cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/f7zk5fk2
title: Data release for Applying the Community Ice Sheet Model to evaluate PMIP3 LGM climatologies over the North American ice sheets

description: The data release consists of a single NetCDF file with results from a suite of ice sheet model simulations. We ran with Community Ice Sheet Model (CISM2) with input from models used in the Palaeoclimate Modelling Intercomparison 3 (PMIP3). The NetCDF file contains output from model year 5000 for a limited number of variables to keep the file size reasonably small. This subset of variables are the ones we focus our analysis and paper on.
DOI: 10.5281/zenodo.6359831
title: Immune parameters in horses under different housing conditions

description: Horses were successively subjected to two different treatments - 1. fission of a stable group, 2. relocation to single housing - and the blood numbers of various leukocytes subsets invesigated. In addition, plasma cortisol concentrations, individual rank, and number of social interactions before and after fission of the group as well as occurrence of stereotypic behavior after relocation to individual stabling was assessed.
DOI: 10.5281/zenodo.6359835
title: Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia)

description: Supplemental data and code for Edie, Collins, and Jablonski, Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia).
description: fixed sourcing error in r/func_Edie_etal_bivalignment.R
DOI: 10.5281/zenodo.5909813
title: Traits, landmarks and outlines: Three congruent sides of a tale on coral reef fish morphology

description: Quantifying the morphology of organisms remains fundamental in ecology given the form-function relationship. Morphology is quantifiable in traits, landmarks, and outlines, and the choice of approach may influence ecological conclusions to an unknown extent. Here, we apply these three approaches to 111 individual coral reef fish of 40 species common in Micronesia. We investigate the major dimensions of morphological variability among individuals, families, and predefined feeding functional groups. We find that although the approaches are complementary, they coincide in capturing elongation as the main dimension of variability. Further, the choice of approach led to different interpretations regarding the degree of morphological differentiation among taxonomic and feeding functional groups. We also use each morphology dataset to compute community-scale morphological diversity on Palauan reefs and investigate how the choice of dataset affects the detection of differences among sites and wave exposure levels. The exact ranking of sites from highest to lowest morphological diversity was sensitive to the approach used, but not the broad spatial pattern of morphological diversity. Conclusions regarding the effect of wave exposure on morphological diversity were robust to the approach used. Biodiversity hotspots (e.g. areas of exceptionally high diversity and/or endemism) are considered important conservation targets but their location may depend on the biodiversity metric used. In the same vein, our results caution against labelling particular sites as morphological diversity hotspots when metrics consider only a single aspect of morphology.
DOI: 10.5281/zenodo.5909812
title: Traits, landmarks and outlines: Three congruent sides of a tale on coral reef fish morphology

description: Quantifying the morphology of organisms remains fundamental in ecology given the form-function relationship. Morphology is quantifiable in traits, landmarks, and outlines, and the choice of approach may influence ecological conclusions to an unknown extent. Here, we apply these three approaches to 111 individual coral reef fish of 40 species common in Micronesia. We investigate the major dimensions of morphological variability among individuals, families, and predefined feeding functional groups. We find that although the approaches are complementary, they coincide in capturing elongation as the main dimension of variability. Further, the choice of approach led to different interpretations regarding the degree of morphological differentiation among taxonomic and feeding functional groups. We also use each morphology dataset to compute community-scale morphological diversity on Palauan reefs and investigate how the choice of dataset affects the detection of differences among sites and wave exposure levels. The exact ranking of sites from highest to lowest morphological diversity was sensitive to the approach used, but not the broad spatial pattern of morphological diversity. Conclusions regarding the effect of wave exposure on morphological diversity were robust to the approach used. Biodiversity hotspots (e.g. areas of exceptionally high diversity and/or endemism) are considered important conservation targets but their location may depend on the biodiversity metric used. In the same vein, our results caution against labelling particular sites as morphological diversity hotspots when metrics consider only a single aspect of morphology.
DOI: 10.5281/zenodo.6341891
title: Simulated exome-sequencing data for a family study of lymphoid cancer

