cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10688894
title: IMC Matched Primary and Metastatic Breast Cancer

description: This repository contains all raw MCD files and the fully annotated dataset file (backup_output.rds) that pertain to imaging mass cytometry analysis of primary and metastatic breast cancers in the manuscript by Grasset et al. "Mapping the breast tumor microenvironment: proximity analysis reveals spatial relationships between macrophage subtypes and metastasis-initiating cancer cells".

Otherlegends.zip contains the antibody panel, maps of ROI assignments for each of the 5 TMAs used, and legends/metadata related to all of the individual ROIs.

R scripts used for the analysis of this dataset are available on https://github.com/wjhlab/BreastMetIMC/
DOI: 10.5281/zenodo.10815895
title: Thesis Supplementary Tables

description: Thesis supplementary tables for chapters 3 and 4. Version 2 .
DOI: 10.5281/zenodo.10116162
title: Thesis Supplementary Tables

description: Thesis supplementary tables for chapters 3 and 4. Version 2 .
DOI: 10.5281/zenodo.10815636
title: Global 1km Land Surface Parameters for Kilometer-Scale Earth System Modeling (LAI_2001_2005)

description: Earth system models (ESMs) are progressively advancing towards the kilometer scale (k-scale). However, the surface parameters for Land Surface Models (LSMs) within ESMs running at the k-scale are typically derived from coarse resolution and outdated datasets. This study aims to develop a new set of global land surface parameters with a resolution of 1 km for multiple years from 2001 to 2020, utilizing the latest and most accurate available datasets. Specifically, the datasets consist of parameters related to land use and land cover, vegetation, soil, and topography. Differences between the newly developed 1k land surface parameters and conventional parameters emphasize their potential for higher accuracy due to the incorporation of the most advanced and latest data sources. To demonstrate the capability of these new parameters, we conducted 1 km resolution simulations using the E3SM Land Model version 2 (ELM2) over the contiguous United States. Our results demonstrate that land surface parameters contribute to significant spatial heterogeneity in ELM2 simulations of soil moisture, latent heat, emitted longwave radiation, and absorbed shortwave radiation. On average, about 31% to 54% of spatial information is lost by upscaling the 1 km ELM2 simulations to a 12 km resolution. Using eXplainable Machine Learning (XML) methods, the influential factors driving the spatial variability and spatial information loss of ELM2 simulations were identified, highlighting the substantial impact of the spatial variability and information loss of various land surface parameters, as well as the mean climate conditions. The comparison against four benchmark datasets indicates that ELM generally performs well in simulating soil moisture and surface energy fluxes. The new land surface parameters are tailored to meet the emerging needs of k-scale LSMs and ESMs modeling with significant implications for advancing our understanding of water, carbon, and energy cycles under global change. 

This data repository is linked to https://zenodo.org/records/10815170
DOI: 10.5281/zenodo.10815637
title: Global 1km Land Surface Parameters for Kilometer-Scale Earth System Modeling (LAI_2001_2005)

description: Earth system models (ESMs) are progressively advancing towards the kilometer scale (k-scale). However, the surface parameters for Land Surface Models (LSMs) within ESMs running at the k-scale are typically derived from coarse resolution and outdated datasets. This study aims to develop a new set of global land surface parameters with a resolution of 1 km for multiple years from 2001 to 2020, utilizing the latest and most accurate available datasets. Specifically, the datasets consist of parameters related to land use and land cover, vegetation, soil, and topography. Differences between the newly developed 1k land surface parameters and conventional parameters emphasize their potential for higher accuracy due to the incorporation of the most advanced and latest data sources. To demonstrate the capability of these new parameters, we conducted 1 km resolution simulations using the E3SM Land Model version 2 (ELM2) over the contiguous United States. Our results demonstrate that land surface parameters contribute to significant spatial heterogeneity in ELM2 simulations of soil moisture, latent heat, emitted longwave radiation, and absorbed shortwave radiation. On average, about 31% to 54% of spatial information is lost by upscaling the 1 km ELM2 simulations to a 12 km resolution. Using eXplainable Machine Learning (XML) methods, the influential factors driving the spatial variability and spatial information loss of ELM2 simulations were identified, highlighting the substantial impact of the spatial variability and information loss of various land surface parameters, as well as the mean climate conditions. The comparison against four benchmark datasets indicates that ELM generally performs well in simulating soil moisture and surface energy fluxes. The new land surface parameters are tailored to meet the emerging needs of k-scale LSMs and ESMs modeling with significant implications for advancing our understanding of water, carbon, and energy cycles under global change. 

