cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13245194.v1
title: Dataset for JGR: solid earth (Huang et al., 2020)

description: We provide the dataset, including the electrical conductivity measurement, 3-D CT image, grain size distribution, and FTIR data to support our research article entitled "Electrical conductivity in texturally equilibrated fluid-bearing forsterite aggregates at 800 °C and 1 GPa: implications for the high electrical conductivity anomalies in mantle wedges".
DOI: 10.6084/m9.figshare.13245319
title: Additional file 1 of Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads

description: Additional file 1. Example configuration file with default values. For the configuration of sub-workflows and applications used by Natrix, a single configuration file is used. Optional parts of the workflow (e.g., the generation of quality reports, clustering of OTUs, or the assignment of taxonomic information) can be disabled. The configuration file is also used to define the protocols used to generate the input data, e.g., whether the data is in single-end or paired-end format and whether a split-sample approach was used during sample preparation. It also contains configuration options to adjust individual parts of the workflow depending on the requirements of the project. An example configuration file with a description and default value for each parameter is shown in the CSV file.
DOI: 10.6084/m9.figshare.13245325
title: Additional file 3 of Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads

description: Additional file 3. Output file descriptions. CSV file containing descriptions of the output files generated by Natrix.
DOI: 10.6084/m9.figshare.13245319.v1
title: Additional file 1 of Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads

description: Additional file 1. Example configuration file with default values. For the configuration of sub-workflows and applications used by Natrix, a single configuration file is used. Optional parts of the workflow (e.g., the generation of quality reports, clustering of OTUs, or the assignment of taxonomic information) can be disabled. The configuration file is also used to define the protocols used to generate the input data, e.g., whether the data is in single-end or paired-end format and whether a split-sample approach was used during sample preparation. It also contains configuration options to adjust individual parts of the workflow depending on the requirements of the project. An example configuration file with a description and default value for each parameter is shown in the CSV file.
DOI: 10.6084/m9.figshare.13245325.v1
title: Additional file 3 of Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads

description: Additional file 3. Output file descriptions. CSV file containing descriptions of the output files generated by Natrix.
DOI: 10.6084/m9.figshare.13245328
title: Additional file 4 of Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads

description: Additional file 4. Configuration parameters used for the flooding experiment. CSV file containing the configuration parameters used in the OTU and ASV variants of the workflow for the processing of the flooding experiment data.
DOI: 10.6084/m9.figshare.13245394
title: Additional file 1 of Correction to: Half-graben inversion tectonics revealed by gravity modeling in the Mikawa Bay region, Central Japan

description: Additional file 1.
DOI: 10.6084/m9.figshare.13245394.v1
title: Additional file 1 of Correction to: Half-graben inversion tectonics revealed by gravity modeling in the Mikawa Bay region, Central Japan

description: Additional file 1.
DOI: 10.6084/m9.figshare.13245446
title: Additional file 2 of Low levels of fine particulate matter increase vascular damage and reduce pulmonary function in young healthy adults

description: Additional file 2: Table S2. Mean percent point change and differences in inflammatory, HRV and cardiac repolarization, lung function, blood chemistry, and lipids measures (95%CI): 1 h after exposure (Post) and approximately 20 h after exposure (Follow-up). Mean change is expressed per 37.8 μg/m3 of PM2.5, which corresponds to average concentrated PM2.5 exposure across subjects. Table S3. Mean values for inflammatory, HRV and cardiac repolarization, lung function, blood chemistry, and lipids measures for air and PM2.5 exposures: Pre-exposure, 1 h after exposure (Post) and approximately 20 h after exposure (Follow-up).
DOI: 10.6084/m9.figshare.13245446.v1
title: Additional file 2 of Low levels of fine particulate matter increase vascular damage and reduce pulmonary function in young healthy adults

