cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7873247.v1
title: Regional patterns of anthropogenic influences on streams and rivers in the conterminous United States, from the early 1970s to 2012

description: This paper introduces a dataset containing consistent time-series measurements of anthropogenic activities potentially affecting stream quality across the conterminous United States and summarizes the most noteworthy trends from 61 variables in 16 categories. Data include measures of atmospheric deposition, agricultural production, livestock, urbanization, irrigation, land use, nutrients from fertilizer, dams/reservoirs, and pesticide use, among others. The trend periods range from 10 to 40 years, beginning as early as 1970 and ending in 2012. Detailed summaries are provided for 1992-2012. Key results include: increase of urbanization and ‘exurbanization’, particularly in the South, Southwest, and Mid-Atlantic; increases in crop production and fertilizer use in much of the Midwest; increases in the concentration of livestock, particularly of hogs/pigs; increases in irrigation, dams, and reservoirs in the Lower Mississippi and Lower Missouri watersheds, widespread increase in the use of the pesticide glyphosate; and widespread decrease in atmospheric deposition of sulfate. These results and others provide a framework for evaluating potential causes of water-quality changes over the past four decades.
DOI: 10.6084/m9.figshare.7873274.v1
title: Mtb and Msm PepNs share high degree of sequence identity.pdf

description: Mtb and Msm PepNs share high degree of sequence identity<br>
DOI: 10.6084/m9.figshare.7873175
title: Chromosome 19 human fasta sequence

description: Chromosome 19 fasta sequencehg38Corresponds to hsa gencode v 29
DOI: 10.6084/m9.figshare.7873175.v1
title: Untitled Item

description: Annotation for chromosome 19
DOI: 10.6084/m9.figshare.7873157
title: High resolution paddy rice maps in cloud-prone Bangladesh and Northeast India using Sentinel-1 data

description: Sentinel-1 SAR- based paddy rice maps for Bangladesh and Northeast India for 2017
DOI: 10.6084/m9.figshare.7873166
title: gencode.v29.primary_assembly.annotation.chr19.gtf.gz

description: Gencode 29 primary annotation from gencode, subset of only human chromosome 19. Annotation gtf
DOI: 10.6084/m9.figshare.7873166.v1
title: gencode.v29.primary_assembly.annotation.chr19.gtf.gz

description: Gencode 29 primary annotation from gencode, subset of only human chromosome 19. Annotation gtf
DOI: 10.6084/m9.figshare.7873175.v3
title: Chromosome 19 human annotations

description: Annotation for chromosome 19
DOI: 10.6084/m9.figshare.7873076
title: MOESM1 of A new seismic survey technology using underwater speaker detected a low-velocity zone near the seafloor: an implication of methane gas accumulation in Tokyo Bay

description: Additional file 1. Seismic reflection data shown in Fig. 2b are available as the additional file with CSV format.
DOI: 10.6084/m9.figshare.7873076.v1
title: MOESM1 of A new seismic survey technology using underwater speaker detected a low-velocity zone near the seafloor: an implication of methane gas accumulation in Tokyo Bay

description: Additional file 1. Seismic reflection data shown in Fig. 2b are available as the additional file with CSV format.
DOI: 10.6084/m9.figshare.7873052
title: Additional file 1: of Inhibition of extracellular proteases improves the production of a xylanase in Parageobacillus thermoglucosidasius

description: Secretory proteins encoded by the genome of P. thermoglucosidasius C56-YS93. Sheet 1: List of secretory proteins, identified by bioinformatics. Sheet 2: List of secretory proteins identified using both bioinformatics and mass spectrometry of the extracellular proteome. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7873052.v1
title: Additional file 1: of Inhibition of extracellular proteases improves the production of a xylanase in Parageobacillus thermoglucosidasius

description: Secretory proteins encoded by the genome of P. thermoglucosidasius C56-YS93. Sheet 1: List of secretory proteins, identified by bioinformatics. Sheet 2: List of secretory proteins identified using both bioinformatics and mass spectrometry of the extracellular proteome. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7873040
title: Additional file 3: of Generation and maintenance of acentric stable double minutes from chromosome arms in inter-species hybrid cells

