cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9994961.v3
title: Model data for article submitted to JGR-Oceans (Feng Tian, Rong-Hua Zhang, Xiujun Wang)

description: Upload are model data submitted to JGR-Oceans， but not been accpted.
DOI: 10.6084/m9.figshare.9994961.v2
title: Model data for article submitted to JGR-Oceans (Feng Tian, Rong-Hua Zhang, Xiujun Wang)

description: Upload are model data submitted to JGR-Oceans
DOI: 10.6084/m9.figshare.9994853
title: Fabrication of core-sheath nanoyarn via touchspinning and its application in wearable piezoelectric nanogenerator

description: A simple and versatile touchspinning method is demonstrated for the fabrication of core-sheath nanofibrous piezoelectric yarns with a single filament electroconductive core. The polyvinylidene fluoride (PVDF) piezoelectric nanofibers are fabricated in a continuous spinning process with relatively controlled structure, orientation, and dimensions to form a sheath layer. The PVDF core-sheath nanoyarn is assembled into a piezoelectric nanogenerator (PNG) capable to convert mechanical energy of body motion into electricity. It was demonstrated that an electrical potential difference of 0.72 V can be generated under compression of 0.33 MPa for a single 3-cm long yarn. The touchspun nanoyarn fabrication method has great potential for the fabrication of functional smart textile products.
DOI: 10.6084/m9.figshare.9994853.v1
title: Fabrication of core-sheath nanoyarn via touchspinning and its application in wearable piezoelectric nanogenerator

description: A simple and versatile touchspinning method is demonstrated for the fabrication of core-sheath nanofibrous piezoelectric yarns with a single filament electroconductive core. The polyvinylidene fluoride (PVDF) piezoelectric nanofibers are fabricated in a continuous spinning process with relatively controlled structure, orientation, and dimensions to form a sheath layer. The PVDF core-sheath nanoyarn is assembled into a piezoelectric nanogenerator (PNG) capable to convert mechanical energy of body motion into electricity. It was demonstrated that an electrical potential difference of 0.72 V can be generated under compression of 0.33 MPa for a single 3-cm long yarn. The touchspun nanoyarn fabrication method has great potential for the fabrication of functional smart textile products.
DOI: 10.6084/m9.figshare.9994826
title: Behavioral data

description: <b>Metadata</b><br>subject: unique participant code<br> trial: trial number <br> run: run number <br> condition: whether the conclusion is an argument or an assertion <br> plausibility: whether the conclusion is necessary, impossible, plausible or implausible <br> category: whether line #2 focuses on a superior (i.e., sup) or an inferior category (i.e., inf). For example, a superior category would be “flowers” and an inferior category would be “roses” <br> form: form of the syllogism <br> response_type: Form of the statement in line #4 (A: All X are Y; I: Some X are Y; E: No X are Y; O: Some X are not Y) <br> characters: characters used in the story <br> story: story framework <br> line: line number <br> agreement: whether the participants agrees (1) or not (0) with the conclusion <br> rt: reading time of the conclusion (in sec) <br> fillers: whether the story is a filler (1) or not (0)<br>environment: whether participants were tested in the MRI scanner (inside_scanner) or not (outside_scanner)
DOI: 10.6084/m9.figshare.9994829
title: Data from Stier et al. 2019 (Ageing before birth: pace and stability of prenatal growth affect telomere dynamics)

description: Datasets used in Stier et al. 2019 (Ageing before birth: pace and stability of prenatal growth affect telomere dynamics). The first excel sheet contains some general information, and specific information about parameters can be found in the publication and ESM<br>
DOI: 10.6084/m9.figshare.9994826.v1
title: Behavioral data

