cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12931229.v3
title: Multiplexing F-actin, MT and IF LatA and Control Data

description: These are SIFTER-generated gel images of separations of cytoskeletal complexes (e.g., F-actin, vimentin intermediate filaments, IF and beta-tubulin microtubules, MT) from monomeric proteins. Files indicate the cell type (U2OS), and whether the cells were drug-treated (LatA) or not (CTRL). Please note that the word "smooth" is included in the file names to indicate images were median filtered (using the Fiji "Remove Outliers" macro with settings: threshold = 50 AFU, and pixel radius = 2). For files labeled "transformed", the image was aligned to the gel image with the same "gel number" using Landmark Correspondence in Fiji, after the gel was stripped and re-probed for beta-tubulin.
DOI: 10.6084/m9.figshare.12931229.v2
title: Multiplexing F-actin, MT and IF LatA and Control Data

description: These are SIFTER-generated gel images of separations of cytoskeletal complexes (e.g., F-actin, vimentin intermediate filaments, IF and beta-tubulin microtubules, MT) from monomeric proteins. Files indicate the cell type (U2OS), and whether the cells were drug-treated (LatA) or not (CTRL). Please note that the word "smooth" is included in the file names to indicate images were median filtered (using the Fiji "Remove Outliers" macro with settings: threshold = 50 AFU, and pixel radius = 2). For files labeled "transformed", the image was aligned to the gel image with the same "gel number" using Landmark Correspondence in Fiji, after the gel was stripped and re-probed for beta-tubulin.
DOI: 10.6084/m9.figshare.12931268
title: Imaging Electrophoresis of GFP-actin and RFP-LifeAct cells

description: These files are timelapse images collected after lysis of either MDA-MB-231 GFP-actin cells or U2OS RFP-LifeAct cells in F-actin stabilization lysis buffer. Upon application of an electric field, F-actin migrates to the microwell edge (for both the U2OS and MDA-MB-231 cells), and G-actin electrophoretically injects into the gel for the MDA-MB-231 GFP-actin cells.
DOI: 10.6084/m9.figshare.12931268.v1
title: Imaging Electrophoresis of GFP-actin and RFP-LifeAct cells

description: These files are timelapse images collected after lysis of either MDA-MB-231 GFP-actin cells or U2OS RFP-LifeAct cells in F-actin stabilization lysis buffer. Upon application of an electric field, F-actin migrates to the microwell edge (for both the U2OS and MDA-MB-231 cells), and G-actin electrophoretically injects into the gel for the MDA-MB-231 GFP-actin cells.
DOI: 10.3886/e115141v2-88480
title: Truth Effect Warnings

description: Data, syntax, and supplemental materials for Only Half of What I’ll Tell You is True: How Experimental Procedures Lead to an Underestimation of the Truth Effect, a manuscript currently under review.
DOI: 10.6084/m9.figshare.14752322.v1
title: Additional file 2 of Delays in reporting and publishing trial results during pandemics: cross sectional analysis of 2009 H1N1, 2014 Ebola, and 2016 Zika clinical trials

description: Additional file 2 Appendix B.
DOI: 10.6084/m9.figshare.14752310.v1
title: Additional file 9 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 9: S7 Table. Summary and list of genes within the DBScan cluster for each chromosome arm.
DOI: 10.6084/m9.figshare.14752307.v1
title: Additional file 8 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 8: S6 Table. List of genes showing Fst &gt; 0.3, 0.4, 0.5 between An. gambiae and An. coluzzii.
DOI: 10.6084/m9.figshare.14752304.v1
title: Additional file 7 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 7: S5 Table. Fst values for each gene in the t-SNE plot.
DOI: 10.6084/m9.figshare.14752301.v1
title: Additional file 6 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 6: S4 Table. Measure of consistency of the t-SNE plot.
DOI: 10.6084/m9.figshare.14747925
title: Supplementary Material for: Immunological Microenvironment Predicts the Survival of the Patients with Hepatocellular Carcinoma Treated with Anti-PD-1 Antibody

