cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19220629
title: Additional file 1 of Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196

description: Additional file 1: This file contains python instructions.
DOI: 10.6084/m9.figshare.19220629.v1
title: Additional file 1 of Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196

description: Additional file 1: This file contains python instructions.
DOI: 10.6084/m9.figshare.19220632.v1
title: Additional file 2 of Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196

description: Additional file 2: This file contains python instructions.
DOI: 10.6084/m9.figshare.19220635
title: Additional file 3 of Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196

description: Additional file 3: This file contains BioProjects and information of all analysed genomes.
DOI: 10.6084/m9.figshare.19220632
title: Additional file 2 of Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196

description: Additional file 2: This file contains python instructions.
DOI: 10.6084/m9.figshare.19220635.v1
title: Additional file 3 of Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196

description: Additional file 3: This file contains BioProjects and information of all analysed genomes.
DOI: 10.6084/m9.figshare.19220641
title: Additional file 5 of Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196

description: Additional file 5: This file contains information regarding core genome single nucleotide polymorphisms, their location and their effect.
DOI: 10.6084/m9.figshare.19220641.v1
title: Additional file 5 of Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196

description: Additional file 5: This file contains information regarding core genome single nucleotide polymorphisms, their location and their effect.
DOI: 10.6084/m9.figshare.19220644
title: Additional file 6 of Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196

description: Additional file 6: This file contains detailed information about the genes that represent the pangenome of Brachyspira hyodysenteriae of sequence type ST196.
DOI: 10.6084/m9.figshare.19220644.v1
title: Additional file 6 of Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196

description: Additional file 6: This file contains detailed information about the genes that represent the pangenome of Brachyspira hyodysenteriae of sequence type ST196.
DOI: 10.6084/m9.figshare.19220647.v1
title: Additional file 7 of Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196

description: Additional file 7: This file contains detailed information about the entire set of genes that constitute the Brachyspira pangenome at the genus level.
DOI: 10.6084/m9.figshare.19220647
title: Additional file 7 of Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196

description: Additional file 7: This file contains detailed information about the entire set of genes that constitute the Brachyspira pangenome at the genus level.
DOI: 10.25345/c5xg9fc2d
title: MassIVE Reanalysis RMSV000000354.4901 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CCDC65 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5sq8qj75
title: MassIVE Reanalysis RMSV000000354.4903 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, IL6R [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5nz80r2x
title: MassIVE Reanalysis RMSV000000354.4905 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CCNY [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19220839
title: Additional file 10 of Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection

description: Additional file 10: Table S6. The primers used in this study.
DOI: 10.6084/m9.figshare.19220839.v1
title: Additional file 10 of Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection

description: Additional file 10: Table S6. The primers used in this study.
DOI: 10.6084/m9.figshare.19220848.v1
title: Additional file 3 of Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection

description: Additional file 3: Table S1. Information of infection stage-specifically expressed lncRNAs.
DOI: 10.6084/m9.figshare.19220851.v1
title: Additional file 4 of Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection

description: Additional file 4: Table S2. Enriched GO terms of infection stage-specifically expressed lncRNA target genes.
DOI: 10.6084/m9.figshare.19220848
title: Additional file 3 of Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection

description: Additional file 3: Table S1. Information of infection stage-specifically expressed lncRNAs.
DOI: 10.6084/m9.figshare.19220851
title: Additional file 4 of Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection

description: Additional file 4: Table S2. Enriched GO terms of infection stage-specifically expressed lncRNA target genes.
DOI: 10.6084/m9.figshare.19220854
title: Additional file 5 of Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection

description: Additional file 5: Table S3. Enriched GO terms of mycelia-specifically expressed lncRNA target genes.
DOI: 10.6084/m9.figshare.19220857.v1
title: Additional file 6 of Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection

description: Additional file 6: Table S4. Contingency table of pathogenesis-related genes matched to PHI-base.
DOI: 10.6084/m9.figshare.19220857
title: Additional file 6 of Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection

description: Additional file 6: Table S4. Contingency table of pathogenesis-related genes matched to PHI-base.
DOI: 10.6084/m9.figshare.19220863
title: Additional file 8 of Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection

description: Additional file 8: Table S5. List of transcripts used as CPAT training set.
DOI: 10.6084/m9.figshare.19220863.v1
title: Additional file 8 of Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection

description: Additional file 8: Table S5. List of transcripts used as CPAT training set.
DOI: 10.48370/ofd/nkas23/xvwnwe
title: Opiętek zielony (Agrilus viridis)1.JPG

