cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7987019.v3
title: Baluk cave (NW China) Holocene speleothem trace element ratios

description: The interpretation of trace element/calcium ratios of speleothems as indicators of local hydroclimatic variability in the vicinity of caves has led to controversy in reconstructing the evolution of moisture conditions in arid central Asia (ACA) during the Holocene. Here we present records of Mg/Ca, Sr/Ca, Ba/Ca, and U/Ca from precisely dated stalagmites from Baluk cave in Xinjiang (northwest China), spanning the past 9370 years. The co-variations of the trace element ratios, together with the slopes of the regression lines of the corresponding logarithmically transformed data, suggest that they are dominated by prior calcite precipitation (PCP) and thus can be used as reliable proxies of changes in moisture/precipitation. The trace element ratios are relatively high during ~9 to 5 ka and lower from 5 ka to the present, indicating a trend of increasing mid–late Holocene moisture in ACA. The long-term trend of variation of the trace element ratios is correlative with two other records of speleothem trace element ratios from caves in ACA: Kesang cave (western Xinjiang) and Ton cave (Uzbekistan). This spatial coherency of the trend of inferred moisture conditions from three caves that are separated by hundreds of kilometers demonstrates that speleothem trace element ratios are indicative of large spatial scale rather than local hydroclimatic variability in ACA during the Holocene. However, the long-term trend of variation of the trace element ratios is the inverse of the corresponding oxygen isotope (δ<sup>18</sup>O) records from the same cave sites, which implies that Holocene speleothem δ<sup>18</sup>O records do not represent changes in the precipitation amount in ACA; rather, they most likely reflect moisture sources and related water vapor transport controlled by Northern Hemisphere summer insolation (NHSI). Our findings provide new evidence for a ‘westerlies-dominated climatic regime’, which influenced hydroclimatic changes in ACA during the Holocene.
DOI: 10.6084/m9.figshare.12873710.v1
title: Additional file 4 of Expression profile analysis of the inflammatory response regulated by hepatocyte nuclear factor 4α

description: Additional file 4:ELK1 and HNF4α binding motifs in HNF4α-regulated genes. This file shows the sequence and position of ELK1 and HNF4α potential binding sites in the group of HNF4α-regulated genes. (XLS 86 KB)
DOI: 10.6084/m9.figshare.7987019.v2
title: Baluk cave (NW China) Holocene speleothem trace element ratios

description: The interpretation of trace element/calcium ratios of speleothems as indicators of local hydroclimatic variability in the vicinity of caves has led to controversy in reconstructing the evolution of moisture conditions in arid central Asia (ACA) during the Holocene. Here we present records of Mg/Ca, Sr/Ca, Ba/Ca, and U/Ca from precisely dated stalagmites from Baluk cave in Xinjiang (northwest China), spanning the past 9370 years. The co-variations of the trace element ratios, together with the slopes of the regression lines of the corresponding logarithmically transformed data, suggest that they are dominated by prior calcite precipitation (PCP) and thus can be used as reliable proxies of changes in moisture/precipitation. The trace element ratios are relatively high during ~9 to 5 ka and lower from 5 ka to the present, indicating a trend of increasing mid–late Holocene moisture in ACA. The long-term trend of variation of the trace element ratios is correlative with two other records of speleothem trace element ratios from caves in ACA: Kesang cave (western Xinjiang) and Ton cave (Uzbekistan). This spatial coherency of the trend of inferred moisture conditions from three caves that are separated by hundreds of kilometers demonstrates that speleothem trace element ratios are indicative of large spatial scale rather than local hydroclimatic variability in ACA during the Holocene. However, the long-term trend of variation of the trace element ratios is the inverse of the corresponding oxygen isotope (δ<sup>18</sup>O) records from the same cave sites, which implies that Holocene speleothem δ<sup>18</sup>O records do not represent changes in the precipitation amount in ACA; rather, they most likely reflect moisture sources and related water vapor transport controlled by Northern Hemisphere summer insolation (NHSI). Our findings provide new evidence for a ‘westerlies-dominated climatic regime’, which influenced hydroclimatic changes in ACA during the Holocene.
DOI: 10.6084/m9.figshare.12873710
title: Additional file 4 of Expression profile analysis of the inflammatory response regulated by hepatocyte nuclear factor 4α

description: Additional file 4:ELK1 and HNF4α binding motifs in HNF4α-regulated genes. This file shows the sequence and position of ELK1 and HNF4α potential binding sites in the group of HNF4α-regulated genes. (XLS 86 KB)
DOI: 10.6084/m9.figshare.12873701.v1
title: Additional file 1 of Expression profile analysis of the inflammatory response regulated by hepatocyte nuclear factor 4α