description: <b>Metadata</b><br>subject: unique participant code<br> trial: trial number <br> run: run number <br> condition: whether the conclusion is an argument or an assertion <br> plausibility: whether the conclusion is necessary, impossible, plausible or implausible <br> category: whether line #2 focuses on a superior (i.e., sup) or an inferior category (i.e., inf). For example, a superior category would be “flowers” and an inferior category would be “roses” <br> form: form of the syllogism <br> response_type: Form of the statement in line #4 (A: All X are Y; I: Some X are Y; E: No X are Y; O: Some X are not Y) <br> characters: characters used in the story <br> story: story framework <br> line: line number <br> agreement: whether the participants agrees (1) or not (0) with the conclusion <br> rt: reading time of the conclusion (in sec) <br> fillers: whether the story is a filler (1) or not (0)<br>environment: whether participants were tested in the MRI scanner (inside_scanner) or not (outside_scanner)
DOI: 10.6084/m9.figshare.9994829.v1
title: Data from Stier et al. 2019 (Ageing before birth: pace and stability of prenatal growth affect telomere dynamics)

description: Datasets used in Stier et al. 2019 (Ageing before birth: pace and stability of prenatal growth affect telomere dynamics). The first excel sheet contains some general information, and specific information about parameters can be found in the publication and ESM<br>
DOI: 10.6084/m9.figshare.9994799
title: Bayesian Inference of Neural Assemblies - Zebrafish functional imaging

description: This figshare project contains the zebrafish functional imaging data used in the PLOS computation publication "Bayesian Inference of neural assemblies". <br>All recordings were of one hour of spontaneous activity from the optic tectum of 7 dpf zebrafish whilst they were in complete darkness. These zebrafish were expressing HuC:GCaMP6s and imaged at 4.8Hz per volume (5 slices in a volume).<br> Here we have 3 files for each fish each with a different suffix denoting the data type: <br>"_centers_cut_ordered.dat" files contain the coordinates of cell bodies for each of the segmented neurons. Columns are coordinates (XYZ) and each row is a neuron. Z coordinates refer to the slice number within the volume (5 slices). <br>"_traces.dat" - raw fluorescence traces for each neuron. This is a Neuron x Time matrix where the rows match the rows in the cell centers file. <br>"_spikes.dat" - Binarised version of "_traces.dat". N x T matrix. These were used as input to the bayesian analysis.
DOI: 10.6084/m9.figshare.9994784
title: File S20. QP-IC Scores Table

description: Contains the QP-IC scores of branches for each locus combination of the 8-bin binning strategy, as well as the complete data set. The most consistent locus is that which produced the largest absolute QP-IC across all loci. Tips do not have QP-IC scores. See File S9 for a mapping of edge numbers to the RAxML phylogeny.
DOI: 10.6084/m9.figshare.9994784.v1
title: File S18. QP-IC Scores Table

description: Contains the QP-IC scores of branches for each locus combination of the 8-bin binning strategy, as well as the complete data set. The most consistent locus is that which produced the largest absolute QP-IC across all loci. Tips do not have QP-IC scores. See File S19 for a mapping of edge numbers to the RAxML phylogeny.
DOI: 10.6084/m9.figshare.9994784.v2
title: File S20. QP-IC Scores Table

description: Contains the QP-IC scores of branches for each locus combination of the 8-bin binning strategy, as well as the complete data set. The most consistent locus is that which produced the largest absolute QP-IC across all loci. Tips do not have QP-IC scores. See File S9 for a mapping of edge numbers to the RAxML phylogeny.
DOI: 10.6084/m9.figshare.9994748
title: File S14. Reduced Probe Sets

description: Contains the reduced probe sets for the 8-bin binning strategy which produced well-supported phylogenies (<i>i.e.</i>, 50 loci, 100 loci, 175 loci, 225 loci) ("8bin_reduced_probe_sets"), as well as all reduced sets (<i>i.e.</i>, 50, 100, 175, 225, 300, 375, 475 loci) for all binning strategies (2-8 bins) ("all_sensitivity_analysis_sets").
DOI: 10.6084/m9.figshare.9994748.v1
title: File S12. Reduced Probe Sets

