, and examined its correlation with clinical features, immune infiltration, and treatment efficacy. The study also explored the expression and impact of the core gene LILRB3 on ccRCC. Our findings indicate that the aberrant expression of LILR family members in ccRCC is associated with tumorigenesis and inhibition of anti-tumor immunity. The risk model enhances long-term survival predictions and supports personalized therapies. These insights establish a foundation for further research into their potential as targets for cancer immunotherapy, improving predictive capabilities and the development of personalized treatments.
DOI: 10.6084/m9.figshare.30060510
title: Construction of a gene–metabolite–microbiome regulatory network reveals novel therapeutic targets in bladder cancer through multi-omics analysis

description: Bladder cancer (BLCA) is a prevalent malignancy with substantial consequences for patient health. This study aimed to elucidate the underlying mechanisms of BLCA through integrated multi-omics analysis. Tumor and adjacent tissues from BLCA patients underwent transcriptomic, whole-exome sequencing, metabolomic, and intratumoral microbiome analyses. These data were integrated with public datasets to identify key genes, metabolites, and microorganisms. Molecular subtypes were defined by key gene expression and compared for pathways, immune profiles, mutations, immunotherapy response, and drug sensitivity. Prognostic relevance was validated in external cohorts. Single-cell sequencing was applied to reveal cellular localization of key genes. Three key genes (<i>AHNAK, CSPG4, NCAM1</i>), 90 metabolites, and two microbes (<i>Sphingomonas koreensis, Rhodospirillaceae</i>) were identified. Key genes negatively correlated with metabolites but not with microbes. BLCA samples were classified into two molecular clusters with distinct ECM organization, metabolic features, immune checkpoint expression, and therapeutic sensitivity. NCAM1 correlated positively with γδ T cells and negatively with M0 macrophages. Single-cell analysis revealed nine major cell types, with fibroblasts displaying the highest expression of key genes, particularly elevated <i>AHNAK</i> in specific fibroblast subtypes. Drug prediction and docking identified candidate compounds targeting these genes with stable binding potential. This comprehensive multi-omics analysis links key genes, metabolites, and microbes to BLCA pathogenesis. Fibroblasts emerge as central regulators, while identified gene–metabolite interactions and microbial associations provide novel insights into tumor heterogeneity. These findings highlight potential biomarkers and therapeutic targets to support precision treatment in BLCA.
DOI: 10.6084/m9.figshare.30060510.v1
title: Construction of a gene–metabolite–microbiome regulatory network reveals novel therapeutic targets in bladder cancer through multi-omics analysis

description: Bladder cancer (BLCA) is a prevalent malignancy with substantial consequences for patient health. This study aimed to elucidate the underlying mechanisms of BLCA through integrated multi-omics analysis. Tumor and adjacent tissues from BLCA patients underwent transcriptomic, whole-exome sequencing, metabolomic, and intratumoral microbiome analyses. These data were integrated with public datasets to identify key genes, metabolites, and microorganisms. Molecular subtypes were defined by key gene expression and compared for pathways, immune profiles, mutations, immunotherapy response, and drug sensitivity. Prognostic relevance was validated in external cohorts. Single-cell sequencing was applied to reveal cellular localization of key genes. Three key genes (<i>AHNAK, CSPG4, NCAM1</i>), 90 metabolites, and two microbes (<i>Sphingomonas koreensis, Rhodospirillaceae</i>) were identified. Key genes negatively correlated with metabolites but not with microbes. BLCA samples were classified into two molecular clusters with distinct ECM organization, metabolic features, immune checkpoint expression, and therapeutic sensitivity. NCAM1 correlated positively with γδ T cells and negatively with M0 macrophages. Single-cell analysis revealed nine major cell types, with fibroblasts displaying the highest expression of key genes, particularly elevated <i>AHNAK</i> in specific fibroblast subtypes. Drug prediction and docking identified candidate compounds targeting these genes with stable binding potential. This comprehensive multi-omics analysis links key genes, metabolites, and microbes to BLCA pathogenesis. Fibroblasts emerge as central regulators, while identified gene–metabolite interactions and microbial associations provide novel insights into tumor heterogeneity. These findings highlight potential biomarkers and therapeutic targets to support precision treatment in BLCA.
DOI: 10.6084/m9.figshare.30344831
title: Spatial immunoprofiling of retroperitoneal leiomyosarcomas reveals intratumoral heterogeneity in immune cell infiltration, checkpoint molecule expression, and tertiary lymphoid structures

