cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5101592
title: Prevalent bee venom genes evolved before the stinger and eusociality

description: Background: Venoms, which have evolved numerous times in animals, are ideal models of convergent trait evolution. However, detailed genomic studies of toxin-encoding genes exist for only a few animal groups. The hyper-diverse hymenopteran insects are the most speciose venomous clade, but investigation of the origin of their venom genes has been largely neglected. Results: Utilising a combination of genomic and proteo-transcriptomic data, we investigated the origin of 11 toxin genes in 29 published and 3 new hymenopteran genomes and compiled an up-to-date list of prevalent bee venom proteins. Observed patterns indicate that bee venom genes predominantly originate through single gene co-option with gene duplication contributing to subsequent diversification. Conclusions: Most Hymenoptera venom genes are shared by all members of the clade and only melittin and the new venom protein family anthophilin1 appear unique to the bee lineage. Most venom proteins thus predate the mega-radiation of hymenopterans and the evolution of the aculeate stinger.
DOI: 10.5281/zenodo.5101593
title: Bee venom genes predominately originated in ancestors of sawfly hymenopterans before the aculeate stinger evolved

description: To study convergent trait evolution, venoms that evolved multiple times in animals are ideal models. However, only few animal groups are studied in detail at the genomic level to understand toxin gene evolution. Hyper-diverse hymenopterans are the most speciose venomous animals, but the origin of their toxin genes has been largely overlooked despite their adaptive significance. We combined genomics with proteo-transcriptomics to compile an up-to-date list of core bee venom proteins and investigated the origin of 11 toxin genes in 30 hymenopteran genomes. We found that bee venom toxins originated predominantly by single gene co-option combined with gene duplication. Only melittin and the new venom protein family anthophilin appear unique to the bee lineage. Other toxins already existed in earliest hymenopterans before aculeates evolved their stinger. We elucidate here toxin gene origin at the genomic level during the mega-radiation of hymenopterans with general implications on the evolution of gene function.
DOI: 10.5281/zenodo.5734574
title: Bee core venom genes predominantly originated before aculeate stingers evolved

description: Venoms have convergently evolved in all major animal lineages and are ideal candidates to unravel the genomic processes underlying convergent trait evolution. However, few animal groups have been studied in detail, and large-scale comparative genomic analyses to address toxin gene evolution are rare. The hyper-diverse hymenopterans are the most speciose group of venomous animals, but the origin of their toxin genes has been largely overlooked. We combined proteo-transcriptomics with comparative genomics compiling an up-to-date list of core bee venom proteins to investigate the origin of 11 venom genes in 30 hymenopteran genomes including two newly sequenced genomes of stingless bees. We found a more distinct pattern in which toxin genes originated predominantly by single gene co-option, a prevalent mechanism in parasitoid wasps. These are always accompanied by parallel expansion events in other bee and hymenopteran sister gene groups. The short toxic peptides melittin and apamin appear to be unique to bees, a result supported by a novel machine learning approach. Based on the syntenic pattern we propose here Anthophilin1 as a bee-unique gene family that includes apamin and MCDP. It appears that bees co-adapted their venom genes which predominantly already existed before the aculeate ovipositor evolved to a stinger which exclusively injects venom. Our results provide insight into the large-scale evolution of bee venom compounds, and we present here the first study revealing general processes of venom evolution at a comparative genomic level for this mega-diverse Hymenoptera.
DOI: 10.5281/zenodo.6998876
title: A common venomous ancestor? Prevalent bee venom genes evolved before the aculeate stinger while few major toxins are bee-specific

