cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7505729
title: cluster_cell_cycle_Info_ADSCs

description: Meta data table includes information such as cell ID, nGene, nUMI, sample, cell cycle phase and cluster
DOI: 10.7284/103504
title: Multibeam Echosounder data collected during research cruise KN204-01 using a SeaBeam 3012-P1 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/103076
title: Multiplexed data collected during research cruise KN204-02 using a WHOI Calliope instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7505729.v1
title: Meta data for single-cell RNA-seq data of cultured ADSCs

description: Meta data table includes information such as cell ID, nGene, nUMI, sample, cell cycle phase and cluster
DOI: 10.6084/m9.figshare.7505720
title: Risk Analysis Research Paper.docx

description: A method is proposed for estimating the risks, safety, reliability and vulnerabiity associated with the operation of complex systems. The method represents a novel approach where graph-theoretic models used in an analysis rest on a hierarchical network of Modules, each module a model of some subsystem. It provides a complete framework for resolving all statistical dependencies and probabilistic uncertainties.In a short series of steps, the method measures the costs, elapsed times, vulnerability scores, and the overall risk, reliability and safety as a threat - or multiple threats - progress through the hierarchy.This stand-alone method is efficient and economical, consisting of at most 100 network vertices, and requiring an insignificant amount of computation time.Four support files needed to collect all the user data and to execute the method have been included with the paper, together with their Document Object Identifier (DOI) for downloading..A detailed user manual has been appended to this research document to assist and guide a user during the application of the method.
DOI: 10.6084/m9.figshare.7505732.v2
title: ADSC_scRNAseq_code.R

description: R code for processing scRNAseq data of ADSCs
DOI: 10.7284/109491
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise KN204-02 using a Hawaii UHDAS instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7505732.v3
title: ADSC_scRNAseq_code.R

description: R code for processing scRNAseq data of ADSCs
DOI: 10.7284/103505
title: Multibeam Echosounder data collected during research cruise KN204-02 using a SeaBeam 3012-P1 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7505612
title: Nie et al full list of genes in Table 2A 12-25-2018

description: Nie et al full list of genes in Table 2A 12-25-2018
DOI: 10.7284/103416
title: Multiplexed data collected during research cruise KN205 using a WHOI Calliope instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7505612.v1
title: Nie et al full list of genes in Table 2A 12-25-2018

description: Nie et al full list of genes in Table 2A 12-25-2018
DOI: 10.7284/109492
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise KN205 using a Hawaii UHDAS instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109493
title: Expendable Probe data collected during research cruise KN205 using a Sippican MK21 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7505324
title: Maternal characteristic according to tertiles of metal(loid)s

description: <b>A prospective study of early pregnancy essential trace metal(loid)s concentrations and gestational glucose levels late in the second trimester -- Supplementary table</b>
DOI: 10.7284/109494
title: Gravimeter data collected during research cruise KN205 using a Bell BGM-3 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7505252
title: Heritability and quantitative trait loci of composition and structural characteristics in sorghum grain

description: Breeding efforts in cereal crops directed toward developing or improving end-use products of grain require assessment of existing phenotypic variance and an understanding of the genetic control of grain quality traits. To this end, a grain sorghum [<i>Sorghum bicolor</i> (L.) Moench] mapping population consisting of 113 F<sub>2:7</sub> recombinant inbred lines (RILs) derived from a cross between Sureño and RTx430 was evaluated in multiple environments for grain composition (fat, fiber, protein, starch) using near-infrared reflectance spectroscopy (NIRS), and size estimates of grain parts (embryo, vitreous endosperm, floury endosperm, kernel area) using an image-based phenotyping software system. Estimates of broad-sense heritability of grain compositional traits ranged from 0.11 to 0.90, whereas those of grain size ranged from 0.16 to 0.72. Composite interval mapping (CIM) was applied to a single nucleotide polymorphism (SNP)-based linkage map to identify marker-trait associations, and through these efforts, a total of 37 quantitative trait loci (QTL) for grain quality were identified across environments. Each QTL explained between 7 and 23% of the phenotypic variation for a given grain trait. Three of the five QTL that colocalized were for traits with significant negative correlation, which included grain protein content that was negatively correlated with grain starch content. In addition, several traits that were positively correlated (e.g. fat and fiber content) also revealed colocalized QTL. Finally, we compared the present study with previous studies identifying grain composition trait loci in an effort to identify genomic regions controlling grain traits across a diversity of environments and sorghum genotypes.
DOI: 10.6084/m9.figshare.7505252.v1
title: Heritability and quantitative trait loci of composition and structural characteristics in sorghum grain

