cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8796419.v2
title: Supplementary Data for Kogay et al. (2019)

description: This dataset contains supplementary figures and tables, sequence alignments, phylogenetic trees and outlier removal calculations used in the bioinformatic analyses presented in:<br> <br> Roman Kogay, Taylor B. Neely, Daniel P. Birnbaum, Camille R. Hankel, Migun Shakya, and Olga Zhaxybayeva. “Machine-learning classification suggests that many alphaproteobacterial prophages may instead be gene transfer agents”, BioRxiv, 2019. (BIORXIV/2019/697243; available at https://www.biorxiv.org/content/10.1101/697243v1)<br><br> <b>File Contents:</b><b><br></b> <b>Supplementary_Figures.pdf: </b>Supplementary Figures S1 and S2 in the manuscript.<br><br> <b>Supplementary_Tables.zip:</b> Supplementary Tables S1-S15 in the manuscript. <b><br> Alignments_for_weight_assignment_GTAs.zip:</b> Alignments of 'true GTA' sequences in the training dataset. These alignments were used to generate pairwise phylogenetic distances for the weighting scheme. The alignments are in FASTA format. The filename prefix (g2, …, g15) refers to the RcGTA gene name (see <b>Supplementary Table S1</b>). <b><br></b><b>Alignments_for_weight_assignment_viruses.zip:</b> Alignments of 'true virus' sequences in the training dataset. These alignments were used to generate pairwise phylogenetic distances for the weighting scheme. The alignments are in FASTA format. The filename prefix (g2, …, g15) refers to the RcGTA gene name (see <b>Supplementary Table S1</b>). <b><br></b><b>Alignments_for_removal_of_outliers.zip:</b> Alignments of ‘true GTA’ and ‘true virus’ sequences in the training datasets. Pairwise phylogenetic distances calculated from these alignments were used to remove GTA homologs that are more closely related to viruses than to other GTAs, as well as to investigate obtained lower accuracies for g6 and g12 (<b>Supplementary Table S11)</b>. The alignments are in FASTA format. The filename prefix (g2, …, g15) refers to the RcGTA gene name (see <b>Supplementary Table S1</b>). <b><br></b><b>Outlier_removal.xlsx</b>: Calculations to identify GTAs that are more closely related to viruses than to other GTAs. The removed sequences are highlighted. <b><br></b><b>Reference_phylogenetic_tree_reconstruction.zip:</b> Concatenated alignment of 83 marker genes in 1,423 taxa in PHYLIP format (concatenated_83markers.phy); information about partitions and substitution models used in phylogenetic reconstruction (partitions.txt); and phylogenetic tree in Newick format (1423_alphaproteobacteria_reference_tree.newick).
DOI: 10.6084/m9.figshare.8796419.v4
title: Supplementary Data for Kogay et al. (2019)

description: This dataset contains supplementary figures and tables, sequence alignments, phylogenetic trees and outlier removal calculations used in the bioinformatic analyses presented in:<br> <br> Roman Kogay, Taylor B. Neely, Daniel P. Birnbaum, Camille R. Hankel, Migun Shakya, and Olga Zhaxybayeva. “Machine-learning classification suggests that many alphaproteobacterial prophages may instead be gene transfer agents”, BioRxiv, 2019. (BIORXIV/2019/697243; available at https://www.biorxiv.org/content/10.1101/697243v1)<br><br> <b>File Contents:</b><b><br></b> <b>Supplementary_Figures.pdf: </b>Supplementary Figures S1 and S2 in the manuscript.<br><br> <b>Supplementary_Tables.zip:</b> Supplementary Tables S1-S15 in the manuscript. <b><br> Alignments_for_weight_assignment_GTAs.zip:</b> Alignments of 'true GTA' sequences in the training dataset. These alignments were used to generate pairwise phylogenetic distances for the weighting scheme. The alignments are in FASTA format. The filename prefix (g2, …, g15) refers to the RcGTA gene name (see <b>Supplementary Table S1</b>). <b><br></b><b>Alignments_for_weight_assignment_viruses.zip:</b> Alignments of 'true virus' sequences in the training dataset. These alignments were used to generate pairwise phylogenetic distances for the weighting scheme. The alignments are in FASTA format. The filename prefix (g2, …, g15) refers to the RcGTA gene name (see <b>Supplementary Table S1</b>). <b><br></b><b>Alignments_for_removal_of_outliers.zip:</b> Alignments of ‘true GTA’ and ‘true virus’ sequences in the training datasets. Pairwise phylogenetic distances calculated from these alignments were used to remove GTA homologs that are more closely related to viruses than to other GTAs, as well as to investigate obtained lower accuracies for g6 and g12 (<b>Supplementary Table S11)</b>. The alignments are in FASTA format. The filename prefix (g2, …, g15) refers to the RcGTA gene name (see <b>Supplementary Table S1</b>). <b><br></b><b>Outlier_removal.xlsx</b>: Calculations to identify GTAs that are more closely related to viruses than to other GTAs. The removed sequences are highlighted. <b><br></b><b>Reference_phylogenetic_tree_reconstruction.zip:</b> Concatenated alignment of 83 marker genes in 1,423 taxa in PHYLIP format (concatenated_83markers.phy); information about partitions and substitution models used in phylogenetic reconstruction (partitions.txt); and phylogenetic tree in Newick format (1423_alphaproteobacteria_reference_tree.newick).
DOI: 10.6084/m9.figshare.8796419.v3
title: Supplementary Data for Kogay et al. (2019)

