cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7294/22203001
title: HBProphage PeerJ 2023

description: Bacterial isolates from the honey bee (Apis mellifera) gut were analyzed for the presence of prophages using a combination of phage analysis programs: VirSorter2 (v2.2.2), CheckV (v.0.7.0), and Vibrant (v1.2.1). Proteins were predicted using prokka (v. 1.14.6) and initially functionally annotated using the PHROGS database (https://phrogs.lmge.uca.fr/index.php, downloaded from http://millardlab.org/2021/11/21/phage-annotation-with-phrogs/ on July 20, 2022). Proteins were then additionally annotated using hidden Markov profiles from the eggNOG v5 (http://eggnog5.embl.de) databases. Associated nucleotide/amino acid sequences and functional annotations of prophage predicted in bacterial isolates are included as files here. Associated code is available at github: https://github.com/ebueren/HBProphage_PeerJ This data is associated with "Characterization of prophages in bacterial genomes from the honey bee (<em>Apis mellifera</em>) gut microbiome", currently in review at PeerJ.
DOI: 10.7294/22203001.v1
title: HBProphage PeerJ 2023

description: Bacterial isolates from the honey bee (Apis mellifera) gut were analyzed for the presence of prophages using a combination of phage analysis programs: VirSorter2 (v2.2.2), CheckV (v.0.7.0), and Vibrant (v1.2.1). Proteins were predicted using prokka (v. 1.14.6) and initially functionally annotated using the PHROGS database (https://phrogs.lmge.uca.fr/index.php, downloaded from http://millardlab.org/2021/11/21/phage-annotation-with-phrogs/ on July 20, 2022). Proteins were then additionally annotated using hidden Markov profiles from the eggNOG v5 (http://eggnog5.embl.de) databases. Associated nucleotide/amino acid sequences and functional annotations of prophage predicted in bacterial isolates are included as files here. Associated code is available at github: https://github.com/ebueren/HBProphage_PeerJ This data is associated with "Characterization of prophages in bacterial genomes from the honey bee (<em>Apis mellifera</em>) gut microbiome", currently in review at PeerJ.
DOI: 10.25810/k55w-7a04.58
title: World Radio Coverage of Climate Change or Global Warming, 2000-2023 - January 2023

description: The Media and Climate Change Observatory Data monitors 130 sources (across newspapers, radio and TV) in 59 countries in seven different regions around the world. Data is assembled by accessing archives through the Lexis Nexis, Proquest and Factiva databases via the University of Colorado libraries. More information may be found at: http://mecco.colorado.edu.
DOI: 10.5281/zenodo.7680624
title: Erosion-classification data for centre-pivot-irrigated fields in Cristalina, Brazil

description: This dataset provides the results from a visual classification of erosion features for centre-pivot-irrigated fields in the municipality of Cristalina, Brazil. A detailed description of the data is provided in the README file. The methodology of the classification is described in detail in the preprint linked to this entry. The shapefiles with the resulting erosion classifications per centre-pivot field were adapted from the freely available geodata provided in the Brazilian Irrigation Atlas, developed by the Brazilian Water Agency: Agência Nacional de Águas e Saneamento Básico (ANA). Atlas Irrigação 2021: Uso da Água na Agricultura Irrigada. Accessed 24 February 2023. &lt;https://metadados.snirh.gov.br/geonetwork/srv/api/records/e2d38e3f-5e62-41ad-87ab-990490841073&gt;.
DOI: 10.5281/zenodo.7680625
title: Erosion-classification data for centre-pivot-irrigated fields in Cristalina, Brazil

description: This dataset provides the results from a visual classification of erosion features for centre-pivot-irrigated fields in the municipality of Cristalina, Brazil. A detailed description of the data is provided in the README file. The methodology of the classification is described in detail in the preprint linked to this entry. The shapefiles with the resulting erosion classifications per centre-pivot field were adapted from the freely available geodata provided in the Brazilian Irrigation Atlas, developed by the Brazilian Water Agency: Agência Nacional de Águas e Saneamento Básico (ANA). Atlas Irrigação 2021: Uso da Água na Agricultura Irrigada. Accessed 24 February 2023. &lt;https://metadados.snirh.gov.br/geonetwork/srv/api/records/e2d38e3f-5e62-41ad-87ab-990490841073&gt;.
DOI: 10.5281/zenodo.7696914
title: Recombinant Expression and Purification of ABHD2 from E. coli