description: Additional file 2: Table S2. Mean percent point change and differences in inflammatory, HRV and cardiac repolarization, lung function, blood chemistry, and lipids measures (95%CI): 1 h after exposure (Post) and approximately 20 h after exposure (Follow-up). Mean change is expressed per 37.8 μg/m3 of PM2.5, which corresponds to average concentrated PM2.5 exposure across subjects. Table S3. Mean values for inflammatory, HRV and cardiac repolarization, lung function, blood chemistry, and lipids measures for air and PM2.5 exposures: Pre-exposure, 1 h after exposure (Post) and approximately 20 h after exposure (Follow-up).
DOI: 10.6084/m9.figshare.13245454
title: Additional file 1 of MyoSight—semi-automated image analysis of skeletal muscle cross sections

description: Additional file 1. Supplementary materials– 1. MyoSight Program. 2. Instruction Manual, Supplementary materials 3. Test image 1. Supplementary materials 4. Test image 2
DOI: 10.6084/m9.figshare.13245475
title: Additional file 1 of Parasite-host ecology: the limited impacts of an intimate enemy on host microbiomes

description: Additional file 1. Type (outplant vs natural colony), location (basal, distal, or scar), and sequencing read count statistics of samples used to assess microbiome composition by Illumina 16S rRNA gene sequencing. Raw counts of paired end sequences per sample (column D) are shown relative to counts after trimming with TrimGalore (column E), after paired-end read merging (column F), and after assignment to an exact sequence variant (ESV) table filtered to remove sequences matching chloroplast and mitochondrial 16S rRNA genes (column G).
DOI: 10.6084/m9.figshare.13245484.v1
title: Additional file 3 of Parasite-host ecology: the limited impacts of an intimate enemy on host microbiomes

description: Additional file 3. Exact sequence variants (ESVs) differing significantly in proportional abundance between coral scar microbiomes from natural coral colonies versus coral scar microbiomes from outplanted corals. Differentially abundant ESVs were identified by DESeq, with significance assessed by a Wald test. The fold change in abundance (expressed as log2) reflects abundance in natural colonies relative to abundance in outplanted corals. ESV classifications are provided at the highest possible taxonomic resolution.
DOI: 10.6084/m9.figshare.13245487
title: Additional file 4 of Parasite-host ecology: the limited impacts of an intimate enemy on host microbiomes

description: Additional file 4. Exact sequence variants (ESVs) differing significantly in proportional abundance between sampling locations on outplanted corals: scar vs. distal microbiomes (Sheet 1), scar vs. basal microbiomes (Sheet 2), and distal vs. basal microbiomes. Differentially abundant ESVs were identified by DESeq, with significance assessed by a Wald test. The fold change in abundance (expressed as log2) reflects abundance in natural colonies relative to abundance in outplanted corals. ESV classifications are provided at the highest possible taxonomic resolution.
DOI: 10.6084/m9.figshare.13245487.v1
title: Additional file 4 of Parasite-host ecology: the limited impacts of an intimate enemy on host microbiomes

description: Additional file 4. Exact sequence variants (ESVs) differing significantly in proportional abundance between sampling locations on outplanted corals: scar vs. distal microbiomes (Sheet 1), scar vs. basal microbiomes (Sheet 2), and distal vs. basal microbiomes. Differentially abundant ESVs were identified by DESeq, with significance assessed by a Wald test. The fold change in abundance (expressed as log2) reflects abundance in natural colonies relative to abundance in outplanted corals. ESV classifications are provided at the highest possible taxonomic resolution.
DOI: 10.6084/m9.figshare.13245484
title: Additional file 3 of Parasite-host ecology: the limited impacts of an intimate enemy on host microbiomes

description: Additional file 3. Exact sequence variants (ESVs) differing significantly in proportional abundance between coral scar microbiomes from natural coral colonies versus coral scar microbiomes from outplanted corals. Differentially abundant ESVs were identified by DESeq, with significance assessed by a Wald test. The fold change in abundance (expressed as log2) reflects abundance in natural colonies relative to abundance in outplanted corals. ESV classifications are provided at the highest possible taxonomic resolution.
DOI: 10.6084/m9.figshare.13245475.v1
title: Additional file 1 of Parasite-host ecology: the limited impacts of an intimate enemy on host microbiomes

