cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10490711
title: dataset_HTB550

description: HTB550(*).csv files recorded a reflected or transmitted wave at each timing during experiment HTB550. The timing when the wave was recorded is mentioned supplement table ST2. HTB0550.csv file recorded shear force, normal force, shear displacement, and normal displacement during experiment HTB550.
DOI: 10.6084/m9.figshare.10490228
title: RNA-seq and ATAC-seq Matrix

description: The emergence of eusociality is one of the major events in evolution. Although several previous studies have investigated the mechanism underlying caste differentiation and social behavior of eusocial insects including ants and honeybees, the molecular circuits governing the sociality of these insects remain obscure. In this study, we profiled the brain transcriptome and chromatin accessibility of all categories of adult castes: queens, males, gynes and workers in Monomorium pharaonis which is a typical caste-dependent eusocial insect. We created a comprehensive dataset including 16 RNA-seq and 16 ATAC-seq profiles from 4 biological replicates. We also demonstrated strong reproducibility of the datasets and identified specific genes and open chromatin regions in the genome that may be associated with caste differentiation. Overall, our data will be a valuable resource for further study of the mechanisms underlying eusocial insect behavior, particularly the role of brain in the control of eusociality.
DOI: 10.6084/m9.figshare.10490711.v1
title: dataset_HTB550

description: HTB550(*).csv files recorded a reflected or transmitted wave at each timing during experiment HTB550. The timing when the wave was recorded is mentioned supplement table ST2. HTB0550.csv file recorded shear force, normal force, shear displacement, and normal displacement during experiment HTB550.
DOI: 10.6084/m9.figshare.10492379
title: dataset_HTB613

description: HTB613(*).csv files recorded a reflected or transmitted wave at each timing during experiment HTB613. The timing when the wave was recorded is mentioned supplement table ST3. HTB0613.csv file recorded shear force, normal force, shear displacement, and normal displacement during experiment HTB613.
DOI: 10.6084/m9.figshare.10482707
title: High dielectric ternary oxides from crystal structure prediction and high-throughput screening

description: The development of new high dielectric materials is essential for advancement in modern electronics. Oxides are generally regarded as the most promising class of high dielectric materials for industrial applications as they possess both high dielectric constants and large band gaps. Most previous researches on high dielectrics were limited to already known materials. In this study, we conducted an extensive search for high dielectrics over a set of ternary oxides by combining crystal structure prediction and density functional perturbation theory calculations. From this search, we adopted multiple stage screening to identify 441 new low-energy high dielectric materials. Among these materials, 33 were identiﬁed as potential high dielectrics favorable for modern device applications. Our research has opened an avenue to explore novel high dielectric materials by combining crystal structure prediction and high throughput screening.<br>
DOI: 10.6084/m9.figshare.10484648
title: dataset_HTB549

description: HTB549(*).csv files recorded a reflected or transmitted wave at each timing during experiment HTB549. The timing when the wave was recorded is mentioned supplement table ST1. HTB0549.csv file recorded shear force, normal force, shear displacement, and normal displacement during experiment HTB549.
DOI: 10.6084/m9.figshare.10482707.v1
title: High dielectric ternary oxides from crystal structure prediction and high-throughput screening

description: The development of new high dielectric materials is essential for advancement in modern electronics. Oxides are generally regarded as the most promising class of high dielectric materials for industrial applications as they possess both high dielectric constants and large band gaps. Most previous researches on high dielectrics were limited to already known materials. In this study, we conducted an extensive search for high dielectrics over a set of ternary oxides by combining crystal structure prediction and density functional perturbation theory calculations. From this search, we adopted multiple stage screening to identify 441 new low-energy high dielectric materials. Among these materials, 33 were identiﬁed as potential high dielectrics favorable for modern device applications. Our research has opened an avenue to explore novel high dielectric materials by combining crystal structure prediction and high throughput screening.<br>
DOI: 10.6084/m9.figshare.10465745
title: SDF-1 preconditioned HPC scaffolds mobilize cartilage-derived progenitors and stimulate meniscal fibrocartilage repair in human explant tissue culture

