cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13342323
title: Deliverable 2.2: Biodiversity indicator database for focus regions

description: To quantify human-driven impacts on biodiversity, we used advanced modeling techniques paired with a few key variables such as habitat quality, vegetation structure, climate, and topography to develop an innovative predictive model that estimates both 1) current biodiversity patterns and distributions and 2) a baseline model of biodiversity. By comparing both of these models, we are able to identify regions with significant human-driven reductions in species richness, endemism, and species composition across both of our focus regions, South America and Africa.


The files provided in this repository (1 km2 resolution) include:


1- Species richness (number of species).


2- Endemism (species rarity). For this metric, we used the corrected weight endemism index, which is the inverse of a species’ range size and effectively assigns higher scores to species with more restricted distributions. For this index, we used species ranges found within our study area (of South America and Africa).


3- Species composition of vertebrates, invertebrates, and plants (which species occur in a given location). This metric, also known as beta diversity, summarizes which sets of species occur at each location. For this, we used the Sorensen index metric, as it does not depend on species absence data.


These results provide a valuable first step in describing human-induced changes in vegetation and biodiversity patterns across both South America and Africa.
description: This project has received funding from the European Research Executive Agency under HORIZON Research and Innovation Actions, grant agreement no101060765
DOI: 10.5281/zenodo.16099762
title: Healthcare Providers' Knowledge on Sickle Cell Disease and its Management: A Pre- and Post-Training Test Evaluation Outcome

description: Healthcare Providers’ Knowledge on Sickle Cell Disease and its Management in a training workshop on Standards of Care for managment of Sickle Cell Disease. A Pre-test was conducted at the begining of the training and a post-Training Test Evaluation done at the end of the training to assess the knowledge.
DOI: 10.5281/zenodo.15266611
title: Data for: Glacial and Periglacial Geomorphology of the Drang Drung, Haskira, and Pensilungpa glaciers, Trans Himalayan Ladakh, India

description: The geopackage contains the glacial and periglacial geomorphological landforms/features of Drang Drung, Haskira and Pensilungpa glacier valleys mapped from a combination of Planetscope images and Pléiades data (images and digital surface model)
DOI: 10.5281/zenodo.15742279
title: Datasets and Code for Assessment of Historical Livability Limitations

description: Datasets for analysis and plotting/visualization of historical livability limitations (associated with high temperature, humidity) assessed using the HEAT-Lim model (Vanos et al., 2023) using hourly ERA5-Land data 1950-2024.

All spatial data (netcdf, or .nc files) are provided at the ERA5-Land spatial resolution (~9-10km grid) over global land areas.

Mets_monthly_min files provide the monthly maximum livability limitations (activity in METs) for all months 1950-2024 for Young_adults and 65_over. Note that the HEAT-Lim model does not provide livability limitations below ~1.5 METs, so any livability values over land below 1.5 METS should be treated as 'survivable but not livable'.

Mets_annual_counts files provide the annual total of hours in each year in which activity would be limited to that activity level (3.3 METs or 2.3 METs) for Young_adults and 65_over.

Python code to calculate rh from ERA5-Land d2m and t2m, calculate livability assessment (METs) from hourly t2m and d2m, create monthly and annual summaries of hourly livability output saved in monthly chunks (nc files), and plot data are provided in the GitHub link.
DOI: 10.5281/zenodo.15792534
title: Dataset and Code for Assessment of Historical Livability Limitations v2

description: NOTE the updated version (v2, uploaded July 2, 2025) includes updated 'mets_monthly_min_1950_2024_1Hour_ERA5-LandNEW_conditions_shade_Young_adult.nc' and mets_monthly_min_1950_2024_1Hour_ERA5-LandNEW_conditions_shade_65_over.nc' - these files properly mask METs when the ERA5-Land 2m air temperature is >25C. These files should be used in place of the older files of the same name in v1 released in June, 2025.

________

Description below is from v1 and applies to data above as well:

Datasets for analysis and plotting/visualization of historical livability limitations (associated with high temperature, humidity) assessed using the HEAT-Lim model (Vanos et al., 2023) using hourly ERA5-Land data 1950-2024.

All spatial data (netcdf, or .nc files) are provided at the ERA5-Land spatial resolution (~9-10km grid) over global land areas.

Mets_monthly_min files provide the monthly maximum livability limitations (activity in METs) for all months 1950-2024 for Young_adults and 65_over. Note that the HEAT-Lim model does not provide livability limitations below ~1.5 METs, so any livability values over land below 1.5 METS should be treated as 'survivable but not livable'.