description: This repository contains all the data files for a simulated exome-sequencing study of 150 families ascertained to contain at least four members affected with lymphoid cancer. The simulated data can be found in the files section below. The files are: SLiM_output.txt - contains the SLiM-simulated, exome-wide, SNV data generated under an American-admixture demographic model, for the American-admixed sub-population only. SLiM_output_chr8&9.txt - contains the SLiM-simulated data above for all source populations as well as the American-admixed sub-population, but only for chromosomes 8 and 9. sample_info.txt - contains pedigree information of all the disease-affected individuals and individuals connecting them along a line of descent, for all 150 ascertained pedigrees. Genotypes.zip - a zipfile that contains 22 text files of genotypes for each chromosome. The genotypes are for simulated single-nucleotide variants on the exome and are in gene-dosage format. SNV maps.zip - a zipfile that contains 22 text files giving the single-nucleotide variant information for each chromosome. familial_cRV.txt - contains the familial causal rare variants for all 150 ascertained pedigrees. study_peds.txt - contains the 150 pedigrees ascertained to contain four or more relatives affected with lymphoid cancer. All the scripts used to generate these data can be found in the GitHub repository archived at https://zenodo.org/record/6347546. We have also uploaded one intermediate .Rdata file, Chromwide.Rdata, to save the user substantial time when running the associated RMarkdown script for the simulation. We recommend loading Chromwide.Rdata into your R work-space rather than generating it from scratch.
description: funding acknowledgement- Natural Sciences and Engineering Research Council of Canada RGPIN-04296-2018
DOI: 10.6084/m9.figshare.19362374.v1
title: Merging imaging technologies and metabarcoding to assess Rhizaria abundances, diversity and contribution to the silicon cycle in the Mediterranean Sea

description: Siliceous Rhizaria (polycystine radiolarians and phaeodarians) are significant contributors to carbon and silicon biogeochemical cycles. Considering their broad taxonomic diversity and their wide size range (from a few micrometres up to several millimetres), a comprehensive evaluation of the entire community to carbon and silicon cycles is challenging. Here, we assess the diversity and contribution of silicified Rhizaria to the global biogenic silica stocks in the upper 500 m of the oligotrophic North-Western Mediterranean Sea using both imaging (FlowCAM, Zooscan and Underwater Vision Profiler) and molecular tools and data. While imaging data revealed that the most abundant organisms were the smallest, molecular results showed that the largest Rhizaria had the highest relative abundances. While this seems contradictory, relative abundance data obtained with molecular methods correlated well with the total biovolume of the organisms. This result reflects a potential link between gene copies number and the volume of a given cell allowing reconciling molecular and imaging data. Using abundance data from imaging methods we estimate that siliceous Rhizaria accounted for up to 6% of the total biogenic silica biomass of the siliceous planktonic community in the upper 500m of the water column. <br>This table gathers the abundances of the ASVs selected to recreate the figure 3 (panel C) from the paper described above.<br>The table has the following structure divided by columns:-sequence: The sequence of the ASV-ASV: the identification of the ASV-taxonomy: the associated PR2 taxonomy-total_presence: the number of samples that the ASV is present in-total_abundance: the total number of reads of the ASV-the remaining columns are the specific samples<br>
DOI: 10.15784/601534
title: Joinville and Livingston Islands - rock and sediment OSL ages

description: detailed results for rock and sediment OSL ages; De calculation; dose rate calculation, fading, signal measurement
DOI: 10.15784/601531
title: Electron Microprobe Analysis of feldspar separates from rock and sediment OSL samples from Joinville and Livingston Island Beaches

description: sediment and rock samples were collected on Joinville and Livingston Islands for OSL dating; feldspar separates were prepared; data set includes Electron microprobe analysis of selected feldspar extracts; includes bmp and tif with elemental maps plus elemental concentrations and Ca:Na:K ratios for feldspar analysis
DOI: 10.15784/601532
title: OSL data - Joinville and Livingston Islands - Raw data

description: raw OSL data for rock and sediment samples collected on Joinville and Livingston Islands
DOI: 10.25345/c5rv0d40q
title: MassIVE MSV000089064 - Fatty Sweet Symphony_gangliosides_RamplerLab_2022
title: Ganglioside profiling (LC-MSn) of MSCs and differentiated adipogenic (fat), chondrogenic (cartilage), and osteogenic (bone) lineage
DOI: 10.6073/pasta/8b92b9c6452698d917f8e104e76e9a97
title: Bonanza Creek LTER: Shrub, Seedling and Sapling Density from 1975 to Present in the Bonanza Creek Experimental Forest near Fairbanks, Alaska