description: :unav
DOI: 10.6084/m9.figshare.19220875
title: Additional file 2 of Large-scale association study on daily weight gain in pigs reveals overlap of genetic factors for growth in humans

description: Additional file 2: Supplementary Table S1.
DOI: 10.6084/m9.figshare.19220875.v1
title: Additional file 2 of Large-scale association study on daily weight gain in pigs reveals overlap of genetic factors for growth in humans

description: Additional file 2: Supplementary Table S1.
DOI: 10.6084/m9.figshare.19220878.v1
title: Additional file 3 of Large-scale association study on daily weight gain in pigs reveals overlap of genetic factors for growth in humans

description: Additional file 3: Supplementary Table S2.
DOI: 10.48370/ofd/nkas23
title: Opiętek zielony (Agrilus viridis (Linnaeus, 1758)), C-334

description: Coleoptera collection
DOI: 10.6084/m9.figshare.19220878
title: Additional file 3 of Large-scale association study on daily weight gain in pigs reveals overlap of genetic factors for growth in humans

description: Additional file 3: Supplementary Table S2.
DOI: 10.6084/m9.figshare.19220953.v1
title: Additional file 3 of An efficient and specific CRISPR-Cas9 genome editing system targeting soybean phytoene desaturase genes

description: Additional file 3. Table S1. Summary of soybean genetic transformations with genome editing constructs.
DOI: 10.6084/m9.figshare.19220956
title: Additional file 4 of An efficient and specific CRISPR-Cas9 genome editing system targeting soybean phytoene desaturase genes

description: Additional file 4. Table S2. Detection of mutations in T0 plants.
DOI: 10.6084/m9.figshare.19220953
title: Additional file 3 of An efficient and specific CRISPR-Cas9 genome editing system targeting soybean phytoene desaturase genes

description: Additional file 3. Table S1. Summary of soybean genetic transformations with genome editing constructs.
DOI: 10.6084/m9.figshare.19220959
title: Additional file 5 of An efficient and specific CRISPR-Cas9 genome editing system targeting soybean phytoene desaturase genes

description: Additional file 5. Table S3. Detection of mutations in GmPDS8 T1 plants.
DOI: 10.6084/m9.figshare.19220959.v1
title: Additional file 5 of An efficient and specific CRISPR-Cas9 genome editing system targeting soybean phytoene desaturase genes

description: Additional file 5. Table S3. Detection of mutations in GmPDS8 T1 plants.
DOI: 10.6084/m9.figshare.19220956.v1
title: Additional file 4 of An efficient and specific CRISPR-Cas9 genome editing system targeting soybean phytoene desaturase genes

description: Additional file 4. Table S2. Detection of mutations in T0 plants.
DOI: 10.6084/m9.figshare.19220962
title: Additional file 6 of An efficient and specific CRISPR-Cas9 genome editing system targeting soybean phytoene desaturase genes

description: Additional file 6. Table S4. Off-target analysis in GmPDS8 T0 plants.
DOI: 10.6084/m9.figshare.19220962.v1
title: Additional file 6 of An efficient and specific CRISPR-Cas9 genome editing system targeting soybean phytoene desaturase genes

description: Additional file 6. Table S4. Off-target analysis in GmPDS8 T0 plants.
DOI: 10.6084/m9.figshare.19220965
title: Additional file 7 of An efficient and specific CRISPR-Cas9 genome editing system targeting soybean phytoene desaturase genes

description: Additional file 7. Table S5. Primers used for cloning and molecular analyses.
DOI: 10.6084/m9.figshare.19220965.v1
title: Additional file 7 of An efficient and specific CRISPR-Cas9 genome editing system targeting soybean phytoene desaturase genes

description: Additional file 7. Table S5. Primers used for cloning and molecular analyses.
DOI: 10.5281/zenodo.6233982
title: AnimalTraits

description: AnimalTraits: a curated animal trait database for body mass, metabolic rate and brain size. This repository contains the animal traits database in CSV format (observations.csv) and Excel format (observations.xlsx), column documentation in CSV format (column-documentation.csv) and a Zip file containing raw data, scripts to compile the database and source for the website (https://animaltraits.org/).
DOI: 10.25345/c5j678x8g
title: MassIVE Reanalysis RMSV000000354.4908 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ARHGAP44 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19221052
title: Additional file 1 of Automatic classification of nerve discharge rhythms based on sparse auto-encoder and time series feature

