cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.18742/29967706
title: Simulation data for "Deciphering the Molecular Mechanisms of Startle Disease: the Role of the Asn46Lys Mutation in the Glycine Receptor"

description: The glycine receptor (GlyR) is a pentameric ligand-gated ion channel that plays important physiological roles in the nervous system. Its malfunction is related to neurological disorders including startle disease (hyperekplexia), which is characterized by exaggerated startle responses to sudden unexpected stimuli, such as noise or touch. Here, we unravel the molecular mechanisms of action of a specific mutation that is linked to startle disease: Asn46Lys (N46K). This residue, in the GlyR extracellular domain, is not directly involved in neurotransmitter binding but can disrupt the neurotransmitter pathway. To understand how, we performed molecular dynamics simulations of the wild-type and mutated extracellular domain of a homomeric α1 GlyR, assessing the effects of the Asn46Lys mutation. We then sampled multiple unbinding and binding events by means of metadynamics simulations, with a funnel restraint to limit the exploration in the solvent. By evaluating the binding free energy landscape, we observed a substantial reduction in neurotransmitter binding affinity, which is consistent with experiments. We suggest that such reduction is linked to the interaction of its crucial glutamic acid residue with the lysine mutation competing with the glycine ligand.
DOI: 10.18742/29967706.v1
title: Simulation data for "Deciphering the Molecular Mechanisms of Startle Disease: the Role of the Asn46Lys Mutation in the Glycine Receptor"

description: The glycine receptor (GlyR) is a pentameric ligand-gated ion channel that plays important physiological roles in the nervous system. Its malfunction is related to neurological disorders including startle disease (hyperekplexia), which is characterized by exaggerated startle responses to sudden unexpected stimuli, such as noise or touch. Here, we unravel the molecular mechanisms of action of a specific mutation that is linked to startle disease: Asn46Lys (N46K). This residue, in the GlyR extracellular domain, is not directly involved in neurotransmitter binding but can disrupt the neurotransmitter pathway. To understand how, we performed molecular dynamics simulations of the wild-type and mutated extracellular domain of a homomeric α1 GlyR, assessing the effects of the Asn46Lys mutation. We then sampled multiple unbinding and binding events by means of metadynamics simulations, with a funnel restraint to limit the exploration in the solvent. By evaluating the binding free energy landscape, we observed a substantial reduction in neurotransmitter binding affinity, which is consistent with experiments. We suggest that such reduction is linked to the interaction of its crucial glutamic acid residue with the lysine mutation competing with the glycine ligand.
DOI: 10.48539/hbm897.hvmv.989
title: 3D Reference Organ for Lymph Node, Female, Left, v1.0

description: This reference organ, Left-lymph-node-female (https://humanatlas.io/3d-reference-library) was created using the<br>Clearing-enhanced 3D (Ce3D) method developed by Dr. Weizhe Li, Laboratory of Immune System Biology, National Institute<br>of Allergy and Infectious Diseases, NIH using data documented in (Li, Germain, and Gerner 2017). While the size and<br>cellular composition of mouse and human lymph nodes varies between species, the overall anatomy is well-conserved.<br><br>**Bibliography:**<br><br>* Li, Weizhe, Ronald N. Germain, and Michael Y. Gerner. 2017. “Multiplex, Quantitative Cellular Analysis in Large Tissue Volumes with Clearing-Enhanced 3D Microscopy (Ce3D).” *Proceedings of the National Academy of Sciences* 114 (35): E7321–30. https://doi.org/10.1073/pnas.1708981114.
DOI: 10.57745/r5apxn
title: Abstract Booklet - 20250310.pdf

description: :unav
DOI: 10.5281/zenodo.17100463
title: Molecular simulations data for: Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy

description: Repository of MD simulations data for: Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy
DOI: 10.5281/zenodo.17100464
title: Molecular simulations data for: Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy

description: Repository of MD simulations data for: Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy
DOI: 10.48539/hbm552.vjgw.787
title: OMAP-5 Organ Mapping Antibody Panel (OMAP)  for Multiplexed Antibody-Based Imaging of Human Liver with SIMS, v1.4

