cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10688953
title: Functional annotation of the reference transcriptome for Prorocentrum cordatum PcorA

description: De novo transcriptomes generated using both Trinity and velvet-oases were merged with CD-HIT-EST to reduce the transcript redundancy to 90% similarity and generate unique genes. Functional annotation was performed using DIAMOND blastp function (Buchfink et al. 2021).
DOI: 10.5281/zenodo.10688954
title: Functional annotation of the reference transcriptome for Prorocentrum cordatum PcorA

description: De novo transcriptomes generated using both Trinity and velvet-oases were merged with CD-HIT-EST to reduce the transcript redundancy to 90% similarity and generate unique genes. Functional annotation was performed using DIAMOND blastp function (Buchfink et al. 2021).
DOI: 10.6084/m9.figshare.25259908
title: Theridiosoma Frontal Release Kinematics Data

description: Kinematics data of frontal releases of Theridiosoma gemmosum, as well as summary sheet of other measurements.
DOI: 10.5281/zenodo.10688965
title: Calculating the high-latitude ionospheric electrodynamics using a machine learning-based field-aligned current model

description: This DOI contains the datasets and codes that are used in the publication "Calculating the high-latitude ionospheric electrodynamics using a machine learning-based field-aligned current model" in Space Weather Journal.
DOI: 10.5281/zenodo.10688966
title: Calculating the high-latitude ionospheric electrodynamics using a machine learning-based field-aligned current model

description: This DOI contains the datasets and codes that are used in the publication "Calculating the high-latitude ionospheric electrodynamics using a machine learning-based field-aligned current model" in Space Weather Journal.
DOI: 10.5287/ora-dakrm9m4e
title: Supporting data for "Thermomechanical characterisation of a thermoplastic polymer and its short glass fibre reinforced composite: Influence of fibre, fibre orientation, strain rates and temperatures"

description: This dataset provides raw data to support the above paper. It is presented in a number of forms:
Origin Data File: .ojpu
Excel file: .xlsx
Thermal image file: .hcc
DMA data: .txt
DOI: 10.25417/uic.22088024.v1
title: Supplementary Figures and Data - Role of NK Cells in Skin Wound Healing of Mice

description: Raw data and Supplementary Figures for paper, Cavalcante-Silva, J., & Koh, T. J. (2023). Role of NK cells in skin wound healing of mice. <em>The Journal of Immunology</em>, <em>210</em>(7), 981-990. 
10.4049/jimmunol.2200637
DOI: 10.25417/uic.22088024
title: Supplementary Figures and Data - Role of NK Cells in Skin Wound Healing of Mice

description: Raw data and Supplementary Figures for paper, Cavalcante-Silva, J., & Koh, T. J. (2023). Role of NK cells in skin wound healing of mice. <em>The Journal of Immunology</em>, <em>210</em>(7), 981-990. 
10.4049/jimmunol.2200637
DOI: 10.5281/zenodo.10688823
title: Example data for our Single-cell RNA sequencing (scRNA-seq) Differential Expression Analysis & Visualization Snakemake Workflow

description: As an example data set for our Single-cell RNA sequencing (scRNA-seq) Differential Expression Analysis & Visualization Snakemake Workflow, we selected a scRNA-seq data set consisting of 15 CRC samples from Lee et al (2020) Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer. Nature Genetics. Downloaded from the Weizmann Institute - Curated Cancer Cell Atlas (3CA) - Colorectal Cancer section.- samples/patients: 15- cells: 21657- features (genes): 22276- preprocessed using the compatible MR.PARETO module for scRNA-seq data processing & visualization.
DOI: 10.5281/zenodo.10688824
title: Example data for our Single-cell RNA sequencing (scRNA-seq) Differential Expression Analysis & Visualization Snakemake Workflow