description: Figure S3. Plots of raw data obtained from microarray analysis using human CytoScanâ ˘ HD Arrays. Data obtained from the analysis using the PartekÂŽ Genomics SuiteÂŽ software was plotted in Excel. X-axis represents position along each chromosome, and each plot coincides the start position of the data. Y-axis represents copy number per cell; normal human genomic DNA and MEF acceptor cells were used as standards to evaluate amplification in COLO 320DM donor cells and each individual clone, respectively. (ZIP 3629 kb)
DOI: 10.6084/m9.figshare.7873040.v1
title: Additional file 3: of Generation and maintenance of acentric stable double minutes from chromosome arms in inter-species hybrid cells

description: Figure S3. Plots of raw data obtained from microarray analysis using human CytoScanâ ˘ HD Arrays. Data obtained from the analysis using the PartekÂŽ Genomics SuiteÂŽ software was plotted in Excel. X-axis represents position along each chromosome, and each plot coincides the start position of the data. Y-axis represents copy number per cell; normal human genomic DNA and MEF acceptor cells were used as standards to evaluate amplification in COLO 320DM donor cells and each individual clone, respectively. (ZIP 3629 kb)
DOI: 10.6084/m9.figshare.7872968
title: Additional file 1: of Analyzing the 3D chromatin organization coordinating with gene expression regulation in B-cell lymphoma

description: This file includes: detailed information from data used, including statistical information of reads and mapping process in RNA-seq and Hi-C analysis (Table S1-S4), gene expression values from heatmap in Additional file 2: Figure S4 (Table S5), gene ontology analysis detailed results (Table S6-S9). (XLSX 85 kb)
DOI: 10.6084/m9.figshare.7872974
title: Additional file 6: of Indication of metabolic inflexibility to food intake in spontaneously overweight Labrador Retriever dogs

description: Phospholipid dataset (nM), n = 118. (XLSX 238 kb)
DOI: 10.6084/m9.figshare.7872965
title: Additional file 5: of Indication of metabolic inflexibility to food intake in spontaneously overweight Labrador Retriever dogs

description: Metabolite dataset (signal areas), n = 6. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7872968.v1
title: Additional file 1: of Analyzing the 3D chromatin organization coordinating with gene expression regulation in B-cell lymphoma

description: This file includes: detailed information from data used, including statistical information of reads and mapping process in RNA-seq and Hi-C analysis (Table S1-S4), gene expression values from heatmap in Additional file 2: Figure S4 (Table S5), gene ontology analysis detailed results (Table S6-S9). (XLSX 85 kb)
DOI: 10.6084/m9.figshare.7872974.v1
title: Additional file 6: of Indication of metabolic inflexibility to food intake in spontaneously overweight Labrador Retriever dogs

description: Phospholipid dataset (nM), n = 118. (XLSX 238 kb)
DOI: 10.6084/m9.figshare.7872965.v1
title: Additional file 5: of Indication of metabolic inflexibility to food intake in spontaneously overweight Labrador Retriever dogs

description: Metabolite dataset (signal areas), n = 6. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7872926
title: Additional file 4: of FitTetra 2.0 â improved genotype calling for tetraploids with multiple population and parental data support

description: An R script containing all the code needed to run comparison between ClusterCall and fitTetra 2.0 on the dataset attached to the ClusterCall manuscript. (R 6 kb)
DOI: 10.6084/m9.figshare.7872920
title: Additional file 3: of FitTetra 2.0 â improved genotype calling for tetraploids with multiple population and parental data support

description: An R script containing all the code needed to run comparison between ClusterCall and fitTetra 2.0 on the dataset attached to fitTetra 2.0. (R 3 kb)
DOI: 10.6084/m9.figshare.7872920.v1
title: Additional file 3: of FitTetra 2.0 â improved genotype calling for tetraploids with multiple population and parental data support

