cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12687299
title: Supplementary Material for: Brain Imaging Signs and Health-Related Quality of Life after Acute Ischemic Stroke: Analysis of ENCHANTED Alteplase Dose Arm

description: <b><i>Background and Purpose:</i></b> The influence of specific brain lesions on health-related quality of life (HRQoL) after acute ischemic stroke (AIS) is uncertain. We aimed to identify imaging predictors of poor HRQoL in alteplase-treated participants of the alteplase dose arm of the Enhanced Control of Hypertension and Thrombolysis Stroke Study (ENCHANTED). <b><i>Methods:</i></b> ENCHANTED was an international trial of low- versus standard-dose intravenous alteplase in AIS patients, with functional outcome (modified Rankin scale [mRS]) and HRQoL on the 5-dimension European Quality of Life Scale (EQ-5D) assessed at 90 days post-randomization. Brain images were analyzed centrally by trained assessors. Multivariable logistic regression was undertaken in the study population randomly divided (2:1) into training (development) and validation (performance) groups, with age (per 10-year increase), ethnicity, baseline National Institutes of Health Stroke Scale (NIHSS) score, diabetes mellitus, premorbid function (mRS score 0 or 1), and proxy respondent, forced into all models. Data are presented with odds ratios (ORs) and 95% confidence intervals (CIs). <b><i>Results:</i></b> Eight prediction models were developed and validated in 2,526 AIS patients (median age 67.5 years; 38.4% female; 61.7% Asian) with complete brain imaging and 90-day EQ-5D utility score data. The best performance model included acute ischemic changes in the right (OR 1.69, 95% CI: 1.24–2.29) and deep (OR 1.50, 95% CI: 1.03–2.19) middle cerebral artery (MCA) regions. Several background features of brain frailty – atrophy, white matter change, and old infarcts – were significantly associated with adverse physical but not emotional HRQoL domains. <b><i>Conclusions:</i></b> In thrombolysed AIS patients, right-sided and deep ischemia within the MCA territory predict poor overall HRQoL, whilst features of old cerebral ischemia are associated with reduced physical HRQoL.
DOI: 10.6084/m9.figshare.12687272
title: Supplementary Material for: Analyses of Intermediate-Stage Hepatocellular Carcinoma Patients Receiving Transarterial Chemoembolization prior to Designing Clinical Trials

description: <b><i>Background:</i></b> Intermediate-stage hepatocellular carcinoma (HCC) has a high frequency of recurrence and progression to advanced stage after transarterial chemoembolization (TACE), particularly in patients with high tumor burden. Promising new results from immune checkpoint inhibitors (ICIs) and ICI-based therapies are expected to replace TACE, especially in HCC patients with high tumor burden. <b><i>Aims:</i></b> The present study aimed to evaluate the effectiveness of TACE with a view to design clinical trials comparing TACE and ICIs. <b><i>Methods:</i></b> We retrospectively identified intermediate-stage HCC patients undergoing TACE from our database and subdivided patients into low- and high-burden groups based on three subclassification models using the diameter of the maximum tumor and the number of tumors. Clinical outcomes were compared between low- and high-burden intermediate-stage HCC. <b><i>Results:</i></b> Of 1,161 newly diagnosed HCC patients, 316 were diagnosed with intermediate-stage disease and underwent TACE. The median overall survival from high-burden intermediate-stage disease was not significantly different by clinical course, reaching high tumor burden in all subclassification models. The prognosis of high-burden patients after initial TACE was poor compared with low-burden patients for two models (except for the up-to-seven criteria). In all three models, high-burden patients showed a poor durable response rate (DRR) both ≥3 months and ≥6 months and poor prognosis after TACE. Moreover, patients with confirmed durable response ≥3 months and ≥6 months showed better survival outcomes for high-burden intermediate-stage HCC. <b><i>Conclusions:</i></b> Our results demonstrate the basis for selecting a population that would not benefit from TACE and setting DRR ≥3 months or ≥6 months as alternative endpoints when designing clinical trials comparing TACE and ICIs.
DOI: 10.6084/m9.figshare.12687272.v1
title: Supplementary Material for: Analyses of Intermediate-Stage Hepatocellular Carcinoma Patients Receiving Transarterial Chemoembolization prior to Designing Clinical Trials

