cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9724070.v4
title: Legal Information as a Complex Network: Improving Topic Modeling through Homophily

description: Natural language processing is a key component to computational legal science. Network analysis is also very important to further understand the structure of references in legal documents. In this paper, we improve topic modeling for legal documents by using homophily derived from two family of references: prior cases and statute laws. We propose a new analysis of a rich data set in order to create these networks. The use of the reference-induced homophily topic modeling improves on prior methods.
DOI: 10.6084/m9.figshare.9723635
title: Additional file 2 of Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line

description: Table S.1. Predicted genes belonging to simplified gene group c. (XLSX 411 kb)
DOI: 10.6084/m9.figshare.9723635.v1
title: Additional file 2 of Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line

description: Table S.1. Predicted genes belonging to simplified gene group c. (XLSX 411 kb)
DOI: 10.6084/m9.figshare.9723614
title: Additional file 2: of An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data

description: GLVM parameter estimates for the gut microbiomes of the four subjects. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.9723617
title: Additional file 3: of An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data

description: OD600 measurements for 10 different species. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9723611
title: Additional file 3: of The effects of pelvic belt use on pelvic alignment during and after pregnancy: a prospective longitudinal cohort study

description: Results of correlation analysis of change in pelvic alignment and birth weight. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9723611.v1
title: Additional file 3: of The effects of pelvic belt use on pelvic alignment during and after pregnancy: a prospective longitudinal cohort study

description: Results of correlation analysis of change in pelvic alignment and birth weight. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9723614.v1
title: Additional file 2: of An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data

description: GLVM parameter estimates for the gut microbiomes of the four subjects. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.9723617.v1
title: Additional file 3: of An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data

description: OD600 measurements for 10 different species. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9723608
title: Additional file 2: of The effects of pelvic belt use on pelvic alignment during and after pregnancy: a prospective longitudinal cohort study

description: The amount of change of pelvic alignment from pregnancy to postpartum periods (The participants who used the belt no less than 7â h were only included to user group). (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9723599
title: Additional file 1: of The effects of pelvic belt use on pelvic alignment during and after pregnancy: a prospective longitudinal cohort study

description: The amount of change of pelvic alignment from pregnancy to postpartum periods. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9723608.v1
title: Additional file 2: of The effects of pelvic belt use on pelvic alignment during and after pregnancy: a prospective longitudinal cohort study

description: The amount of change of pelvic alignment from pregnancy to postpartum periods (The participants who used the belt no less than 7â h were only included to user group). (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9723599.v1
title: Additional file 1: of The effects of pelvic belt use on pelvic alignment during and after pregnancy: a prospective longitudinal cohort study

description: The amount of change of pelvic alignment from pregnancy to postpartum periods. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9723590
title: Additional file 6: of Different copies of SENSITIVITY TO RED LIGHT REDUCED 1 show strong subfunctionalization in Brassica napus

description: Primer sequences. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9723593
title: Additional file 7: of Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake

description: Dataset 3. Species representative MAGs that encode for S-cycling marker genes. Basis for Fig.Â 3. KEGG number assignment, CheckM-completeness, and CheckM-contamination are given. X, gene absent; V, gene present. (XLSX 53 kb)
DOI: 10.6084/m9.figshare.9723587
title: Additional file 6: of Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake

description: Dataset 2. Phylogenetic tree of all bacterial MAGs obtained in this study and in [35] based on 16 ribosomal proteins. References included in the tree were obtained from [98]. (TRE 269 kb)
DOI: 10.6084/m9.figshare.9723590.v1
title: Additional file 6: of Different copies of SENSITIVITY TO RED LIGHT REDUCED 1 show strong subfunctionalization in Brassica napus

description: Primer sequences. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9723593.v1
title: Additional file 7: of Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake

description: Dataset 3. Species representative MAGs that encode for S-cycling marker genes. Basis for Fig.Â 3. KEGG number assignment, CheckM-completeness, and CheckM-contamination are given. X, gene absent; V, gene present. (XLSX 53 kb)
DOI: 10.6084/m9.figshare.9723587.v1
title: Additional file 6: of Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake

description: Dataset 2. Phylogenetic tree of all bacterial MAGs obtained in this study and in [35] based on 16 ribosomal proteins. References included in the tree were obtained from [98]. (TRE 269 kb)
DOI: 10.6084/m9.figshare.9723572
title: Additional file 4: of Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake

description: Dataset 1. Metrics and Genbank accession numbers on the obtained metagenome-assembled genomes (MAGs). The total size of the MAG (Mb), the number of contains (# Contigs), the contig N50 (kb), maximum contig length (kb), estimated mean coverage, average G+C mol%, total number of 5S, 16S and 23S rRNAs, total number of tRNAs and estimated percentages of CheckM-completeness (Compl), CheckM-contamination (Cont), and strain heterogeneity (Str het) are given. The final given name used for the Genbank submission (NCBI organism name) was derived from the Genome Taxonomy Database (GTDP) classification according to [89] and where possible verified with the 16S rRNA gene classification according to the SILVA database (see column â Proposed name (GTDB)â ). For the latter, BLAST results are reported: taxonomy of the best hit, identity with this best hit (%), e value of the match, the length of the query (number of nucleotides), and the coverage with the hit (%). (XLSX 182 kb)
DOI: 10.6084/m9.figshare.9723572.v1
title: Additional file 4: of Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake

description: Dataset 1. Metrics and Genbank accession numbers on the obtained metagenome-assembled genomes (MAGs). The total size of the MAG (Mb), the number of contains (# Contigs), the contig N50 (kb), maximum contig length (kb), estimated mean coverage, average G+C mol%, total number of 5S, 16S and 23S rRNAs, total number of tRNAs and estimated percentages of CheckM-completeness (Compl), CheckM-contamination (Cont), and strain heterogeneity (Str het) are given. The final given name used for the Genbank submission (NCBI organism name) was derived from the Genome Taxonomy Database (GTDP) classification according to [89] and where possible verified with the 16S rRNA gene classification according to the SILVA database (see column â Proposed name (GTDB)â ). For the latter, BLAST results are reported: taxonomy of the best hit, identity with this best hit (%), e value of the match, the length of the query (number of nucleotides), and the coverage with the hit (%). (XLSX 182 kb)
DOI: 10.6084/m9.figshare.9723527
title: Additional file 10: of Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake

description: Dataset 4. Presence-absence of marker genes for central metabolic pathways and environmentally relevant element transformations in a selection of MAGs. MAGs were selected based on the presence of markers for dissimilatory sulfur cycling. KEGG number assignment, CheckM-completeness, and CheckM-contamination, as well as species delineation (based on average nucleotide identity, see the â Methodsâ section) are given. X, gene absent; V, gene present. (XLSX 261 kb)
DOI: 10.6084/m9.figshare.9723527.v1
title: Additional file 10: of Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake

description: Dataset 4. Presence-absence of marker genes for central metabolic pathways and environmentally relevant element transformations in a selection of MAGs. MAGs were selected based on the presence of markers for dissimilatory sulfur cycling. KEGG number assignment, CheckM-completeness, and CheckM-contamination, as well as species delineation (based on average nucleotide identity, see the â Methodsâ section) are given. X, gene absent; V, gene present. (XLSX 261 kb)
DOI: 10.6084/m9.figshare.9723470
title: MOESM5 of Revision of the species composition and distribution of Turkish sand flies using DNA barcodes

description: Additional file 5: Table S2. Interspecific and intraspecific (diagonal line) cox1 sequence divergence based on K2P model obtained for Turkish sand flies.
DOI: 10.6084/m9.figshare.9723470.v1
title: MOESM5 of Revision of the species composition and distribution of Turkish sand flies using DNA barcodes

description: Additional file 5: Table S2. Interspecific and intraspecific (diagonal line) cox1 sequence divergence based on K2P model obtained for Turkish sand flies.
DOI: 10.6084/m9.figshare.9723443
title: MOESM1 of Revision of the species composition and distribution of Turkish sand flies using DNA barcodes

description: Additional file 1: Table S1. Information regarding the sand fly collection sites and the number of traps used in each locality.
DOI: 10.6084/m9.figshare.9723443.v1
title: MOESM1 of Revision of the species composition and distribution of Turkish sand flies using DNA barcodes