description: α/β Hydrolase domain-containing protein 2 (ABHD2), is a member of the metabolic serine hydrolases superfamily & a progesterone membrane receptor. In sperm, it supports the activation of CatSper which leads to sperm hypermotility. ABHD2 is 425 aa and has a N-terminal transmembrane domain followed by an extracellular facing domain. Here we report the recombinant expression and purification of ABHD2 amino acids 33-435 from <em>E. coli</em>. To the best of our knowledge, we are the first to have recombinantly purified active ABHD2.
DOI: 10.5281/zenodo.7696913
title: Recombinant Expression and Purification of ABHD2 from E. coli

description: α/β Hydrolase domain-containing protein 2 (ABHD2), is a member of the metabolic serine hydrolases superfamily & a progesterone membrane receptor. In sperm, it supports the activation of CatSper which leads to sperm hypermotility. ABHD2 is 425 aa and has a N-terminal transmembrane domain followed by an extracellular facing domain. Here we report the recombinant expression and purification of ABHD2 amino acids 33-435 from <em>E. coli</em>. To the best of our knowledge, we are the first to have recombinantly purified active ABHD2.
DOI: 10.6073/pasta/31ecbf6e3f9a68ce001a21328db9f078
title: ASD05 Stream discharge measured at the flumes on watershed N01B at Konza Prairie

description: Stream discharge is measured on a catchment (N01B), with 1-year fire return interval and grazed by bison since 1992. Measurements are taken at 5 minute intervals at a triangular throated flume. The prairie streams are 3rd-order and are intermittent. Daily and stormflow discharge records are available.
DOI: 10.5066/p92omgpn
title: Acute and chronic toxicity of two perfluoroalkyl substances to Neocloeon triangulifer

description: Dataset consists of 4-day, 14-day, and full life responses of laboratory cultured mayflies (Neocloeon triangulifer) to perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA).� Responses were measured as survival at 4 days, 14 days, pre-emergent nymph (PEN) stage, and emergence; 14-day length; number of days to PEN stage, and imago live weight.� Water quality and analytical chemistry results associated with toxicity data are included.
DOI: 10.25422/azu.data.17054063
title: Data and Code for "Comprehensive Radar Mapping of Malaspina Glacier (Sít' Tlein), Alaska—The World's Largest Piedmont Glacier—Reveals Potential for Instability"

description: Malaspina Glacier, located on the coast of southern Alaska, is the world's largest piedmont glacier. A narrow ice-cored foreland zone undergoing rapid thermokarst erosion separates the glacier from the relatively warm waters of the Gulf of Alaska. Glacier-wide thinning rates for Malaspina are greater than 1 m/yr, and previous geophysical investigations indicated that bed elevation exceeds 300 m below sea level in some places. These observations together give rise to the question of glacial stability. To address this question, glacier evolution models are dependent upon detailed observations of Malaspina's subglacial topography. Here, we map 2,000 line-km of the glacier's bed using airborne radar sounding data collected by NASA's Operation IceBridge. When compared to gridded radar measurements, we find that glaciological models overestimate Malaspina's volume by more than 30%. While we report a mean bed elevation 100 m greater than previous models, we find that Malaspina inhabits a broad basin largely grounded below sea level. Several subglacial channels dissect the glacier's bed: the most prominent of these channels extends at least 35 km up-glacier from the terminus toward the throat of Seward Glacier. Provided continued foreland erosion, an ice-ocean connection may promote rapid retreat along these overdeepened subglacial channels, with a global sea-level rise potential of 1.4 mm. <em>For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu</em><br>
DOI: 10.25422/azu.data.17054063.v2
title: Data and Code for "Comprehensive Radar Mapping of Malaspina Glacier (Sít' Tlein), Alaska—The World's Largest Piedmont Glacier—Reveals Potential for Instability"