description: Venoms, which have evolved numerous times in animals, are ideal models of convergent trait evolution. However, detailed genomic studies of toxin-encoding genes exist for only a few animal groups. The hyper-diverse hymenopteran insects are the most speciose venomous clade, but investigation of the origin of their venom genes has been largely neglected. Utilising a combination of genomic and proteo-transcriptomic data, we investigated the origin of 11 toxin genes in 29 published and three new hymenopteran genomes and compiled an up-to-date list of prevalent bee venom proteins. Observed patterns indicate that bee venom genes predominantly originate through single gene co-option with gene duplication contributing to subsequent diversification. Most Hymenoptera venom genes are shared by all members of the clade and only melittin and the new venom protein family anthophilin appear unique to the bee lineage. Most venom proteins thus predate the mega-radiation of hymenopterans and the evolution of the aculeate stinger.
DOI: 10.5281/zenodo.7934577
title: A common venomous ancestor? Prevalent bee venom genes evolved before the aculeate stinger while few major toxins are bee-specific

description: Venoms, which have evolved numerous times in animals, are ideal models of convergent trait evolution. However, detailed genomic studies of toxin-encoding genes exist for only a few animal groups. The hyper-diverse hymenopteran insects are the most speciose venomous clade, but investigation of the origin of their venom genes has been largely neglected. Utilising a combination of genomic and proteo-transcriptomic data, we investigated the origin of 11 toxin genes in 29 published and three new hymenopteran genomes and compiled an up-to-date list of prevalent bee venom proteins. Observed patterns indicate that bee venom genes predominantly originate through single gene co-option with gene duplication contributing to subsequent diversification. Most Hymenoptera venom genes are shared by all members of the clade and only melittin and the new venom protein family anthophilin appear unique to the bee lineage. Most venom proteins thus predate the mega-radiation of hymenopterans and the evolution of the aculeate stinger.
DOI: 10.5281/zenodo.8052397
title: Prevalent bee venom genes evolved before the stinger and eusociality

description: Background: Venoms, which have evolved numerous times in animals, are ideal models of convergent trait evolution. However, detailed genomic studies of toxin-encoding genes exist for only a few animal groups. The hyper-diverse hymenopteran insects are the most speciose venomous clade, but investigation of the origin of their venom genes has been largely neglected. Results: Utilising a combination of genomic and proteo-transcriptomic data, we investigated the origin of 11 toxin genes in 29 published and 3 new hymenopteran genomes and compiled an up-to-date list of prevalent bee venom proteins. Observed patterns indicate that bee venom genes predominantly originate through single gene co-option with gene duplication contributing to subsequent diversification. Conclusions: Most Hymenoptera venom genes are shared by all members of the clade and only melittin and the new venom protein family anthophilin1 appear unique to the bee lineage. Most venom proteins thus predate the mega-radiation of hymenopterans and the evolution of the aculeate stinger.
DOI: 10.34740/kaggle/dsv/6019863
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.34740/kaggle/dsv/6019875
title: 2021 World Population (updated daily)
DOI: 10.5281/zenodo.7936404
title: Data Analysis files for "Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action"

description: Data analysis files for the manuscript "Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action", Nature Communications <strong>14</strong>, 3784 (2023), or arXiv:2210.12443 (2022) This contains the raw data, the data analysis files, and the figure generation files of the manuscript, which includes the following three parts, 0. Data preparation The total size of the raw dataset is around 120GB. The raw data is pre-processed via digital down-conversion at 40MHz to obtain the optical/microwave transient response of the electro-optical device in the presence of strong optical pulses at different powers and frequencies. The processed data is adopted for data analysis of the response measurements for convenience. 1. Data Analysis Detailed data analysis of the electro-optical (microwave and optical) responses in presence of the optical pump pulses for different mode and probing configurations. 2. Figures for the manuscripts. Figures for the optical characterizations Figures for the coherent responses for different configurations Figures for the excess back-action Figures for the theoretical curves in the Supplementary Information
DOI: 10.5281/zenodo.7936405
title: Data Analysis files for "Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action"

