cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17140813
title: Additional file 1 of Expression of plasma IFN signaling-related miRNAs during acute SARS-CoV-2 infection and its association with RBD-IgG antibody response

description: Additional file 1: Table S1. List of human miRNAs with target gene and miRNAs seed binding site on COVID-19 isolates.
DOI: 10.6084/m9.figshare.17141032
title: Additional file 5 of Rice Carbohydrate-Binding Malectin-Like Protein, OsCBM1, Contributes to Drought-Stress Tolerance by Participating in NADPH Oxidase-Mediated ROS Production

description: Additional file 5: Table S3. The original data of RNA-seq experiments.
DOI: 10.6084/m9.figshare.19762387.v1
title: Bone mesenchymal stem cells (BMSCs)-derived exosomal microRNA-21-5p regulates Kruppel-like factor 3 (KLF3) to promote osteoblast proliferation <i>in vitro</i>

description: Bone mesenchymal stem cells (BMSCs)-derived exosomes (Exos) play important roles in osteoporosis, while the regulation of microRNA (miR)-21-5p remains unclear. The BMSCs-derived exosomes were isolated from femoral bone marrow of trauma patients, which were then used to stimulate human osteoblasts (hFOB1.19 cells). The miR-21-5p mimic or inhibitor was transfected into BMSCs to overexpress or knockdown miR-21-5p. The functions of miR-21-5p in osteoporosis were assessed by cell counting kit-8 (CCK-8) assay, alkaline phosphatase (ALP) staining and alizarin red staining assays. We found that BMSCs-derived exosomes could enhance proliferation, osteoblastic differentiation and ALP activity of hFOB1.19 cells. BMSCs-derived exosomes with upregulated miR-21-5p could further enhance these protective impacts compared with that in BMSCs-derived exosomes, while BMSCs-derived exosomes with downregulated miR-21-5p reduced these cell phenotypes. MiR-21-5p could directly bind to the 3’-untranslated region (UTR) of Kruppel-like factor 3 (KLF3), and knockdown of KLF3 obviously attenuated these inhibitory effects of BMSCs-derived exosomes with downregulated miR-21-5p on osteoblastic differentiation and ALP activity of hFOB1.19 cells. In summary, BMSCs-derived exosomal miR-21-5p improved osteoporosis through regulating KLF3, providing a potential therapeutic strategy for osteoporosis.
DOI: 10.6084/m9.figshare.15567948.v1
title: Additional file 4 of A modified Delphi study to enhance and gain international consensus on the Physical Activity Messaging Framework (PAMF) and Checklist (PAMC)

description: Additional file 4. Survey 1 qualitative analysis.
DOI: 10.6084/m9.figshare.19762387.v2
title: Bone mesenchymal stem cells (BMSCs)-derived exosomal microRNA-21-5p regulates Kruppel-like factor 3 (KLF3) to promote osteoblast proliferation <i>in vitro</i>

description: Bone mesenchymal stem cells (BMSCs)-derived exosomes (Exos) play important roles in osteoporosis, while the regulation of microRNA (miR)-21-5p remains unclear. The BMSCs-derived exosomes were isolated from femoral bone marrow of trauma patients, which were then used to stimulate human osteoblasts (hFOB1.19 cells). The miR-21-5p mimic or inhibitor was transfected into BMSCs to overexpress or knockdown miR-21-5p. The functions of miR-21-5p in osteoporosis were assessed by cell counting kit-8 (CCK-8) assay, alkaline phosphatase (ALP) staining and alizarin red staining assays. We found that BMSCs-derived exosomes could enhance proliferation, osteoblastic differentiation and ALP activity of hFOB1.19 cells. BMSCs-derived exosomes with upregulated miR-21-5p could further enhance these protective impacts compared with that in BMSCs-derived exosomes, while BMSCs-derived exosomes with downregulated miR-21-5p reduced these cell phenotypes. MiR-21-5p could directly bind to the 3’-untranslated region (UTR) of Kruppel-like factor 3 (KLF3), and knockdown of KLF3 obviously attenuated these inhibitory effects of BMSCs-derived exosomes with downregulated miR-21-5p on osteoblastic differentiation and ALP activity of hFOB1.19 cells. In summary, BMSCs-derived exosomal miR-21-5p improved osteoporosis through regulating KLF3, providing a potential therapeutic strategy for osteoporosis.
DOI: 10.6084/m9.figshare.15567675
title: Additional file 3 of Mechanism of interaction between virus and host is inferred from the changes of gene expression in macrophages infected with African swine fever virus CN/GS/2018 strain

