cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22445212.v1
title: Well-fed or nearly dead? Using quantitative PCR to detect dietary stress in Daphnia pulex.

description: Nutrition is at the center of interactions between organisms and their environment. During this time of unprecedented anthropogenic environmental change, biological indicators of nutritional changes and their effects on ecosystems are crucial if we are to understand and mitigate these changes. In this study, we developed a qPCR assay to examine nutritional responsiveness of ten genes identified as potential indicators of nutritional state in the freshwater zooplankton <em>Daphnia pulex</em>. We grew animals in six ecologically relevant treatments: nutrient replete, low carbon (food), low phosphorus, low nitrogen, low calcium, and high Cyanobacteria. We selected ten nutrient sensitive genes, two per limiting nutrient, and two reference genes from an RNA sequencing dataset. We found that using the nutrient-specific pairs of genes for single nutrient limitation assays showed mixed results with some treatments (calcium, nitrogen, carbon) with high levels of treatment discrimination, but gene responses designed for other treatments (phosphorus and Cyanobacteria) showed little to no treatment discrimination. However, when we used all ten genes as a single nutritional state assay, we could discriminate between our six nutritional states with high levels of accuracy. These results represent a compelling proof of concept for the use of gene-based nutritional biomarkers, paving the way for the use of genetically based nutritional state biomarkers in the study of ecology
DOI: 10.5281/zenodo.6821243
title: Cross-phyla protein annotation by structural prediction and alignment

description: <strong>Background:</strong> Protein annotation is a major goal in molecular biology, yet experimentally determined knowledge is typically limited to a few model organisms. In non-model species, the sequence-based prediction of gene orthology can be used to infer protein identity, however this approach loses predictive power at longer evolutionary distances. Here we propose a workflow for protein annotation using structural similarity, exploiting the fact that similar protein structures often reflect homology and are more conserved than protein sequences. <strong>Results:</strong> We propose a workflow of openly available tools for the functional annotation of proteins via structural similarity (MorF: <strong>Mor</strong>pholog<strong>F</strong>inder) and use it to annotate the complete proteome of a sponge. Sponges are highly relevant for inferring the early history of animals, yet their proteomes remain sparsely annotated. MorF accurately predicts the functions of proteins with known homology in &gt;90% cases, and annotates an additional 50% of the proteome beyond standard sequence-based methods. We uncover new functions for sponge cell types, including extensive FGF, TGF and Ephrin signalling in sponge epithelia, and redox metabolism and control in myopeptidocytes. Notably, we also annotate genes specific to the enigmatic sponge mesocytes, proposing they function to digest cell walls. <strong>Conclusions:</strong> Our work demonstrates that structural similarity is a powerful approach that complements and extends sequence similarity searches to identify homologous proteins over long evolutionary distances. We anticipate this to be a powerful approach that boosts discovery in numerous -omics datasets, especially for non-model organisms.
description: we upload two more tables that contain the yeast and Arabidopsis proteins with similar structures to human proteins, as well as information on whether they are homologs or not.
description: {"references": ["Ruperti, Fabian and Papadopoulos, Nikolaos, et al. (2022). Data related to https://doi.org/10.1101/2022.07.05.498892"]}
DOI: 10.21227/pxft-3480
title: Data for archetypes

description: Data for the alluvial charts and clustering
DOI: 10.5281/zenodo.7781913
title: Gene/Protein BridgeDb ID Mapping Database (Ensembl 108)

description: Ensembl 108 derived ID mapping databases for use with BridgeDb.<br> <br> The scripts used to create these databases based on Ensembl BioMart can be found at https://github.com/bridgedb/create-bridgedb-genedb.
DOI: 10.5281/zenodo.7781912
title: Gene/Protein BridgeDb ID Mapping Database (Ensembl 108)

description: Ensembl 108 derived ID mapping databases for use with BridgeDb.<br> <br> The scripts used to create these databases based on Ensembl BioMart can be found at https://github.com/bridgedb/create-bridgedb-genedb.
DOI: 10.5066/p9gotc10
title: Elevation and Mangrove Cover Projections under Sea-Level Rise Scenarios at J.N. Ding Darling National Wildlife Refuge, Sanibel Island, Florida, 2020-2100