description: OMAP-5 was designed for Secondary Ionization Mass Spectrometry (SIMS) imaging of fresh frozen human liver samples<br>(Tian et al. 2022). The panel contains 20 antibodies and a cationic nucleic acid intercalator that contains<br>natural-abundance iridium. An antibody directed against Na/K ATPase was used for cell segmentation and image<br>alignment. This OMAP provides spatial context for the anatomical structures, metabolic zonation, and cell types<br>present in the ASCT+B liver table v1.0 (Masci, Kendall, and Suzuki 2021). This OMAP does not yet contain antibodies<br>for NK cells, dendritic cells, portal fibroblasts, MAIT cells, gamma delta T cells, and hepatic oval cells. Antigens<br>were detected using lanthanide tagged primary antibodies where the metal tags were detected by specific mass channels<br>using C60 SIMS. Details on the antibody staining method can be found here (Tian 2022). Image registration and cell<br>segmentation were performed using Deepcell. Cell segmentation was performed using nuclear and membrane marker<br>channels. Integrated protein expression was used to determine thresholds for cellular classification. An antibody<br>directed against EGFR was originally included in OMAP-5 v1.0 and v1.1, but was removed due to inconsistent labeling. A<br>representative dataset using this OMAP can be found here: (Tian and Tarolli 2023).<br><br>**Bibliography:**<br><br>* Masci, Anna Maria, Tim Kendall, and Ayako Suzuki. 2021. “Liver (v1.0) Graph Data, v1.0.” https://lod.humanatlas.io/asct-b/liver/v1.0/.<br>* Tian, Hua. 2022. “Liver Tissue Staining with Multiple Lanthanides-Tagged Antibodies,” February. https://www.protocols.io/view/liver-tissue-staining-with-multiple-lanthanides-ta-b5qmq5u6.<br>* Tian, Hua, Presha Rajbhandari, Jay Tarolli, Aubrianna M. Decker, Taruna V. Neelakantan, Tina Angerer, Fereshteh Zandkarimi, et al. 2022. “Multi-Modal Mass Spectrometry Imaging Reveals Single-Cell Metabolic States in Mammalian Liver.” bioRxiv. https://doi.org/10.1101/2022.09.26.508878.<br>* Tian, Hua, and Jay Tarolli. 2023. “Multiplexed Staining Dataset - OMAP 5 - Liver-Lanthanides-Conjugated Antibodies and C60-Secondary Ion Mass Spectrometry Imaging.” Zenodo. https://zenodo.org/records/8084259.
DOI: 10.15468/dl.cjuxvu
title: Occurrence Download

description: A dataset containing 93877 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helianthus annuus"
 ]
}

 The dataset includes 93877 records from 971 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053563-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48539/hbm476.bqcc.574
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Liver, 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/hbm765.jwfb.892
title: 3D Reference Organ for Kidney, Female, Left, 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/hbm554.czzx.885
title: OMAP-23: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of vermiform appendix (FFPE) with MICS on MACSima, v1.1

