cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11775780.v1
title: Additional file 3 of Repetitive DNA content in the maize genome is uncoupled from population stratification at SNP loci

description: Additional file 3 Cluster read counts by inbred. A file listing cluster name and the number of reads from each inbred that contributed to the given cluster.
DOI: 10.6084/m9.figshare.11775771
title: Additional file 2 of Repetitive DNA content in the maize genome is uncoupled from population stratification at SNP loci

description: Additional file 2 Cluster annotation information. File listing clusters and their associated annotation as determined by sequence matches to RepBase
DOI: 10.6084/m9.figshare.11775771.v1
title: Additional file 2 of Repetitive DNA content in the maize genome is uncoupled from population stratification at SNP loci

description: Additional file 2 Cluster annotation information. File listing clusters and their associated annotation as determined by sequence matches to RepBase
DOI: 10.6084/m9.figshare.11775759
title: Additional file 1 of Repetitive DNA content in the maize genome is uncoupled from population stratification at SNP loci

description: Additional file 1 List of ex-PVP Zea mays spp mays inbreds used in this study. A list of the public names for ex-PVP inbreds used in this study, as well as their SRA sample names.
DOI: 10.6084/m9.figshare.11775759.v1
title: Additional file 1 of Repetitive DNA content in the maize genome is uncoupled from population stratification at SNP loci

description: Additional file 1 List of ex-PVP Zea mays spp mays inbreds used in this study. A list of the public names for ex-PVP inbreds used in this study, as well as their SRA sample names.
DOI: 10.6084/m9.figshare.11775738
title: Additional file 1 of Effect of air-polishing on surface roughness of composite dental restorative material â€“ comparison of three different air-polishing powders

description: Additional file 1. Roughness parameters.
DOI: 10.6084/m9.figshare.11775738.v1
title: Additional file 1 of Effect of air-polishing on surface roughness of composite dental restorative material â€“ comparison of three different air-polishing powders

description: Additional file 1. Roughness parameters.
DOI: 10.6084/m9.figshare.11775633
title: Additional file 1 of A highly sensitive and specific workflow for detecting rare copy-number variants from exome sequencing data

description: Additional file 1: Table S1. Details of the high-quality true-positive CNVs from SNP array and the exome validation status. Table S2. List of exons in disease-associated genes that were excluded based on a mean mappabilty score of 0.75 or less. Table S3. Details of the CNVs used for false-discovery rate estimation against WGS data. Table S4. Details of the ES false negatives and SNP array false positive CNVs. Table S5. Details of CNVs that overlapped 10 SNPs in the SNP array and reviewed for determining false-discovery rate against SNP array.
DOI: 10.6084/m9.figshare.11775636
title: Additional file 1 of Comparative genomic analysis of the secondary flagellar (flag-2) system in the order Enterobacterales

description: Additional file 1: Table S1. Presence/absence of flag-2 loci among 4028 strains belonging to eight families and 72 genera. The presence of flag-1 loci is also indicated. The previous taxonomy denotes the taxonomy according to the NCBI genome database, while the current taxonomy is according to the Genome Taxonomy Database (GTDB). The isolation source as well as habitat/lifestyles of the different strains are given. Table S2. Molecular characteristics of the flag-2 loci among 592 taxa in the Enterobacterales. The sizes of the flag-2 loci, variable regions VR1 and VR2, their G + C contents (%) and G + C deviation (%) from the genome are shown. The number of predicted proteins encoded on each of these flag-2 fractions are also shown. Table S3. Characteristics of the cargo genes encoded in the variable regions VR1 and VR2 and elsewhere in the enterobacterial flag-2 loci. The number of strains and the families/genera in which each protein occurs within the flag-2 loci are indicated, as well as the average amino acid identities among enterobacterial orthologues. Conserved domains present in each cargo protein as determined by BlastP analysis against the Conserved Domain Database are shown.
DOI: 10.6084/m9.figshare.11775636.v1
title: Additional file 1 of Comparative genomic analysis of the secondary flagellar (flag-2) system in the order Enterobacterales