description: Elevation projections from the WARMER-Mangroves model for J N. "Ding" Darling National Wildlife Refuge across a range of sea-level rise scenarios (53, 115, and 183 cm by 2100). The model was calibrated using dated soil cores sampled from the basin hydrologic zone. These data support the following publication: Buffington, K.J., Thorne, K.M., Krauss, K.W., Conrad, J.K., Drexler, J.Z., and Zhu, Z., in-review. Vulnerability of Sanibel Island's mangrove resources to sea-level rise (Florida, USA).
DOI: 10.25345/c5rx93p9m
title: MassIVE MSV000091607 - Effect of salinity stress on the exoproteome profile of Bacillus amyloliquefaciens EB2003A
title: The study investigated the effect of 200 mM NaCl on the exoproteome profile of Bacillus amyloliquefaciens. 0 mM NaCl was the control.
DOI: 10.5281/zenodo.7789856
title: Thermal plasticity of the sea urchin Salmacis sphaeroides

description: Data of metabolic rates of sea urchin acclimated to two different temperatures.
DOI: 10.5281/zenodo.7789855
title: Thermal plasticity of the sea urchin Salmacis sphaeroides

description: Data of metabolic rates of sea urchin acclimated to two different temperatures.
DOI: 10.7281/t1/zhg9bb/nb7vx9
title: 20170816_Deidentified booklet data codebook.pdf

description: A codebook to guide users of the datasets in Turnbull_Deidentifed data sets.zip. (The codebook is also included within the dataset folder.)
DOI: 10.7281/t1/zhg9bb/pl1b1n
title: Turnbull_Phase I Study Deidentified data sets.zip

description: Three datasets containing an anonymized version of the data used to create all tables and figures in this publication.
DOI: 10.6084/m9.figshare.22457470
title: Supplementary Data for "Ribosomes as molecular thermometers: metal-binding sites in ribosomal proteins as a proxy of bacterial adaptation to heat and cold"

description: This data complement the manuscript "Ribosomes as molecular thermometers: metal-binding sites in ribosomal proteins as a proxy of bacterial adaptation to heat and cold".
DOI: 10.6084/m9.figshare.22457470.v1
title: Supplementary Data for "Ribosomes as molecular thermometers: metal-binding sites in ribosomal proteins as a proxy of bacterial adaptation to heat and cold"

description: This data complement the manuscript "Ribosomes as molecular thermometers: metal-binding sites in ribosomal proteins as a proxy of bacterial adaptation to heat and cold".
DOI: 10.6084/m9.figshare.22457965
title: oldH5CtrlStim.rds

description: old liger object
DOI: 10.6084/m9.figshare.22457965.v1
title: oldH5CtrlStim.rds

description: old liger object
DOI: 10.5066/p9kv6fmq
title: Bias-Corrected Topobathymetric Elevation Model for South Florida, 2018

description: Accurate elevation data in coastal ecosystems are crucial for understanding vulnerability to sea-level rise. Lidar has become increasingly available; however, in tidal wetlands such as mangroves and salt marsh, vertical bias from dense vegetation reduces accuracy of the delivered 'base earth' products. To increase accuracy of elevation models across south Florida, we applied the LEAN technique to six different lidar collections from 2007-2018. On average, LEAN correction increased DEM accuracy by 46.1 percent, reducing the vertical bias. After correction and post-processing, the DEMs were merged together with a bathymetric dataset to create a seamless topobathy product.
DOI: 10.6084/m9.figshare.21941558.v3
title: README_US_bee_completeness_paper.md

description: README.md file for all data files listed under this project
DOI: 10.6084/m9.figshare.22457977
title: Supplementary Tables S1-S19 for PhD Thesis (Anton Kalyuzhnyy)

description: Supplementary Tables S1-S19 for PhD Thesis (Anton Kalyuzhnyy)
DOI: 10.6084/m9.figshare.22457977.v1
title: Supplementary Tables S1-S19 for PhD Thesis (Anton Kalyuzhnyy)

description: Supplementary Tables S1-S19 for PhD Thesis (Anton Kalyuzhnyy)
DOI: 10.15156/bio/sh0888655.09fu
title: SH0888655.09FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.6084/m9.figshare.21941558
title: README_US_bee_completeness_paper.md

description: README.md file for all data files listed under this project
DOI: 10.6084/m9.figshare.21941558.v4
title: README_US_bee_completeness_paper.md

description: README.md file for all data files listed under this project
DOI: 10.7281/t1/tlebvw/8f2sbn
title: 2-04_DynamicRegA.D6.IC1.zip

description: Dynamic Simulation data used in publication of doi:10.5194/wes-2016-58 (4 of 10)
DOI: 10.7281/t1/tlebvw/ljufag
title: 2-01_DynamicRegA.D4.IC1.zip

description: Dynamic Simulation data used in publication of doi:10.5194/wes-2016-58 (1 of 10)
DOI: 10.7281/t1/tlebvw/remsg0
title: 2-03_DynamicRegA.D4.IC3.zip

