cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5dz03b9z
title: MassIVE MSV000092689 - Case study for MOSS algorithm: LC-MS raw data of bourbon
title: A Thermo Vanquish UPLC system (ThermoFisher, Waltham, MA, USA) coupled with a Hybrid Quadrupole Orbitrap Q Exactive mass spectrometer (ThermoFisher) was used for small molecule analysis of study samples. Bourbon molecules were separated using an Xbridge BEH Amide (2.5 um, 2.1 x 150 mm, Waters, Milford, MA, USA) column. The mobile phases consisted of solvents A and B, where A contained 5 mM ammonium acetate, 0.1% acetic acid in 90% H2O/10% acetonitrile (ACN) and B contained 5 mM ammonium acetate, 0.1% acetic acid in 10% H2O/90% ACN. A gradient of mobile phase injection was used for 20 minutes at a flow rate of 0.3 mL/min, starting with 30% of mobile phase A and increasing to 70% at 5 min. The proportion of mobile phase A was maintained at 70% until 9 min, and then started to decrease to 30% until 11 min. The percentage of solvent A was then kept at 70% until 20 min, after which it gradually returned to 30% to prepare for the next injection. To observe and prove the consistency of the instrument during testing and to enable data normalization, a pooled quality control (QC) was added to the sample tray after every ten sample injections in both sequences. A blank sample was added after each QC sample.
DOI: 10.5281/zenodo.8264548
title: Supplementary data for "Chamber studies of OH + dimethyl sulfoxide and dimethyl disulfide: insights into the dimethyl sulfide oxidation mechanism."

description: This page contains public data for the peer-reviewed publication:<br> Matthew B. Goss and Jesse H. Kroll: "Chamber studies of OH + dimethyl sulfoxide and dimethyl disulfide: insights into the dimethyl sulfide oxidation mechanism." ACP, XX, XXXX–XXXX, 202X. Submitted. These data files are intended as additional supplementary information for this publication. If you would like to use any data herein in a publication, please contact the corresponding author (Matthew Goss, mgoss@mit.edu) first. Data files contain product concentration timeseries. Time is reported in seconds after UV lights were turned on. All data, except for ozone and NOx timeseries, have been corrected for chamber dilution. Product concentrations are reported in parts per billion. If you have any more questions, please contact the corresponding author, Matthew Goss at mgoss@mit.edu.
DOI: 10.5281/zenodo.8264547
title: Supplementary data for "Chamber studies of OH + dimethyl sulfoxide and dimethyl disulfide: insights into the dimethyl sulfide oxidation mechanism."

description: This page contains public data for the peer-reviewed publication:<br> Matthew B. Goss and Jesse H. Kroll: "Chamber studies of OH + dimethyl sulfoxide and dimethyl disulfide: insights into the dimethyl sulfide oxidation mechanism." ACP, XX, XXXX–XXXX, 202X. Submitted. These data files are intended as additional supplementary information for this publication. If you would like to use any data herein in a publication, please contact the corresponding author (Matthew Goss, mgoss@mit.edu) first. Data files contain product concentration timeseries. Time is reported in seconds after UV lights were turned on. All data, except for ozone and NOx timeseries, have been corrected for chamber dilution. Product concentrations are reported in parts per billion. If you have any more questions, please contact the corresponding author, Matthew Goss at mgoss@mit.edu.
DOI: 10.17909/har4-7y03
title: Data used in TOI-1420b discovery paper
DOI: 10.5281/zenodo.8264583
title: accipiter_francesiae_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8264582
title: accipiter_francesiae_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8263172
title: PyPSA-PL: Limited flexibility of the Polish power system

description: This record contains all the scripts and data from the PyPSA-PL modelling exercise that supported the report: Kubiczek P. (2023). Praca w podstawie. Modelowanie kosztów niskiej elastyczności polskiego systemu<br> elektroenergetycznego. Instrat Policy Paper 04/2023. https://www.instrat.pl/praca-w-podstawie The record structure is based on the PyPSA-PL repository https://github.com/instrat-pl/pypsa-pl (v2.0 with changes).
DOI: 10.5281/zenodo.8263171
title: PyPSA-PL: Limited flexibility of the Polish power system

