cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25573/data.23284901
title: DNA sequences

description: Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimens. Species identifications were verified based on taxonomic, phenotypic, and genotypic data, and sequences are associated with voucher specimens, live-color photographs, and genetic samples catalogued at Smithsonian Institution, National Museum of Natural History. Specimens, photographs, and genetic samples are available for analyses; see contact information below. <br> Katherine E. Bemis (1,2), Matthew G. Girard (2,3), Mudjekeewis D. Santos (4), Kent E. Carpenter (5), Jonathan R. Deeds (6), Diane E. Pitassy (2), Nicko Amor L. Flores (4), Elizabeth S. Hunter (6), Amy C. Driskell (7), Kenneth S. Macdonald III (7), Lee A. Weigt (7), Jeffrey T. Williams (2) <br> 1. National Systematics Laboratory, Office of Science and Technology, NOAA Fisheries, Washington, D.C. 20560, U.S.A. <br> 2. Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560, U.S.A. <br> 3. Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045, U.S.A. <br> 4. Genetic Fingerprinting Laboratory, National Fisheries Research and Development Institute, Quezon City, 1103, Philippines. <br> 5. Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, 23529, U.S.A. <br> 6. Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, 20740, U.S.A. <br> 7. Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560, U.S.A. <br> Corresponding authors: Katherine E. Bemis (bemisk@si.edu), Matthew G. Girard (girardmg@si.edu), Jeffrey T. Williams (jtwfish@gmail.com)
DOI: 10.25573/data.23284901.v1
title: DNA sequences

description: Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimens. Species identifications were verified based on taxonomic, phenotypic, and genotypic data, and sequences are associated with voucher specimens, live-color photographs, and genetic samples catalogued at Smithsonian Institution, National Museum of Natural History. Specimens, photographs, and genetic samples are available for analyses; see contact information below. <br> Katherine E. Bemis (1,2), Matthew G. Girard (2,3), Mudjekeewis D. Santos (4), Kent E. Carpenter (5), Jonathan R. Deeds (6), Diane E. Pitassy (2), Nicko Amor L. Flores (4), Elizabeth S. Hunter (6), Amy C. Driskell (7), Kenneth S. Macdonald III (7), Lee A. Weigt (7), Jeffrey T. Williams (2) <br> 1. National Systematics Laboratory, Office of Science and Technology, NOAA Fisheries, Washington, D.C. 20560, U.S.A. <br> 2. Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560, U.S.A. <br> 3. Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045, U.S.A. <br> 4. Genetic Fingerprinting Laboratory, National Fisheries Research and Development Institute, Quezon City, 1103, Philippines. <br> 5. Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, 23529, U.S.A. <br> 6. Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, 20740, U.S.A. <br> 7. Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560, U.S.A. <br> Corresponding authors: Katherine E. Bemis (bemisk@si.edu), Matthew G. Girard (girardmg@si.edu), Jeffrey T. Williams (jtwfish@gmail.com)
DOI: 10.34740/kaggle/ds/2043128
title: PAS_Dataset
DOI: 10.6084/m9.figshare.21401115
title: LC3-dependent EV loading and secretion (LDELS) promotes TFRC (transferrin receptor) secretion via extracellular vesicles

description: LC3-dependent EV loading and secretion (LDELS) is a secretory autophagy pathway in which the macroautophagy/autophagy machinery facilitates the packaging of cytosolic cargos, such as RNA-binding proteins, into extracellular vesicles (EVs) for secretion outside of the cell. Here, we identify TFRC (transferrin receptor), one of the first proteins found to be secreted via EVs, as a transmembrane cargo of the LDELS pathway. Similar to other LDELS targets, TFRC secretion via EVs genetically requires components of the MAP1LC3/LC3-conjugation machinery but is independent of other <i>ATG</i>s involved in classical autophagosome formation. Furthermore, the packaging and secretion of this transmembrane protein into EVs depends on multiple ESCRT pathway components and the small GTPase RAB27A. Based on these results, we propose that the LDELS pathway promotes TFRC incorporation into EVs and its secretion outside the cell. <b>Abbreviations:</b> ATG: autophagy related; ESCRT: endosomal sorting complexes required for transport; EV: extracellular vesicle; EVP: extracellular vesicle and particle; ILV: intralumenal vesicle; LDELS: LC3-dependent EV loading and secretion; LIR: LC3-interacting region; MVE: multivesicular endosome; RBP: RNA-binding protein; TMT: tandem mass tag; TFRC: transferrin receptor.
DOI: 10.6084/m9.figshare.21401115.v1
title: LC3-dependent EV loading and secretion (LDELS) promotes TFRC (transferrin receptor) secretion via extracellular vesicles

description: LC3-dependent EV loading and secretion (LDELS) is a secretory autophagy pathway in which the macroautophagy/autophagy machinery facilitates the packaging of cytosolic cargos, such as RNA-binding proteins, into extracellular vesicles (EVs) for secretion outside of the cell. Here, we identify TFRC (transferrin receptor), one of the first proteins found to be secreted via EVs, as a transmembrane cargo of the LDELS pathway. Similar to other LDELS targets, TFRC secretion via EVs genetically requires components of the MAP1LC3/LC3-conjugation machinery but is independent of other <i>ATG</i>s involved in classical autophagosome formation. Furthermore, the packaging and secretion of this transmembrane protein into EVs depends on multiple ESCRT pathway components and the small GTPase RAB27A. Based on these results, we propose that the LDELS pathway promotes TFRC incorporation into EVs and its secretion outside the cell. <b>Abbreviations:</b> ATG: autophagy related; ESCRT: endosomal sorting complexes required for transport; EV: extracellular vesicle; EVP: extracellular vesicle and particle; ILV: intralumenal vesicle; LDELS: LC3-dependent EV loading and secretion; LIR: LC3-interacting region; MVE: multivesicular endosome; RBP: RNA-binding protein; TMT: tandem mass tag; TFRC: transferrin receptor.
DOI: 10.5517/ccdc.csd.cc26tyhh
title: CCDC 2050727: Experimental Crystal Structure Determination