description: Breeding efforts in cereal crops directed toward developing or improving end-use products of grain require assessment of existing phenotypic variance and an understanding of the genetic control of grain quality traits. To this end, a grain sorghum [<i>Sorghum bicolor</i> (L.) Moench] mapping population consisting of 113 F<sub>2:7</sub> recombinant inbred lines (RILs) derived from a cross between Sureño and RTx430 was evaluated in multiple environments for grain composition (fat, fiber, protein, starch) using near-infrared reflectance spectroscopy (NIRS), and size estimates of grain parts (embryo, vitreous endosperm, floury endosperm, kernel area) using an image-based phenotyping software system. Estimates of broad-sense heritability of grain compositional traits ranged from 0.11 to 0.90, whereas those of grain size ranged from 0.16 to 0.72. Composite interval mapping (CIM) was applied to a single nucleotide polymorphism (SNP)-based linkage map to identify marker-trait associations, and through these efforts, a total of 37 quantitative trait loci (QTL) for grain quality were identified across environments. Each QTL explained between 7 and 23% of the phenotypic variation for a given grain trait. Three of the five QTL that colocalized were for traits with significant negative correlation, which included grain protein content that was negatively correlated with grain starch content. In addition, several traits that were positively correlated (e.g. fat and fiber content) also revealed colocalized QTL. Finally, we compared the present study with previous studies identifying grain composition trait loci in an effort to identify genomic regions controlling grain traits across a diversity of environments and sorghum genotypes.
DOI: 10.6084/m9.figshare.7505324.v1
title: Table S1.docx

description: <b>A prospective study of early pregnancy essential trace metal(loid)s concentrations and gestational glucose levels late in the second trimester -- Supplementary table</b>
DOI: 10.7284/103506
title: Multibeam Echosounder data collected during research cruise KN205 using a SeaBeam 3012-P1 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109499
title: Multiplexed data collected during research cruise KN206 using a WHOI Calliope instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109496
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise KN206 using a Hawaii UHDAS instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7505093
title: Statistical approaches in surface finishing. Part 2. non-parametric methods for data analysis

description: This paper is the second of a short series of articles aimed towards describing some of the various statistical methods and approaches that have been used in surface finishing. The methods fall broadly into two areas: analysis and design-of-experiments. In the first paper, the subject was briefly introduced followed by a discussion of parametric statistics hypothesis testing. This second paper logically continues with descriptions of the various non-parametric tests and situations where these could be applied, all within the context of surface finishing applications.
DOI: 10.7284/109495
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise KN206 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7505093.v1
title: Statistical approaches in surface finishing. Part 2. non-parametric methods for data analysis

description: This paper is the second of a short series of articles aimed towards describing some of the various statistical methods and approaches that have been used in surface finishing. The methods fall broadly into two areas: analysis and design-of-experiments. In the first paper, the subject was briefly introduced followed by a discussion of parametric statistics hypothesis testing. This second paper logically continues with descriptions of the various non-parametric tests and situations where these could be applied, all within the context of surface finishing applications.
DOI: 10.6084/m9.figshare.7504907
title: The human RNA helicase DHX37 is required for release of the U3 snoRNP from pre-ribosomal particles

description: Ribosome synthesis is an essential cellular process, and perturbation of human ribosome production is linked to cancer and genetic diseases termed ribosomopathies. During their assembly, pre-ribosomal particles undergo numerous structural rearrangements, which establish the architecture present in mature complexes and serve as key checkpoints, ensuring the fidelity of ribosome biogenesis. RNA helicases are essential mediators of such remodelling events and here, we demonstrate that the DEAH-box RNA helicase DHX37 is required for maturation of the small ribosomal subunit in human cells. Our data reveal that the presence of DHX37 in early pre-ribosomal particles is monitored by a quality control pathway and that failure to recruit DHX37 leads to pre-rRNA degradation. Using an <i>in vivo</i> crosslinking approach, we show that DHX37 binds directly to the U3 small nucleolar RNA (snoRNA) and demonstrate that the catalytic activity of the helicase is required for dissociation of the U3 snoRNA from pre-ribosomal complexes. This is an important event during ribosome assembly as it enables formation of the central pseudoknot structure of the small ribosomal subunit. We identify UTP14A as a direct interaction partner of DHX37 and our data suggest that UTP14A can act as a cofactor that stimulates the activity of the helicase in the context of U3 snoRNA release.
DOI: 10.6084/m9.figshare.7504907.v1
title: The human RNA helicase DHX37 is required for release of the U3 snoRNP from pre-ribosomal particles