description: This dataset contains supplementary figures and tables, sequence alignments, phylogenetic trees and outlier removal calculations used in the bioinformatic analyses presented in:<br> <br> Roman Kogay, Taylor B. Neely, Daniel P. Birnbaum, Camille R. Hankel, Migun Shakya, and Olga Zhaxybayeva. “Machine-learning classification suggests that many alphaproteobacterial prophages may instead be gene transfer agents”, BioRxiv, 2019. (BIORXIV/2019/697243; available at https://www.biorxiv.org/content/10.1101/697243v1)<br><br> <b>File Contents:</b><b><br></b> <b>Supplementary_Figures.pdf: </b>Supplementary Figures S1 and S2 in the manuscript.<br><br> <b>Supplementary_Tables.zip:</b> Supplementary Tables S1-S15 in the manuscript. <b><br> Alignments_for_weight_assignment_GTAs.zip:</b> Alignments of 'true GTA' sequences in the training dataset. These alignments were used to generate pairwise phylogenetic distances for the weighting scheme. The alignments are in FASTA format. The filename prefix (g2, …, g15) refers to the RcGTA gene name (see <b>Supplementary Table S1</b>). <b><br></b><b>Alignments_for_weight_assignment_viruses.zip:</b> Alignments of 'true virus' sequences in the training dataset. These alignments were used to generate pairwise phylogenetic distances for the weighting scheme. The alignments are in FASTA format. The filename prefix (g2, …, g15) refers to the RcGTA gene name (see <b>Supplementary Table S1</b>). <b><br></b><b>Alignments_for_removal_of_outliers.zip:</b> Alignments of ‘true GTA’ and ‘true virus’ sequences in the training datasets. Pairwise phylogenetic distances calculated from these alignments were used to remove GTA homologs that are more closely related to viruses than to other GTAs, as well as to investigate obtained lower accuracies for g6 and g12 (<b>Supplementary Table S11)</b>. The alignments are in FASTA format. The filename prefix (g2, …, g15) refers to the RcGTA gene name (see <b>Supplementary Table S1</b>). <b><br></b><b>Outlier_removal.xlsx</b>: Calculations to identify GTAs that are more closely related to viruses than to other GTAs. The removed sequences are highlighted. <b><br></b><b>Reference_phylogenetic_tree_reconstruction.zip:</b> Concatenated alignment of 83 marker genes in 1,423 taxa in PHYLIP format (concatenated_83markers.phy); information about partitions and substitution models used in phylogenetic reconstruction (partitions.txt); and phylogenetic tree in Newick format (1423_alphaproteobacteria_reference_tree.newick).
DOI: 10.6084/m9.figshare.8796344.v1
title: Thermal-hydro coupling model of immiscible two-phase flow in heterogeneous porous structures at high temperature

description: This file includes the figures, tables and equations that underlie the conclusions of our paper.
DOI: 10.6084/m9.figshare.8796302
title: 异常关系指标前20家餐厅完整评论数据集

description: Top 20 restaurants of anomalous relation online comment dataset
DOI: 10.6084/m9.figshare.8796296
title: 美团网广州粤菜类餐厅基本信息.xlsx

description: basic information list about Cantonese restaurants on Meituan website
DOI: 10.6084/m9.figshare.8796302.v1
title: 异常关系指标前20家餐厅完整评论数据集

description: Top 20 restaurants of anomalous relation online comment dataset
DOI: 10.6084/m9.figshare.8796263
title: istribution Characteristics of Dimethylated Sulfur Compounds and Turnover of Dimethylsulfide in the northern South China Sea during Summer