description: Contains the reduced probe sets for the 8-bin binning strategy which produced well-supported phylogenies (<i>i.e.</i>, 50 loci, 100 loci, 175 loci, 225 loci) ("8bin_reduced_probe_sets"), as well as all reduced sets (<i>i.e.</i>, 50, 100, 175, 225, 300, 375, 475 loci) for all binning strategies (2-8 bins) ("all_sensitivity_analysis_sets").
DOI: 10.6084/m9.figshare.9994748.v3
title: File S14. Reduced Probe Sets

description: Contains the reduced probe sets for the 8-bin binning strategy which produced well-supported phylogenies (<i>i.e.</i>, 50 loci, 100 loci, 175 loci, 225 loci) ("8bin_reduced_probe_sets"), as well as all reduced sets (<i>i.e.</i>, 50, 100, 175, 225, 300, 375, 475 loci) for all binning strategies (2-8 bins) ("all_sensitivity_analysis_sets").
DOI: 10.6084/m9.figshare.9994748.v2
title: File S14. Reduced Probe Sets

description: Contains the reduced probe sets for the 8-bin binning strategy which produced well-supported phylogenies (<i>i.e.</i>, 50 loci, 100 loci, 175 loci, 225 loci) ("8bin_reduced_probe_sets"), as well as all reduced sets (<i>i.e.</i>, 50, 100, 175, 225, 300, 375, 475 loci) for all binning strategies (2-8 bins) ("all_sensitivity_analysis_sets").
DOI: 10.6084/m9.figshare.9994703
title: File S6. NEXUS Tree Files

description: Contains all the phylogenies constructed in this study in NEXUS format. Note: the QP-IC scores are stored in such a way that FigTree 1.4.3 does not readily display them. Use a text editor and/or some other software to view these values.
DOI: 10.6084/m9.figshare.9994691
title: File S5. Complete DNA Alignment

description: Contains the complete alignment of nucleotide data for all taxa and all loci used to construct phylogenies in PHYLIP format.
DOI: 10.6084/m9.figshare.9994706.v1
title: Benchmark analysis of coiled-coil prediction tools

description: This repository contains the raw data for the publication "Protein function prediction in genomes: Critical assessment of coiled-coil predictions based on protein structure data". The tar file contains all the millions of files, sorted by the first letters of the PDB ids, containing the PDBs, sequences, and predictions. The database dump contains the database.<br>
DOI: 10.6084/m9.figshare.9994685
title: File S4 - Individual Loci Alignments

description: Individual alignments of each of the 729 recovered loci in the NOC1 probe kit in PHYLIP format.
DOI: 10.6084/m9.figshare.9994652
title: File S3 - Probe Set Details Table

description: Contains information about which probes were recovered from each taxon (“Probe Recovery Profile”), the number of taxa recovered by each probe (“Probe Recovery Summary Stats”), and various probe statistics (“Probe Statistics”; <i>e.g.</i>, length, GC content).<br>
DOI: 10.6084/m9.figshare.9994691.v1
title: File S4. Complete DNA Alignment

description: Contains the complete alignment of nucleotide data for all taxa and all loci used to construct phylogenies in PHYLIP format.
DOI: 10.6084/m9.figshare.9994703.v1
title: File S5. NEXUS Tree Files

description: Contains all the phylogenies constructed in this study in NEXUS format. Note: the QP-IC scores are stored in such a way that FigTree 1.4.3 does not readily display them. Use a text editor and/or some other software to view these values.
DOI: 10.6084/m9.figshare.9994685.v1
title: File S3 - Individual Loci Alignments

description: Individual alignments of each of the 729 recovered loci in the ARC-ToL probe kit in PHYLIP format.
DOI: 10.6084/m9.figshare.9994646
title: File S1 - Taxon Sampling Table

description: The first sheet contains information about the taxa used for Anchored Hybrid Enrichment, including collection localities and read recovery for each taxon. The second sheet contains information about the samples used in the analysis of COI, including information for the samples obtained from GenBank.<br>
DOI: 10.6084/m9.figshare.9994691.v2
title: File S5. Complete DNA Alignment