description: Additional file 3. ASFV 24h vs. MOCK 24h. Information of differentially expressed genes at 24 hpi.
DOI: 10.6084/m9.figshare.9277517
title: Additional file 3: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S3. Mean marker density of Illumina SNP markers genotyped in a canola GWAS panel of 368 accessions. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.25249777
title: Supplementary Material for: Opinions over targets for blood pressure control after mechanical thrombectomy in patients with acute ischemic stroke: baseline survey for the ENCHANTED2/MT trial in China

description: Background: Although guidelines recommend a target blood pressure 185-180/105-110 mmHg after mechanical thrombectomy for acute ischemic stroke (AIS), there is limited randomized evidence to support this level. We surveyed candidate institutions about the approach to blood pressure management in this patient group in preparation for inviting them to participate in the Enhanced Blood Pressure Control after Endovascular Thrombectomy for the Acute Ischemic Stroke Trial (ENCHANTED2/MT). 
Methods: Physicians from a professional network of institutions that met mechanical thrombectomy qualification requirements were invited to participate in an online questionnaire covering basic clinical information as well as questions on blood pressure management. 
Results: We invited 88 sites to participate with 44 (50%) ultimately joining the trial, and a total of 88 physicians finished the survey. The median number of annual mechanical thrombectomy cases performed per site was 89 [IQR 65-150]. Only 38 (43%) institutions strictly adhere to guidelines when managing the blood pressure of mechanical thrombectomy patients. The most popular blood pressure target for reperfusion patients was 140-160 mmHg (n=47, 53%), and &lt;120 mmHg (n=28, 32%). Fewer hospital stroke beds (40 [21–57] vs. 60 [39–110], p = 0.01) and lower proportion of elevated blood pressure after mechanical thrombectomy (25% [10%–50%] vs. 50% [20%–70%], p = 0.02) were related to a more aggressive blood pressure target (&lt;120 mmHg). Urapidil (n=82, 93%) and calcium channel blockers (CCBs) (n = 87, 99%), were the most widely used antihypertensive drugs, respectively.
Conclusions: According to the survey, unstandardized blood pressure management protocols are performed in mechanical thrombectomy patients at institutions across China, which is different from prior survey from another country. More high-quality studies are needed to guide clinical practice.
DOI: 10.6084/m9.figshare.9277517.v1
title: Additional file 3: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S3. Mean marker density of Illumina SNP markers genotyped in a canola GWAS panel of 368 accessions. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.9277526
title: Additional file 4: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S4. PCR primers used for expression analysis by RT-qPCR (Guo et al. 2014) (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9277526.v1
title: Additional file 4: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S4. PCR primers used for expression analysis by RT-qPCR (Guo et al. 2014) (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9277529
title: Additional file 5: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S5. Brassica napus genome BLAT HITs against the Arabidopsis thaliana FLOWERING LOCUS T (AT1G65480.1, RSB8/FT/chr1:24331428â 24333935) using Darmor reference assembly ( http://www.genoscope.cns.fr/blat-server/cgi-bin/colza/webBlat ). FT paralogs identified in a previous study (Schiessl et al. 2014 [45]) are also shown for comparison. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.9277529.v1
title: Additional file 5: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S5. Brassica napus genome BLAT HITs against the Arabidopsis thaliana FLOWERING LOCUS T (AT1G65480.1, RSB8/FT/chr1:24331428â 24333935) using Darmor reference assembly ( http://www.genoscope.cns.fr/blat-server/cgi-bin/colza/webBlat ). FT paralogs identified in a previous study (Schiessl et al. 2014 [45]) are also shown for comparison. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.9277535
title: Additional file 6: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S6. (A) Natural variation in flowering time in a GWAS panel of 368 lines of B. napus grown under controlled environment cabinets under short day (8 h light and 16 h dark) and long day (16 h light and 8 h dark); (B) Natural variation in flowering time in a GWAS panel of 300 lines of B. napus grown under field conditions. - represents to missing data and (C) Broad sense heritability of flowering time under controlled and field condition among canola accessions. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.9277535.v1
title: Additional file 6: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S6. (A) Natural variation in flowering time in a GWAS panel of 368 lines of B. napus grown under controlled environment cabinets under short day (8 h light and 16 h dark) and long day (16 h light and 8 h dark); (B) Natural variation in flowering time in a GWAS panel of 300 lines of B. napus grown under field conditions. - represents to missing data and (C) Broad sense heritability of flowering time under controlled and field condition among canola accessions. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.9277541
title: Additional file 7: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S7. Marker LD across B. napus genome. (CSV 1575 kb)
DOI: 10.6084/m9.figshare.9277541.v1
title: Additional file 7: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S7. Marker LD across B. napus genome. (CSV 1575 kb)
DOI: 10.6084/m9.figshare.9277547
title: Additional file 8: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S8. Familial relationships between pairs of accessions used for GWAS. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.9277547.v1
title: Additional file 8: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S8. Familial relationships between pairs of accessions used for GWAS. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.9277556
title: Additional file 9: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S9. Marker trait association identified for flowering time and photoperiodic response in a GWAS panel of canola. Response to photoperiod was assessed under controlled environment conditions, LD: Long day conditions (16 h light, 8 h dark at 20 degree); SD (8 h light, 16 h dark at 20 degree). Flowering time was also evaluated under field conditions at three sites: Wagga Wagga (irrigation, NSW, Australia), Wagga Wagga (lateral move irrigation site) and Condobolin (rainfed site, NSW, Australia) Days to flowering was used for GWAS analysis using GAPIT program in R and Golden Helix (SVS, with and without principal component analysis). (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9277556.v1
title: Additional file 9: of GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