description: This dataset contains the original data of dimethylated sulfur compounds concentrations in the northern South China Sea, including the ones of the surface seawater and of two vertical transects.
DOI: 10.6084/m9.figshare.8796119
title: Supplementary Information for the paper "Individual behavioral type captured by a Bayesian model comparison of cap making by sponge crabs"

description: The code as an output html from a Rmarkdown, the data as a csv file are included.
DOI: 10.6084/m9.figshare.8796119.v1
title: Supplementary Information for the paper "Individuality emerging in cap making by sponge crab"

description: The code as an output html from a Rmarkdown, the data as a csv file are included.
DOI: 10.6084/m9.figshare.8796119.v2
title: Supplementary Information for the paper "Individuality emerging in cap making by sponge crab"

description: The code as an output html from a Rmarkdown, the data as a csv file are included.
DOI: 10.6084/m9.figshare.8796119.v3
title: Supplementary Information for the paper "Individual behavioral type captured by a Bayesian model comparison in cap making by sponge crab"

description: The code as an output html from a Rmarkdown, the data as a csv file are included.
DOI: 10.6084/m9.figshare.8796119.v4
title: Supplementary Information for the paper "Individual behavioral type captured by a Bayesian model comparison in cap making by sponge crab"

description: The code as an output html from a Rmarkdown, the data as a csv file are included.
DOI: 10.6084/m9.figshare.8796119.v5
title: Supplementary Information for the paper "Individual behavioral type captured by a Bayesian model comparison of cap making by sponge crabs"

description: The code as an output html from a Rmarkdown, the data as a csv file are included.
DOI: 10.6084/m9.figshare.8796119.v6
title: Supplementary Information for the paper "Individual behavioral type captured by a Bayesian model comparison of cap making by sponge crabs"

description: The code as an output html from a Rmarkdown, the data as a csv file are included.
DOI: 10.6084/m9.figshare.8795816
title: Additional file 1: of New therapeutic targeting of Alzheimer’s disease with the potential use of proline-rich polypeptide complex to modulate an innate immune response - preliminary study

description: Data set. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8795816.v1
title: Additional file 1: of New therapeutic targeting of Alzheimer’s disease with the potential use of proline-rich polypeptide complex to modulate an innate immune response - preliminary study

description: Data set. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8795750
title: Additional file 4: of Surface PEGylation suppresses pulmonary effects of CuO in allergen-induced lung inflammation

description: Table S4. Lists of the differentially expressed genes from the microarray experiment. Experimental groups treated with modified CuO materials were compared against the groups treated with the corresponding dose of core CuO in PBS-challenged or OVA-challenged mice. The tables with the differentially expressed genes of each pairwise comparison are reported in sheets of the Microsoft Excel archive, named accordingly. In each table, the significantly differentially expressed genes (Benjamini and Hochberg post hoc corrected p-value â 0.58) are ordered according to the decreasing log2 fold change. The Agilent probe IDs and gene symbols are shown. Additionally, for each significant gene, the average expression across the microarray samples, the t-test value, the nominal P value, the adjusted P value and the B value are also reported. (XLSX 338 kb)
DOI: 10.6084/m9.figshare.8795744
title: Additional file 3: of Surface PEGylation suppresses pulmonary effects of CuO in allergen-induced lung inflammation

description: Table S3 Lists of the differentially expressed genes from the microarray experiment. Experimental groups of PBS-challenged or OVA-challenged mice that were treated with the same CuO material were combined and compared against their corresponding controls. The tables with the differentially expressed genes of each pairwise comparison are reported in sheets of the Microsoft Excel archive, named accordingly. In each table, the significantly differentially expressed genes (Benjamini and Hochberg post hoc corrected p-value â 0.58) are ordered according to the decreasing log2 fold change. The Agilent probe IDs and gene symbols are shown. Additionally, for each significant gene, the average expression across the microarray samples, the t-test value, the nominal P value, the adjusted P value and the B value are also reported. (XLSX 256 kb)
DOI: 10.6084/m9.figshare.8795750.v1
title: Additional file 4: of Surface PEGylation suppresses pulmonary effects of CuO in allergen-induced lung inflammation

description: Table S4. Lists of the differentially expressed genes from the microarray experiment. Experimental groups treated with modified CuO materials were compared against the groups treated with the corresponding dose of core CuO in PBS-challenged or OVA-challenged mice. The tables with the differentially expressed genes of each pairwise comparison are reported in sheets of the Microsoft Excel archive, named accordingly. In each table, the significantly differentially expressed genes (Benjamini and Hochberg post hoc corrected p-value â 0.58) are ordered according to the decreasing log2 fold change. The Agilent probe IDs and gene symbols are shown. Additionally, for each significant gene, the average expression across the microarray samples, the t-test value, the nominal P value, the adjusted P value and the B value are also reported. (XLSX 338 kb)
DOI: 10.6084/m9.figshare.8795738
title: Additional file 2: of Surface PEGylation suppresses pulmonary effects of CuO in allergen-induced lung inflammation