description: <b>Purpose</b>: The purpose of this study was to characterize the influence of SDF-1 on cell migration/adhesion and temporal gene expression of human cartilage mesenchymal progenitor cells (C-PCs); and to utilize SDF-1 conditioned mesenchymal progenitors to stimulate reintegration of human meniscus fibrocartilage breaks. <b>Materials and Methods</b>: Characterization of SDF-1-induced cell migration was achieved using hydroxypropyl cellulose (HPC) scaffolds pretreated with SDF-1. Fluorescence microscopy and cell counting were used to visualize and quantify the extent of cell migration into scaffolds, respectively. Relative mRNA expression analysis was used to characterize the temporal effects of SDF-1 on C-PCs. Tissue reintegration experiments were conducted using cylindrical human meniscal tissue punches, which were then placed back together with an HPC scaffold embedded with C-PCs. Tensile testing was used to evaluate the extent of tissue reintegration stimulated by human mesenchymal progenitors. <b>Results</b>: C-PCs migrate into scaffolds in response to SDF-1 with the same efficiency as mesenchymal progenitors from human marrow (BM-MSCs). SDF-1 treatment of C-PCs did not significantly alter the expression of early and late stage chondrogenic differentiation genes. Scaffolds containing SDF-1 pre-conditioned C-PCs successfully adhered to fibrocartilage breaks and migrated from the scaffold into the tissue. Tensile testing demonstrated that SDF-1 preconditioned C-PCs stimulate reintegration of fibrocartilage tears. <b>Conclusion</b>: C-PCs migrate in response to SDF-1. Exposure to SDF-1 does not significantly alter the unique mRNA profile of C-PCs that make them desirable for cartilaginous tissue repair applications. SDF-1 pretreated mesenchymal progenitors successfully disperse into injured tissues to help facilitate tissue reintegration.
DOI: 10.6084/m9.figshare.10462310
title: Effects of ascorbic acid on dental pulp stem cells from human deciduous (SHED) and permanent teeth (DPSC)

description: Cytotoxicity: Concentration screened were 10, 30, 50, 80, 100, 150, 250, 500 ug/mL ascorbic acid (AA) on SHED and DPSC. Based on IC50 values, SHED can withstand higher AA concentration compared to DPSC. Both cells survived in 10-150 ug/mL but died in 250 and 500 ug/mL AA. <br>Osteoblast differentiation:We performed viability (MTT assay), ALP specific enzyme activity, von Kossa stain and RT-PCR for bone molecular markers. Ascorbic acid could differentiate SHED and DPSC to osteoblast. Its effects were similar to the positive control of the study (AA+BGP)
DOI: 10.6084/m9.figshare.10462310.v1
title: Effects of ascorbic acid on dental pulp stem cells from human deciduous (SHED) and permanent teeth (DPSC)

description: Cytotoxicity: Concentration screened were 10, 30, 50, 80, 100, 150, 250, 500 ug/mL ascorbic acid (AA) on SHED and DPSC. Based on IC50 values, SHED can withstand higher AA concentration compared to DPSC. Both cells survived in 10-150 ug/mL but died in 250 and 500 ug/mL AA. <br>Osteoblast differentiation:We performed viability (MTT assay), ALP specific enzyme activity, von Kossa stain and RT-PCR for bone molecular markers. Ascorbic acid could differentiate SHED and DPSC to osteoblast. Its effects were similar to the positive control of the study (AA+BGP)
DOI: 10.6084/m9.figshare.10461464
title: Processive DNA synthesis is associated with localized decompaction of constitutive heterochromatin at the sites of DNA replication and repair

description: Constitutive heterochromatin is considered as a functionally inert genome compartment, important for its architecture and stability. How such stable structure is maintained is not well understood. Here, we apply four different visualization schemes to label it and investigate its dynamics during DNA replication and repair. We show that replisomes assemble over the heterochromatin in a temporally ordered manner. Furthermore, heterochromatin undergoes transient decompaction locally at the active sites of DNA synthesis. Using selective laser microirradiation conditions that lead to damage repaired via processive DNA synthesis, we measured similarly local decompaction of heterochromatin. In both cases, we could not observe large-scale movement of heterochromatin to the domain surface. Instead, the processive DNA synthesis machinery assembled at the replication/repair sites. Altogether, our data are compatible with a progression of DNA replication/repair along the chromatin in a dynamic mode with localized and transient decompaction that does not globally remodels the whole heterochromatin compartment.
DOI: 10.6084/m9.figshare.10461464.v1
title: Processive DNA synthesis is associated with localized decompaction of constitutive heterochromatin at the sites of DNA replication and repair