description: <b><i>Introduction:</i></b> Although immune checkpoint inhibitors (ICIs) have been considered as promising agents for the treatment of advanced hepatocellular carcinoma (HCC), previous clinical trials revealed that the response to anti-programmed cell death protein 1 (anti-PD-1) monotherapy was as low as 20%. Identifying subgroups that respond well to ICIs is clinically important. Here, we studied the prognostic factors for anti-PD-1 antibody treatment based on the molecular and immunological features of HCC. <b><i>Methods:</i></b> Patients who were administered anti-PD1 antibody for advanced HCC at Kindai University Hospital were included. Clinicopathological backgrounds and antitumor responses were examined in 34 cases where tumor tissues before treatment were available. Transcriptome analysis was performed using 40 HCC samples obtained from surgical resection, and immune status was compared between 20 HCCs with activating mutations in β-catenin and those without the mutations using transcriptome-based immunogram. <b><i>Results:</i></b> Univariate analysis showed that the disease control rate was significantly better in patients with α-fetoprotein &lt; 400 ng/mL, negative for β-catenin/glutamate synthetase (GS) staining, high combined positive score (CPS) of programmed death-ligand 1 (PD-L1), and increased infiltration of CD8<sup>+</sup> cells in tumor tissues. Among them, negative staining of β-catenin/GS, CPS of PD-L1 ≥ 1, and high degree of CD8<sup>+</sup> tumor-infiltrating lymphocytes (TILs) were significantly associated with longer survival in both progression-free survival (PFS) and overall survival (OS). The combination of these factors well stratified the survival of the patients on anti-PD-1 antibody in both PFS and OS (<i>p</i> &lt; 0.0001 and <i>p</i> = 0.0048 for PFS and OS, respectively). In addition, the immunogram revealed that tumor-carrying mutations in β-catenin showed downregulation of immune-related genes, especially in those related to priming and activation by dendritic cells, interferon-γ response, inhibitory molecules, and regulatory T cells. <b><i>Discussion/Conclusion:</i></b> The combined score including Wnt/β-catenin activation, CPS of PD-L1, and degree of CD8<sup>+</sup> TILs in HCC is informative for predicting the response to ICI in HCC cases. Constitutive activation of β-catenin can induce an immune cold phenotype with downregulation of immune-related genes, and immunohistochemistry-based evaluation is beneficial for identifying the subgroup that shows a good response to ICI.
DOI: 10.6084/m9.figshare.14747925.v1
title: Supplementary Material for: Immunological Microenvironment Predicts the Survival of the Patients with Hepatocellular Carcinoma Treated with Anti-PD-1 Antibody

description: <b><i>Introduction:</i></b> Although immune checkpoint inhibitors (ICIs) have been considered as promising agents for the treatment of advanced hepatocellular carcinoma (HCC), previous clinical trials revealed that the response to anti-programmed cell death protein 1 (anti-PD-1) monotherapy was as low as 20%. Identifying subgroups that respond well to ICIs is clinically important. Here, we studied the prognostic factors for anti-PD-1 antibody treatment based on the molecular and immunological features of HCC. <b><i>Methods:</i></b> Patients who were administered anti-PD1 antibody for advanced HCC at Kindai University Hospital were included. Clinicopathological backgrounds and antitumor responses were examined in 34 cases where tumor tissues before treatment were available. Transcriptome analysis was performed using 40 HCC samples obtained from surgical resection, and immune status was compared between 20 HCCs with activating mutations in β-catenin and those without the mutations using transcriptome-based immunogram. <b><i>Results:</i></b> Univariate analysis showed that the disease control rate was significantly better in patients with α-fetoprotein &lt; 400 ng/mL, negative for β-catenin/glutamate synthetase (GS) staining, high combined positive score (CPS) of programmed death-ligand 1 (PD-L1), and increased infiltration of CD8<sup>+</sup> cells in tumor tissues. Among them, negative staining of β-catenin/GS, CPS of PD-L1 ≥ 1, and high degree of CD8<sup>+</sup> tumor-infiltrating lymphocytes (TILs) were significantly associated with longer survival in both progression-free survival (PFS) and overall survival (OS). The combination of these factors well stratified the survival of the patients on anti-PD-1 antibody in both PFS and OS (<i>p</i> &lt; 0.0001 and <i>p</i> = 0.0048 for PFS and OS, respectively). In addition, the immunogram revealed that tumor-carrying mutations in β-catenin showed downregulation of immune-related genes, especially in those related to priming and activation by dendritic cells, interferon-γ response, inhibitory molecules, and regulatory T cells. <b><i>Discussion/Conclusion:</i></b> The combined score including Wnt/β-catenin activation, CPS of PD-L1, and degree of CD8<sup>+</sup> TILs in HCC is informative for predicting the response to ICI in HCC cases. Constitutive activation of β-catenin can induce an immune cold phenotype with downregulation of immune-related genes, and immunohistochemistry-based evaluation is beneficial for identifying the subgroup that shows a good response to ICI.
DOI: 10.6084/m9.figshare.14752298.v1
title: Additional file 5 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 5: S3 Table. Summary of missing data per gene.
DOI: 10.6084/m9.figshare.14752295.v1
title: Additional file 4 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 4: S2 Table. Number of SNPs, genomic location and coordinates for each gene in the t-SNE plot.
DOI: 10.6084/m9.figshare.14752292.v1
title: Additional file 3 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 3: S1 Table. Sample information, data from the Ag1000G.
DOI: 10.6084/m9.figshare.14752283.v1
title: Additional file 11 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 11: S9 Table. GO enrichment analysis.
DOI: 10.6084/m9.figshare.14752280.v1
title: Additional file 10 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 10: S8 Table. Guinea-Bissau cluster.
DOI: 10.6084/m9.figshare.14752271.v1
title: Additional file 3 of Effects of FUdR on gene expression in the C. elegans bacterial diet OP50