description: Data analysis files for the manuscript "Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action", Nature Communications <strong>14</strong>, 3784 (2023), or arXiv:2210.12443 (2022) This contains the raw data, the data analysis files, and the figure generation files of the manuscript, which includes the following three parts, 0. Data preparation The total size of the raw dataset is around 120GB. The raw data is pre-processed via digital down-conversion at 40MHz to obtain the optical/microwave transient response of the electro-optical device in the presence of strong optical pulses at different powers and frequencies. The processed data is adopted for data analysis of the response measurements for convenience. 1. Data Analysis Detailed data analysis of the electro-optical (microwave and optical) responses in presence of the optical pump pulses for different mode and probing configurations. 2. Figures for the manuscripts. Figures for the optical characterizations Figures for the coherent responses for different configurations Figures for the excess back-action Figures for the theoretical curves in the Supplementary Information
DOI: 10.6084/m9.figshare.23576178
title: <strong>Population genetic structure of </strong><em><strong>Torreya grandis</strong></em>

description: The EST-SSR genotype dataset of Torreya grandis.
DOI: 10.5281/zenodo.8079096
title: Multi-horizon forecasting of average daily PM2.5 concentration using LSTM: A case study of air pollution in Singapore

description: Data and code used in the study.
DOI: 10.5281/zenodo.8079097
title: Multi-horizon forecasting of average daily PM2.5 concentration using LSTM: A case study of air pollution in Singapore

description: Data and code used in the study.
DOI: 10.5281/zenodo.8079237
title: Multi-horizon forecasting of average daily PM2.5 concentration using LSTM: A case study of air pollution in Singapore

description: Data and code used in the study.
DOI: 10.6084/m9.figshare.23565954
title: gwhd2021jpg.zip

description: Global Wheat Head Dataset 2021 (jpg compressed) The jpg compressed version of Global Wheat Head Dataset 2021. Converting all the images from png to jpg resulted in compression of abt. 10Gb to 1Gb. File name in the csv annotation file were also converted. Conversion script is included in this zip file (png2jpg.py). This should aid the download waiting time to a certain extent, however I do not assure any data loss upon image compression. I do not claim any rights regarding this dataset. https://zenodo.org/record/5092309
DOI: 10.25345/c5ms3kb6k
title: MassIVE MSV000092261 - Proteome of LPS and IFNg-treated murine bone marrow-derived macrophages
title: Proteomic analysis of murine bone marrow-derived macrophages (BMDMs) incubated with LPS, LPS/IFNg and IFNg for 6 h and 24 h. Cells were stimulated with 100 ng/ml LPS E.coli (Sigma, L2880) and/or 2 ng/ml recombinant mouse IFN-gamma protein (R&D Systems inc., 485-MI/CF) for either 6 h or 24 h, lysed in SDS lysis buffer (2% SDS in 100 mM TEAB) and boiled (15 min, 95 C, 350 rpm). DNA was sheared with Benzonase Nuclease (Merck Millipore) and 2 mM MgCl2 at 37 C (30 min, 500 rpm). Reversibly oxidized cysteines were reduced with 10 mM TCEP followed by alkylation with 20 mM IAA (each step 30 min, 22 C, 600 rpm, in the dark). Proteins were cleaned with the SP3 method using the KingFisher Flex system (Thermo Scientific) and digested overnight with LysC/trypsin (1:50 protease:protein ratio, 37 C, 1000 rpm). Peptides were purified using the in-Stage Tip (iST) 96x Sample Preparation Kit from PreOmics, resuspended in the LC-Load solution of the kit and analysed on an Orbitrap Lumos Fusion Tribrid mass spectrometer (Thermo Scientific) in data-independent acquisition (DIA) mode with 33 dynamic isolation windows. A sample-specific spectral library was created by mixing aliquots of all samples followed by fractionation using high pH reversed phase chromatography. Peptides were collected into total 96 fractions, which were concatenated into 24 fractions and measured using DIA.
DOI: 10.5281/zenodo.6593136
title: WaterGAP2.2d model derived Potential evapotranspiration and Renewable water resources variables with standard and modified PET calculation methods

