cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26208/1hv3-4s20
title: Focused Isoprene Experiment at the California Institute of Technology (FIXCIT) photochemical box modeling

description: These experimental data and Matlab computer code were used to model the atmospheric isoprene chemistry observed during the Focused Isoprene Experiment at the Caltech environmental chamber, called FIXCIT. The model using five different chemical mechanisms and observations were compared for OH, hydroperoxyl (HO2), and isoprene oxidation products that occur at different stages of the oxidation sequence – isoprene hydroxyhydroperoxide (ISOPOOH), isoprene epoxydiol (IEPOX), hydroxyacetone, formaldehyde, methacrolein, and methyl vinyl ketone. The model code is in the F0AM format (Wolfe, G. M., Marvin, M. R., Roberts, S. J., Travis, K. R., & Liao, J. (2016). The Framework for 0‐D Atmospheric Modeling (F0AM) v3.1., Geoscientific Model Development, 9, 3309–3319. https://doi.org/10.5194/gmd‐9‐3309‐2016), the chemical files for the five model mechanisms, and the FIXCIT input merged file used to initialize the model. The data are in Matlab format.

To run the model, run FIX_multiruns_XXX_YYY.mat. It will call the F0AM model input program FIX_F0AM_20240529_ivard24hl0wvar_Jtest2.m. One or the other of these two programs calls the programs FIX_events_v3_2.m, FFIX_experiment_times_isop_v2.m, FIX_replace_initvals.m, and FIX_CombineInterpData_v4.m.

The first step is to change the directories, both input and output, in these programs to the ones being used on your computer. Second, check that the file names and dates are consistent in the FIX_multiruns_XXX_YYY.m file. Third, check that the model switches, such as ModelOptions, and tgauss and kdil in Met, are set to the desired values. Then start FIX_multiruns_XXX_YYY.m.

To replicate the figures in the manuscript and its supplement, change directories in FIX_daily_plots_v20240529_1stmanuscript_varwall.m and run it. It will call FIX_conc_compare_4dailyplots_v5.m and FIX_more_stats_v9.m. The result will be the daily comparison plots and the heatmaps in the manuscript.
DOI: 10.15468/dl.qvx77q
title: Occurrence Download

description: A dataset containing 54 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((141.47656 -36.64218,141.89573 -36.64218,141.89573 -36.39187,141.47656 -36.39187,141.47656 -36.64218))",
 "TaxonKey is Euphrasia collina subsp. tetragona (R.Br.) W.R.Barker"
 ]
}

 The dataset includes 54 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007074-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18120/qjf7-tc63
title: Movement Disorders - ERNA in STN & GPi
DOI: 10.15468/dl.em4gdp
title: Occurrence Download

description: A dataset containing 67597426 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is North America"
 ]
}

 The dataset includes 67597426 records from 3640 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007049-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13145/bacdive14657.20240916.9.1
title: Staphylococcus hominis subsp. novobiosepticus Kloos et al. 1998

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14658.20240916.9.1
title: Mammaliicoccus vitulinus (Webster et al. 1994) Madhaiyan et al. 2020

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14659.20240916.9.1
title: Mammaliicoccus vitulinus (Webster et al. 1994) Madhaiyan et al. 2020

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14660.20240916.9.1
title: Mammaliicoccus vitulinus (Webster et al. 1994) Madhaiyan et al. 2020

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14661.20240916.9.1
title: Staphylococcus equorum Schleifer et al. 1985 emend. Jeong et al. 2013

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14662.20240916.9.1
title: Staphylococcus equorum Schleifer et al. 1985 emend. Jeong et al. 2013

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14663.20240916.9.1
title: Staphylococcus equorum Schleifer et al. 1985 emend. Jeong et al. 2013

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14664.20240916.9.1
title: Mammaliicoccus sciuri (Kloos et al. 1976) Madhaiyan et al. 2020

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14665.20240916.9.1
title: Staphylococcus simiae Pant??ek et al. 2005

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14666.20240510.9
title: Staphylococcus simiae Pant??ek et al. 2005