description: Additional file 3: Table S2. Common bacterial genes in OP50 E. coli regulated in response to FUdR and in specific hosts.
DOI: 10.6084/m9.figshare.14752270.v1
title: Additional file 1 of Change theory in STEM higher education: a systematic review

description: Additional file 1.
DOI: 10.6084/m9.figshare.14752265.v1
title: Additional file 1 of Effects of FUdR on gene expression in the C. elegans bacterial diet OP50

description: Additional file 1: Table S1. The top 158 differentially expressed genes in OP50 E. coli exposed to FUdR.
DOI: 10.6084/m9.figshare.14752226.v1
title: Additional file 2 of Gene set enrichment analysis for genome-wide DNA methylation data

description: Additional file 2. Supplementary tables.
DOI: 10.6084/m9.figshare.14752216.v1
title: Additional file 2 of Unbiased profiling of CRISPR RNA-guided transposition products by long-read sequencing

description: Additional file 2: Supplementary Table 1. SMRT Sequencing and Analysis Statistics.
DOI: 10.6084/m9.figshare.14752208.v1
title: Additional file 3 of Characterization of nucleic acids from extracellular vesicle-enriched human sweat

description: Additional file 3: Supplementary Table 2. Comparison of top 1% RNA identified in Illumina and Ion Torrent.
DOI: 10.6084/m9.figshare.14752205.v1
title: Additional file 2 of Characterization of nucleic acids from extracellular vesicle-enriched human sweat

description: Additional file 2: Supplementary Table 1. Transcripts identified in at least 18 samples.
DOI: 10.6084/m9.figshare.14752148.v1
title: Additional file 6 of Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection

description: Additional file 6: PM- and DM-responsive lncRNAs as putative targets and endogenous target mimics of Vitis vinifera miRNAs. PM- and DM-responsive protein coding sequences (which are coexpressing with PM- and DM-responsive lncRNAs) as putative targets of Vitis vinifera miRNAs.
DOI: 10.6084/m9.figshare.14752145.v1
title: Additional file 5 of Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection

description: Additional file 5: Pathway enrichment analysis for lncRNAs co-expressing with CDS in response to powdery and downy mildew.
DOI: 10.6084/m9.figshare.14752142.v1
title: Additional file 4 of Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection

description: Additional file 4: Gene Ontology distribution for all 3 categories for mRNAs coexpressing with PM and DM-responsive lncRNAs and direct Gene Ontology (GO) Count representing the most frequent GO terms in the Biological Processes category.
DOI: 10.6084/m9.figshare.14752139.v1
title: Additional file 3 of Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection

description: Additional file 3: Co-expressing powdery and downy mildew-responsive Vitis vinifera lncRNAs and mature mRNAs at Pearson correlation coefficient &gt;= 0.9 (using CoExpress v1.5), including all the positively and negatively co-related co-expressing pairs based on Pearson correlation coefficient using the PERL Script.
DOI: 10.6084/m9.figshare.14752133.v1
title: Additional file 1 of Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection

description: Additional file 1: Table S1. Details of transcriptomic data collected from NCBI-SRA database.
DOI: 10.6084/m9.figshare.14752129.v1
title: Additional file 8 of Plasma metabolomic profiling in patients with rheumatoid arthritis identifies biochemical features predictive of quantitative disease activity

description: Additional file 8: Supplementary Table 6. Metabolites displaying significant changes in abundances in patients without clinical improvement (n = 48).
DOI: 10.6084/m9.figshare.14752126.v1
title: Additional file 7 of Plasma metabolomic profiling in patients with rheumatoid arthritis identifies biochemical features predictive of quantitative disease activity

description: Additional file 7: Supplementary Table 5. Metabolites displaying significant changes in abundances in patients with clinical improvement (n = 16).
DOI: 10.6084/m9.figshare.14752123.v1
title: Additional file 6 of Plasma metabolomic profiling in patients with rheumatoid arthritis identifies biochemical features predictive of quantitative disease activity

description: Additional file 6: Supplementary Table 4. Differentially abundant metabolites between lower (DAS28-CRP ≤ 3.2) and higher (DAS28-CRP &gt; 3.2) disease activity groups.
DOI: 10.6084/m9.figshare.14752120.v1
title: Additional file 5 of Plasma metabolomic profiling in patients with rheumatoid arthritis identifies biochemical features predictive of quantitative disease activity

description: Additional file 5: Supplementary Table 3. Demographic characteristics of discovery cohort samples (n = 128) divided into lower (DAS28-CRP ≤ 3.2) and higher disease activity (DAS28-CRP &gt; 3.2).
DOI: 10.6084/m9.figshare.14752114.v1
title: Additional file 3 of Plasma metabolomic profiling in patients with rheumatoid arthritis identifies biochemical features predictive of quantitative disease activity

description: Additional file 3: Supplementary Table 2. Subject characteristics of 12 patients (12 samples) from the validation cohort.
DOI: 10.6084/m9.figshare.14752111.v1
title: Additional file 2 of Plasma metabolomic profiling in patients with rheumatoid arthritis identifies biochemical features predictive of quantitative disease activity

description: Additional file 2: Supplementary Table 1. Subject characteristics of 64 patients (128 samples) from the discovery cohort.
DOI: 10.6084/m9.figshare.14752061.v1
title: Additional file 1 of SaQuant: a real-time PCR assay for quantitative assessment of Staphylococcus aureus

description: Additional file 1.
DOI: 10.6084/m9.figshare.14752039.v1
title: Additional file 1 of Conspecific odor cues induce different vocal responses in serrate-legged small treefrogs, but only in the absence of acoustic signals

description: Additional file 1.
DOI: 10.6084/m9.figshare.14752036.v1
title: Additional file 4 of Analysis of single-cell RNA sequencing data based on autoencoders

description: Additional file 4. Excel file of the metrics calculated for the MCA datasets. Each tab is related to a tested approach and shows the calculated metrics and used method.
DOI: 10.6084/m9.figshare.14752033.v1
title: Additional file 3 of Analysis of single-cell RNA sequencing data based on autoencoders

description: Additional file 3. Excel file of the metrics calculated for the PIC datasets. Each tab is related to a tested approach and shows the calculated metrics and used method.
DOI: 10.6084/m9.figshare.14752030.v1
title: Additional file 2 of Analysis of single-cell RNA sequencing data based on autoencoders

description: Additional file 2. Excel file of the metrics calculated for the PBMC datasets. Each tab is related to a tested approach and shows the calculated metrics and used method.
DOI: 10.6084/m9.figshare.14752322
title: Additional file 2 of Delays in reporting and publishing trial results during pandemics: cross sectional analysis of 2009 H1N1, 2014 Ebola, and 2016 Zika clinical trials

description: Additional file 2 Appendix B.
DOI: 10.17909/t9-gxy4-t088
title: PG1407+265 ACS image