description: An R script containing all the code needed to run comparison between ClusterCall and fitTetra 2.0 on the dataset attached to fitTetra 2.0. (R 3 kb)
DOI: 10.6084/m9.figshare.7872926.v1
title: Additional file 4: of FitTetra 2.0 â improved genotype calling for tetraploids with multiple population and parental data support

description: An R script containing all the code needed to run comparison between ClusterCall and fitTetra 2.0 on the dataset attached to the ClusterCall manuscript. (R 6 kb)
DOI: 10.6084/m9.figshare.7872908
title: Additional file 2: of FitTetra 2.0 â improved genotype calling for tetraploids with multiple population and parental data support

description: A zip archive containing all the data and code needed to run the comparisons. (ZIP 33420 kb)
DOI: 10.6084/m9.figshare.7872899
title: Additional file 1: of FitTetra 2.0 â improved genotype calling for tetraploids with multiple population and parental data support

description: A tar archive containing fitTetra 2.0 package. (GZ 46494 kb)
DOI: 10.6084/m9.figshare.7872908.v1
title: Additional file 2: of FitTetra 2.0 â improved genotype calling for tetraploids with multiple population and parental data support

description: A zip archive containing all the data and code needed to run the comparisons. (ZIP 33420 kb)
DOI: 10.6084/m9.figshare.7872899.v1
title: Additional file 1: of FitTetra 2.0 â improved genotype calling for tetraploids with multiple population and parental data support

description: A tar archive containing fitTetra 2.0 package. (GZ 46494 kb)
DOI: 10.6084/m9.figshare.7872821
title: Additional file 3: of On and off the rocks: persistence and ecological diversification in a tropical Australian lizard radiation

description: Appendix 1. Full list of samples included in genetic and morphological analyses inlcuding GenBank accession details. Samples which were assigned to genetic lineages based on locality (no DNA) are indicated with an asterisk. (XLSX 135 kb)
DOI: 10.6084/m9.figshare.7872824
title: MOESM3 of Construction of a large-scale semi-field facility to study genotypic differences in deep root growth and resources acquisition

description: Additional file 3. Two-way ANOVA model output of biomass and root data from the 2017 season including the effect of the unit in the analysis.
DOI: 10.6084/m9.figshare.7872815
title: Additional file 2: of On and off the rocks: persistence and ecological diversification in a tropical Australian lizard radiation

description: Distribution of sampling (in kmz file format) for generalist taxa in the G. australis group in this paper. (KMZ 8 kb)
DOI: 10.6084/m9.figshare.7872818
title: MOESM2 of Construction of a large-scale semi-field facility to study genotypic differences in deep root growth and resources acquisition

description: Additional file 2. Texture and chemical properties of top and subsoil in each unit of the RadiMax facility (Fine soil fraction
DOI: 10.6084/m9.figshare.7872821.v1
title: Additional file 3: of On and off the rocks: persistence and ecological diversification in a tropical Australian lizard radiation

description: Appendix 1. Full list of samples included in genetic and morphological analyses inlcuding GenBank accession details. Samples which were assigned to genetic lineages based on locality (no DNA) are indicated with an asterisk. (XLSX 135 kb)
DOI: 10.6084/m9.figshare.7872824.v1
title: MOESM3 of Construction of a large-scale semi-field facility to study genotypic differences in deep root growth and resources acquisition

description: Additional file 3. Two-way ANOVA model output of biomass and root data from the 2017 season including the effect of the unit in the analysis.
DOI: 10.6084/m9.figshare.7872818.v1
title: MOESM2 of Construction of a large-scale semi-field facility to study genotypic differences in deep root growth and resources acquisition

description: Additional file 2. Texture and chemical properties of top and subsoil in each unit of the RadiMax facility (Fine soil fraction
DOI: 10.6084/m9.figshare.7872806
title: Additional file 1: of On and off the rocks: persistence and ecological diversification in a tropical Australian lizard radiation