description: This record contains all the scripts and data from the PyPSA-PL modelling exercise that supported the report: Kubiczek P. (2023). Praca w podstawie. Modelowanie kosztów niskiej elastyczności polskiego systemu<br> elektroenergetycznego. Instrat Policy Paper 04/2023. https://www.instrat.pl/praca-w-podstawie The record structure is based on the PyPSA-PL repository https://github.com/instrat-pl/pypsa-pl (v2.0 with changes).
DOI: 10.5281/zenodo.8264491
title: Zr–O Ab Initio Training Data Created by Molecular Dynamics, Contour Exploration, and Dimer Searches

description: These density functional theory calculations span a diverse set of structures in the Zr–O system which was used as machine-learned interatomic potential (MLIP) training data. This data set was used to benchmark different structural evolution methods (molecular dynamics, contour exploration, and dimer searches) for the quality and accuracy of MLIPs trained on them. The data is provided in the .traj format from ASE. Along with data set used in our publication, we provide a large set of extra unused data and a small Python script example for parsing the data set. The set contains 120,068 structures which contain a total of 3,154,158 atoms. For more details, please see our paper:<br> Michael J Waters and James M Rondinelli, <em>J. Phys.: Condens. Matter</em> <strong>34</strong> 385901(2022) (https://dx.doi.org/10.1088/1361-648X/ac7f73)
DOI: 10.5281/zenodo.8264492
title: Zr–O Ab Initio Training Data Created by Molecular Dynamics, Contour Exploration, and Dimer Searches

description: These density functional theory calculations span a diverse set of structures in the Zr–O system which was used as machine-learned interatomic potential (MLIP) training data. This data set was used to benchmark different structural evolution methods (molecular dynamics, contour exploration, and dimer searches) for the quality and accuracy of MLIPs trained on them. The data is provided in the .traj format from ASE. Along with data set used in our publication, we provide a large set of extra unused data and a small Python script example for parsing the data set. The set contains 120,068 structures which contain a total of 3,154,158 atoms. For more details, please see our paper:<br> Michael J Waters and James M Rondinelli, <em>J. Phys.: Condens. Matter</em> <strong>34</strong> 385901(2022) (https://dx.doi.org/10.1088/1361-648X/ac7f73)
DOI: 10.5281/zenodo.8220182
title: UAV Canyelles Vineyard Dataset 2023-06-09

description: The dataset encompasses the following data: Orthomosaic Images: ortho_230609.jpg: A detailed RGB orthomosaic of the entire vineyard. This orthomosaic was meticulously generated using Agisoft Metashape, employing images from the RGB.zip folder. The creation process involved medium accuracy settings. ortho_230609_ndvi.jpg: An orthomosaic captured in Near-Infrared (NIR) spectrum, portraying the entirety of the vineyard. This NIR orthomosaic was crafted through Agisoft Metashape, utilizing both NIR images and the Red channel of the RGB images from the NIR.zip and RGB.zip folders. The generation process employed medium accuracy settings. Drone-Captured Image Folders: RGB.zip: A collection of RGB images obtained using a DJI MAVIC 3M drone. These images were gathered during a flight at an altitude of 10 meters, ensuring 80% frontal and side overlap between each image. NIR.zip: A compilation of Near-Infrared (NIR) images collected through the same manual drone flight process. The data collection procedure involved flying the DJI MAVIC 3M drone over the vineyard in Canyelles in Catalonia, Spain. The flight took place under sunny weather conditions with an average temperature of 26 degrees Celsius.
DOI: 10.5281/zenodo.8220183
title: UAV Canyelles Vineyard Dataset 2023-06-09

description: The dataset encompasses the following data: Orthomosaic Images: ortho_230609.jpg: A detailed RGB orthomosaic of the entire vineyard. This orthomosaic was meticulously generated using Agisoft Metashape, employing images from the RGB.zip folder. The creation process involved medium accuracy settings. ortho_230609_ndvi.jpg: An orthomosaic captured in Near-Infrared (NIR) spectrum, portraying the entirety of the vineyard. This NIR orthomosaic was crafted through Agisoft Metashape, utilizing both NIR images and the Red channel of the RGB images from the NIR.zip and RGB.zip folders. The generation process employed medium accuracy settings. Drone-Captured Image Folders: RGB.zip: A collection of RGB images obtained using a DJI MAVIC 3M drone. These images were gathered during a flight at an altitude of 10 meters, ensuring 80% frontal and side overlap between each image. NIR.zip: A compilation of Near-Infrared (NIR) images collected through the same manual drone flight process. The data collection procedure involved flying the DJI MAVIC 3M drone over the vineyard in Canyelles in Catalonia, Spain. The flight took place under sunny weather conditions with an average temperature of 26 degrees Celsius.
DOI: 10.5281/zenodo.8264619
title: clanga_hastata_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8264618
title: clanga_hastata_spades_01.fasta.gz