description: Constitutive heterochromatin is considered as a functionally inert genome compartment, important for its architecture and stability. How such stable structure is maintained is not well understood. Here, we apply four different visualization schemes to label it and investigate its dynamics during DNA replication and repair. We show that replisomes assemble over the heterochromatin in a temporally ordered manner. Furthermore, heterochromatin undergoes transient decompaction locally at the active sites of DNA synthesis. Using selective laser microirradiation conditions that lead to damage repaired via processive DNA synthesis, we measured similarly local decompaction of heterochromatin. In both cases, we could not observe large-scale movement of heterochromatin to the domain surface. Instead, the processive DNA synthesis machinery assembled at the replication/repair sites. Altogether, our data are compatible with a progression of DNA replication/repair along the chromatin in a dynamic mode with localized and transient decompaction that does not globally remodels the whole heterochromatin compartment.
DOI: 10.6084/m9.figshare.10465745.v2
title: SDF-1 preconditioned HPC scaffolds mobilize cartilage-derived progenitors and stimulate meniscal fibrocartilage repair in human explant tissue culture

description: <b>Purpose</b>: The purpose of this study was to characterize the influence of SDF-1 on cell migration/adhesion and temporal gene expression of human cartilage mesenchymal progenitor cells (C-PCs); and to utilize SDF-1 conditioned mesenchymal progenitors to stimulate reintegration of human meniscus fibrocartilage breaks. <b>Materials and Methods</b>: Characterization of SDF-1-induced cell migration was achieved using hydroxypropyl cellulose (HPC) scaffolds pretreated with SDF-1. Fluorescence microscopy and cell counting were used to visualize and quantify the extent of cell migration into scaffolds, respectively. Relative mRNA expression analysis was used to characterize the temporal effects of SDF-1 on C-PCs. Tissue reintegration experiments were conducted using cylindrical human meniscal tissue punches, which were then placed back together with an HPC scaffold embedded with C-PCs. Tensile testing was used to evaluate the extent of tissue reintegration stimulated by human mesenchymal progenitors. <b>Results</b>: C-PCs migrate into scaffolds in response to SDF-1 with the same efficiency as mesenchymal progenitors from human marrow (BM-MSCs). SDF-1 treatment of C-PCs did not significantly alter the expression of early and late stage chondrogenic differentiation genes. Scaffolds containing SDF-1 pre-conditioned C-PCs successfully adhered to fibrocartilage breaks and migrated from the scaffold into the tissue. Tensile testing demonstrated that SDF-1 preconditioned C-PCs stimulate reintegration of fibrocartilage tears. <b>Conclusion</b>: C-PCs migrate in response to SDF-1. Exposure to SDF-1 does not significantly alter the unique mRNA profile of C-PCs that make them desirable for cartilaginous tissue repair applications. SDF-1 pretreated mesenchymal progenitors successfully disperse into injured tissues to help facilitate tissue reintegration.
DOI: 10.6084/m9.figshare.10465745.v1
title: SDF-1 preconditioned HPC scaffolds mobilize cartilage-derived progenitors and stimulate meniscal fibrocartilage repair in human explant tissue culture

description: <b>Purpose</b>: The purpose of this study was to characterize the influence of SDF-1 on cell migration/adhesion and temporal gene expression of human cartilage mesenchymal progenitor cells (C-PCs); and to utilize SDF-1 conditioned mesenchymal progenitors to stimulate reintegration of human meniscus fibrocartilage breaks. <b>Materials and Methods</b>: Characterization of SDF-1-induced cell migration was achieved using hydroxypropyl cellulose (HPC) scaffolds pretreated with SDF-1. Fluorescence microscopy and cell counting were used to visualize and quantify the extent of cell migration into scaffolds, respectively. Relative mRNA expression analysis was used to characterize the temporal effects of SDF-1 on C-PCs. Tissue reintegration experiments were conducted using cylindrical human meniscal tissue punches, which were then placed back together with an HPC scaffold embedded with C-PCs. Tensile testing was used to evaluate the extent of tissue reintegration stimulated by human mesenchymal progenitors. <b>Results</b>: C-PCs migrate into scaffolds in response to SDF-1 with the same efficiency as mesenchymal progenitors from human marrow (BM-MSCs). SDF-1 treatment of C-PCs did not significantly alter the expression of early and late stage chondrogenic differentiation genes. Scaffolds containing SDF-1 pre-conditioned C-PCs successfully adhered to fibrocartilage breaks and migrated from the scaffold into the tissue. Tensile testing demonstrated that SDF-1 preconditioned C-PCs stimulate reintegration of fibrocartilage tears. <b>Conclusion</b>: C-PCs migrate in response to SDF-1. Exposure to SDF-1 does not significantly alter the unique mRNA profile of C-PCs that make them desirable for cartilaginous tissue repair applications. SDF-1 pretreated mesenchymal progenitors successfully disperse into injured tissues to help facilitate tissue reintegration.
DOI: 10.6084/m9.figshare.10458665
title: MOESM9 of A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