description: Table S2. Lists of the differentially expressed genes from the microarray experiment. The tables with the differentially expressed genes in each of the relevant pairwise comparisons (each experimental group compared against corresponding PBS-challenged or OVA-challenged controls) are reported in sheets of the Microsoft Excel archive, named accordingly. In each table, the significantly differentially expressed genes (Benjamini and Hochberg post hoc corrected P value â 0.58) are ordered according to the decreasing log2 fold change. The Agilent probe IDs and gene symbols are shown. Additionally, for each significant gene, the average expression across the microarray samples, the t-test value, the nominal P value, the adjusted P value and the B value are also reported. (XLSX 1842 kb)
DOI: 10.6084/m9.figshare.8795744.v1
title: Additional file 3: of Surface PEGylation suppresses pulmonary effects of CuO in allergen-induced lung inflammation

description: Table S3 Lists of the differentially expressed genes from the microarray experiment. Experimental groups of PBS-challenged or OVA-challenged mice that were treated with the same CuO material were combined and compared against their corresponding controls. The tables with the differentially expressed genes of each pairwise comparison are reported in sheets of the Microsoft Excel archive, named accordingly. In each table, the significantly differentially expressed genes (Benjamini and Hochberg post hoc corrected p-value â 0.58) are ordered according to the decreasing log2 fold change. The Agilent probe IDs and gene symbols are shown. Additionally, for each significant gene, the average expression across the microarray samples, the t-test value, the nominal P value, the adjusted P value and the B value are also reported. (XLSX 256 kb)
DOI: 10.6084/m9.figshare.8795738.v1
title: Additional file 2: of Surface PEGylation suppresses pulmonary effects of CuO in allergen-induced lung inflammation

description: Table S2. Lists of the differentially expressed genes from the microarray experiment. The tables with the differentially expressed genes in each of the relevant pairwise comparisons (each experimental group compared against corresponding PBS-challenged or OVA-challenged controls) are reported in sheets of the Microsoft Excel archive, named accordingly. In each table, the significantly differentially expressed genes (Benjamini and Hochberg post hoc corrected P value â 0.58) are ordered according to the decreasing log2 fold change. The Agilent probe IDs and gene symbols are shown. Additionally, for each significant gene, the average expression across the microarray samples, the t-test value, the nominal P value, the adjusted P value and the B value are also reported. (XLSX 1842 kb)
DOI: 10.6084/m9.figshare.8795717
title: Additional file 3: of flam piRNA precursors channel from the nucleus to the cytoplasm in a temporally regulated manner along Drosophila oogenesis

description: Table S1. Number of cells and follicles analyzed for quantifications presented in Figs.Â 1a-b, 2b, 3b, 4b (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8795717.v1
title: Additional file 3: of flam piRNA precursors channel from the nucleus to the cytoplasm in a temporally regulated manner along Drosophila oogenesis

description: Table S1. Number of cells and follicles analyzed for quantifications presented in Figs.Â 1a-b, 2b, 3b, 4b (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8795675
title: Additional file 1: of Fit 4 surgery, a bespoke app with biofeedback delivers rehabilitation at home before and after elective lung resection

description: Users guide to Fit 4 Surgery app booklet. (ZIP 1123 kb)
DOI: 10.6084/m9.figshare.8795675.v1
title: Additional file 1: of Fit 4 surgery, a bespoke app with biofeedback delivers rehabilitation at home before and after elective lung resection

description: Users guide to Fit 4 Surgery app booklet. (ZIP 1123 kb)
DOI: 10.6084/m9.figshare.8795666
title: Additional file 1: of QTL-mapping and genomic prediction for bovine respiratory disease in U.S. Holsteins using sequence imputation and feature selection

description: Table S1. Prediction accuracies and regressions of phenotype on genomic predictions for risk of BRD according to training and validation phenotype subsets and genotype subsets. This file contains Pearson correlation coefficients, regression slopes and intercepts for the regression of BRD case/control phenotype on genomic predictions for BRD risk for the Bovine HD, WGS imputed and feature selection genotype sets. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8795666.v1
title: Additional file 1: of QTL-mapping and genomic prediction for bovine respiratory disease in U.S. Holsteins using sequence imputation and feature selection