description: Dynamic Simulation data used in publication of doi:10.5194/wes-2016-58 (3 of 10)
DOI: 10.7281/t1/tlebvw/uc4wgg
title: 2-02_DynamicRegA.D4.IC2.zip

description: Dynamic Simulation data used in publication of doi:10.5194/wes-2016-58 (2 of 10)
DOI: 10.7281/t1/tlebvw/1sgu04
title: 2-05_DynamicRegD.D4.IC1.zip

description: Simulation data used in publication of doi:10.5194/wes-2016-58 (5 of 10)
DOI: 10.7281/t1/tlebvw/dgcr7r
title: 2-07_DynamicRegD.D4.IC3.zip

description: Dynamic Simulation data used in publication of doi:10.5194/wes-2016-58 (7 of 10)
DOI: 10.7281/t1/tlebvw/n8nwrj
title: 2-08_DynamicRegD.D6.IC1.zip

description: Dynamic Simulation data used in publication of doi:10.5194/wes-2016-58 (8 of 10)
DOI: 10.7281/t1/tlebvw/p6s0x8
title: 2-06_DynamicRegD.D4.IC2.zip

description: Dynamic Simulation data used in publication of doi:10.5194/wes-2016-58 (6 of 10)
DOI: 10.7281/t1/tlebvw/xfxkom
title: 2-09_DynamicRegD.D6.IC2.zip

description: Dynamic Simulation data used in publication of doi:10.5194/wes-2016-58 (9 of 10)
DOI: 10.7281/t1/tlebvw/bgrxd3
title: 1_Codebook_wes-2016-58.zip

description: Description of simulation data files used in publication of doi:10.5194/wes-2016-58
DOI: 10.7281/t1/tlebvw/odqenk
title: 3-02_StaticRegD.zip

description: Static Simulation data used in publication of doi:10.5194/wes-2016-58 (2 of 2)
DOI: 10.7281/t1/tlebvw/qvwwzn
title: 3-01_StaticRegA.zip

description: Static Simulation data used in publication of doi:10.5194/wes-2016-58 (1 of 2)
DOI: 10.7281/t1/tlebvw/yygjsq
title: 2-10_DynamicRegD.D6.IC3.zip

description: Dynamic Simulation data used in publication of doi:10.5194/wes-2016-58 (10 of 10)
DOI: 10.6084/m9.figshare.22455616
title: Full Dataset prior to Cleaning

description: This dataset includes all of the data downloaded from GBIF (DOIs provided in README.md as well as below, downloaded Feb 2021) as well as data downloaded from SCAN. This dataset has 2,808,432 records and can be used as a reference to the verbatim data before it underwent the cleaning process. The only modifications made to this datset after direct download from the data portals are the following: <br> 1) for GBIF records, I renamed the countryCode column to be "country" so that the column title is consistent across both GBIF and SCAN 2) A source column was added where I specify if the record came from GBIF or SCAN 3) Duplicate records across SCAN and GBIF were removed by identifying identical instances "catalogNumber" and "institutionCode" 4) Only the Darwin core columns (DwC) that were shared across downloaded datasets were retained. GBIF contained ~249 DwC variables, and SCAN data contained fewer, so this combined dataset only includes the ~80 columns shared between the two datasets <br> ------------- <br> For GBIF, we downloaded the data in three separate chunks, therefore there are three DOIs. See below: <br> GBIF.org (3 February 2021) GBIF Occurrence Downloadhttps://doi.org/10.15468/dl.6cxfsw GBIF.org (3 February 2021) GBIF Occurrence Downloadhttps://doi.org/10.15468/dl.b9rfa7 GBIF.org (3 February 2021) GBIF Occurrence Downloadhttps://doi.org/10.15468/dl.w2nndm
DOI: 10.5281/zenodo.7789185
title: An exploratory survey about using ChatGPT in education, healthcare, and research

description: Survey responses dataset associated with paper, 'An exploratory survey about using ChatGPT in education, healthcare, and research.'
DOI: 10.5281/zenodo.7789186
title: An exploratory survey about using ChatGPT in education, healthcare, and research

description: Survey responses dataset associated with paper, 'An exploratory survey about using ChatGPT in education, healthcare, and research.'
DOI: 10.5519/qd.qykgqmdw
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (76 records)
DOI: 10.35078/hdsfv6
title: Replication Data for: Ficha epidemiológica de localidade: Distrito: Varginha | Município: Deresópolis