description: Additional file 1: Table S1. Presence/absence of flag-2 loci among 4028 strains belonging to eight families and 72 genera. The presence of flag-1 loci is also indicated. The previous taxonomy denotes the taxonomy according to the NCBI genome database, while the current taxonomy is according to the Genome Taxonomy Database (GTDB). The isolation source as well as habitat/lifestyles of the different strains are given. Table S2. Molecular characteristics of the flag-2 loci among 592 taxa in the Enterobacterales. The sizes of the flag-2 loci, variable regions VR1 and VR2, their G + C contents (%) and G + C deviation (%) from the genome are shown. The number of predicted proteins encoded on each of these flag-2 fractions are also shown. Table S3. Characteristics of the cargo genes encoded in the variable regions VR1 and VR2 and elsewhere in the enterobacterial flag-2 loci. The number of strains and the families/genera in which each protein occurs within the flag-2 loci are indicated, as well as the average amino acid identities among enterobacterial orthologues. Conserved domains present in each cargo protein as determined by BlastP analysis against the Conserved Domain Database are shown.
DOI: 10.6084/m9.figshare.11775633.v1
title: Additional file 1 of A highly sensitive and specific workflow for detecting rare copy-number variants from exome sequencing data

description: Additional file 1: Table S1. Details of the high-quality true-positive CNVs from SNP array and the exome validation status. Table S2. List of exons in disease-associated genes that were excluded based on a mean mappabilty score of 0.75 or less. Table S3. Details of the CNVs used for false-discovery rate estimation against WGS data. Table S4. Details of the ES false negatives and SNP array false positive CNVs. Table S5. Details of CNVs that overlapped 10 SNPs in the SNP array and reviewed for determining false-discovery rate against SNP array.
DOI: 10.6084/m9.figshare.11775516
title: Additional file 5 of Proteins involved in the biosynthesis of lipophosphoglycan in Leishmania: a comparative genomic and evolutionary analysis

description: Additional file 5: Table S5. Orthologs genes information (ID, protein products, organism, corresponding open reading frames coordinates and strand).
DOI: 10.6084/m9.figshare.11775513
title: Additional file 4 of Proteins involved in the biosynthesis of lipophosphoglycan in Leishmania: a comparative genomic and evolutionary analysis

description: Additional file 4: Table S4. Information on re-annotated genes and newly predicted open reading frames.
DOI: 10.6084/m9.figshare.11775516.v1
title: Additional file 5 of Proteins involved in the biosynthesis of lipophosphoglycan in Leishmania: a comparative genomic and evolutionary analysis

description: Additional file 5: Table S5. Orthologs genes information (ID, protein products, organism, corresponding open reading frames coordinates and strand).
DOI: 10.6084/m9.figshare.11775507
title: Additional file 3 of Proteins involved in the biosynthesis of lipophosphoglycan in Leishmania: a comparative genomic and evolutionary analysis

description: Additional file 3: Table S3. Metadata about the genes chosen as query in orthologous searches.
DOI: 10.6084/m9.figshare.11775513.v1
title: Additional file 4 of Proteins involved in the biosynthesis of lipophosphoglycan in Leishmania: a comparative genomic and evolutionary analysis

description: Additional file 4: Table S4. Information on re-annotated genes and newly predicted open reading frames.
DOI: 10.6084/m9.figshare.11775507.v1
title: Additional file 3 of Proteins involved in the biosynthesis of lipophosphoglycan in Leishmania: a comparative genomic and evolutionary analysis

description: Additional file 3: Table S3. Metadata about the genes chosen as query in orthologous searches.
DOI: 10.6084/m9.figshare.11775495
title: Additional file 2 of Proteins involved in the biosynthesis of lipophosphoglycan in Leishmania: a comparative genomic and evolutionary analysis

description: Additional file 2: Table S2. Metadata of the RNA-seq gene expression studies re-analyzed in the work.
DOI: 10.6084/m9.figshare.11775495.v1
title: Additional file 2 of Proteins involved in the biosynthesis of lipophosphoglycan in Leishmania: a comparative genomic and evolutionary analysis

description: Additional file 2: Table S2. Metadata of the RNA-seq gene expression studies re-analyzed in the work.
DOI: 10.6084/m9.figshare.11775486
title: Additional file 1 of Proteins involved in the biosynthesis of lipophosphoglycan in Leishmania: a comparative genomic and evolutionary analysis

description: Additional file 1: Table S1. Metadata of the genomes included in the study.
DOI: 10.6084/m9.figshare.11775486.v1
title: Additional file 1 of Proteins involved in the biosynthesis of lipophosphoglycan in Leishmania: a comparative genomic and evolutionary analysis

description: Additional file 1: Table S1. Metadata of the genomes included in the study.
DOI: 10.6084/m9.figshare.11775126
title: blueJeans-PNAS2020

description: Data associated with "Assessing the Reliability of a Clothing-Based Forensic Identification"
DOI: 10.6084/m9.figshare.11775318
title: Simulated significant wave height (3-hourly, 2015.01-2100.12) from FIO-ESM v2.0 ssp585 experiment r1i1p1f1

