cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16649839
title: Supplementary material

description: Table S01. Metadata. The table provides the SRA experiment identifiers for the reference and Gulf metagenomes, including the related MG-RAST identifier, geographical location, latitude, longitude, depth, library instrument, library layout, and PubMed references.<br><br>Table S02. PDF describing the annotated enzymes in the reference. The table shows the PDF describing the behavior of each enzyme in the reference metagenomes (normal, log-normal, gamma, and Weibull distributions).<br><br>Table S03. PDF of enzymes in metabolic pathways. The table shows the PDF describing the behavior of each enzyme in the reference metagenomes for which a metabolic pathway is described.<br><br>Table S04. EZSs of enzymes found in metabolic pathways. Enzymes with an assigned EZS were classified into the corresponding KEGG BRITE classes and metabolic maps.<br><br>Table S05. Statistical properties of enzymes grouped into BRITE classes. A summary of the measures of the central tendency and quartiles is shown in the table with the enzymes grouped into the BRITE classes.<br><br>Table S06. EC equivalences. We show the enzyme names associated with ECs related to the figures in the main text.<br><br>
DOI: 10.6084/m9.figshare.16649839.v1
title: Supplementary material

description: Table S01. Metadata. The table provides the SRA experiment identifiers for the reference and Gulf metagenomes, including the related MG-RAST identifier, geographical location, latitude, longitude, depth, library instrument, library layout, and PubMed references.<br><br>Table S02. PDF describing the annotated enzymes in the reference. The table shows the PDF describing the behavior of each enzyme in the reference metagenomes (normal, log-normal, gamma, and Weibull distributions).<br><br>Table S03. PDF of enzymes in metabolic pathways. The table shows the PDF describing the behavior of each enzyme in the reference metagenomes for which a metabolic pathway is described.<br><br>Table S04. EZSs of enzymes found in metabolic pathways. Enzymes with an assigned EZS were classified into the corresponding KEGG BRITE classes and metabolic maps.<br><br>Table S05. Statistical properties of enzymes grouped into BRITE classes. A summary of the measures of the central tendency and quartiles is shown in the table with the enzymes grouped into the BRITE classes.<br><br>Table S06. EC equivalences. We show the enzyme names associated with ECs related to the figures in the main text.<br><br>
DOI: 10.17909/t9-rd26-dv46
title: HST Data from "Tidal Distortions in NGC1052-DF2 and NGC1052-DF4: Independent Evidence for a Lack of Dark Matter"

description: We use Hubble Space Telescope (HST) Advanced Camera for Surveys (ACS) imaging to study the morphology of the galaxies' inner regions. These observations, as detailed in Danieli et al. 2020 and Shen et al. 2021, were taken during Cycles 24 (program 14644), 26 (program 15695), and 27 (program 15851), imaging NGC1052-DF4 over 8 orbits in the F814W filter and 4 orbits in the F606W filter and NGC1052-DF2 over 20 orbits in each filter.
DOI: 10.6084/m9.figshare.16649884
title: Supplementary Data File 2 targetaml_raw_mat.csv

description: transcriptome data sets of targetaml
DOI: 10.6084/m9.figshare.16649890
title: Supplementary Data File 3 laml_raw_mat.csv

description: transcriptome data sets of Laml
DOI: 10.6084/m9.figshare.16649887
title: Supplementary Data File 1 beataml_raw_mat.csv

description: transcriptome data sets of BeatAMl
DOI: 10.6084/m9.figshare.16649857.v1
title: Methylation_Phasing_Test.tar

description: This is a test nanopore dataset for methylation phasing tutorial. A tiny subset for chr11:1000000-3000000 from NA12858 dataset at Nanopore WGS consortium GitHub (https://github.com/nanopore-wgs-consortium/NA12878).
DOI: 10.6084/m9.figshare.16649857
title: Methylation_Phasing_Test.tar

description: This is a test nanopore dataset for methylation phasing tutorial. A tiny subset for chr11:1000000-3000000 from NA12858 dataset at Nanopore WGS consortium GitHub (https://github.com/nanopore-wgs-consortium/NA12878).
DOI: 10.5281/zenodo.5518246
title: Reprocessed genomics data sets at different read depths

description: Six tracks that are reprocessed versions at different read depths from a single set of bams.
DOI: 10.5281/zenodo.5518245
title: Reprocessed genomics data sets at different read depths