description: Lehner et al ACS observation of PG1407+265
DOI: 10.6084/m9.figshare.14752310
title: Additional file 9 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 9: S7 Table. Summary and list of genes within the DBScan cluster for each chromosome arm.
DOI: 10.6084/m9.figshare.14752307
title: Additional file 8 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 8: S6 Table. List of genes showing Fst &gt; 0.3, 0.4, 0.5 between An. gambiae and An. coluzzii.
DOI: 10.6084/m9.figshare.14752304
title: Additional file 7 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 7: S5 Table. Fst values for each gene in the t-SNE plot.
DOI: 10.6084/m9.figshare.14752301
title: Additional file 6 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 6: S4 Table. Measure of consistency of the t-SNE plot.
DOI: 10.6084/m9.figshare.14752298
title: Additional file 5 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 5: S3 Table. Summary of missing data per gene.
DOI: 10.6084/m9.figshare.14752295
title: Additional file 4 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 4: S2 Table. Number of SNPs, genomic location and coordinates for each gene in the t-SNE plot.
DOI: 10.6084/m9.figshare.14752292
title: Additional file 3 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 3: S1 Table. Sample information, data from the Ag1000G.
DOI: 10.6084/m9.figshare.14752283
title: Additional file 11 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 11: S9 Table. GO enrichment analysis.
DOI: 10.6084/m9.figshare.14752280
title: Additional file 10 of Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

description: Additional file 10: S8 Table. Guinea-Bissau cluster.
DOI: 10.6084/m9.figshare.14752271
title: Additional file 3 of Effects of FUdR on gene expression in the C. elegans bacterial diet OP50

description: Additional file 3: Table S2. Common bacterial genes in OP50 E. coli regulated in response to FUdR and in specific hosts.
DOI: 10.6084/m9.figshare.14752270
title: Additional file 1 of Change theory in STEM higher education: a systematic review

description: Additional file 1.
DOI: 10.6084/m9.figshare.14752265
title: Additional file 1 of Effects of FUdR on gene expression in the C. elegans bacterial diet OP50

description: Additional file 1: Table S1. The top 158 differentially expressed genes in OP50 E. coli exposed to FUdR.
DOI: 10.5281/zenodo.4915584
title: data for the submission in Marine Geology MARGO-S-21-00281

description: Data used for the plots can be found in the submission in Marine Geology MARGO-S-21-00281. The bathymetric data are saved as sufer and excel data files. 1) 202011.srf is used for figure 1b. 2) large bar elevation.xlsx is used for figure 2.
DOI: 10.5281/zenodo.4915583
title: data for the submission in Marine Geology MARGO-S-21-00281

description: Data used for the plots can be found in the submission in Marine Geology MARGO-S-21-00281. The bathymetric data are saved as sufer and excel data files. 1) 202011.srf is used for figure 1b. 2) large bar elevation.xlsx is used for figure 2.
DOI: 10.6084/m9.figshare.14752226
title: Additional file 2 of Gene set enrichment analysis for genome-wide DNA methylation data

description: Additional file 2. Supplementary tables.
DOI: 10.6084/m9.figshare.14752216
title: Additional file 2 of Unbiased profiling of CRISPR RNA-guided transposition products by long-read sequencing

description: Additional file 2: Supplementary Table 1. SMRT Sequencing and Analysis Statistics.
DOI: 10.6084/m9.figshare.14752208
title: Additional file 3 of Characterization of nucleic acids from extracellular vesicle-enriched human sweat

description: Additional file 3: Supplementary Table 2. Comparison of top 1% RNA identified in Illumina and Ion Torrent.
DOI: 10.6084/m9.figshare.14752205
title: Additional file 2 of Characterization of nucleic acids from extracellular vesicle-enriched human sweat

description: Additional file 2: Supplementary Table 1. Transcripts identified in at least 18 samples.
DOI: 10.6084/m9.figshare.14752148
title: Additional file 6 of Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection

description: Additional file 6: PM- and DM-responsive lncRNAs as putative targets and endogenous target mimics of Vitis vinifera miRNAs. PM- and DM-responsive protein coding sequences (which are coexpressing with PM- and DM-responsive lncRNAs) as putative targets of Vitis vinifera miRNAs.
DOI: 10.6084/m9.figshare.14752145
title: Additional file 5 of Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection

description: Additional file 5: Pathway enrichment analysis for lncRNAs co-expressing with CDS in response to powdery and downy mildew.