Mets_annual_counts files provide the annual total of hours in each year in which activity would be limited to that activity level (3.3 METs or 2.3 METs) for Young_adults and 65_over.

Python code to calculate rh from ERA5-Land d2m and t2m, calculate livability assessment (METs) from hourly t2m and d2m, create monthly and annual summaries of hourly livability output saved in monthly chunks (nc files), and plot data are provided in the GitHub link.
DOI: 10.5281/zenodo.8321185
title: Occupational exposure dataset for TiO2, carbon black and TiO2 and Ag;X

description: The size-resolved emission rate distributions of the nanomaterials supported by occupational exposure web application (https://aerosol.cloud.nanosolveit.eu/) hosted on NanoSolveIT Cloud Platform.  distributions are based on experimental data from:


A. J. Koivisto, T. Hussein, R. Niemelä, T. Tuomi and K. Hämeri, Impact of particle emissions of new laser printers on modeled office room, Atmos. Environ., 2010, 44(17), 2140–2146.

V. Gomez, M. Levin, A. T. Saber, S. Irusta, M. Dal Maso and R. Hanoi, et al., Comparison of Dust Release from Epoxy and Paint Nanocomposites and Conventional Products during Sanding and Sawing, Ann. Occup. Hyg., 2014, 58(8), 983–994.

A. J. Koivisto, A. C. Ø. Jensen, K. I. Kling, J. Kling, H. C. Budtz and I. K. Koponen, et al., Particle emission rates during electrostatic spray deposition of TiO2 nanoparticlebased photoactive coating, J. Hazard. Mater., 2018, 341, 218–227.

1 A. J. Koivisto, K. I. Kling, A. S. Fonseca, A. B. Bluhme, M. Moreman and M. Yu, et al., Dip coating of air purifier ceramic honeycombs with photocatalytic TiO2 nanoparticles: A case study for occupational exposure, Sci. Total Environ., 2018, 630, 1283–1291.


Details for the usage of the database can be found in:

P. Tsiros, N. Cheimarios, A. Tsoumanis, A.C.O. Jensen, G. Melagraki, I. Lynch, H. Sarimveis, A. Afantitis, “Towards an in silico Integrated Approach for Testing and Assessment of nanomaterials: from predicted indoor air concentrations to lung dose and biodistribution”, Environmental Science: Nano, 9, 1282, (2022).
https://pubs.rsc.org/en/content/articlelanding/2022/en/d1en00956g
DOI: 10.5281/zenodo.14249455
title: Data for: Glacial and Periglacial Geomorphology of the Drang Drung, Haskira, and Pensilungpa glaciers, Trans Himalayan Ladakh, India

description: The geopackage contains the glacial and periglacial geomorphological landforms/features of Drang Drung, Haskira and Pensilungpa glacier valleys mapped from a combination of Planetscope images and Pléiades data (images and digital surface model)
DOI: 10.5281/zenodo.15267518
title: Data for: Glacial and Periglacial Geomorphology of the Drang Drung, Haskira, and Pensilungpa glaciers, Trans-Himalayan Ladakh, India

description: The geopackage contains the glacial and periglacial geomorphological landforms/features of Drang Drung, Haskira and Pensilungpa glacier valleys mapped from a combination of Planetscope images and Pléiades data (images and digital surface model)
DOI: 10.5281/zenodo.15231920
title: Bibliometric Analysis of Sustainable Project Management (dataset as of April 2025)
DOI: 10.22002/aj5py-ey572
title: H. pylori 26695 / AGS

description: Grid box YWC054
description: <strong>Tilt Series Date:</strong> 2013-11-25</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 210.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> H.pylori prepared by Lee Rettberg</p>
<strong>Purification / Growth Conditions / Treatment:</strong> H.pylori cells grown in BLBB + 10% heat inactivated fetal bovine serum at 37 degrees in microaerobic chamber with GasPak EZ Campy Sachets for 2 days, OD600=0.4AGS cells cultivated on QF Au finder grid for 2 day in DMEM + 10% FBS. Infect by pylori for 6 hr.</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 37 C, 3µl BSA treated gold (1 ml gold resuspent in 30 ul). Manual blot by Whatman 40 filter paper. Ethane/propane mix.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-11-25-50/rawdata/</p>20131125_YWC054_10050.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-11-25-50/rawdata/20131125_YWC054_10050.mrc"
        > <i class="download icon"></i> Download </a></p>