description: OMAP-23 was developed for MICS (MACSima Imaging Cyclic Staining) imaging of human formalin-fixed, paraffin-embedded<br>(FFPE) vermiform appendix tissue. Tissue fixation and antigen retrieval methods are outlined in Neil et al. (2023),<br>while details of the MACSima platform and imaging approach are provided in Kinkhabwala et al. (2022). The panel<br>contains 28 antibodies and the nuclear marker DAPI, used for image alignment and nuclear segmentation. All antibodies<br>in this panel are recombinant human IgG1 with Fc receptor binding removed to prevent non-specific binding and<br>eliminate the need for blocking steps. This recombinant format also allows inclusion of non-human monoclonal<br>antibodies followed by species-specific fluorophore-labeled secondary antibodies. The newly introduced dye VioB515 is<br>used to label one marker and is removed through chemical cleavage after imaging. OMAP-23 follows the structure and<br>approach of previous MICS-based OMAPs (OMAP-10 and OMAP-21) and expands upon OMAP-21 with the inclusion of markers<br>targeting non-immune cell types. It provides spatial context for all anatomical structures and most cell types within<br>the vermiform appendix. Reagents were sourced exclusively from Miltenyi Biotec and validated through a rigorous<br>internal QC process, thus lot numbers are not included. Data analysis was performed using the MACSIQ View Analysis<br>software described in Kinkhabwala et al. (2022). The software suite processes raw MACSima images, generates stitched<br>views, and enables downstream analyses including segmentation, gating, normalization, dimensionality reduction (tSNE,<br>UMAP), heatmaps, and clustering. This is the third OMAP designed for the MACSima platform. A representative dataset<br>for OMAP-23 is available at Zenodo (Müller, Femel, and Bosio 2024).<br><br>**Bibliography:**<br><br>* Kinkhabwala, Ali, Christoph Herbel, Jennifer Pankratz, Dmytro A. Yushchenko, Silvia Rüberg, Paurush Praveen, Sandy Reiß, et al. 2022. “MACSima Imaging Cyclic Staining (MICS) Technology Reveals Combinatorial Target Pairs for CAR T Cell Treatment of Solid Tumors.” *Scientific Reports* 12 (1): 1911. https://doi.org/10.1038/s41598-022-05841-4.<br>* Muller, Werner, Julia Femel, and Andreas Bosio. 2024. “OMAP-23: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Vermiform Appendix (FFPE) with MICS on MACSima.” Zenodo. https://zenodo.org/records/14008816.<br>* Neil, Emily, Dongju Park, Rebecca C. Hennessey, Eric C. DiBiasio, Michael DiBuono, Hanna Lafayette, Erica Lloyd, et al. 2023. “Spatial Protein and RNA Analysis on the Same Tissue Section Using MICS Technology.” bioRxiv. https://doi.org/10.1101/2023.10.27.564191.
DOI: 10.34740/kaggle/dsv/13030298
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.48539/hbm224.qjkz.987
title: Anatomical Structures, Cell Types and Biomarkers (ASCT+B) Tables to 3D Reference Object Library Crosswalk, v1.6

description: This lookup table maps [Anatomical Structures, Cell Types and Biomarkers (ASCT+B)<br>Table](https://humanatlas.io/asctb-tables) terms to anatomical structure terms used in the [3D Reference Object<br>Library](https://humanatlas.io/3d-reference-library).
DOI: 10.48539/hbm868.dwjz.874
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Lung, 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/hbm494.klqk.628
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Eye, 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>characterize cell types. The tables are authored and reviewed by an international team of experts.
DOI: 10.48539/hbm244.bcmq.737
title: OMAP-23: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of vermiform appendix (FFPE) with MICS on MACSima, v1.0

description: OMAP-23 was designed for MICS (MACSima imaging cyclic staining) imaging of FFPE human vermiform appendix<br>sample. Tissue fixation and antigen retrieval is described in (Spatial protein and RNA analysis on the same tissue<br>section using MICS technology). The MACSima technology is described in detail in the following publication (MACSima<br>imaging cyclic staining (MICS) technology reveals combinatorial target pairs for CAR T cell treatment of solid<br>tumors). All, antibodies in this panel are recombinant antibodies with a mutated human IgG1 constant region, removing<br>Fc receptor binding capacity of human IgG1, eliminating the need for additional blocking steps and reducing<br>non-specific binding. The use of human IgG1 recombinant antibodies allows for the addition of uncoupled monoclonal<br>antibodies from other species followed by a fluorescence labelled secondary reagent specific for the species of the<br>monoclonal antibody. The multiplex system has been described already for OMAP-10 and OMAP-21. A new dye VioB515 is<br>used for one reagents. The fluorescence is removed by cleavage. The panel contains 28 antibodies and the nuclear<br>marker DAPI for image alignment and nuclear segmentation. This OMAP provides a spatial context for all anatomical<br>structures and most cell types present in the vermiform appendix. OMAP-23 follows OMAP-21, with fewer antibodies but<br>adding antibodies for non-immune cells. All reagents are from Miltenyi Biotec and have been rigorously tested through<br>an internal quality control system to have minimal variation between lots. For this reason, lot information is not<br>included in this table. Analysis was performed by an accompanied software package MACSIQ View Analysis also described<br>in the MACSima publication (https://doi.org/10.1038/s41598-022-05841-4). The MACSima system is continuously evolving,<br> this is the third OMAP for the MACSima system.
DOI: 10.48539/hbm375.wfjn.332
title: OMAP-8: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Placenta with Imaging Mass Cytometry (IMC), v1.0

