cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9247409
title: Additional file 14: of Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

description: Virus-host associations. A listing of all associations (Hi-C linkage or long-read alignment) between predicted viral contigs and non-viral contigs. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.9247415
title: Additional file 15: of Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

description: ARG allele predictions. A listing of all predicted candidate antibiotic resistance gene (ARG) alleles in the short- and long-read assemblies. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.9247418.v1
title: Additional file 16: of Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

description: Long-read assembly ARG allele similarities. A percent identity matrix of detected ARG alleles to show high degrees of similarity between alleles. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.9247409.v1
title: Additional file 14: of Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

description: Virus-host associations. A listing of all associations (Hi-C linkage or long-read alignment) between predicted viral contigs and non-viral contigs. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.9247415.v1
title: Additional file 15: of Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

description: ARG allele predictions. A listing of all predicted candidate antibiotic resistance gene (ARG) alleles in the short- and long-read assemblies. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.9247397
title: Additional file 13: of Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

description: Long-read assembly Prodigal ORF predictions. This file contains all Prodigal ORF predictions for the long-read MQ bins. (GZ 18904 kb)
DOI: 10.6084/m9.figshare.9247391
title: Additional file 1: of Customized tracheal design using 3D printing of a polymer hydrogel: influence of UV laser cross-linking on mechanical properties

description: Complementary information on UV cross linkage and mechanical properties. (ZIP 464 kb)
DOI: 10.6084/m9.figshare.9247397.v1
title: Additional file 13: of Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

description: Long-read assembly Prodigal ORF predictions. This file contains all Prodigal ORF predictions for the long-read MQ bins. (GZ 18904 kb)
DOI: 10.6084/m9.figshare.9247391.v1
title: Additional file 1: of Customized tracheal design using 3D printing of a polymer hydrogel: influence of UV laser cross-linking on mechanical properties

description: Complementary information on UV cross linkage and mechanical properties. (ZIP 464 kb)
DOI: 10.6084/m9.figshare.9247379
title: Additional file 12: of Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

description: Short-read assembly Prodigal ORF predictions. This file contains all Prodigal ORF predictions for the short-read MQ bins. (GZ 87178 kb)
DOI: 10.6084/m9.figshare.9247376
title: Additional file 11: of Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

description: Hypergeometric test of contig alignment depth. These are the results of an enrichment test designed to identify differences in community abundance/composition between several public rumen datasets (see AdditionalÂ fileÂ 1: Supplementary methods). The short-read assembly and long-read assembly results are listed on separate tabs. Enrichment was determined by the Hypergeometric mean test using a Benjamini-Hochberg-corrected alpha. (XLSX 224 kb)
DOI: 10.6084/m9.figshare.9247376.v1
title: Additional file 11: of Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

description: Hypergeometric test of contig alignment depth. These are the results of an enrichment test designed to identify differences in community abundance/composition between several public rumen datasets (see AdditionalÂ fileÂ 1: Supplementary methods). The short-read assembly and long-read assembly results are listed on separate tabs. Enrichment was determined by the Hypergeometric mean test using a Benjamini-Hochberg-corrected alpha. (XLSX 224 kb)
DOI: 10.6084/m9.figshare.9247379.v1
title: Additional file 12: of Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

description: Short-read assembly Prodigal ORF predictions. This file contains all Prodigal ORF predictions for the short-read MQ bins. (GZ 87178 kb)
DOI: 10.6084/m9.figshare.9247367
title: Additional file 10: of Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

description: Long-read unique rumen assembly sequence. A listing of the long-read contigs that did not have reciprocal alignments to the Hungate1000 or Stewart et al. rumen microbial assemblies. (GZ 9 kb)
DOI: 10.6084/m9.figshare.9247367.v1
title: Additional file 10: of Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

description: Long-read unique rumen assembly sequence. A listing of the long-read contigs that did not have reciprocal alignments to the Hungate1000 or Stewart et al. rumen microbial assemblies. (GZ 9 kb)
DOI: 10.6084/m9.figshare.9247310
title: MOESM3 of Effectiveness of ecotechnologies for recovery of nitrogen and phosphorus from anaerobic digestate and effectiveness of the recovery products as fertilisers: a systematic review protocol