This data repository is linked to https://zenodo.org/records/10815170
DOI: 10.6084/m9.figshare.25419391
title: Water vapor isotopic data from the ALMA Observatory

description: This is a CSV file of water vapor isotopic data collected at the ALMA Observatory in 2015, The data are 1-minute averages and are corrected for drift and normalized to the VSMOW/SLAP scale. This data is used the Galewsky, 2024 paper on Shannon Entropy
DOI: 10.6084/m9.figshare.25419391.v1
title: Water vapor isotopic data from the ALMA Observatory

description: This is a CSV file of water vapor isotopic data collected at the ALMA Observatory in 2015, The data are 1-minute averages and are corrected for drift and normalized to the VSMOW/SLAP scale. This data is used the Galewsky, 2024 paper on Shannon Entropy
DOI: 10.5066/p9gj25ec
title: Pesticides in tree swallows from the Milwaukee Estuary, WI

description: Legacy contaminants and contaminants of emerging concern (CECs) were assessed in tree swallow (Tachycineta bicolor) tissue and diet samples from three drainages in the Milwaukee Estuary, Wisconsin to understand exposures and possible effects.
DOI: 10.5281/zenodo.10813260
title: Additional Resources for End-user Comprehension of Transfer Risks in Smart Contracts
DOI: 10.5281/zenodo.10813261
title: Additional Resources for End-user Comprehension of Transfer Risks in Smart Contracts
DOI: 10.5281/zenodo.10816090
title: Integrated Modeling of Flow, Soil Erosion, and Nutrient Dynamics in a Regional Watershed: Assessing Natural and Human-Induced Impacts

description: Attached file is the verification data for the submitted manuscript "Integrated Modeling of Flow, Soil Erosion, and Nutrient Dynamics in a Regional Watershed: Assessing Natural and Human-Induced Impacts" .
DOI: 10.5281/zenodo.10816089
title: Integrated Modeling of Flow, Soil Erosion, and Nutrient Dynamics in a Regional Watershed: Assessing Natural and Human-Induced Impacts

description: Attached file is the verification data for the submitted manuscript "Integrated Modeling of Flow, Soil Erosion, and Nutrient Dynamics in a Regional Watershed: Assessing Natural and Human-Induced Impacts" .
DOI: 10.5281/zenodo.10816044
title: CD crossdock benchmark set for DiffBindFR

description: The CD benchmark set represents a comprehensive, large-scale benchmark dataset specifically designed for cross-docking evaluations in DiffBindFR paper. It is uniquely equipped to handle a variety of cross-docking scenarios, including Apo-Holo, Holo-Holo, and AF2-Holo cross-docking. The dataset, as released, encompasses several subsets: Ensemble (including three targets: CDK2, EGFR, and FXA), ApoRef, CASF2016, GPCR-AF2, and DUDE27-HoloEns. Each cross-docking system within these subsets is comprehensively equipped with a well prepared receptor PDB file, ligand SDF file, and Mol2 file. Every system has been assigned a unique ID with the format of [Lig ID][Alt ID]_[Apo PDB ID]_[Cross-Docking ID], and Cross-Docking ID can help users identify cross-docking scenario.
DOI: 10.5281/zenodo.10816043
title: CD crossdock benchmark set for DiffBindFR

description: The CD benchmark set represents a comprehensive, large-scale benchmark dataset specifically designed for cross-docking evaluations in DiffBindFR paper. It is uniquely equipped to handle a variety of cross-docking scenarios, including Apo-Holo, Holo-Holo, and AF2-Holo cross-docking. The dataset, as released, encompasses several subsets: Ensemble (including three targets: CDK2, EGFR, and FXA), ApoRef, CASF2016, GPCR-AF2, and DUDE27-HoloEns. Each cross-docking system within these subsets is comprehensively equipped with a well prepared receptor PDB file, ligand SDF file, and Mol2 file. Every system has been assigned a unique ID with the format of [Lig ID][Alt ID]_[Apo PDB ID]_[Cross-Docking ID], and Cross-Docking ID can help users identify cross-docking scenario.
DOI: 10.5281/zenodo.10100579
title: Transpiration response under drought conditions of sedlings exposed to EMF

description: Supplementary information of the manuscript: 10.1093/treephys/tpae029

Dataset of seedlings exposed to ectomycorrhizal fungi (EMF) containing: transpiration rate and needle water potential time-series, fluorescence, dry biomass, and root morphology traits.