description: Simulated significant wave height (3-hourly, 2015.01-2100.12) from FIO-ESM v2.0 ssp585 experiment (one of future scenarios) r1i1p1f1. The grid, named gx1v6, is the displaced pole (the North Pole displaced to the Greenland) grid with 1.1 degree in longitude and 0.27-0.54 degree in latitude.
DOI: 10.6084/m9.figshare.11775081
title: TESS Extended Mission Yield Simulations

description: TESS planet yield simulations.Changes from Barclay, Pepper & Quintana:- Uses TIC 8 (based on Gaia)- Uses Petigura 2018 for the FGK occurrence rate- Use conservative detection threshold<br>Might be others that I've forgotten.<br>
DOI: 10.6084/m9.figshare.11775126.v1
title: blueJeans-PNAS2020

description: Data associated with "Assessing the Reliability of a Clothing-Based Forensic Identification"
DOI: 10.6084/m9.figshare.11775126.v2
title: blueJeans-PNAS2020

description: Data associated with "Assessing the Reliability of a Clothing-Based Forensic Identification"
DOI: 10.6084/m9.figshare.11775126.v3
title: blueJeans-PNAS2020

description: Data associated with "Assessing the Reliability of a Clothing-Based Forensic Identification"
DOI: 10.6084/m9.figshare.11775009
title: Primary Studies List

description: Primary Studies List
DOI: 10.6084/m9.figshare.11775009.v1
title: Primary Studies List

description: Primary Studies List
DOI: 10.6084/m9.figshare.11775006
title: Quality Assessment List

description: Quality Assessment
DOI: 10.6084/m9.figshare.11775006.v1
title: Quality Assessment List

description: Quality Assessment
DOI: 10.6084/m9.figshare.11774958
title: NCLDV species trees

description: These two trees were generated from the same alignment using different models in IQ-TREE. The alignment is also provided. <br>
DOI: 10.26180/5e664140c4ab1
title: BiDaML_Study.7z

description: User study results for evaluating BiDaML tool - conducted on 29 August 2019
DOI: 10.6084/m9.figshare.11774844
title: Ragweed transcriptome

description: Isoform- and gene-level transcriptomes for common ragweed.<br>After filtering out low quality reads and sequencing adapters with Trimmomatic, a total of 11.8 million read pairs from a single genotype (from Oklahoma) were used in the transcriptome assembly with Trinity. After the primary transcriptome-assembly, we combined isoforms into contigs covering entire length of the genes. First, isoforms that were &gt; 95% identical, potentially representing allelic splitting, were merged with CD-HIT, and the resulting contigs (93,857) used to make “SuperTranscripts” with Lace. The final gene-level transcriptome consists of 58,644 contigs with a E90N50 (N50 estimated for contigs comprising 90% of the total expression) of 2510 bp. The isoform (after CD-HIT) and gene (after LACE) level transcriptomes are provided.
DOI: 10.6084/m9.figshare.11774844.v1
title: Ragweed transcriptome

description: Isoform and gene level transcriptomes for common ragweed.<br>After filtering out low quality reads and sequencing adapters with Trimmomatic, a total of 11.8 million read pairs from a single genotype (from Oklahoma) were used in the transcriptome assembly with Trinity. After the primary transcriptome-assembly, we combined isoforms into contigs covering entire length of the genes. First, isoforms that were &gt; 95% identical, potentially representing allelic splitting, were merged with CD-HIT, and the resulting contigs (93,857) used to make “SuperTranscripts” with Lace. The final gene-level transcriptome consists of 58,644 contigs with a E90N50 (N50 estimated for contigs comprising 90% of the total expression) of 2510 bp. The isoform (after CD-HIT) and gene (after LACE) level transcriptomes are provided.
DOI: 10.6084/m9.figshare.11774793
title: RuCl3_Raman.zip

description: Raman Data of RuCl3 Kitaev boundary
DOI: 10.6084/m9.figshare.11774778
title: Data from Keiser et al 2015 - Arthropod-Plant Interactions.xlsx

description: Data associated with behavioral assays and mesocosm experiment.<br>
DOI: 10.6084/m9.figshare.11774778.v1
title: Data from Keiser et al 2015 - Arthropod-Plant Interactions.xlsx

description: Data associated with behavioral assays and mesocosm experiment.<br>
DOI: 10.6084/m9.figshare.11774793.v1
title: RuCl3_Raman.zip

description: Raman Data of RuCl3 Kitaev boundary
DOI: 10.6084/m9.figshare.11774652
title: Data used in A History of Population Health.xlsx

