cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.59naxd
title: Occurrence Download

description: A dataset containing 606 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Heracleum mantegazzianum",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 606 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014801-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.19703529
title: Proteome Changes Associated with the VEGFR Pathway and Immune System in Diabetic Macular Edema Patients at Different Diabetic Retinopathy Stages

description: Diabetic macular edema (DME) is a major cause of vision loss in all stages of diabetic retinopathy (DR). However, there is limited recognition of aqueous humor (AH) proteome profiles of DME patients at different DR stages. In this study, we aimed to investigate the AH proteome changes between DME patients at the nonproliferative diabetic retinopathy (NPDR) stage and those at the proliferative diabetic retinopathy (PDR) stage. A label-free data-independent acquisition based liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis was performed to profile the abundances of AH proteins in 73 eyes from DME patients at different DR stages. Enzyme-linked immunosorbent assay (ELISA) was used to confirm the proteomics results with AH samples from non-diabetic patients and DME patients at the NPDR or PDR stage. LC-MS/MS results showed significantly changed expression of 308 proteins between DME patients in the NPDR and PDR groups. Compared to the NPDR group, the proteins relatively up-regulated in the PDR group are involved in the immune system and/or negative regulation of the cell cycle, while proteins relatively down-regulated in the PDR group are associated with the vascular endothelial growth factor receptor (VEGFR) pathway and/or metabolism. ELISA results further verified the proteomic result of down-regulated expression of the immune-associated protein cystatin C (CST3) in the PDR group compared to that in the NPDR and non-diabetic groups. In this study, we reported for the first time the decreased abundances of AH proteins associated with the VEGFR pathway and both down- and up-regulated expression of AH proteins associated with the immune system in the PDR group compared to that in the NPDR group. Furthermore, we found negative correlations of immune-associated protein, CST3 concentration in AH with DR severity and central retinal thickness, suggesting CST3 as a promising target independent of the VEGFR pathway in DME-involved DR treatment.
DOI: 10.6084/m9.figshare.12362492
title: Additional file 2 of Expression profiling of spinal cord dorsal horn in a rat model of complex regional pain syndrome type-I uncovers potential mechanisms mediating pain and neuroinflammation responses

description: Additional file 2: Suppl. Table 2. DEGs.
DOI: 10.6084/m9.figshare.12362495
title: Additional file 3 of Expression profiling of spinal cord dorsal horn in a rat model of complex regional pain syndrome type-I uncovers potential mechanisms mediating pain and neuroinflammation responses

description: Additional file 3: Suppl. Table 3. BP result of the upregulated DEGs in CPIP.
DOI: 10.6084/m9.figshare.12362498.v1
title: Additional file 4 of Expression profiling of spinal cord dorsal horn in a rat model of complex regional pain syndrome type-I uncovers potential mechanisms mediating pain and neuroinflammation responses

description: Additional file 4: Suppl. Table 4. BP result of the downregulated DEGs in CPIP.
DOI: 10.6084/m9.figshare.12362501.v1
title: Additional file 5 of Expression profiling of spinal cord dorsal horn in a rat model of complex regional pain syndrome type-I uncovers potential mechanisms mediating pain and neuroinflammation responses

description: Additional file 5: Suppl. Table 5. CC result of the upregulated DEGs in CPIP.
DOI: 10.6084/m9.figshare.12362489.v1
title: Additional file 1 of Expression profiling of spinal cord dorsal horn in a rat model of complex regional pain syndrome type-I uncovers potential mechanisms mediating pain and neuroinflammation responses

description: Additional file 1: Suppl. Table 1. All expressed transcripts.
DOI: 10.6084/m9.figshare.12362492.v1
title: Additional file 2 of Expression profiling of spinal cord dorsal horn in a rat model of complex regional pain syndrome type-I uncovers potential mechanisms mediating pain and neuroinflammation responses

description: Additional file 2: Suppl. Table 2. DEGs.
DOI: 10.6084/m9.figshare.12362513.v1
title: Additional file 9 of Expression profiling of spinal cord dorsal horn in a rat model of complex regional pain syndrome type-I uncovers potential mechanisms mediating pain and neuroinflammation responses

description: Additional file 9: Suppl. Table 9. KEGG analysis.
DOI: 10.6084/m9.figshare.14983944
title: A conserved genetic architecture among populations of the maize progenitor, teosinte, was radically altered by domestication

