cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14342789
title: Metagenome assembled genomes co_6-Bin_15_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14551008.v2
title: ecologically_omnipresent_genes

description: Information on the 1,864 pan-ecological genes we identified in our 30% gene catalog, including annotations to the Genome Taxonomy Database bac120 genes and functional annotations.
DOI: 10.6084/m9.figshare.14342789.v1
title: Metagenome assembled genomes co_6-Bin_15_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342801.v1
title: Metagenome assembled genomes co_1-Bin_14_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342798
title: Metagenome assembled genomes co_5-Bin_5_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342804
title: Metagenome assembled genomes co_7-Bin_12_2.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342798.v1
title: Metagenome assembled genomes co_5-Bin_5_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342801
title: Metagenome assembled genomes co_1-Bin_14_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342804.v1
title: Metagenome assembled genomes co_7-Bin_12_2.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342834.v1
title: Metagenome assembled genomes co_7-Bin_40_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342834
title: Metagenome assembled genomes co_7-Bin_40_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6073/pasta/4e65443dda8e180fae3077b8f6502d3f
title: Time series of dissolved methane and carbon dioxide concentrations for Falling Creek Reservoir and Beaverdam Reservoir in southwestern Virginia, USA during 2015-2020

description: Surface samples and depth profiles of carbon dioxide and methane concentrations were sampled during the ice-free period from 2015 to 2020 in two drinking water reservoirs in southwestern Virginia, USA: Beaverdam Reservoir (Vinton, Virginia) and Falling Creek Reservoir (Vinton, Virginia). Both reservoirs are owned and operated by the Western Virginia Water Authority as primary or secondary drinking water sources for Roanoke, Virginia. The dataset consists of depth profiles of dissolved greenhouse gas (carbon dioxide, methane) samples measured at the deepest site of each reservoir adjacent to the dam. Additional samples were collected at a gauged weir on Falling Creek Reservoir's primary inflow tributary as well as surface samples from a wetland adjacent to Falling Creek Reservoir. At Beaverdam Reservoir, additional samples were collected at the outflow below the dam. Samples were collected approximately fortnightly from March-April, weekly from May-October, and monthly in November at Falling Creek Reservoir and Beaverdam Reservoir. In 2019, surface samples along the stream and reservoir continuum from both Falling Creek Reservoir and Beaverdam Reservoir were collected monthly during the summer stratified period.
DOI: 10.15468/yt8p5x
title: The easternmost record of Macratriinae LeConte, 1862 (Coleoptera: Anthicidae) with a new species from Fiji and a genus-rank synonymy in Macratriini LeConte 1862

description: This dataset contains the digitized treatments in Plazi based on the original journal article Telnov, Dmitry (2021): The easternmost record of Macratriinae LeConte, 1862 (Coleoptera: Anthicidae) with a new species from Fiji and a genus-rank synonymy in Macratriini LeConte 1862. Zootaxa 4965 (1): 191-200, DOI: https://doi.org/10.11646/zootaxa.4965.1.10
DOI: 10.5281/zenodo.4729075
title: PathDSP: Explainable drug sensitivity prediction through cancer pathway enrichment

description: A deep learning model for predicting drug response of cancer cell lines with cancer signaling pathway enrichment
DOI: 10.5281/zenodo.4729068
title: PathDSP: Explainable drug sensitivity prediction through cancer pathway enrichment

description: A deep learning model for predicting drug response of cancer cell lines with cancer signaling pathway enrichment
DOI: 10.6084/m9.figshare.14342846.v1
title: Metagenome assembled genomes co_9-Bin_15.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342846
title: Metagenome assembled genomes co_9-Bin_15.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342912
title: Metagenome assembled genomes co_2-Bin_21_2.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342912.v1
title: Metagenome assembled genomes co_2-Bin_21_2.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342915
title: Metagenome assembled genomes co_8-Bin_15_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342915.v1
title: Metagenome assembled genomes co_8-Bin_15_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342918.v1
title: Metagenome assembled genomes co_5-Bin_43_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342918
title: Metagenome assembled genomes co_5-Bin_43_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342921
title: Metagenome assembled genomes co_3-Bin_43_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342921.v1
title: Metagenome assembled genomes co_3-Bin_43_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342924.v1
title: Metagenome assembled genomes co_3-Bin_9_2.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342924
title: Metagenome assembled genomes co_3-Bin_9_2.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342927
title: Metagenome assembled genomes co_7-Bin_52_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342927.v1
title: Metagenome assembled genomes co_7-Bin_52_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14551011
title: Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques

description: The emergence of several SARS-CoV-2 variants has caused global concerns about increased transmissibility, increased pathogenicity and decreased efficacy of medical countermeasures. Animal models can be used to assess phenotypical changes in the absence of confounding factors that affect observed pathogenicity and transmissibility data in the human population. Here, we studied the pathogenicity of variants of concern (VOC) B.1.1.7 and B.1.351 in rhesus macaques and compared it to a recent clade B.1 SARS-CoV-2 isolate containing the D614G substitution in spike. The B.1.1.7 VOC behaved similarly to the D614G with respect to clinical disease, virus shedding and virus replication in the respiratory tract. The B.1.351 isolate resulted in lower clinical scores in rhesus macaques that correlated with lower virus titers in the lungs, less severe histologic lung lesions and less viral antigen detected in the lungs. We observed differences in the local innate immune response to infection. In bronchoalveolar lavages, cytokines and chemokines were upregulated on day 4 in animals inoculated with D614G and B.1.1.7 but not in those inoculated with B.1.351. In nasal samples, we did not detect upregulation of cytokines and chemokines in D614G or B.1.351-inoculated animals. However, cytokines and chemokines were upregulated in the noses of B.1.1.7-inoculated animals. Taken together, our comparative pathogenicity study suggests that ongoing circulation under diverse evolutionary pressure favors transmissibility and immune evasion rather than an increase in intrinsic pathogenicity.
DOI: 10.6084/m9.figshare.14551011.v1
title: Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques

description: The emergence of several SARS-CoV-2 variants has caused global concerns about increased transmissibility, increased pathogenicity and decreased efficacy of medical countermeasures. Animal models can be used to assess phenotypical changes in the absence of confounding factors that affect observed pathogenicity and transmissibility data in the human population. Here, we studied the pathogenicity of variants of concern (VOC) B.1.1.7 and B.1.351 in rhesus macaques and compared it to a recent clade B.1 SARS-CoV-2 isolate containing the D614G substitution in spike. The B.1.1.7 VOC behaved similarly to the D614G with respect to clinical disease, virus shedding and virus replication in the respiratory tract. The B.1.351 isolate resulted in lower clinical scores in rhesus macaques that correlated with lower virus titers in the lungs, less severe histologic lung lesions and less viral antigen detected in the lungs. We observed differences in the local innate immune response to infection. In bronchoalveolar lavages, cytokines and chemokines were upregulated on day 4 in animals inoculated with D614G and B.1.1.7 but not in those inoculated with B.1.351. In nasal samples, we did not detect upregulation of cytokines and chemokines in D614G or B.1.351-inoculated animals. However, cytokines and chemokines were upregulated in the noses of B.1.1.7-inoculated animals. Taken together, our comparative pathogenicity study suggests that ongoing circulation under diverse evolutionary pressure favors transmissibility and immune evasion rather than an increase in intrinsic pathogenicity.
DOI: 10.6084/m9.figshare.14342930
title: Metagenome assembled genomes co_5-Bin_38_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342930.v1
title: Metagenome assembled genomes co_5-Bin_38_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342933
title: Metagenome assembled genomes co_7-Bin_37_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342933.v1
title: Metagenome assembled genomes co_7-Bin_37_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342936.v1
title: Metagenome assembled genomes co_8-Bin_21_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342936
title: Metagenome assembled genomes co_8-Bin_21_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342939
title: Metagenome assembled genomes co_6-Bin_5_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342939.v1
title: Metagenome assembled genomes co_6-Bin_5_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342942
title: Metagenome assembled genomes co_5-Bin_30_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342942.v1
title: Metagenome assembled genomes co_5-Bin_30_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342945
title: Metagenome assembled genomes co_7-Bin_1_4.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342945.v1
title: Metagenome assembled genomes co_7-Bin_1_4.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342948.v1
title: Metagenome assembled genomes co_8-Bin_38_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342948
title: Metagenome assembled genomes co_8-Bin_38_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342951
title: Metagenome assembled genomes co_6-Bin_13_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342951.v1
title: Metagenome assembled genomes co_6-Bin_13_1.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.
DOI: 10.6084/m9.figshare.14342954
title: Metagenome assembled genomes co_3-Bin_34_2.fa

description: Co-assemblies were binned with CONCOCT within anvi’o v5.1 by clustering scaffolds 2500 bp or longer into metagenome assembled genomes (MAGs) and manually refining them within the anvi’o platform. Furthermore, dRep v2.3.2 was used to dereplicate MAGs and obtain representative genomes with flags ‘-comp 50 -con 10’ and default values.