cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4602627
title: Simulated maps for paper " Detecting Protein and DNA/RNA Structures in Cryo-EM Maps of Intermediate Resolution Using Deep Learning"

description: These folders include simulated EM map files at 6 A and 10 A for 1056 protein-RNA/RNA complex structures. Maps of 6 A are stored in the 'SIMU6' directory while those simulated at 10 A are saved in the 'SIMU10' directory.<br> To verify all the files are downloaded, please go to "SIMU6" and "SIMU10" directory and run the checking script verify_utils.py by "python3 verify_utils.py" to see if the downloading is successful or not.<br> These simulated maps were used in the following paper: Xiao Wang, Eman Alnabati, Tunde W Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi & Daisuke Kihara. Detecting Protein and DNA/RNA Structures in Cryo-EM Maps of Intermediate Resolution Using Deep Learning. Nature Communications (2021).<br> The simulated maps were generated by the pdb2vol program of the SITUS package. Please read the papers for more details.<br> For each PDB entry, 3 files are included: .pdb (PDB file), mrc (simulated map file), and _reso (simulated resolution).<br> For any questions or further assistance, please contact by email to Daisuke Kihara: dkihara@purdue.edu.<br>
DOI: 10.5281/zenodo.4599656
title: Simulated maps for paper " Detecting Protein and DNA/RNA Structures in Cryo-EM Maps of Intermediate Resolution Using Deep Learning"

description: These folders include simulated EM map files at 6 A and 10 A for 1056 protein-RNA/RNA complex structures. Maps of 6 A are stored in the 'SIMU6' directory while those simulated at 10 A are saved in the 'SIMU10' directory.<br> To verify all the files are downloaded, please go to "SIMU6" and "SIMU10" directory and run the checking script verify_utils.py by "python3 verify_utils.py" to see if the downloading is successful or not.<br> These simulated maps were used in the following paper: Xiao Wang, Eman Alnabati, Tunde W Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi & Daisuke Kihara. Detecting Protein and DNA/RNA Structures in Cryo-EM Maps of Intermediate Resolution Using Deep Learning. Nature Communications (2021).<br> The simulated maps were generated by the pdb2vol program of the SITUS package. Please read the papers for more details.<br> For each PDB entry, 3 files are included: .pdb (PDB file), mrc (simulated map file), and _reso (simulated resolution).<br> For any questions or further assistance, please contact by email to Daisuke Kihara: dkihara@purdue.edu.<br>
DOI: 10.5281/zenodo.4469785
title: Deconvolving clinically relevant cellular immune crosstalk from bulk gene expression using CODEFACS and LIRICS

description: All the processed data generated in the manuscript "Deconvolving clinically relevant cellular immune crosstalk from bulk gene expression using CODEFACS and LIRICS" are uploaded here. Please see the README for details.
DOI: 10.5281/zenodo.4602631
title: Replication Package - Assessing Perceived Sentiment in Pull Requests with Emoji: Evidence from Tools and Developer Eye Movements

description: Replication Package for the study <em>Assessing Perceived Sentiment in Pull Requests with Emoji: Evidence from Tools and Developer Eye Movements</em>
DOI: 10.5281/zenodo.4602630
title: Replication Package - Assessing Perceived Sentiment in Pull Requests with Emoji: Evidence from Tools and Developer Eye Movements

description: Replication Package for the study <em>Assessing Perceived Sentiment in Pull Requests with Emoji: Evidence from Tools and Developer Eye Movements</em>
DOI: 10.6084/m9.figshare.14211179
title: mBio_Wang_etal_2020_supplement_TableS1

description: <b>Supplemental Table S1. Number of genes per TPM bin from RNA-Seq of 21 <i>C. albicans </i>isolates.</b>
DOI: 10.6084/m9.figshare.14211218
title: mBio_Wang_etal_2020_supplement_TableS2

description: <b>Supplemental Table S2. Number of differentially expressed genes in all pairwise combinations among <i>C. albicans </i>isolates. </b>Differentially expressed genes were defined by a q-value &lt; 0.05 and ≥ 2-fold change.
DOI: 10.6084/m9.figshare.14211224
title: mBio_Wang_etal_2020_supplement_TableS3