description: Ribosome synthesis is an essential cellular process, and perturbation of human ribosome production is linked to cancer and genetic diseases termed ribosomopathies. During their assembly, pre-ribosomal particles undergo numerous structural rearrangements, which establish the architecture present in mature complexes and serve as key checkpoints, ensuring the fidelity of ribosome biogenesis. RNA helicases are essential mediators of such remodelling events and here, we demonstrate that the DEAH-box RNA helicase DHX37 is required for maturation of the small ribosomal subunit in human cells. Our data reveal that the presence of DHX37 in early pre-ribosomal particles is monitored by a quality control pathway and that failure to recruit DHX37 leads to pre-rRNA degradation. Using an <i>in vivo</i> crosslinking approach, we show that DHX37 binds directly to the U3 small nucleolar RNA (snoRNA) and demonstrate that the catalytic activity of the helicase is required for dissociation of the U3 snoRNA from pre-ribosomal complexes. This is an important event during ribosome assembly as it enables formation of the central pseudoknot structure of the small ribosomal subunit. We identify UTP14A as a direct interaction partner of DHX37 and our data suggest that UTP14A can act as a cofactor that stimulates the activity of the helicase in the context of U3 snoRNA release.
DOI: 10.7284/109497
title: Expendable Probe data collected during research cruise KN206 using a Sippican MK21 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109498
title: Gravimeter data collected during research cruise KN206 using a Bell BGM-3 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504922.v1
title: Transcriptional dynamics of microRNAs and their targets during Drosophila neurogenesis

description: During <i>Drosophila melanogaster</i> embryogenesis, tight regulation of gene expression in time and space is required for the orderly emergence of specific cell types. While the general importance of microRNAs in regulating eukaryotic gene expression has been well-established, their role in early neurogenesis remains to be addressed. In this survey, we investigate the transcriptional dynamics of microRNAs and their target transcripts during neurogenesis of <i>Drosophila melanogaster</i> . To this end, we use the recently developed <i>DIV-MARIS</i> protocol, a method for enriching specific cell types from the <i>Drosophila</i> embryo <i>in vivo</i>, to sequence cell-type-specific transcriptomes. We generate dedicated small and total RNA-seq libraries for neuroblasts, neurons and glia cells at early (6–8 h after egg laying (AEL)) and late (18–22 h AEL) stage. This allows us to directly compare these transcriptomes and investigate the potential functional roles of individual microRNAs with spatio-temporal resolution genome-wide, which is beyond the capabilities of existing <i>in-situ</i> hybridization studies. Overall, we identify 74 microRNAs that are significantly differentially expressed between the three cell types and the two developmental stages. In all cell types, predicted target genes of down-regulated microRNAs show a significant enrichment of their target genes related to neurogenesis. We also investigate how microRNAs regulate the transcriptome by targeting transcription factors and find many candidate microRNAs with putative roles in neurogenesis. Our survey highlights the roles of miRNAs as regulators of differentiation and glioneurognesis in the fruit fly and provides distinct starting points for dedicated functional follow-up studies.
DOI: 10.7284/109500
title: Multibeam Echosounder data collected during research cruise KN206 using a SeaBeam 3012-P1 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504922.v2
title: Transcriptional dynamics of microRNAs and their targets during Drosophila neurogenesis

