cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14337319.v1
title: Tectonic cycles of the New England Orogen, eastern Australia: A Review

description: The New England Orogen (NEO), the youngest of the orogens of the Tasmanides of eastern Australia, is defined by two main cycles of compression–extension. The compression component involves thrust tectonics and advance of the arc towards the continental plate, while extension is characterised by rifting, basin formation, thermal relaxation and retreat of the arc towards the oceanic plate. A compilation of 623 records of U–Pb zircon geochronology rock ages from Geoscience Australia, the geological surveys of Queensland and New South Wales and other published research throughout the orogen, has helped to clarify its complex tectonic history. This contribution focuses on the entire NEO and is aimed at those who are unfamiliar with the details of the orogen and who could benefit from a summary of current knowledge. It aims to fill a gap in recent literature between broad-scale overviews of the orogen incorporated as part of wider research on the Tasmanides and detailed studies usually specific to either the northern or southern parts of the orogen. Within the two main cycles of compression–extension, six accepted and distinct tectonic phases are defined and reviewed. Maps of geological processes active during each phase reveal the centres of activity during each tectonic phase, and the range in U–Pb zircon ages highlights the degree of diachronicity along the length of the NEO. In addition, remnants of the early Permian offshore arc formed during extensive slab rollback, are identified by the available geochronology. Estimates of the beginning of the Hunter-Bowen phase of compression, generally thought to commence around 265 Ma are complicated by the presence of extensional-type magmatism in eastern Queensland that occurred between 270 and 260 Ma.
DOI: 10.21227/6n45-g439
title: Web API and Mashup Dataset

description: Web API and Mushup dataset from ProgrammableWeb
DOI: 10.6084/m9.figshare.14336753.v1
title: Peltigera lichens from Navarino Island, Magallanes Region, Chile (2020, Patagonian steppe)

description: Peltigera lichen samples collected by the Microbial Ecology Lab (Universidad de Chile), from a Patagonina steppe in Navarino Island in 2020.
DOI: 10.25919/m4bs-xj60
title: Parkes pulsar observations with undefined project IDs for 2020OCTS_08

description: Parkes pulsar observations with undefined project IDs for 2020OCTS. This collection contains data from the ToO project PX071.
DOI: 10.5281/zenodo.4646471
title: MEDICINE

description: Additional file 1: Table S1. Ingenuity Canonical Pathways(XLSX 11 kb)<br> Additional file 2: Table S2.Upstream Analysis (XLSX 11 kb)<br> Additional file 3: Table S3. Sequences of the oligonucleotide primers used for quantitative PCR. (XLSX 11 kb)<br>
DOI: 10.5281/zenodo.4646470
title: MEDICINE

description: Additional file 1: Table S1. Ingenuity Canonical Pathways(XLSX 11 kb)<br> Additional file 2: Table S2.Upstream Analysis (XLSX 11 kb)<br> Additional file 3: Table S3. Sequences of the oligonucleotide primers used for quantitative PCR. (XLSX 11 kb)<br>
DOI: 10.5281/zenodo.4646469
title: Data of "Physics-constrained deep learning recognition of geochemical patterns"

description: The raw data of paper "Physics-constrained deep learning recognition of geochemical patterns"
DOI: 10.5281/zenodo.4646468
title: Data of "Physics-constrained deep learning recognition of geochemical patterns"

description: The raw data of paper "Physics-constrained deep learning recognition of geochemical patterns"
DOI: 10.6084/m9.figshare.14337405
title: Additional file 1 of Cutaneous melanoma: cost of illness under Brazilian health system perspectives

description: Additional file 1.
DOI: 10.6084/m9.figshare.14337405.v1
title: Additional file 1 of Cutaneous melanoma: cost of illness under Brazilian health system perspectives

description: Additional file 1.
DOI: 10.5281/zenodo.4646488
title: Supplementary material

description: Supplementary material to the paper ”A graph-based semi-supervised approach for predicting eukaryotic essential genes”.
DOI: 10.5281/zenodo.4646487
title: Supplementary material

description: Supplementary material to the paper ”A graph-based semi-supervised approach for predicting eukaryotic essential genes”.
DOI: 10.6084/m9.figshare.14337478
title: Additional file 1 of Transcriptional profiling reveals potential involvement of microvillous TRPM5-expressing cells in viral infection of the olfactory epithelium