description: Table S9. Marker trait association identified for flowering time and photoperiodic response in a GWAS panel of canola. Response to photoperiod was assessed under controlled environment conditions, LD: Long day conditions (16 h light, 8 h dark at 20 degree); SD (8 h light, 16 h dark at 20 degree). Flowering time was also evaluated under field conditions at three sites: Wagga Wagga (irrigation, NSW, Australia), Wagga Wagga (lateral move irrigation site) and Condobolin (rainfed site, NSW, Australia) Days to flowering was used for GWAS analysis using GAPIT program in R and Golden Helix (SVS, with and without principal component analysis). (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8229050
title: Methionine restriction delays senescence and suppresses the senescence-associated secretory phenotype in the kidney through endogenous hydrogen sulfide

description: Aging is a risk factor for various acute and chronic kidney injuries. Kidney aging is accompanied by the secretion of growth factors, proteases, and inflammatory cytokines, known as the senescence-associated secretory phenotype (SASP). These factors accelerate the aging process and senescence-associated changes. Delaying kidney senescence may prevent acute and chronic kidney injury. Methionine restriction (MR) was found to be an effective intervention for delaying senescence. However, the mechanism of MR remains unclear. In this study, we investigated the effect of MR on the survival rate and renal aging of C57BL/6 mice and examined the relevant mechanisms. MR increased the survival rate and decreased the levels of senescence markers in the aging kidney. Both in vivo and in vitro, MR upregulated the transsulfuration pathway to increase H<sub>2</sub>S production, downregulated senescence markers and the SASP, and activated AMPK. The ability of MR to delay aging was reduced when AMPK was inhibited. These results suggest that MR may slow animal aging and kidney senescence through H<sub>2</sub>S production and AMPK pathway activation. <b>Abbreviations</b>: DR: diet restriction; MR: methionine restriction; SASP: senescence-associated secretory phenotype; AL: ad libitum; CKD, chronic kidney disease; AKI: acute kidney disease; TSP: transsulfuration pathway; CGL: cystathionine g-lyase; H<sub>2</sub>S: hydrogen sulfide; AMPK: AMP-activated protein kinase; mTOR: mammalian target of rapamycin; IS: indoxyl sulfate; CC: compound C.
DOI: 10.6084/m9.figshare.8229050.v1
title: Methionine restriction delays senescence and suppresses the senescence-associated secretory phenotype in the kidney through endogenous hydrogen sulfide