description: Additional file 9. A-Lister source code.
DOI: 10.6084/m9.figshare.10458665.v1
title: MOESM9 of A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

description: Additional file 9. A-Lister source code.
DOI: 10.6084/m9.figshare.10458659
title: MOESM8 of A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

description: Additional file 8. Use case 3 result.
DOI: 10.6084/m9.figshare.10458656
title: MOESM3 of Deletion of the fungus specific protein phosphatase Z1 exaggerates the oxidative stress response in Candida albicans

description: Additional file 3:Dataset S1. for Additional figures. Dataset S2. for Fig. 1. Dataset S3. for Table 1. Dataset S4. for Fig. 2. Dataset S5. for Table 2. Dataset S6. for Fig. 3. Dataset S7. for Table 3. DNA chip and RNA-Seq. Dataset S8. for Table 3. RT-qPCR.
DOI: 10.6084/m9.figshare.10458653
title: MOESM7 of A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

description: Additional file 7. Use case 2 result.
DOI: 10.6084/m9.figshare.10458647
title: MOESM6 of A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

description: Additional file 6. Name-List file B.
DOI: 10.6084/m9.figshare.10458656.v1
title: MOESM3 of Deletion of the fungus specific protein phosphatase Z1 exaggerates the oxidative stress response in Candida albicans

description: Additional file 3:Dataset S1. for Additional figures. Dataset S2. for Fig. 1. Dataset S3. for Table 1. Dataset S4. for Fig. 2. Dataset S5. for Table 2. Dataset S6. for Fig. 3. Dataset S7. for Table 3. DNA chip and RNA-Seq. Dataset S8. for Table 3. RT-qPCR.
DOI: 10.6084/m9.figshare.10458659.v1
title: MOESM8 of A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

description: Additional file 8. Use case 3 result.
DOI: 10.6084/m9.figshare.10458647.v1
title: MOESM6 of A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

description: Additional file 6. Name-List file B.
DOI: 10.6084/m9.figshare.10458653.v1
title: MOESM7 of A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

description: Additional file 7. Use case 2 result.
DOI: 10.6084/m9.figshare.10458641
title: MOESM5 of A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

description: Additional file 5. Name-List file A.
DOI: 10.6084/m9.figshare.10458623
title: MOESM2 of A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

description: Additional file 2. DE-Sample sample input file.
DOI: 10.6084/m9.figshare.10458641.v1
title: MOESM5 of A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

description: Additional file 5. Name-List file A.
DOI: 10.6084/m9.figshare.10458632
title: MOESM3 of A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

description: Additional file 3. DE-Series sample input file.
DOI: 10.6084/m9.figshare.10458623.v1
title: MOESM2 of A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

description: Additional file 2. DE-Sample sample input file.
DOI: 10.6084/m9.figshare.10458632.v1
title: MOESM3 of A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

description: Additional file 3. DE-Series sample input file.
DOI: 10.6084/m9.figshare.10458617
title: MOESM1 of A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

description: Additional file 1. Name-List sample input file.
DOI: 10.6084/m9.figshare.10458617.v1
title: MOESM1 of A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

description: Additional file 1. Name-List sample input file.
DOI: 10.6084/m9.figshare.10458602
title: MOESM1 of Sporting programs aimed at inactive population groups in the Netherlands: factors influencing their long-term sustainability in the organized sports setting