description: <b><i>Background:</i></b> Intermediate-stage hepatocellular carcinoma (HCC) has a high frequency of recurrence and progression to advanced stage after transarterial chemoembolization (TACE), particularly in patients with high tumor burden. Promising new results from immune checkpoint inhibitors (ICIs) and ICI-based therapies are expected to replace TACE, especially in HCC patients with high tumor burden. <b><i>Aims:</i></b> The present study aimed to evaluate the effectiveness of TACE with a view to design clinical trials comparing TACE and ICIs. <b><i>Methods:</i></b> We retrospectively identified intermediate-stage HCC patients undergoing TACE from our database and subdivided patients into low- and high-burden groups based on three subclassification models using the diameter of the maximum tumor and the number of tumors. Clinical outcomes were compared between low- and high-burden intermediate-stage HCC. <b><i>Results:</i></b> Of 1,161 newly diagnosed HCC patients, 316 were diagnosed with intermediate-stage disease and underwent TACE. The median overall survival from high-burden intermediate-stage disease was not significantly different by clinical course, reaching high tumor burden in all subclassification models. The prognosis of high-burden patients after initial TACE was poor compared with low-burden patients for two models (except for the up-to-seven criteria). In all three models, high-burden patients showed a poor durable response rate (DRR) both ≥3 months and ≥6 months and poor prognosis after TACE. Moreover, patients with confirmed durable response ≥3 months and ≥6 months showed better survival outcomes for high-burden intermediate-stage HCC. <b><i>Conclusions:</i></b> Our results demonstrate the basis for selecting a population that would not benefit from TACE and setting DRR ≥3 months or ≥6 months as alternative endpoints when designing clinical trials comparing TACE and ICIs.
DOI: 10.6084/m9.figshare.12687197
title: Additional file 4 of Seed characterization and early nitrogen metabolism performance of seedlings from Altiplano and coastal ecotypes of Quinoa

description: Additional file 4: Table S1. Raw metabolomics data used for heatmap and metabolite clustering analysis.
DOI: 10.6084/m9.figshare.12687230.v1
title: Reclamation_shapefile.rar

description: This datasets include the shapefiles of Aquaculture zone, Agricultural/build-up land and Natural water of lakes in middle and lower reaches of Yangtze River Basin in every three-year interval (1973, 1976, 1979, 1982, 1985, 1988, 1991, 1994, 1997, 2000, 2003, 2006, 2009, 2013, 2015, 2018)
DOI: 10.6084/m9.figshare.12687197.v1
title: Additional file 4 of Seed characterization and early nitrogen metabolism performance of seedlings from Altiplano and coastal ecotypes of Quinoa

description: Additional file 4: Table S1. Raw metabolomics data used for heatmap and metabolite clustering analysis.
DOI: 10.6084/m9.figshare.12687185
title: Additional file 1 of Wound closure in epidermolysis bullosa: data from the vehicle arm of the phase 3 ESSENCE Study

description: Additional file 1. ESSENCE individual baseline characteristics of the vehicle group. Contains individual de-identified data of patients who were randomly assigned to the vehicle group in the current study.
DOI: 10.6084/m9.figshare.12687230.v2
title: Reclamation_shapefile.rar

description: Datasets associated with a paper published in Remote Sensing of Environment, titled “Anthropogenic transformation of Yangtze Plain freshwater lakes: patterns, drivers and impacts”.<br> <br> This datasets include the shapefiles of Aquaculture zone, Agricultural/build-up land and Natural water of lakes in middle and lower reaches of Yangtze River Basin in every three-year interval (1973, 1976, 1979, 1982, 1985, 1988, 1991, 1994, 1997, 2000, 2003, 2006, 2009, 2013, 2015, 2018)
DOI: 10.6084/m9.figshare.12687182
title: Additional file 9 of Sub-fertility in crossbred bulls: deciphering testicular level transcriptomic alterations between zebu (Bos indicus) and crossbred (Bos taurus x Bos indicus) bulls