description: Contains the complete alignment of nucleotide data for all taxa and all loci used to construct phylogenies in PHYLIP format.
DOI: 10.6084/m9.figshare.9994685.v3
title: File S4 - Individual Loci Alignments

description: Individual alignments of each of the 729 recovered loci in the NOC1 probe kit in PHYLIP format.
DOI: 10.6084/m9.figshare.9994652.v1
title: File S2 - Probe Set Details Table

description: Contains information about which probes were recovered from each taxon (“Probe Recovery Profile”), the number of taxa recovered by each probe (“Probe Recovery Summary Stats”), and various probe statistics (“Probe Statistics”; <i>e.g.</i>, length, GC content).<br>
DOI: 10.6084/m9.figshare.9994685.v2
title: File S4 - Individual Loci Alignments

description: Individual alignments of each of the 729 recovered loci in the ARC-ToL probe kit in PHYLIP format.
DOI: 10.6084/m9.figshare.9994703.v2
title: File S6. NEXUS Tree Files

description: Contains all the phylogenies constructed in this study in NEXUS format. Note: the QP-IC scores are stored in such a way that FigTree 1.4.3 does not readily display them. Use a text editor and/or some other software to view these values.
DOI: 10.6084/m9.figshare.9994652.v3
title: File S3 - Probe Set Details Table

description: Contains information about which probes were recovered from each taxon (“Probe Recovery Profile”), the number of taxa recovered by each probe (“Probe Recovery Summary Stats”), and various probe statistics (“Probe Statistics”; <i>e.g.</i>, length, GC content).<br>
DOI: 10.6084/m9.figshare.9994586
title: Divergent effects of translation termination factor eRF3A and nonsense-mediated mRNA decay factor UPF1 on the expression of uORF carrying mRNAs and ribosome protein genes

description: In addition to its role in translation termination, eRF3A has been implicated in the nonsense-mediated mRNA decay (NMD) pathway through its interaction with UPF1. NMD is a RNA quality control mechanism, which detects and degrades aberrant mRNAs as well as some normal transcripts including those that harbour upstream open reading frames in their 5ʹ leader sequence. In this study, we used RNA-sequencing and ribosome profiling to perform a genome wide analysis of the effect of either eRF3A or UPF1 depletion in human cells. Our bioinformatics analyses allow to delineate the features of the transcripts controlled by eRF3A and UPF1 and to compare the effect of each of these factors on gene expression. We find that eRF3A and UPF1 have very different impacts on the human transcriptome, less than 250 transcripts being targeted by both factors. We show that eRF3A depletion globally derepresses the expression of mRNAs containing translated uORFs while UPF1 knockdown derepresses only the mRNAs harbouring uORFs with an AUG codon in an optimal context for translation initiation. Finally, we also find that eRF3A and UPF1 have opposite effects on ribosome protein gene expression. Together, our results provide important elements for understanding the impact of translation termination and NMD on the human transcriptome and reveal novel determinants of ribosome biogenesis regulation.
DOI: 10.6084/m9.figshare.9994652.v2
title: File S3 - Probe Set Details Table

description: Contains information about which probes were recovered from each taxon (“Probe Recovery Profile”), the number of taxa recovered by each probe (“Probe Recovery Summary Stats”), and various probe statistics (“Probe Statistics”; <i>e.g.</i>, length, GC content).<br>
DOI: 10.6084/m9.figshare.9994568
title: SILVA v132 + v138, NR99, in ARB+UDB11 format

description: SILVA release 132 and 138 non-redundant (clustered at 99%) database including typestrains in both ARB and UDB (usearch11) formats. For use with https://github.com/KasperSkytte/AutoTax
DOI: 10.6084/m9.figshare.9994586.v1
title: Divergent effects of translation termination factor eRF3A and nonsense-mediated mRNA decay factor UPF1 on the expression of uORF carrying mRNAs and ribosome protein genes