description: Levantamento Triatomínico com operações de campo ocorridas em Minas Gerais pela Superintendência de Campanhas de Saúde Pública (SUCAM) e FUNASA (Fundação Nacional de Saúde), no período de 1979 a 1999, objetivando a busca da presença de vetores da doença de Chagas ou de vestígios dessa presença. A partir dela são orientadas as operações com inseticida (pt) Triatomine survey with field operations carried out in Minas Gerais by the Public Health Campaigns Superintendence (SUCAM) and FUNASA (National Health Foundation), from 1979 to 1999, aiming to search for the presence of Chagas disease vectors or traces of that presence. From it, operations with insecticide are guided (en) Encuesta de triatominos con operaciones de campo realizada en Minas Gerais por la Superintendencia de Campañas de Salud Pública (SUCAM) y FUNASA (Fundación Nacional de Salud), de 1979 a 1999, con el objetivo de buscar la presencia de vectores de la enfermedad de Chagas o rastros de esa presencia. Desde ella se orientan las operaciones con insecticida (es)
DOI: 10.5281/zenodo.7789868
title: Data from : Quantifying the Effect Size of Management Actions on Aboveground Carbon Stocks in Forest Plantations

description: These data were extracted from publications listed in the supplemental data associated with the manuscript. The data include information on the aboveground carbon biomass of individual tree crops in pure versus interplanted stands, the aboveground biomass stocks of NPK fertilized versus unfertilized forest plantations, and the aboveground carbon stocks of thinned versus unthinned forest plantations. Additionally, the data contains other attributes of the studies that were used as moderator variables in the meta-analysis. For further details on how missing standard deviations were imputed, please refer to the methods section of the manuscript.
DOI: 10.5281/zenodo.7789867
title: Data from : Quantifying the Effect Size of Management Actions on Aboveground Carbon Stocks in Forest Plantations

description: These data were extracted from publications listed in the supplemental data associated with the manuscript. The data include information on the aboveground carbon biomass of individual tree crops in pure versus interplanted stands, the aboveground biomass stocks of NPK fertilized versus unfertilized forest plantations, and the aboveground carbon stocks of thinned versus unthinned forest plantations. Additionally, the data contains other attributes of the studies that were used as moderator variables in the meta-analysis. For further details on how missing standard deviations were imputed, please refer to the methods section of the manuscript.
DOI: 10.5281/zenodo.7789885
title: Data set to support the DSML measure

description: Two datasets for the factor analysis which has been conducted to develop the Diversity of Strategies for Motivation in Learning (DSML), as it has been published in the Behavioral Sciences Journal by Caroline Hands and Maria Limniou (2013).
DOI: 10.5281/zenodo.7789884
title: Data set to support the DSML measure

description: Two datasets for the factor analysis which has been conducted to develop the Diversity of Strategies for Motivation in Learning (DSML), as it has been published in the Behavioral Sciences Journal by Caroline Hands and Maria Limniou (2013).
DOI: 10.34740/kaggle/dsv/5280197
title: Balochi Language to English Translation Dataset
DOI: 10.18112/openneuro.ds004547.v1.0.0
title: Older Adult Structual and functional MRI data
DOI: 10.25739/sg2m-ky55
title: Bucksch_Liu_ThePlantPhenomeJournal_2023

description: Raw data to reproduce the results published in the corresponding paper
DOI: 10.6084/m9.figshare.22448341
title: Soybean Expression Atlas v2

description: <strong>Overview</strong> This directory contains important files created during the construction of the Soybean Expression Atlas v2. <br> <strong>Directory structure</strong> Here, you can find the following files: <br> - `se_atlas_gene.rda`: A *SummarizedExperiment* object containing gene-level transcript abundances in TPM and bias-corrected counts, which are stored in the `gene_TPM` and `gene_counts` assays, respectively. <br> - `se_atlas_transcript.rda`: A *SummarizedExperiment* object containing transcript-level transcript abundances in TPM and counts, which are stored in the `tx_TPM` and `tx_counts` assays, respectively. <br> - `equivalence_classes.tar.gz`: A compressed directory containing equivalence classes generated by salmon for all BioSamples. Equivalence classes are typically used for differential transcript usage analyses. <br> - `parquet_dir.tar.gz`: A partitioned .parquet directory with the gene-level transcript abundances in TPM and bias-corrected counts created with the *arrow* package. <br>
DOI: 10.17909/y06k-3f04
title: TESS observations for TKS XVI

description: TESS 2-min cadence observations for "The TESS-Keck Survey. XVI. Mass Measurements for 12 Planets in Eight Systems and Tentative Evidence of a Gap in the Mass-Radius Distribution of Small Planets"
DOI: 10.5281/zenodo.7788072
title: Replication package for "Ride-Sharing and the Geography of Consumption Industries"