description: Additional file 1: Table S1. Information regarding the sand fly collection sites and the number of traps used in each locality.
DOI: 10.5281/zenodo.4002478
title: Rat BAT Xenotransplantation Recovers the Fertility and Metabolic Health of PCOS Mice

description: <strong>Supplementary dataset 1</strong> This file contains datasets for all 230 overlapped DEGs (Fig. 6A and B) among RTM, MTM, and control group compared with the PCOS group in F0 model mice. It has two sheets: "F0 up-regulated DEGs" contained all DEGs that have significantly higher (|log2| &gt; 1) expression levels in RTM, MTM, and control group than PCOS group; "F0 down-regulated DEGs" contained all DEGs that have significantly lower (|log2| &gt; 1) expression level in RTM, MTM, and control group than PCOS group. For each gene, both FPKM of each repeat and the average FPKM of three repeats are shown. <strong>Supplementary dataset 2</strong> This file, corresponding to Fig. 7, contains 4 sheets of datasets for all DEGs that overlapped between human PCOS studies and corrent study. From left to right, in sheet 1, the datasets from column A-AB are for the DEGs in current study; the datasets from column AD-BL are for the DEGs in Lan et al (36). In sheet 2, the datasets from column A-AA are for the DEGs in our study; the datasets from column AC-AI are for the DEGs in Wissing et al (37). In sheet 3, the datasets from column A-AB are for the DEGs in our study; the datasets from column AD-AL are for the DEGs in Lu et al (38). In sheet 4, the datasets from column A-AB are for the DEGs in our study; the datasets from column AD-AG are for the DEGs in Kaur et al (39). For a clear distinguishment between our data and the reference data, column AC in sheet 1, column AB in sheet 2, column AC in sheet 3, and column AC in sheet 4 are left blank and highlighted in green; Two columns with title "symbol" and red typed in each sheet list all overlapping DEGs between our data and reference data. <strong>Supplementary dataset </strong><strong>3</strong> This file contains 4 sheets. Each sheet includes KEGG information for the DEGs that overlapped between human PCOS studies and current study. <strong>Supplementary dataset </strong><strong>4</strong> This dataset contains all 126 overlapped DEGs (Supplementary Fig. 6A and B) among RTM, MTM, and control group compared with the PCOS group in F1 model mice. It has two sheets: "F1 up-regulated DEGs" contained all DEGs that have significantly higher (|log2| &gt; 1) expression level in RTM, MTM, and control group than in PCOS group; "F1 down-regulated DEGs" contained all DEGs that have significantly lower (|log2| &gt; 1) expression level in RTM, MTM, and control group than in PCOS group. For each gene, both FPKM of each repeat and the average FPKM of three repeats are shown.
DOI: 10.5281/zenodo.4002477
title: Rat BAT Xenotransplantation Recovers the Fertility and Metabolic Health of PCOS Mice

description: <strong>Supplementary dataset 1</strong> This file contains datasets for all 230 overlapped DEGs (Fig. 6A and B) among RTM, MTM, and control group compared with the PCOS group in F0 model mice. It has two sheets: "F0 up-regulated DEGs" contained all DEGs that have significantly higher (|log2| &gt; 1) expression levels in RTM, MTM, and control group than PCOS group; "F0 down-regulated DEGs" contained all DEGs that have significantly lower (|log2| &gt; 1) expression level in RTM, MTM, and control group than PCOS group. For each gene, both FPKM of each repeat and the average FPKM of three repeats are shown. <strong>Supplementary dataset 2</strong> This file, corresponding to Fig. 7, contains 4 sheets of datasets for all DEGs that overlapped between human PCOS studies and corrent study. From left to right, in sheet 1, the datasets from column A-AB are for the DEGs in current study; the datasets from column AD-BL are for the DEGs in Lan et al (36). In sheet 2, the datasets from column A-AA are for the DEGs in our study; the datasets from column AC-AI are for the DEGs in Wissing et al (37). In sheet 3, the datasets from column A-AB are for the DEGs in our study; the datasets from column AD-AL are for the DEGs in Lu et al (38). In sheet 4, the datasets from column A-AB are for the DEGs in our study; the datasets from column AD-AG are for the DEGs in Kaur et al (39). For a clear distinguishment between our data and the reference data, column AC in sheet 1, column AB in sheet 2, column AC in sheet 3, and column AC in sheet 4 are left blank and highlighted in green; Two columns with title "symbol" and red typed in each sheet list all overlapping DEGs between our data and reference data. <strong>Supplementary dataset </strong><strong>3</strong> This file contains 4 sheets. Each sheet includes KEGG information for the DEGs that overlapped between human PCOS studies and current study. <strong>Supplementary dataset </strong><strong>4</strong> This dataset contains all 126 overlapped DEGs (Supplementary Fig. 6A and B) among RTM, MTM, and control group compared with the PCOS group in F1 model mice. It has two sheets: "F1 up-regulated DEGs" contained all DEGs that have significantly higher (|log2| &gt; 1) expression level in RTM, MTM, and control group than in PCOS group; "F1 down-regulated DEGs" contained all DEGs that have significantly lower (|log2| &gt; 1) expression level in RTM, MTM, and control group than in PCOS group. For each gene, both FPKM of each repeat and the average FPKM of three repeats are shown.
DOI: 10.6084/m9.figshare.9723377
title: Additional file 5: of Arm-less mitochondrial tRNAs conserved for over 30 millions of years in spiders