description: In addition to its role in translation termination, eRF3A has been implicated in the nonsense-mediated mRNA decay (NMD) pathway through its interaction with UPF1. NMD is a RNA quality control mechanism, which detects and degrades aberrant mRNAs as well as some normal transcripts including those that harbour upstream open reading frames in their 5ʹ leader sequence. In this study, we used RNA-sequencing and ribosome profiling to perform a genome wide analysis of the effect of either eRF3A or UPF1 depletion in human cells. Our bioinformatics analyses allow to delineate the features of the transcripts controlled by eRF3A and UPF1 and to compare the effect of each of these factors on gene expression. We find that eRF3A and UPF1 have very different impacts on the human transcriptome, less than 250 transcripts being targeted by both factors. We show that eRF3A depletion globally derepresses the expression of mRNAs containing translated uORFs while UPF1 knockdown derepresses only the mRNAs harbouring uORFs with an AUG codon in an optimal context for translation initiation. Finally, we also find that eRF3A and UPF1 have opposite effects on ribosome protein gene expression. Together, our results provide important elements for understanding the impact of translation termination and NMD on the human transcriptome and reveal novel determinants of ribosome biogenesis regulation.
DOI: 10.6084/m9.figshare.9994418
title: Open Data for Social Resilience in Victoria

description: This is an open data set for Social Resilience of communities in Victoria, Australia. Social Resilience is the capacity for groups and communities to preserve and sustain their wellbeing in the face of adverse challenges. This dataset describes the resilience of communities based on eleven socio-economic variables. <br>These variables and their distribution are describes by these Jupyter notebooks across three different statistical areas:<br><b>SA2: </b>https://nbviewer.jupyter.org/github/soda-lab/social-resilience/blob/master/cluster_sa2_preview.ipynb<br><br><b>SA3:</b> https://nbviewer.jupyter.org/github/soda-lab/social-resilience/blob/master/cluster_sa3_preview.ipynb<br><br><b>SA4: </b>https://nbviewer.jupyter.org/github/soda-lab/social-resilience/blob/master/cluster_sa4_preview.ipynb<br><br><br>Input to this program is available in this open AARNet datasets: https://cloudstor.aarnet.edu.au/plus/s/1LPSBl1eyGfc8KK<br><br><br>
DOI: 10.6084/m9.figshare.9994568.v1
title: SILVA132+typestrains, in ARB+UDB11 format

description: SILVA version 132 non-redundant (clustered at 99%) database including typestrains in both ARB and UDB (usearch11) formats. For use with https://github.com/KasperSkytte/AutoTax
DOI: 10.6084/m9.figshare.9994568.v2
title: SILVA132+typestrains, in ARB+UDB11 format

description: SILVA release 132 and 138 non-redundant (clustered at 99%) database including typestrains in both ARB and UDB (usearch11) formats. For use with https://github.com/KasperSkytte/AutoTax
DOI: 10.6084/m9.figshare.9994073
title: MOESM9 of A systematic review and meta-analyses of risk factors associated with lameness in dairy cows

description: Additional file 9. Data set used for the systematic review .
DOI: 10.6084/m9.figshare.9994073.v1
title: MOESM9 of A systematic review and meta-analyses of risk factors associated with lameness in dairy cows

description: Additional file 9. Data set used for the systematic review .
DOI: 10.6084/m9.figshare.9994043
title: MOESM2 of A systematic review and meta-analyses of risk factors associated with lameness in dairy cows

description: Additional file 2. Application of the STROBE guidelines for each of the 120 scrutinized publications.
DOI: 10.6084/m9.figshare.9994043.v1
title: MOESM2 of A systematic review and meta-analyses of risk factors associated with lameness in dairy cows

description: Additional file 2. Application of the STROBE guidelines for each of the 120 scrutinized publications.
DOI: 10.6084/m9.figshare.9994022
title: MOESM10 of A systematic review and meta-analyses of risk factors associated with lameness in dairy cows

description: Additional file 10. Data set used for meta-analyses.
DOI: 10.6084/m9.figshare.9994022.v1
title: MOESM10 of A systematic review and meta-analyses of risk factors associated with lameness in dairy cows

description: Additional file 10. Data set used for meta-analyses.
DOI: 10.6084/m9.figshare.9993995
title: MOESM9 of Genetic mechanisms in the repression of flowering by gibberellins in apple (Malus x domestica Borkh.)