description: This study is a survey of the density of tall shrubs, saplings, and seedlings at Bonanza Creek LTER Control Plots. Densities have been measured at some sites since 1975 while others began in the mid 1980's. In 2006 methodology was changed in attempt to better capture the spatial variability of shrub and tree species within the research sites. The current method, presented here, uses a 2 meter wide transect along two site boundaries covering 220m2. All seedlings, saplings, and tall shrubs &gt;1m (regardless of species) are counted by species and size class along the transect. The previous method used 4m2 circular plots at 20 points on a 10mx10m grid within the control plot for an area of 80m2. The circular method measured all seedlings, saplings, and a certain set of "tall shrubs", regardless of height. The height requirement creates an issue when comparing the old and new methods for early successional stands. For Alnus and Salix this is likely only a problem in the FP0 sites as they are the only sites with a high density of shrubs shorter than 1m. Shrub community changes at these early successional sites should be analyzed using percent cover data. At the later successional sites most Alnus and Salix shrubs are greater than 1m so the transect method likely does not underrepresent density. The metadata and raw data from the circular method can be found in Vegetation Plots of the Bonanza Creek LTER Control Plots: Species Count (1975 - 2004) .
DOI: 10.6084/m9.figshare.19352609
title: Figure 3. Table Summarizing DnaSP Data

description: Table summarizing DnaSP Ka/Ks results. Data focused on notable Ka/Ks values only, noting the number of Ka/Ks values greater than one over the entire sequence. Coding sequences obtained from Ensembl via BLASTn. Re-aligned as translated amino acids via MUSCLE in Aliview. Species were run against each other one at a time - data from each comparison were collected and entered into Microsoft Excel to create this table.
DOI: 10.6084/m9.figshare.19352609.v1
title: Figure 3. Table Summarizing DnaSP Data

description: Table summarizing DnaSP Ka/Ks results. Data focused on notable Ka/Ks values only, noting the number of Ka/Ks values greater than one over the entire sequence. Coding sequences obtained from Ensembl via BLASTn. Re-aligned as translated amino acids via MUSCLE in Aliview. Species were run against each other one at a time - data from each comparison were collected and entered into Microsoft Excel to create this table.
DOI: 10.6073/pasta/e6e78093f1ad86da897585f5f6d32222
title: Bonanza Creek LTER: Point Bar Vegetation Survey of Bonanza Creek LTER Research Plots (2007-Present)

description: Beginning in 2007 ocular vegetation estimates were replaced by the point bar system. The point bar is meant to be a more objective way of carrying out annual vegetation surveys. In particular because you are placing the point bar in the same location every time a site is visited, a better understanding of vegetation change over time is possible. This method replaces the old system of estimating percent cover visually ( Vegetation Plots of the Bonanza Creek LTER Control Plots: Species Percent Cover (1975 - 2009) ), which is often subject to personal bias and small shifts in species composition are often overlooked. Data from both methods were collected during the 2007, 2008, and 2009 field seasons, and regression analysis shows unique and statistically significant relationships between the two methods depending on growth form. At each site, growth forms were evaluated separately, and at each site there is a specific regression model for each growth form. In this way a user can correlate the two methods and data collected before 2007 can be compared to data collected after the new protocol was established.
DOI: 10.6084/m9.figshare.19352633.v1
title: Figure 6. Table Cross-referencing between DnaSP and HMMER Data

description: Table cross-referencing DnaSP data from species with high Ka/Ks values only with coding and amino acid sequences in Aliview and HMMER data. Nucleotide positions taken from DnaSP data tables and cross-referenced with Aliview. Nucleotide positions were highlighted and translated to amino acid view in order to view non-synonymous substitutions. Amino acids positions were compared to HMMER analysis to determine which domain the high Ka/Ks values were located in.
DOI: 10.6084/m9.figshare.19352633
title: Figure 6. Table Cross-referencing between DnaSP and HMMER Data