description: <b>Supplemental Table S3. Differentially expressed genes among <i>C. albicans </i>isolates. </b>Differentially expressed genes were defined by a q-value &lt; 0.05 and ≥ 2-fold change. LogFC is log<sub>2</sub> fold change, logCPM is log2 counts per million differences, PValue is the p-value for the gene, and FDR indicates the false discovery rate corrected p-value. Positive LogFC value indicate higher expression in the second strain in the tab title and negative value indicate lower expression.
DOI: 10.6084/m9.figshare.14211233
title: mBio_Wang_etal_2020_supplement_TableS4

description: <b>Supplemental Table S4. Gene ontology (GO) terms associated with differentially expressed genes. </b>The first column denotes the GO term, the second column identifies the number of pairwise comparison with significant enrichment for that term, and the third column identifies all pairwise comparisons in which the GO term was identified. Tabs are broken out by “Component”, “Process”, and “Function”.
DOI: 10.6084/m9.figshare.14211239
title: mBio_Wang_etal_2020_supplement_TableS5

description: <b>Supplemental Table S5. Gene ontology (GO) terms associated with uniformly expressed genes across the 21 <i>C. albicans </i>isolates. </b>The columns of each page include “GOID”, “GO term”, “Cluster frequency” to indicate the number of genes within the GO term among the 2036 identically expressed genes, “background Frequency” to indicate the total number of 6473 annotated genes in the <i>C. albicans </i>genome assigned to that GO term, “Corrected p-value” “False Discovery Rate”, and “Genes annotated to the term” to define the genes that contribute to the “Cluster Frequency” column. Tabs are broken out by “Component”, “Process”, and “Function”.
DOI: 10.6084/m9.figshare.14211242
title: mBio_Wang_etal_2020_supplement_TableS6

description: <b>Supplemental Table S6. Gene ontology (GO) terms associated with strain-specific expression. </b>The columns of each page include “GOID”, “GO term”, “Cluster frequency” to indicate the number of genes within the GO term among the 2036 identically expressed genes, “background Frequency” to indicate the total number of 6473 annotated genes in the <i>C. albicans </i>genome assigned to that GO term, “Corrected p-value” “False Discovery Rate”, and “Genes annotated to the term” to define the genes that contribute to the “Cluster Frequency” column. Tabs are broken out by “Strain_component/process/function”.
DOI: 10.6084/m9.figshare.14211248
title: mBio_Wang_etal_2020_supplement_TableS7

description: <b>Supplemental Table S7. Average 5’ UTR lengths for all detectable genes across the 21 <i>C. albicans </i>isolates.</b>
DOI: 10.6084/m9.figshare.14211251
title: mBio_Wang_etal_2020_supplement_TableS8

description: <b>Supplemental Table S8. Average 3’ UTR lengths for all detectable genes across the 21 <i>C. albicans </i>isolates.</b>
DOI: 10.6084/m9.figshare.14211263
title: mBio_Wang_etal_2020_supplement_TableS9

description: <b>Supplemental Table S9. <i>C. albicans </i>genes with significantly elevated expression plasticity. </b>Each gene is listed with the coefficient of variation (CV) for expression for the gene across all isolates.
DOI: 10.6084/m9.figshare.14211266
title: mBio_Wang_etal_2020_supplement_TableS10

description: <b>Supplemental Table S10. Genes differentially expressed between extreme phenotypic groups in the 21 <i>C. albicans </i>isolates<i>. </i></b>Each tab is associated with a different phenotype. Row 1 indicates the strains used for comparison and the criteria that defined each set in the comparison. LogFC is log<sub>2</sub> fold change, logCPM is log2 counts per million differences, PValue is the p-value for the gene, and FDR indicates the false discovery rate corrected p-value. Positive LogFC value indicate higher expression in the second strain in the tab title and negative value indicate lower expression.
DOI: 10.6084/m9.figshare.14211275
title: mBio_Wang_etal_2020_supplement_TableS11

description: <b>Supplemental Table S11. Gene ontology (GO) terms associated with differentially expressed genes between extreme phenotypic groups in the 21 <i>C. albicans </i>isolates. </b>Each tab identifies the phenotype and GO category (component, function, or process) for each comparison made with significant enrichment of GO terms. The columns of each page include “GOID”, “GO term”, “Cluster frequency” to indicate the number of genes within the GO term among the 2036 identically expressed genes, “background Frequency” to indicate the total number of 6473 annotated genes in the <i>C. albicans </i>genome assigned to that GO term, “Corrected p-value” “False Discovery Rate”, and “Genes annotated to the term” to define the genes that contribute to the “Cluster Frequency” column.
DOI: 10.6084/m9.figshare.14211278
title: mBio_Wang_etal_2020_supplement_TableS12

