cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13309409.v1
title: Supplemental Table S1-S5

description: <b>All animal procedures were reviewed and approved by the Animal Care and Use Committee and were carried out in accordance with the Sichuan Agricultural University. A In consideration of the dysregulation of BA homeostasis was mainly occurred during the second or third trimester of pregnancy, this study was conducted from day 60 of gestation (G60) till farrowing (L0). VAN group was orally administered with vancomycin (20mg/kg diet), which was mixed with corn starch to 10 gram, from G60 to G114, while the control group (CON) orally received 10 gram corn starch. The feed intake from G60 to G90 was 2.45kg/d and thereafter 3.06kg/d. Blood samples of pregnant sows were collected from precaval vein every 7 to 8 days via catheters implanted at cephalic vein or via ear vein when catheters didn’t work after 12-hours fasting. In consideration of the barely faeces found at L0, maternal faeces were collected at G60, G90 and G105, respectively. Placental tissues, ileum tissues and fetal blood (umbilical cord vein) samples were collected after 8-hours fasting at G60 and G90, respectively, when pregnant swine were laparotomized and under deep isoflurane-induced anesthesia, and during parturition.</b> <b>Primary pig hepatocytes were isolated from 2~5 day old female pigs using 2-step perfusion method with a minor modification. Cell concentration was determined and 1.5 105 per well were plated in 24-well plates or 5 105 per well were plated in 6-well plates. Cells were grown in complete medium containing DMEM medium, 2.5% dextran-coated, charcoal-stripped fetal bovine serum.</b> <b>The total BA (TBA) was measured by the enzymatic cycling method assay kits in Model 3100 automatic biochemical analyzer (Hitachi, Tokyo, Japan). Bile acids profile was measured by UPLC-MS/MS.</b> <b>Estradiol was measured by estradiol radioimmunoassay KIT according to the manufacturer’s specifications.</b><b></b>
DOI: 10.5281/zenodo.4299389
title: Phenological and climate data for herbarium specimens of Streptanthus tortuosus (Brasicaceae)

description: These data represent phenological data derived from herbarium specimens of Streptanthus tortuous collected between 1903 and 2013 in California. The associated temperature and precipitation related climate data during the year of specimen collection at the location of collection are also included.
DOI: 10.5281/zenodo.4299388
title: Phenological and climate data for herbarium specimens of Streptanthus tortuosus (Brasicaceae)

description: These data represent phenological data derived from herbarium specimens of Streptanthus tortuous collected between 1903 and 2013 in California. The associated temperature and precipitation related climate data during the year of specimen collection at the location of collection are also included.
DOI: 10.6084/m9.figshare.13310092.v1
title: Additional file 1 of MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis

description: Additional file 1: Table S1. Known miRNAs identified in this study.
DOI: 10.6084/m9.figshare.13310086.v1
title: Additional file 10 of MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis

description: Additional file 10: Table S10. Oligonucleotide primers used for qRT-PCR assays in this study.
DOI: 10.6084/m9.figshare.13310086
title: Additional file 10 of MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis

description: Additional file 10: Table S10. Oligonucleotide primers used for qRT-PCR assays in this study.
DOI: 10.6084/m9.figshare.13310104
title: Additional file 4 of MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis

description: Additional file 4: Table S4. Expression pattern of differentially expressed miRNAs in Anyu 5 and target function identified by degradome.
DOI: 10.6084/m9.figshare.13310107
title: Additional file 5 of MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis

description: Additional file 5: Table S5. Expression pattern of differentially expressed miRNAs in Ye 478 × Huangzaosi and target function identified by degradome.
DOI: 10.6084/m9.figshare.13310098.v1
title: Additional file 2 of MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis

description: Additional file 2: Table S2. Novel miRNAs identified in this study.
DOI: 10.6084/m9.figshare.13310104.v1
title: Additional file 4 of MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis

description: Additional file 4: Table S4. Expression pattern of differentially expressed miRNAs in Anyu 5 and target function identified by degradome.
DOI: 10.6084/m9.figshare.13310098
title: Additional file 2 of MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis

description: Additional file 2: Table S2. Novel miRNAs identified in this study.
DOI: 10.6084/m9.figshare.13310101.v1
title: Additional file 3 of MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis

description: Additional file 3: Table S3. Expression pattern of differentially expressed miRNAs in Zhengdan 958 and target function identified by degradome.
DOI: 10.6084/m9.figshare.13310107.v1
title: Additional file 5 of MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis

description: Additional file 5: Table S5. Expression pattern of differentially expressed miRNAs in Ye 478 × Huangzaosi and target function identified by degradome.
DOI: 10.6084/m9.figshare.13310092
title: Additional file 1 of MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis

description: Additional file 1: Table S1. Known miRNAs identified in this study.
DOI: 10.6084/m9.figshare.13310101
title: Additional file 3 of MicroRNA transcriptomic analysis of the sixth leaf of maize (Zea mays L.) revealed a regulatory mechanism of jointing stage heterosis

description: Additional file 3: Table S3. Expression pattern of differentially expressed miRNAs in Zhengdan 958 and target function identified by degradome.
DOI: 10.6084/m9.figshare.13310218
title: Additional file 1 of Reproductive consequences of an extra long-term sperm storage organ

description: Additional file 1: Table S1. Number of sperm per spermathecae. If no number is listed for the "SP3" column, that female only had two spermathecae. "Day" is the number of days after fertilization at which the spermathecae's sperm numbers were scored. "Female #" is a designated number for each female scored. "SP1-3" are the three separate spermathecae, with a number (1-3) randomly assigned to each spermathecae. Table S2. Number of offspring for each time interval (days 0-5, 5.5-10, 10.5-15, and 15.5-20) for female with two vs. three spermathecae (SP#). Females that were not scored for the last time interval have that value left blank. Note that "Female #" is a designated number for each female scored and does not represent the same numbered female as in Table S1.
DOI: 10.6084/m9.figshare.13310218.v1
title: Additional file 1 of Reproductive consequences of an extra long-term sperm storage organ

description: Additional file 1: Table S1. Number of sperm per spermathecae. If no number is listed for the "SP3" column, that female only had two spermathecae. "Day" is the number of days after fertilization at which the spermathecae's sperm numbers were scored. "Female #" is a designated number for each female scored. "SP1-3" are the three separate spermathecae, with a number (1-3) randomly assigned to each spermathecae. Table S2. Number of offspring for each time interval (days 0-5, 5.5-10, 10.5-15, and 15.5-20) for female with two vs. three spermathecae (SP#). Females that were not scored for the last time interval have that value left blank. Note that "Female #" is a designated number for each female scored and does not represent the same numbered female as in Table S1.
DOI: 10.6084/m9.figshare.13310323.v1
title: Additional file 1 of Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains

description: Additional file 1. Table S1.
DOI: 10.6084/m9.figshare.13310329.v1
title: Additional file 3 of Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains

description: Additional file 3. Table S3.
DOI: 10.6084/m9.figshare.13310338.v1
title: Additional file 6 of Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains

description: Additional file 6. Table S5.
DOI: 10.6084/m9.figshare.13310329
title: Additional file 3 of Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains

description: Additional file 3. Table S3.
DOI: 10.6084/m9.figshare.13310323
title: Additional file 1 of Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains

description: Additional file 1. Table S1.
DOI: 10.6084/m9.figshare.13310338
title: Additional file 6 of Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains

description: Additional file 6. Table S5.
DOI: 10.5281/zenodo.4299373
title: MoMA Collection - Automatic Monthly Update

description: Temporary Description
DOI: 10.5281/zenodo.4299372
title: MoMA Collection - Automatic Monthly Update

description: Temporary Description
DOI: 10.6084/m9.figshare.13310377
title: Additional file 7 of Developmental programming in human umbilical cord vein endothelial cells following fetal growth restriction

description: Additional file 7. Table S5: All MsigDB gene modules, as determined by CAMERA, in gene list ranked based on a comparison of: differential expression of FGR versus control (FGR–control). Modules sorted by significance.
DOI: 10.6084/m9.figshare.13310377.v1
title: Additional file 7 of Developmental programming in human umbilical cord vein endothelial cells following fetal growth restriction

description: Additional file 7. Table S5: All MsigDB gene modules, as determined by CAMERA, in gene list ranked based on a comparison of: differential expression of FGR versus control (FGR–control). Modules sorted by significance.
DOI: 10.6084/m9.figshare.13310374
title: Additional file 6 of Developmental programming in human umbilical cord vein endothelial cells following fetal growth restriction

description: Additional file 6. Table S4: differential expression of FGR versus control (FGR–control).
DOI: 10.6084/m9.figshare.13310374.v1
title: Additional file 6 of Developmental programming in human umbilical cord vein endothelial cells following fetal growth restriction

description: Additional file 6. Table S4: differential expression of FGR versus control (FGR–control).
DOI: 10.6084/m9.figshare.13310452
title: Additional file 2 of Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis

description: Additional file 2: Supplemental file 2. (tab) – CRISPR reconstructions highlighting 1) global structure and position of IS6110 insertions [‘IS6110’ sheet]; 2) spacer variants [‘spacer’ sheet]; 3) DR variants [‘DR’ sheet]; 4) Duplicated DVR [‘Duplic’ sheet].
DOI: 10.6084/m9.figshare.13310452.v1
title: Additional file 2 of Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis

description: Additional file 2: Supplemental file 2. (tab) – CRISPR reconstructions highlighting 1) global structure and position of IS6110 insertions [‘IS6110’ sheet]; 2) spacer variants [‘spacer’ sheet]; 3) DR variants [‘DR’ sheet]; 4) Duplicated DVR [‘Duplic’ sheet].
DOI: 10.6084/m9.figshare.13310569.v1
title: Additional file 2 of Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature

description: Additional file 2: Supplementary File 1.
DOI: 10.6084/m9.figshare.13310578.v1
title: Additional file 3 of Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature

description: Additional file 3: Supplementary File 2.
DOI: 10.6084/m9.figshare.13310569
title: Additional file 2 of Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature

description: Additional file 2: Supplementary File 1.
DOI: 10.6084/m9.figshare.13310578
title: Additional file 3 of Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature

description: Additional file 3: Supplementary File 2.
DOI: 10.6084/m9.figshare.13310599.v1
title: Additional file 1 of Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline

description: Additional file 1: Gene count estimates. Model (negative binomial generalized linear mixed models) based estimates of gene counts from models using different normalization strategies. ensemblid: Ensembl gene identifiers; normalization_model: Indicates normalization model: lib_size_normalized, gene counts are modeled with study conditions as fixed effects and participant id as random effects and with the addition of library size as a fixed effect. tissue_offset_lib_size_normalized, same as lib_size_normalized but with the addition of tissue weight used in library prep as an offset. The non-normalized model is not included in the data set; interaction_model: Indicates if the coefficient is estimated in a model containing the interaction between volume condition and time. If FALSE, the model only contains time as a fixed effect (in addition to any normalization, see above), coefficients should in this case be interpreted as averages over volume conditions; coefficient: Names of coefficients (fixed effects, time and volume conditions). timew2pre and timew12 indicate differences from timew0 (intercept) in rested state models. timew2post indicates differences from timew2pre (intercept) in acute exercise models. setsmultiple indicates interaction effects, the difference between setssingle (reference level) and setsmultiple; estimate: Estimates on the natural log scale; se: Standard errors (SE) on the natural log scale; zvalue: Z-values; pvalue: Un-adjusted P-values; pvalue_adjust: Adjusted P-values (FDR) per model/normalization method and coefficient.
DOI: 10.6084/m9.figshare.13310599
title: Additional file 1 of Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline

description: Additional file 1: Gene count estimates. Model (negative binomial generalized linear mixed models) based estimates of gene counts from models using different normalization strategies. ensemblid: Ensembl gene identifiers; normalization_model: Indicates normalization model: lib_size_normalized, gene counts are modeled with study conditions as fixed effects and participant id as random effects and with the addition of library size as a fixed effect. tissue_offset_lib_size_normalized, same as lib_size_normalized but with the addition of tissue weight used in library prep as an offset. The non-normalized model is not included in the data set; interaction_model: Indicates if the coefficient is estimated in a model containing the interaction between volume condition and time. If FALSE, the model only contains time as a fixed effect (in addition to any normalization, see above), coefficients should in this case be interpreted as averages over volume conditions; coefficient: Names of coefficients (fixed effects, time and volume conditions). timew2pre and timew12 indicate differences from timew0 (intercept) in rested state models. timew2post indicates differences from timew2pre (intercept) in acute exercise models. setsmultiple indicates interaction effects, the difference between setssingle (reference level) and setsmultiple; estimate: Estimates on the natural log scale; se: Standard errors (SE) on the natural log scale; zvalue: Z-values; pvalue: Un-adjusted P-values; pvalue_adjust: Adjusted P-values (FDR) per model/normalization method and coefficient.
DOI: 10.6084/m9.figshare.13310602.v1
title: Additional file 2 of Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline

description: Additional file 2: Functional annotation using gene ontology terms. Significance tests for functional annotation using rank-based and over-representation based analysis. ID: Gene ontology (GO) id; go_category: GO category, bp, Biological process; cc, cellular component; mf, molecular function; name: Descriptive GO name; normalization_model: Indicate normalization model used to test enrichment: lib_size_normalized, gene counts are modeled with study conditions as fixed effects and participant id as random effects and with the addition of library size as a fixed effect, tissue_offset_lib_size_normalized, same as lib_size_normalized but with the addition of tissue weight used in library prep as an offset. The non-normalized model is not included; coefficient: Names of coefficients used to test enrichment (fixed effects, time and volume conditions). timew2pre and timew12 indicates differences from timew0 (intercept) in rested state models. timew2post indicates differences from timew2pre (intercept) in acute exercise models. setsmultiple indicates interaction effects, the difference between setssingle (reference level) and setsmultiple; cerno_statistic: Test statistic from the rank-based cerno-test; cerno_auc: Area under the curve from the Cerno test (see tmod documentation for details, https://CRAN.R-project.org/package=tmod ); cerno_pval: Un-adjusted P-values from cerno test, cerno_padj: Adjusted P-values (default settings in tmodCERNOtest, see tmod documentation); fgsea_pval: Un-adjusted P-values from gene set enrichment tests performed with the fgsea package; fgsea_padj: Adjusted fgsea P-values; NES: Normalized enrichment scores from gene set enrichment tests; set_size: Size of gene sets using genes expressed in the present data set; ora_geneRatio: Gene ratio in over-representation analysis of genes identified as differentially expressed; ora_padj: Adjusted p-values from over-representation analysis.
DOI: 10.6084/m9.figshare.13310617
title: Additional file 2 of Prediction of the incubation period for COVID-19 and future virus disease outbreaks