description: Additional file 9. List of differentially expressed transcripts between Zebu and crossbred bull testis (1.5-fold change)
DOI: 10.6084/m9.figshare.12687182.v1
title: Additional file 9 of Sub-fertility in crossbred bulls: deciphering testicular level transcriptomic alterations between zebu (Bos indicus) and crossbred (Bos taurus x Bos indicus) bulls

description: Additional file 9. List of differentially expressed transcripts between Zebu and crossbred bull testis (1.5-fold change)
DOI: 10.6084/m9.figshare.12687230
title: Datasets associated with a paper published in Remote Sensing of Environment, titled “Anthropogenic transformation of Yangtze Plain freshwater lakes: patterns, drivers and impacts" https://www.sciencedirect.com/science/article/abs/pii/S0034425720303680

description: This datasets include the shapefiles of Aquaculture zone, Agricultural/build-up land and Natural water of lakes in middle and lower reaches of Yangtze River Basin in every three-year interval (1973, 1976, 1979, 1982, 1985, 1988, 1991, 1994, 1997, 2000, 2003, 2006, 2009, 2013, 2015, 2018)
DOI: 10.6084/m9.figshare.12687154
title: Additional file 2 of Environmental hazard testing of nanobiomaterials

description: Additional file 2: Table S1. Representative bionanomaterials list types. Table S2. Overview of key terrestrial species and standard guidelines. Table S3. Overview of key microbial activity standard guidelines. Table S4. ISO Standard methods available in soil microbiology. Table S5. Overview of key aquatic species and standard guidelines. Table S6. Overview of available tests for effect assessment for soil invertebrates.
DOI: 10.6084/m9.figshare.12687154.v1
title: Additional file 2 of Environmental hazard testing of nanobiomaterials

description: Additional file 2: Table S1. Representative bionanomaterials list types. Table S2. Overview of key terrestrial species and standard guidelines. Table S3. Overview of key microbial activity standard guidelines. Table S4. ISO Standard methods available in soil microbiology. Table S5. Overview of key aquatic species and standard guidelines. Table S6. Overview of available tests for effect assessment for soil invertebrates.
DOI: 10.6084/m9.figshare.12687143
title: Additional file 5 of The oilseed rape developmental expression resource: a resource for the investigation of gene expression dynamics during the floral transition in oilseed rape

description: Additional file 5: Table S1. Genomic location and homology information for all BnAP1 and BnAGL24 genes in the ORDER database. Except for the “Brassica napus gene name” column, this table represents the data available from the ORDER table view.
DOI: 10.6084/m9.figshare.12687146
title: Additional file 6 of The oilseed rape developmental expression resource: a resource for the investigation of gene expression dynamics during the floral transition in oilseed rape

description: Additional file 6: Table S2. Genomic location and homology information for all BLAST hits to RsFLC1, RsFLC2, and RsFLC3 identified in the ORDER database.
DOI: 10.6084/m9.figshare.12687146.v1
title: Additional file 6 of The oilseed rape developmental expression resource: a resource for the investigation of gene expression dynamics during the floral transition in oilseed rape

description: Additional file 6: Table S2. Genomic location and homology information for all BLAST hits to RsFLC1, RsFLC2, and RsFLC3 identified in the ORDER database.
DOI: 10.6084/m9.figshare.12687143.v1
title: Additional file 5 of The oilseed rape developmental expression resource: a resource for the investigation of gene expression dynamics during the floral transition in oilseed rape

description: Additional file 5: Table S1. Genomic location and homology information for all BnAP1 and BnAGL24 genes in the ORDER database. Except for the “Brassica napus gene name” column, this table represents the data available from the ORDER table view.
DOI: 10.6084/m9.figshare.12687109
title: Additional file 2 of Alternative methylation of intron motifs is associated with cancer-related gene expression in both canine mammary tumor and human breast cancer