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14667.20240510.9
title: Staphylococcus simiae Pant??ek et al. 2005

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14668.20240510.9
title: Staphylococcus simiae Pant??ek et al. 2005

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14669.20240916.9.1
title: Staphylococcus saprophyticus subsp. bovis Hájek et al. 1996

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14670.20240916.9.1
title: Staphylococcus pseudintermedius Devriese et al. 2005

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.57841/casdc.0004594
title: FIGURE 11. Stenus iustus Puthz, 1976. A in Taxonomic study on the Chinese Steninae (Coleoptera, Staphylinidae), with descriptions of three new species of the Genus Stenus Latreille
DOI: 10.13145/bacdive14671.20240916.9.1
title: Staphylococcus pettenkoferi Trülzsch et al. 2007

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14672.20240916.9.1
title: Staphylococcus microti Nováková et al. 2010

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14673.20240916.9.1
title: Staphylococcus massiliensis Al Masalma et al. 2010

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14674.20240916.9.1
title: Staphylococcus rostri Riesen and Perreten 2010

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14675.20240510.9
title: Staphylococcus rostri Riesen and Perreten 2010

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14676.20240916.9.1
title: Staphylococcus devriesei Supré et al. 2010

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14677.20240916.9.1
title: Staphylococcus agnetis Taponen et al. 2012

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14678.20240510.9
title: Staphylococcus agnetis Taponen et al. 2012

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14679.20240510.9
title: Staphylococcus agnetis Taponen et al. 2012

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14680.20240916.9.1
title: Mammaliicoccus stepanovicii (Hauschild et al. 2012) Madhaiyan et al. 2020

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14681.20240916.9.1
title: Nosocomiicoccus ampullae Morais et al. 2008

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14682.20240916.9.1
title: Lactovum miscens Matthies et al. 2005

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14683.20240916.9.1
title: Lactococcus garvieae subsp. garvieae (Collins et al. 1984) Varsha and Nampoothiri 2016

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14684.20240916.9.1
title: Lactococcus garvieae (Collins et al. 1984) Schleifer et al. 1986

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14685.20240916.9.1
title: Lactococcus garvieae (Collins et al. 1984) Schleifer et al. 1986

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14686.20240916.9.1
title: Lactococcus garvieae subsp. garvieae (Collins et al. 1984) Varsha and Nampoothiri 2016

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14687.20240916.9.1
title: Lactococcus garvieae (Collins et al. 1984) Schleifer et al. 1986

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14688.20240510.9
title: Lactococcus lactis subsp. cremoris (Orla-Jensen 1919) Schleifer et al. 1986

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14689.20240510.9
title: Lactococcus lactis subsp. cremoris (Orla-Jensen 1919) Schleifer et al. 1986

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14690.20240510.9
title: Lactococcus lactis subsp. cremoris (Orla-Jensen 1919) Schleifer et al. 1986

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14691.20240916.9.1
title: Lactococcus cremoris subsp. cremoris (Orla-Jensen 1919) Li et al. 2021

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14692.20240510.9
title: Lactococcus cremoris subsp. cremoris (Orla-Jensen 1919) Li et al. 2021

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15468/dl.bj2fbs
title: Occurrence Download

description: A dataset containing 905 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Solanum dulcamara",
 "Country is New Zealand",
 "HasCoordinate is true"
 ]
}

 The dataset includes 905 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053609-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48539/hbm896.twpt.542
title: 3D Reference Organ for Thymus, Female, v1.0

description: [This reference organ](https://humanatlas.io/3d-reference-library) was created using data from the Visible Human<br>Female provided by the National Library of Medicine.
DOI: 10.48539/hbm974.qwfp.588
title: OMAP-18: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of human lymph node with Cell DIVE-IBEX, v1.0