description: Additional file 3. Data extraction sheet.
DOI: 10.6084/m9.figshare.9247304
title: MOESM2 of Effectiveness of ecotechnologies for recovery of nitrogen and phosphorus from anaerobic digestate and effectiveness of the recovery products as fertilisers: a systematic review protocol

description: Additional file 2. Scoping exercise.
DOI: 10.6084/m9.figshare.9247310.v1
title: MOESM3 of Effectiveness of ecotechnologies for recovery of nitrogen and phosphorus from anaerobic digestate and effectiveness of the recovery products as fertilisers: a systematic review protocol

description: Additional file 3. Data extraction sheet.
DOI: 10.6084/m9.figshare.9247304.v1
title: MOESM2 of Effectiveness of ecotechnologies for recovery of nitrogen and phosphorus from anaerobic digestate and effectiveness of the recovery products as fertilisers: a systematic review protocol

description: Additional file 2. Scoping exercise.
DOI: 10.6084/m9.figshare.9247295
title: MOESM1 of Effectiveness of ecotechnologies for recovery of nitrogen and phosphorus from anaerobic digestate and effectiveness of the recovery products as fertilisers: a systematic review protocol

description: Additional file 1. ROSES form for systematic review protocols.
DOI: 10.6084/m9.figshare.9247295.v1
title: MOESM1 of Effectiveness of ecotechnologies for recovery of nitrogen and phosphorus from anaerobic digestate and effectiveness of the recovery products as fertilisers: a systematic review protocol

description: Additional file 1. ROSES form for systematic review protocols.
DOI: 10.6084/m9.figshare.9247250
title: MOESM2 of The relative effectiveness of seed addition methods for restoring or re-creating species rich grasslands: a systematic review protocol

description: Additional file 2. ROSES form.
DOI: 10.6084/m9.figshare.9247250.v1
title: MOESM2 of The relative effectiveness of seed addition methods for restoring or re-creating species rich grasslands: a systematic review protocol

description: Additional file 2. ROSES form.
DOI: 10.6084/m9.figshare.9247241
title: MOESM1 of Effect of community led total sanitation and hygiene (CLTSH) implementation program on latrine utilization among adult villagers of North Ethiopia: a cross-sectional study

description: Additional file 1. Minimal data set included in the manuscript.
DOI: 10.6084/m9.figshare.9247241.v1
title: MOESM1 of Effect of community led total sanitation and hygiene (CLTSH) implementation program on latrine utilization among adult villagers of North Ethiopia: a cross-sectional study

description: Additional file 1. Minimal data set included in the manuscript.
DOI: 10.6084/m9.figshare.9247202
title: Additional file 6: of Exploring the molecular basis of neuronal excitability in a vocal learner

description: Sequence recovery BED track. A taeGut1 BED track of the sequence recovered from aligning chicken models. (TXT 19 kb)
DOI: 10.6084/m9.figshare.9247202.v1
title: Additional file 6: of Exploring the molecular basis of neuronal excitability in a vocal learner

description: Sequence recovery BED track. A taeGut1 BED track of the sequence recovered from aligning chicken models. (TXT 19 kb)
DOI: 10.6084/m9.figshare.9247169
title: Additional file 1: of Exploring the molecular basis of neuronal excitability in a vocal learner

description: Table S1. Documents synteny analysis, chicken orthologs, model completeness, sequence recovery data, and EST evidence for ion channel genes in the zebra finch genome. Table S2. details evidence supporting gene loss conclusions. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.9247169.v1
title: Additional file 1: of Exploring the molecular basis of neuronal excitability in a vocal learner

description: Table S1. Documents synteny analysis, chicken orthologs, model completeness, sequence recovery data, and EST evidence for ion channel genes in the zebra finch genome. Table S2. details evidence supporting gene loss conclusions. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.9247160
title: MOESM4 of A customizable method to characterize Arabidopsis thaliana transpiration under drought conditions