description: <b>Supplemental Table S12. Genes significantly correlated with a linear model of gene expression for 23 phenotypic measurements in the 21 <i>C. albicans </i>isolates. </b>Each tab describes the phenotype correlated against gene expression. The columns of each page include “Slope” of the linear regression, “Intercept” on the y-axis, “rSquared” correlation value, “pValue”, and “qValue” to indicate the corrected p-value.
DOI: 10.6084/m9.figshare.14211281
title: mBio_Wang_etal_2020_supplement_TableS13

description: <b>Supplemental Table S13. Gene ontology (GO) terms associated with linear modeled genes in the 21 <i>C. albicans </i>isolates. </b>Each tab identifies the phenotype and GO category (component, function, or process) for each comparison made with significant enrichment of GO terms. The columns of each page include “GO term”, “Cluster frequency” to indicate the number of genes within the GO term among the 2036 identically expressed genes, “background Frequency” to indicate the total number of 6473 annotated genes in the <i>C. albicans </i>genome assigned to that GO term, “Corrected p-value” “False Discovery Rate”, and “Genes annotated to the term” to define the genes that contribute to the “Cluster Frequency” column.
DOI: 10.6084/m9.figshare.14211287
title: mBio_Wang_etal_2020_supplement_TableS14

description: <b>Supplemental Table S14. Gene lists for <i>C. albicans </i>co-expression modules.</b>
DOI: 10.6084/m9.figshare.14211290
title: mBio_Wang_etal_2020_supplement_TableS15

description: <b>Supplemental Table S15. Gene ontology (GO) terms enriched within each co-expression module. </b>Each module is denoted as “MEX_component/process/function” in separate tabs. The columns of each page include “GOID”, “GO term”, “Cluster frequency” to indicate the number of genes within the GO term among the 2036 identically expressed genes, “background Frequency” to indicate the total number of 6473 annotated genes in the <i>C. albicans </i>genome assigned to that GO term, “Corrected p-value” “False Discovery Rate”, “Genes annotated to the term” to define the genes that contribute to the “Cluster Frequency” column, and “Directly Annotated GOID list” includes the list of GO IDs connected to the GO ID in that row.
DOI: 10.6084/m9.figshare.14211296
title: mBio_Wang_etal_2020_supplement_TableS16

description: <b>Supplemental</b> <b>Table S16. <i>C. albicans </i>strains used in this study.</b>
DOI: 10.6084/m9.figshare.14211299
title: mBio_Wang_etal_2020_supplement_TableS17

description: <b>Supplemental Table S17. Oligonucleotides used in this study.</b>
DOI: 10.6084/m9.figshare.14211305
title: mBio_Wang_etal_2020_supplement_TableS18

description: <b>Supplemental Table S18. Plasmids used in this study.</b>
DOI: 10.6084/m9.figshare.14211396
title: Additional file 1 of Somatic variants for seed and fruit set in grapevine

description: Additional file 1: Table S1. Genotyping of variant pairs with SSR markers. Table S2. Statistical analysis of bunch, berry and seed traits upon open-pollination. Table S3. Bunch compactness according to the OIV 204 descriptor. Table S4. Spearman correlation between bunch compactness and other traits evaluated in this work. Table S5. Statistical analysis of length, width and length/width ratio of the apparently normal seeds extracted from berries at veraison. Table S6. Statistical analysis of length, width and length/width ratio of the ovule/seed traces extracted from berries at veraison. Table S7. Statistical analysis of seed and fruit set in open- and self-pollination conditions. Table S8. Microsatellite profile of Sangiovese, Gamay and Nebbiolo seedlings derived from self-pollination and emasculation with inflorescence bagging. Table S9. Corinto Nero offspring analyzed for ploidy level and microsatellite genotyping. Table S10. Single nucleotide polymorphisms and insertions/deletions identified in the five amplicons containing the RNA-Seq SNPs that distinguish Sangiovese and Corinto Nero. Table S11. Results of the tests for the presence of viruses.
DOI: 10.6084/m9.figshare.14211396.v1
title: Additional file 1 of Somatic variants for seed and fruit set in grapevine