description: OMAP-8 was designed for Imaging Mass Cytometry (IMC) (https://pubmed.ncbi.nlm.nih.gov/24584193/) of formalin-fixed<br>paraffin-embedded (FFPE) human term-placenta samples. The tissue slides were prepared with a two-step antigen<br>retrieval process (pH 6 and pH 9, as described https://dx.doi.org/10.17504/protocols.io.bpwumpew). OMAP antibodies<br>validated by immunohistochemistry and IMC were conjugated to polymers containing metal isotopes. Conjugated antibodies<br>were used to stain processed human term-placenta tissue simultaneously. Regions of the processed tissue were then<br>acquired on the imaging mass cytometer (Hyperion; Standard BioTools) by laser ablation and visualized. The panel<br>contains 26 antibodies conjugated to unique metal isotopes and iridium marks the DNA. This OMAP provides a spatial<br>context for key placenta cell types in the [ASCT+B v.1.0<br>table](https://doi.org/10.48539/HBM446.WGLG.755). Single-cell RNA sequencing data were used to guide marker selection<br>for multiplexed tissue imaging. For example, ASCL2, HLA-G, PD-L1, CD68 and LYVE1 allow functionally specialized cell<br>types to be visualized and quantified in the placenta. Note that one of our core antibodies is to LYVE1 but, unlike in<br>other tissues where it is used to mark lymphatic vasculature, here we use it to mark the macrophage of the placenta<br>(Hofbauer cells) – there should be no lymphatics in the placenta.
DOI: 10.15468/dl.qbcmtp
title: Occurrence Download

description: A dataset containing 680 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Brazil",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chrysocyon brachyurus"
 ]
}

 The dataset includes 680 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053613-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48539/hbm763.qfrb.477
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Spleen, v1.3

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. The spleen ASCT+B<br>tables are derived from published literature, public datasets, unpublished studies from table authors, and input<br>provided by Dr. Birte Steiniger, an early reviewer and leader in the field of spleen anatomy. The gene biomarkers are<br>primarily derived from one landmark publication in humans: [(Madissoon et al.<br>2019)](https://doi.org/10.1186/s13059-019-1906-x). The anatomical structures and cell types of the spleen were highly<br>influenced by work from Dr. Steiniger including: [(Steiniger 2015)](https://doi.org/10.1111/imm.12469), [(Steiniger et<br>al. 2018)](https://doi.org/10.1038/s41598-018-34105-3), and [(Steiniger et al.<br>2007)](https://doi.org/10.1007/s00418-007-0320-8). Whenever possible, we used multiple sources to confirm gene and<br>protein biomarkers and united them across cell types. Cell phenotypes, especially for protein-based assays, are highly<br>granular with several markers listed at different expression levels. We anticipate further revision and refinement<br>from multimodal studies that pair sequencing and imaging studies from the same human sample. In total, this table<br>reports 37 anatomical structures, 60 cell types, and 194 biomarkers.
DOI: 10.48539/hbm453.mfsj.554
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Kidney, v1.5