description: Additional file 4. Photographs with the overlapping segmentation of the leaf area obtained as output of Easy Leaf Area to be processed by Leaf-GP from a replicate experiment.
DOI: 10.6084/m9.figshare.9247166
title: MOESM5 of A customizable method to characterize Arabidopsis thaliana transpiration under drought conditions

description: Additional file 5. Excel with raw data and calculation of the results of a replicate of the whole experiment.
DOI: 10.6084/m9.figshare.9247166.v1
title: MOESM5 of A customizable method to characterize Arabidopsis thaliana transpiration under drought conditions

description: Additional file 5. Excel with raw data and calculation of the results of a replicate of the whole experiment.
DOI: 10.6084/m9.figshare.9247154
title: MOESM3 of A customizable method to characterize Arabidopsis thaliana transpiration under drought conditions

description: Additional file 3. Excel with the whole output of Leaf-GP comprising parameters as individual leaf area, number of leaves and perimeters.
DOI: 10.6084/m9.figshare.9247160.v1
title: MOESM4 of A customizable method to characterize Arabidopsis thaliana transpiration under drought conditions

description: Additional file 4. Photographs with the overlapping segmentation of the leaf area obtained as output of Easy Leaf Area to be processed by Leaf-GP from a replicate experiment.
DOI: 10.6084/m9.figshare.9247148
title: MOESM2 of A customizable method to characterize Arabidopsis thaliana transpiration under drought conditions

description: Additional file 2. Photographs with the overlapping segmentation of the leaf area obtained as output of Easy Leaf Area to be processed by Leaf-GP.
DOI: 10.6084/m9.figshare.9247151
title: Additional file 1: of Estimating the annual risk of infection with Mycobacterium tuberculosis among adolescents in Western Kenya in preparation for TB vaccine trials

description: Annual risk of TB infection (ARTI). The data set provides all the variables that were used for analysis of the results in this manuscript. (CSV 1400 kb)
DOI: 10.6084/m9.figshare.9247154.v1
title: MOESM3 of A customizable method to characterize Arabidopsis thaliana transpiration under drought conditions

description: Additional file 3. Excel with the whole output of Leaf-GP comprising parameters as individual leaf area, number of leaves and perimeters.
DOI: 10.6084/m9.figshare.9247151.v1
title: Additional file 1: of Estimating the annual risk of infection with Mycobacterium tuberculosis among adolescents in Western Kenya in preparation for TB vaccine trials

description: Annual risk of TB infection (ARTI). The data set provides all the variables that were used for analysis of the results in this manuscript. (CSV 1400 kb)
DOI: 10.6084/m9.figshare.9247148.v1
title: MOESM2 of A customizable method to characterize Arabidopsis thaliana transpiration under drought conditions

description: Additional file 2. Photographs with the overlapping segmentation of the leaf area obtained as output of Easy Leaf Area to be processed by Leaf-GP.
DOI: 10.6084/m9.figshare.9243557
title: 学生成绩.xls

description: scores
DOI: 10.6084/m9.figshare.9241775
title: AMT_12,1–8, 2019

description: Dataset related to the publication in AMT number 12, 1–8, 2019
DOI: 10.6084/m9.figshare.9241688
title: Juniper distribution in SE South Dakota and NE Nebraska

description: The juniper distribution map was generated from two Landsat 8 scenes collected from path/row 29/30 on 07JAN2015 and from path/row 30/30 on 01JAN2016. Both scenes had &gt;95% snow cover. Matched filtering, a partial unmixing technique, was used to calculated juniper fractions based on a set of endmember pixels, and a threshold was applied to create the classified map. Classification accuracy was 91% for path/row 29/30 and 88% for path/row 30/30. <br>The juniper map is stored as the GeoTIFF file "Juniper_Map_Final.tif". The dataset has a raster cell size of 30 m and is in the UTM projection, zone 14N.<br>
DOI: 10.6084/m9.figshare.9241775.v1
title: AMT_12,1–8, 2019