description: Additional file 1. Type (outplant vs natural colony), location (basal, distal, or scar), and sequencing read count statistics of samples used to assess microbiome composition by Illumina 16S rRNA gene sequencing. Raw counts of paired end sequences per sample (column D) are shown relative to counts after trimming with TrimGalore (column E), after paired-end read merging (column F), and after assignment to an exact sequence variant (ESV) table filtered to remove sequences matching chloroplast and mitochondrial 16S rRNA genes (column G).
DOI: 10.6084/m9.figshare.13245520
title: Additional file 5 of Activating transcription factor-2 (ATF2) is a key determinant of resistance to endocrine treatment in an in vitro model of breast cancer

description: Additional file 5: Supplementary file 3. Drug targets after siATF2 in TAMR.
DOI: 10.6084/m9.figshare.13245511.v1
title: Additional file 3 of Activating transcription factor-2 (ATF2) is a key determinant of resistance to endocrine treatment in an in vitro model of breast cancer

description: Additional file 3: Supplementary file 1. MvsT_DE Genes and Pathway analysis.
DOI: 10.6084/m9.figshare.13245514.v1
title: Additional file 4 of Activating transcription factor-2 (ATF2) is a key determinant of resistance to endocrine treatment in an in vitro model of breast cancer

description: Additional file 4: Supplementary file 2. siATF2 MvsT_DE Genes and Pathway analysis.
DOI: 10.6084/m9.figshare.13245511
title: Additional file 3 of Activating transcription factor-2 (ATF2) is a key determinant of resistance to endocrine treatment in an in vitro model of breast cancer

description: Additional file 3: Supplementary file 1. MvsT_DE Genes and Pathway analysis.
DOI: 10.6084/m9.figshare.13245520.v1
title: Additional file 5 of Activating transcription factor-2 (ATF2) is a key determinant of resistance to endocrine treatment in an in vitro model of breast cancer

description: Additional file 5: Supplementary file 3. Drug targets after siATF2 in TAMR.
DOI: 10.6084/m9.figshare.13245514
title: Additional file 4 of Activating transcription factor-2 (ATF2) is a key determinant of resistance to endocrine treatment in an in vitro model of breast cancer

description: Additional file 4: Supplementary file 2. siATF2 MvsT_DE Genes and Pathway analysis.
DOI: 10.6084/m9.figshare.13245535
title: Additional file 3 of Sperm miRNAs— potential mediators of bull age and early embryo development

description: Additional file 3: Table S1. Total RNA extracted from bovine spermatozoa. Table S2. Differentially expressed miRNA in the two contrasts. Table S3. Dataset of targets expressed in 2-cell embryo of 10vs16 months contrast for IPA. Table S4. Dataset of targets expressed in 2-cell embryo of 12vs16 months contrast for IPA. Table S5. Dataset of targets related to 2-cell embryo competence of 10vs16 months contrast for IPA. Table S6. Dataset of targets related to 2-cell embryo competence of 12vs16 months contrast for IPA. Table S7. Dataset of targets expressed in blastocyst of 10vs16 months contrast for IPA. Table S8. Dataset of targets expressed in blastocyst of 12vs16 months contrast for IPA.
DOI: 10.6084/m9.figshare.13245607
title: Additional file 1 of Mantodea oasis of Palaearctic region: biogeographical analysis of Mantodea in Egypt

description: Additional file 1. Mantodea records of Egypt. The sheet contains 428 records of Mantodea with their coordinates and the source of each record.
DOI: 10.6084/m9.figshare.13245607.v1
title: Additional file 1 of Mantodea oasis of Palaearctic region: biogeographical analysis of Mantodea in Egypt

description: Additional file 1. Mantodea records of Egypt. The sheet contains 428 records of Mantodea with their coordinates and the source of each record.
DOI: 10.6084/m9.figshare.13245622
title: Additional file 1 of Spatial modelling improves genetic evaluation in smallholder breeding programs

description: Additional file 1. Simulation code available from https://doi.org/10.6084/m9.figshare.12403898 .
DOI: 10.6084/m9.figshare.13245622.v1
title: Additional file 1 of Spatial modelling improves genetic evaluation in smallholder breeding programs