description: As an example data set for our Single-cell RNA sequencing (scRNA-seq) Differential Expression Analysis & Visualization Snakemake Workflow, we selected a scRNA-seq data set consisting of 15 CRC samples from Lee et al (2020) Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer. Nature Genetics. Downloaded from the Weizmann Institute - Curated Cancer Cell Atlas (3CA) - Colorectal Cancer section.- samples/patients: 15- cells: 21657- features (genes): 22276- preprocessed using the compatible MR.PARETO module for scRNA-seq data processing & visualization.
DOI: 10.6084/m9.figshare.23061029
title: Optimal gene trees

description: Maximum likelihood optimal gene trees based on analyses of locus alignments that did not violate phylogenetic assumptions (all "good" and "bad" loci are also included for reference in the 50p_good+bad_genetrees folder). 
When using this data, cite:
DOI: 10.6084/m9.figshare.23060765
title: Concatenated alignments

description: Concatenated alignment files in phylip format. 
When using this data, cite:
<br>
DOI: 10.6084/m9.figshare.23061029.v1
title: Optimal gene trees

description: Maximum likelihood optimal gene trees based on analyses of locus alignments that did not violate phylogenetic assumptions (all "good" and "bad" loci are also included for reference in the 50p_good+bad_genetrees folder). 
When using this data, cite:
DOI: 10.25417/uic.24279613
title: Data - Women enrollment barriers in a post-stroke study

description: Dataset underlying the results for, "Barriers to enrollment in a post-stroke neuromodulation and walking study: implications for recruiting women."
DOI: 10.26207/28et-1e58
title: Datasets to simulate data-driven models for filling the temporal gaps in the low-frequency nitrate data
DOI: 10.6084/m9.figshare.23060633
title: Locus alignments

description: Trimmed locus alignment files in nexus format. When using this data, cite:
DOI: 10.6084/m9.figshare.23059979
title: ASTRAL species tree files

description: ASTRAL species tree files. When using this data, cite:
DOI: 10.6084/m9.figshare.23059868
title: Maximum likelihood tree files

description: IQTREE maximum likelihood tree files.When using this data, cite:Forthman, M., Phan, H., Miller, C.W., Kimball, R.T. (In press). Phylogenetic placement of the leaf-footed bug tribes Agriopocorini, Amorbini, and Manocoreini (Heteroptera: Coreoidea) using ultraconserved elements. <i>Zool. J. Linn. Soc.</i>
DOI: 10.6084/m9.figshare.23059868.v1
title: Maximum likelihood tree files

description: IQTREE maximum likelihood tree files.When using this data, cite:Forthman, M., Phan, H., Miller, C.W., Kimball, R.T. (In press). Phylogenetic placement of the leaf-footed bug tribes Agriopocorini, Amorbini, and Manocoreini (Heteroptera: Coreoidea) using ultraconserved elements. <i>Zool. J. Linn. Soc.</i>
DOI: 10.5281/zenodo.10688892
title: Dataset: Engineered Step-Pool Sequences: Geometry, Failure Modes, and Stability

description: The data set includes results from flume experiments on engineered step-pool sequences conducted at the Laboratory of Hydraulics, Hydrology, and Glaciology (VAW) at ETH Zurich.
DOI: 10.5281/zenodo.10688893
title: Dataset: Engineered Step-Pool Sequences: Geometry, Failure Modes, and Stability

description: The data set includes results from flume experiments on engineered step-pool sequences conducted at the Laboratory of Hydraulics, Hydrology, and Glaciology (VAW) at ETH Zurich.
DOI: 10.6084/m9.figshare.24764403.v1
title: Learning-dependent navigation strategies and neural computation in C. elegans

description: Data set for analysis and to generate figures in the paper
DOI: 10.5281/zenodo.10685606
title: E3SMv2 hourly outputs Part II for paper: Representing the effects of giant aerosol in droplet nucleation in E3SMv2

