cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5643484
title: Additional file 2 Table S2. of A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

description: List of genera binned by aerotolerance. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5643484.v1
title: Additional file 2 Table S2. of A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

description: List of genera binned by aerotolerance. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5643475
title: Additional file 4: of RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars

description: High quality SNPs occurring in differentially expressed genes in Duroc. The SNPs are presented with Ensembl gene id, gene name, significance level (FDR) of differentially expressed gene, chromosome (SSC), position, reference allele and alternate allele, as well as effect, impact according to SnpEff and dbSNP ID. (XLSX 117 kb)
DOI: 10.6084/m9.figshare.5643475.v1
title: Additional file 4: of RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars

description: High quality SNPs occurring in differentially expressed genes in Duroc. The SNPs are presented with Ensembl gene id, gene name, significance level (FDR) of differentially expressed gene, chromosome (SSC), position, reference allele and alternate allele, as well as effect, impact according to SnpEff and dbSNP ID. (XLSX 117 kb)
DOI: 10.6084/m9.figshare.5643454
title: Additional file 1: Table S1. of A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

description: Clinical metadata for samples collected at Massachusetts General Hospital. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.5643454.v1
title: Additional file 1: Table S1. of A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

description: Clinical metadata for samples collected at Massachusetts General Hospital. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.5643451
title: MOESM2 of Optimization of quantitative proteomic analysis of clots generated from plasma of patients with venous thromboembolism

description: Additional file 2: Table 2. The list of proteins identified by MaxQuant software in plasma fibrin clots from patients with VTE, which were measured using pipet-tip strong anion exchange (SAX) protocol combined with LC-MS/MS and Total Protein Approach (TPA) (n = 4 per group)
DOI: 10.6084/m9.figshare.5643451.v1
title: MOESM2 of Optimization of quantitative proteomic analysis of clots generated from plasma of patients with venous thromboembolism

description: Additional file 2: Table 2. The list of proteins identified by MaxQuant software in plasma fibrin clots from patients with VTE, which were measured using pipet-tip strong anion exchange (SAX) protocol combined with LC-MS/MS and Total Protein Approach (TPA) (n = 4 per group)
DOI: 10.6084/m9.figshare.5643448
title: Additional file 3: of RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars

description: High quality SNPs occurring in differentially expressed genes in Landrace. The SNPs are presented with Ensembl gene id, gene name, FDR value of differentially expressed gene, chromosome (SSC), position, reference allele and alternate allele, as well as effect, impact according to SnpEff and dbSNP ID. (XLSX 100 kb)
DOI: 10.6084/m9.figshare.5643448.v1
title: Additional file 3: of RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars

description: High quality SNPs occurring in differentially expressed genes in Landrace. The SNPs are presented with Ensembl gene id, gene name, FDR value of differentially expressed gene, chromosome (SSC), position, reference allele and alternate allele, as well as effect, impact according to SnpEff and dbSNP ID. (XLSX 100 kb)
DOI: 10.6084/m9.figshare.5643439
title: Additional file 1 of Predicting cancer type from tumour DNA signatures

description: Shown are 50 genes selected via stability selection. A list of 50 genes that are most frequently ranked highly by SVM-RFE, their brief descriptions and whether they have been identified as cancer driver genes. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.5643439.v1
title: Additional file 1 of Predicting cancer type from tumour DNA signatures

description: Shown are 50 genes selected via stability selection. A list of 50 genes that are most frequently ranked highly by SVM-RFE, their brief descriptions and whether they have been identified as cancer driver genes. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.12739160.v2
title: Data about power and gas system.xlsx

description: The attahed file includes the data of a coupled electric and gas networks for 5 cases.
DOI: 10.6084/m9.figshare.5643430
title: Additional file 2: of RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars

description: Differentially expressed genes for DFI in Duroc. The results are presented with Ensembl gene id, gene symbol, gene name, fold change and significance level (FDR). (XLSX 34 kb)
DOI: 10.6084/m9.figshare.5643430.v1
title: Additional file 2: of RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars

description: Differentially expressed genes for DFI in Duroc. The results are presented with Ensembl gene id, gene symbol, gene name, fold change and significance level (FDR). (XLSX 34 kb)
DOI: 10.6084/m9.figshare.5643424
title: MOESM1 of Optimization of quantitative proteomic analysis of clots generated from plasma of patients with venous thromboembolism

description: Additional file 1: Table 1. The list of proteins identified by MaxQuant software in plasma fibrin clots from patients with VTE, which were measured using MED FASP (LysC + Typsin + Chymotrypsin) method combined with LC-MS/MS and Total Protein Approach (TPA) (n = 4 per group)
DOI: 10.6084/m9.figshare.5643424.v1
title: MOESM1 of Optimization of quantitative proteomic analysis of clots generated from plasma of patients with venous thromboembolism

description: Additional file 1: Table 1. The list of proteins identified by MaxQuant software in plasma fibrin clots from patients with VTE, which were measured using MED FASP (LysC + Typsin + Chymotrypsin) method combined with LC-MS/MS and Total Protein Approach (TPA) (n = 4 per group)
DOI: 10.6084/m9.figshare.5643412
title: Additional file 1: of RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars

description: Differentially expressed genes for DFI in Landrace. The results are presented with Ensembl gene id, gene symbol, gene name, fold change and significance level (FDR). (XLSX 31 kb)
DOI: 10.6084/m9.figshare.5643412.v1
title: Additional file 1: of RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars

description: Differentially expressed genes for DFI in Landrace. The results are presented with Ensembl gene id, gene symbol, gene name, fold change and significance level (FDR). (XLSX 31 kb)
DOI: 10.6084/m9.figshare.5643328
title: acoustic_BEAK_w_region from Beaked whales demonstrate a marked acoustic response to the use of shipboard echosounders

description: Data associated with “definitive” beaked whale acoustics detections
DOI: 10.6084/m9.figshare.5643328.v1
title: acoustic_BEAK_w_region from Beaked whales demonstrate a marked acoustic response to the use of shipboard echosounders

description: Data associated with “definitive” beaked whale acoustics detections
DOI: 10.6084/m9.figshare.5643325
title: acoustic_ALL_w_region from Beaked whales demonstrate a marked acoustic response to the use of shipboard echosounders

description: Data associated with all beaked whale acoustic detections
DOI: 10.6084/m9.figshare.5643325.v1
title: acoustic_ALL_w_region from Beaked whales demonstrate a marked acoustic response to the use of shipboard echosounders

description: Data associated with all beaked whale acoustic detections
DOI: 10.6084/m9.figshare.5643322
title: visual_groups_w_region from Beaked whales demonstrate a marked acoustic response to the use of shipboard echosounders

description: Data associated with visual sightings
DOI: 10.6084/m9.figshare.5643322.v1
title: visual_groups_w_region from Beaked whales demonstrate a marked acoustic response to the use of shipboard echosounders

description: Data associated with visual sightings
DOI: 10.6084/m9.figshare.5643319
title: RSOS_17049_Visual_data_code_201711 from Beaked whales demonstrate a marked acoustic response to the use of shipboard echosounders

description: R code and associated output for the statistical modeling for the visual data
DOI: 10.6084/m9.figshare.5643319.v1
title: RSOS_17049_Visual_data_code_201711 from Beaked whales demonstrate a marked acoustic response to the use of shipboard echosounders

description: R code and associated output for the statistical modeling for the visual data
DOI: 10.6084/m9.figshare.5643316
title: RSOS_170940_Acoustic_data_code_201711 from Beaked whales demonstrate a marked acoustic response to the use of shipboard echosounders

description: R code and associated output for the statistical modeling for the acoustic data
DOI: 10.6084/m9.figshare.5643304
title: Nonlinear Spectral Mixture Effects for Photosynthetic/Non-photosynthetic Vegetation Cover Estimates of Typical Desert Vegetation in Western China