description: Malaspina Glacier, located on the coast of southern Alaska, is the world's largest piedmont glacier. A narrow ice-cored foreland zone undergoing rapid thermokarst erosion separates the glacier from the relatively warm waters of the Gulf of Alaska. Glacier-wide thinning rates for Malaspina are greater than 1 m/yr, and previous geophysical investigations indicated that bed elevation exceeds 300 m below sea level in some places. These observations together give rise to the question of glacial stability. To address this question, glacier evolution models are dependent upon detailed observations of Malaspina's subglacial topography. Here, we map 2,000 line-km of the glacier's bed using airborne radar sounding data collected by NASA's Operation IceBridge. When compared to gridded radar measurements, we find that glaciological models overestimate Malaspina's volume by more than 30%. While we report a mean bed elevation 100 m greater than previous models, we find that Malaspina inhabits a broad basin largely grounded below sea level. Several subglacial channels dissect the glacier's bed: the most prominent of these channels extends at least 35 km up-glacier from the terminus toward the throat of Seward Glacier. Provided continued foreland erosion, an ice-ocean connection may promote rapid retreat along these overdeepened subglacial channels, with a global sea-level rise potential of 1.4 mm. <em>For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu</em><br>
DOI: 10.25422/azu.data.17054063.v1
title: Data and Code for "Comprehensive Radar Mapping of Malaspina Glacier (Sít' Tlein), Alaska – the World's Largest Piedmont Glacier – Reveals Potential for Instability"

description: Malaspina Glacier, located on the coast of southern Alaska, is the world’s largest piedmont glacier. A narrow ice-cored foreland zone undergoing rapid thermokarst erosion separates the glacier from the relatively warm waters of the Gulf of Alaska. Glacier-wide thinning rates for Malaspina are greater than 1 m/yr, and previous geophysical investigations indicated that bed elevation exceeds 300 m below sea level in some places. These observations together give rise to the question of glacial stability. To address this question, glacier evolution models are dependent upon detailed observations of Malaspina's subglacial topography. Here, we map over 3,250 line-km of the glacier's bed using airborne radar sounding data collected by NASA's Operation IceBridge. When compared to gridded radar measurements, we find that glaciological models overestimate Malaspina's volume by more than 30%. While we report a mean bed elevation 100 m greater than previous models, we find that Malaspina inhabits a broad basin largely grounded below sea level. Several subglacial channels dissect the glacier's bed: the most prominent of these channels extends at least 35 km up-glacier from the terminus towards the throat of Seward Glacier. Provided continued foreland erosion, an ice-ocean connection may promote rapid retreat along these overdeepened subglacial channels, with a global sea level rise potential of 1.4 mm.<br> <em>For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu</em><br>
DOI: 10.5281/zenodo.6957644
title: Supplementary data for: "The influence of reef isostasy, dynamic topography, and glacial isostatic adjustment on the Last Interglacial sea-level record of Northeastern Australia"

description: This repository contains supplementary information and data for the paper: ""The influence of reef isostasy, dynamic topography, and glacial isostatic adjustment on the Last Interglacial sea-level record of Northeastern Australia", submitted to Communications Earth & Environment.
DOI: 10.6084/m9.figshare.22213495
title: Table S2. Extended comparison of ARRDC3 residues near the C182Y position in the Gnathostomes.