description: Dataset related to the publication in AMT number 12, 1–8, 2019
DOI: 10.6084/m9.figshare.9236408
title: Consistently up-regulated proteins in FLG kd organoids

description: Consistently up-regulated proteins in FLG kd organoids
DOI: 10.6084/m9.figshare.9236102
title: Consistently down-regulated proteins in FLG kd organoids

description: Consistently down-regulated proteins in FLG kd organoids
DOI: 10.6084/m9.figshare.9235142
title: Excel macros and data example

description: Macros for organizing raw data from LabView software that logs timestamps for every rotation of a flight mill arms and then summarizes the time of individual flight bouts.
DOI: 10.6084/m9.figshare.9233633
title: Data used in Guzy et al_2019_Ecological ApplicationsData used in Guzy et al_2019_Ecological Applications

description: Data used in hierarchical community occupancy model Guzy et al_2019_Differential responses of amphibian and reptile assemblages to size of riparian buffers within managed forests.<br>Species occurrence files (n=37 species) are stored as a .csv for each species which includes presence-absence data for 102 sites during 4 surveys.<br>Also included here is a short bit of R Code that reads in each species and compiles one large encounter matrix ('X') which can be sent to the model.<br>Site covariates are provided in file titled "Site Covariates"Sampling covariates are provided in the files titled "pc1" and "pc2".<br>Data used in hierarchical community occupancy model Guzy et al_2019_Differential responses of amphibian and reptile assemblages to size of riparian buffers within managed forests.<br>Species occurrence files (n=37 species) are stored as a .csv for each species which includes presence-absence data for 102 sites during 4 surveys.<br>Also included here is a short bit of R Code that reads in each species and compiles one large encounter matrix ('X') which gets sent to the model.<br>Site covariates are provided in file titled "Site Covariates"Sampling covariates are provided in the files titled "pc1" and "pc2".
DOI: 10.6084/m9.figshare.9232142
title: Growth-chamber experiments: Influence of wetland plants on sediment oxygen and denitrification (Long Island, NY, USA)

description: This project contatins data from growth-chamber experiments conducted at Stony Brook University to determine the influence of marsh plant Spartina alterniflora on sediment oxygen availability and rates of microbial denitrification. A manuscript associated with these data is currently under review.<br>"20150312_ProfileData.csv" contains vertical sediment data in 3 cm increments, including porewater chemistry and root and rhizome characteristics. We also measured microbial processes (mineralization, nitrification, and denitrification), sediment moisture, sediment organic content, and dissolved O<sub>2</sub> and N<sub>2</sub> concentrations at 6 and 12 cm below the sediment surface.<br>"20150622_MesoScaleData.csv" contains measurements conducted at the scale of the whole mesocosms, including aboveground plant traits, mean sediment characteristics, porewater nutrient concentrations, and microbial process rates.
DOI: 10.6084/m9.figshare.9232610
title: Insights on the response of microbial communities to vegetation and biogeochemical properties in amended and unamended acid-generating mine wastes

description: Understanding the structure of microbial communities in acidic, metal contaminated tailings and waste rock in cool, continental northern temperate climates is important for identifying their potential for use in phytostabilization and bioremediation programs. In this study, microbial community compositions across two large mine waste sites in the Sudbury basin were analyzed along gradients of barren-to-vegetated tailings and waste rock. Microbial communities were less diverse, more homogenous, and mainly chemolithoautotrophic in barren sites, transitioning to more diverse communities of organoheterotrophs, nitrogen-fixing/plant-growth promoting bacteria, and ectomycorrhizal fungi in the vegetated areas. Network interaction analyses of microbial communities demonstrated higher levels of interactions of microbial groups in the barren tailings, which were related to the extreme environmental and chemical conditions and restricted anabolic nutrient availability of the substrates. We also show that vegetation and plant-derived organic matter in the tailings are associated with the shifts observed in the structure of microbial communities towards more soil-like communities, which sequentially further aids in the establishment of vegetation. These findings have implications for the optimization of phytoestablishment and bioremediation in mine tailings and waste rock in the cool, continental northern temperate and boreal climates.
DOI: 10.6084/m9.figshare.9232142.v1
title: Growth-chamber experiments: Influence of wetland plants on sediment oxygen and denitrification (Long Island, NY, USA)