description: Table S1. Prediction accuracies and regressions of phenotype on genomic predictions for risk of BRD according to training and validation phenotype subsets and genotype subsets. This file contains Pearson correlation coefficients, regression slopes and intercepts for the regression of BRD case/control phenotype on genomic predictions for BRD risk for the Bovine HD, WGS imputed and feature selection genotype sets. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8795660
title: Additional file 1: of Research trends in Korean medicine based on temporal and network analysis

description: Keyword. Full list of 41,873 keywords used in our study. Table 1. Full list of 1,123 keywords and their frequencies. Table 2. Full list of the appearance frequencies for the keywords. Figure S1-S8. All cluster images. Table2-5y. Appearance frequencies of the keywords by five-year periods. Table2-10y. Appearance frequencies of the keywords by ten-year periods. (ZIP 8463 kb)
DOI: 10.6084/m9.figshare.8795657
title: Additional file 11: of Correction to: Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta

description: HMM profiles used for Hmmsearch. (ZIP 1469 kb)
DOI: 10.6084/m9.figshare.8795657.v1
title: Additional file 11: of Correction to: Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta

description: HMM profiles used for Hmmsearch. (ZIP 1469 kb)
DOI: 10.6084/m9.figshare.8795660.v1
title: Additional file 1: of Research trends in Korean medicine based on temporal and network analysis

description: Keyword. Full list of 41,873 keywords used in our study. Table 1. Full list of 1,123 keywords and their frequencies. Table 2. Full list of the appearance frequencies for the keywords. Figure S1-S8. All cluster images. Table2-5y. Appearance frequencies of the keywords by five-year periods. Table2-10y. Appearance frequencies of the keywords by ten-year periods. (ZIP 8463 kb)
DOI: 10.6084/m9.figshare.8795633
title: Additional file 1: of Sleep SAAF: a responsive parenting intervention to prevent excessive weight gain and obesity among African American infants

description: Data and safety monitoring plan, Research maternal informed consent and parental permission for infant document. (ZIP 477 kb)
DOI: 10.6084/m9.figshare.8795633.v1
title: Additional file 1: of Sleep SAAF: a responsive parenting intervention to prevent excessive weight gain and obesity among African American infants

description: Data and safety monitoring plan, Research maternal informed consent and parental permission for infant document. (ZIP 477 kb)
DOI: 10.6084/m9.figshare.8795624
title: Additional file 2: of Is the non-identity problem relevant to public health and policy? An online survey

description: Statistical analyses. (SPS 9 kb)
DOI: 10.6084/m9.figshare.8795618
title: Additional file 1: of Is the non-identity problem relevant to public health and policy? An online survey

description: Raw data. (CSV 411 kb)
DOI: 10.6084/m9.figshare.8795624.v1
title: Additional file 2: of Is the non-identity problem relevant to public health and policy? An online survey

description: Statistical analyses. (SPS 9 kb)
DOI: 10.6084/m9.figshare.8795618.v1
title: Additional file 1: of Is the non-identity problem relevant to public health and policy? An online survey

description: Raw data. (CSV 411 kb)
DOI: 10.6084/m9.figshare.8795606
title: Additional file 1: of Pleural thickening on screening chest X-rays: a single institutional study

description: Table S1. Top 10 most common abnormal findings on screening chest X-rays. Table S2. Distribution and laterality of pleural thickening. Table S3. Pleural thickening and sex. Table S4. Pleural thickening and age distribution. Table S5. Pleural thickening and smoking status. Table S6. Pleural thickening and BMI. (XLSX 18 kb)
DOI: 10.25582/data.2024-04.3088201/2555176
title: Data for EMSL Project 60201 from April 2024
DOI: 10.25582/data.2024-04.3088202/2555177
title: Data for EMSL Project 60201 from April 2024
DOI: 10.25582/data.2024-04.3088204/2555178
title: Data for EMSL Project 60201 from April 2024
DOI: 10.25582/data.2024-04.3088207/2555179
title: Data for EMSL Project 60201 from April 2024
DOI: 10.25582/data.2024-04.3088208/2555180
title: Data for EMSL Project 60201 from April 2024
DOI: 10.25582/data.2024-04.3088210/2555181
title: Data for EMSL Project 60201 from April 2024
DOI: 10.25582/data.2024-04.3088212/2555182
title: Data for EMSL Project 60201 from April 2024
DOI: 10.25582/data.2024-04.3088220/2555183
title: Data for EMSL Project 60201 from April 2024