description: Leiomyosarcoma (LMS) is a rare, aggressive cancer with limited treatment options at the metastatic stage. The response to immune checkpoint inhibitors (ICIs) is inconsistent, likely due to intratumoral heterogeneity, which is more pronounced in large tumours such as retroperitoneal LMS. This study examined heterogeneity in four large treatment-naive LMS tumours (ten samples per tumour) by analysing immune cells, tertiary lymphoid structures (TLSs), checkpoint molecules, and cytokine secretion across different tumour regions. Significant region-dependent differences were observed in immune components, with TLSs present only at tumour margins and inconsistently across samples from the same tumour. Expression levels of programmed cell death 1 (PD-1) and programmed death ligand 1 (PD-L1) varied within individual tumours, and shared immune patterns were identified in specific regions, including elevated indoleamine 2,3-dioxygenase 1, absence of a particular macrophage subpopulation, and reduced PD-1 and lymphocyte activation gene 3 (LAG-3) expression at organ-adjacent margins. Anti-LAG-3 blockade altered cytokine and checkpoint molecule levels in a region-specific manner. These findings highlight substantial intratumoral heterogeneity, which may contribute to the variable response to ICI therapy. As immune checkpoint molecule expression influences treatment eligibility, multiple biopsies from different tumour regions may be necessary to assess immune infiltration accurately and guide therapy decisions.
DOI: 10.6084/m9.figshare.30344831.v1
title: Spatial immunoprofiling of retroperitoneal leiomyosarcomas reveals intratumoral heterogeneity in immune cell infiltration, checkpoint molecule expression, and tertiary lymphoid structures

description: Leiomyosarcoma (LMS) is a rare, aggressive cancer with limited treatment options at the metastatic stage. The response to immune checkpoint inhibitors (ICIs) is inconsistent, likely due to intratumoral heterogeneity, which is more pronounced in large tumours such as retroperitoneal LMS. This study examined heterogeneity in four large treatment-naive LMS tumours (ten samples per tumour) by analysing immune cells, tertiary lymphoid structures (TLSs), checkpoint molecules, and cytokine secretion across different tumour regions. Significant region-dependent differences were observed in immune components, with TLSs present only at tumour margins and inconsistently across samples from the same tumour. Expression levels of programmed cell death 1 (PD-1) and programmed death ligand 1 (PD-L1) varied within individual tumours, and shared immune patterns were identified in specific regions, including elevated indoleamine 2,3-dioxygenase 1, absence of a particular macrophage subpopulation, and reduced PD-1 and lymphocyte activation gene 3 (LAG-3) expression at organ-adjacent margins. Anti-LAG-3 blockade altered cytokine and checkpoint molecule levels in a region-specific manner. These findings highlight substantial intratumoral heterogeneity, which may contribute to the variable response to ICI therapy. As immune checkpoint molecule expression influences treatment eligibility, multiple biopsies from different tumour regions may be necessary to assess immune infiltration accurately and guide therapy decisions.
DOI: 10.6084/m9.figshare.29234855
title: A reassessment of existing systematic reviews evaluating the effectiveness of cryotherapy in patients following total knee arthroplasty

description: This study reassessed systematic reviews on cryotherapy efficacy following total knee arthroplasty (TKA). Ten databases were searched from January 1, 2018 to September 15, 2023 for relevant systematic reviews. Two researchers independently screened articles and extracted data. Five systematic reviews were included. Two of the studies were found to exhibit high methodological quality, while the remaining three demonstrated exceedingly low methodological quality. The deficiencies in quality were attributed to several factors, including the lack of a predefined research protocol, absence of exclusion criteria, unclarified funding sources for the included studies, and potential for publication bias. Of the 18 outcome indicators, Swelling was intermediate-quality evidence , Hemoglobin, Pain score within 24 hours after surgery, Pain score within 48 hours after surgery, Pain score within 72 hours after surgery, Blood loss volume, Pain score on the next day of surgery and Range of Motion (ROM) were low-quality evidence, and other outcome indicators were exceedingly low-quality evidence. Cryotherapy appears to offer benefits such as pain relief, reduction in joint swelling, and improved joint mobility during the initial post-operative phase following TKA. However, further high-quality studies are required to validate the efficacy and safety of cryotherapy for patients undergoing TKA, given the identified limitations in the quality of the available outcome indicators.
DOI: 10.6084/m9.figshare.29234855.v1
title: A reassessment of existing systematic reviews evaluating the effectiveness of cryotherapy in patients following total knee arthroplasty

description: This study reassessed systematic reviews on cryotherapy efficacy following total knee arthroplasty (TKA). Ten databases were searched from January 1, 2018 to September 15, 2023 for relevant systematic reviews. Two researchers independently screened articles and extracted data. Five systematic reviews were included. Two of the studies were found to exhibit high methodological quality, while the remaining three demonstrated exceedingly low methodological quality. The deficiencies in quality were attributed to several factors, including the lack of a predefined research protocol, absence of exclusion criteria, unclarified funding sources for the included studies, and potential for publication bias. Of the 18 outcome indicators, Swelling was intermediate-quality evidence , Hemoglobin, Pain score within 24 hours after surgery, Pain score within 48 hours after surgery, Pain score within 72 hours after surgery, Blood loss volume, Pain score on the next day of surgery and Range of Motion (ROM) were low-quality evidence, and other outcome indicators were exceedingly low-quality evidence. Cryotherapy appears to offer benefits such as pain relief, reduction in joint swelling, and improved joint mobility during the initial post-operative phase following TKA. However, further high-quality studies are required to validate the efficacy and safety of cryotherapy for patients undergoing TKA, given the identified limitations in the quality of the available outcome indicators.