cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7755755.v1
title: MOESM4 of Enhancing co-translational folding of heterologous protein by deleting non-essential ribosomal proteins in Pichia pastoris

description: Additional file 4: Table S6. mRNA fold-change (log2) for chaperone genes. Table S7. RNC-mRNA fold-change (log2) for chaperone genes. P-values of differential expression were calculated using edgeR software.
DOI: 10.6084/m9.figshare.11950062
title: Graphene oxide nanoparticles induce hepatic dysfunction through the regulation of innate immune signaling in zebrafish (<i>Danio rerio</i>)

description: Graphene oxide (GO) is an increasingly important nanomaterial that exhibits great promise in the area of bionanotechnology and nanobiomedicine. However, the toxic effects of GO on the vertebrate developmental system are still poorly understood. Here, we aimed to investigate the toxic effects and molecular mechanisms of GO exposure in larval and adult zebrafish. The results showed that the major hepatotoxic phenotype induced by GO in zebrafish embryos was a significant decrease in liver area and a dose-dependent decrease in the hepatocytes. Moreover, the number of macrophages and neutrophils in zebrafish embryos were reduced but the expressions of pro-inflammatory cytokines were increased after GO treatment. High through-put RNA-Seq identified 314 differentially expressed genes (DEGs) in GO-induced zebrafish embryos including 192 up-regulated and 122 down-regulated. KEGG and GO functional analysis revealed that steroid hormone biosynthesis, lipoprotein metabolic process, and PPAR signaling pathway were significantly enriched. Most of the lipid metabolism genes were down-regulated while majority of the immune genes were up-regulated after GO treatment. Moreover, GO induced NF-κB p65 into the nucleus and increased the protein levels of NF-κB p65, JAK2, STAT3, and Bcl2 in adult zebrafish liver. In addition, pharmacological experiments showed that inhibition of ROS and blocking the MAPK signaling could rescue the hepatotoxic phenotypes induced by GO exposure. On the contrary, pharmacological activation of PPAR-α expression have increased the hepatotoxic effects in GO-induced larval and adult zebrafish. Taken together, these informations demonstrated that GO induced hepatic dysfunction mainly through the ROS and PPAR-α mediated innate immune signaling in zebrafish.
DOI: 10.6084/m9.figshare.11950062.v1
title: Graphene oxide nanoparticles induce hepatic dysfunction through the regulation of innate immune signaling in zebrafish (<i>Danio rerio</i>)

description: Graphene oxide (GO) is an increasingly important nanomaterial that exhibits great promise in the area of bionanotechnology and nanobiomedicine. However, the toxic effects of GO on the vertebrate developmental system are still poorly understood. Here, we aimed to investigate the toxic effects and molecular mechanisms of GO exposure in larval and adult zebrafish. The results showed that the major hepatotoxic phenotype induced by GO in zebrafish embryos was a significant decrease in liver area and a dose-dependent decrease in the hepatocytes. Moreover, the number of macrophages and neutrophils in zebrafish embryos were reduced but the expressions of pro-inflammatory cytokines were increased after GO treatment. High through-put RNA-Seq identified 314 differentially expressed genes (DEGs) in GO-induced zebrafish embryos including 192 up-regulated and 122 down-regulated. KEGG and GO functional analysis revealed that steroid hormone biosynthesis, lipoprotein metabolic process, and PPAR signaling pathway were significantly enriched. Most of the lipid metabolism genes were down-regulated while majority of the immune genes were up-regulated after GO treatment. Moreover, GO induced NF-κB p65 into the nucleus and increased the protein levels of NF-κB p65, JAK2, STAT3, and Bcl2 in adult zebrafish liver. In addition, pharmacological experiments showed that inhibition of ROS and blocking the MAPK signaling could rescue the hepatotoxic phenotypes induced by GO exposure. On the contrary, pharmacological activation of PPAR-α expression have increased the hepatotoxic effects in GO-induced larval and adult zebrafish. Taken together, these informations demonstrated that GO induced hepatic dysfunction mainly through the ROS and PPAR-α mediated innate immune signaling in zebrafish.
DOI: 10.6084/m9.figshare.7231481
title: Additional file 10 of The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

description: Table S8. Soil and site characteristics associated with each of the soil samples collected in this study. MAT = mean annual temperature. MAP = mean annual precipitation, MMT = mean monthly temperature, MMP = mean monthly precipitation (the data we used is the month data we sampled at that site or the mean value of 2-month data if the sampling date was at the beginning or the end of a month), RST = real-time soil temperature, RAT = real-time air temperature, DOC = dissolved organic carbon, Olsen-P = rapid available phosphorus, Ph = rice plant height, FD = flooding depth. MAT, MAP, MMT, and MMP were 22-years observation date obtained from http://neo.sci.gsfc.nasa.gov. The total carbon (TC), total nitrogen (TN), and total phosphorus (TP) were on dry basis while the RAP was on wet basis. Field moisture was measured immediately after sample collection. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.7231481.v1
title: Additional file 10: of The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

