cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.15089942.v1
title: A ferroptosis-related gene signature for graft loss prediction following renal allograft

description: Allogeneic kidney transplantation (renal allograft) is the most effective treatment for advanced kidney disease. Previous studies have indicated that ferroptosis participates in the progression of acute kidney injury and renal transplant failure. However, few studies have evaluated the prognostic value of ferroptosis on renal transplantation outcomes. In this study, a total of 22 differentially expressed ferroptosis-related genes (DFGs) were identified, which were mainly enriched in infection-related pathways. Next, a ferroptosis-related gene signature, including GA-binding protein transcription factor subunit beta 1 (GABPB1), cyclin-dependent kinase inhibitor 1A (CDKN1A), Toll-like receptor 4 (TLR4), C-X-C motif chemokine ligand 2 (CXCL2), caveolin 1 (CAV1), and ribonucleotide reductase subunit M2 (RRM2), was constructed to predict graft loss following renal allograft. Moreover, receiver operating characteristic (ROC) curves (area under the ROC curve [AUC] &gt; 0.8) demonstrated the accuracy of the gene signature and univariate Cox analysis suggested that the gene signature could play an independent role in graft loss (p &lt; 0.05). Furthermore, the nomogram and calibration plots also indicated the good prognostic capability of the gene signature. Finally, immune-related and cytokine signaling pathways were mostly enriched in renal allograft patients with poor outcomes. Considered together, a ferroptosis-related gene signature and nomogram based on DFGs were created to predict the 1-, 2- and 3- year graft loss probability of renal allograft patients.The gene signature could serve as a valuable biomarker for predicting graft loss, contributing to improving the outcome of allogeneic kidney transplantation.
DOI: 10.6084/m9.figshare.19808140
title: Additional file 13 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 13: Table S12. GO Annotation Enrichment Analysis in CP53_vs_BP45.
DOI: 10.6084/m9.figshare.19808158
title: Additional file 4 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 4: Table S3. GO enrich for BT45vsAT37.
DOI: 10.6073/pasta/a45c6bdadc8d23a6c907561cc101efd8
title: Sea ice thickness, snow depth, and sea ice freeboard in lagoon sites along the Alaska Beaufort Sea coast, 2019-ongoing

description: Physical parameters related to snow and sea ice have implications for lagoon circulation, sea-air heat exchange, and underwater light regimes. To understand these relationships and their greater effect on ecosystem function, the Beaufort Lagoon Ecosystem LTER (BLE LTER) uses in situ methods to assess snow depth, ice freeboard, and ice thickness in select water bodies across the Beaufort Sea coast (Elson Lagoon, Simpson Lagoon, Kaktovik Lagoon, Jago Lagoon, and Stefansson Sound). Sea ice thickness is the distance from sea ice bottom to top, not including snow. Freeboard, determined in the same drilled hole, is the distance from the surface of the water to the top of the ice, not including snow cover. These measurements are made annually, close to maximum ice thickness (typically April).
DOI: 10.6084/m9.figshare.19808131
title: Additional file 10 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 10: Table S9. List of DEPs.
DOI: 10.6084/m9.figshare.15090026
title: ZEB2, interacting with MDM2, contributes to the dysfuntion of brain microvascular endothelial cells and brain injury after intracerebral hemorrhage

description: ZEB2 has been shown to be upregulated in the brain tissues of rats with intracerebral hemorrhage (ICH), but its role in ICH-caused brain injury remains unclear. Here, an ICH rat model was established via intracerebral injection of autologous blood, and the lentivirus-mediated ZEB2 short hairpin RNA (sh-ZEB2) or negative control (scramble) were administered 0.5 hours after ICH. Silencing ZEB2 alleviated ICH-induced neurologic deficits and the increase of BBB permeability, brain water content and ZEB2 expression. Next, OGD (oxygen glucose deprivation) plus hemin was used to treat primary brain microvascular endothelial cells (BMECs) to simulate the ICH condition <i>in vitro</i>. OGD plus hemin upregulated ZEB2 expression and apoptosis, but reduced cell viability, migration, TEER (transendothelial electric resistance) and the expression of vascular-endothelial (VE-) cadherin, occludin and claudin-5, which was reversed by inhibiting ZEB2. Mechanism researches showed that ZEB2 interacted with MDM2 to up-regulate MDM2 protein expression, and then increased E2F1 protein level by suppressing its ubiquitination, which in turn promoted the transcription of ZEB2 to induce its protein expression, so as to enhance the interaction between ZEB2 and MDM2, thereby contributing to OGD plus hemin-induced endothelial dysfunction. Additionally, the joint interference of ZEB2 and MDM2 <i>in vivo</i> had better mitigative effects on ICH-induced brain injury compared with silencing ZEB2 alone. In summary, ZEB2 interacted with MDM2 to promote BMEC dysfunction and brain damage after ICH.
DOI: 10.6084/m9.figshare.19808143
title: Additional file 14 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 14: Table S13. Differentially expressed metabolites.
DOI: 10.6084/m9.figshare.8274266
title: Additional file 1: of Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle

description: Table S1. Phenotype records and metadata for each individual. (XLSX 171 kb)
DOI: 10.6084/m9.figshare.15090012
title: Digitisation of Yeh and Lindau Photoionisation Cross Section Tabulated Data CSV Format

description: This document provides a digitised version of the tabulated atomic subshell photoionisation cross section data calculated by Yeh and Lindau (1985). The data from the original paper was manually mined and deposited into a CSV format for easy access.
DOI: 10.6084/m9.figshare.19808152
title: Additional file 2 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 2: Table S1. The data set summary of transcriptome sequence.
DOI: 10.6084/m9.figshare.19808155.v1
title: Additional file 3 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 3: Table S2. The summary of DEGs.
DOI: 10.6084/m9.figshare.15090026.v1
title: ZEB2, interacting with MDM2, contributes to the dysfuntion of brain microvascular endothelial cells and brain injury after intracerebral hemorrhage

description: ZEB2 has been shown to be upregulated in the brain tissues of rats with intracerebral hemorrhage (ICH), but its role in ICH-caused brain injury remains unclear. Here, an ICH rat model was established via intracerebral injection of autologous blood, and the lentivirus-mediated ZEB2 short hairpin RNA (sh-ZEB2) or negative control (scramble) were administered 0.5 hours after ICH. Silencing ZEB2 alleviated ICH-induced neurologic deficits and the increase of BBB permeability, brain water content and ZEB2 expression. Next, OGD (oxygen glucose deprivation) plus hemin was used to treat primary brain microvascular endothelial cells (BMECs) to simulate the ICH condition <i>in vitro</i>. OGD plus hemin upregulated ZEB2 expression and apoptosis, but reduced cell viability, migration, TEER (transendothelial electric resistance) and the expression of vascular-endothelial (VE-) cadherin, occludin and claudin-5, which was reversed by inhibiting ZEB2. Mechanism researches showed that ZEB2 interacted with MDM2 to up-regulate MDM2 protein expression, and then increased E2F1 protein level by suppressing its ubiquitination, which in turn promoted the transcription of ZEB2 to induce its protein expression, so as to enhance the interaction between ZEB2 and MDM2, thereby contributing to OGD plus hemin-induced endothelial dysfunction. Additionally, the joint interference of ZEB2 and MDM2 <i>in vivo</i> had better mitigative effects on ICH-induced brain injury compared with silencing ZEB2 alone. In summary, ZEB2 interacted with MDM2 to promote BMEC dysfunction and brain damage after ICH.
DOI: 10.6084/m9.figshare.15090023.v1
title: Uncovering antiobesity-related hypertension targets and mechanisms of metformin, an antidiabetic medication

description: Metformin, a common clinical drug used to treat diabetes mellitus, is found with potential antiobese actions as reported in increasing evidences. However, the detailed mechanisms of metformin-antiobesity-related hypertension remain unrevealed. We have utilized the bioinformatics strategy, including network pharmacology and molecular docking analyses, to uncover pharmacological targets and molecular pathways of bioactive compounds against clinical disorders, such as cancers, coronavirus disease 2019. In this report, the <i>in-silico</i> approaches using network pharmacology and molecular docking was utilized to identify the core targets, pharmacological functions and mechanisms of metformin against obesity-related hypertension. The networking analysis identified 154 differentially expressed genes of obesity and hypertension, and 21 interaction genes, 6 core genes of metformin treating obesity-related hypertension. As results, molecular docking findings indicated the binding capability of metformin with key proteins, including interleukin 6 (IL-6) and chemokine (C-C motif) Ligand 2 (CCL2) expressed in obesity- and hypertension-dependent tissues. Metformin-exerted antihypertension/obesity actions involved in metabolic regulation, inflammatory suppression. And antihypertension/obesity mechanisms of metformin were revealed, including regulation of inflammatory and immunological signaling pathways for ameliorating microenvironmental homeostasis in targeting tissues. In conclusion, our current bioinformatics findings have uncovered all pharmacological targets, biological functions and signaling pathways of metformin treating obesity-related hypertension, thus promoting its clinical application in future.
DOI: 10.6084/m9.figshare.15090023
title: Uncovering antiobesity-related hypertension targets and mechanisms of metformin, an antidiabetic medication

