cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21522121.v1
title: Additional file 6 of Evolution and function of developmentally dynamic pseudogenes in mammals

description: Additional file 6: Table S5. GO enrichment for coding genes co-expressed with non-dynamic pseudogenes.
DOI: 10.6084/m9.figshare.21522124
title: Additional file 7 of Evolution and function of developmentally dynamic pseudogenes in mammals

description: Additional file 7: Table S6. The detailed information of pseudogene ORF.
DOI: 10.6084/m9.figshare.21522124.v1
title: Additional file 7 of Evolution and function of developmentally dynamic pseudogenes in mammals

description: Additional file 7: Table S6. The detailed information of pseudogene ORF.
DOI: 10.6084/m9.figshare.21522130
title: Additional file 8 of Evolution and function of developmentally dynamic pseudogenes in mammals

description: Additional file 8: Table S7. Number of expressed pseudogenes, Iso-seq detected pseudogenes, and DDPs.
DOI: 10.6084/m9.figshare.21522130.v1
title: Additional file 8 of Evolution and function of developmentally dynamic pseudogenes in mammals

description: Additional file 8: Table S7. Number of expressed pseudogenes, Iso-seq detected pseudogenes, and DDPs.
DOI: 10.6084/m9.figshare.21522133
title: Additional file 9 of Evolution and function of developmentally dynamic pseudogenes in mammals

description: Additional file 9: Table S8. DDPs among different tissues in human.
DOI: 10.6084/m9.figshare.21522133.v1
title: Additional file 9 of Evolution and function of developmentally dynamic pseudogenes in mammals

description: Additional file 9: Table S8. DDPs among different tissues in human.
DOI: 10.6084/m9.figshare.21522142
title: Additional file 1 of Pan-cancer landscape of aberrant DNA Methylation across childhood Cancers: Molecular Characteristics and Clinical relevance

description: Additional file 1: Supplementary Table 1-7: Supplementary Table 1. Characteristics of methylation and gene expression data sets used in this study. Supplementary Table 2. Numbers of differentially methylated CpG sites identified in pediatric cancers. Supplementary Table 3. The list of SDMCs. Supplementary Table 4. Differentially methylated SDMCs in adult cancers. Supplementary Table 5. Co-location and enrichment of SDMCs in Genomic features. Supplementary Table 6. Associations between SDMCs and gene transcription. Supplementary Table 7. Pathway enrichment analysis of SDMCs.
DOI: 10.6084/m9.figshare.21522142.v1
title: Additional file 1 of Pan-cancer landscape of aberrant DNA Methylation across childhood Cancers: Molecular Characteristics and Clinical relevance

description: Additional file 1: Supplementary Table 1-7: Supplementary Table 1. Characteristics of methylation and gene expression data sets used in this study. Supplementary Table 2. Numbers of differentially methylated CpG sites identified in pediatric cancers. Supplementary Table 3. The list of SDMCs. Supplementary Table 4. Differentially methylated SDMCs in adult cancers. Supplementary Table 5. Co-location and enrichment of SDMCs in Genomic features. Supplementary Table 6. Associations between SDMCs and gene transcription. Supplementary Table 7. Pathway enrichment analysis of SDMCs.
DOI: 10.6084/m9.figshare.19425014
title: Additional file 2 of Relationship between modifiable lifestyle factors and chronic kidney disease: a bibliometric analysis of top-cited publications from 2011 to 2020

description: Additional file 2: Supplementary Table 2. Keywords merging details. Supplementary Table 3. Bibliometric information of the top 100-cited articles on the impact of modifiable lifestyles on CKD.
DOI: 10.6084/m9.figshare.19425014.v2
title: Additional file 2 of Relationship between modifiable lifestyle factors and chronic kidney disease: a bibliometric analysis of top-cited publications from 2011 to 2020

description: Additional file 2: Supplementary Table 2. Keywords merging details. Supplementary Table 3. Bibliometric information of the top 100-cited articles on the impact of modifiable lifestyles on CKD.
DOI: 10.6084/m9.figshare.19425014.v1
title: Additional file 2 of Relationship between modifiable lifestyle factors and chronic kidney disease: a bibliometric analysis of top-cited publications from 2011 to 2020