description: .
DOI: 10.34740/kaggle/dsv/6326203
title: US counties COVID 19 dataset
DOI: 10.5281/zenodo.8264621
title: symplocos_macrophylla_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8264620
title: symplocos_macrophylla_spades_01.fasta.gz

description: .
DOI: 10.25345/c5959cj5k
title: MassIVE MSV000092690 - Systematic investigation on the effect of O-GlcNAcylation on condensate formation under heat stress and recovery
title: O-GlcNAc is known to regulate the aggregation and condensate formation of several proteins, but how O-GlcNAc regulates protein solubilities globally has yet to be systematically investigated. Here, we employed a chemoproteomic workflow integrating selective enrichment and multiplex proteomics to quantify the solubilities of O-GlcNAcylated and non-modified proteins, as well as their role in RNA condensate formation. The solubilities were also quantified after heat stress and recovery to investigate the condensate formation during heat stress response. Surprisingly. we found O-GlcNAc leads to dramatic solubility decrease of the modified proteins, and the degree of solubility drop is related to the protein localization and functions. Site-specific analysis found the adjacent residues and secondary structures of the glycosites are pivotal for the effect of O-GlcNAc for solubility change, and the number of acidic residues is related to the different effect of O-GlcNAc in heat stress and recovery. Additionally, it was found that O-GlcNAc promotes the dissociation of RNA condensates during heat stress, while it enhances the formation of RNA condensates in the recovery phase. The glycosites that facilitate the dissociation or the formation of the RNA condensates are distinct, and the physiological properties of their surroundings residues are diverse. This work advances our understanding of the role of O-GlcNAc in regulating biomolecular condensates and will be a useful resource for future research in biomolecular condensates.
DOI: 10.25345/c55h7c45n
title: MassIVE MSV000092691 - State-dependent protein-protein interactions mediating 4-1BB CAR Signaling
title: We define a network of protein interactions engaged by chimeric antigen receptors following target binding, and show that the magnitude of network activation correlates with IL-2 secretion, a proxy measure for CAR T cell function.
DOI: 10.5281/zenodo.8264633
title: alipiopsitta_xanthops_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8264632
title: alipiopsitta_xanthops_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8264647
title: portunus_pelagicus_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8264646
title: portunus_pelagicus_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8264655
title: accipiter_rhodogaster_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8264654
title: accipiter_rhodogaster_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8263947
title: DTM, REM, and LiDAR of Five Sites in the St. Vrain Watershed

description: Digital terrain models (drone and LiDAR) and the corresponding uav relative elevation model for Julia and Lindsay's project with The Watershed Center.
DOI: 10.5281/zenodo.8263946
title: DTM, REM, and LiDAR of Five Sites in the St. Vrain Watershed

description: Digital terrain models (drone and LiDAR) and the corresponding uav relative elevation model for Julia and Lindsay's project with The Watershed Center.
DOI: 10.5281/zenodo.8264665
title: lophaetus_occipitalis_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.8264664
title: lophaetus_occipitalis_spades_01.fasta.gz

description: .
DOI: 10.17592/001.2023020601
title: Conductivity, temperature, pressure, and dissolved oxygen data off Sabrina Coast measured by CTD on JARE59 Shirase cruise in the 2017/18 season

description: This is a conductivity, temperature, pressure, and dissolved oxygen dataset measured at CTD stations off Sabrina Coast on the Shirase cruise of the 59th Japanese Antarctic Research Expedition (JARE59, 2017/18 season) by using CTD system.
DOI: 10.17592/001.2023020602
title: Stable oxygen isotope ratio of seawaters at the Totten Ice Shelf front off Sabrina Coast by rosette-multi-water sampler on JARE59 Shirase cruise in the 2017/18 season