        20131125_YWC054_10050_full.rec,  Reconstruction (Pixel Size 1.92 nm), 712.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-11-25-50/3dimage_35113/20131125_YWC054_10050_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.13342009
title: Deliverable 2.2: Biodiversity indicator database for focus regions

description: To quantify human-driven impacts on biodiversity, we used advanced modeling techniques paired with a few key variables such as habitat quality, vegetation structure, climate, and topography to develop an innovative predictive model that estimates both 1) current biodiversity patterns and distributions and 2) a baseline model of biodiversity. By comparing both of these models, we are able to identify regions with significant human-driven reductions in species richness, endemism, and species composition across both of our focus regions, South America and Africa.


The files provided in this repository (1 km2 resolution) include:


1- Species richness (number of species).


2- Endemism (species rarity). For this metric, we used the corrected weight endemism index, which is the inverse of a species’ range size and effectively assigns higher scores to species with more restricted distributions. For this index, we used species ranges found within our study area (of South America and Africa).


3- Species composition of vertebrates, invertebrates, and plants (which species occur in a given location). This metric, also known as beta diversity, summarizes which sets of species occur at each location. For this, we used the Sorensen index metric, as it does not depend on species absence data.


These results provide a valuable first step in describing human-induced changes in vegetation and biodiversity patterns across both South America and Africa.
description: This project has received funding from the European Research Executive Agency under HORIZON Research and Innovation Actions, grant agreement no101060765
DOI: 10.5281/zenodo.15699871
title: Oceanographic time series of innermost station for Nuup Kangerlua (SW Greenland)

description: This data is collected during monthly transect by the Greenland Climate Research Centre (https://gcrc.gl/), part of the long-term hydrographic research program in Nuup Kangerlua. For more information reach out to John Mortensen (jomo@natur.gl) or Lorenz Meire (LoMe@natur.gl).Data is from period 2008-05-13 to 2023-12-05. 

# name 1 = Cast: Cast name# name 2 = Date: YYYYMMDD, date of collection# name 3 = Latitude: Latitude in decimal degrees# name 4 = Longitude: Longitude in decimal degrees# name 5 = Year: year# name 6 = Month: month# name 7= Day: day of the month# name 8= Time: time (format HH:MM) in UTC# name 9 = SBEtime: time in julian days from start of year# name 10 = Pressure: Pressure, Strain Gauge [db]# name 11 = Temperature: Temperature [ITS-90, deg C]# name 12 = Salinity: Salinity, Practical [PSU]# name 13 = Density: Density [density, kg/m^3]
DOI: 10.5281/zenodo.8300431
title: Open database on traits and phylogenetic data on European pollinators

description: (subtitle) data on wild bees, hoverflies and butterflies


(abstract) This dataset was produced in the framework of the work package 1 (task 2) of the Horizon EU project Safeguard. The dataset encompassess trait data for three groups of pollinators: wild bees, hoverflies and butterflies, as well as phylogenetic data extracted from the GenBank. Information on traits comes from different literature sources, as well as direct measurements in collections and published databases. Some of the traits are common accross different species groups, while some traits are unique for particular group.


(method) Litherature search and direct measurments on specimens.


(dataset) This dataset compiles trait data for European wild bee, hoveverfly and butterfly species, and includes different categorical or numerical values for particular traits. It also contains phylogenetic information for species.
DOI: 10.5281/zenodo.13353482
title: Dataset for paper: Prognostic Stratification by the Meet-URO Score in Real-World Older Patients With Metastatic Renal Cell Carcinoma (mRCC) Receiving Cabozantinib: A Subanalysis of the Prospective ZEBRA Study (Meet-URO 9)

description: Dataset for paper: Prognostic Stratification by the Meet-URO Score in Real-World Older Patients With Metastatic Renal Cell Carcinoma (mRCC) Receiving Cabozantinib: A Subanalysis of the Prospective ZEBRA Study (Meet-URO 9)
DOI: 10.22002/pk10w-ymh32
title: Myxococcus xanthus delta-pilT

description: grid box YWC063
description: <strong>Tilt Series Date:</strong> 2013-12-21</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain form Lotte Sogaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 48 hr in shaking CTT medium at 30 degrees without antibiotics. OD600=0.7</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. -4 offset, 4 sec blot time, 1s drain. Ethane/propane mix. Grid: Quantifoil Cu 2/2 Finder. 10 nm gold beads.</p>
  ycw2013-12-21-30_slicer8551.jpg: Ring .  Bullseye .  Myxococcus Xanthus
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-12-21-30/rawdata/</p>20131221_YWC063_10030.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-12-21-30/rawdata/20131221_YWC063_10030.mrc"
        > <i class="download icon"></i> Download </a></p>