Pine seedlings were exposed to EMF and then subject to drought stress for 10 days followed by 14 days of recovery. 

Transpiration was measured by weight loss, and needle water potential using a pressure chamber

Fluorescence measurements were done at the National Plant Phenotyping Infrastructure (NaPPI) facilities at the University of Helsinki
DOI: 10.5281/zenodo.10100580
title: Transpiration response under drought conditions of sedlings exposed to EMF

description: Supplementary information of the manuscript: 10.1093/treephys/tpae029

Dataset of seedlings exposed to ectomycorrhizal fungi (EMF) containing: transpiration rate and needle water potential time-series, fluorescence, dry biomass, and root morphology traits.

Pine seedlings were exposed to EMF and then subject to drought stress for 10 days followed by 14 days of recovery. 

Transpiration was measured by weight loss, and needle water potential using a pressure chamber

Fluorescence measurements were done at the National Plant Phenotyping Infrastructure (NaPPI) facilities at the University of Helsinki
DOI: 10.5281/zenodo.10691339
title: Supplementary data - The "sand rose brick" paper
DOI: 10.5281/zenodo.10717797
title: Supplementary data - "Rebuilding with sand roses" paper
DOI: 10.5281/zenodo.8260492
title: Data from: Effectiveness of Online Off-the-Job Training in Attracting Participants and Video-On-Demand Streaming in Improving Work-Life Balance: A Study Focusing on Medical Technologists

description: The Nara Association of Medical Technologists has introduced online Off-Job Training (Off-JT) starting from FY2020 in response to the COVID-19 pandemic. This study aims to evaluate the online Off-JT, which differs from the traditional face-to-face format. Firstly, we compared the online format's ability to attract participants with the face-to-face format based on the number of training sessions and attendees. Despite having fewer training sessions (40.8% less), the online format had an average attendance of 105.4% higher (39.7 vs. 19.3) than the face-to-face format. To enhance participant convenience, we offered a limited number of live and video-on-demand (VOD) sessions on YouTube, evaluating their usefulness through an online survey focusing on work-life balance (WLB). The survey results showed that 81.9% (458/559) of respondents reported an improvement in WLB. The effect on WLB improvement varied depending on the viewing method, with VOD sessions showing 84.1% (376/447) and live sessions showing 73.2% (82/112). We believe that the increased ability to attract participants in the online Off-JT is mainly due to the elimination of travel burdens through internet-connected devices. The combination of live and VOD sessions on YouTube allowed participants to adjust their viewing time, leading to better allocation of free time and improved WLB. The online Off-JT and VOD delivery have shown to enhance convenience for participants by removing geographical and time constraints, resulting in positive effects.
DOI: 10.5281/zenodo.8260491
title: Data from: Effectiveness of Online Off-the-Job Training in Attracting Participants and Video-On-Demand Streaming in Improving Work-Life Balance: A Study Focusing on Medical Technologists

description: The Nara Association of Medical Technologists has introduced online Off-Job Training (Off-JT) starting from FY2020 in response to the COVID-19 pandemic. This study aims to evaluate the online Off-JT, which differs from the traditional face-to-face format. Firstly, we compared the online format's ability to attract participants with the face-to-face format based on the number of training sessions and attendees. Despite having fewer training sessions (40.8% less), the online format had an average attendance of 105.4% higher (39.7 vs. 19.3) than the face-to-face format. To enhance participant convenience, we offered a limited number of live and video-on-demand (VOD) sessions on YouTube, evaluating their usefulness through an online survey focusing on work-life balance (WLB). The survey results showed that 81.9% (458/559) of respondents reported an improvement in WLB. The effect on WLB improvement varied depending on the viewing method, with VOD sessions showing 84.1% (376/447) and live sessions showing 73.2% (82/112). We believe that the increased ability to attract participants in the online Off-JT is mainly due to the elimination of travel burdens through internet-connected devices. The combination of live and VOD sessions on YouTube allowed participants to adjust their viewing time, leading to better allocation of free time and improved WLB. The online Off-JT and VOD delivery have shown to enhance convenience for participants by removing geographical and time constraints, resulting in positive effects.
DOI: 10.5281/zenodo.10726910
title: Data and code associated with the publication "Emotional states elicited by wolf videos are diverse and explain general attitudes towards wolves", Arbieu et al., People and Nature 2024