description: Six tracks that are reprocessed versions at different read depths from a single set of bams.
DOI: 10.6084/m9.figshare.16649800.v1
title: Native herbivores indirectly facilitate the growth of invasive Spartina in a eutrophic saltmarsh

description: These data were collected to explain how eutrophication interact with native herbivores to facilitate the growth of a globally invasive species <i>Spartina alterniflora</i> in coastal China by using a two year field nitrogen (N)-enrichment X crab exclusion experiment.
DOI: 10.5281/zenodo.5518253
title: Bathymetry beneath the Amery ice shelf, East Antarctica, revealed by airborne gravity

description: We estimated the seafloor topography beneath the Amery Ice Shelf, East Antarctica, from airborne gravity anomaly through a nonlinear inversion method called simulated annealing. The estimation results provide a view of the seafloor beneath the Amery Ice Shelf, where direct bathymetric observations are rare. The model, 'gravity_estimated_seafloor_topography_beneath_the_Amery_Ice_Shelf.nc', is in NetCDF format which can be read through MATLAB commands "ncdisp" and "ncread". Contents of the model can be found in "contents.txt". The MATLAB program "nc2mat.m" reads the NetCDF ".nc" format model and saves the variables in the model to a MATLAB ".mat" format file.
description: {"references": ["Yang, J. et al. (2021). Bathymetry beneath the Amery Ice Shelf, East Antarctica, revealed by airborne gravity. Geophysical Research Letters. (under review)"]}
DOI: 10.5281/zenodo.5518252
title: Bathymetry beneath the Amery ice shelf, East Antarctica, revealed by airborne gravity

description: We estimated the seafloor topography beneath the Amery Ice Shelf, East Antarctica, from airborne gravity anomaly through a nonlinear inversion method called simulated annealing. The estimation results provide a view of the seafloor beneath the Amery Ice Shelf, where direct bathymetric observations are rare. The model, 'gravity_estimated_seafloor_topography_beneath_the_Amery_Ice_Shelf.nc', is in NetCDF format which can be read through MATLAB commands "ncdisp" and "ncread". Contents of the model can be found in "contents.txt". The MATLAB program "nc2mat.m" reads the NetCDF ".nc" format model and saves the variables in the model to a MATLAB ".mat" format file.
description: {"references": ["Yang, J. et al. (2021). Bathymetry beneath the Amery Ice Shelf, East Antarctica, revealed by airborne gravity. Geophysical Research Letters. (under review)"]}
DOI: 10.6084/m9.figshare.16649800.v2
title: Native herbivores indirectly facilitate the growth of invasive Spartina in a eutrophic saltmarsh

description: These data were collected to explain how eutrophication interact with native herbivores to facilitate the growth of a globally invasive species <i>Spartina alterniflora</i> in coastal China by using a two year field nitrogen (N)-enrichment X crab exclusion experiment.
DOI: 10.6084/m9.figshare.16649800.v3
title: Native herbivores indirectly facilitate the growth of invasive Spartina in a eutrophic saltmarsh

description: These data were collected to explain how eutrophication interact with native herbivores to facilitate the growth of a globally invasive species <i>Spartina alterniflora</i> in coastal China by using a two year field nitrogen (N)-enrichment X crab exclusion experiment.
DOI: 10.26180/16621096
title: Supplementary Figure 3 data

description: Supplementary Figure 3 data
DOI: 10.26180/16621096.v1
title: Supplementary Figure 3 data

description: Supplementary Figure 3 data
DOI: 10.3886/e112931v1-96620
title: Replication data for: Delinking Land Rights from Land Use: Certification and Migration in Mexico

description: In many developing countries property rights over rural land are maintained through continuous personal use instead of by land titles. We show that removing the link between land use and land rights through the issuance of ownership certificates can result in large-scale adjustments to labor and land allocations. Using the rollout of the Mexican land certification program from 1993 to 2006, we find that households obtaining certificates were subsequently 28 percent more likely to have a migrant member. We also show that even though land certification induced migration, it had little effect on cultivated area due to consolidation of farm units. (JEL O13, O17, P14, Q15, Q18, Q24, Q28)
DOI: 10.6084/m9.figshare.16649981
title: Additional file 1 of Waardenburg syndrome type 2A in a large Iranian family with a novel MITF gene mutation

description: Additional file 1. Peer review reports.
DOI: 10.6084/m9.figshare.16649981.v1
title: Additional file 1 of Waardenburg syndrome type 2A in a large Iranian family with a novel MITF gene mutation