description: Table S1. Gene orders found in the 32 mitogenomes available in GenBank and MetAMiGA, that retrieved from Parachtes and Harpactocrates plus the ancestral patterns for Pancrustanea, Arthropoda and Chelicetata . (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9723377.v1
title: Additional file 5: of Arm-less mitochondrial tRNAs conserved for over 30 millions of years in spiders

description: Table S1. Gene orders found in the 32 mitogenomes available in GenBank and MetAMiGA, that retrieved from Parachtes and Harpactocrates plus the ancestral patterns for Pancrustanea, Arthropoda and Chelicetata . (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9723365
title: Additional file 1: of Anti-PD-1 monoclonal antibody MEDI0680 in a phase I study of patients with advanced solid malignancies

description: Figure S1. Study design and pharmacokinetic/pharmacodynamic assessment. (a) phase I study design. (b) Overview of pharmacokinetic and pharmacodynamic profile assessment. Figure S2. MEDI0680 binding and specificity for PD-1. (a) MEDI0680 binding to activated primary human T cells. (b) Binding specificity of MEDI0680 to recombinant human proteins that share amino acid sequence homology with PD-1. Figure S3. Inhibition of ligand binding to native PD-1 by MEDI0680. (a) Blockade by MEDI0680 of recombinant human PD-L1 or (b) recombinant human PD-L2 binding to CHO cells expressing human PD-1 protein. Figure S4. In vitro T-cell activation and cytotoxicity mediated by MEDI0680. (a) IFNÎł release into cell culture media of allogeneic dendritic cellâ T cell mixed lymphocyte reactions. (b) Cellular cytotoxicity mediated by EBV-reactive CD8 T cells over time, as determined by non-invasive electrical impedance measurement in an xCelligence RTCA MP instrument as a surrogate for cell death. Figure S5. Representative examples of flow cytometry of peripheral blood from patients treated with MEDI0680. (a) Ki67 staining in CD4+ and CD8+ T cells at cycle 1 day 1 pre-treatment (C1D1) and at cycle 1 day 8 post-treatment, as indicated. (b) HLA-DR and CD38 co-staining on CD4+ effector memory T cells (CD4+ TEM) at the same time points. Figure S6. Lack of correlation between changes in peripheral pharmacodynamic markers and objective clinical response. (a) Fold change in the indicated cytokine and chemokine markers in all cohorts or (b) only in the 10 and 20mg/kg cohorts or (c) the fold change in T-cell proliferation and CD4+ TEM CD38high HLA-DRhigh (activated) T cells with respect to objective clinical responses are shown. Table S1. Key eligibility criteria. Table S2. Patient characteristics and samples evaluated for pharmacodynamic analysis. Table S3. In silico identification of PD-1 paralogs using the protein Basic Local Alignment Search Tool BLASTp. Table S4. Study disposition (as-treated population). (ZIP 5.02 mb)
DOI: 10.6084/m9.figshare.9723365.v1
title: Additional file 1: of Anti-PD-1 monoclonal antibody MEDI0680 in a phase I study of patients with advanced solid malignancies