description: The genotypes and phenotypes for teosinte and maize landrace populations are included.
DOI: 10.6084/m9.figshare.12362504.v1
title: Additional file 6 of Expression profiling of spinal cord dorsal horn in a rat model of complex regional pain syndrome type-I uncovers potential mechanisms mediating pain and neuroinflammation responses

description: Additional file 6: Suppl. Table 6. CC result of the downregulated DEGs in CPIP.
DOI: 10.6084/m9.figshare.20226892.v1
title: Additional file 1 of A bioinformatic analysis study of m7G regulator-mediated methylation modification patterns and tumor microenvironment infiltration in glioblastoma

description: Additional file 1.
DOI: 10.6084/m9.figshare.12362504
title: Additional file 6 of Expression profiling of spinal cord dorsal horn in a rat model of complex regional pain syndrome type-I uncovers potential mechanisms mediating pain and neuroinflammation responses

description: Additional file 6: Suppl. Table 6. CC result of the downregulated DEGs in CPIP.
DOI: 10.6084/m9.figshare.20226901.v1
title: Additional file 4 of A bioinformatic analysis study of m7G regulator-mediated methylation modification patterns and tumor microenvironment infiltration in glioblastoma

description: Additional file 4.
DOI: 10.6084/m9.figshare.18130887
title: The circ-PITX1 promotes non-small cell lung cancer development via the miR-30e-5p/ITGA6 axis

description: Non-small cell lung cancer (NSCLC) is one of the most prevalent tumors with high incidence and mortality across the globe. Recently, increasing studies have demonstrated that circular RNAs (circRNAs) exert outstanding functions in NSCLC progression. Notwithstanding, we are still in the dark about the function and exact mechanism of circ-PITX1, a newly discovered circRNA. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) confirmed the profile of circ-PITX1 in NSCLC tissues and adjacent normal tissues. Gain- and loss- of function assay verified the impact of circ-PITX1 and miR-30e-5p on the proliferation, invasion, and migration of NSCLC cells (H1975 and A549). Bioinformatics analysis corroborated the downstream mechanisms of circ-PITX1. Dual-luciferase reporter gene assay and RNA immunoprecipitation (RIP) examined the interactions between circ-PITX1 and miR-30e-5p, miR-30e-5p and ITGA6. The protein levels of ITGA6, PI3K, AKT were determined by Western blot. circ-PITX1 was substantially up-regulated in NSCLC tissues and cells, and circ-PITX1 up-regulation was correlated with NSCLC patients’ poor survival. Functionally, circ-PITX1 overexpression or miR-30e-5p inhibition markedly facilitated proliferation, migration, invasion, epithelial-mesenchymal transition (EMT), reduced apoptosis, and enhanced ITGA6/PI3K/AKT expression in NSCLC cells, whereas circ-PITX1 knockdown or miR-30e-5p up-regulation resulted in the opposite results. Mechanistically, circ-PITX1 acted as a sponge of miR-30e-5p, which targeted the 3ʹuntranslated region (UTR) of ITGA6. Knockdown of circ-PITX1 or overexpressing miR-30e-5p reduced ITGA6/PI3K/AKT axis. circ-PITX1 modulates the miR-30e-5p/ITGA6 axis to boost NSCLC progression, hence functioning as an oncogene.
DOI: 10.6084/m9.figshare.11315150
title: MOESM2 of A novel epigenetic signature for overall survival prediction in patients with breast cancer

description: Additional file 2.Â Calculation procedure for lasso COX regression
DOI: 10.6084/m9.figshare.11315150.v1
title: MOESM2 of A novel epigenetic signature for overall survival prediction in patients with breast cancer

description: Additional file 2.Â Calculation procedure for lasso COX regression
DOI: 10.34740/kaggle/dsv/7635716
title: AutoXGB
DOI: 10.34740/kaggle/dsv/7635717
title: OnlineFree
DOI: 10.6084/m9.figshare.20226956.v1
title: Additional file 5 of Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection

description: Additional file 5. Prediction results of the target genes of DEmiRNAs.
DOI: 10.6084/m9.figshare.20226947
title: Additional file 2 of Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection

description: Additional file 2. Overview of the small RNA sequencing data.
DOI: 10.6084/m9.figshare.20226953
title: Additional file 4 of Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection

description: Additional file 4. Prediction results of the target genes of DElncRNAs.
DOI: 10.6084/m9.figshare.12362513
title: Additional file 9 of Expression profiling of spinal cord dorsal horn in a rat model of complex regional pain syndrome type-I uncovers potential mechanisms mediating pain and neuroinflammation responses

description: Additional file 9: Suppl. Table 9. KEGG analysis.
DOI: 10.6084/m9.figshare.19178373
title: Spatial Accessibility Patterns to Public Hospitals in Shanghai: An Improved Gravity Model

description: The spatial distribution of public hospitals is a crucial factor in patient access and thus important to health equity, especially amid the COVID-19 pandemic crisis. In China, a major issue is to improve accessibility to public health care in the face of the limited space for further growth of cities. Therefore, this study assesses the current spatial accessibility patterns to public hospitals in Shanghai, using point density analysis and the comprehensively improved gravity model. The results identify the challenges of inadequate and imbalanced spatial distribution of public hospitals at the district level and show that the central urban area has more high-quality public health care resources and also has higher accessibility levels. Based on the comparisons in each district, the study also summarizes four policy implications for future public hospital and public health care system optimization in Shanghai, which can also be leveraged for the planning of public hospitals in other cities or other public service facilities. The first is to deploy public hospitals in areas with a large population and to introduce branches of top-level hospitals to noncentral areas. The second is the full utilization of community health service centers to relieve the burden of public hospitals to improve accessibility.
DOI: 10.6084/m9.figshare.17082405
title: ALDOA maintains NLRP3 inflammasome activation by controlling AMPK activation

description: Dysregulated NLRP3 inflammasome activity results in uncontrolled inflammation, which is the basis of many chronic diseases. Although the regulatory mechanism has been gradually clarified after a long period of research, the metabolic regulation of NLRP3 inflammasome is still a mystery. Here, we find that ALDOA, as a monitor of glycolysis, regulates NLRP3 inflammasome by sensing changes in glycolytic flux to participate in the formation of AXIN-based AMPK-activation complex on the lysosomal surface. In this process, ALDOA restricts PRKN/parkin-dependent mitophagy through controlling AMPK activation to maintain mitochondrial damage caused by NLRP3 agonists. Furthermore, ALDOA also regulates the transcription of <i>SQSTM1/p62</i>, a receptor for mitophagy, through AMPK-FOXO3 signaling. In addition to studying the mechanism by which ALDOA regulated NLRP3 inflammasome, we also screened ALDOA inhibitors and found that LYG-202, a synthetic flavonoid compound, inhibited ALDOA enzyme activity by occupying the position involved in Schiff base intermediate formation, thus preventing FBP from combining with ALDOA. In vitro, LYG-202 suppressed NLRP3 inflammasome via activating the AMPK-mitophagy signaling pathway. In vivo, LYG-202 attenuated sterile inflammation and fulminant hepatitis, and suppressed the activation of NLRP3 inflammasome activation. Therefore, our study demonstrated that the glycolytic enzyme ALDOA maintained NLRP3 inflammasome activation by monitoring the glycolytic flux to control AMPK activation during the classical activation of NLRP3. ALDOA: aldolase A; AMPK: AMP-activated protein kinase; ATG: autophagy related; ATG5: autophagy related 5; ATP: adenosine triphosphate; BMDMs: bone marrow-derived macrophages; CALCOCO2: calcium binding and coiled-coil domain 2; CASP1: caspase 1; CQ: chloroquine; FOXO3: forkhead box O3; IL1B: interleukin 1 beta; LPS: lipopolysaccharide; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MT: mutant; mtDNA: mitochondrial DNA; MTORC1: mechanistic target of rapamycin kinase complex 1; mtROS: mitochondrial reactive oxygen species; NLRP3: NLR family, pyrin domain containing 3; OPTN: optineurin; PBS: phosphate-buffered saline; PRKN/Parkin: parkin RBR E3 ubiquitin protein ligase; SN: supernatant; SQSTM1/p62: sequestosome 1; STK11/LKB1: serine/threonine kinase 11; TOMM20: translocase of outer mitochondrial membrane 20; ULK1: unc-51 like autophagy activating kinase 1; v-ATPase: vacuolar type H+-ATPase; WT: wild-type.
DOI: 10.6084/m9.figshare.20226815
title: Additional file 12 of Combined nature and human selections reshaped peach fruit metabolome