description: Aging is a risk factor for various acute and chronic kidney injuries. Kidney aging is accompanied by the secretion of growth factors, proteases, and inflammatory cytokines, known as the senescence-associated secretory phenotype (SASP). These factors accelerate the aging process and senescence-associated changes. Delaying kidney senescence may prevent acute and chronic kidney injury. Methionine restriction (MR) was found to be an effective intervention for delaying senescence. However, the mechanism of MR remains unclear. In this study, we investigated the effect of MR on the survival rate and renal aging of C57BL/6 mice and examined the relevant mechanisms. MR increased the survival rate and decreased the levels of senescence markers in the aging kidney. Both in vivo and in vitro, MR upregulated the transsulfuration pathway to increase H<sub>2</sub>S production, downregulated senescence markers and the SASP, and activated AMPK. The ability of MR to delay aging was reduced when AMPK was inhibited. These results suggest that MR may slow animal aging and kidney senescence through H<sub>2</sub>S production and AMPK pathway activation. <b>Abbreviations</b>: DR: diet restriction; MR: methionine restriction; SASP: senescence-associated secretory phenotype; AL: ad libitum; CKD, chronic kidney disease; AKI: acute kidney disease; TSP: transsulfuration pathway; CGL: cystathionine g-lyase; H<sub>2</sub>S: hydrogen sulfide; AMPK: AMP-activated protein kinase; mTOR: mammalian target of rapamycin; IS: indoxyl sulfate; CC: compound C.
DOI: 10.6084/m9.figshare.9277649
title: MOESM1 of A network pharmacology-based study on the anti-hepatoma effect of Radix Salviae Miltiorrhizae

description: Additional file 1: Table S1. List of active ingredients in Radix Salviae Miltiorrhizae (RSM).
DOI: 10.6084/m9.figshare.9277649.v1
title: MOESM1 of A network pharmacology-based study on the anti-hepatoma effect of Radix Salviae Miltiorrhizae

description: Additional file 1: Table S1. List of active ingredients in Radix Salviae Miltiorrhizae (RSM).
DOI: 10.6084/m9.figshare.9277655
title: MOESM2 of A network pharmacology-based study on the anti-hepatoma effect of Radix Salviae Miltiorrhizae

description: Additional file 2: Table S2. List of the chemical compounds and putative targets of RSM following screening.
DOI: 10.6084/m9.figshare.9277655.v1
title: MOESM2 of A network pharmacology-based study on the anti-hepatoma effect of Radix Salviae Miltiorrhizae

description: Additional file 2: Table S2. List of the chemical compounds and putative targets of RSM following screening.
DOI: 10.6084/m9.figshare.9277658
title: MOESM3 of A network pharmacology-based study on the anti-hepatoma effect of Radix Salviae Miltiorrhizae

description: Additional file 3: Table S3. List of hepatocellular carcinoma (HCC)-related targets identified from the GeneCards and OMIM databases and common targets of RSM and HCC.
DOI: 10.6084/m9.figshare.9277658.v1
title: MOESM3 of A network pharmacology-based study on the anti-hepatoma effect of Radix Salviae Miltiorrhizae

description: Additional file 3: Table S3. List of hepatocellular carcinoma (HCC)-related targets identified from the GeneCards and OMIM databases and common targets of RSM and HCC.
DOI: 10.6084/m9.figshare.9277661
title: MOESM4 of A network pharmacology-based study on the anti-hepatoma effect of Radix Salviae Miltiorrhizae

description: Additional file 4: Table S4. Gene ontology (GO) terms and pathways.
DOI: 10.6084/m9.figshare.9277661.v1
title: MOESM4 of A network pharmacology-based study on the anti-hepatoma effect of Radix Salviae Miltiorrhizae