description: Additional file 1.
DOI: 10.6084/m9.figshare.14337478.v1
title: Additional file 1 of Transcriptional profiling reveals potential involvement of microvillous TRPM5-expressing cells in viral infection of the olfactory epithelium

description: Additional file 1.
DOI: 10.6084/m9.figshare.14337483.v1
title: Additional file 1 of Actionability of commercial laboratory sequencing panels for newborn screening and the importance of transparency for parental decision-making

description: Additional file 1. An excel spreadsheet containing four tabs with Supplemental Tables S1-S4. Table S1. provides a list of the 74 gene-disease pairs included on all commercial panels with ASQM criteria scores, total score, and designated category for each gene-disease pair. Table S2. lists 88 additional gene-disease pairs that were scored for this manuscript following the publication by Milko et al. [19], including individual ASQM criteria scores, total score, and designated category for each gene-disease pair. Table S3. lists the 77 genes that appeared on one or more commercial laboratory NBS panels, but were designated by our group as ASQM Category 2 because they have childhood-onset but lower or no actionability. Table S4. includes 249 genes that were designated by our group as ASQM Category 1 due to childhood onset and high actionability, but were not listed on any of the four commercial lab NBS panels.
DOI: 10.6084/m9.figshare.14337483
title: Additional file 1 of Actionability of commercial laboratory sequencing panels for newborn screening and the importance of transparency for parental decision-making

description: Additional file 1. An excel spreadsheet containing four tabs with Supplemental Tables S1-S4. Table S1. provides a list of the 74 gene-disease pairs included on all commercial panels with ASQM criteria scores, total score, and designated category for each gene-disease pair. Table S2. lists 88 additional gene-disease pairs that were scored for this manuscript following the publication by Milko et al. [19], including individual ASQM criteria scores, total score, and designated category for each gene-disease pair. Table S3. lists the 77 genes that appeared on one or more commercial laboratory NBS panels, but were designated by our group as ASQM Category 2 because they have childhood-onset but lower or no actionability. Table S4. includes 249 genes that were designated by our group as ASQM Category 1 due to childhood onset and high actionability, but were not listed on any of the four commercial lab NBS panels.
DOI: 10.6084/m9.figshare.14337525.v1
title: Additional file 1 of Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing

description: Additional file 1: Table S1. Per-scaffold statistics. Table S2. Contaminations found in smaller scaffold of the OKI2018_I69 assembly. Table S3. Statistics results for the analysis of sequence properties across chromosome-scale scaffolds. Table S4. BUSCO scores. Table S5. List of missing BUSCO genes in OKI2018_I69, OdB3 and OSKA2016 genome assemblies. Table S6. List of oikopleurid gene homologs uploaded to ZENBU.
DOI: 10.6084/m9.figshare.14337525
title: Additional file 1 of Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing

description: Additional file 1: Table S1. Per-scaffold statistics. Table S2. Contaminations found in smaller scaffold of the OKI2018_I69 assembly. Table S3. Statistics results for the analysis of sequence properties across chromosome-scale scaffolds. Table S4. BUSCO scores. Table S5. List of missing BUSCO genes in OKI2018_I69, OdB3 and OSKA2016 genome assemblies. Table S6. List of oikopleurid gene homologs uploaded to ZENBU.
DOI: 10.6084/m9.figshare.14337571
title: Additional file 2 of High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains

description: Additional file 2: Supplementary Table S1. Similar OPR counts at the attL and attR sites verify an origin of sequencing reads from circularised phage genomes. Supplementary Table S2. Collection of strains and microbiota community used in this study. Supplementary Table S3. Homologous core sequences of the attachment sites of induced prophages. Supplementary Table S4. Packaging site and its location in the lysogenic host genome.
DOI: 10.21227/4q34-sh69
title: February-1-Rivera-Sergio

description: February-1-Rivera-Sergio
DOI: 10.6084/m9.figshare.14337574
title: Additional file 3 of High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains

description: Additional file 3. Blautia coccoides YL58 phage 1. Flavonifractor plautii YL31 phage 1. Flavonifractor plautii YL31 phage 2. Salmonella enterica serovar Typhimurium LT2 p22. Salmonella enterica serovar Typhimurium LT2 FELS-1. Salmonella enterica serovar Typhimurium LT2 FELS-2. Escherichia coli HS phage 1. Acutalibacter muris KB18 phage 1. Akkermansia muciniphila YL44 phage 1. Akkermansia muciniphila YL44 phage 1 (assembly virion enrichment). Akkermansia muciniphila YL44 phage 2. Akkermansia muciniphila YL44 phage 2 (assembly virion enrichment)
DOI: 10.6084/m9.figshare.14337577
title: Additional file 4 of High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains

description: Additional file 4: Supplementary Table S5. Prophage predicted by VIBRANT. Supplementary Table S6. Prophage predicted by VirSorter. Supplementary Table S7. Prophage predicted by Prophage Hunter. Supplementary Table S8. Prophage predicted by PHASTER
DOI: 10.6084/m9.figshare.14337577.v1
title: Additional file 4 of High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains

description: Additional file 4: Supplementary Table S5. Prophage predicted by VIBRANT. Supplementary Table S6. Prophage predicted by VirSorter. Supplementary Table S7. Prophage predicted by Prophage Hunter. Supplementary Table S8. Prophage predicted by PHASTER
DOI: 10.6084/m9.figshare.14337574.v1
title: Additional file 3 of High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains

description: Additional file 3. Blautia coccoides YL58 phage 1. Flavonifractor plautii YL31 phage 1. Flavonifractor plautii YL31 phage 2. Salmonella enterica serovar Typhimurium LT2 p22. Salmonella enterica serovar Typhimurium LT2 FELS-1. Salmonella enterica serovar Typhimurium LT2 FELS-2. Escherichia coli HS phage 1. Acutalibacter muris KB18 phage 1. Akkermansia muciniphila YL44 phage 1. Akkermansia muciniphila YL44 phage 1 (assembly virion enrichment). Akkermansia muciniphila YL44 phage 2. Akkermansia muciniphila YL44 phage 2 (assembly virion enrichment)
DOI: 10.6084/m9.figshare.14337571.v1
title: Additional file 2 of High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains

description: Additional file 2: Supplementary Table S1. Similar OPR counts at the attL and attR sites verify an origin of sequencing reads from circularised phage genomes. Supplementary Table S2. Collection of strains and microbiota community used in this study. Supplementary Table S3. Homologous core sequences of the attachment sites of induced prophages. Supplementary Table S4. Packaging site and its location in the lysogenic host genome.
DOI: 10.6084/m9.figshare.14337652
title: Additional file 2 of A universal power law for modelling the growth and form of teeth, claws, horns, thorns, beaks, and shells

description: Additional file 2: Data S1. Distance and cross-sectional area data for vertebrate teeth, cusps and tooth rows. Taxonomy, specimen number, institution, tooth type/position and measurements of cross-sectional area for 10 distances from tip of tooth.
DOI: 10.6084/m9.figshare.14337652.v1
title: Additional file 2 of A universal power law for modelling the growth and form of teeth, claws, horns, thorns, beaks, and shells

description: Additional file 2: Data S1. Distance and cross-sectional area data for vertebrate teeth, cusps and tooth rows. Taxonomy, specimen number, institution, tooth type/position and measurements of cross-sectional area for 10 distances from tip of tooth.
DOI: 10.6084/m9.figshare.14337655
title: Additional file 3 of A universal power law for modelling the growth and form of teeth, claws, horns, thorns, beaks, and shells

description: Additional file 3: Data S2. Distance and cross-sectional area data for developmental simulations of seal teeth from model by Savriama et al. [41]. Model parameters and measurements of cross-sectional area for 10 distances from tip of tooth. Starting from the ringed seal model of Savriama et al. [41], parameters were increased and decreased to show the effect of each parameter on tooth shape. The central cusp on each model was measured for the power cascade. Parameters: Act, activator; Boy, buoyancy; Deg, degradation of activator; Egr, epithelial growth; Inh, inhibitor.
DOI: 10.6084/m9.figshare.14337658
title: Additional file 4 of A universal power law for modelling the growth and form of teeth, claws, horns, thorns, beaks, and shells

description: Additional file 4: Data S3. Distance and cross-sectional area data for non-tooth structures: antlers, beaks, chelicera, claws, hooves, horns, prickles, shells, spine and thorn. Taxonomy, specimen number, institution, structure type and measurements of cross-sectional area for 10 distances from tip of structure.
DOI: 10.6084/m9.figshare.14337655.v1
title: Additional file 3 of A universal power law for modelling the growth and form of teeth, claws, horns, thorns, beaks, and shells