description: Additional file 9: Table S8. Results of Blastx using transcript models and the Arabidopsis TAIR10 non-redundant protein database.
DOI: 10.6084/m9.figshare.9993986
title: MOESM8 of Genetic mechanisms in the repression of flowering by gibberellins in apple (Malus x domestica Borkh.)

description: Additional file 8. Enriched GO bioprocess terms (Table S6) and KEGG pathway terms (Table S7) for GA-responsive genes. Gene Ontology bioprocess and KEGG pathway enrichment analysis were carried out using annotated terms for the most homologous Arabidopsis protein. All Arabidopsis homologs of apple genes supporting the enrichment terms are listed. GA-related terms are highlighted in red. The P values for enrichment, as well as the Bonferroni and Benjamini corrected p values are shown.
DOI: 10.6084/m9.figshare.9993995.v1
title: MOESM9 of Genetic mechanisms in the repression of flowering by gibberellins in apple (Malus x domestica Borkh.)

description: Additional file 9: Table S8. Results of Blastx using transcript models and the Arabidopsis TAIR10 non-redundant protein database.
DOI: 10.6084/m9.figshare.9993986.v1
title: MOESM8 of Genetic mechanisms in the repression of flowering by gibberellins in apple (Malus x domestica Borkh.)

description: Additional file 8. Enriched GO bioprocess terms (Table S6) and KEGG pathway terms (Table S7) for GA-responsive genes. Gene Ontology bioprocess and KEGG pathway enrichment analysis were carried out using annotated terms for the most homologous Arabidopsis protein. All Arabidopsis homologs of apple genes supporting the enrichment terms are listed. GA-related terms are highlighted in red. The P values for enrichment, as well as the Bonferroni and Benjamini corrected p values are shown.
DOI: 10.6084/m9.figshare.9993980
title: MOESM7 of Genetic mechanisms in the repression of flowering by gibberellins in apple (Malus x domestica Borkh.)

description: Additional file 7: Table S5. Differentially expressed genes in the apple bourse shoot apices in response to GA. This file contains the differentially expressed genes (DEGs) in response to GA, their coordinates, Arabidopsis homologs, gene description, expression (FPKM), Log2(Fold Change), and significance (p value, and q value, which is adjusted p value).
DOI: 10.6084/m9.figshare.9993980.v1
title: MOESM7 of Genetic mechanisms in the repression of flowering by gibberellins in apple (Malus x domestica Borkh.)

description: Additional file 7: Table S5. Differentially expressed genes in the apple bourse shoot apices in response to GA. This file contains the differentially expressed genes (DEGs) in response to GA, their coordinates, Arabidopsis homologs, gene description, expression (FPKM), Log2(Fold Change), and significance (p value, and q value, which is adjusted p value).
DOI: 10.6084/m9.figshare.9993965
title: MOESM6 of Genetic mechanisms in the repression of flowering by gibberellins in apple (Malus x domestica Borkh.)

description: Additional file 6. A revised feature coordinate map (GFF3) including previously annotated transcripts and transcripts identified in this study.
DOI: 10.6084/m9.figshare.9993959
title: MOESM5 of Genetic mechanisms in the repression of flowering by gibberellins in apple (Malus x domestica Borkh.)

description: Additional file 5: Table S2. Classification of transcript models using GffCompare. Class codes were assigned to each transcript based on the relationship between this transcript and its closest reference transcript. Table S3. Best hits for unannotated transcripts (class codes: i, y, p, u) from BlastN and the NCBI non-redundant nucleotide collection database (nt). Table S4. Sequence length and expression of unannotated transcripts that have no hit from the nt database.