description: Table cross-referencing DnaSP data from species with high Ka/Ks values only with coding and amino acid sequences in Aliview and HMMER data. Nucleotide positions taken from DnaSP data tables and cross-referenced with Aliview. Nucleotide positions were highlighted and translated to amino acid view in order to view non-synonymous substitutions. Amino acids positions were compared to HMMER analysis to determine which domain the high Ka/Ks values were located in.
DOI: 10.7488/9613095a-674e-41f7-9e86-e68c6e3570e7
title: Formulating and testing a strategy for introducing Pulmonary Rehabilitation (PR) for Chronic Obstructive Pulmonary Disease management in a rural Indian setting

description: PR is proven to be the most effective strategy to improve shortness of breath, health status and exercise tolerance as well as reduce readmissions and mortality in recent exacerbations patients. There is no therapeutic or rehabilitative government health program for COPD management while in the private sector PR is often incompletely advised. Most of the PR centres are in the urban area and studies are rarely done in the rural population to understand the feasibility of PR. To further formulate and test a PR strategy, we aimed to assess the need for PR from the perspective of people with COPD and HCP in a rural Indian setting.
DOI: 10.12751/g-node.i20kyh
title: 1024-channel electrophysiological recordings in macaque V1 and V4 during resting state

description: We provide electrophysiological recordings in Macaque V1 and V4 cortex with 16 Utah arrays in two subjects.
description: IsDescribedBy: Chen, X., Morales-Gregorio, A., Sprenger, J., Kleinjohann, A., Sridhar, S., van Albada, S. J., Grün, S., Roelfsema, P. R. (2022) 1024-channel electrophysiological recordings in macaque V1 and V4 during resting state. Scientific Data Vol. 9, Article 77. (https://doi.org/10.1038/s41597-022-01180-1)
description: IsReferencedBy: Chen, X., Wang, F., Fernandez, E., Roelfsema, P. R. (2020). Shape perception via a high-channel-count neuroprosthesis in monkey visual cortex. Science Vol. 370, Issue 6521, pp. 1191-1196. (https://doi.org/10.1126/science.abd7435)
DOI: 10.6084/m9.figshare.19362569
title: Species cGAS sequences

description: Species cGAS sequences. A file of the cGAS coding nucleotide sequences of the species and homologs used in the analyses.
DOI: 10.6084/m9.figshare.19362569.v1
title: Species cGAS sequences

description: Species cGAS sequences. A file of the cGAS coding nucleotide sequences of the species and homologs used in the analyses.
DOI: 10.5281/zenodo.6359891
title: Genomic, transcriptomic and proteomic comparison of MRSA CC398 isolates collected from human and wild animal samples (Genome assembly and annotation dataset)

description: This dataset includes the assembled contigs (.fasta and .gbk files), the nucleotide sequences of the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) (.ffn files) and the respective amino acid sequences of the translated CDS sequences (.faa files) for the following methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) strains: MRSA CC398 isolates recovered from humans, namely C5621 and C9017, and from a wild boar, namely OR418. All raw sequence reads used in this study were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB35102).
DOI: 10.5281/zenodo.6359890
title: Genomic, transcriptomic and proteomic comparison of MRSA CC398 isolates collected from human and wild animal samples (Genome assembly and annotation dataset)

description: This dataset includes the assembled contigs (.fasta and .gbk files), the nucleotide sequences of the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) (.ffn files) and the respective amino acid sequences of the translated CDS sequences (.faa files) for the following methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) strains: MRSA CC398 isolates recovered from humans, namely C5621 and C9017, and from a wild boar, namely OR418. All raw sequence reads used in this study were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB35102).
DOI: 10.5287/bodleian:pvmvn90da
title: The role of PEG-40-stearate in the production, morphology and stability of microbubbles
DOI: 10.23708/a8xmbj
title: ECOMED Database description

description: ECOMED Database structure description
DOI: 10.5281/zenodo.6359909
title: Dataset for map in "Endangered languages in Brazil in 2021"