description: Bovine congestive heart failure (BCHF) has become increasingly prevalent among feedlot cattle in the Western Great Plains of North America with up to 7% mortality in affected herds. BCHF is an untreatable complex condition involving pulmonary hypertension that culminates in right ventricular failure and death. Genes associated with BCHF in feedlot cattle have not been previously identified. Our aim was to search for genomic regions associated with this disease. A retrospective, matched case-control design with 102 clinical BCHF cases and their unaffected penmates was used in a genome-wide association study. Paired nominal data from approximately 560k filtered single nucleotide polymorphisms (SNPs) were analyzed with McNemar’s test. The most significant genome-wide association was in the arrestin domain-containing 3 protein gene (ARRDC3), followed by the nuclear factor IA gene (NFIA, mid-p-values, 1x10E-8 and 2x10E-7, respectively). Animals with homozygous risk alleles at either gene were approximately 8-fold more likely to have BCHF than their matched penmates without those risk alleles (CI95 = 3-17). Animals with homozygous risk alleles at both genes were 28-fold more likely to have BCHF than all others (p-value = 1x10E-7, CI95 = 4-206). A linked missense variant in ARRDC3 (C182Y) represents a potential functional variant since C182 is conserved among all other jawed vertebrate species observed. A DNA test with two markers showed 29% of 273 BCHF cases had homozygous risk alleles in both genes, compared to 2.5% in 198 similar unaffected feedlot cattle. This DNA test may be useful for identifying feedlot animals with the highest risk for BCHF in the environments described here. Although pathogenic roles for ARRDC3 and NFIA variants associated with BCHF are unknown, their discovery facilitates classifying animals by genetic risk and allows cattle producers to make informed decisions for selective breeding and animal health management.
DOI: 10.6084/m9.figshare.22213495.v1
title: Table S2. Extended comparison of ARRDC3 residues near the C182Y position in the Gnathostomes.

description: Bovine congestive heart failure (BCHF) has become increasingly prevalent among feedlot cattle in the Western Great Plains of North America with up to 7% mortality in affected herds. BCHF is an untreatable complex condition involving pulmonary hypertension that culminates in right ventricular failure and death. Genes associated with BCHF in feedlot cattle have not been previously identified. Our aim was to search for genomic regions associated with this disease. A retrospective, matched case-control design with 102 clinical BCHF cases and their unaffected penmates was used in a genome-wide association study. Paired nominal data from approximately 560k filtered single nucleotide polymorphisms (SNPs) were analyzed with McNemar’s test. The most significant genome-wide association was in the arrestin domain-containing 3 protein gene (ARRDC3), followed by the nuclear factor IA gene (NFIA, mid-p-values, 1x10E-8 and 2x10E-7, respectively). Animals with homozygous risk alleles at either gene were approximately 8-fold more likely to have BCHF than their matched penmates without those risk alleles (CI95 = 3-17). Animals with homozygous risk alleles at both genes were 28-fold more likely to have BCHF than all others (p-value = 1x10E-7, CI95 = 4-206). A linked missense variant in ARRDC3 (C182Y) represents a potential functional variant since C182 is conserved among all other jawed vertebrate species observed. A DNA test with two markers showed 29% of 273 BCHF cases had homozygous risk alleles in both genes, compared to 2.5% in 198 similar unaffected feedlot cattle. This DNA test may be useful for identifying feedlot animals with the highest risk for BCHF in the environments described here. Although pathogenic roles for ARRDC3 and NFIA variants associated with BCHF are unknown, their discovery facilitates classifying animals by genetic risk and allows cattle producers to make informed decisions for selective breeding and animal health management.
DOI: 10.6073/pasta/db1ec40e57f043b0c113498e20f3cb2d
title: ASD06 Stream discharge measured at the flumes on watershed N02B at Konza Prairie

description: Stream discharge is measured on a catchment (N02B), with 2-year fire return interval and grazed by bison since 1992. Measurements are taken at 5 minute intervals at a triangular throated flume. The prairie streams are 3rd-order and are intermittent. Daily and stormflow discharge records are available.
DOI: 10.5281/zenodo.5726876
title: Campagne Océanographique Seamount 1. Compte-rendu et liste des stations.

description: Cruise report and station list
DOI: 10.5281/zenodo.7696883
title: Representative sequences for colorectal cancer additive log ratios

description: Representative sequences and corresponding feature rank tables calculated in Debelius et al, The local tumor microbiome is associated with survival in late-stage colorectal cancer patients (doi: https://doi.org/10.1101/2022.09.16.22279353) file_s1_tissue_alr_sequences.fasta goes with tissue_only_ranks.tsv and corresponds to Figure 1 in the manuscript. file_s2_interaction_dr_sequences.fasta corresponds to figure 2 and links to interaction_models_interaction_ranks.tsv and interaction_models_tissue_ranks.tsv file_s3_tumor_rPCA_alr_sequences.fasta corresponds to Figure 3 and links to tumor_survival_index_ranks_file3.tsv. The rank files provide the rank and rank group; the fasta files provide the reference sequences for the data.
description: {"references": ["Debelius, J. et al (2022). \"The local tumor microbiome is associated with survival in late-stage colorectal cancer patients\". medRxiV. doi: https://doi.org/10.1101/2022.09.16.22279353"]}
DOI: 10.5281/zenodo.7696882
title: Representative sequences for colorectal cancer additive log ratios