description: Additional file 1:Genes that respond to the treatment of HNF4α knock-down and/or cytokines. This file includes four sub-tables showing the genes with significantly altered expression and fold changes in four categories (Category A to D). (XLS 2 MB)
DOI: 10.6084/m9.figshare.12873701
title: Additional file 1 of Expression profile analysis of the inflammatory response regulated by hepatocyte nuclear factor 4α

description: Additional file 1:Genes that respond to the treatment of HNF4α knock-down and/or cytokines. This file includes four sub-tables showing the genes with significantly altered expression and fold changes in four categories (Category A to D). (XLS 2 MB)
DOI: 10.6084/m9.figshare.7986557
title: Additional file 1: of Microcirculatory perfusion disturbances following cardiac surgery with cardiopulmonary bypass are associated with in vitro endothelial hyperpermeability and increased angiopoietin-2 levels

description: Supplemental methods. Figure S1. Changes in renal endothelial cell structures following post-CPB plasma exposure. Figure S2. Changes in pulmonary endothelial cell structures following post-CPB plasma exposure. (ZIP 280 kb)
DOI: 10.6084/m9.figshare.12873740.v1
title: Additional file 3 of De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing

description: Additional file 3:Contigs from de novo assembly of 383,918 reads from the current study. The contig sequences obtained from the de novo assembly of 3, 83,918 reads from Jatropha curcas were given as FASTA format in TXT file. (TXT 16 MB)
DOI: 10.6084/m9.figshare.12873743.v1
title: Additional file 4 of De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing

description: Additional file 4:Contigs from de novo assembly of 991,050 reads from Sato et al. , 2011[9]. The contig sequences obtained from the de novo assembly of 991,050 reads from Sato et al., 2011 [9] were given as FASTA format in TXT file. (TXT 4 MB)
DOI: 10.6084/m9.figshare.12873743
title: Additional file 4 of De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing

description: Additional file 4:Contigs from de novo assembly of 991,050 reads from Sato et al. , 2011[9]. The contig sequences obtained from the de novo assembly of 991,050 reads from Sato et al., 2011 [9] were given as FASTA format in TXT file. (TXT 4 MB)
DOI: 10.6084/m9.figshare.7986557.v1
title: Additional file 1: of Microcirculatory perfusion disturbances following cardiac surgery with cardiopulmonary bypass are associated with in vitro endothelial hyperpermeability and increased angiopoietin-2 levels

description: Supplemental methods. Figure S1. Changes in renal endothelial cell structures following post-CPB plasma exposure. Figure S2. Changes in pulmonary endothelial cell structures following post-CPB plasma exposure. (ZIP 280 kb)
DOI: 10.6084/m9.figshare.12873740
title: Additional file 3 of De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing

description: Additional file 3:Contigs from de novo assembly of 383,918 reads from the current study. The contig sequences obtained from the de novo assembly of 3, 83,918 reads from Jatropha curcas were given as FASTA format in TXT file. (TXT 16 MB)
DOI: 10.6084/m9.figshare.12873761.v6
title: Additional file of De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing

description: Additional file of De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing
DOI: 10.6084/m9.figshare.12873761.v5
title: Additional file of De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing

description: Additional file of De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing
DOI: 10.6084/m9.figshare.12873770.v15
title: Additional file of Mycoplasma mycoides, from "mycoides Small Colony" to "capri". A microevolutionary perspective

description: Additional file of Mycoplasma mycoides, from "mycoides Small Colony" to "capri". A microevolutionary perspective
DOI: 10.6084/m9.figshare.7986476
title: Additional file 8: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S4. Summary statistics of 15 agronomic traits in 419 upland cotton accessions. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7986476.v1
title: Additional file 8: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S4. Summary statistics of 15 agronomic traits in 419 upland cotton accessions. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7986464
title: Additional file 5: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S1. Summary of 299 SSR polymorphisms. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7986464.v1
title: Additional file 5: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S1. Summary of 299 SSR polymorphisms. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7986446
title: Additional file 3: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S3. List of 299 SSR markers was used in this study and their position information and genetic diversity. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.12873770.v16
title: Additional file of Mycoplasma mycoides, from "mycoides Small Colony" to "capri". A microevolutionary perspective