description: Table S8. Soil and site characteristics associated with each of the soil samples collected in this study. MAT = mean annual temperature. MAP = mean annual precipitation, MMT = mean monthly temperature, MMP = mean monthly precipitation (the data we used is the month data we sampled at that site or the mean value of 2-month data if the sampling date was at the beginning or the end of a month), RST = real-time soil temperature, RAT = real-time air temperature, DOC = dissolved organic carbon, Olsen-P = rapid available phosphorus, Ph = rice plant height, FD = flooding depth. MAT, MAP, MMT, and MMP were 22-years observation date obtained from http://neo.sci.gsfc.nasa.gov . The total carbon (TC), total nitrogen (TN), and total phosphorus (TP) were on dry basis while the RAP was on wet basis. Field moisture was measured immediately after sample collection. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.7231481.v2
title: Additional file 10 of The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

description: Table S8. Soil and site characteristics associated with each of the soil samples collected in this study. MAT = mean annual temperature. MAP = mean annual precipitation, MMT = mean monthly temperature, MMP = mean monthly precipitation (the data we used is the month data we sampled at that site or the mean value of 2-month data if the sampling date was at the beginning or the end of a month), RST = real-time soil temperature, RAT = real-time air temperature, DOC = dissolved organic carbon, Olsen-P = rapid available phosphorus, Ph = rice plant height, FD = flooding depth. MAT, MAP, MMT, and MMP were 22-years observation date obtained from http://neo.sci.gsfc.nasa.gov. The total carbon (TC), total nitrogen (TN), and total phosphorus (TP) were on dry basis while the RAP was on wet basis. Field moisture was measured immediately after sample collection. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.7231505
title: Additional file 10: of Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploids

description: Table S2. Tissue-specific silencing (a) and development-specific silencing (b) at different growth stages. Mean percentages of tissues showing tissue-specific silence of alleles/homeologs at different stages. (XLS 41 kb)
DOI: 10.6084/m9.figshare.7231505.v1
title: Additional file 10: of Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploids

description: Table S2. Tissue-specific silencing (a) and development-specific silencing (b) at different growth stages. Mean percentages of tissues showing tissue-specific silence of alleles/homeologs at different stages. (XLS 41 kb)
DOI: 10.6084/m9.figshare.7755803
title: Additional file 1: of Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history

description: Table S1. Sequencing summary of 480 peach accessions. Table S8. Putative domestication sweeps. Table S9. Putative improvement sweeps. Table S10. Genes in putative domestication sweeps. Table S11. Genes in putative improvement sweeps. Table S15. Putative selective sweeps for low CR breeding. Table S16. Chilling requirement test by classifying accessions into low (1) and non-low CR (0). Table S17. Putative improvement sweeps in western improved group. Table S18. Putative improvement sweeps in eastern improved group. (XLSX 576 kb)
DOI: 10.6084/m9.figshare.7755803.v1
title: Additional file 1: of Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history

description: Table S1. Sequencing summary of 480 peach accessions. Table S8. Putative domestication sweeps. Table S9. Putative improvement sweeps. Table S10. Genes in putative domestication sweeps. Table S11. Genes in putative improvement sweeps. Table S15. Putative selective sweeps for low CR breeding. Table S16. Chilling requirement test by classifying accessions into low (1) and non-low CR (0). Table S17. Putative improvement sweeps in western improved group. Table S18. Putative improvement sweeps in eastern improved group. (XLSX 576 kb)
DOI: 10.6084/m9.figshare.7231517
title: Additional file 1: of Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploids

description: Table S1. Genes used in Sequenom MassARRAY assays. (XLS 42 kb)
DOI: 10.6084/m9.figshare.7231517.v1
title: Additional file 1: of Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploids

description: Table S1. Genes used in Sequenom MassARRAY assays. (XLS 42 kb)
DOI: 10.6084/m9.figshare.7231520
title: Additional file 12 of The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

description: Table S9. Basic information of the metagenomic sequencing. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7231520.v2
title: Additional file 12 of The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

description: Table S9. Basic information of the metagenomic sequencing. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7231520.v1
title: Additional file 12: of The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

description: Table S9. Basic information of the metagenomic sequencing. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8280113
title: Additional file 1: of Characterization of genes required for both Rpg1 and rpg4-mediated wheat stem rust resistance in barley