description: Additional file 3: Data S2. Distance and cross-sectional area data for developmental simulations of seal teeth from model by Savriama et al. [41]. Model parameters and measurements of cross-sectional area for 10 distances from tip of tooth. Starting from the ringed seal model of Savriama et al. [41], parameters were increased and decreased to show the effect of each parameter on tooth shape. The central cusp on each model was measured for the power cascade. Parameters: Act, activator; Boy, buoyancy; Deg, degradation of activator; Egr, epithelial growth; Inh, inhibitor.
DOI: 10.6084/m9.figshare.14337658.v1
title: Additional file 4 of A universal power law for modelling the growth and form of teeth, claws, horns, thorns, beaks, and shells

description: Additional file 4: Data S3. Distance and cross-sectional area data for non-tooth structures: antlers, beaks, chelicera, claws, hooves, horns, prickles, shells, spine and thorn. Taxonomy, specimen number, institution, structure type and measurements of cross-sectional area for 10 distances from tip of structure.
DOI: 10.6084/m9.figshare.14337679
title: Additional file 2 of Population structure and uropathogenic potential of extended-spectrum cephalosporin-resistant Escherichia coli from retail chicken meat

description: Additional file 2.
DOI: 10.6084/m9.figshare.14337679.v1
title: Additional file 2 of Population structure and uropathogenic potential of extended-spectrum cephalosporin-resistant Escherichia coli from retail chicken meat

description: Additional file 2.
DOI: 10.6084/m9.figshare.14337682.v1
title: Additional file 1 of Differential influences of (±) anatoxin-a on photolocomotor behavior and gene transcription in larval zebrafish and fathead minnows

description: Additional file 1: Table S1. List of genes and associated primer sequences used in this study for gene transcription analysis focusing on neurotoxicity, oxidative stress, DNA damage, and hepatotoxicity. In the table, ZF refers to zebrafish specific sequences, while FHM refers to fathead minnow specific sequences. Gene sequences that were not used from literature were designed for this study using the NCBI Primer-BLAST tool. *Efficiencies were determined using a standard curve of Ct values acquired from a 4-fold dilution series of cDNA (1, 1:4, 1:16) in duplicate.
DOI: 10.6084/m9.figshare.14337682
title: Additional file 1 of Differential influences of (±) anatoxin-a on photolocomotor behavior and gene transcription in larval zebrafish and fathead minnows

description: Additional file 1: Table S1. List of genes and associated primer sequences used in this study for gene transcription analysis focusing on neurotoxicity, oxidative stress, DNA damage, and hepatotoxicity. In the table, ZF refers to zebrafish specific sequences, while FHM refers to fathead minnow specific sequences. Gene sequences that were not used from literature were designed for this study using the NCBI Primer-BLAST tool. *Efficiencies were determined using a standard curve of Ct values acquired from a 4-fold dilution series of cDNA (1, 1:4, 1:16) in duplicate.
DOI: 10.6084/m9.figshare.13357850
title: Additional file 1 of You don’t have the guts: a diverse set of fungi survive passage through Macrotermes bellicosus termite guts

description: Additional file 1: Table S1. Collection information of substrates and colonies used for both experiments.
DOI: 10.6084/m9.figshare.13357853.v1
title: Additional file 2 of You don’t have the guts: a diverse set of fungi survive passage through Macrotermes bellicosus termite guts

description: Additional file 2: Table S2. Amplicon Sequence Variants (ASVs) identified from the MiSeq analyses of all forage substrates (experiment a, noted as ICF), as well as the fungus comb experiment (experiment c, noted as FC). The file contains four worksheets. The first is a merged file consisting of the sequence, the taxonomic assignment and the abundance of each ASV per sample. The next three worksheets are the metadata, taxonomy table and OTU table respectively, ready to be used with the Phyloseq package.
DOI: 10.6084/m9.figshare.13357856
title: Additional file 3 of You don’t have the guts: a diverse set of fungi survive passage through Macrotermes bellicosus termite guts

description: Additional file 3: Table S3. Fungal genera identified through isolations from guts. Each row contains a sequenced sample, its sequence, its closest match in GenBank and its metadata.
DOI: 10.6084/m9.figshare.13357853
title: Additional file 2 of You don’t have the guts: a diverse set of fungi survive passage through Macrotermes bellicosus termite guts