description: Data used in <i>A History of Population Health</i>
DOI: 10.6084/m9.figshare.11774652.v1
title: Data used in A History of Population Health.xlsx

description: Data used in <i>A History of Population Health</i>
DOI: 10.6084/m9.figshare.11774640.v1
title: iriR: Client for the EU Industrial Research and Industry Scoreboard

description: The Economics of Industrial Research & Innovation (IRI) is a scientific project carried out within the Directorate B: Growth and Innovation, one of the seven scientific institutes of the European Commission's Joint Research Centre (JRC) (). 'iriR' objective is to allows an easy connection with R to the European Commission's Economics of Industrial Research and Innovation data.
DOI: 10.6084/m9.figshare.11774640.v2
title: iriR: A R Package for the EU Industrial Research and Industry Scoreboard

description: The Economics of Industrial Research & Innovation (IRI) is a scientific project carried out within the Directorate B: Growth and Innovation, one of the seven scientific institutes of the European Commission's Joint Research Centre (JRC) (). 'iriR' objective is to allows an easy connection with R to the European Commission's Economics of Industrial Research and Innovation data.
DOI: 10.6084/m9.figshare.11774586
title: Variation in Sensory Attributes and Volatile Compounds in Beers Brewed from Genetically Distinct Malts: An Integrated Sensory and Non-Targeted Metabolomics Approach

description: Previous research demonstrates that barley genetics can influence beer flavor. However, the chemical basis for differences in beer flavor attributed to barley is not well defined. Here, the associations between beer volatile compounds and sensory descriptors were investigated in a controlled experiment, whereby barley genotype was the main driver of variation in the system. Beer was brewed from three advanced barley breeding lines and compared to a CDC Copeland control. Sensory studies were performed via three independent panels (a consumer, brewery, and laboratory panel). The results suggest that the four beer samples have distinct flavor profiles that could be discriminated by the three sensory panels. Volatile compounds for the four beers were characterized using HS/SPME-GC-MS; quantitation and annotation were performed using a non-targeted metabolomics approach on 397 detected compounds. The O2PLS data analysis supports that alkane/alkenes, benzenoids, amides/amines, and fatty acid esters were associated with the most desirable lager traits, compared to Maillard Reaction Products that were more abundant in the beers with “non-ideal” lager traits. Taken together, these data further support the role of barley genetics in beer flavor and provide new information on the types of volatile metabolites that can vary in controlled systems.
DOI: 10.6084/m9.figshare.11774586.v1
title: Variation in Sensory Attributes and Volatile Compounds in Beers Brewed from Genetically Distinct Malts: An Integrated Sensory and Non-Targeted Metabolomics Approach

description: Previous research demonstrates that barley genetics can influence beer flavor. However, the chemical basis for differences in beer flavor attributed to barley is not well defined. Here, the associations between beer volatile compounds and sensory descriptors were investigated in a controlled experiment, whereby barley genotype was the main driver of variation in the system. Beer was brewed from three advanced barley breeding lines and compared to a CDC Copeland control. Sensory studies were performed via three independent panels (a consumer, brewery, and laboratory panel). The results suggest that the four beer samples have distinct flavor profiles that could be discriminated by the three sensory panels. Volatile compounds for the four beers were characterized using HS/SPME-GC-MS; quantitation and annotation were performed using a non-targeted metabolomics approach on 397 detected compounds. The O2PLS data analysis supports that alkane/alkenes, benzenoids, amides/amines, and fatty acid esters were associated with the most desirable lager traits, compared to Maillard Reaction Products that were more abundant in the beers with “non-ideal” lager traits. Taken together, these data further support the role of barley genetics in beer flavor and provide new information on the types of volatile metabolites that can vary in controlled systems.
DOI: 10.6084/m9.figshare.11774520
title: Severe obesity and the impact of medical weight loss on estimated glomerular filtration rate