description: Representative sequences and corresponding feature rank tables calculated in Debelius et al, The local tumor microbiome is associated with survival in late-stage colorectal cancer patients (doi: https://doi.org/10.1101/2022.09.16.22279353) file_s1_tissue_alr_sequences.fasta goes with tissue_only_ranks.tsv and corresponds to Figure 1 in the manuscript. file_s2_interaction_dr_sequences.fasta corresponds to figure 2 and links to interaction_models_interaction_ranks.tsv and interaction_models_tissue_ranks.tsv file_s3_tumor_rPCA_alr_sequences.fasta corresponds to Figure 3 and links to tumor_survival_index_ranks_file3.tsv. The rank files provide the rank and rank group; the fasta files provide the reference sequences for the data.
description: {"references": ["Debelius, J. et al (2022). \"The local tumor microbiome is associated with survival in late-stage colorectal cancer patients\". medRxiV. doi: https://doi.org/10.1101/2022.09.16.22279353"]}
DOI: 10.5281/zenodo.7697134
title: cathorops_aguadulce_2_ragtag_1.fasta.gz

description: .
DOI: 10.5281/zenodo.7697133
title: cathorops_aguadulce_2_ragtag_1.fasta.gz

description: .
DOI: 10.5281/zenodo.7697118
title: Synthetic parcel data for Lyon

description: This data set contains a synthetic parcel data set for Lyon that has been generated during the Horizon 2020 project LEAD. It represents individual parcels that need to be delivered during an average day in Lyon with individual coordinates, based on a synthetic population for the city.
DOI: 10.5281/zenodo.7697117
title: Synthetic parcel data for Lyon

description: This data set contains a synthetic parcel data set for Lyon that has been generated during the Horizon 2020 project LEAD. It represents individual parcels that need to be delivered during an average day in Lyon with individual coordinates, based on a synthetic population for the city.
DOI: 10.5281/zenodo.7697123
title: Mission océanographique SEAMOUNT 2. Compte-rendu et liste des stations

description: Cruise report and station list
DOI: 10.34943/b572358a-7528-4de9-ac57-d929f82d049c
title: ODP 1026 Broadband Seismometer Deployed 2010-10-06

description: The Guralp CMG-IT Broadband Seismometer 2533 was deployed on 2010-10-06 at ODP 1026. ODP 1026 is a borehole site used to pinpoint an area within Cascadia. This device is a Broadband Seismometer. Broadband Seismometers measure seismic waves over a broad frequency range depending on the device (e.g. 0.00278 Hz - 250 Hz). A broadband seismometer facilitates measurement of seismic events in the widest frequency band possible. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.6084/m9.figshare.7591376.v1
title: Yield characteristics of cherry tomato cultivated with and without shading screen at different irrigation levels

description: ABSTRACT The use of shading screen in vegetable crops sensitive to the radiation excess, associated with the effective water use via irrigation, allows for yield gains. This study aimed to evaluate the yield characteristics of cherry tomato cultivated with and without shading screen and different irrigation levels. A randomized block design was used, in a 4 x 2 factorial arrangement, with four irrigation levels (140 %, 160 %, 180 % and 200 % of the reference evapotranspiration - ETo) and two cherry tomato hybrids (Wanda and Dolcetto). The irrigation level corresponding to 200 % of the ETo provided the highest values for number of flowers and clusters formed, number of fruits per plant and fruit diameter. The Wanda hybrid was more fruitful, with a higher emission of clusters, while Dolcetto was more floriferous. The use of shade screen for cultivating cherry tomato provides an increase in the yield characteristics, if compared to the cultivation in open areas.