description: This dataset contains hourly output Part II from E3SMv2 nudged simulations used in the article "Representing the effects of giant aerosol in droplet nucleation in E3SMv2". The manuscript is submitted to Geoscientific Model Development.  Part II is for the dataset of the simulation values over Southern ocean region. This dataset includes four nudged run cases:  ga.00 for control run, ga.02 for GCCN run with assuming 2 um diameter for GCCN, ga.03 for GCCN run with assuming 3 um diameter for GCCN and ga.04 for GCCN run with assuming 4 um diameter for GCCN.
DOI: 10.5281/zenodo.10685607
title: E3SMv2 hourly outputs Part II for paper: Representing the effects of giant aerosol in droplet nucleation in E3SMv2

description: This dataset contains hourly output Part II from E3SMv2 nudged simulations used in the article "Representing the effects of giant aerosol in droplet nucleation in E3SMv2". The manuscript is submitted to Geoscientific Model Development.  Part II is for the dataset of the simulation values over Southern ocean region. This dataset includes four nudged run cases:  ga.00 for control run, ga.02 for GCCN run with assuming 2 um diameter for GCCN, ga.03 for GCCN run with assuming 3 um diameter for GCCN and ga.04 for GCCN run with assuming 4 um diameter for GCCN.
DOI: 10.5281/zenodo.10672152
title: E3SMv2 climatology outputs for paper: Representing the effects of giant aerosol in droplet nucleation in E3SMv2

description: This dataset contains climatological output from E3SMv2 model simulations used in the article ``Representing the effects of giant aerosol in droplet nucleation in E3SMv2". The manuscript is submitted to Geoscientific Model Development. There are two directories in this dataset: PD and PI. For each directory, there are seven files.
DOI: 10.5281/zenodo.10672153
title: E3SMv2 climatology outputs for paper: Representing the effects of giant aerosol in droplet nucleation in E3SMv2

description: This dataset contains climatological output from E3SMv2 model simulations used in the article ``Representing the effects of giant aerosol in droplet nucleation in E3SMv2". The manuscript is submitted to Geoscientific Model Development. There are two directories in this dataset: PD and PI. For each directory, there are seven files.
DOI: 10.5281/zenodo.10672096
title: E3SMv2 hourly outputs Part I for paper: Representing the effects of giant aerosol in droplet nucleation in E3SMv2

description: This dataset contains hourly output PartI from E3SMv2 nudged simulations used in the article "Representing the effects of giant aerosol in droplet nucleation in E3SMv2". The manuscript is submitted to Geoscientific Model Development.  Part I is for the dataset of the simulation values over the Atlantic ocean region to the west of Africa continent. This dataset includes four nudged run cases:  ga.00 for control run, ga.02 for GCCN run with assuming 2 um diameter for GCCN, ga.03 for GCCN run with assuming 3 um diameter for GCCN and ga.04 for GCCN run with assuming 4 um diameter for GCCN.
DOI: 10.5281/zenodo.10672097
title: E3SMv2 hourly outputs Part I for paper: Representing the effects of giant aerosol in droplet nucleation in E3SMv2

description: This dataset contains hourly output PartI from E3SMv2 nudged simulations used in the article "Representing the effects of giant aerosol in droplet nucleation in E3SMv2". The manuscript is submitted to Geoscientific Model Development.  Part I is for the dataset of the simulation values over the Atlantic ocean region to the west of Africa continent. This dataset includes four nudged run cases:  ga.00 for control run, ga.02 for GCCN run with assuming 2 um diameter for GCCN, ga.03 for GCCN run with assuming 3 um diameter for GCCN and ga.04 for GCCN run with assuming 4 um diameter for GCCN.
DOI: 10.5281/zenodo.10684291
title: BAM files for Alkallas and Najafabadi, Methods Mol Biol 2022, 2515:129-150 (part 1)
DOI: 10.5281/zenodo.10684292
title: BAM files for Alkallas and Najafabadi, Methods Mol Biol 2022, 2515:129-150 (part 1)
DOI: 10.6084/m9.figshare.25102763.v3
title: sounddatabase