description: Desert vegetation plays significant roles in securing the ecological integrity of oasis ecosystems in western China. Timely monitoring of photosynthetic/non-photosynthetic desert vegetation cover is necessary to guide management practices on land desertification and research into the mechanisms driving vegetation recession. In this study, nonlinear spectral mixture effects for photosynthetic/non-photosynthetic vegetation cover estimates are investigated through comparing the performance of linear and nonlinear spectral mixture models with different endmembers applied to field spectral measurements of two types of typical desert vegetation, namely, <i>Nitraria</i> shrubs and <i>Haloxylon</i>. The main results were as follows. (1) The correct selection of endmembers is important for improving the accuracy of vegetation cover estimates, and in particular, shadow endmembers cannot be neglected. (2) For both the <i>Nitraria</i> shrubs and <i>Haloxylon</i>, the Kernel-based Nonlinear Spectral Mixture Model (KNSMM) with nonlinear parameters was the best unmixing model. In consideration of the computational complexity and accuracy requirements, the Linear Spectral Mixture Model (LSMM) could be adopted for <i>Nitraria</i> shrubs plots, but this will result in significant errors for the <i>Haloxylon</i> plots since the nonlinear spectral mixture effects were more obvious for this vegetation type. (3) The vegetation canopy structure (planophile or erectophile) determines the strength of the nonlinear spectral mixture effects. Therefore, no matter for Nitraria shrubs or Haloxylon, the non-linear spectral mixing effects between the photosynthetic / non-photosynthetic vegetation and the bare soil do exist, and its strength is dependent on the three-dimensional structure of the vegetation canopy. The choice of linear or nonlinear spectral mixture models is up to the consideration of computational complexity and the accuracy requirement.
DOI: 10.6084/m9.figshare.5643304.v1
title: Nonlinear Spectral Mixture Effects for Photosynthetic/Non-photosynthetic Vegetation Cover Estimates of Typical Desert Vegetation in Western China

description: Desert vegetation plays significant roles in securing the ecological integrity of oasis ecosystems in western China. Timely monitoring of photosynthetic/non-photosynthetic desert vegetation cover is necessary to guide management practices on land desertification and research into the mechanisms driving vegetation recession. In this study, nonlinear spectral mixture effects for photosynthetic/non-photosynthetic vegetation cover estimates are investigated through comparing the performance of linear and nonlinear spectral mixture models with different endmembers applied to field spectral measurements of two types of typical desert vegetation, namely, <i>Nitraria</i> shrubs and <i>Haloxylon</i>. The main results were as follows. (1) The correct selection of endmembers is important for improving the accuracy of vegetation cover estimates, and in particular, shadow endmembers cannot be neglected. (2) For both the <i>Nitraria</i> shrubs and <i>Haloxylon</i>, the Kernel-based Nonlinear Spectral Mixture Model (KNSMM) with nonlinear parameters was the best unmixing model. In consideration of the computational complexity and accuracy requirements, the Linear Spectral Mixture Model (LSMM) could be adopted for <i>Nitraria</i> shrubs plots, but this will result in significant errors for the <i>Haloxylon</i> plots since the nonlinear spectral mixture effects were more obvious for this vegetation type. (3) The vegetation canopy structure (planophile or erectophile) determines the strength of the nonlinear spectral mixture effects. Therefore, no matter for Nitraria shrubs or Haloxylon, the non-linear spectral mixing effects between the photosynthetic / non-photosynthetic vegetation and the bare soil do exist, and its strength is dependent on the three-dimensional structure of the vegetation canopy. The choice of linear or nonlinear spectral mixture models is up to the consideration of computational complexity and the accuracy requirement.
DOI: 10.6084/m9.figshare.5643247
title: NL4-3 env SMRT sequences and references

description: Full-length Pacific Biosciences SMRT CCS reads of HIV-1 NL4-3 <i>env</i>. Originally published as part of Laird Smith, Melissa, et al. "Rapid sequencing of complete <i>env</i> genes from primary HIV-1 samples." <i>Virus Evolution</i> 2.2 (2016): vew018.<br><br>FASTQ file contains only the NL4-3 reads from the NL4-3/CH040 mixture originally used to evaluate PCR recombination.<br><br>Also contains a FASTA file of reference sequences, including NL4-3, HXB2, and others.<br><br>These data were used to validate RIFRAF, a novel consensus algorithm.<br><br><br>
DOI: 10.6084/m9.figshare.5643247.v2
title: NL4-3 env SMRT sequences and references