description: Additional file 2: Supplementary Tables. Table S1. Information for CMT tissue samples. Table S2. Quality check for MBD-sequencing. Table S3. List of CMT-DMRs (68,741) and their genomic features. Table S4. List of Subtype-DMRs (68,741) and their genomic features. Table S5. Differentially methylated genes anti-correlated with expression. Table S6. Functional annotations for CMT-DMGs in 'Disease Perturbations from GEO down'. Table S7 GO terms in CMT-DMGs. Table S8. List of nearest genes from hypomethylated intergenic regions in each subtype. Table S9. GO terms in Subtype DMGs. Table S10. GO terms in the nearest genes from intergenic CMT-DMRs. Table S11. KEGG pathways in intergenic Subtype-DMRs. Table S12. Motifs enriched in hypermethylated intron bins (169, p-val &lt; 0.01). Table S13. Motifs enriched in hypomethylated intron bins (83, p-val &lt; 0.01). Table S14. Genes containing Pax5 motifs in their hypermethylated intronic regions. Table S15. Genes containing Pax6 motifs in their hypomethylated intronic regions. Table S16. Putative target genes with differentially methylated intron motifs. Table S17. Motif enrichment in each Subtype-DMR. Table S18. Validation target genes with differentially methylated PAX motifs. Table S19. Primers designed for BS-conversion PCR. Table S20. Validation of single CpG methylation by BS-seq in CDH5 and LRIG1 genes
DOI: 10.6084/m9.figshare.12687109.v1
title: Additional file 2 of Alternative methylation of intron motifs is associated with cancer-related gene expression in both canine mammary tumor and human breast cancer

description: Additional file 2: Supplementary Tables. Table S1. Information for CMT tissue samples. Table S2. Quality check for MBD-sequencing. Table S3. List of CMT-DMRs (68,741) and their genomic features. Table S4. List of Subtype-DMRs (68,741) and their genomic features. Table S5. Differentially methylated genes anti-correlated with expression. Table S6. Functional annotations for CMT-DMGs in 'Disease Perturbations from GEO down'. Table S7 GO terms in CMT-DMGs. Table S8. List of nearest genes from hypomethylated intergenic regions in each subtype. Table S9. GO terms in Subtype DMGs. Table S10. GO terms in the nearest genes from intergenic CMT-DMRs. Table S11. KEGG pathways in intergenic Subtype-DMRs. Table S12. Motifs enriched in hypermethylated intron bins (169, p-val &lt; 0.01). Table S13. Motifs enriched in hypomethylated intron bins (83, p-val &lt; 0.01). Table S14. Genes containing Pax5 motifs in their hypermethylated intronic regions. Table S15. Genes containing Pax6 motifs in their hypomethylated intronic regions. Table S16. Putative target genes with differentially methylated intron motifs. Table S17. Motif enrichment in each Subtype-DMR. Table S18. Validation target genes with differentially methylated PAX motifs. Table S19. Primers designed for BS-conversion PCR. Table S20. Validation of single CpG methylation by BS-seq in CDH5 and LRIG1 genes
DOI: 10.6084/m9.figshare.12687094
title: Additional file 8 of Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site

description: Additional file 8. Individual data for Figure 5c.
DOI: 10.6084/m9.figshare.12687097
title: Additional file 9 of Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site

description: Additional file 9. Individual data for Figure 6a.
DOI: 10.6084/m9.figshare.12687094.v1
title: Additional file 8 of Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site

description: Additional file 8. Individual data for Figure 5c.
DOI: 10.6084/m9.figshare.12687097.v1
title: Additional file 9 of Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site

description: Additional file 9. Individual data for Figure 6a.
DOI: 10.6084/m9.figshare.12687091
title: Additional file 7 of Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site

description: Additional file 7. Individual data for Figure 5a.
DOI: 10.6084/m9.figshare.12687091.v1
title: Additional file 7 of Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site

description: Additional file 7. Individual data for Figure 5a.
DOI: 10.6084/m9.figshare.12687070
title: Additional file 12 of Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site

description: Additional file 12. Individual data for Figure S3 B.
DOI: 10.6084/m9.figshare.12687064
title: Additional file 10 of Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site

description: Additional file 10. Individual data for figure 6e.
DOI: 10.6084/m9.figshare.12687067
title: Additional file 11 of Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site

description: Additional file 11. Individual data for Figure S3 A.
DOI: 10.6084/m9.figshare.12687070.v1
title: Additional file 12 of Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site

description: Additional file 12. Individual data for Figure S3 B.
DOI: 10.6084/m9.figshare.12687064.v1
title: Additional file 10 of Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site