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. The kidney ASCT+B<br>tables are generated from a variety of publicly available human kidney datasets and from data generated by HuBMAP and<br>KPMP consortia. Most of the markers listed are observed in more than one study or orthogonally validated. Note that<br>these are predicted markers and a single marker to annotate a cell type is not likely sufficient or specific.<br>Therefore, these are just a guide, more accurate annotation should be done using the entire set of enriched genes in a<br>cluster. The cell types shown here are at much higher granularity, although general markers for many of the<br>structures are also shown. There is a tradeoff in uncertainty of cell type annotation with higher granularity and as<br>spatial validation approaches become more robust we will be accordingly revising these.
DOI: 10.24403/jp.1497808
title: Matthias Eifler: Die Bibliothek des Erfurter Petersklosters im späten Mittelalter : Buchkultur und Literaturrezeption im Kontext der Bursfelder Klosterreform ; Teilband 1: Darstellung. - Teilband 2: Kataloge und Anhänge. - Veröffentlichungen der Historischen Kommission für Thüringen, Kleine Reihe ; Bd. 51. - Köln ; Weimar ; Wien : Böhlau Verlag, 2017 / [rezensiert von] Anja Freckmann
DOI: 10.48539/hbm657.rthq.837
title: OMAP-9: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Kidney with CODEX, v1.4

description: OMAP-9 was designed for CO-Detection by indEXing (CODEX) imaging of fresh frozen human kidney tissue using the<br>protocol described by Sabo et al. (2023a). The panel includes 41 antibodies and the nuclear marker DAPI for image<br>alignment and nuclear segmentation. OMAP-9 provides a spatial context for all anatomical structures and most cell<br>types present in the ASCT+B kidney table v1.1. This OMAP expands upon OMAP-3 (Neumann and Farrow 2024), which used an<br>18-plex CODEX panel, by incorporating additional markers that enable granular phenotyping of key kidney cells. These<br>include structural cells (e.g., Podocalyxin, LRP2, E-cadherin, SLC12A3, Na/K ATPase, Cytokeratin 8), T cells (e.g.,<br>CD3D, CD4, CD45RO, CD8, FOXP3, GATA-3), myeloid cells (e.g., CD11c, CD68, CD206, HLA-DR, Myeloperoxidase), and B cells<br>(CD20). Antibodies against injury-related markers (e.g., KIM1, IGFBP7, Osteopontin, PLSCR1, VCAM1, MCP1,<br>phospho-c-JUN, phospho-MLKL, Fibronectin, Collagen IV, LC3, Cystatin 3, PROM1) support profiling of disease<br>progression and tissue repair. Antibody clones for vimentin, beta-catenin, and uromodulin differ from those in OMAP-3.<br>Mesangial cells in the glomerulus are not targeted due to the lack of suitable CODEX-compatible antibodies. Additional<br>details on tissue preparation and the CODEX multiplexing workflow are provided by Sabo et al. (2023b). OMAP-9 v1.1<br>corrects author names, and v1.5 updates the UniProt accession number for CD45RO to P08575-4, differentiating it from<br>CD45. A representative dataset is available via Barwinska, Sabo, and EL-Achkar (2024).<br><br>**Bibliography:**<br><br>* Barwinska, Daria, Angela Sabo, and Tarek EL-Achkar. 2024. “OMAP-9.” Zenodo. https://doi.org/10.5281/zenodo.14537009.<br>* Neumann, Elizabeth K., and Melissa Farrow. 2024. “3-Kidney-Codex (v1.3) Graph Data, v1.3.” https://lod.humanatlas.io/omap/3-kidney-codex/v1.3/.<br>* Sabo, Angela R., Connor J. Gulbronson, Daria Barwinska, Michael J. Ferkowicz, William Bowen, Seth Winfree, and Tarek Ashkar. 2023a. “Indiana University Adapted Akoya Phenocycler-Fusion Tissue Staining and Imaging Protocol for Fresh Frozen Kidney Tissue,” March. https://www.protocols.io/view/indiana-university-adapted-akoya-phenocycler-fusio-cpchvit6.<br>* Sabo, Angela R., Connor J. Gulbronson, Daria Barwinska, Michael J. Ferkowicz, William Bowen, Seth Winfree, and Tarek Ashkar. 2023b. “Indiana University Adapted Akoya Phenocycler-Fusion Tissue Staining and Imaging Protocol for Fresh Frozen Kidney Tissue,” March. https://www.protocols.io/view/indiana-university-adapted-akoya-phenocycler-fusio-cpchvit6.