description: This data set is produced as a part of the ''Improving the quantification of climate change hazards by hydrological models: A simple ensemble approach for considering the uncertain effect of vegetation response to climate change on potential evapotranspiration" journal publication (in preparation). WaterGAP2.2d global hydrological model with two different settings; 1) with standard PET method Priestley-Taylor (PT) and 2) with modified approach (PT-MA) (please refer to the publication for more details on the method) used to derive the data set. The bias-adjusted GCM-derived (GFDL-ESM2M, HadGEM2-ES, IPSL-CM5A-LR, and MIROC5) climate data under RCP2.6 and RCP8.5 emission scenarios were used as the input. The model-derived potential evapotranspiration and the renewable water resources variables are available from 1981 to 2099 on the monthly scale for each land grid cell (spatial resolution: 0.5 degrees x 0.5 degrees). The data files are in the netCDF format (.nc4).
DOI: 10.5281/zenodo.6593135
title: WaterGAP2.2d model derived Potential evapotranspiration and Renewable water resources variables with standard and modified PET calculation methods

description: This data set is produced as a part of the ''Improving the quantification of climate change hazards by hydrological models: A simple ensemble approach for considering the uncertain effect of vegetation response to climate change on potential evapotranspiration" journal publication (in preparation). WaterGAP2.2d global hydrological model with two different settings; 1) with standard PET method Priestley-Taylor (PT) and 2) with modified approach (PT-MA) (please refer to the publication for more details on the method) used to derive the data set. The bias-adjusted GCM-derived (GFDL-ESM2M, HadGEM2-ES, IPSL-CM5A-LR, and MIROC5) climate data under RCP2.6 and RCP8.5 emission scenarios were used as the input. The model-derived potential evapotranspiration and the renewable water resources variables are available from 1981 to 2099 on the monthly scale for each land grid cell (spatial resolution: 0.5 degrees x 0.5 degrees). The data files are in the netCDF format (.nc4).
DOI: 10.34740/kaggle/dsv/6020305
title: COVID Vaccination in World (updated daily)
DOI: 10.5519/qd.xm9efsh2
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (10017 records)
DOI: 10.5281/zenodo.8077124
title: Maven Central Analysis

description: The structure of the Maven ecosystem provides a valuable source of data to study and analyze the distribution of Java libraries. In this study we scrutinize four different categories of information available on Maven; packaging types content of the libraries, Java aspects of builds, required space by the packages, and finally, version control reproducibility of the libraries.
DOI: 10.5281/zenodo.8077125
title: Maven Central Analysis

description: The structure of the Maven ecosystem provides a valuable source of data to study and analyze the distribution of Java libraries. In this study we scrutinize four different categories of information available on Maven; packaging types content of the libraries, Java aspects of builds, required space by the packages, and finally, version control reproducibility of the libraries.
DOI: 10.6084/m9.figshare.20217581
title: Spatiotemporal Flow L-function

description: This zip contains the code and data used in the simulation experiment and case study mentioned in the paper " Spatiotemporal Flow L-function: a new method for identifying spatiotemporal clusters in geogrphical flow data".
DOI: 10.5281/zenodo.8079292
title: Dataset corresponding to "Heavy quasiparticles and cascades without symmetry breaking in twisted bilayer graphene"

description: Data corresponding to the figures in the manuscript "Heavy quasiparticles and cascades without symmetry breaking in twisted bilayer graphene" published in Nature Communications (2023)
DOI: 10.5281/zenodo.8079291
title: Dataset corresponding to "Heavy quasiparticles and cascades without symmetry breaking in twisted bilayer graphene"

description: Data corresponding to the figures in the manuscript "Heavy quasiparticles and cascades without symmetry breaking in twisted bilayer graphene" published in Nature Communications (2023)
DOI: 10.5281/zenodo.8079380
title: Ocean Gateways and Ocean Circulation Dynamics: Unveiling the Deep Water-Mass properties in the Western Equatorial Pacific and Eastern Indian Ocean since the middle