description: Additional file of Mycoplasma mycoides, from "mycoides Small Colony" to "capri". A microevolutionary perspective
DOI: 10.6084/m9.figshare.12873815.v1
title: Additional file 7 of Mycoplasma mycoides, from "mycoides Small Colony" to "capri". A microevolutionary perspective

description: Additional file 7:"List of gene clusters identified as orthologous". This additional table lists the names of genes found orthologous by the Microbial Genome Database for Comparative Analysis http://mbgd.genome.ad.jp/ (XLS 236 KB)
DOI: 10.6084/m9.figshare.12873818.v1
title: Additional file 8 of Mycoplasma mycoides, from "mycoides Small Colony" to "capri". A microevolutionary perspective

description: Additional file 8:"List of CDS in Mmc strains GM12 and 95010 showing less than 90% similarity with each other". This additional table lists the names of genes that are not highly similar in two strains belonging to the same subspecies, M. mycoides subsp. capri. (XLS 44 KB)
DOI: 10.6084/m9.figshare.7986440
title: Additional file 2: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S5. Mean squares of the ANOVA of 15 agronomic traits measurements in 6 environments. “*”, “**” indicate significance at the probability levels of P
DOI: 10.6084/m9.figshare.12873818
title: Additional file 8 of Mycoplasma mycoides, from "mycoides Small Colony" to "capri". A microevolutionary perspective

description: Additional file 8:"List of CDS in Mmc strains GM12 and 95010 showing less than 90% similarity with each other". This additional table lists the names of genes that are not highly similar in two strains belonging to the same subspecies, M. mycoides subsp. capri. (XLS 44 KB)
DOI: 10.6084/m9.figshare.7986437
title: Additional file 1: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S2. List of 419 upland cotton accessions was used in this study and their cluster information. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.12873815
title: Additional file 7 of Mycoplasma mycoides, from "mycoides Small Colony" to "capri". A microevolutionary perspective

description: Additional file 7:"List of gene clusters identified as orthologous". This additional table lists the names of genes found orthologous by the Microbial Genome Database for Comparative Analysis http://mbgd.genome.ad.jp/ (XLS 236 KB)
DOI: 10.6084/m9.figshare.7986431
title: Additional file 16: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S9. Summary of 2 types of favorable alleles in key agronomic traits. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7986446.v1
title: Additional file 3: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S3. List of 299 SSR markers was used in this study and their position information and genetic diversity. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.7986440.v1
title: Additional file 2: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S5. Mean squares of the ANOVA of 15 agronomic traits measurements in 6 environments. “*”, “**” indicate significance at the probability levels of P
DOI: 10.6084/m9.figshare.7986431.v1
title: Additional file 16: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S9. Summary of 2 types of favorable alleles in key agronomic traits. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7986425
title: Additional file 15: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S8. Categorization of accessions containing more than one rare favorable allele (RFA) and non-RFA accessions. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.7986437.v1
title: Additional file 1: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S2. List of 419 upland cotton accessions was used in this study and their cluster information. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.7986416
title: Additional file 14: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S7. Favorable alleles for the top 5% and bottom 5% accessions in 4 yield and fiber quality traits. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.12873824.v3
title: Additional file of In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis

description: Additional file of In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis
DOI: 10.6084/m9.figshare.12873824.v5
title: Additional file of In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis

description: Additional file of In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis
DOI: 10.6084/m9.figshare.7986425.v1
title: Additional file 15: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S8. Categorization of accessions containing more than one rare favorable allele (RFA) and non-RFA accessions. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.7986416.v1
title: Additional file 14: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S7. Favorable alleles for the top 5% and bottom 5% accessions in 4 yield and fiber quality traits. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7986404
title: Additional file 13: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S6. The frequency of favorable alleles in 3 breeding periods. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.12873824.v2
title: Additional file of In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis

description: Additional file of In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis
DOI: 10.6084/m9.figshare.12873833
title: Additional file 2 of In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis

description: Additional file 2:Table S2: Significant GO identifiers detected based on the differentially expressed transcripts in cluster 1 for the acute phase response to E. coli infection. A hypergeometric gene set enrichment test was performed based on cluster 1 of the contrast T24 vs. C24. Overrepresentation of gene sets defined by the GO database http://www.geneontology.org/ was tested using the Fisher's exact test. A gene set was considered significant if P &lt; 0.05. (HTML 32 KB)
DOI: 10.6084/m9.figshare.12873836.v1
title: Additional file 3 of In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis

description: Additional file 3:Table S3: Significant GO identifiers detected based on the differentially expressed transcripts in cluster 2 for the acute phase response to E. coli infection. A hypergeometric gene set enrichment test was performed based on cluster 2 of the contrast T24 vs. C24. A gene set was considered significant if P &lt; 0.05. (HTML 15 KB)
DOI: 10.6084/m9.figshare.12873824.v1
title: Additional file of In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis

description: Additional file of In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis
DOI: 10.6084/m9.figshare.7986404.v1
title: Additional file 13: of Identifying favorable alleles for improving key agronomic traits in upland cotton

description: Table S6. The frequency of favorable alleles in 3 breeding periods. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.12873830.v1
title: Additional file 1 of In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis

description: Additional file 1:Table S1: Differentially expressed transcripts for the acute phase response to E. coli infection in the bovine udder. (XLS 124 KB)
DOI: 10.6084/m9.figshare.12873830
title: Additional file 1 of In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis

description: Additional file 1:Table S1: Differentially expressed transcripts for the acute phase response to E. coli infection in the bovine udder. (XLS 124 KB)
DOI: 10.6084/m9.figshare.12873842.v1
title: Additional file 5 of In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis

description: Additional file 5:Table S4: Overlap of differentially expressed genes between three studies of E. coli infection in the bovine udder. Data from T = 24 h post-infection in three different studies: 1) "This study": the study described in this paper; 2) "Mitterhuemer": the study described by Mitterhuemer et al. [14]; and 3) "Rinaldi": the study described by Rinaldi et al. [15]. (XLS 21 KB)
DOI: 10.6084/m9.figshare.12873842
title: Additional file 5 of In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis

description: Additional file 5:Table S4: Overlap of differentially expressed genes between three studies of E. coli infection in the bovine udder. Data from T = 24 h post-infection in three different studies: 1) "This study": the study described in this paper; 2) "Mitterhuemer": the study described by Mitterhuemer et al. [14]; and 3) "Rinaldi": the study described by Rinaldi et al. [15]. (XLS 21 KB)
DOI: 10.6084/m9.figshare.12873833.v1
title: Additional file 2 of In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis

description: Additional file 2:Table S2: Significant GO identifiers detected based on the differentially expressed transcripts in cluster 1 for the acute phase response to E. coli infection. A hypergeometric gene set enrichment test was performed based on cluster 1 of the contrast T24 vs. C24. Overrepresentation of gene sets defined by the GO database http://www.geneontology.org/ was tested using the Fisher's exact test. A gene set was considered significant if P &lt; 0.05. (HTML 32 KB)
DOI: 10.6084/m9.figshare.12873836
title: Additional file 3 of In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis

description: Additional file 3:Table S3: Significant GO identifiers detected based on the differentially expressed transcripts in cluster 2 for the acute phase response to E. coli infection. A hypergeometric gene set enrichment test was performed based on cluster 2 of the contrast T24 vs. C24. A gene set was considered significant if P &lt; 0.05. (HTML 15 KB)
DOI: 10.6084/m9.figshare.7986365
title: Additional file 5: of An improved protein extraction method applied to cotton leaves is compatible with 2-DE and LC-MS

description: List of all proteins identified by the high-throughput LC-MS/MS. (XLS 5478 kb)
DOI: 10.6084/m9.figshare.7986365.v1
title: Additional file 5: of An improved protein extraction method applied to cotton leaves is compatible with 2-DE and LC-MS

description: List of all proteins identified by the high-throughput LC-MS/MS. (XLS 5478 kb)
DOI: 10.6084/m9.figshare.7986353
title: Additional file 3: of An improved protein extraction method applied to cotton leaves is compatible with 2-DE and LC-MS

description: MS/MS identification of the 50 pairs of protein spots from the TCA and TCA-B gels. (XLS 373 kb)
DOI: 10.6084/m9.figshare.7986347
title: Additional file 2: of An improved protein extraction method applied to cotton leaves is compatible with 2-DE and LC-MS

description: Protein concentrations and yields from the three different protein extraction methods. (XLS 65 kb)
DOI: 10.6084/m9.figshare.7986353.v1
title: Additional file 3: of An improved protein extraction method applied to cotton leaves is compatible with 2-DE and LC-MS

description: MS/MS identification of the 50 pairs of protein spots from the TCA and TCA-B gels. (XLS 373 kb)
DOI: 10.6084/m9.figshare.7986347.v1
title: Additional file 2: of An improved protein extraction method applied to cotton leaves is compatible with 2-DE and LC-MS

description: Protein concentrations and yields from the three different protein extraction methods. (XLS 65 kb)