description: Additional file 12: Table S11. List of the 185 accessions used in transcriptome sequencing and eQTL analysis.
DOI: 10.6084/m9.figshare.20226947.v1
title: Additional file 2 of Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection

description: Additional file 2. Overview of the small RNA sequencing data.
DOI: 10.6084/m9.figshare.12362507.v1
title: Additional file 7 of Expression profiling of spinal cord dorsal horn in a rat model of complex regional pain syndrome type-I uncovers potential mechanisms mediating pain and neuroinflammation responses

description: Additional file 7: Suppl. Table 7. MF result of the upregulated DEGs in CPIP.
DOI: 10.6084/m9.figshare.20226962.v1
title: Additional file 6 of Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection

description: Additional file 6. Innate immunity-related target genes of DElncRNAs.
DOI: 10.6084/m9.figshare.20226956
title: Additional file 5 of Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection

description: Additional file 5. Prediction results of the target genes of DEmiRNAs.
DOI: 10.6084/m9.figshare.20226812
title: Additional file 11 of Combined nature and human selections reshaped peach fruit metabolome

description: Additional file 11: Table S10. Number of associated SNPs in each non-overlapping 1-Mb sliding windows across the peach genome.
DOI: 10.6084/m9.figshare.20226907
title: Additional file 6 of A bioinformatic analysis study of m7G regulator-mediated methylation modification patterns and tumor microenvironment infiltration in glioblastoma

description: Additional file 6.
DOI: 10.6084/m9.figshare.20226893.v1
title: Additional file 4 of Combined nature and human selections reshaped peach fruit metabolome

description: Additional file 4: Table S3. Detailed information of metabolites evaluated in 2015 related to Fig. 1d and e.
DOI: 10.6084/m9.figshare.20226965.v1
title: Additional file 7 of Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection

description: Additional file 7. Innate immunity-related target genes of DEmiRNAs.
DOI: 10.6084/m9.figshare.20226898
title: Additional file 3 of A bioinformatic analysis study of m7G regulator-mediated methylation modification patterns and tumor microenvironment infiltration in glioblastoma

description: Additional file 3.
DOI: 10.6084/m9.figshare.20226970
title: Additional file 5 of Increased CSF-decorin predicts brain pathological changes driven by Alzheimer’s Aβ amyloidosis

description: Additional file 5: Table S4. Significantly altered ECM associated proteins in mouse CSF determined by PEA.
DOI: 10.6084/m9.figshare.20226979.v1
title: Additional file 8 of Increased CSF-decorin predicts brain pathological changes driven by Alzheimer’s Aβ amyloidosis

description: Additional file 8: Table S7. Proteome comparison of AppNL-F/NL-F and AppNL-G-F/NL-G-F mice vs NC/MCI/AD (abnormal-amyloid/normal-tau subjects).
DOI: 10.6084/m9.figshare.20226904.v1
title: Additional file 5 of A bioinformatic analysis study of m7G regulator-mediated methylation modification patterns and tumor microenvironment infiltration in glioblastoma

description: Additional file 5.
DOI: 10.6084/m9.figshare.20226884
title: Additional file 32 of Combined nature and human selections reshaped peach fruit metabolome

description: Additional file 32: Table S31. List of metabolites highly correlated with inhibition rates of all four cancer cell lines.
DOI: 10.6084/m9.figshare.20226854
title: Additional file 24 of Combined nature and human selections reshaped peach fruit metabolome

description: Additional file 24: Table S23. Selective sweeps related to peach domestication and improvement, and differentiation between eastern and western improved varieties.
DOI: 10.6084/m9.figshare.20226944
title: Additional file 1 of Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection

description: Additional file 1. Overview of the RNA sequencing data.
DOI: 10.6084/m9.figshare.20226970.v1
title: Additional file 5 of Increased CSF-decorin predicts brain pathological changes driven by Alzheimer’s Aβ amyloidosis

description: Additional file 5: Table S4. Significantly altered ECM associated proteins in mouse CSF determined by PEA.
DOI: 10.6084/m9.figshare.20226809
title: Additional file 10 of Combined nature and human selections reshaped peach fruit metabolome

description: Additional file 10: Table S9. Statistics of lead SNPs associated with each metabolite in the two seasons.
DOI: 10.6084/m9.figshare.20226833
title: Additional file 18 of Combined nature and human selections reshaped peach fruit metabolome