description: Full-length Pacific Biosciences SMRT CCS reads of HIV-1 NL4-3 <i>env</i>. Originally published as part of Laird Smith, Melissa, et al. "Rapid sequencing of complete <i>env</i> genes from primary HIV-1 samples." <i>Virus Evolution</i> 2.2 (2016): vew018.<br><br>FASTQ file contains only the NL4-3 reads from the NL4-3/CH040 mixture originally used to evaluate PCR recombination.<br><br>Also contains a FASTA file of reference sequences, including NL4-3, HXB2, and others.<br><br>These data were used to validate RIFRAF, a novel consensus algorithm.<br><br><br>
DOI: 10.6084/m9.figshare.5643247.v1
title: NL4-3 SMRT sequences and references

description: Full-length Pacific Biosciences SMRT CCS reads of HIV-1 NL4-3 env. Originally published as part of Laird Smith, Melissa, et al. "Rapid sequencing of complete env genes from primary HIV-1 samples." <i>Virus Evolution</i> 2.2 (2016): vew018.<br><br>FASTQ file contains only the NL4-3 reads from the NL4-3/CH040 mixture originally used to evaluate PCR recombination.<br><br>Also contains a FASTA file of reference sequences, including NL4-3, HXB2, and others.<br><br>These data were used to validate RIFRAF, a novel consensus algorithm.<br><br><br>
DOI: 10.6084/m9.figshare.5643214
title: Dataset for: Model for pressure drop and flow deflection in the numerical simulation of stents in aneurysm

description: The numerical simulation of flow diverters like stents contributes to the development and improvement of endovascular stenting procedures, leading ultimately to an improved treatment of intracranial aneurysms. Due to the scale difference between the struts of flow diverters and the full artery, it is common to avoid fully resolved simulations at the level of the stent porosity. Instead, the effect of stents on the flow is represented by a heuristic continuum model. However, the commonly used porous media models describe the properties of flow diverters only partially, because they do not explicitly account for the deflection of the flow direction by the stent. We show that this deficiency can be circumvented by adopting the theoretical framework of screen models. The article first reviews existing screen models. It then proposes an explicit formula for the drag and the deflection coefficient, as predicted by each model, for both perpendicular and inclined angles. The results of 2D numerical simulations are used to formulate a generalization of these formulas, to achieve best results in the case of stent modeling. The obtained model is then validated, again through 2D numerical simulation.
DOI: 10.6084/m9.figshare.5643214.v1
title: Dataset for: Model for pressure drop and flow deflection in the numerical simulation of stents in aneurysm

description: The numerical simulation of flow diverters like stents contributes to the development and improvement of endovascular stenting procedures, leading ultimately to an improved treatment of intracranial aneurysms. Due to the scale difference between the struts of flow diverters and the full artery, it is common to avoid fully resolved simulations at the level of the stent porosity. Instead, the effect of stents on the flow is represented by a heuristic continuum model. However, the commonly used porous media models describe the properties of flow diverters only partially, because they do not explicitly account for the deflection of the flow direction by the stent. We show that this deficiency can be circumvented by adopting the theoretical framework of screen models. The article first reviews existing screen models. It then proposes an explicit formula for the drag and the deflection coefficient, as predicted by each model, for both perpendicular and inclined angles. The results of 2D numerical simulations are used to formulate a generalization of these formulas, to achieve best results in the case of stent modeling. The obtained model is then validated, again through 2D numerical simulation.
DOI: 10.23641/asha.5643076
title: Early Development of Emotional Competence (EDEC) assessment tool (Na et al., 2017)