description: This package replicates all the analysis of the associated manuscript. The output is all the figures and tables provided in the paper. All the non-confidential data are also provided in this package.
DOI: 10.5281/zenodo.7788071
title: Replication package for "Ride-Sharing and the Geography of Consumption Industries"

description: This package replicates all the analysis of the associated manuscript. The output is all the figures and tables provided in the paper. All the non-confidential data are also provided in this package.
DOI: 10.6084/m9.figshare.22404567
title: Doxorubicin-treated Cardiomyocytes - Molecular Cartography 100 genes

description: We utilized a chemically defined protocol to differentiate human induced pluripotent stem cells (iPSCs) into beating cardiomyocytes and treated them with either DMSO (vehicle) or 2.5 μM DOX for twelve hours before fixation. Single molecule spatial transcriptomes were measured by Resolve Bioscience using Molecular Cartography for 100 genes important for cardiomyocyte health and function. <br> Replicates A1 and A2 correspond to vehicles while replicates B1 and B2 correspond to DOX treated samples.
DOI: 10.6084/m9.figshare.22463218
title: Supplemental data_Table 1_AJP.xlsx

description: RNAseq Data <br> Supplemental Data Table 1: <strong>All of the genes that significantly changed during PRA</strong> <br> Supplemental Data Table 2: <strong>All of the genes that significantly changed in </strong><em><strong>IL-6-/-</strong></em> <strong>PRA versus WT PRA</strong>
DOI: 10.34740/kaggle/dsv/5280338
title: Queue Waiting Time Prediction
DOI: 10.5281/zenodo.7789909
title: Enriched OpenAlex Data for Universidad de Antioquia

description: Advanced user API output from http://impactu.colav.co for the Institutional Profile "Universidad de Antioquia"
DOI: 10.5281/zenodo.7789908
title: Enriched OpenAlex Data for Universidad de Antioquia

description: Advanced user API output from http://impactu.colav.co for the Institutional Profile "Universidad de Antioquia"
DOI: 10.6084/m9.figshare.22463890
title: Coastal Biodiversity Priority Areas 2023

description: This dataset is the first version of cross-realm biodiversity priority developed for the South African coastal zone, aiming to align land-based and marine CBA Maps through the land-sea (including estuaries) interface. It was developed by doing cross-realm biodiversity planning for the coastal zone (using Marxan).
DOI: 10.6084/m9.figshare.16649695.v1
title: Network: lter, Domain: mcmurdo

description: MacroSheds timeseries data, shapefiles, and metadata for domain: mcmurdo, within network: lter
DOI: 10.6084/m9.figshare.19638642
title: Using genomics, morphometrics, and environmental niche modeling to test the validity of a narrow-range endemic snail, Patera nantahala (Gastropoda, Polygyridae)

description: Datasets from Whelan et al. "Using genomics, morphometrics, and environmental niche modeling to test the validity of a narrow-range endemic snail". See README and publication for details on specific files.
DOI: 10.6084/m9.figshare.19638642.v1
title: Using genomics, morphometrics, and environmental niche modeling to test the validity of a narrow-range endemic snail, Patera nantahala (Gastropoda, Polygyridae)

description: Datasets from Whelan et al. "Using genomics, morphometrics, and environmental niche modeling to test the validity of a narrow-range endemic snail". See README and publication for details on specific files.
DOI: 10.18112/openneuro.ds004547.v1.1.0
title: Older Adult Structual and functional MRI data
DOI: 10.34740/kaggle/dsv/5234184
title: Nifty Total Market stocks, 1D, max price history
DOI: 10.5281/zenodo.7789999
title: How does thermal pressurization of pore fluids affect 3D strike-slip earthquake dynamics and ground motions?

description: BSSA-TP-31Mar2023-zenodo.tar.gz has all the input files required to simulate forty-nine dynamic rupture models. Note that "SeisSol_release_generatedKernels_dhsw_hybrid_none_9_5" and "TP-3D-final_withXML" are SeisSol executable (compiled on Shaheen II at KAUST) and mesh files respectively. Every simulation folder should have empty "logs" and "output" folders where simulation outputs will be stored.
DOI: 10.5281/zenodo.7789998
title: How does thermal pressurization of pore fluids affect 3D strike-slip earthquake dynamics and ground motions?

description: BSSA-TP-31Mar2023-zenodo.tar.gz has all the input files required to simulate forty-nine dynamic rupture models. Note that "SeisSol_release_generatedKernels_dhsw_hybrid_none_9_5" and "TP-3D-final_withXML" are SeisSol executable (compiled on Shaheen II at KAUST) and mesh files respectively. Every simulation folder should have empty "logs" and "output" folders where simulation outputs will be stored.