description: This is a dataset of stable oxygen isotope ratio of seawaters obtained at CTD stations off Sabrina Coast on the Shirase cruise of the 59th Japanese Antarctic Research Expedition (JARE59, 2017/18 season) by using CTD system. SBE19/SBE55 ECO Water Sampler system of Sea-Bird Electronics, Inc. was used. After transporting the water samples to laboratory, stable oxygen isotope ratio, reference to VSMOW2, was measured by Isoprime (Elementar, U.K.) at Institute of Low Temperature Science, Hokkaido University.
DOI: 10.17592/001.2023020603
title: Conductivity, temperature, pressure, and dissolved oxygen data off Sabrina Coast measured by CTD on JARE61 Shirase cruise in the 2019/20 season

description: This is a conductivity, temperature, pressure, and dissolved oxygen dataset measured at CTD stations off Sabrina Coast on the Shirase cruise of the 61st Japanese Antarctic Research Expedition (JARE61, 2019/20 season) by using CTD system.
DOI: 10.17592/001.2023020604
title: Mooring observation data at the Totten Ice Shelf front from December 2019 to March 2020 (JARE61, 2019/20 season)

description: This is a time-series oceanographic data by a mooring deployed at the Totten Ice Shelf front from December 2019 to March 2020 (at East Totten Trough, JARE61, 2019/20 season).
DOI: 10.17592/001.2023020605
title: Bathymetric dataset for "On-Shelf Circulation of Warm Water Toward the Totten Ice Shelf, East Antarctica"

description: This is a bathymetric dataset for "On-Shelf Circulation of Warm Water Toward the Totten Ice Shelf, East Antarctica" (Hirano et al., Nature Communications, in revision). The dataset includes two types of bathymetry data; high-resolution (200 m in horizontal) bathymetry data gridded from multibeam echo sounder observations and compiled bathymetry data for the physical oceanographic modeling off the Sabrina Coast, East Antarctica. See the detail of the dataset for the Method Section in the paper above (Hirano et al.).
DOI: 10.17592/001.2023013105
title: Conductivity, temperature, pressure, and dissolved oxygen data off Sabrina Coast measured by CTD on JARE63 Shirase cruise in the 2021/22 season

description: This is a conductivity, temperature, pressure, and dissolved oxygen dataset measured at CTD stations off Sabrina Coast on the Shirase cruise of the 63rd Japanese Antarctic Research Expedition (JARE63, 2021/22 season) by using CTD system.
DOI: 10.17592/001.2023013106
title: Conductivity, temperature, and depth data off Sabrina Coast measured by expendable CTD (XCTD) system on JARE63 Shirase cruise in the 2021/22 season

description: This is a conductivity, temperature, and depth dataset off Budd and Sabrina Coasts on the Shirase cruise of the 63rd Japanese Antarctic Research Expedition (JARE63, 2021/22 season) measured by the eXpendable CTD (XCTD) system. The XCTD data is obtained by the collaborative observation of the JARE's Prioritized Research Project Science Program (ROBOTICA) and Hydrographic and Oceanographic Department, Japan Coast Guard.
DOI: 10.17592/001.2023021702
title: Soil moisture at Spasskaya Pad

description: The datasets are daily data of soil moisture water equivalent at Spasskaya Pad Experimental Forest in northeastern Siberia during the summer period from 1998 to 2019. Soil mositure water equivalent was estimated from the observations at 4 sites by the similar method developed by Sugimoto et al. 2003, from the regression relationships of TDR measurements between manual (Moisture Point) and automatic observations by three measurement systems (TRIME IMKO P2, Decagon ECH2O, Sentek EnviroSmart).
DOI: 10.17592/001.2023021701
title: Larch needle C/N and carbon and nitrogen isotopes at Spasskaya Pad

description: The dataset is C/N ratio and carbon and nitrogen isotopes of larch needles observed at Spasskaya Pad Experimental Forest in northeastern Siberia during the period from 1999 to 2019. Larch needles were sampled from four to eight trees in August and average values were calculated.
DOI: 10.17592/001.2021070803
title: Conductivity, temperature, and depth data off Budd/Sabrina Coasts measured by expendable CTD (XCTD) system on JARE61 Shirase cruise in the 2019/20 season

description: This is a conductivity, temperature, and depth dataset off Budd and Sabrina Coasts on the Shirase cruise of the 61st Japanese Antarctic Research Expedition (JARE61) measured by the eXpendable CTD (XCTD) system. The XCTD data is obtained by the collaborative observation of the JARE's Prioritized Research Project Science Program (ROBOTICA) and Hydrographic and Oceanographic Department, Japan Coast Guard.
DOI: 10.5281/zenodo.7672132
title: heteromormyrus_pauciradiatus_zanfona_1.fasta.gz