description: During <i>Drosophila melanogaster</i> embryogenesis, tight regulation of gene expression in time and space is required for the orderly emergence of specific cell types. While the general importance of microRNAs in regulating eukaryotic gene expression has been well-established, their role in early neurogenesis remains to be addressed. In this survey, we investigate the transcriptional dynamics of microRNAs and their target transcripts during neurogenesis of <i>Drosophila melanogaster</i>. To this end, we use the recently developed <i>DIV-MARIS</i> protocol, a method for enriching specific cell types from the <i>Drosophila</i> embryo <i>in vivo</i>, to sequence cell type-specific transcriptomes. We generate dedicated small and total RNA-seq libraries for neuroblasts, neurons and glia cells at early (6–8 h after egg laying (AEL)) and late (18–22 h AEL) stage. This allows us to directly compare these transcriptomes and investigate the potential functional roles of individual microRNAs with spatiotemporal resolution genome-wide, which is beyond the capabilities of existing <i>in situ</i> hybridization methods. Overall, we identify 74 microRNAs that are significantly differentially expressed between the three cell types and the two developmental stages. In all cell types, predicted target genes of down-regulated microRNAs show a significant enrichment of Gene Ontology terms related to neurogenesis. We also investigate how microRNAs regulate the transcriptome by targeting transcription factors and find many candidate microRNAs with putative roles in neurogenesis. Our survey highlights the roles of microRNAs as regulators of differentiation and glioneurognesis in the fruit fly and provides distinct starting points for dedicated functional follow-up studies.
DOI: 10.7284/106820
title: Multiplexed data collected during research cruise KN207-01 using a WHOI Calliope instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109502
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise KN207-01 using a Hawaii UHDAS instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109501
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise KN207-01 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504757
title: Communicative signaling of occupational fitness: How innovative ability is expressed and assessed

description: This study investigates how individuals working in the innovation field communicatively define the nature of their work and make assessments of others’ innovative ability. Drawing on signaling theory, this work explores what communicative signals are valued within an ambiguous professional context. Interviews with 36 innovation workers revealed that individuals perceive this emerging occupational role as comprised of skills and traits that vary in how easily they are communicatively expressed, and in turn what forms of communication allow these dimensions to be evaluated. These findings inform the development of a grounded model for communicatively assessing innovative ability. This work extends our theoretical understanding of how signals of professionalism are actively, and communicatively expressed and assessed in new occupational settings.
DOI: 10.6084/m9.figshare.7504757.v1
title: Communicative signaling of occupational fitness: How innovative ability is expressed and assessed

description: This study investigates how individuals working in the innovation field communicatively define the nature of their work and make assessments of others’ innovative ability. Drawing on signaling theory, this work explores what communicative signals are valued within an ambiguous professional context. Interviews with 36 innovation workers revealed that individuals perceive this emerging occupational role as comprised of skills and traits that vary in how easily they are communicatively expressed, and in turn what forms of communication allow these dimensions to be evaluated. These findings inform the development of a grounded model for communicatively assessing innovative ability. This work extends our theoretical understanding of how signals of professionalism are actively, and communicatively expressed and assessed in new occupational settings.
DOI: 10.7284/109503
title: Gravimeter data collected during research cruise KN207-01 using a Bell BGM-3 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504748
title: Metabolite BridgeDb ID Mapping Database (20181224)

description: BridgeDb ID mapping database for metabolites, using HMDB 4.0 (Release of 29-09-2018), ChEBI 170 (Release of 03 Dec. 2018), and Wikidata (24 Dec. 2018) as data sources.<br>Several updated mappings, with additional test to eliminate double mappings in WikiPathways (from Wikidata to any other type of included database) and additional test cases in the test pathway from WikiPathways (https://www.wikipathways.org/index.php/Pathway:WP2582).<br><i>This work was funded by ELIXIR, the research infrastructure for life-science data.</i>
DOI: 10.7284/106805
title: Multibeam Echosounder data collected during research cruise KN207-01 using a SeaBeam 3012-P1 instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106821
title: Multiplexed data collected during research cruise KN207-02 using a WHOI Calliope instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109504
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise KN207-02 using a Hawaii UHDAS instrument system onboard the platform RV Knorr

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7504715
title: Three-way interaction model with switching mechanism as an effective strategy for tracing functionally-related genes

description: <b>Introduction</b>: Identification of functionally-related genes is an important step in understanding biological systems. The most popular strategy to infer functional dependence is to study pairwise correlations between gene expression levels. However, certain functionally-related genes may have a low expression correlation due to their nonlinear interactions. The use of a three-way interaction (3WI) model with switching mechanism (SM) is a relatively new strategy to trace functionally-related genes. The 3WI model traces the dynamic and nonlinear nature of the co-expression relationship of two genes by introducing their link to the expression level of a third gene. <b>Areas covered</b>: In this paper, we reviewed a variety of existing methods for tracing the 3WIs. Furthermore, we provide a comprehensive review of the previous biological studies based on 3WI models. <b>Expert commentary</b>: Comparison of features of these methods indicates that the modified liquid association algorithm has the best efficiency for tracing 3WI between others. The limited number of biological studies based on the 3WI suggests that high computational demand of the available algorithms is a major challenge to apply this approach for analyzing high-throughput omics data.