description: Additional file 2: Supplementary Table 2. Keywords merging details. Supplementary Table 3. Bibliometric information of the top 100-cited articles on the impact of modifiable lifestyles on CKD.
DOI: 10.6084/m9.figshare.19425036
title: Additional file 2 of Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height

description: Additional file 2: Table S1. DEGs in D vs. W, H vs. W and H vs. D.
DOI: 10.24403/jp.1341900
title: Kritische Revision der "Thlaspi”-Arten Europas, Afrikas und Vorderasiens. Spezieller Teil : V) Noccidium / Friedrich Karl Meyer
DOI: 10.6084/m9.figshare.19425036.v1
title: Additional file 2 of Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height

description: Additional file 2: Table S1. DEGs in D vs. W, H vs. W and H vs. D.
DOI: 10.6084/m9.figshare.19425039
title: Additional file 3 of Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height

description: Additional file 3: Table S2. GO enrichment analysis of differentially expressed genes of D vs. W, H vs. W and H vs. D of Sophora davidii.
DOI: 10.6084/m9.figshare.19425039.v1
title: Additional file 3 of Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height

description: Additional file 3: Table S2. GO enrichment analysis of differentially expressed genes of D vs. W, H vs. W and H vs. D of Sophora davidii.
DOI: 10.6084/m9.figshare.19425042
title: Additional file 4 of Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height

description: Additional file 4: Table S3. Relative changes in the expression of lignin biosynthesis-related genes.
DOI: 10.6084/m9.figshare.19425042.v1
title: Additional file 4 of Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height

description: Additional file 4: Table S3. Relative changes in the expression of lignin biosynthesis-related genes.
DOI: 10.6084/m9.figshare.19425045
title: Additional file 5 of Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height

description: Additional file 5: Table S4. DEGs involved in phythormone biosynthesis and signal transduction pathways.
DOI: 10.6084/m9.figshare.19425045.v1
title: Additional file 5 of Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height

description: Additional file 5: Table S4. DEGs involved in phythormone biosynthesis and signal transduction pathways.
DOI: 10.6084/m9.figshare.19425048
title: Additional file 6 of Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height

description: Additional file 6: Table S5. DEGs involved in flavonoid biosynthesis and phenylpropanoid biosynthesis.
DOI: 10.6084/m9.figshare.19425048.v1
title: Additional file 6 of Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height

description: Additional file 6: Table S5. DEGs involved in flavonoid biosynthesis and phenylpropanoid biosynthesis.
DOI: 10.6084/m9.figshare.19425051
title: Additional file 7 of Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height

description: Additional file 7: Table S6. Fifty-seven significantly different metabolites in both the dwarf and tall mutants.
DOI: 10.6084/m9.figshare.19425051.v1
title: Additional file 7 of Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height

description: Additional file 7: Table S6. Fifty-seven significantly different metabolites in both the dwarf and tall mutants.
DOI: 10.6084/m9.figshare.19425054
title: Additional file 8 of Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height

description: Additional file 8: Table S7. Gene-specific primers used in gene expression analysis by qPCR.
DOI: 10.6084/m9.figshare.19425054.v1
title: Additional file 8 of Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height

description: Additional file 8: Table S7. Gene-specific primers used in gene expression analysis by qPCR.
DOI: 10.6084/m9.figshare.21522209
title: Additional file 3 of Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family

description: Additional file 3: Table S2. Specific data of enrichment analysis.
DOI: 10.6084/m9.figshare.21522209.v1
title: Additional file 3 of Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family

description: Additional file 3: Table S2. Specific data of enrichment analysis.
DOI: 10.6084/m9.figshare.21522212
title: Additional file 4 of Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family

description: Additional file 4: Table S3. Statistical analysis of promoter distribution.
DOI: 10.6084/m9.figshare.21522212.v1
title: Additional file 4 of Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family

description: Additional file 4: Table S3. Statistical analysis of promoter distribution.
DOI: 10.6084/m9.figshare.21522214
title: Additional file 6 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

description: Additional file 6: Table S1. Characteristics of CAR T-cell products.
DOI: 10.6084/m9.figshare.21522214.v1
title: Additional file 6 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

description: Additional file 6: Table S1. Characteristics of CAR T-cell products.
DOI: 10.6084/m9.figshare.21522217
title: Additional file 7 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

description: Additional file 7: Table S2. Differentially expressed genes in non-transduced and transduced CAR T-cell products.
DOI: 10.6084/m9.figshare.21522217.v1
title: Additional file 7 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