description: Additional file 1. Simulation code available from https://doi.org/10.6084/m9.figshare.12403898 .
DOI: 10.6084/m9.figshare.13245683
title: Additional file 1 of PathoSPOT genomic epidemiology reveals under-the-radar nosocomial outbreaks

description: Additional file 1. This file contains Supplementary Table S1, which lists the bacterial genome assembly details.
DOI: 10.6084/m9.figshare.13245683.v1
title: Additional file 1 of PathoSPOT genomic epidemiology reveals under-the-radar nosocomial outbreaks

description: Additional file 1. This file contains Supplementary Table S1, which lists the bacterial genome assembly details.
DOI: 10.6084/m9.figshare.13245716.v1
title: Additional file 4 of TREM2 Alzheimer’s variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophages

description: Additional file 4 Results of RNA-seq differential gene expression analysis with DESeq2. DESeq2 output for R47H TREM2 vs WT and TREM2 KO vs WT, with gene name, relative expression (“Base Mean”), log-2-fold-change from the WT, and Benjamini-Hochberg-adjusted p values indicated.
DOI: 10.6084/m9.figshare.13245719
title: Additional file 5 of TREM2 Alzheimer’s variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophages

description: Additional file 5. Results of RNA-seq Ingenuity Pathways Analysis on TREM2 KO PPI groups. For each PPI group separate files give information about the genes assigned to that group (suffix “_Genes”), the predicted upstream regulators with Activation Z-score indicating whether the change mimics (+) or opposes (−) TREM2 KO transcriptional effects (suffix “_UpstreamAnalysis”), and the relationship of predicted upstream regulators to disease/functions (suffix “_RegulatorEffects”).
DOI: 10.6084/m9.figshare.13245694
title: Additional file 10 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

description: Additional file 10. Significant markers identified in genome wide association studies, genetic and physical position, p value, allele frequency, phenotypic effect and founder genotypes associated with 9 traits in the MAGIC population evaluated in 2013, 2014 and 2016. Favorable alleles are colored in green.
DOI: 10.6084/m9.figshare.13245716
title: Additional file 4 of TREM2 Alzheimer’s variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophages

description: Additional file 4 Results of RNA-seq differential gene expression analysis with DESeq2. DESeq2 output for R47H TREM2 vs WT and TREM2 KO vs WT, with gene name, relative expression (“Base Mean”), log-2-fold-change from the WT, and Benjamini-Hochberg-adjusted p values indicated.
DOI: 10.6084/m9.figshare.13245703
title: Additional file 13 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

description: Additional file 13. Phenotypic performance of top 10 RILs of the common bean MAGIC population and their genotypes at 12 major QTL. Phenotypic values for each of the top ten MAGIC RIL lines are shown for each trial, color coded from desirable (green) to undesirable (red) values. For each RIL line founder haplotypes for the top 12 QTL are shown together with the haplotype effects color coded from desirable (blue) to undesirable (red) QTL effects. The data mean phenotype for each parental haplotype in the main QTL and maximum and minimum trait values or haplotype effects are shown below. Letters indicate significant differences using Tukey test (α = 0.05).
DOI: 10.6084/m9.figshare.13245694.v1
title: Additional file 10 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

description: Additional file 10. Significant markers identified in genome wide association studies, genetic and physical position, p value, allele frequency, phenotypic effect and founder genotypes associated with 9 traits in the MAGIC population evaluated in 2013, 2014 and 2016. Favorable alleles are colored in green.
DOI: 10.6084/m9.figshare.13245697.v1
title: Additional file 11 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

description: Additional file 11. Details of QTL identified by interval mapping, genetic and physical position, LOD, phenotypic variation explained, and founders’ allelic effects mapped for 7 traits in the MAGIC population evaluated in 2013, 2014 and 2016.
DOI: 10.6084/m9.figshare.13245703.v1
title: Additional file 13 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