description: Metformin, a common clinical drug used to treat diabetes mellitus, is found with potential antiobese actions as reported in increasing evidences. However, the detailed mechanisms of metformin-antiobesity-related hypertension remain unrevealed. We have utilized the bioinformatics strategy, including network pharmacology and molecular docking analyses, to uncover pharmacological targets and molecular pathways of bioactive compounds against clinical disorders, such as cancers, coronavirus disease 2019. In this report, the <i>in-silico</i> approaches using network pharmacology and molecular docking was utilized to identify the core targets, pharmacological functions and mechanisms of metformin against obesity-related hypertension. The networking analysis identified 154 differentially expressed genes of obesity and hypertension, and 21 interaction genes, 6 core genes of metformin treating obesity-related hypertension. As results, molecular docking findings indicated the binding capability of metformin with key proteins, including interleukin 6 (IL-6) and chemokine (C-C motif) Ligand 2 (CCL2) expressed in obesity- and hypertension-dependent tissues. Metformin-exerted antihypertension/obesity actions involved in metabolic regulation, inflammatory suppression. And antihypertension/obesity mechanisms of metformin were revealed, including regulation of inflammatory and immunological signaling pathways for ameliorating microenvironmental homeostasis in targeting tissues. In conclusion, our current bioinformatics findings have uncovered all pharmacological targets, biological functions and signaling pathways of metformin treating obesity-related hypertension, thus promoting its clinical application in future.
DOI: 10.6084/m9.figshare.24002939
title: Additional file 2 of An atlas of associations between 14 micronutrients and 22 cancer outcomes: Mendelian randomization analyses

description: Additional file 2: Table S1. Characteristics of genome-wide association studies of exposures. Table S2. Details of instrumental variables used in mendelian randomization analyses. Table S3. Details of all mendelian randomization analyses associations. Table S4. Effects of instrumental variables on major risk factors of cancer (potential confounders).
DOI: 10.6084/m9.figshare.8274299.v1
title: Additional file 6: of Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle

description: Table S6. Relative abundance and heritability estimates of detected rumen microbial taxa, and factors (breed, sex, diet, and age) driving their variation. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.24002939.v1
title: Additional file 2 of An atlas of associations between 14 micronutrients and 22 cancer outcomes: Mendelian randomization analyses

description: Additional file 2: Table S1. Characteristics of genome-wide association studies of exposures. Table S2. Details of instrumental variables used in mendelian randomization analyses. Table S3. Details of all mendelian randomization analyses associations. Table S4. Effects of instrumental variables on major risk factors of cancer (potential confounders).
DOI: 10.21942/uva.25272889
title: ATP raw data corresponding to article Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models (10.1016/j.antiviral.2024.105798).

description: ATP raw data corresponding to article Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models (10.1016/j.antiviral.2024.105798).
DOI: 10.21942/uva.25272889.v1
title: ATP raw data corresponding to article Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models (10.1016/j.antiviral.2024.105798).

description: ATP raw data corresponding to article Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models (10.1016/j.antiviral.2024.105798).
DOI: 10.21942/uva.25273084.v1
title: LDH raw data corresponding to article Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models (10.1016/j.antiviral.2024.105798).

description: LDH raw data corresponding to article Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models (10.1016/j.antiviral.2024.105798).
DOI: 10.58032/agh/xl9mjb
title: Scimago Journal Country Rank service data on 3 years citations per document collected in November 2023, for the period 2000-2020, including titles for which full data is available for these 21 years

description: Citations per document counts the number of citations received by documents from a journal and divides them by the total number of documents published in that journal.
DOI: 10.21942/uva.25273084
title: LDH raw data corresponding to article Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models (10.1016/j.antiviral.2024.105798).

description: LDH raw data corresponding to article Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models (10.1016/j.antiviral.2024.105798).
DOI: 10.6084/m9.figshare.8274299
title: Additional file 6: of Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle

description: Table S6. Relative abundance and heritability estimates of detected rumen microbial taxa, and factors (breed, sex, diet, and age) driving their variation. (XLSX 25 kb)
DOI: 10.21942/uva.25272880
title: TCID50 raw data corresponding to article Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models (10.1016/j.antiviral.2024.105798).

description: TCID50 raw data corresponding to article Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models (10.1016/j.antiviral.2024.105798).
DOI: 10.21942/uva.25272880.v1
title: TCID50 raw data corresponding to article Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models (10.1016/j.antiviral.2024.105798).

description: TCID50 raw data corresponding to article Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models (10.1016/j.antiviral.2024.105798).
DOI: 10.21942/uva.25272865
title: qPCR raw data corresponding to article Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models (10.1016/j.antiviral.2024.105798).

description: qPCR raw data corresponding to article Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models (10.1016/j.antiviral.2024.105798).
DOI: 10.21942/uva.25272865.v1
title: qPCR raw data corresponding to article Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models (10.1016/j.antiviral.2024.105798).