description: Additional file 1. Training datasets: Training datasets composed of different types of ISI sequences simulated by theoretical models, and the Category labels of Training datasets.
DOI: 10.6084/m9.figshare.19221052.v1
title: Additional file 1 of Automatic classification of nerve discharge rhythms based on sparse auto-encoder and time series feature

description: Additional file 1. Training datasets: Training datasets composed of different types of ISI sequences simulated by theoretical models, and the Category labels of Training datasets.
DOI: 10.6084/m9.figshare.19221055
title: Additional file 2 of Automatic classification of nerve discharge rhythms based on sparse auto-encoder and time series feature

description: Additional file 2. Testing datasets: Testing datasets composed of different types of ISI sequences simulated by theoretical models, and the Category labels of Training datasets.
DOI: 10.6084/m9.figshare.19221055.v1
title: Additional file 2 of Automatic classification of nerve discharge rhythms based on sparse auto-encoder and time series feature

description: Additional file 2. Testing datasets: Testing datasets composed of different types of ISI sequences simulated by theoretical models, and the Category labels of Training datasets.
DOI: 10.25345/c5df6k44r
title: MassIVE Reanalysis RMSV000000354.4909 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, IFNA10 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c58p5vb13
title: MassIVE Reanalysis RMSV000000354.4906 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ASMTL [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.48370/ofd/w5eksw/718xdx
title: Opiętek osikowy (Agrilus suvorovi).JPG

description: :unav
DOI: 10.48370/ofd/w5eksw
title: Opiętek osikowy (Agrilus suvorovi (Obenberger, 1935)), C-335

description: Coleoptera collection
DOI: 10.25345/c5513tx0k
title: MassIVE Reanalysis RMSV000000354.4912 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, MME [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c51834373
title: MassIVE Reanalysis RMSV000000354.4910 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ACADS [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5wh2dg17
title: MassIVE Reanalysis RMSV000000354.4911 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CKMT1A [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5rr1pn60
title: MassIVE Reanalysis RMSV000000354.4913 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C12orf53 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.48370/ofd/xmoqsj/bmttxg
title: Opiętek osikowy (Agrilus suvorovi) 1.JPG

description: :unav
DOI: 10.48370/ofd/xmoqsj
title: Opiętek osikowy (Agrilus suvorovi (Obenberger, 1935)), C-336

description: Coleoptera collection
DOI: 10.25345/c5n00zv25
title: MassIVE Reanalysis RMSV000000354.4915 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TAT [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5h70819p
title: MassIVE Reanalysis RMSV000000354.4907 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, METTL21A [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19221165
title: Supplementary Material for: High-Throughput Metabolomics and Diabetic Kidney Disease Progression: Evidence from the Chronic Renal Insufficiency (CRIC) Study

description: <b><i>Introduction:</i></b> Metabolomics could offer novel prognostic biomarkers and elucidate mechanisms of diabetic kidney disease (DKD) progression. Via metabolomic analysis of urine samples from 995 CRIC participants with diabetes and state-of-the-art statistical modeling, we aimed to identify metabolites prognostic to DKD progression. <b><i>Methods:</i></b> Urine samples (<i>N</i> = 995) were assayed for relative metabolite abundance by untargeted flow-injection mass spectrometry, and stringent statistical criteria were used to eliminate noisy compounds, resulting in 698 annotated metabolite ions. Utilizing the 698 metabolites’ ion abundance along with clinical data (demographics, blood pressure, HbA1c, eGFR, and albuminuria), we developed univariate and multivariate models for the eGFR slope using penalized (lasso) and random forest models. Final models were tested on time-to-ESKD (end-stage kidney disease) via cross-validated C-statistics. We also conducted pathway enrichment analysis and a targeted analysis of a subset of metabolites. <b><i>Results:</i></b> Six eGFR slope models selected 9–30 variables. In the adjusted ESKD model with highest C-statistic, valine (or betaine) and 3-(4-methyl-3-pentenyl)thiophene were associated (<i>p</i> &lt; 0.05) with 44% and 65% higher hazard of ESKD per doubling of metabolite abundance, respectively. Also, 13 (of 15) prognostic amino acids, including valine and betaine, were confirmed in the targeted analysis. Enrichment analysis revealed pathways implicated in kidney and cardiometabolic disease. <b><i>Conclusions:</i></b> Using the diverse CRIC sample, a high-throughput untargeted assay, followed by targeted analysis, and rigorous statistical analysis to reduce false discovery, we identified several novel metabolites implicated in DKD progression. If replicated in independent cohorts, our findings could inform risk stratification and treatment strategies for patients with DKD.