description: Additional file 4: Table S4. Gene ontology (GO) terms and pathways.
DOI: 10.6084/m9.figshare.9277688
title: Additional file 2 of MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations

description: : Table S1. Computing resources required for each method on four real metagenomic datasets are provided. MaxRSS refers to the maximum memory used by the corresponding method. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9277688.v1
title: Additional file 2 of MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations

description: : Table S1. Computing resources required for each method on four real metagenomic datasets are provided. MaxRSS refers to the maximum memory used by the corresponding method. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9277697
title: Additional file 3 of MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations

description: : Table S2. Number of assembled contigs from unmapped reads and number of detected viral contigs by VirFinder for each dataset are provided. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9277697.v1
title: Additional file 3 of MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations

description: : Table S2. Number of assembled contigs from unmapped reads and number of detected viral contigs by VirFinder for each dataset are provided. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9277706
title: Additional file 4 of MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations

description: : Table S3. Significantly associated microbes selected by Boruta feature selection method for each dataset are provided. The table also shows the mean abundance in cases and controls for each selected microbes together with a FDR-adjusted WMW test p value for differences in the mean abundances. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.9277706.v1
title: Additional file 4 of MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations

description: : Table S3. Significantly associated microbes selected by Boruta feature selection method for each dataset are provided. The table also shows the mean abundance in cases and controls for each selected microbes together with a FDR-adjusted WMW test p value for differences in the mean abundances. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.9277715
title: Additional file 5 of MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations

description: : Table S4. A genus-level assignment for each MAG generated from four metagenomic datasets is given. The corresponding Mash distance and p value are also provided. A MAG with multiple hits in the database is reported in the table only if all of its hits belong to a common microbial genus in the taxonomy tree. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.9277715.v1
title: Additional file 5 of MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations

description: : Table S4. A genus-level assignment for each MAG generated from four metagenomic datasets is given. The corresponding Mash distance and p value are also provided. A MAG with multiple hits in the database is reported in the table only if all of its hits belong to a common microbial genus in the taxonomy tree. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.8229143
title: Data (vegetation, seed bank and soil environmental data).xlsx

description: The related paper has been accept by Ecological Applications.
DOI: 10.6084/m9.figshare.15567763.v1
title: Additional file 1 of Time series analysis of hemorrhagic fever with renal syndrome in mainland China by using an XGBoost forecasting model

description: Additional file 1. Monthly cases of hemorrhagic fever with renal syndrome in Mainland China from 2004 to 2018.
DOI: 10.5281/zenodo.3981104
title: Topological Network of the Dutch Fairway Information System

description: Topological fairway network derived from the Dutch Fairway Information System. The data is processed to be topological connected and usable for transport network analysis.  


Files


network_digital_twin_v0.3.json This is the json (for web) file for the Rhine corridor extending from Rotterdam (NLD) to Basel (Switzerland).


network_digital_twin_v0.3.pickle This is the pickled (for performance) file for the Rhine corridor extending from Rotterdam (NLD) to Basel (Switzerland).


network_digital_twin_v0.3.zip This is the shapefile (for gis) file for the Rhine corridor extending from Rotterdam (NLD) to Basel (Switzerland).


Methodological information


For details about the creation of the network see Build_FIS_network.ipynb.


Updates in version 0.3.0:


- Added information on discharge dependent velocities and waterlevels in river_waterlevel.geojson and river_velocity.geojson


- Moved information on bathymetry to separate fileedges_0.3_with_bathy.geojson


- More structures added (fix in source dataset)


- Edge and node id's are now always strings


- Removed yaml file. It was not efficient enough and reading functionality is removed from networkx


 


Updates in version 0.2.0:


- added bathymetry info: mean, standard deviation , percentiles [0 (min), 5,  10, 50 (median),  90, 95, 100 (max)]


- added new output formats: added shapely compatible geometry type


Source data for the network is available at https://www.vaarweginformatie.nl/.


Sharing and Access information


CC BY-SA 4.0 license applies: https://creativecommons.org/licenses/by-sa/4.0/.