description: Additional file 18: Table S17. Metabolites evaluated in 2016 correlated with different gene co-expression modules.
DOI: 10.6084/m9.figshare.20226976
title: Additional file 7 of Increased CSF-decorin predicts brain pathological changes driven by Alzheimer’s Aβ amyloidosis

description: Additional file 7: Table S6. Proteome comparison of AppNL-F/NL-F and AppNL-G-F/NL-G-F mice vs NC/MCI/AD (abnormal-amyloid/abnormal-tau subjects).
DOI: 10.6084/m9.figshare.20226824
title: Additional file 15 of Combined nature and human selections reshaped peach fruit metabolome

description: Additional file 15: Table S14. List of candidate genes within 25-kb flanking regions of the lead SNPs associated with metabolites identified in 2016.
DOI: 10.6084/m9.figshare.20226833.v1
title: Additional file 18 of Combined nature and human selections reshaped peach fruit metabolome

description: Additional file 18: Table S17. Metabolites evaluated in 2016 correlated with different gene co-expression modules.
DOI: 10.6084/m9.figshare.11315297
title: MOESM1 of Identification of key genes in invasive clinically non-functioning pituitary adenoma by integrating analysis of DNA methylation and mRNA expression profiles

description: Additional file 1: Table S1. Clinical information of 68 patients with NFPA. Table S2. List of differentially methylated probes. Table S3. List of differentially methylated genes in the promoter region. Table S4. List of differentially expressed genes. Table S5. Pearson analyses results of 69 significant genes. Table S6. GO and KEGG analyses of 115 genes. Table S7. GO and KEGG analyses of 58 genes. Table S8. Pyrosequencing primers of 19 genes. Table S9. RT-PCR primers of 20 genes (including thr control). Table S10. Distribution of differential methylated probes.
DOI: 10.6084/m9.figshare.19178373.v1
title: Spatial Accessibility Patterns to Public Hospitals in Shanghai: An Improved Gravity Model

description: The spatial distribution of public hospitals is a crucial factor in patient access and thus important to health equity, especially amid the COVID-19 pandemic crisis. In China, a major issue is to improve accessibility to public health care in the face of the limited space for further growth of cities. Therefore, this study assesses the current spatial accessibility patterns to public hospitals in Shanghai, using point density analysis and the comprehensively improved gravity model. The results identify the challenges of inadequate and imbalanced spatial distribution of public hospitals at the district level and show that the central urban area has more high-quality public health care resources and also has higher accessibility levels. Based on the comparisons in each district, the study also summarizes four policy implications for future public hospital and public health care system optimization in Shanghai, which can also be leveraged for the planning of public hospitals in other cities or other public service facilities. The first is to deploy public hospitals in areas with a large population and to introduce branches of top-level hospitals to noncentral areas. The second is the full utilization of community health service centers to relieve the burden of public hospitals to improve accessibility.
DOI: 10.6084/m9.figshare.20226892
title: Additional file 1 of A bioinformatic analysis study of m7G regulator-mediated methylation modification patterns and tumor microenvironment infiltration in glioblastoma

description: Additional file 1.
DOI: 10.6084/m9.figshare.20226904
title: Additional file 5 of A bioinformatic analysis study of m7G regulator-mediated methylation modification patterns and tumor microenvironment infiltration in glioblastoma

description: Additional file 5.
DOI: 10.6084/m9.figshare.11315297.v1
title: MOESM1 of Identification of key genes in invasive clinically non-functioning pituitary adenoma by integrating analysis of DNA methylation and mRNA expression profiles

description: Additional file 1: Table S1. Clinical information of 68 patients with NFPA. Table S2. List of differentially methylated probes. Table S3. List of differentially methylated genes in the promoter region. Table S4. List of differentially expressed genes. Table S5. Pearson analyses results of 69 significant genes. Table S6. GO and KEGG analyses of 115 genes. Table S7. GO and KEGG analyses of 58 genes. Table S8. Pyrosequencing primers of 19 genes. Table S9. RT-PCR primers of 20 genes (including thr control). Table S10. Distribution of differential methylated probes.
DOI: 10.6084/m9.figshare.20226821
title: Additional file 14 of Combined nature and human selections reshaped peach fruit metabolome

description: Additional file 14: Table S13. Correlation between gene expression and metabolite contents evaluated in 2016.