description: Additional file 2: Table S2. Amplicon Sequence Variants (ASVs) identified from the MiSeq analyses of all forage substrates (experiment a, noted as ICF), as well as the fungus comb experiment (experiment c, noted as FC). The file contains four worksheets. The first is a merged file consisting of the sequence, the taxonomic assignment and the abundance of each ASV per sample. The next three worksheets are the metadata, taxonomy table and OTU table respectively, ready to be used with the Phyloseq package.
DOI: 10.6084/m9.figshare.13357856.v1
title: Additional file 3 of You don’t have the guts: a diverse set of fungi survive passage through Macrotermes bellicosus termite guts

description: Additional file 3: Table S3. Fungal genera identified through isolations from guts. Each row contains a sequenced sample, its sequence, its closest match in GenBank and its metadata.
DOI: 10.6084/m9.figshare.13357850.v1
title: Additional file 1 of You don’t have the guts: a diverse set of fungi survive passage through Macrotermes bellicosus termite guts

description: Additional file 1: Table S1. Collection information of substrates and colonies used for both experiments.
DOI: 10.5281/zenodo.4646251
title: Coupled Aqua and Ridge Planets in the Community Earth System Model

description: This dataset contains two case directories of idealized Community Earth System Model, and the respective quasi-equilibrated climatologies of simulated Year 401-500.
DOI: 10.5281/zenodo.4646250
title: Coupled Aqua and Ridge Planets in the Community Earth System Model

description: This dataset contains two case directories of idealized Community Earth System Model, and the respective quasi-equilibrated climatologies of simulated Year 401-500.
DOI: 10.6084/m9.figshare.14337771.v1
title: Additional file 2 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes

description: Additional file 1. Clustering information for 3,378 gut phages identified in the study. Phage genomes were dereplicated at 95% identity over 80% of the contig length. The GenBank accession codes for each phage and the representative sequence is provided in columns 1 and 3, respectively.
DOI: 10.6084/m9.figshare.14337771
title: Additional file 2 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes

description: Additional file 1. Clustering information for 3,378 gut phages identified in the study. Phage genomes were dereplicated at 95% identity over 80% of the contig length. The GenBank accession codes for each phage and the representative sequence is provided in columns 1 and 3, respectively.
DOI: 10.6084/m9.figshare.14337774
title: Additional file 3 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes

description: Additional file 2. Taxonomic information for 1,886 representative phage genomes. Each taxonomically classified phage genome was scored by ViralVerify, Seeker and vcontact2 and the assignments are provided in columns 9-10, 11 and 12-13, respectively.
DOI: 10.6084/m9.figshare.14337774.v1
title: Additional file 3 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes

description: Additional file 2. Taxonomic information for 1,886 representative phage genomes. Each taxonomically classified phage genome was scored by ViralVerify, Seeker and vcontact2 and the assignments are provided in columns 9-10, 11 and 12-13, respectively.
DOI: 10.6084/m9.figshare.14337783
title: Additional file 6 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes

description: Additional file 5. Candidate anti-CRISPR (Acr) proteins encoded on each phage genome. Proteins predicted to be an Acr with high confidence (score &gt; 0.9) and meeting all other heuristic criteria are listed along with their inferred host. For the Bifidobacteria phages (see the main text), the nucleotide coordinates of closely related prophages integrated in their host genome are provided in columns 6-8.
DOI: 10.6084/m9.figshare.14337780
title: Additional file 5 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes

description: Additional file 4. Host ranges inferred from CRISPR-spacer matches. The nucleotide coordinates of the protospacer are provided in columns 2 and 3. The sequence of the CRISPR spacer and protospacer are provided in columns 4 and 5. The taxonomic information of the host is listed in the subsequent columns.
DOI: 10.6084/m9.figshare.14337780.v1
title: Additional file 5 of Thousands of previously unknown phages discovered in whole-community human gut metagenomes

description: Additional file 4. Host ranges inferred from CRISPR-spacer matches. The nucleotide coordinates of the protospacer are provided in columns 2 and 3. The sequence of the CRISPR spacer and protospacer are provided in columns 4 and 5. The taxonomic information of the host is listed in the subsequent columns.