description: Additional file 7: Table S2. Differentially expressed genes in non-transduced and transduced CAR T-cell products.
DOI: 10.6084/m9.figshare.21522220
title: Additional file 8 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

description: Additional file 8: Table S3. Differential alternative splicing transcripts with viral integration.
DOI: 10.6084/m9.figshare.21522220.v1
title: Additional file 8 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

description: Additional file 8: Table S3. Differential alternative splicing transcripts with viral integration.
DOI: 10.6084/m9.figshare.21522223
title: Additional file 9 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

description: Additional file 9: Table S4. Differential integration sites at gene locus based on clinical outcomes.
DOI: 10.6084/m9.figshare.21522223.v1
title: Additional file 9 of Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

description: Additional file 9: Table S4. Differential integration sites at gene locus based on clinical outcomes.
DOI: 10.24403/jp.1341902
title: Kritische Revision der "Thlaspi”-Arten Europas, Afrikas und Vorderasiens. Spezieller Teil : VI) Kotschyella / Friedrich Karl Meyer
DOI: 10.6084/m9.figshare.19425143
title: Additional file 2 of Diversity and antimicrobial activities of culturable actinomycetes from Odontotermes formosanus (Blattaria: Termitidae)

description: Additional file 2: Table S2. List of all actinobacterial strains isolated from Odontotermes formosanus and combs.
DOI: 10.6084/m9.figshare.19425143.v1
title: Additional file 2 of Diversity and antimicrobial activities of culturable actinomycetes from Odontotermes formosanus (Blattaria: Termitidae)

description: Additional file 2: Table S2. List of all actinobacterial strains isolated from Odontotermes formosanus and combs.
DOI: 10.6084/m9.figshare.13133715
title: DNA methylation biomarker selected by an ensemble machine learning approach predicts mortality risk in an HIV-positive veteran population

description: <b>Background</b>: With the improved life expectancy of people living with HIV (PLWH), identifying vulnerable subpopulations at high mortality risk is important. Evidences showed that DNA methylation (DNAm) is associated with mortality in non-HIV populations. Here, we established a panel of DNAm biomarkers that can predict mortality risk among PLWH. <b>Methods</b>: 1,081 HIV-positive participants from the Veterans Ageing Cohort Study (VACS) were divided into training (N = 460), validation (N = 114), and testing (N = 507) sets. VACS index was used as a measure of mortality risk among PLWH. Model training and fine-tuning were conducted using the ensemble method in the training and validation sets and prediction performance was assessed in the testing set. The survival analysis comparing the predicted high and low mortality risk groups and the Gene Ontology enrichment analysis of the predictive CpG sites were performed. <b>Results</b>: We selected a panel of 393 CpGs for the ensemble prediction model that showed excellent performance in predicting high mortality risk with an auROC of 0.809 (95%CI: 0.767,0.851) and a balanced accuracy of 0.653 (95%CI: 0.611, 0.693) in the testing set. The high mortality risk group was significantly associated with 10-year mortality (hazard ratio = 1.79, p = 4E-05) compared with low risk group. These 393 CpGs were located in 280 genes enriched in immune and inflammation response pathways. <b>Conclusions</b>: We identified a panel of DNAm features associated with mortality risk in PLWH. These DNAm features may serve as predictive biomarkers for mortality risk among PLWH. <b>Abbreviations</b>: AUC: Area Under Curve; CI: Confidence interval; DMR: differentially methylated region; DNA: Deoxyribonucleic acid; DNAm: DNA methylation; DAVID: Database for Annotation, Visualization, and Integrated Discovery; EWA: epigenome-wide association; FDR: False discovery rate; FWER: Family-wise error rate; GLMNET: elastic-net-regularized generalized linear models; GO: Gene ontology; HIV: Human immunodeficiency virus; HM450K: Human Methylation 450 K BeadChip; k-NN: k-nearest neighbours; NK: Natural killer; PC: Principal component; PLWH: people living with HIV; QC: Quality control; SVM: Support Vector Machines; VACS: Veterans Ageing Cohort Study; XGBoost: Extreme Gradient Boosting Tree
DOI: 10.6084/m9.figshare.13133715.v1
title: DNA methylation biomarker selected by an ensemble machine learning approach predicts mortality risk in an HIV-positive veteran population