description: Additional file 1. Theoretical framework of factors. Presents an overview of factors influencing the sustainability of health promotion programs from previous literature, ordered per main theme and subthemes.
DOI: 10.6084/m9.figshare.10458602.v1
title: MOESM1 of Sporting programs aimed at inactive population groups in the Netherlands: factors influencing their long-term sustainability in the organized sports setting

description: Additional file 1. Theoretical framework of factors. Presents an overview of factors influencing the sustainability of health promotion programs from previous literature, ordered per main theme and subthemes.
DOI: 10.6084/m9.figshare.10458581
title: MOESM6 of Comparative transcriptome analysis of matched primary and distant metastatic ovarian carcinoma

description: Additional file 5: Table S5. Univariate cox proportional hazard analysis for our 100 metastatic genes performed from TCGA data.
DOI: 10.6084/m9.figshare.10458581.v1
title: MOESM6 of Comparative transcriptome analysis of matched primary and distant metastatic ovarian carcinoma

description: Additional file 5: Table S5. Univariate cox proportional hazard analysis for our 100 metastatic genes performed from TCGA data.
DOI: 10.6084/m9.figshare.10458575
title: MOESM5 of Comparative transcriptome analysis of matched primary and distant metastatic ovarian carcinoma

description: Additional file 4: Table S4. Upstream regulators identified in our data using Ingenuity Pathway Analysis.
DOI: 10.6084/m9.figshare.10458566
title: MOESM4 of Comparative transcriptome analysis of matched primary and distant metastatic ovarian carcinoma

description: Additional file 3: Table S3. Number of upstream transcription factor motifs predicted within (+/− 1.5 kb of TSS) or around (+/− 50 kb from TSS) promoters of IPA predicted target genes.
DOI: 10.6084/m9.figshare.10458575.v1
title: MOESM5 of Comparative transcriptome analysis of matched primary and distant metastatic ovarian carcinoma

description: Additional file 4: Table S4. Upstream regulators identified in our data using Ingenuity Pathway Analysis.
DOI: 10.6084/m9.figshare.10458566.v1
title: MOESM4 of Comparative transcriptome analysis of matched primary and distant metastatic ovarian carcinoma

description: Additional file 3: Table S3. Number of upstream transcription factor motifs predicted within (+/− 1.5 kb of TSS) or around (+/− 50 kb from TSS) promoters of IPA predicted target genes.
DOI: 10.6084/m9.figshare.10458557
title: MOESM3 of Comparative transcriptome analysis of matched primary and distant metastatic ovarian carcinoma

description: Additional file 2: Table S2. Gene Ontology Analysis (Diseases or Functions Annotation) of differentially expressed genes performed using Ingenuity Pathway Analysis.
DOI: 10.6084/m9.figshare.10458557.v1
title: MOESM3 of Comparative transcriptome analysis of matched primary and distant metastatic ovarian carcinoma

description: Additional file 2: Table S2. Gene Ontology Analysis (Diseases or Functions Annotation) of differentially expressed genes performed using Ingenuity Pathway Analysis.
DOI: 10.6084/m9.figshare.10458548
title: MOESM2 of Comparative transcriptome analysis of matched primary and distant metastatic ovarian carcinoma

description: Additional file 1: Table S1. The differentially expressed genes identified in our analysis.
DOI: 10.6084/m9.figshare.10458548.v1
title: MOESM2 of Comparative transcriptome analysis of matched primary and distant metastatic ovarian carcinoma

description: Additional file 1: Table S1. The differentially expressed genes identified in our analysis.
DOI: 10.6084/m9.figshare.10458539
title: MOESM1 of Clinical significance of stromal ER and PR expression in periampullary adenocarcinoma

description: Additional file 1: Data 1. Specification of the targeted gene panel, showing types of mutations and tumor morphology in each case for every 70 genes sequenced.
DOI: 10.6084/m9.figshare.10458524
title: MOESM7 of Genetic dynamics in untreated CLL patients with either stable or progressive disease: a longitudinal study

description: Additional file 7: Table S7. SNPs and mutations detected by Haloplex SureDesign Panel.
DOI: 10.6084/m9.figshare.10458539.v1
title: MOESM1 of Clinical significance of stromal ER and PR expression in periampullary adenocarcinoma

description: Additional file 1: Data 1. Specification of the targeted gene panel, showing types of mutations and tumor morphology in each case for every 70 genes sequenced.