description: Distribution of sampling (in kmz file format) for saxicoline taxa in the G. australis group in this paper. (KMZ 6 kb)
DOI: 10.6084/m9.figshare.7872815.v1
title: Additional file 2: of On and off the rocks: persistence and ecological diversification in a tropical Australian lizard radiation

description: Distribution of sampling (in kmz file format) for generalist taxa in the G. australis group in this paper. (KMZ 8 kb)
DOI: 10.6084/m9.figshare.7872806.v1
title: Additional file 1: of On and off the rocks: persistence and ecological diversification in a tropical Australian lizard radiation

description: Distribution of sampling (in kmz file format) for saxicoline taxa in the G. australis group in this paper. (KMZ 6 kb)
DOI: 10.6084/m9.figshare.7872779
title: MOESM1 of Functional and transcriptomic characterization of carboplatin-resistant A2780 ovarian cancer cell line

description: Additional file 1: Table S1. Gene list of 156 transcripts.
DOI: 10.6084/m9.figshare.7872779.v1
title: MOESM1 of Functional and transcriptomic characterization of carboplatin-resistant A2780 ovarian cancer cell line

description: Additional file 1: Table S1. Gene list of 156 transcripts.
DOI: 10.6084/m9.figshare.7872731
title: Additional file 1: of PMAMCA: prediction of microRNA-disease association utilizing a matrix completion approach

description: Table S1. Notation. Table S2. Top-50 candidate miRNAs for breast cancer predicted by PMAMCA. Table S3. Top-50 candidate miRNAs for lung cancer predicted by PMAMCA. Table S4. List of validated cancer hallmark-based signature and their genes. Table S5. List of confirmed driver and passenger genes. (additional experimental result) Table S6. Top-50 candidate miRNAs for colon cancer predicted by PMAMCA. (additional experimental result). Figure S1. The workflow for prioritizing candidate miRNAs. Figure S2. Applying matrix factorization into miRNA-disease association extraction. Figure S3. Performance comparisons between PMAMCA and four state-of-the-art methods. Figure S4. Performance of PMAMCA with different values of k. Figure S5. Numbers of correctly retrieved known disease-related miRNAs for various rank thresholds. (ZIP 2223 kb)
DOI: 10.6084/m9.figshare.7872731.v1
title: Additional file 1: of PMAMCA: prediction of microRNA-disease association utilizing a matrix completion approach

description: Table S1. Notation. Table S2. Top-50 candidate miRNAs for breast cancer predicted by PMAMCA. Table S3. Top-50 candidate miRNAs for lung cancer predicted by PMAMCA. Table S4. List of validated cancer hallmark-based signature and their genes. Table S5. List of confirmed driver and passenger genes. (additional experimental result) Table S6. Top-50 candidate miRNAs for colon cancer predicted by PMAMCA. (additional experimental result). Figure S1. The workflow for prioritizing candidate miRNAs. Figure S2. Applying matrix factorization into miRNA-disease association extraction. Figure S3. Performance comparisons between PMAMCA and four state-of-the-art methods. Figure S4. Performance of PMAMCA with different values of k. Figure S5. Numbers of correctly retrieved known disease-related miRNAs for various rank thresholds. (ZIP 2223 kb)
DOI: 10.25345/c5wt98
title: MassIVE MSV000086028 - 1_HILIC LC MS_MS of 244 fecal samples of infants_part I
title: Sillner et al. : Longitudinal profiles of dietary and microbial metabolites in formula- and breastfed infants - https://doi.org/10.1101/2020.05.11.086546 HILIC LC-MS/MS for generating non-targeted metabolomics data of 244 fecal samples of infants during first year of life and a follow-up (24 month) Data dependent AutoMSMS function of maXis in negative ionisation mode with 10eV collision energy
DOI: 10.6084/m9.figshare.7872560
title: gVCF_HG00154

description: 1000 Genomes gVCF mapped to hs37d5 for HG00154.
DOI: 10.6084/m9.figshare.7872560.v1
title: gVCF_HG00154

description: 1000 Genomes gVCF mapped to hs37d5 for HG00154.
DOI: 10.6084/m9.figshare.7872515
title: gVCF_HG00149