description: Table S1. Seedling QCCJ phenotyping and root length measurement data on Hv584/rpr9 F2:6 RIL population. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.8280113.v1
title: Additional file 1: of Characterization of genes required for both Rpg1 and rpg4-mediated wheat stem rust resistance in barley

description: Table S1. Seedling QCCJ phenotyping and root length measurement data on Hv584/rpr9 F2:6 RIL population. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.7231541
title: Additional file 13 of The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

description: Table S10. Statistics information of metagenomic assembly for each metagenomic sample. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7231541.v2
title: Additional file 13 of The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

description: Table S10. Statistics information of metagenomic assembly for each metagenomic sample. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7231541.v1
title: Additional file 13: of The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

description: Table S10. Statistics information of metagenomic assembly for each metagenomic sample. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8280119
title: Additional file 2: of Characterization of genes required for both Rpg1 and rpg4-mediated wheat stem rust resistance in barley

description: Table S2. List of 2701 redundant loci across the seven chromosomes of barley used for the genetic map construction. (XLSX 73 kb)
DOI: 10.6084/m9.figshare.8280119.v1
title: Additional file 2: of Characterization of genes required for both Rpg1 and rpg4-mediated wheat stem rust resistance in barley

description: Table S2. List of 2701 redundant loci across the seven chromosomes of barley used for the genetic map construction. (XLSX 73 kb)
DOI: 10.5066/p98x9grb
title: Disturbance, energy, climate partitions, cultivars and species habitat data for the Colorado Plateau and environs

description: These data were compiled to support and inform the Bureau of Land Management&rsquo;s Colorado Plateau Native Plant Program and to guide future management action when selecting regions to collect and increase seed for native plant materials development. The objective of our study was to develop geospatial datasets to aid land managers and restoration practitioners in identifying areas that will need to be restored in the future (currently disturbed) as well as areas to source new native plant materials for propagation with increased climate similarity to these areas across the Colorado Plateau, Arizona/New Mexico Mountains, and Arizona/New Mexico Plateaus. These data represent species distribution models for 12 high priority restoration species on the Colorado Plateau and environs, source locations of commonly available germplasms for those 12 high priority restoration species, climatic suitability of those restoration species based on the source locations, areas disturbed by grazing, energy production, and wildfires, as well as climatic partitions within each species habitat to illustrate areas for new collections for grow out. This data was collected and analyzed electronically. Disturbance data was collected from the US Energy Information Administration, Homeland Infrastructure Foundation Level Data, the Bureau of Land Management, the US Forest Service, and the National Interagency Fire Center. Species distribution models were created using species occurrence data sourced from SEINET, 19 bioclimatic variables sourced from the WorldClim historical dataset, and were created using MaxEnt software. Climate similarity (referred to as well suited habitat throughout) and climate partitioning models were created using the Seed Mapping Toolkit. This data can be used to investigate suitable habitat for priority restoration species, identify landscape level disturbances, identify suitability of currently available native plant materials (NPMs), and to prioritize locations for seed collection to fill gaps in existing native plant material suitability.
DOI: 10.6084/m9.figshare.8280140
title: Additional file 6: of Characterization of genes required for both Rpg1 and rpg4-mediated wheat stem rust resistance in barley

description: Table S3. List of 487 exome capture target genes under the rpr9 QTL with their physical position and gene orientation on barley ch. 3H. Exome capture reads for Q21861-wt and Q21861-rpr9 mutant and their coverage ratio for each target is given. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.25274098
title: Interviews

description: The research was qualitative in approach and sought to understand the conceptions of university teachers about the use of bibliographic managers. To achieve this objective, interviews were conducted with university teachers from three Latin American countries, who responded to the questions posed in the interview guide, which were transcribed in the document presented here.
DOI: 10.6084/m9.figshare.25274098.v1
title: Interviews

description: The research was qualitative in approach and sought to understand the conceptions of university teachers about the use of bibliographic managers. To achieve this objective, interviews were conducted with university teachers from three Latin American countries, who responded to the questions posed in the interview guide, which were transcribed in the document presented here.
DOI: 10.6084/m9.figshare.8280140.v1
title: Additional file 6: of Characterization of genes required for both Rpg1 and rpg4-mediated wheat stem rust resistance in barley

description: Table S3. List of 487 exome capture target genes under the rpr9 QTL with their physical position and gene orientation on barley ch. 3H. Exome capture reads for Q21861-wt and Q21861-rpr9 mutant and their coverage ratio for each target is given. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.7231565
title: Additional file 1: of The ultrasound-guided selective nerve block in the upper arm: an approach of retaining the motor function in elbow