description: Figure S1. Study design and pharmacokinetic/pharmacodynamic assessment. (a) phase I study design. (b) Overview of pharmacokinetic and pharmacodynamic profile assessment. Figure S2. MEDI0680 binding and specificity for PD-1. (a) MEDI0680 binding to activated primary human T cells. (b) Binding specificity of MEDI0680 to recombinant human proteins that share amino acid sequence homology with PD-1. Figure S3. Inhibition of ligand binding to native PD-1 by MEDI0680. (a) Blockade by MEDI0680 of recombinant human PD-L1 or (b) recombinant human PD-L2 binding to CHO cells expressing human PD-1 protein. Figure S4. In vitro T-cell activation and cytotoxicity mediated by MEDI0680. (a) IFNÎł release into cell culture media of allogeneic dendritic cellâ T cell mixed lymphocyte reactions. (b) Cellular cytotoxicity mediated by EBV-reactive CD8 T cells over time, as determined by non-invasive electrical impedance measurement in an xCelligence RTCA MP instrument as a surrogate for cell death. Figure S5. Representative examples of flow cytometry of peripheral blood from patients treated with MEDI0680. (a) Ki67 staining in CD4+ and CD8+ T cells at cycle 1 day 1 pre-treatment (C1D1) and at cycle 1 day 8 post-treatment, as indicated. (b) HLA-DR and CD38 co-staining on CD4+ effector memory T cells (CD4+ TEM) at the same time points. Figure S6. Lack of correlation between changes in peripheral pharmacodynamic markers and objective clinical response. (a) Fold change in the indicated cytokine and chemokine markers in all cohorts or (b) only in the 10 and 20mg/kg cohorts or (c) the fold change in T-cell proliferation and CD4+ TEM CD38high HLA-DRhigh (activated) T cells with respect to objective clinical responses are shown. Table S1. Key eligibility criteria. Table S2. Patient characteristics and samples evaluated for pharmacodynamic analysis. Table S3. In silico identification of PD-1 paralogs using the protein Basic Local Alignment Search Tool BLASTp. Table S4. Study disposition (as-treated population). (ZIP 5.02 mb)
DOI: 10.6084/m9.figshare.9723344
title: Additional file 2: of Doctorsâ attitudes to, beliefs about, and experiences of the regulation of professional competence: a scoping review protocol

description: Data charting form. Form to be used for data charting process. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9723344.v1
title: Additional file 2: of Doctorsâ attitudes to, beliefs about, and experiences of the regulation of professional competence: a scoping review protocol

description: Data charting form. Form to be used for data charting process. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9723326
title: Additional file 3: of Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome

description: Classification and pI values of the different types of proteins retrieved from the eight prokaryotes used in the electrostatic surface potential and pI comparisons. The pIs of the different proteins, their transmembrane domain topology and presence/absence of signal peptides are shown. (XLSX 784 kb)
DOI: 10.6084/m9.figshare.9723326.v1
title: Additional file 3: of Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome

description: Classification and pI values of the different types of proteins retrieved from the eight prokaryotes used in the electrostatic surface potential and pI comparisons. The pIs of the different proteins, their transmembrane domain topology and presence/absence of signal peptides are shown. (XLSX 784 kb)
DOI: 10.6084/m9.figshare.9723317
title: Additional file 2: of Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome

description: Prokaryotic genomes used in this study. Name of the genome, accession/Genbank number (NCBI), habitat, isolation/origin, reference, type of genome and taxonomy fields are provided. Habitat, phyla and Isoelectric point relative frequencies of each microbe. Statistical analysis of the compared dataset (Bray-Curtis+PERMANOVA, Principal Component Analysis, Averageâ +â Standard Deviation). (XLSX 60 kb)
DOI: 10.6084/m9.figshare.9723317.v1
title: Additional file 2: of Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome

description: Prokaryotic genomes used in this study. Name of the genome, accession/Genbank number (NCBI), habitat, isolation/origin, reference, type of genome and taxonomy fields are provided. Habitat, phyla and Isoelectric point relative frequencies of each microbe. Statistical analysis of the compared dataset (Bray-Curtis+PERMANOVA, Principal Component Analysis, Averageâ +â Standard Deviation). (XLSX 60 kb)