description: Additional file 2. GenBank file with the reference genomes used for each of the studied viruses.
DOI: 10.6084/m9.figshare.13310602
title: Additional file 2 of Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline

description: Additional file 2: Functional annotation using gene ontology terms. Significance tests for functional annotation using rank-based and over-representation based analysis. ID: Gene ontology (GO) id; go_category: GO category, bp, Biological process; cc, cellular component; mf, molecular function; name: Descriptive GO name; normalization_model: Indicate normalization model used to test enrichment: lib_size_normalized, gene counts are modeled with study conditions as fixed effects and participant id as random effects and with the addition of library size as a fixed effect, tissue_offset_lib_size_normalized, same as lib_size_normalized but with the addition of tissue weight used in library prep as an offset. The non-normalized model is not included; coefficient: Names of coefficients used to test enrichment (fixed effects, time and volume conditions). timew2pre and timew12 indicates differences from timew0 (intercept) in rested state models. timew2post indicates differences from timew2pre (intercept) in acute exercise models. setsmultiple indicates interaction effects, the difference between setssingle (reference level) and setsmultiple; cerno_statistic: Test statistic from the rank-based cerno-test; cerno_auc: Area under the curve from the Cerno test (see tmod documentation for details, https://CRAN.R-project.org/package=tmod ); cerno_pval: Un-adjusted P-values from cerno test, cerno_padj: Adjusted P-values (default settings in tmodCERNOtest, see tmod documentation); fgsea_pval: Un-adjusted P-values from gene set enrichment tests performed with the fgsea package; fgsea_padj: Adjusted fgsea P-values; NES: Normalized enrichment scores from gene set enrichment tests; set_size: Size of gene sets using genes expressed in the present data set; ora_geneRatio: Gene ratio in over-representation analysis of genes identified as differentially expressed; ora_padj: Adjusted p-values from over-representation analysis.
DOI: 10.6084/m9.figshare.13310620
title: Additional file 3 of Prediction of the incubation period for COVID-19 and future virus disease outbreaks

description: Additional file 3. Accessions of the nucleotide sequences used for each of the 14 viruses studied. The sequence alignments are available through Zenodo ( https://zenodo.org/record/4239675 ).
DOI: 10.6084/m9.figshare.13310620.v1
title: Additional file 3 of Prediction of the incubation period for COVID-19 and future virus disease outbreaks

description: Additional file 3. Accessions of the nucleotide sequences used for each of the 14 viruses studied. The sequence alignments are available through Zenodo ( https://zenodo.org/record/4239675 ).
DOI: 10.6084/m9.figshare.13310617.v1
title: Additional file 2 of Prediction of the incubation period for COVID-19 and future virus disease outbreaks

description: Additional file 2. GenBank file with the reference genomes used for each of the studied viruses.
DOI: 10.6084/m9.figshare.13310701
title: Additional file 12 of Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions

description: Additional file 12: Table S6. Primer sequences used in this study.
DOI: 10.6084/m9.figshare.13310695
title: Additional file 11 of Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions

description: Additional file 11: Table S5. Accessions used in this study.
DOI: 10.6084/m9.figshare.13310701.v1
title: Additional file 12 of Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions

description: Additional file 12: Table S6. Primer sequences used in this study.
DOI: 10.6084/m9.figshare.13310719
title: Additional file 1 of Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions

description: Additional file 1: Table S1. Sequencing coverage for each nucleotide position in the experiment.
DOI: 10.6084/m9.figshare.13310695.v1
title: Additional file 11 of Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions

description: Additional file 11: Table S5. Accessions used in this study.
DOI: 10.6084/m9.figshare.13310716
title: Additional file 14 of Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions

description: Additional file 14: Table S7. Correspondence between Illumina indexes and accession pools used in this study.
DOI: 10.6084/m9.figshare.13310716.v1
title: Additional file 14 of Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions

description: Additional file 14: Table S7. Correspondence between Illumina indexes and accession pools used in this study.
DOI: 10.6084/m9.figshare.13310740
title: Additional file 4 of Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions

description: Additional file 4: Table S2. Allele frequencies and number of accessions harboring alleles of predicted deleterious variants common to GATK, SNVer and CRISP.