description: <b>Objective</b>: To assess the impact of obesity, glucose tolerance, and weight loss on renal function, we measured serum creatinine and cystatin C and estimated glomerular filtration rate (GFR) indexed to 1.73m<sup>2</sup> body surface area (BSA) and GFR indexed to actual BSA in subjects with normal and abnormal glucose tolerance before and up to 2 years after medical weight loss. <b>Methods: </b>We studied 146 subjects at baseline and 3-to-6 months after 18% reduction in weight; 43 were also studied at 2-years. GFR was estimated using the MDRD, CKD-EPI<sub>Cr</sub>, CKD-EPI<sub>CysCr</sub>, and the CKD-EPI<sub>Cys</sub> equations. <b>Results</b>: eGFR was consistently lower when creatinine-based rather than cystatin C-based estimating equations were used. eGFR was lower when creatinine-based or cystatin C-based equations were indexed to 1.73m<sup>2</sup> BSA than when they were indexed to actual BSA. eGFR indexed to actual BSA was more likely to demonstrate hyperfiltration (eGFR ≥135 ml/min) than eGFR indexed to 1.73m<sup>2</sup> BSA and decreased into the normal range with weight loss. eGFR was highest in subjects with impaired fasting glucose but there was little difference in the patterns of change in eGFR across groups by glucose tolerance status. <b>Conclusions</b>: With severe obesity, high fat-free mass and BSA result in low estimates of eGFR indexed to 1.73m<sup>2</sup> BSA, especially when creatinine-based estimating equations are used. GFR indexed to actual BSA is approximately 50% higher. When eGFR is indexed to actual BSA, many subjects display evidence of renal hyperfiltration which improves with weight loss. In subjects with severe obesity undergoing medical weight loss, estimating equations that use cystatin C and are indexed to actual BSA may provide a more accurate assessment of renal function.
DOI: 10.6084/m9.figshare.11774472
title: autosomal_single_exons.6367.trees

description: Maximum Likelihood (PhyML) gene trees generated from individual exons over 500bp in length (as opposed to exons concatenated into entire protein coding genes).
DOI: 10.6084/m9.figshare.11774472.v1
title: autosomal_single_exons.6367.trees

description: Maximum Likelihood (PhyML) gene trees generated from individual exons over 500bp in length (as opposed to exons concatenated into entire protein coding genes).
DOI: 10.6084/m9.figshare.11771643
title: data archive contents.xlsx

description: none
DOI: 10.6084/m9.figshare.11771643.v1
title: data archive contents.xlsx

description: none
DOI: 10.6084/m9.figshare.11771619
title: What cortical areas are responsible for blindsight in hemianopic patients?

description: The data that support the findings of the study "What cortical areas are responsible for blindsight in hemianopic patients?"<em><br></em>
DOI: 10.6084/m9.figshare.11771565
title: Supplementary tables from Evolutionary Genomics of Metchnikovella incurvata (Metchnikovellidae): An Early Branching Microsporidium

description: Supplementary tables from Evolutionary Genomics of Metchnikovella incurvata (Metchnikovellidae): An Early Branching Microsporidium
DOI: 10.6084/m9.figshare.11771565.v1
title: Supplementary tables from Evolutionary Genomics of Metchnikovella incurvata (Metchnikovellidae): An Early Branching Microsporidium

description: Supplementary tables from Evolutionary Genomics of Metchnikovella incurvata (Metchnikovellidae): An Early Branching Microsporidium
DOI: 10.6084/m9.figshare.11771289
title: Egg transcriptome assembly of Meloidogyne enterolobii (INRA/JKI)

description: From the raw Illumina reads, adapters and low quality regions (Phred score &lt;30) as well as regions that contained 2 or more consecutive ambiguous nucleotides were cropped using prinseq resulting in 54,424,802 cleaned paired-end reads. The clean reads were assembled using CLC Genomics Workbench 9.0 (https://www.qiagenbioinformatics.com/) with automatic bubble size and word size estimation, in simple contig mode, and minimum contig length of 200.
DOI: 10.6084/m9.figshare.11771295
title: J2 stage transcriptome assembly of Meloidogyne enterolobii (INRA/JKI)

description: Transcriptome assembly of second stage pre-parasitic juveniles of M. entereolobii. From the raw illulmina reads, adapters and low quality regions (Phred score &lt;30) as well as regions that contained 2 or more consecutive ambiguous nucleotides were cropped using prinseq resulting in 54,424,802 cleaned paired-end reads for. The clean reads were assembled using CLC Genomics Workbench 9.0 (https://www.qiagenbioinformatics.com/) with automatic bubble size and word size estimation, in simple contig mode, and minimum contig length of 200.
DOI: 10.6084/m9.figshare.11771286
title: Molecular dynamics simulations of coronavirus 2019-nCoV protease model in complex with G75 and G82 ligands

description: Molecular dynamics simulations (300 ps MD at 300 K) of comparative model of novel coronavirus 2019-nCoV protease Mpro in complex with the ligands G75 and G82. The starting position of the ligands has been respectively copied from 3SZN and 3TIU PDB structures.<br>The archives contain also an heatmap representing the protein-ligand contact frequencies. Green-boxed occurrences in the heatmap represent hydrogen bond formation during the simulation.<br>