description: This project contatins data from growth-chamber experiments conducted at Stony Brook University to determine the influence of marsh plant Spartina alterniflora on sediment oxygen availability and rates of microbial denitrification. A manuscript associated with these data is currently under review.<br>"20150312_ProfileData.csv" contains vertical sediment data in 3 cm increments, including porewater chemistry and root and rhizome characteristics. We also measured microbial processes (mineralization, nitrification, and denitrification), sediment moisture, sediment organic content, and dissolved O<sub>2</sub> and N<sub>2</sub> concentrations at 6 and 12 cm below the sediment surface.<br>"20150622_MesoScaleData.csv" contains measurements conducted at the scale of the whole mesocosms, including aboveground plant traits, mean sediment characteristics, porewater nutrient concentrations, and microbial process rates.
DOI: 10.6084/m9.figshare.9232115
title: AMR GAVI VIS Extended data

description: This dataset contains two files:1) The excel file that contains the background information that was sent to all participants in the study; the questionnaire that asked participants to enter the vaccine and criteria scores; and participants anonymised details2) The body of an email that was sent to all participants in the study<br>
DOI: 10.6084/m9.figshare.9232610.v1
title: 16S_OTU table.csv

description: 16S OTU_table
DOI: 10.6084/m9.figshare.9232610.v2
title: 16S_OTU table.csv

description: 16S OTU_table
DOI: 10.6084/m9.figshare.9232610.v3
title: Insights on the response of microbial communities to vegetation and biogeochemical properties in amended and unamended acid-generating mine wastes

description: Understanding the structure of microbial communities in acidic, metal contaminated tailings and waste rock in cool, continental northern temperate climates is important for identifying their potential for use in phytostabilization and bioremediation programs. In this study, microbial community compositions across two large mine waste sites in the Sudbury basin were analyzed along gradients of barren-to-vegetated tailings and waste rock. Microbial communities were less diverse, more homogenous, and mainly chemolithoautotrophic in barren sites, transitioning to more diverse communities of organoheterotrophs, nitrogen-fixing/plant-growth promoting bacteria, and ectomycorrhizal fungi in the vegetated areas. Network interaction analyses of microbial communities demonstrated higher levels of interactions of microbial groups in the barren tailings, which were related to the extreme environmental and chemical conditions and restricted anabolic nutrient availability of the substrates. We also show that vegetation and plant-derived organic matter in the tailings are associated with the shifts observed in the structure of microbial communities towards more soil-like communities, which sequentially further aids in the establishment of vegetation. These findings have implications for the optimization of phytoestablishment and bioremediation in mine tailings and waste rock in the cool, continental northern temperate and boreal climates.
DOI: 10.6084/m9.figshare.9228869
title: Northern elephant seal blubber proteome (repeated ACTH challenge)

description: Juvenile northern elephant seals received once-daily injections of synthetic adrenocorticotropic hormone (ACTH) for four consecutive days. Blubber samples were collected immediately prior to and four hours after the first and fourth ACTH administrations. Proteins were isolated from the inner, metabolically active half (closest to muscle) of each blubber sample from two study animals for which transcriptomes have been published. Blubber was homogenized in Qiazol and proteins were precipitated from the organic phase after phase extraction with chloroform. Denatured, trypsinized, and alkylated peptides were labeled with iTRAQ 8plex and fractionated off-line using a high pH reverse-phase peptide fractionation kit. Fractions were pooled in pairs and injected onto a C18 LC column. Mass spectrometry analysis was performed on a Thermo Orbitrap Fusion Tribrid mass spectrometer in DDA mode with HCD collision. MS/MS data analysis (SEQUEST search against SwissProt UniProt database) and iTRAQ-labeled peptide quantification at the MS2 level were conducted using Proteome Discoverer v2.2.