description: OMAP-18 was designed for Cell DIVE imaging (https://doi.org/10.1073/pnas.1300136110) of human FFPE lymph node samples<br>using the IBEX (Iterative Bleaching Extends multi-pleXity) dye inactivation protocol. The resulting method, termed<br>Cell DIVE-IBEX, allows complete signal elimination without tissue loss using IBEX compatible fluorophores<br>(https://doi.org/10.1038/s41596-021-00644-9). The panel consists of 3 cycles of 11 primary antibodies, 4 secondary<br>antibodies, a streptavidin conjugate to detect a biotinylated KI67 antibody (Thermo Fisher Scientific S21384), and<br>nuclear label Hoechst for image alignment and nuclear segmentation. This OMAP provides a spatial context for 15<br>anatomical structures and 11 cell types present in the ASCT+B lymph node table, v1.1<br>(https://doi.org/10.48539/HBM573.SHCQ.259). OMAP-18 was designed using OMAP-1<br>(https://doi.org/10.48539/HBM458.NSWR.957) as a reference and therefore contains all the biomarkers included in<br>OMAP-1. However, OMAP-18 is limited to essential markers for evaluating changes in lymph node architecture and immune<br>cell composition arising from malignancy based on discovery studies using OMAP-1. For this reason, OMAP-18 does not<br>allow granular phenotyping of fibroblastic reticular cells, T regulatory cells, T helper cells, blood and lymphatic<br>endothelial cells, and dendritic cells but can easily be expanded in the future. Importantly, this panel utilizes the<br>BCL2 clone preferred by pathologists (clone SP66), providing additional value for translational studies. Human FFPE<br>samples were prepared using a dual antigen retrieval approach consisting of 30 minutes with Epitope Retrieval Solution<br>1 (pH 6, 100C) and then 30 minutes with Epitope Retrieval Solution 2 (pH 9, 100C) performed on the Leica Bond. More<br>details on the antigen retrieval protocol and step-by-step application of antibodies can be found on the IBEX Imaging<br>Community site (https://doi.org/10.5281/zenodo.7693278). Detailed B cell follicle and cellular community analysis was<br>performed as described in the accompanying manuscript (https://doi.org/10.1016/j.ccell.2024.02.001). Representative<br>datasets can be accessed on Image Data Resource (https://idr.openmicroscopy.org) under accession number idr0158 and<br>querying images with the prefix “CellDIVE_IBEX_Immune.”
DOI: 10.48539/hbm894.fgqn.237
title: 3D Reference Organ for Heart, Female, v1.0

description: [This reference organ](https://humanatlas.io/3d-reference-library) was created using data from the Visible Human<br>Female provided by the National Library of Medicine.
DOI: 10.48539/hbm368.fbrw.337
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Fallopian Tube, v1.2

description: [Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables](https://humanatlas.io/asctb-tables) aim to<br>capture the nested *part_of* structure of anatomical human body parts, the typology of cells, and biomarkers used to<br>identify cell types. The tables are authored and reviewed by an international team of experts.
DOI: 10.48539/hbm426.gzpn.888
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Vasculature, v1.0

description: [Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables](https://humanatlas.io/asctb-tables) aim to<br>capture the nested *part_of* structure of anatomical human body parts, the typology of cells, and biomarkers used to<br>identify cell types. The tables are authored and reviewed by an international team of experts.
DOI: 10.48539/hbm655.dgsw.887
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Blood Vasculature, v1.1

description: [Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables](https://humanatlas.io/asctb-tables) aim to<br>capture the nested *part_of* structure of anatomical human body parts, the typology of cells, and biomarkers used to<br>identify cell types. The tables are authored and reviewed by an international team of experts.
DOI: 10.21227/dyg7-4631
title: "IIBC simulation and experiment"

description: "This dataset contains the partial simulation and experiment data from the research presented in the paper \"Integrating Identification and Regulation: A Balance Control Framework for Biped Robots Under Unknown Load Conditions\". The data was collected from the humanoid robot performing standing and walking tasks while carrying various unknown loads.The dataset includes:1. Time-series data from simulations, including estimated load parameters, robot joint states, and Center of Mass (CoM) trajectories.2. Time-series data from experiments, including force\/torque sensor readings, IMU data, and robot joint states.All data is provided in CSV and TXT formats. This dataset can be used to validate and benchmark algorithms for real-time load identification and balance control in bipedal robots."
DOI: 10.48539/hbm243.rgbp.396
title: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Skin with Cell DIVE, v1.1

