cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/npc2c3m8ff.1
title: Data for: An Integrated Gaussian Graphical Model to Evaluate the Impact of Exposures on Metabolic Networks

description: Attached is a zip file containing codes for simulated data generation, Lasso implementation and accuracy measurement
DOI: 10.25606/surf.578c6039-00534b69
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-440)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 440 of the 2048³ resolution collection.
DOI: 10.5281/zenodo.3406796
title: Distinguishing mutations and null alleles from genotyping errors using mother progeny comparisons in Brazilian pine (Araucaria angustifolia)

description: The use of microsatellite markers provides a window into the evolutionary processes of a given species. As such, these markers are widely used in scientific and applied research and are praised for their practicality and ease of use, however, the unavoidable incidence of genotyping deviations has been broadly neglected in the literature. Therefore, the present study aimed to estimate the rate of null alleles, mutations and genotyping errors in microsatellite loci, using Araucaria angustifolia, a threatened species, as a case study. We estimated the rates of the different types of genotyping deviations using mother-progeny genotype comparison from 50 seed-trees and their respective progeny (seeds). A total of 2336 A. angustifolia samples were genotyped, and we found that the rate of null alleles was 0.045. From the 1972 mother-progeny comparisons, the overall genotype deviation rate was 1.58%, consisting of 145 inconsistences (mutations), 339 null alleles and 210 genotyping errors. In terms of seed numbers, 128 (6.5%) showed inconsistencies in at least one locus, 118 (6.0%) null alleles, and 321 (16.3%) genotyping errors. This is the first study to describe the inconsistences (mutations) between mother-progeny genotypes for A. angustifolia, and the outcome makes it clear that an understanding of these genotyping deviations must be considered in assessing the accuracy of inferences made based on population genetics analyses.
description: The present data brings considerable information with 2336 genotyped individuals, including mother and progeny (seeds) of Araucaria angustifolia, an economically and ecologically important tree species. All progenies (seeds) were collected directly from the respective seed-tree (mother).
DOI: 10.5281/zenodo.3406797
title: Distinguishing mutations and null alleles from genotyping errors using mother progeny comparisons in Brazilian pine (Araucaria angustifolia)

description: The use of microsatellite markers provides a window into the evolutionary processes of a given species. As such, these markers are widely used in scientific and applied research and are praised for their practicality and ease of use, however, the unavoidable incidence of genotyping deviations has been broadly neglected in the literature. Therefore, the present study aimed to estimate the rate of null alleles, mutations and genotyping errors in microsatellite loci, using Araucaria angustifolia, a threatened species, as a case study. We estimated the rates of the different types of genotyping deviations using mother-progeny genotype comparison from 50 seed-trees and their respective progeny (seeds). A total of 2336 A. angustifolia samples were genotyped, and we found that the rate of null alleles was 0.045. From the 1972 mother-progeny comparisons, the overall genotype deviation rate was 1.58%, consisting of 145 inconsistences (mutations), 339 null alleles and 210 genotyping errors. In terms of seed numbers, 128 (6.5%) showed inconsistencies in at least one locus, 118 (6.0%) null alleles, and 321 (16.3%) genotyping errors. This is the first study to describe the inconsistences (mutations) between mother-progeny genotypes for A. angustifolia, and the outcome makes it clear that an understanding of these genotyping deviations must be considered in assessing the accuracy of inferences made based on population genetics analyses.
description: The present data brings considerable information with 2336 genotyped individuals, including mother and progeny (seeds) of Araucaria angustifolia, an economically and ecologically important tree species. All progenies (seeds) were collected directly from the respective seed-tree (mother).
DOI: 10.17632/pb4fj9fjjv.1
title: Data for: Smallholder farmers’ willingness to pay for scale-appropriate farm mechanization: Evidence from the mid-hills of Nepal

description: Meta data and data used in this article.
DOI: 10.25606/surf.578c6039-b6a7e573
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-189)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 189 of the 2048³ resolution collection.
DOI: 10.5061/dryad.g01j27q/1
title: Dryad Item 10.5061/DRYAD.G01J27Q/1

description: (:tba)
DOI: 10.5061/dryad.g01j27q/2
title: Dryad Item 10.5061/DRYAD.G01J27Q/2

description: (:tba)
DOI: 10.17632/sfmbxcn8z4.1
title: Data for: A comparison of separation routines for Benders optimality cuts for two-level facility location problems

description: This compressed file contains the source code, data, and complete achieved results for the paper "A comparison of separation routines for Benders optimality cuts for two-level facility location problems". Note that CPLEX was used as our solver.
DOI: 10.25606/surf.578c6039-0ba1bb99
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-185)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 185 of the 2048³ resolution collection.
DOI: 10.25606/surf.578c6039-30d71bd9
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-537)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 537 of the 2048³ resolution collection.
DOI: 10.25606/surf.578c6039-987ce417
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-743)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 743 of the 2048³ resolution collection.
DOI: 10.25606/surf.578c6039-ca39b4a2
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-154)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 154 of the 2048³ resolution collection.
DOI: 10.5061/dryad.16f5v10/1
title: Dryad Item 10.5061/DRYAD.16F5V10/1