description: we manually listened to all the sounds and classified them into four categories: [Type-0] Sounds that are completely irrelevant to the corresponding labels; [Type-1] Earcon (The identification of Earcon is based on the guideline of Earcons design reported by Blattner, Sumikawa and Greenberg); [Type-2] Auditory icon (which is made by capturing the sounds in everyday life); [Type-3] Music/vocal/other sounds that are relevant to the label description. To study the relationship between semantic descriptors and sound features of Earcon, we first obtained 270 earcons with short, structured musical messages from a mixed database containing 1053 sound samples with different types.
DOI: 10.18739/a2n00zv96
title: Carbon dioxide flux measurements from Small Mammal Experiment Summer 2019 (Nome and Toolik, Alaska)

description: We conducted a field experiment in which small mammal density was manipulated at two locations (near Toolik, and Nome, Alaska) with three replicate sites at each location. The motivation for collecting this carbon dioxide (CO2) flux dataset was to understand and quantify the impact of the most abundant herbivores, small rodents (voles and lemmings) on tussock tundra vegetation community composition and canopy structure in the Arctic. In July of 2018, at each site we set up an 8 meter (m) x 8 m fenced exclosure with a 0.635 centimeter (cm) square mesh to prevent herbivore grazing and increase vegetation cover (Exclosure treatment (EX)), set up a 20 m x 20 m enclosure that was stocked with up to 4 voles from spring snowmelt through September in 2018 and 2019 (Press treatment (PR)), and identified an 8 m x 8 m unfenced control plot marked at each corner with pin flags at each site (Control (CT)). In 2019, at the Toolik sites only, we set up a 20 m x 20 m enclosure at each replicate site that was stocked with up to 4 voles from spring snowmelt through September in 2019 only, after which voles were removed and the fences served to exclude voles from 2020-2023 (Pulse treatment (PU)).
 Within each treatment at each site, we collected CO2 flux data from circular subplots (0.5m^2 footprint) at three distinct locations during the period of peak leaf out (~July) in 2019.
DOI: 10.5281/zenodo.10688975
title: De novo transcriptome assembly for Prorocentrum cordatum PcorA

description: Raw reads were pre-processed by removing the adaptors and low-quality reads using BBMap. The filtered reads were normalized for depth based on kmer counts using BBNorm function. De novo transcriptomes were generated using both Trinity and velvet-oases. CD-HIT-EST was used to merge the resulting two de novo transcriptomes and reduce the transcript redundancy to 90% similarity and unique genes were predicted using transdecoder. Raw reads can be found in GenBank PRJNA1077943.
DOI: 10.5281/zenodo.10688974
title: De novo transcriptome assembly for Prorocentrum cordatum PcorA

description: Raw reads were pre-processed by removing the adaptors and low-quality reads using BBMap. The filtered reads were normalized for depth based on kmer counts using BBNorm function. De novo transcriptomes were generated using both Trinity and velvet-oases. CD-HIT-EST was used to merge the resulting two de novo transcriptomes and reduce the transcript redundancy to 90% similarity and unique genes were predicted using transdecoder. Raw reads can be found in GenBank PRJNA1077943.
DOI: 10.18739/a2h70825v
title: Pointframe measurements of vegetation species and height from Small Mammal Experiment Summer 2018 and 2019 near Utqiagvik (Barrow), Alaska