description: This folder contains the data and R scripts needed to replicate the analysis of the publication entitled "Emotional states elicited by wolf videos are diverse and explain general attitudes towards wolves". This dataset represents a social survey in rural populations of 24 randomly selected cities in France (n=795) to (i) quantify emotional diversity and (ii) test the relationship between emotional states and attitudes towards wolves, accounting for individual and regional factors. All data were collected between November 2018 and May 2019.
DOI: 10.5281/zenodo.10726909
title: Data and code associated with the publication "Emotional states elicited by wolf videos are diverse and explain general attitudes towards wolves", Arbieu et al., People and Nature 2024

description: This folder contains the data and R scripts needed to replicate the analysis of the publication entitled "Emotional states elicited by wolf videos are diverse and explain general attitudes towards wolves". This dataset represents a social survey in rural populations of 24 randomly selected cities in France (n=795) to (i) quantify emotional diversity and (ii) test the relationship between emotional states and attitudes towards wolves, accounting for individual and regional factors. All data were collected between November 2018 and May 2019.
DOI: 10.5281/zenodo.10816180
title: Phased T2T reference genome and pangenome reveal expanded resistance gene analogs in apple domestication
title: Comparative genomics analysis

description: Phased T2T reference genome and pangenome reveal expanded resistance gene analogs in apple domesticationThe data contains two files, namely genome file and genome annotation file:1. Genome:This file contains 12 genomes for 5 species (cultivar), namely: Malus domestica cv. ‘Golden Delicious’ (GD), Malus domestica cv. ‘Gala’ (Gala), Malus domestica cv. ‘Honeycrisp’ (HC), Malus domestica cv. ‘HFTH1’ (HFTH1), Malus baccata (Mba), Malus sieversii (Msi), and Malus sylvestris (Msy)

2. Genome annotation:Corresponding to the genome file.Note: Hap1 and hap2 represent two haplotypes of a species (cultivar), all data used for the construction of pan-genomes and comparative genomics analysis.
DOI: 10.5281/zenodo.10816179
title: Phased T2T reference genome and pangenome reveal expanded resistance gene analogs in apple domestication
title: Comparative genomics analysis

description: Phased T2T reference genome and pangenome reveal expanded resistance gene analogs in apple domesticationThe data contains two files, namely genome file and genome annotation file:1. Genome:This file contains 12 genomes for 5 species (cultivar), namely: Malus domestica cv. ‘Golden Delicious’ (GD), Malus domestica cv. ‘Gala’ (Gala), Malus domestica cv. ‘Honeycrisp’ (HC), Malus domestica cv. ‘HFTH1’ (HFTH1), Malus baccata (Mba), Malus sieversii (Msi), and Malus sylvestris (Msy)

2. Genome annotation:Corresponding to the genome file.Note: Hap1 and hap2 represent two haplotypes of a species (cultivar), all data used for the construction of pan-genomes and comparative genomics analysis.
DOI: 10.5281/zenodo.10816305
title: Phased T2T reference genome and pangenome reveal expanded resistance gene analogs in apple domestication
title: The genome of Golden Delicious

description: Two haplotypes of the T2T genome of Golden Delicious apple and their annotation files
DOI: 10.5281/zenodo.10816304
title: Phased T2T reference genome and pangenome reveal expanded resistance gene analogs in apple domestication
title: The genome of Golden Delicious

description: Two haplotypes of the T2T genome of Golden Delicious apple and their annotation files
DOI: 10.5281/zenodo.10816159
title: Liquid water content and vertical velocity from RICO-based LES simulations

description: The RICO-based simulations by implementing the LES module of WRF model 4.0 generate the raw data. The simulation continued for 40 hours with a time step of 0.5 second. The domain size is 12.8×12.8×4 km3, with a resolution of 50 m and 40 m in the horizontal and vertical orientation, respectively. The outputs during 8~40 hour were retained every 20 minutes. Two parameters (LWC and vertical velocity) were then extracted by using MATLAB to create the following dataset. Additionally, LWC at 1 min before each moment was also uploaded for tracking. The "q" and "w" in the filename represent LWC and vertical velocity, respectively, and the number in the filename represents the corresponding hour and minute (e.g. "q24_20" means LWC value at 24h20m). The unit of "q" and "w" are "kg/kg" and "m/s' respectively.
DOI: 10.5281/zenodo.10816160
title: Liquid water content and vertical velocity from RICO-based LES simulations