description: (:tba)
DOI: 10.6073/pasta/65d2f5bf78c6144a2ed0bc3bd67514a9
title: Cone production of upper slope conifers in the Cascade Range of Oregon and Washington, 1959 to present

description: Seed supply is a key feature of tree population dynamics, and seed production may be indicative of environmental and biological drivers. This study examines cone production in upper-slope, true fir-hemlock forests of the Pacific Northwest, starting in 1959 to the present. Annual surveys of cone counts of Abies spp. (A. amabilis, A. concolor, A. grandis, A. lasiocarpa, A. magnifica, A. procera), Pinus spp. (P. engelmannii, P. lamberti, P. monticola), and Tsuga spp. (T mertsiana) have been conducted at sixty-one plots in 37 locations in nine national forests in Washington and Oregon (originally 10 national forests, but Mt. Baker and Snoqualimie were combined). At each site, a visual count is made of cone production in each of a number (20-30) trees in a stand of one tree species. At some plots, additional trees were added in the 1980s. Primary data include numbers of counts per tree per year, periodic measurements of tree diameter, and the names of the sites. These data illustrate the periodicity of cone production cycles, as well as longer trends associated with climate change and variability in the region.
DOI: 10.25606/surf.578c6039-920394ff
title: The Cosmogrid Simulation: Statistical Properties of Small Dark Matter Halos (2048-158)

description: We present the results of the "Cosmogrid" cosmological N-body simulation suites based on the concordance LCDM model. The Cosmogrid simulation was performed in a 30 Mpc box with 2048³ particles. The mass of each particle is 1.28x10^5 Msun, which is sufficient to resolve ultra-faint dwarfs. We found that the halo mass function shows good agreement with the Sheth & Tormen fitting function down to ~10^7 Msun. We have analyzed the spherically averaged density profiles of the three most massive halos which are of galaxy group size and contain at least 170 million particles. The slopes of these density profiles become shallower than -1 at the inner most radius. We also find a clear correlation of halo concentration with mass. The mass dependence of the concentration parameter cannot be expressed by a single power law, however a simple model based on the Press-Schechter theory proposed by Navarro et al. gives reasonable agreement with this dependence. The spin parameter does not show a correlation with the halo mass. The probability distribution functions for both concentration and spin are well fitted by the log-normal distribution for halos with the masses larger than ~10^8 Msun. The subhalo abundance depends on the halo mass. Galaxy-sized halos have 50% more subhalos than ~10^11 Msun halos have. This is snapshot 158 of the 2048³ resolution collection.
DOI: 10.5061/dryad.97h25b0/1
title: Dryad Item 10.5061/DRYAD.97H25B0/1

description: (:tba)
DOI: 10.5281/zenodo.3406736
title: Lidar data at Sapelo Island, Georgia, USA

description: This is the data corresponding to figure 9 of the paper: Sergio Fagherazzi, Giulio Mariotti, Nicoletta Leonardi, Alberto Canestrelli, William Nardin, William S. Kearney, Morphodynamics of salt marshes in a period of accelerated sea level rise, Submitted to Journal of Geophysical Research, Centennial Edition.
DOI: 10.5281/zenodo.3406737
title: Lidar data at Sapelo Island, Georgia, USA

description: This is the data corresponding to figure 9 of the paper: Sergio Fagherazzi, Giulio Mariotti, Nicoletta Leonardi, Alberto Canestrelli, William Nardin, William S. Kearney, Morphodynamics of salt marshes in a period of accelerated sea level rise, Submitted to Journal of Geophysical Research, Centennial Edition.
DOI: 10.5281/zenodo.3406885
title: Supplementary of Bayesian Evaluation of Incomplete Fission Yields

description: This part employ a code to read parameters of the trained Bayesian neural network which are stored in the log file, and output the averaged function values and Confidence Interval (CI) of fission yields. The instructions are given in the attached BNN-fission.PDF file.
DOI: 10.5281/zenodo.3406886
title: Supplementary of Bayesian Evaluation of Incomplete Fission Yields

description: This part employ a code to read parameters of the trained Bayesian neural network which are stored in the log file, and output the averaged function values and Confidence Interval (CI) of fission yields. The instructions are given in the attached BNN-fission.PDF file.
DOI: 10.5281/zenodo.3406975
title: The pan-genome of Saccharomyces cerevisiae