description: Additional file 1: Table S1. Genotyping of variant pairs with SSR markers. Table S2. Statistical analysis of bunch, berry and seed traits upon open-pollination. Table S3. Bunch compactness according to the OIV 204 descriptor. Table S4. Spearman correlation between bunch compactness and other traits evaluated in this work. Table S5. Statistical analysis of length, width and length/width ratio of the apparently normal seeds extracted from berries at veraison. Table S6. Statistical analysis of length, width and length/width ratio of the ovule/seed traces extracted from berries at veraison. Table S7. Statistical analysis of seed and fruit set in open- and self-pollination conditions. Table S8. Microsatellite profile of Sangiovese, Gamay and Nebbiolo seedlings derived from self-pollination and emasculation with inflorescence bagging. Table S9. Corinto Nero offspring analyzed for ploidy level and microsatellite genotyping. Table S10. Single nucleotide polymorphisms and insertions/deletions identified in the five amplicons containing the RNA-Seq SNPs that distinguish Sangiovese and Corinto Nero. Table S11. Results of the tests for the presence of viruses.
DOI: 10.6084/m9.figshare.14211503
title: Additional file 2 of Novel ERCC2 variant in trichothiodystrophy infant: the first case report in China

description: Additional file 2: Supplementary Table 2. The output SNP information during whole exome sequencing.
DOI: 10.6084/m9.figshare.14211503.v1
title: Additional file 2 of Novel ERCC2 variant in trichothiodystrophy infant: the first case report in China

description: Additional file 2: Supplementary Table 2. The output SNP information during whole exome sequencing.
DOI: 10.6084/m9.figshare.14211540
title: Additional file 1 of Repurposing novel therapeutic candidate drugs for coronavirus disease-19 based on protein-protein interaction network analysis

description: Additional file 1.
DOI: 10.6084/m9.figshare.14211540.v1
title: Additional file 1 of Repurposing novel therapeutic candidate drugs for coronavirus disease-19 based on protein-protein interaction network analysis

description: Additional file 1.
DOI: 10.6084/m9.figshare.14211546
title: Additional file 3 of Repurposing novel therapeutic candidate drugs for coronavirus disease-19 based on protein-protein interaction network analysis

description: Additional file 3.
DOI: 10.6084/m9.figshare.14211543
title: Additional file 2 of Repurposing novel therapeutic candidate drugs for coronavirus disease-19 based on protein-protein interaction network analysis

description: Additional file 2.
DOI: 10.6084/m9.figshare.14211552
title: Additional file 5 of Repurposing novel therapeutic candidate drugs for coronavirus disease-19 based on protein-protein interaction network analysis

description: Additional file 5.
DOI: 10.6084/m9.figshare.14211549.v1
title: Additional file 4 of Repurposing novel therapeutic candidate drugs for coronavirus disease-19 based on protein-protein interaction network analysis

description: Additional file 4.
DOI: 10.6084/m9.figshare.14211552.v1
title: Additional file 5 of Repurposing novel therapeutic candidate drugs for coronavirus disease-19 based on protein-protein interaction network analysis

description: Additional file 5.
DOI: 10.6084/m9.figshare.14211549
title: Additional file 4 of Repurposing novel therapeutic candidate drugs for coronavirus disease-19 based on protein-protein interaction network analysis

description: Additional file 4.
DOI: 10.6084/m9.figshare.14211546.v1
title: Additional file 3 of Repurposing novel therapeutic candidate drugs for coronavirus disease-19 based on protein-protein interaction network analysis

description: Additional file 3.
DOI: 10.6084/m9.figshare.14211555.v1
title: Additional file 6 of Repurposing novel therapeutic candidate drugs for coronavirus disease-19 based on protein-protein interaction network analysis

description: Additional file 6.
DOI: 10.6084/m9.figshare.14211558.v1
title: Additional file 7 of Repurposing novel therapeutic candidate drugs for coronavirus disease-19 based on protein-protein interaction network analysis

description: Additional file 7.
DOI: 10.6084/m9.figshare.14211555
title: Additional file 6 of Repurposing novel therapeutic candidate drugs for coronavirus disease-19 based on protein-protein interaction network analysis

description: Additional file 6.
DOI: 10.6084/m9.figshare.14211558
title: Additional file 7 of Repurposing novel therapeutic candidate drugs for coronavirus disease-19 based on protein-protein interaction network analysis

description: Additional file 7.
DOI: 10.6084/m9.figshare.14211543.v1
title: Additional file 2 of Repurposing novel therapeutic candidate drugs for coronavirus disease-19 based on protein-protein interaction network analysis

description: Additional file 2.
DOI: 10.6084/m9.figshare.14211597
title: Additional file 1 of Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.)