description: The RICO-based simulations by implementing the LES module of WRF model 4.0 generate the raw data. The simulation continued for 40 hours with a time step of 0.5 second. The domain size is 12.8×12.8×4 km3, with a resolution of 50 m and 40 m in the horizontal and vertical orientation, respectively. The outputs during 8~40 hour were retained every 20 minutes. Two parameters (LWC and vertical velocity) were then extracted by using MATLAB to create the following dataset. Additionally, LWC at 1 min before each moment was also uploaded for tracking. The "q" and "w" in the filename represent LWC and vertical velocity, respectively, and the number in the filename represents the corresponding hour and minute (e.g. "q24_20" means LWC value at 24h20m). The unit of "q" and "w" are "kg/kg" and "m/s' respectively.
DOI: 10.5281/zenodo.10816245
title: event_person_reid_dataset
DOI: 10.5281/zenodo.10816246
title: event_person_reid_dataset
DOI: 10.5281/zenodo.10530505
title: Data on authorship issues in Cochrane manuscripts

description: Anonymized data on authorship issues in Cochrane manuscripts after inplementation of an authorship declaration form in Cochrane Colorectal Group.
DOI: 10.57745/4xvckk
title: EJP_citizen science_data.tab

description: We conducted a web-based survey. This excel sheet includes questions and answers from respondants.
DOI: 10.57745/uhhst3
title: EJP_citizen science_script R.R

description: All statistical analyses were performed using this R script (R version 4.2.2)
DOI: 10.5281/zenodo.10307480
title: SensoDat: Simulation-based Sensor Dataset of Self-driving Cars

description: GitHub: https://github.com/christianbirchler-org/sensodat

Developing tools in the context of autonomous systems, such as self-driving cars (SDCs), is time-consuming and costly since researchers and practitioners rely on expensive computing hardware and simulation software. We propose SensoDat, a dataset of 32,580 executed simulation-based SDC test cases generated with state-of-the-art test generators for SDCs. The dataset consists of trajectory logs and a variety of sensor data from the SDCs (e.g., rpm, wheel speed, brake thermals, transmission, etc.) represented as a time series. In total, SensoDat provides data from 81 different simulated sensors. Future research in the domain of SDCs does not necessarily depend on executing expensive test cases when using SensoDat. Furthermore, with the high amount and variety of sensor data, we think SensoDat can contribute to research, particularly for AI development, regression testing techniques for simulation-based SDC testing, flakiness in simulation, etc.
DOI: 10.5281/zenodo.10816480
title: Anticancer bioactive peptide combined with oxaliplatin against gastric cancer by regulation of PI3K/AKT signaling via inhibition of TPX2
DOI: 10.5281/zenodo.10816479
title: Anticancer bioactive peptide combined with oxaliplatin against gastric cancer by regulation of PI3K/AKT signaling via inhibition of TPX2
DOI: 10.5281/zenodo.10805481
title: Dataset: Partial discharge and interference discrimination in gas-insulated systems using electric and magnetic sensors

description: Data set for the experiments in the published paper https://doi.org/10.1016/j.ijepes.2024.109911
description: "This project 19ENG02 FutureEnergy has received funding from the EMPIR programme co-financed by the Participating States and from the European Union's Horizon 2020 research and innovation programme"
DOI: 10.5281/zenodo.10805482
title: Dataset: Partial discharge and interference discrimination in gas-insulated systems using electric and magnetic sensors

description: Data set for the experiments in the published paper https://doi.org/10.1016/j.ijepes.2024.109911
description: "This project 19ENG02 FutureEnergy has received funding from the EMPIR programme co-financed by the Participating States and from the European Union's Horizon 2020 research and innovation programme"
DOI: 10.5281/zenodo.10816634
title: PyMedPhys - Dicom-to-delivery NPCA file

description: https://github.com/pymedphys/pymedphys/issues/1047
DOI: 10.5281/zenodo.10816635
title: PyMedPhys - Dicom-to-delivery NPCA file

description: https://github.com/pymedphys/pymedphys/issues/1047
DOI: 10.5281/zenodo.10816365
title: Extended Data Fig. 2-27 Geographical information of bioinformatic predicted samples based on the analysis of 16S rRNA gene in four PE degrading bacteria
DOI: 10.5281/zenodo.10816366
title: Extended Data Fig. 2-27 Geographical information of bioinformatic predicted samples based on the analysis of 16S rRNA gene in four PE degrading bacteria
DOI: 10.48324/dandi.000934/0.240315.1754
title: 20240331_AIBS_Patchseq_nonhuman_primate

description: HMBA Lein PatchSeq upload (nonhuman primate) (Q1 2024)