description: File contains a dataset related to census counts and stable isotopes that we used to write our manuscript.
DOI: 10.5281/zenodo.8079379
title: Ocean Gateways and Ocean Circulation Dynamics: Unveiling the Deep Water-Mass properties in the Western Equatorial Pacific and Eastern Indian Ocean since the middle

description: File contains a dataset related to census counts and stable isotopes that we used to write our manuscript.
DOI: 10.5281/zenodo.8079378
title: Data Estudios retención abandono universitario en Perú 2003 2022

description: Data de Estudios sobre retención abandono universitario en Perú entre los años 2003 2022. Corresponde a los artículos seleccionados finalmente para el estudio.
DOI: 10.5281/zenodo.8079377
title: Data Estudios retención abandono universitario en Perú 2003 2022

description: Data de Estudios sobre retención abandono universitario en Perú entre los años 2003 2022. Corresponde a los artículos seleccionados finalmente para el estudio.
DOI: 10.34740/kaggle/dsv/6020584
title: Electric Vehicle Data (1997-2024) (update version)
DOI: 10.5281/zenodo.8079387
title: Dataset Artifact for Prodigy: Towards Unsupervised Anomaly Detection in Production HPC Systems

description: The dataset contains a small set of application runs from Eclipse supercomputer. The applications run with and without synthetic HPC performance anomalies. More detailed information regarding synthetic anomalies can be found at: https://github.com/peaclab/HPAS. We have chosen four applications, namely LAMMPS, sw4, sw4Lite, and ExaMiniMD, to encompass both real and proxy applications. We have executed each application five times on four compute nodes without introducing any anomalies. To showcase our experiment, we have specifically selected the "memleak" anomaly as it is one of the most commonly occurring types. Additionally, we have also executed each application five times with the chosen anomaly. The dataset we have collected consists of a total of 160 samples, with 80 samples labeled as anomalous and 80 samples labeled as healthy. For the details of applications please refer to the paper. The applications were run on Eclipse, which is situated at Sandia National Laboratories. Eclipse comprises 1488 compute nodes, each equipped with 128GB of memory and two sockets. Each socket contains 18 E5-2695 v4 CPU cores with 2-way hyperthreading, providing substantial computational power for scientific and engineering applications.
DOI: 10.15468/dl.krps6p
title: Occurrence Download

description: A dataset containing 164262 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Continent is Europe",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Valeriana officinalis L."
 ]
}

 The dataset includes 164262 records from 641 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049122-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pv5zpe
title: Occurrence Download

description: A dataset containing 86 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllodactylus bugastrolepis Dixon, 1966"
 ]
}

 The dataset includes 86 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005212-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-63170
title: Redemption tidings, vol. 43, nos. 1-52, 6 Jan. - 28 Dec. 1967

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle for vol. 43, nos. 1-39 (6 Jan. - 29 Sept. 1967).
DOI: 10.15468/dl.7jba9g
title: Occurrence Download

description: A dataset listing the 8721 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Lithuania",
 "GadmGid is LTU"
 ]
}

 The dataset's 8721 records were derived from 155 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000841-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-62263
title: Redemption tidings, vol. 42, nos. 1-52, 1 Jan. - 23 Dec. 1966

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.ytk8nb
title: Occurrence Download

description: A dataset containing 32429 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Material sample, Specimen, Material citation, Occurrence evidence)",
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Echinodermata"
 ]
}

 The dataset includes 32429 records from 99 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038926-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zurzmv
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Microgecko latifi (Leviton & Anderson, 1972)"
 ]
}

 The dataset includes 24 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002337-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-63336
title: Redemption tidings, vol. 43, nos. 1-52, 6 Jan. - 28 Dec. 1967

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle for vol. 43, nos. 1-39 (6 Jan. - 29 Sept. 1967).