description: Data set and R script used to produce the map of Brazilian indigenous languages in "Endangered languages in Brazil in 2021" by Sebastian Drude, Joshua Birchall, Ana Vilacy Galúcio, Denny Moore and Hein van der Voort. This is a chapter in the book <em>Endangered Languages in the 21<sup>st</sup> Century </em>edited by Eda Derhemi and Chris Moseley and to be published by Routledge in 2022.
DOI: 10.18112/openneuro.ds003216.v2.0.1
title: Whole brain layer-fMRI connectome: An open dataset
DOI: 10.23708/rznaos
title: ECOMED DATABASE SCHEMA

description: ECOMED Database structure schema
DOI: 10.6073/pasta/af6ac21436f2e0f080f987c4ed56e2f8
title: Counts of potential nest predators from Black-throated Blue Warbler territories, Hubbard Brook Experimental Forest, 1997 – 2019

description: This dataset provides counts of potential nest predators recorded on surveys conducted in black-throated blue warbler territories at the Hubbard Brook Experimental Forest. Surveys occurred on three gridded study plots at the HBEF: low elevation (250-350 m; 85 ha), middle elevation (450-600 m; 65 ha), and high elevation (750-850 m; 35 ha). See Rodenhouse et al. 2003 for plot details. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
DOI: 10.6084/m9.figshare.19352534
title: Figure 11, H5N1 Susceptible Species/Biotic environments

description: Figure 11, Raw data collected from various pieces of literature describing biotic environment of multiple H5N1-suseptible avian species. Contains scientific name of each species studied and describes habitat and potential interactions with their environment. Literature references included.
DOI: 10.6084/m9.figshare.19352534.v1
title: Figure 11, H5N1 Susceptible Species/Biotic environments

description: Figure 11, Raw data collected from various pieces of literature describing biotic environment of multiple H5N1-suseptible avian species. Contains scientific name of each species studied and describes habitat and potential interactions with their environment. Literature references included.
DOI: 10.6084/m9.figshare.19352546
title: Figure 12, H5N1 Resistant Species/Biotic Environments

description: Figure 12, Raw data collected from various pieces of literature describing biotic environment of multiple H5N1-resistant avian species. Contains scientific name of each species studied and describes habitat and potential interactions with their environment. Literature references included.
DOI: 10.6084/m9.figshare.19352546.v1
title: Figure 12, H5N1 Resistant Species/Biotic Environments

description: Figure 12, Raw data collected from various pieces of literature describing biotic environment of multiple H5N1-resistant avian species. Contains scientific name of each species studied and describes habitat and potential interactions with their environment. Literature references included.
DOI: 10.6084/m9.figshare.18335813.v7
title: Supplementary Files and Tables

description: Supplemental tables and files.
DOI: 10.6084/m9.figshare.17712398
title: Metabolomics GWAS Raw Data

description: Raw GWAS output of 111 Metabolites for 178 DGRP strains on AL or DR diets.
DOI: 10.6084/m9.figshare.17712398.v2
title: Metabolomics GWAS Raw Data

description: Raw GWAS output of 111 Metabolites for 178 DGRP strains on AL or DR diets.
DOI: 10.6084/m9.figshare.17712398.v1
title: Metabolomics GWAS Raw Data

description: Raw GWAS output of 111 Metabolites for 178 DGRP strains on AL or DR diets.
DOI: 10.6084/m9.figshare.19358723
title: Figure 10. Collection of TLR7 coding sequences of avian species analyzed in the study

description: These are the coding sequences for the TLR7 in the avian species those are analyzed within the study. These sequences are obtained from Ensembl and NCBI database via BlastN search using the TLR7 of Anas platyrhonchos coding sequence as a base sequence to search the other species' TLR7 coding sequence.
DOI: 10.6084/m9.figshare.19358723.v1
title: Fig 10. Collection of TLR7 coding sequences of avian species analyzed in the study

description: These are the coding sequences for the TLR7 in the avian species those are analyzed within the study. These sequences are obtained from Ensembl and NCBI database via BlastN search using the TLR7 of Anas platyrhonchos coding sequence as a base sequence to search the other species' TLR7 coding sequence.
DOI: 10.15468/dl.d9qsy8
title: Occurrence Download

description: A dataset containing 134 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alyxia hurlimannii Guillaumin"
 ]
}

 The dataset includes 134 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003742-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.