description: Characteristics of Arm Group and Axillary Group (n = 12). This is the data about patients’ motor block scale and duration of motor blockade of the elbow and shoulder,the onset and the duration of sensory blockade (Musculocutaneous nerves; Radial nerve; Ulnar nerve; Medial antebrachial cutaneous nerves; Median nerve), patients’ satisfaction. (XLS 22 kb)
DOI: 10.6084/m9.figshare.7231565.v1
title: Additional file 1: of The ultrasound-guided selective nerve block in the upper arm: an approach of retaining the motor function in elbow

description: Characteristics of Arm Group and Axillary Group (n = 12). This is the data about patients’ motor block scale and duration of motor blockade of the elbow and shoulder,the onset and the duration of sensory blockade (Musculocutaneous nerves; Radial nerve; Ulnar nerve; Medial antebrachial cutaneous nerves; Median nerve), patients’ satisfaction. (XLS 22 kb)
DOI: 10.6084/m9.figshare.7231571
title: Additional file 2 of The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

description: Table S1. Statistics of DOM extraction and annotation of soil samples collected in this study. Peak number a = number of peaks after filtering blank peaks and singletons. Peak number b = number of peaks after filtering blank peaks and those present in less than 10 samples, which is further introduced to annotation procedure. Peak number c = number of peaks assigned to putative formulas. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7231571.v2
title: Additional file 2 of The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

description: Table S1. Statistics of DOM extraction and annotation of soil samples collected in this study. Peak number a = number of peaks after filtering blank peaks and singletons. Peak number b = number of peaks after filtering blank peaks and those present in less than 10 samples, which is further introduced to annotation procedure. Peak number c = number of peaks assigned to putative formulas. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7231571.v1
title: Additional file 2: of The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

description: Table S1. Statistics of DOM extraction and annotation of soil samples collected in this study. Peak number a = number of peaks after filtering blank peaks and singletons. Peak number b = number of peaks after filtering blank peaks and those present in less than 10 samples, which is further introduced to annotation procedure. Peak number c = number of peaks assigned to putative formulas. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8280158
title: Additional file 9: of Characterization of genes required for both Rpg1 and rpg4-mediated wheat stem rust resistance in barley

description: Table S4. List of fifteen annotated high confidence SKP-1 like genes in barley whole genome assembly. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.8280158.v1
title: Additional file 9: of Characterization of genes required for both Rpg1 and rpg4-mediated wheat stem rust resistance in barley

description: Table S4. List of fifteen annotated high confidence SKP-1 like genes in barley whole genome assembly. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.7231589
title: Additional file 3 of The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

description: Table S2. Multivariate analysis of bacterial data and drivers using canonical correspondence analysis (CCA) and non-metric multidimensional scaling (NMDS). Constrained (CCA) and unconstrained methods (NMDS and envfit) were used to compare and interpret effects of edaphic, geographical, and DOM factors on the microbial diversity. CCA1, CCA2, MDS1, and MDS2 stand for the angle cosines of variables and the axes. Pvals.1, empirical P values of fit statistic of environmental variables in CCA; Pvals.2, empirical P values of fit statistic using envfit to present environmental variables in NMDS; r2, goodness of fit statistic. Variables with Pvals.2 ≤ 0.001 were ticked on the “Fig. 3c” column and shown on Fig. 3c. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7231589.v1
title: Additional file 3: of The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

description: Table S2. Multivariate analysis of bacterial data and drivers using canonical correspondence analysis (CCA) and non-metric multidimensional scaling (NMDS). Constrained (CCA) and unconstrained methods (NMDS and envfit) were used to compare and interpret effects of edaphic, geographical, and DOM factors on the microbial diversity. CCA1, CCA2, MDS1, and MDS2 stand for the angle cosines of variables and the axes. Pvals.1, empirical P values of fit statistic of environmental variables in CCA; Pvals.2, empirical P values of fit statistic using envfit to present environmental variables in NMDS; r2, goodness of fit statistic. Variables with Pvals.2 ≤ 0.001 were ticked on the “Fig. 3c” column and shown on Fig. 3c. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7231589.v2
title: Additional file 3 of The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

description: Table S2. Multivariate analysis of bacterial data and drivers using canonical correspondence analysis (CCA) and non-metric multidimensional scaling (NMDS). Constrained (CCA) and unconstrained methods (NMDS and envfit) were used to compare and interpret effects of edaphic, geographical, and DOM factors on the microbial diversity. CCA1, CCA2, MDS1, and MDS2 stand for the angle cosines of variables and the axes. Pvals.1, empirical P values of fit statistic of environmental variables in CCA; Pvals.2, empirical P values of fit statistic using envfit to present environmental variables in NMDS; r2, goodness of fit statistic. Variables with Pvals.2 ≤ 0.001 were ticked on the “Fig. 3c” column and shown on Fig. 3c. (XLSX 16 kb)