description: 1000 Genomes gVCF mapped to hs37d5 for HG00149.
DOI: 10.6084/m9.figshare.7872524
title: gVCF_HG00150

description: 1000 Genomes gVCF mapped to hs37d5 for HG00150.
DOI: 10.6084/m9.figshare.7872551
title: gVCF_HG00151

description: 1000 Genomes gVCF mapped to hs37d5 for HG00151.
DOI: 10.6084/m9.figshare.7872515.v1
title: gVCF_HG00149

description: 1000 Genomes gVCF mapped to hs37d5 for HG00149.
DOI: 10.6084/m9.figshare.7872524.v1
title: gVCF_HG00150

description: 1000 Genomes gVCF mapped to hs37d5 for HG00150.
DOI: 10.6084/m9.figshare.7872551.v1
title: gVCF_HG00151

description: 1000 Genomes gVCF mapped to hs37d5 for HG00151.
DOI: 10.6084/m9.figshare.7872584.v1
title: Transcriptome profiling reveals association of peripheral adipose tissue pathology with type-2 diabetes in asian Indians

description: Type 2 Diabetes (T2D) is a complex disease with an elusive link between its molecular etiology and clinical presentation. Although, the role of visceral adipose tissue in the pathogenesis of insulin resistance and T2D is well known, only a limited information is available on the role of peripheral subcutaneous adipose tissue especiallyin Asian Indians. In this microarray based study of diabetic and normal glucose tolerant (NGT) Asian Indians, we generated the transcription profile of their thigh subcutaneous adipose tissue and further analyzed the diffrentially expressed genes (DEGs) using weighted gene co-expression network analysis (WGCNA) approach. Through WGCNA, we identified the perturbed pathways implicated by these DEGs in relevant co-expression modules by using a topology-based enrichment method. We also attempted to link these pathways with known aspects of T2D pathophysiology in terms of their association with some of their intermediate traits, namely; clinical diagnosis of diabetes, adipocyte size, HOMA-B, and HOMA-R, glycated hemoglobin (Hb1Ac), insulin, glocose level, proinflamatory markers – TNF-α, IL-6, lipid profile markers – Very Low Density Lipids (VLDL), Low Density Lipids (LDL), High Density Lipids (HDL), and Non Esterified Fatty Acids (NEFA). It was observed in this study that several modules of co-expressed genes show an association with diabetes and some of its intermediate phenotypic traits mentioned above. Therefore, these findings suggest a role of peripheral subcutaneous adipose tissue in the pathophsiology of T2D in Asian Indians. Additionally, our study indicated that the peripheral subcutaneous adipose tissue in diabetics shows pathologic changes characterized by adipocyte hypertrophy and upregulation of inflammation related pathways. Graphical Abstract
DOI: 10.6084/m9.figshare.7872407
title: gVCF_HG00146

description: 1000 Genomes gVCF mapped to hs37d5 for HG00146.
DOI: 10.6084/m9.figshare.7872449
title: gVCF_HG00148

description: 1000 Genomes gVCF mapped to hs37d5 for HG00148.
DOI: 10.6084/m9.figshare.7872407.v1
title: gVCF_HG00146

description: 1000 Genomes gVCF mapped to hs37d5 for HG00146.
DOI: 10.6084/m9.figshare.7872449.v1
title: gVCF_HG00148

description: 1000 Genomes gVCF mapped to hs37d5 for HG00148.
DOI: 10.6084/m9.figshare.7872584.v2
title: Transcriptome profiling reveals association of peripheral adipose tissue pathology with type-2 diabetes in Asian Indians