description: Additional file 1. Peer review reports.
DOI: 10.6084/m9.figshare.16649984
title: Additional file 1 of Analysing the impact of the two most common SARS-CoV-2 nucleocapsid protein variants on interactions with membrane protein in silico

description: Supplementary Table 1A. – Complete list of closely situated residues from mutant N protein and M protein in the docked complex.
DOI: 10.6084/m9.figshare.16649984.v1
title: Additional file 1 of Analysing the impact of the two most common SARS-CoV-2 nucleocapsid protein variants on interactions with membrane protein in silico

description: Supplementary Table 1A. – Complete list of closely situated residues from mutant N protein and M protein in the docked complex.
DOI: 10.6084/m9.figshare.16649990
title: Additional file 2 of Analysing the impact of the two most common SARS-CoV-2 nucleocapsid protein variants on interactions with membrane protein in silico

description: Supplementary Table 1B. – Complete list of closely situated residues from wild type N protein and M protein in the docked complex.
DOI: 10.6084/m9.figshare.16649990.v1
title: Additional file 2 of Analysing the impact of the two most common SARS-CoV-2 nucleocapsid protein variants on interactions with membrane protein in silico

description: Supplementary Table 1B. – Complete list of closely situated residues from wild type N protein and M protein in the docked complex.
DOI: 10.6084/m9.figshare.16650098
title: Additional file 4 of Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus

description: Additional file 4: Table S2. Genes differentially expressed between EC and leaf.
DOI: 10.6084/m9.figshare.16650098.v1
title: Additional file 4 of Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus

description: Additional file 4: Table S2. Genes differentially expressed between EC and leaf.
DOI: 10.6084/m9.figshare.16650104
title: Additional file 5 of Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus

description: Additional file 5: Table S3. TE families differentially expressed between EC and leaf.
DOI: 10.6084/m9.figshare.16650104.v1
title: Additional file 5 of Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus

description: Additional file 5: Table S3. TE families differentially expressed between EC and leaf.
DOI: 10.6084/m9.figshare.16650110.v1
title: Additional file 1 of Validation of multiple equations for estimating low-density lipoprotein cholesterol levels in Korean adults

description: Additional file 1: Supplementary Material S1. LDL calculators for the 12 equations.
DOI: 10.6084/m9.figshare.16650110
title: Additional file 1 of Validation of multiple equations for estimating low-density lipoprotein cholesterol levels in Korean adults

description: Additional file 1: Supplementary Material S1. LDL calculators for the 12 equations.
DOI: 10.6084/m9.figshare.16650116.v1
title: Additional file 2 of Validation of multiple equations for estimating low-density lipoprotein cholesterol levels in Korean adults

description: Additional file 2: Supplementary Table S1. Intraclass correlation coefficient and systemic differences among the 12 equations in comparison with directly measured LDL. Supplementary Table S2. Limits of agreement and absolute error among the 12 equations in comparison with directly measured LDL. Supplementary Table S3. Intraclass correlation coefficient and systemic differences among the 12 equations in comparison with directly measured LDL (LDLdirect) by subgroup of LDL concentration. Supplementary Table S4. Limits of agreement and absolute error among the 12 equations in comparison with directly measured LDL by subgroup of LDL concentration. Supplementary Table S5. Intraclass correlation coefficient and systemic differences among the 12 equations in comparison with directly measured LDL according to subgroup by triglyceride (TG) concentration. Supplementary Table S6. Limit of agreement and absolute percentage errors among the 12 equations in comparison with directly measured LDL according to subgroups by triglyceride (TG) concentration. Supplementary Fig. S1. Bland–Altman plots for the 12 equations with directly measured LDL concentration. Supplementary Fig. S2. Overall agreement of categorization according to the NCEP ATP III between calculated LDL and directly measured LDL by LDL subgroup. Supplementary Fig. S3. Overall agreement of categorization according to the NCEP ATP III between calculated LDL and directly measured LDL by TG subgroup.
DOI: 10.6084/m9.figshare.16650119.v1
title: Additional file 1 of Rare novel LPL mutations are associated with neonatal onset lipoprotein lipase (LPL) deficiency in two cases

description: Additional file 1.
DOI: 10.6084/m9.figshare.16650119
title: Additional file 1 of Rare novel LPL mutations are associated with neonatal onset lipoprotein lipase (LPL) deficiency in two cases