description: qPCR raw data corresponding to article Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models (10.1016/j.antiviral.2024.105798).
DOI: 10.58032/agh/kc5yyp
title: Scimago Journal Country Rank service data on 2 years citations per document collected in November 2023, for the period 2000-2020, including titles for which full data is available for these 21 years

description: Citations per document counts the number of citations received by documents from a journal and divides them by the total number of documents published in that journal.
DOI: 10.6084/m9.figshare.21905895
title: Data for the manuscript "Combining paleomagnetic and Re-Os isotope data to quantify the process from hydrocarbon generation to accumulation"

description:  The files here include the data of carbonate reservoir rocks in the Longmen Shan belt, South China. In detail, Table S1 is the data of isothermal remanent magnetization component uxmixing analysis (Table S1); Table S2 is the result of Total Organic Content (TOC) and natural remanent magnetism (NRM) values for hydrocarbon-bearing carbonate samples; Table S3 is the result of vitrinite reflectance in oil (Ro) value. Table S4 is the reuslt of Sr isotope values. There are also files, including the raw data for demagnetization, and their directions.
DOI: 10.6084/m9.figshare.24002721.v1
title: Additional file 2 of Knockdown of long noncoding RNA SAN rejuvenates aged adipose-derived stem cells via miR-143-3p/ADD3 axis

description: Additional file 2. Differentially expressed lncRNAs.
DOI: 10.6084/m9.figshare.24002724.v1
title: Additional file 3 of Knockdown of long noncoding RNA SAN rejuvenates aged adipose-derived stem cells via miR-143-3p/ADD3 axis

description: Additional file 3. Gene list in Fig. 5a.
DOI: 10.58032/agh/fbsl0s
title: Scimago Journal Country Rank service data on Scimago Journal Rank collected in July 2023, for the period 2000-2020, including titles for which full data is available for these 21 years

description: The Scimago Journal Rank (SJR) indicator expresses the average number of weighted citations received in a selected year to the number of documents published in the selected journal in the three previous years.
DOI: 10.6084/m9.figshare.7750202
title: The HGF-MET axis coordinates liver cancer metabolism and autophagy for chemotherapeutic resistance

description: Notwithstanding the numerous drugs available for liver cancer, emerging evidence suggests that chemotherapeutic resistance is a significant issue. HGF and its receptor MET play critical roles in liver carcinogenesis and metastasis, mainly dependent on the activity of receptor tyrosine kinase. However, for unknown reasons, all HGF-MET kinase activity-targeted drugs have failed or have been suspended in clinical trials thus far. Macroautophagy/autophagy is a protective ‘self-eating’ process for resisting metabolic stress by recycling obsolete components, whereas the impact of autophagy-mediated reprogrammed metabolism on therapeutic resistance is largely unclear, especially in liver cancer. In the present study, we first observed that HGF stimulus facilitated the Warburg effect and glutaminolysis to promote biogenesis in multiple liver cancer cells. We then identified the pyruvate dehydrogenase complex (PDHC) and GLS/GLS1 as crucial substrates of HGF-activated MET kinase; MET-mediated phosphorylation inhibits PDHC activity but activates GLS to promote cancer cell metabolism and biogenesis. We further found that the key residues of kinase activity in MET (Y1234/1235) also constitute a conserved LC3-interacting region motif (Y1234-Y1235-x-V1237). Therefore, on inhibiting HGF-mediated MET kinase activation, Y1234/1235-dephosphorylated MET induced autophagy to maintain biogenesis for cancer cell survival. Moreover, we verified that Y1234/1235-dephosphorylated MET correlated with autophagy in clinical liver cancer. Finally, a combination of MET inhibitor and autophagy suppressor significantly improved the therapeutic efficiency of liver cancer <i>in vitro</i> and in mice. Together, our findings reveal an HGF-MET axis-coordinated functional interaction between tyrosine kinase signaling and autophagy, and establish a MET-autophagy double-targeted strategy to overcome chemotherapeutic resistance in liver cancer. <b>Abbreviations:</b> ALDO: aldolase, fructose-bisphosphate; CQ: chloroquine; DLAT/PDCE2: dihydrolipoamide S-acetyltransferase; EMT: epithelial-mesenchymal transition; ENO: enolase; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GLS/GLS1: glutaminase; GLUL/GS: glutamine-ammonia ligase; GPI/PGI: glucose-6-phosphate isomerase; HCC: hepatocellular carcinoma; HGF: hepatocyte growth factor; HK: hexokinase; LDH: lactate dehydrogenase; LIHC: liver hepatocellular carcinoma; LIR: LC3-interacting region; PDH: pyruvate dehydrogenase; PDHA1: pyruvate dehydrogenase E1 alpha 1 subunit; PDHX: pyruvate dehydrogenase complex component X; PFK: phosphofructokinase; PK: pyruvate kinase; RTK: receptor tyrosine kinase; TCGA: The Cancer Genome Atlas