        20131221_YWC063_10030_full.rec,  Reconstruction (Pixel Size 1.56 nm), 712.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-12-21-30/3dimage_36398/20131221_YWC063_10030_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/egrf0-2km37
title: Myxococcus xanthus PilO-sfGFP

description: Strain SA4088Grid box YWC092
description: <strong>Tilt Series Date:</strong> 2014-03-10</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -8.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain form Lotte Sogaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 48 hr in shaking CTT medium at 30 degrees without antibiotics. OD600=0.8</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. -3.5 offset, 4 sec blot time, no drain. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
  ycw2014-03-10-7_slicer7478.jpg: T6SS in Myxococcus xanthus PilO-sfGFP ycw2014-03-10-7_slicer7479.jpg: unknown tube in Myxococcus xanthus PilO-sfGFP
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2014-03-10-7/rawdata/</p>20140310_YWC092_10007.mrc,  Tilt Series (Pixel Size 3.9 nm), 3.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2014-03-10-7/rawdata/20140310_YWC092_10007.mrc"
        > <i class="download icon"></i> Download </a></p>

        20140310_YWC092_10007_part131_8.rec,  Reconstruction (Pixel Size 15.6 nm), 712.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2014-03-10-7/3dimage_39919/20140310_YWC092_10007_part131_8.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/317r1-hy724
title: Bdellovibrio/E.coli mini cell

description: Something wrong with the dosage setting.
description: <strong>Tilt Series Date:</strong> 2013-09-10</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Bdellovibrio bacteriovorus</p>
<strong>Strain:</strong> HD100</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 2.0°, constant angular increment, dosage: 20.0 eV/Å²,  defocus: -8.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain from Liz Sockett, Cells prepared by Lee Rettberg</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown in S17-1 prey solution at 30 degrees, OD600=0.2, filtered by 0.22 um filter, mixed with purified WM3433 mini E. coli for 10 min before freezing</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 nm BSA treated gold. -3 offset, 4 sec blot time, no drain. Ethane/propane mix. Quantifoil Cu Finder grid</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-09-10-25/rawdata/</p>20130910_Janelia_Bdellovibrio_WM34330004.mrc,  Tilt Series (Pixel Size 0.42 nm), 1.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-09-10-25/rawdata/20130910_Janelia_Bdellovibrio_WM34330004.mrc"
        > <i class="download icon"></i> Download </a></p>

        20130910_Janelia_Bdellovibrio_WM34330004.rec,  Reconstruction (Pixel Size 1.68 nm), 1.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-09-10-25/3dimage_30767/20130910_Janelia_Bdellovibrio_WM34330004.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/ftmvj-7w041
title: Bdellovibrio attack-phase

description: Bdellovibrio in the mixture with Vibrio cholerae MKW1383.Imaged by Janelia farm Titan Krios.
description: <strong>Tilt Series Date:</strong> 2013-05-01</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Bdellovibrio bacteriovorus</p>
<strong>Strain:</strong> HD100</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -8.0 μm,  magnification: 26000x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Bdellovibrio bacteriovorus HD100 strain from Liz Sockett, Vibrio cholerae MKW1383 strain from Matthew Waldor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Bdellovibrio cells grown in S17-1 prey solution at 30 degrees, then filtered by 0.45 um filter. Vibrio MKW 1383 grown in LB for overnight. Bdellovibrio + Vibrio cholerae MKW1383 in Ca-HEPES buffer at 30 C for 16hr</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 nm BSA treated gold. -3 offset, 4 sec blot time, no drain. Ethane/propane mix.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-05-01-40/rawdata/</p>grid3-tiltseries_30007.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-05-01-40/rawdata/grid3-tiltseries_30007.mrc"
        > <i class="download icon"></i> Download </a></p>

        grid3-tiltseries_30007_full.rec,  Reconstruction (Pixel Size 1.68 nm), 516.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-05-01-40/3dimage_26440/grid3-tiltseries_30007_full.rec"
        > <i class="download icon"></i> Download </a></p>