description: <b>Background</b>: With the improved life expectancy of people living with HIV (PLWH), identifying vulnerable subpopulations at high mortality risk is important. Evidences showed that DNA methylation (DNAm) is associated with mortality in non-HIV populations. Here, we established a panel of DNAm biomarkers that can predict mortality risk among PLWH. <b>Methods</b>: 1,081 HIV-positive participants from the Veterans Ageing Cohort Study (VACS) were divided into training (N = 460), validation (N = 114), and testing (N = 507) sets. VACS index was used as a measure of mortality risk among PLWH. Model training and fine-tuning were conducted using the ensemble method in the training and validation sets and prediction performance was assessed in the testing set. The survival analysis comparing the predicted high and low mortality risk groups and the Gene Ontology enrichment analysis of the predictive CpG sites were performed. <b>Results</b>: We selected a panel of 393 CpGs for the ensemble prediction model that showed excellent performance in predicting high mortality risk with an auROC of 0.809 (95%CI: 0.767,0.851) and a balanced accuracy of 0.653 (95%CI: 0.611, 0.693) in the testing set. The high mortality risk group was significantly associated with 10-year mortality (hazard ratio = 1.79, p = 4E-05) compared with low risk group. These 393 CpGs were located in 280 genes enriched in immune and inflammation response pathways. <b>Conclusions</b>: We identified a panel of DNAm features associated with mortality risk in PLWH. These DNAm features may serve as predictive biomarkers for mortality risk among PLWH. <b>Abbreviations</b>: AUC: Area Under Curve; CI: Confidence interval; DMR: differentially methylated region; DNA: Deoxyribonucleic acid; DNAm: DNA methylation; DAVID: Database for Annotation, Visualization, and Integrated Discovery; EWA: epigenome-wide association; FDR: False discovery rate; FWER: Family-wise error rate; GLMNET: elastic-net-regularized generalized linear models; GO: Gene ontology; HIV: Human immunodeficiency virus; HM450K: Human Methylation 450 K BeadChip; k-NN: k-nearest neighbours; NK: Natural killer; PC: Principal component; PLWH: people living with HIV; QC: Quality control; SVM: Support Vector Machines; VACS: Veterans Ageing Cohort Study; XGBoost: Extreme Gradient Boosting Tree
DOI: 10.6084/m9.figshare.24143817
title: Additional file 3 of Physiological, metabolomic, and transcriptomic reveal metabolic pathway alterations in Gymnocypris przewalskii due to cold exposure

description: Additional file 3.
DOI: 10.6084/m9.figshare.24143817.v1
title: Additional file 3 of Physiological, metabolomic, and transcriptomic reveal metabolic pathway alterations in Gymnocypris przewalskii due to cold exposure

description: Additional file 3.
DOI: 10.6084/m9.figshare.24143820
title: Additional file 4 of Physiological, metabolomic, and transcriptomic reveal metabolic pathway alterations in Gymnocypris przewalskii due to cold exposure

description: Additional file 4.
DOI: 10.6084/m9.figshare.24143820.v1
title: Additional file 4 of Physiological, metabolomic, and transcriptomic reveal metabolic pathway alterations in Gymnocypris przewalskii due to cold exposure

description: Additional file 4.
DOI: 10.6084/m9.figshare.12085161
title: Additional file 2 of MSX2 suppression through inhibition of TGFβ signaling enhances hematopoietic differentiation of human embryonic stem cells

description: Additional file 2 : Supplementary Table S1- S5. Supplementary Table S1: The sequences for CRISPR sgRNAs and genotyping primers. Supplementary Table S2: The source of fluorochrome-conjugated antibodies used in flow cytometry. Supplementary Table S3: The primers used for real-time PCR. Supplementary Table S4: The primers used for CHIP-qPCR. Supplementary Table S5: RNA-seq of CD31+ endothelial cells derived from WT and MSX2−/− hESCs.
DOI: 10.6084/m9.figshare.12085161.v1
title: Additional file 2 of MSX2 suppression through inhibition of TGFβ signaling enhances hematopoietic differentiation of human embryonic stem cells