description: Additional file 1 List of the 108 DgNAC genes identified in orchardgrass.
DOI: 10.6084/m9.figshare.14211597.v1
title: Additional file 1 of Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.)

description: Additional file 1 List of the 108 DgNAC genes identified in orchardgrass.
DOI: 10.6084/m9.figshare.14211600
title: Additional file 2 of Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.)

description: Additional file 2. Analysis and distribution of conserved motifs in orchardgrass NAC proteins.
DOI: 10.6084/m9.figshare.14211600.v1
title: Additional file 2 of Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.)

description: Additional file 2. Analysis and distribution of conserved motifs in orchardgrass NAC proteins.
DOI: 10.6084/m9.figshare.14211603
title: Additional file 3 of Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.)

description: Additional file 3. One-to-one orthologous relationships between orchardgrass and other plants.
DOI: 10.6084/m9.figshare.14211609
title: Additional file 5 of Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.)

description: Additional file 5 Expression (FPKM) of DgNAC genes in different tissues.
DOI: 10.6084/m9.figshare.14211606
title: Additional file 4 of Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.)

description: Additional file 4. Sequences of the primers used in this study.
DOI: 10.6084/m9.figshare.14211612
title: Additional file 6 of Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.)

description: Additional file 6 Expression (FPKM) of DgNAC genes in different floral bud development stages.
DOI: 10.6084/m9.figshare.14211615
title: Additional file 7 of Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.)

description: Additional file 7 RNA-seq data of the orchardgrass-specific NAC genes that were used in this study.
DOI: 10.6084/m9.figshare.14211609.v1
title: Additional file 5 of Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.)

description: Additional file 5 Expression (FPKM) of DgNAC genes in different tissues.
DOI: 10.6084/m9.figshare.14211612.v1
title: Additional file 6 of Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.)

description: Additional file 6 Expression (FPKM) of DgNAC genes in different floral bud development stages.
DOI: 10.6084/m9.figshare.14211606.v1
title: Additional file 4 of Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.)

description: Additional file 4. Sequences of the primers used in this study.
DOI: 10.6084/m9.figshare.14211615.v1
title: Additional file 7 of Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.)

description: Additional file 7 RNA-seq data of the orchardgrass-specific NAC genes that were used in this study.
DOI: 10.6084/m9.figshare.14211603.v1
title: Additional file 3 of Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.)

description: Additional file 3. One-to-one orthologous relationships between orchardgrass and other plants.
DOI: 10.6084/m9.figshare.14211671.v1
title: Additional file 2 of An epithelial-mesenchymal transition-related 5-gene signature predicting the prognosis of hepatocellular carcinoma patients

description: Additional file 2. Modes of interaction in PPI network.
DOI: 10.6084/m9.figshare.14211671
title: Additional file 2 of An epithelial-mesenchymal transition-related 5-gene signature predicting the prognosis of hepatocellular carcinoma patients

description: Additional file 2. Modes of interaction in PPI network.
DOI: 10.6084/m9.figshare.14211720
title: Additional file 1 of Composition and origins of decorated glass from Umayyad Cordoba (Spain)

description: Additional file 1: Table S1. LA-ICP-MS data of Piscinas Municipales de Poniente glass, oxides and chlorine are given in [wt% ], elements in [ppm]. Table S2. Average LA-ICP-MS data of glass standards compared to published values for Corning reference glasses A, B, C, D, and NIST SRM 612.
DOI: 10.6084/m9.figshare.14211720.v1
title: Additional file 1 of Composition and origins of decorated glass from Umayyad Cordoba (Spain)

description: Additional file 1: Table S1. LA-ICP-MS data of Piscinas Municipales de Poniente glass, oxides and chlorine are given in [wt% ], elements in [ppm]. Table S2. Average LA-ICP-MS data of glass standards compared to published values for Corning reference glasses A, B, C, D, and NIST SRM 612.
DOI: 10.6084/m9.figshare.14211770
title: Additional file 6 of Consistent ultra-long DNA sequencing with automated slow pipetting

description: Additional file 6: Supplementary Table 2. Ten longest mapped reads for four exemplary libraries. Length is displayed in base pairs and was calculated after programmatic fusion of split reads (see methods).