description: .
DOI: 10.5281/zenodo.7672131
title: heteromormyrus_pauciradiatus_zanfona_1.fasta.gz

description: .
DOI: 10.18119/n97g8t
title: Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks
DOI: 10.6084/m9.figshare.21905670.v1
title: Data from: Phenotypic plasticity evolves at multiple biological levels in response to environmental predictability in a long-term experiment with a halotolerant microalga

description: Phenotypic plasticity, the change in the phenotype of a given genotype in response to its environment of development, is a ubiquitous feature of life, enabling organisms to cope with variation in their environment. Theoretical studies predict that, under stationary environmental variation, the level of plasticity should evolve to match the predictability of selection at the timing of development. However, the extent to which patterns of evolution of plasticity for more integrated traits are mirrored by their underlying molecular mechanisms remains unclear, especially in response to well-characterized selective pressures exerted by environmental predictability. Here, we used experimental evolution with the microalgae <em>Dunaliella salina</em> under controlled environmental fluctuations, to test whether the evolution of phenotypic plasticity in responses to environmental predictability (as measured by the squared autocorrelation <em>ρ</em><sup><em>2</em></sup>) occurred across biological levels, going from DNA methylation to gene expression to cell morphology. Transcriptomic analysis indicates clear effects of salinity and <em>ρ</em><sup><em>2</em></sup>×salinity interaction on gene expression, thus identifying sets of genes involved in plasticity and its evolution. These transcriptomic effects were independent of DNA methylation changes in <em>cis.</em> However we did find <em>ρ</em><sup><em>2</em></sup><em>-</em>specific responses of DNA methylation to salinity change, albeit weaker than for gene expression. Overall, we found consistent evolution of reduced plasticity in less predictable environments for DNA methylation, gene expression, and cell morphology. Our results provide the first clear empirical signature of plasticity evolution at multiple levels in response to environmental predictability, and highlight the importance of experimental evolution to address predictions from evolutionary theory, as well as investigate the molecular basis of plasticity evolution.
DOI: 10.6084/m9.figshare.21905670
title: Data from: Phenotypic plasticity evolves at multiple biological levels in response to environmental predictability in a long-term experiment with a halotolerant microalga

description: Phenotypic plasticity, the change in the phenotype of a given genotype in response to its environment of development, is a ubiquitous feature of life, enabling organisms to cope with variation in their environment. Theoretical studies predict that, under stationary environmental variation, the level of plasticity should evolve to match the predictability of selection at the timing of development. However, the extent to which patterns of evolution of plasticity for more integrated traits are mirrored by their underlying molecular mechanisms remains unclear, especially in response to well-characterized selective pressures exerted by environmental predictability. Here, we used experimental evolution with the microalgae <em>Dunaliella salina</em> under controlled environmental fluctuations, to test whether the evolution of phenotypic plasticity in responses to environmental predictability (as measured by the squared autocorrelation <em>ρ</em><sup><em>2</em></sup>) occurred across biological levels, going from DNA methylation to gene expression to cell morphology. Transcriptomic analysis indicates clear effects of salinity and <em>ρ</em><sup><em>2</em></sup>×salinity interaction on gene expression, thus identifying sets of genes involved in plasticity and its evolution. These transcriptomic effects were independent of DNA methylation changes in <em>cis.</em> However we did find <em>ρ</em><sup><em>2</em></sup><em>-</em>specific responses of DNA methylation to salinity change, albeit weaker than for gene expression. Overall, we found consistent evolution of reduced plasticity in less predictable environments for DNA methylation, gene expression, and cell morphology. Our results provide the first clear empirical signature of plasticity evolution at multiple levels in response to environmental predictability, and highlight the importance of experimental evolution to address predictions from evolutionary theory, as well as investigate the molecular basis of plasticity evolution.
DOI: 10.5517/ccdc.csd.cc2dpl6x
title: CCDC 2225279: Experimental Crystal Structure Determination

description: Related Article: Juba Ghouilem, Sokna Bazzi, Nicolas Grimblat, Pascal Retailleau, Vincent Gandon, Samir Messaoudi|2023|Chem.Commun.|59|2497|doi:10.1039/D3CC00046J
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.