description: <b>Purpose: </b>This article introduces and provides initial data supporting “The Early Development of Emotional Competence (EDEC): A tool for children with complex communication needs (CCNs).” The EDEC was developed to raise awareness about the relation of language and emotional competence and to maximize the likelihood that intervention includes language to discuss emotions in ways that are consistent with the values and goals of the family.<b>Method: </b>First, the theoretical and clinical foundations of the EDEC development were discussed. Then, a description of preferred translation practices was provided, with examples of Korean and Mandarin Chinese translations. Finally, initial data from a pilot study with two sociocultural communities (i.e., 10 American and 10 Korean mothers of children developing typically) were presented to demonstrate the potential of the tool.<b>Results: </b>The pilot test offered preliminary support for the sensitivity of the EDEC. The tool solicited responses reflecting cultural differences between American and Korean mothers’ perception of a child’s emotional skills and mother-child conversation about emotions as predicted based on many cross-cultural studies in emotion.<b>Conclusions: </b>The information elicited from the EDEC shows promise for enabling culturally natural conversation about emotions with appropriate vocabulary and phrases in their augmentative and alternative communication systems.<br><b>Supplemental Material S1. </b>English version of the Early Development of Emotional Competence (EDEC).<br><b>Supplemental Material S2.</b> Korean version of the Early Development of Emotional Competence (EDEC).<br><b>Supplemental Material S3.</b> Mandarin Chinese version of the Early Development of Emotional Competence (EDEC). <b><br></b><b>Supplemental Material S4. </b>Codebook for the Early Development of Emotional Competence (EDEC). <br>Na, J. Y., Wilkinson, K., & Liang, J. (2017). Early Development of Emotional Competence (EDEC) assessment tool for children with complex communication needs: Development and evidence. <i>American Journal of Speech-Language Pathology, 27,</i> 24–36. https://doi.org/10.1044/2017_AJSLP-16-0058
DOI: 10.6084/m9.figshare.5643052
title: Microscopic Characterization of Shale

description: The data presents the results of scratch tests carried out on gas shale materials. The goal is to quantify the resistance to fracture using brittleness indices as well as nonlinear fracture mechanics modeling.
DOI: 10.6084/m9.figshare.5643052.v1
title: Microscopic Characterization of Shale

description: The data presents the results of scratch tests carried out on gas shale materials. The goal is to quantify the resistance to fracture using brittleness indices as well as nonlinear fracture mechanics modeling.
DOI: 10.6084/m9.figshare.5640988
title: Reconstructing an African haploid genome from the 18th century (all files)

description: This file set presents supporting data for the paper titled "Reconstructing an African haploid genome from the 18th century". The dataset presents the data underpinning the reconstructed genome of Icelandic man Hans Jonatan (HJ), b. 1784, based on both single nucleotide polymorphism (SNP) chips and whole genome sequenced (WGS) of his descendants.<br>Datasets provided map the descendants in HJ's genealogy to identifiers used in the associated paper, African fragments in HJ descendants as determined by HAPMIX statistical software and the different African microarray SNP datasets used as reference populations to determine the origin of HJ’s haploid African genome.<br>Formats<br>Files are provided in either .xls, .pdf (both datasets) or .docx (figures) formats.<br>HAPMIX is an application for accurately inferring chromosomal segments of distinct ancestry in admixed populations, using dense genetic data. ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.
DOI: 10.6084/m9.figshare.5640988.v1
title: Reconstructing an African haploid genome from the 18th century (all files)

description: This file set presents supporting data for the paper titled "Reconstructing an African haploid genome from the 18th century". The dataset presents the data underpinning the reconstructed genome of Icelandic man Hans Jonatan (HJ), b. 1784, based on both single nucleotide polymorphism (SNP) chips and whole genome sequenced (WGS) of his descendants.<br>Datasets provided map the descendants in HJ's genealogy to identifiers used in the associated paper, African fragments in HJ descendants as determined by HAPMIX statistical software and the different African microarray SNP datasets used as reference populations to determine the origin of HJ’s haploid African genome.<br>Formats<br>Files are provided in either .xls, .pdf (both datasets) or .docx (figures) formats.<br>HAPMIX is an application for accurately inferring chromosomal segments of distinct ancestry in admixed populations, using dense genetic data. ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.
DOI: 10.6084/m9.figshare.5640895
title: Supplementary Table 1. SNP Genotyping

description: Illumina micro-array chips used to genotype Hans Jonatan (HJ) descendants
DOI: 10.6084/m9.figshare.5640895.v1
title: Supplementary Table 1. SNP Genotyping

description: Illumina micro-array chips used to genotype Hans Jonatan (HJ) descendants