description: Type 2 diabetes (T2D) is a complex disease with an elusive link between its molecular aetiology and clinical presentation. Although, the role of visceral adipose tissue in insulin-resistance and T2D is known, limited information is available on the role of peripheral-subcutaneous adipose tissue especially in Asian Indians. In this microarray-based study of diabetic and normal glucose tolerant Asian Indians, we generated the transcriptome of their thigh adipose tissue and analyzed differentially expressed genes (DEGs) using weighted gene co-expression network analysis; further we identified perturbed pathways implicated by these DEGs in relevant co-expression modules. We also attempted to link these pathways with known aspects of T2D pathophysiology in terms of their association with some of their intermediate traits, namely; adipocyte size, HOMA-B, HOMA-R, Hb1Ac, insulin, glucose-level, TNF-α, IL-6, VLDLs, LDLs, HDLs, and NEFAs. It was observed that several modules of co-expressed genes show an association with diabetes and some of its intermediate phenotypic traits mentioned above. Therefore, these findings suggest a role of peripheral subcutaneous adipose tissue in the pathophsiology of T2D in Asian Indians. Additionally, our study indicated that the peripheral subcutaneous adipose tissue in diabetics shows pathologic changes characterized by adipocyte hypertrophy and up-regulation of inflammation-related pathways.
DOI: 10.6084/m9.figshare.7872332
title: gVCF_HG00233

description: 1000 Genomes gVCF mapped to hs37d5 for HG00233.
DOI: 10.6084/m9.figshare.7872344
title: gVCF_HG00145

description: 1000 Genomes gVCF mapped to hs37d5 for HG00145.
DOI: 10.6084/m9.figshare.7872344.v1
title: gVCF_HG00145

description: 1000 Genomes gVCF mapped to hs37d5 for HG00145.
DOI: 10.6084/m9.figshare.7872239
title: gVCF_HG00143

description: 1000 Genomes gVCF mapped to hs37d5 for HG00143.
DOI: 10.6084/m9.figshare.7872239.v1
title: gVCF_HG00143

description: 1000 Genomes gVCF mapped to hs37d5 for HG00143.
DOI: 10.6084/m9.figshare.7872242
title: Right Heart Catheterization During Exercise in Patients with COPD—An Overview of Clinical Results and Methodological Aspects

description: While right heart catheterization (RHC) at rest is the gold standard to assess pulmonary hemodynamics in patients with chronic obstructive pulmonary disease (COPD) and pulmonary hypertension (PH), the invasive measurement of exercise hemodynamics is less well established in this group. Since exercise hemodynamics are increasingly recognized as important clinical information in patients with PH, our goal was to review the literature in this field to provide a basis for clinical use, further studies, and future recommendations. We identified 69 studies (published since 1968) reporting RHC data in 2819 patients with COPD, of whom 2561 underwent exercise testing. Few studies simultaneously measured gas exchange during exercise. Overall, these studies showed large variations in the patient populations and research questions studied and the methods and definitions employed. Despite these limitations, the data consistently demonstrated the presence of precapillary PH at rest in up to 38% of patients with COPD. With exercise, a relevant proportion of patients developed an abnormal hemodynamic response, depending on the definition used. Furthermore, some studies assessed right ventricular function during exercise and showed a blunted increase in right ventricular ejection fraction. Drug effects and the impact of interventional procedures were also studied. Again, due to large variations in the patients studied and the methods used, firm conclusions are difficult to derive. Despite the limitations of this dataset, several recommendations with respect to technical aspects (body position, exercise protocol, and data acquisition) can be inferred for this challenging patient population and may be helpful for further studies or recommendations.
DOI: 10.6084/m9.figshare.7872269
title: gVCF_HG00232

description: 1000 Genomes gVCF mapped to hs37d5 for HG00232.
DOI: 10.6084/m9.figshare.7872269.v1
title: gVCF_HG00232

description: 1000 Genomes gVCF mapped to hs37d5 for HG00232.
DOI: 10.6084/m9.figshare.7872332.v1
title: gVCF_HG00233

description: 1000 Genomes gVCF mapped to hs37d5 for HG00233.
DOI: 10.6084/m9.figshare.7872230
title: gVCF_HG00190

description: 1000 Genomes gVCF mapped to hs37d5 for HG00190.
DOI: 10.6084/m9.figshare.7872233
title: gVCF_HG00142

description: 1000 Genomes gVCF mapped to hs37d5 for HG00142.