description: Additional file 13. Phenotypic performance of top 10 RILs of the common bean MAGIC population and their genotypes at 12 major QTL. Phenotypic values for each of the top ten MAGIC RIL lines are shown for each trial, color coded from desirable (green) to undesirable (red) values. For each RIL line founder haplotypes for the top 12 QTL are shown together with the haplotype effects color coded from desirable (blue) to undesirable (red) QTL effects. The data mean phenotype for each parental haplotype in the main QTL and maximum and minimum trait values or haplotype effects are shown below. Letters indicate significant differences using Tukey test (α = 0.05).
DOI: 10.6084/m9.figshare.13245719.v1
title: Additional file 5 of TREM2 Alzheimer’s variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophages

description: Additional file 5. Results of RNA-seq Ingenuity Pathways Analysis on TREM2 KO PPI groups. For each PPI group separate files give information about the genes assigned to that group (suffix “_Genes”), the predicted upstream regulators with Activation Z-score indicating whether the change mimics (+) or opposes (−) TREM2 KO transcriptional effects (suffix “_UpstreamAnalysis”), and the relationship of predicted upstream regulators to disease/functions (suffix “_RegulatorEffects”).
DOI: 10.6084/m9.figshare.13245709.v1
title: Additional file 15 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

description: Additional file 15. Significant polymorphisms in major QTL identified by both methods MLM GWAS and QTL mapping based on haplotypes that affect protein coding regions of candidate genes with moderate or high effect as defined by SnpEff (v4.3). Gene expression data added from O’Rourke et al. [105] and Phytozome.org (v12.1.6).
DOI: 10.6084/m9.figshare.13245709
title: Additional file 15 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

description: Additional file 15. Significant polymorphisms in major QTL identified by both methods MLM GWAS and QTL mapping based on haplotypes that affect protein coding regions of candidate genes with moderate or high effect as defined by SnpEff (v4.3). Gene expression data added from O’Rourke et al. [105] and Phytozome.org (v12.1.6).
DOI: 10.6084/m9.figshare.13245730
title: Additional file 7 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

description: Additional file 7. Haplotype composition of the MAGIC lines. The parental source, the length and genomic construction of each haplotype in each MAGIC line is shown, using the method proposed by Kover et al. [10].
DOI: 10.6084/m9.figshare.13245697
title: Additional file 11 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

description: Additional file 11. Details of QTL identified by interval mapping, genetic and physical position, LOD, phenotypic variation explained, and founders’ allelic effects mapped for 7 traits in the MAGIC population evaluated in 2013, 2014 and 2016.
DOI: 10.6084/m9.figshare.13245718
title: Additional file 3 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

description: Additional file 3. Phenotypic variability, least significant difference (LSD) and broad-sense heritability (H2) for best linear unbiased predictors (BLUPs) of the evaluated traits in the trials of 2013, 2014 and 2016 of the MAGIC population.
DOI: 10.6084/m9.figshare.13245718.v1
title: Additional file 3 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

description: Additional file 3. Phenotypic variability, least significant difference (LSD) and broad-sense heritability (H2) for best linear unbiased predictors (BLUPs) of the evaluated traits in the trials of 2013, 2014 and 2016 of the MAGIC population.
DOI: 10.6084/m9.figshare.13245730.v1
title: Additional file 7 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

description: Additional file 7. Haplotype composition of the MAGIC lines. The parental source, the length and genomic construction of each haplotype in each MAGIC line is shown, using the method proposed by Kover et al. [10].
DOI: 10.6084/m9.figshare.13245721
title: Additional file 4 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

description: Additional file 4. Distribution of markers per chromosome obtained from WGS of the eight founder lines. Markers from GBS of the whole population and the resulting thinned markers used to construct the genetic map for QTL analysis are listed.
DOI: 10.6084/m9.figshare.13245721.v1
title: Additional file 4 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

description: Additional file 4. Distribution of markers per chromosome obtained from WGS of the eight founder lines. Markers from GBS of the whole population and the resulting thinned markers used to construct the genetic map for QTL analysis are listed.
DOI: 10.6084/m9.figshare.13245784
title: Additional file 2 of iCLIP analysis of RNA substrates of the archaeal exosome

description: Additional file 2:. iCLIP and RNA-Seq statistics.