description: Additional file 1.
DOI: 10.6084/m9.figshare.16650116
title: Additional file 2 of Validation of multiple equations for estimating low-density lipoprotein cholesterol levels in Korean adults

description: Additional file 2: Supplementary Table S1. Intraclass correlation coefficient and systemic differences among the 12 equations in comparison with directly measured LDL. Supplementary Table S2. Limits of agreement and absolute error among the 12 equations in comparison with directly measured LDL. Supplementary Table S3. Intraclass correlation coefficient and systemic differences among the 12 equations in comparison with directly measured LDL (LDLdirect) by subgroup of LDL concentration. Supplementary Table S4. Limits of agreement and absolute error among the 12 equations in comparison with directly measured LDL by subgroup of LDL concentration. Supplementary Table S5. Intraclass correlation coefficient and systemic differences among the 12 equations in comparison with directly measured LDL according to subgroup by triglyceride (TG) concentration. Supplementary Table S6. Limit of agreement and absolute percentage errors among the 12 equations in comparison with directly measured LDL according to subgroups by triglyceride (TG) concentration. Supplementary Fig. S1. Bland–Altman plots for the 12 equations with directly measured LDL concentration. Supplementary Fig. S2. Overall agreement of categorization according to the NCEP ATP III between calculated LDL and directly measured LDL by LDL subgroup. Supplementary Fig. S3. Overall agreement of categorization according to the NCEP ATP III between calculated LDL and directly measured LDL by TG subgroup.
DOI: 10.6084/m9.figshare.16650209
title: Additional file 1 of The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells

description: Additional file 1: Supplemental Table S1. FIMO analysis of immediate signaling-dependent TF motifs among promoters of early-responding TFs that are more expressed at 2 h vs steady state.
DOI: 10.6084/m9.figshare.16650209.v1
title: Additional file 1 of The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells

description: Additional file 1: Supplemental Table S1. FIMO analysis of immediate signaling-dependent TF motifs among promoters of early-responding TFs that are more expressed at 2 h vs steady state.
DOI: 10.6084/m9.figshare.16650212
title: Additional file 2 of The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells

description: Additional file 2: Supplemental Table S2. FIMO analysis of immediate signaling-dependent TF motifs among promoters of early-responding TFs that are less expressed at 2 h vs steady state.
DOI: 10.6084/m9.figshare.16650212.v1
title: Additional file 2 of The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells

description: Additional file 2: Supplemental Table S2. FIMO analysis of immediate signaling-dependent TF motifs among promoters of early-responding TFs that are less expressed at 2 h vs steady state.
DOI: 10.6084/m9.figshare.16650218
title: Additional file 3 of The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells

description: Additional file 3: Supplemental Table S3. FIMO analysis of early-responding TF motif presence in promoters of up-regulated late-responding TF genes.
DOI: 10.6084/m9.figshare.16650218.v1
title: Additional file 3 of The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells

description: Additional file 3: Supplemental Table S3. FIMO analysis of early-responding TF motif presence in promoters of up-regulated late-responding TF genes.
DOI: 10.6084/m9.figshare.16650230
title: Additional file 5 of The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells

description: Additional file 5: Supplemental Table S5. Functional cluster analysis with 661 CpG-dependent TF genes.
DOI: 10.6084/m9.figshare.16650227.v1
title: Additional file 4 of The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells

description: Additional file 4: Supplemental Table S4. FIMO analysis of early-responding TF motif presence in promoters of down-regulated late-responding TF genes.
DOI: 10.6084/m9.figshare.16650227
title: Additional file 4 of The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells

description: Additional file 4: Supplemental Table S4. FIMO analysis of early-responding TF motif presence in promoters of down-regulated late-responding TF genes.
DOI: 10.6084/m9.figshare.16650230.v1
title: Additional file 5 of The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells

description: Additional file 5: Supplemental Table S5. Functional cluster analysis with 661 CpG-dependent TF genes.
DOI: 10.6084/m9.figshare.16650236
title: Additional file 6 of The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells

description: Additional file 6: Supplemental Table S6. Centrimo motif enrichment analysis using the HOCOMOCO database and 2174 gene promoter associated regions with increased chromatin accessibility after pDC activation.
DOI: 10.6084/m9.figshare.16650236.v1
title: Additional file 6 of The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells

description: Additional file 6: Supplemental Table S6. Centrimo motif enrichment analysis using the HOCOMOCO database and 2174 gene promoter associated regions with increased chromatin accessibility after pDC activation.
DOI: 10.6084/m9.figshare.16650242
title: Additional file 7 of The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells

description: Additional file 7: Supplemental Table S7. FIMO analysis of immediate signaling-dependent TF motifs among promoters of early-responding TFs that are more expressed and have more accessible chromatin at 2 h vs steady state.
DOI: 10.6084/m9.figshare.16650242.v1
title: Additional file 7 of The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells

description: Additional file 7: Supplemental Table S7. FIMO analysis of immediate signaling-dependent TF motifs among promoters of early-responding TFs that are more expressed and have more accessible chromatin at 2 h vs steady state.
DOI: 10.5281/zenodo.5518301
title: RibSeg Dataset

description: This dataset is mistakenly uploaded, please see the RibSeg dataset in https://zenodo.org/record/5336592#.YUlTYLj0kac
DOI: 10.5281/zenodo.5518300
title: RibSeg Dataset

description: This dataset is mistakenly uploaded, please see the RibSeg dataset in https://zenodo.org/record/5336592#.YUlTYLj0kac
DOI: 10.6084/m9.figshare.16650329
title: Additional file 3 of Overexpression of a Novel ERF-X-Type Transcription Factor, OsERF106MZ, Reduces Shoot Growth and Tolerance to Salinity Stress in Rice

description: Additional file 3. Data S1 OsERF106-related DEGs.
DOI: 10.6084/m9.figshare.16650335
title: Additional file 4 of Overexpression of a Novel ERF-X-Type Transcription Factor, OsERF106MZ, Reduces Shoot Growth and Tolerance to Salinity Stress in Rice

description: Additional file 4. Data S2 Common DEGs.
DOI: 10.6084/m9.figshare.16650329.v1
title: Additional file 3 of Overexpression of a Novel ERF-X-Type Transcription Factor, OsERF106MZ, Reduces Shoot Growth and Tolerance to Salinity Stress in Rice

description: Additional file 3. Data S1 OsERF106-related DEGs.
DOI: 10.6084/m9.figshare.16650335.v1
title: Additional file 4 of Overexpression of a Novel ERF-X-Type Transcription Factor, OsERF106MZ, Reduces Shoot Growth and Tolerance to Salinity Stress in Rice

description: Additional file 4. Data S2 Common DEGs.
DOI: 10.6084/m9.figshare.16650344
title: Additional file 1 of Patient-centered infertility questionnaire for female clients (PCIQ-F): part I: questionnaire development

description: Additional file 1: Item pool with face validity index for calrity and importance, and the decision taken. FVI and S-FVI/Ave after deleting items. Content validity index with items decision. The items for draft patient-centered infertility care questionnaire for female clients (PCIQ-F), with item and domain content validity index.
DOI: 10.6084/m9.figshare.16650344.v1
title: Additional file 1 of Patient-centered infertility questionnaire for female clients (PCIQ-F): part I: questionnaire development

description: Additional file 1: Item pool with face validity index for calrity and importance, and the decision taken. FVI and S-FVI/Ave after deleting items. Content validity index with items decision. The items for draft patient-centered infertility care questionnaire for female clients (PCIQ-F), with item and domain content validity index.
DOI: 10.6084/m9.figshare.14889694
title: Additional file 1 of Transcriptome signature of miRNA-26b KO mouse model suggests novel targets

description: Additional file 1.
DOI: 10.6084/m9.figshare.14889694.v1
title: Additional file 1 of Transcriptome signature of miRNA-26b KO mouse model suggests novel targets

description: Additional file 1.
DOI: 10.6084/m9.figshare.16650365
title: Additional file 1 of A cancer-unique glycan: de-N-acetyl polysialic acid (dPSA) linked to cell surface nucleolin depends on re-expression of the fetal polysialyltransferase ST8SIA2 gene

description: Additional file 1:. LC/MS/MS Cluster Report Data File.
DOI: 10.6084/m9.figshare.16650365.v1
title: Additional file 1 of A cancer-unique glycan: de-N-acetyl polysialic acid (dPSA) linked to cell surface nucleolin depends on re-expression of the fetal polysialyltransferase ST8SIA2 gene

description: Additional file 1:. LC/MS/MS Cluster Report Data File.