description: Additional file 10. Individual data for figure 6e.
DOI: 10.6084/m9.figshare.12687067.v1
title: Additional file 11 of Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site

description: Additional file 11. Individual data for Figure S3 A.
DOI: 10.6084/m9.figshare.12687003
title: Additional file 9 of Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data

description: Additional file 9: Paired t-test for mapped reads in default compared to sex chromosome complement reference genome. Mean difference in expression for average total reads mapped for each tissue and each sex when aligned to a sex chromosome informed versus a default reference genome. Paired t-test to test for significant difference in total reads mapped for the whole transcriptome (WT), chromosome 8, and chromosome X. Nonparametric Wilcox single rank sum test was used to test for significant difference in total reads mapped on the Y chromosome for male samples in each tissue separately.
DOI: 10.6084/m9.figshare.12686991
title: Additional file 5 of Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data

description: Additional file 5: List of samples that were removed from downstream analysis. Samples that did not cluster with the reported sex or clustered in unexpected ways were removed from the differential expression analysis. One male XY whole blood, 4 female XX and 4 male XY brain cortex, and one female XX breast sample were removed.
DOI: 10.6084/m9.figshare.12687003.v1
title: Additional file 9 of Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data

description: Additional file 9: Paired t-test for mapped reads in default compared to sex chromosome complement reference genome. Mean difference in expression for average total reads mapped for each tissue and each sex when aligned to a sex chromosome informed versus a default reference genome. Paired t-test to test for significant difference in total reads mapped for the whole transcriptome (WT), chromosome 8, and chromosome X. Nonparametric Wilcox single rank sum test was used to test for significant difference in total reads mapped on the Y chromosome for male samples in each tissue separately.
DOI: 10.6084/m9.figshare.12686991.v1
title: Additional file 5 of Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data

description: Additional file 5: List of samples that were removed from downstream analysis. Samples that did not cluster with the reported sex or clustered in unexpected ways were removed from the differential expression analysis. One male XY whole blood, 4 female XX and 4 male XY brain cortex, and one female XX breast sample were removed.
DOI: 10.6084/m9.figshare.12686976
title: Additional file 1 of Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data

description: Additional file 1: Sample IDs. RNA-Seq whole blood, brain cortex, breast, liver, and thyroid tissue samples from 20 genetic female (46, XX) and 20 genetic male (46, XY) individuals were downloaded from the Genotype-Tissue Expression (GTEx) project [19] for a total of 200 RNA-Seq tissue samples.
DOI: 10.6084/m9.figshare.12686967
title: Additional file 17 of Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data

description: Additional file 17: GO analysis of differentially expressed genes in female and male samples with STAR aligner. Gene enrichment analysis of genes that are more highly expressed in one sex versus the other sex for each tissue, whole blood, brain cortex, breast, liver and thyroid, when samples were aligned to a default or sex chromosome complement informed reference genome using STAR.
DOI: 10.6084/m9.figshare.12686964
title: Additional file 16 of Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data

description: Additional file 16: GO analysis of differentially expressed genes in female and male samples with HISAT aligner. Gene enrichment analysis of genes that are more highly expressed in one sex versus the other sex for each tissue, whole blood, brain cortex, breast, liver and thyroid, when samples were aligned to a default or sex chromosome complement informed reference genome using HISAT.
DOI: 10.6084/m9.figshare.12686967.v1
title: Additional file 17 of Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data

description: Additional file 17: GO analysis of differentially expressed genes in female and male samples with STAR aligner. Gene enrichment analysis of genes that are more highly expressed in one sex versus the other sex for each tissue, whole blood, brain cortex, breast, liver and thyroid, when samples were aligned to a default or sex chromosome complement informed reference genome using STAR.
DOI: 10.6084/m9.figshare.12686976.v1
title: Additional file 1 of Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data

description: Additional file 1: Sample IDs. RNA-Seq whole blood, brain cortex, breast, liver, and thyroid tissue samples from 20 genetic female (46, XX) and 20 genetic male (46, XY) individuals were downloaded from the Genotype-Tissue Expression (GTEx) project [19] for a total of 200 RNA-Seq tissue samples.