description: Additional file 2 : Supplementary Table S1- S5. Supplementary Table S1: The sequences for CRISPR sgRNAs and genotyping primers. Supplementary Table S2: The source of fluorochrome-conjugated antibodies used in flow cytometry. Supplementary Table S3: The primers used for real-time PCR. Supplementary Table S4: The primers used for CHIP-qPCR. Supplementary Table S5: RNA-seq of CD31+ endothelial cells derived from WT and MSX2−/− hESCs.
DOI: 10.24403/jp.1341904
title: Heterothalamus wagenitzii (Compositae, Astereae), a new species from Brazil / Frank H. Hellwig
DOI: 10.5281/zenodo.10623223
title: Paradoxical activation of oncogenic signaling as a cancer treatment strategy - scRNA-seq dataset

description: Cancer homeostasis depends on a balance between activated oncogenic pathways driving tumorigenesis and engagement of stress-response programs that counteract the inherent toxicity of such aberrant signaling. While inhibition of oncogenic signaling pathways has been explored extensively, there is increasing evidence that overactivation of the same pathways can also disrupt cancer homeostasis and cause lethality. We show here that inhibition of Protein Phosphatase 2A (PP2A) hyperactivates multiple oncogenic pathways and engages stress responses in colon cancer cells. Genetic and compound screens identify combined inhibition of PP2A and WEE1 as synergistic in multiple cancer models by collapsing DNA replication and triggering premature mitosis followed by cell death. This combination also suppressed the growth of patient-derived tumors in vivo. Remarkably, acquired resistance to this drug combination suppressed the ability of colon cancer cells to form tumors in vivo. Our data suggest that paradoxical activation of oncogenic signaling can result in tumor suppressive resistance.
DOI: 10.5281/zenodo.10623222
title: Paradoxical activation of oncogenic signaling as a cancer treatment strategy - scRNA-seq dataset

description: Cancer homeostasis depends on a balance between activated oncogenic pathways driving tumorigenesis and engagement of stress-response programs that counteract the inherent toxicity of such aberrant signaling. While inhibition of oncogenic signaling pathways has been explored extensively, there is increasing evidence that overactivation of the same pathways can also disrupt cancer homeostasis and cause lethality. We show here that inhibition of Protein Phosphatase 2A (PP2A) hyperactivates multiple oncogenic pathways and engages stress responses in colon cancer cells. Genetic and compound screens identify combined inhibition of PP2A and WEE1 as synergistic in multiple cancer models by collapsing DNA replication and triggering premature mitosis followed by cell death. This combination also suppressed the growth of patient-derived tumors in vivo. Remarkably, acquired resistance to this drug combination suppressed the ability of colon cancer cells to form tumors in vivo. Our data suggest that paradoxical activation of oncogenic signaling can result in tumor suppressive resistance.
DOI: 10.6084/m9.figshare.22618057
title: Additional file 3 of Comprehensive analysis of the laccase gene family in tea plant highlights its roles in development and stress responses

description: Additional file 3: Table S3. Proteins interacting with LAC proteins in Arabidopsis and C. sinensis.
DOI: 10.6084/m9.figshare.22618057.v1
title: Additional file 3 of Comprehensive analysis of the laccase gene family in tea plant highlights its roles in development and stress responses

description: Additional file 3: Table S3. Proteins interacting with LAC proteins in Arabidopsis and C. sinensis.
DOI: 10.24403/jp.1341906
title: Two new Pinguicula species (Lentibulariaceae) from East Cuba (Cuba oriental) / S. Jost Casper
DOI: 10.6084/m9.figshare.5793876
title: Real-time freehand 3D ultrasound imaging

description: Real-time freehand 3D ultrasound (US) has attracted much attention in clinical practices because it provides interactive feedback to help the clinicians acquire not only high-quality images but also timely information of the scanning area, which is necessary in intraoperative examinations. In this study, we developed a real-time freehand 3D US imaging system which can obtain volume reconstruction and visualisation during data acquisition at real-time level. Based on two popular algorithms, i.e. squared distance weighted interpolation (SDW) and Bezier interpolation, we designed corresponding parallel computing methods that were implemented on the graphics processing unit (GPU) to incrementally reconstruct and display the tissues being scanned using Visualisation toolkits (VTK). With a typical B-scan image size of 302 × 268 at an acquisition rate of 25 Hz and a preset volume size of 90 × 81 × 192, the system achieved an incremental reconstruction-visualisation rate of up to 32 frames/s and 119 frames/s for the SDW and Bezier algorithms, respectively, achieving the real-time 3D US.