description: These datasets are related to 'The pan-genome of <em>Saccharomyces cerevisiae</em>' (Li G., Ji B., and Nielsen J.). This deposition contains following datasets: (1) Genomes.tar.gz: a compressed file containing 1392 <em>Saccharomyces cerevisiae </em>genome assembles analyzed (2) genome_information_2.0.tsv: a tab-separated text file that contains the basic information of above genomes, including genomeSize, contigNums, N50, busco_C(%), busco_S(%), busco_D(%), busco_F(%), busco_M(%), busco_n, number_of_genes, number_of_partial_genes, download_from, Eco_Source, Ploidy, Aneuploidies. (3) ClusterFasta.tar.gz: a compressed file that contains a list of fasta files. Each fasta file contains protein sequences in a cluster. The name of the fasta file is the name of the representative sequence of that cluster. (4) sc_gene_cluster_info_0.7_v4.tsv: a tab-separated text file that contains the properties of gene clusters. (5) gene_presence_absence_v4.tsv: a tab-separated text file that contains the gene-presence/absence information. Each columns is a gene cluster. Each row is a genome. Y/N is used to present presence/absence. (6) gene_num_in_clusters_of_each_strain_v4.tsv: a tab-sparated text file that contains the gene number of each genome in each cluster (copy number). Each columns is a gene cluster. Each row is a genome. (7) feature_importances_cv5_pa_cnv.tsv: a tab-separated file that contains the feature importance from a random forest classifier in a 5-fold cross-validation approach. The classifier was trained on gene presence/absence table (PA) or copy number table (CNV). The columns 'pa_x' indicate the feature importance in each fold of cross-validation on PA dataset. The columns 'cnv_x' indicate the feature importance in each fold of cross-validation on CNV dataset.
DOI: 10.5281/zenodo.3406810
title: Videos of mice and squirrels handling various seeds and trained DeepLabCut models for tracking the digits

description: Videos of freely moving and head-fixed mice handling flaxseeds, wheat berries, millet grains, couscous pellets, black-eyed peas, and peanut fragments, as well as wild squirrels handling peanuts, as used in Barrett et. al., "Manual dexterity of mice during food-handling involves the thumb and a set of fast basic movements", in preparation, plus trained DeepLabCut (DLC) models for tracking the digits of the mice during behaviour. The ZIP file "seed handling videos.zip" contains the videos analysed in the paper as H.264-encoded MP4s with a constant rate factor of 20, which has been shown to not significantly affect DLC tracking results (https://www.biorxiv.org/content/10.1101/457242v1). The ZIP file "squirrel seed handling videos.zip" contains the squirrel peanut handling videos in the same format. Each remaining ZIP file contains one or more DLC project folders (minus the videos subfolder), each containing a trained model for tracking the nose and digits 1-4 on both hands during seed handling. SeedHandling-John-2019-07-02.zip is for front view videos, SeedHandling-John-2019-07-04.zip bottom view, and SeedHandling-John-2019-07-05.zip head-fixed side view. "squirrel deeplabcut.zip" contains models for each set of squirrel videos (SeedHandling-John-2019-03-15\ for 20180921*.mp4 and SeedHandling-John-2019-05-20\ for20190424*.mp4). To use on your own data, simply unzip and use the analyze_videos function in DeepLabCut, setting the config file path to the folder you unzipped the model to. For more details on DeepLabCut, see Mathis et. al. (2018), Nat. Neurosci (https://www.nature.com/articles/s41593-018-0209-y) and http://www.mousemotorlab.org/deeplabcut.
DOI: 10.5281/zenodo.3406813
title: DWD European Weather 2

description: opendata.dwd.de - OpenData by Deutscher Wetter Dienst Conditions: https://www.dwd.de/EN/service/copyright/copyright_node.html dates and times are UTC.
DOI: 10.18716/nmrshiftdb2/60004113/nmredata_mrc_cd3od
title: NMReDATA_MRC NMR dataset for (3,5,7,12)-Cholestane-3,7,12,26,27-pentol, 26-(hydrogen sulfate)/sodium salt; 5-cyprinol sulfate in Methanol-D4 (CD3OD)
DOI: 10.5519/qd.nknm4on4
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5281/zenodo.3406990
title: Dataset for "Gross primary productivity of four European ecosystems constrained by joint CO2 and COS flux measurements"

description: Data of measurements and model output of the publication "Gross primary productivity of four European ecosystems constrained by joint CO<sub>2</sub> and COS flux measurements". Data consists of micrometeorological data, COS and CO<sub>2</sub> flux measurements for 4 sites including filters for the fluxes. The sites include: a managed temperate mountain grassland in Austria (18.06.-21.08.2015), a Mediterranean savanna ecosystem in Spain(29.04.-24.05.2016)), a Temperate beach forest in Denmark(07.06.-03.07.2016) and an agricultural soy bean field in Italy(03.07.-01.08.2017). Version 2: param2950** are now correct (were filled with the same values for all field sites) For additional information please contact: Georg.Wohlfahrt@uibk.ac.at
description: Additional funding: Austrian Science Fund (FWF): Georg Wohlfahrt I03859; Tyrolian Science Fund: Florian Kitz UNI-0404/1801; Det Frie Forskningsråd (DFF): Andreas Ibrom 1323-00182; Alexander von Humboldt-Stiftung (Humboldt Foundation); University of Innsbruck: Georg Wohlfahrt; University of Innsbruck: Albin Hammerle; University of Innsbruck: Felix Maximilian Spielmann