description: OMAP-22 was developed for Cell DIVE multiplexed imaging of human formalin-fixed, paraffin-embedded (FFPE) skin tissue.<br>Cell DIVE enables highly multiplexed, antibody-based imaging and single-cell analysis, as outlined in Gerdes et al.<br>(2013). Tissue slides were processed with a dual antigen retrieval method using pH 6 and pH 9 buffers, as described in<br>McDonough et al. (2020), and antigens were detected with either dye-conjugated primary antibodies or unlabeled<br>primaries with fluorophore-conjugated secondaries. A detailed protocol is available in Pryhuber et al. (2022). The<br>panel comprises 34 antibodies and the nuclear marker DAPI for image registration and nuclear segmentation. This<br>updated v1.1 OMAP builds on OMAP-4 (McDonough, Chadwick, and Ginty 2024) and expands biomarker coverage by including<br>CD103, CD14, CD1a, CD207, CD34, F13A1, CDKN1A, KRT1, KRT5, KRT7, KRT10, MLANA, PDPN, TPSAB1, and VWF. These additions<br>enable identification of specific keratinocyte populations, dermal dendritic cells, melanocytes, mast cells, and<br>Langerhans cells. Protein biomarkers such as DDB2, CDKN1A, and p53 allow profiling of aging and skin damage responses.<br>Updates also include the use of commercially available conjugates when possible, replacing custom-labeled clones, and<br>correction of CD3 marker specification from CD3D to CD3E. This OMAP provides spatial context for most anatomical<br>structures and cell types listed in the ASCT+B skin table v1.3 (Ginty et al. 2023). Representative datasets are<br>publicly available on the HuBMAP data portal.<br><br>**Bibliography:**<br><br>* Gerdes, Michael J., Christopher J. Sevinsky, Anup Sood, Sudeshna Adak, Musodiq O. Bello, Alexander Bordwell, Ali Can, et al. 2013. “Highly Multiplexed Single-Cell Analysis of Formalin-Fixed, Paraffin-Embedded Cancer Tissue.” *Proceedings of the National Academy of Sciences* 110 (29): 11982–87. https://doi.org/10.1073/pnas.1300136110.<br>* Ginty, Fiona, Jonhan Ho, Joel Sunshine, and Arivarasan Karunamurthy. 2023. “Skin (v1.3) Graph Data, v1.3.” 2023. https://lod.humanatlas.io/asct-b/skin/v1.3/.<br>* McDonough, Elizabeth, Chrystal Chadwick, and Fiona Ginty. 2024. “4-Skin-Cell-Dive (v1.3) Graph Data, v1.3.” 2024. https://lod.humanatlas.io/omap/4-skin-cell-dive/v1.3/.<br>* McDonough, Liz, Chrystal Chadwick, Fiona Ginty, Christine Surrette, and Anup Sood. 2020. “Cell DIVETM Platform | Slide Clearing and Antigen Retrieval,” December. https://www.protocols.io/view/cell-dive-platform-slide-clearing-and-antigen-retr-bpwumpew.<br>* Pryhuber, Gloria, Gail Deutsch, Christine Surrette, Lisa Lowery, Heidie Huyck, and Cory Poole. 2022. “HuBMAP | GE/URMC/SCH Cell DIVETM Modality Overview,” February. https://www.protocols.io/view/hubmap-ge-urmc-sch-cell-dive-modality-overview-b4kgqutw.
DOI: 10.15468/dl.x7basd
title: Occurrence Download

description: A dataset containing 430 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Rana zhenhaiensis",
 "Year 2000-2025"
 ]
}

 The dataset includes 430 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053612-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d9wumw
title: Occurrence Download

description: A dataset containing 18984 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Asystasia gangetica"
 ]
}

 The dataset includes 18984 records from 378 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053610-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.