description: We conducted a field experiment in which small mammal density was manipulated at three replicate sites at near Utqiagvik, Alaska. The motivation for collecting this pointframe dataset was to understand and quantify the impact of the most abundant herbivores, small rodents (voles and lemmings) on tussock tundra vegetation community composition and canopy structure in the Arctic. In July of 2018, at each site we set up an 8 meter (m) x 8 m fenced exclosure with a 0.635 centimeter (cm) square mesh to prevent herbivore grazing and increase vegetation cover (Exclosure treatment (EX)), set up a 20 m x 20 m enclosure that was stocked with up to 4 voles from spring snowmelt through September in 2018 and 2019 (Press treatment (PR)), and identified an 8 m x 8 m unfenced control plot marked at each corner with pin flags at each site (Control (CT)). In 2019, at each site we set up a 20 m x 20 m enclosure that was stocked with up to 4 voles from spring snowmelt through September in 2019 only, after which voles were removed and the fences served to exclude voles from 2020-2023 (Pulse treatment (PU)).
 Within each treatment at each site, we collected vegetation species and height data from pointframe measurements (62 points, 80cm across with a 0.5m^2 footprint) at three distinct locations during the period of peak leaf out (~July) in 2018 and 2019.
DOI: 10.6084/m9.figshare.12981297
title: Molecular phylogenetic analysis of New Zealand mosquito species

description: Taxonomic information for New Zealand mosquito species is predominantly morphological with very few molecular data available to date. In this study, the mitochondrial <i>COI</i> gene and nuclear ITS1 were amplified and sequenced from DNA templates representing 17 species; 15 previously known New Zealand species, a newly discovered undescribed <i>Aedes</i> species from the Chatham Islands and a recently eradicated invader, <i>Ae. camptorhynchus</i>. This paper provides DNA barcoding sequences for the entire known New Zealand mosquito fauna, the first for the majority of these species. Phylogenetic analysis of <i>COI</i> and ITS1 indicated that the endemic species are all genetically distinct from the exotic species examined including vector species of pathogens of human diseases. The genus <i>Opifex</i> is distant from the genus <i>Aedes</i> based on analysis of ITS1 sequences, and <i>Ae. chathamicus</i> is more closely related to species within <i>Aedes</i> than to the genus <i>Opifex</i>. Results show <i>Culex asteliae</i> to be a valid species but <i>Cx. rotoruae</i> is not necessarily so. The <i>Aedes</i> species appears to be closely related to <i>Ae. subalbirostris</i>. The introduced <i>Cx. quinquefasciatus</i> was clearly shown to be related <i>to Cx. pipiens</i>; however, the endemic <i>Cx. pervigilans</i> was not. No evidence of population variation based on geographic location was detected.
DOI: 10.6084/m9.figshare.12981297.v1
title: Molecular phylogenetic analysis of New Zealand mosquito species

description: Taxonomic information for New Zealand mosquito species is predominantly morphological with very few molecular data available to date. In this study, the mitochondrial <i>COI</i> gene and nuclear ITS1 were amplified and sequenced from DNA templates representing 17 species; 15 previously known New Zealand species, a newly discovered undescribed <i>Aedes</i> species from the Chatham Islands and a recently eradicated invader, <i>Ae. camptorhynchus</i>. This paper provides DNA barcoding sequences for the entire known New Zealand mosquito fauna, the first for the majority of these species. Phylogenetic analysis of <i>COI</i> and ITS1 indicated that the endemic species are all genetically distinct from the exotic species examined including vector species of pathogens of human diseases. The genus <i>Opifex</i> is distant from the genus <i>Aedes</i> based on analysis of ITS1 sequences, and <i>Ae. chathamicus</i> is more closely related to species within <i>Aedes</i> than to the genus <i>Opifex</i>. Results show <i>Culex asteliae</i> to be a valid species but <i>Cx. rotoruae</i> is not necessarily so. The <i>Aedes</i> species appears to be closely related to <i>Ae. subalbirostris</i>. The introduced <i>Cx. quinquefasciatus</i> was clearly shown to be related <i>to Cx. pipiens</i>; however, the endemic <i>Cx. pervigilans</i> was not. No evidence of population variation based on geographic location was detected.
DOI: 10.18739/a2cf9j82n
title: Pointframe measurements of vegetation species and height from Small Mammal Experiment Summer 2018 and 2019 near Toolik Lake, Alaska

description: We conducted a field experiment in which small mammal density was manipulated at three replicate sites near Toolik Lake, Alaska. The motivation for collecting this pointframe dataset was to understand and quantify the impact of the most abundant herbivores, small rodents (voles and lemmings) on tussock tundra vegetation community composition and canopy structure in the Arctic. In July of 2018, at each site we set up an 8 meter (m) x 8 m fenced exclosure with a 0.635 centimeter (cm) square mesh to prevent herbivore grazing and increase vegetation cover (Exclosure treatment (EX)), set up a 20 m x 20 m enclosure that was stocked with up to 4 voles from spring snowmelt through September in 2018 and 2019 (Press treatment (PR)), and identified an 8 m x 8 m unfenced control plot marked at each corner with pin flags at each site (Control (CT)). In 2019, at each site we set up a 20 m x 20 m enclosure that was stocked with up to 4 voles from spring snowmelt through September in 2019 only, after which voles were removed and the fences served to exclude voles from 2020-2023 (Pulse treatment (PU)).
 Within each treatment at each site, we collected vegetation species and height data from pointframe measurements (62 points, 80cm across with a 0.5m^2 footprint) at three distinct locations during the period of peak leaf out (~July) in 2018 and 2019.
DOI: 10.18739/a27s7ht97
title: Pointframe measurements of vegetation species and height from Small Mammal Experiment Summer 2018 and 2019 from Nome, Alaska

description: We conducted a field experiment in which small mammal density was manipulated at three replicate sites near Nome, Alaska. The motivation for collecting this pointframe dataset was to understand and quantify the impact of the most abundant herbivores, small rodents (voles and lemmings) on tussock tundra vegetation community composition and canopy structure in the Arctic. In July of 2018, at each site we set up an 8 meter (m) x 8 m fenced exclosure with a 0.635 centimeter (cm) square mesh to prevent herbivore grazing and increase vegetation cover (Exclosure treatment (EX)), set up a 20 m x 20 m enclosure that was stocked with up to 4 voles from spring snowmelt through September in 2018 and 2019 (Press treatment (PR)), and identified an 8 m x 8 m unfenced control plot marked at each corner with pin flags at each site (Control (CT)). Within each treatment at each site, we collected vegetation species and height data from pointframe measurements (62 points, 80cm across with a 0.5m^2 footprint) at three distinct locations during the period of peak leaf out (~July) in 2019
DOI: 10.6073/pasta/8b904f5a90dc060eed3969fbc33df702
title: Gastropod Biomass and Densities found at Rabbit Key Basin, Florida Bay (FCE) from March 2000 to April 2001

description: Grazing gastropod biomass and shell morphology were measured from 1 m2 plots within Thalassia seagrass meadow in Rabbit Key Basin, Florida Bay, Everglades National Park.
DOI: 10.5281/zenodo.10689058
title: drug prevalence among student

description: the data was render anonymous for confidentiality purposes
DOI: 10.5281/zenodo.10689059
title: drug prevalence among student

description: the data was render anonymous for confidentiality purposes
DOI: 10.6084/m9.figshare.12457262
title: Additional file 1 of Can the anatomy of abnormal flowers elucidate relationships of the androecial members in the ginger (Zingiberaceae)?

description: Additional file 1: Table S1. Tests for significant saturation of the loci matrices for Zingiberales taxon samples. Table S2. Publication of the floral vascular system in Zingiberales. Table S3. The herbarium vouchers of the Alpinia intermedia in SCBG. Table S4. GeneBank accession numbers for previously sequenced species used for phylogenetic analysis in this study.
DOI: 10.6084/m9.figshare.12457262.v1
title: Additional file 1 of Can the anatomy of abnormal flowers elucidate relationships of the androecial members in the ginger (Zingiberaceae)?

description: Additional file 1: Table S1. Tests for significant saturation of the loci matrices for Zingiberales taxon samples. Table S2. Publication of the floral vascular system in Zingiberales. Table S3. The herbarium vouchers of the Alpinia intermedia in SCBG. Table S4. GeneBank accession numbers for previously sequenced species used for phylogenetic analysis in this study.