description: Related Article: Carl Schiller, Daniel Sieh, Nils Lindenmaier, Michel Stephan, Natascha Junker, Edward Reijerse, Alexander A. Granovsky, Peter Burger|2023|J.Am.Chem.Soc.|145|11392|doi:10.1021/jacs.3c02781
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc26tyjj
title: CCDC 2050728: Experimental Crystal Structure Determination

description: Related Article: Carl Schiller, Daniel Sieh, Nils Lindenmaier, Michel Stephan, Natascha Junker, Edward Reijerse, Alexander A. Granovsky, Peter Burger|2023|J.Am.Chem.Soc.|145|11392|doi:10.1021/jacs.3c02781
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc270rz0
title: CCDC 2056322: Experimental Crystal Structure Determination

description: Related Article: Mithilesh Kumar Nayak, Benedict J. Elvers, Debdeep Mandal, Ayan Das, Raghunathan Ramakrishnan, Kaustubh R. Mote, Carola Schulzke, Cem Burak Yildiz, Anukul Jana|2023|Chem.Commun.|59|6698|doi:10.1039/D3CC00891F
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc270s02
title: CCDC 2056323: Experimental Crystal Structure Determination

description: Related Article: Mithilesh Kumar Nayak, Benedict J. Elvers, Debdeep Mandal, Ayan Das, Raghunathan Ramakrishnan, Kaustubh R. Mote, Carola Schulzke, Cem Burak Yildiz, Anukul Jana|2023|Chem.Commun.|59|6698|doi:10.1039/D3CC00891F
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2cyvsz
title: CCDC 2203442: Experimental Crystal Structure Determination

description: Related Article: Feng Pan, Haohu Li, Xiaohua Wang, Liwen Luo, Yanfei Lin, Qingkai Yu, Wenlin Xie, Lianpeng Zhang|2023|RSC Advances|13|13911|doi:10.1039/D3RA02247A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d1nbg
title: CCDC 2206125: Experimental Crystal Structure Determination

description: Related Article: Fei Wang, Xiangling Shi, Yi Zhang, Wei Zhou, Aimin Li, Yuanchu Liu, Jonathan L. Sessler, Qing He|2023|J.Am.Chem.Soc.|145|10943|doi:10.1021/jacs.3c01066
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.13020/reqb-y062
title: Supporting data for Core−Shell Gyroid in ABC Bottlebrush Block Terpolymers

description: These files contain primary data supporting all results reported in Cui et al. "Core−shell gyroid in ABC bottlebrush block terpolymers." A series of bottlebrush block polymers containing 24 PEP-PS diblock copolymers and 109 PEP-PS-PEO triblock terpolymers were synthesized by ring-opening metathesis polymerization (ROMP) of norbornene-functionalized poly(ethylene-alt-propylene) (PEP), poly(styrene) (PS), and poly(ethylene oxide) (PEO) macromonomers. The molecular weights of the three macromonomers were around 1 kg/mol. The relatively modest total backbone degrees of polymerization ranged from ca. 20 to 40. Morphologies of these bottlebrush block polymers were characterized by small-angle X-ray scattering (SAXS). The PEP-PS diblocks exhibited only cylindrical (HEX) and lamellar (LAM) morphologies; the desired network phases did not appear in these materials, consistent with previous experimental studies. However, adding variable-length bottlebrush PEO blocks to diblocks containing 30% to 50% PS led to a substantial core-shell double gyroid (GYR) phase window in the ternary phase portrait. Encouragingly, the GYR unit cell dimensions increased almost linearly with the backbone degree of polymerization, portending the ability to access larger network dimensions than previously obtained with linear block polymers. This finding demonstrates a periodic network phase in bottlebrush block polymers for the first time and highlights extraordinary opportunities associated with applying facile ROMP chemistry to multiblock bottlebrush polymers.
description: The data folder contains all small-angle X-ray scattering (SAXS) data, as well as proton nuclear magnetic resonance (1H NMR), size exclusion chromatography (SEC), differential scanning calorimetry (DSC), and transmission electron microscopy (TEM) data. The nomenclature is consistent with that used in the manuscript. See the readme.txt file for further details.
DOI: 10.34740/kaggle/dsv/5832496
title: Mahanagar Yatayat Dataset
DOI: 10.5281/zenodo.7998732
title: hERG Kv11.1 and Janus Kinase 2 interplay in retinoblastoma cell migration

description: Docking poses, Molecular Dynamics simulation starting structures and MD trajectories
DOI: 10.5281/zenodo.7998731
title: hERG Kv11.1 and Janus Kinase 2 interplay in retinoblastoma cell migration

description: Docking poses, Molecular Dynamics simulation starting structures and MD trajectories
DOI: 10.5281/zenodo.7884215
title: KsgA facilitates ribosomal small subunit maturation by proofreading a key structural lesion

description: Weights, z files, poses, indices, CTF info, and particles for cryoDRGN training on KsgA-treated and untreated datasets in "KsgA facilitates ribosomal small subunit maturation by proofreading a key structural lesion"
DOI: 10.5281/zenodo.7884214
title: KsgA facilitates ribosomal small subunit maturation by proofreading a key structural lesion

description: Weights, z files, poses, indices, CTF info, and particles for cryoDRGN training on KsgA-treated and untreated datasets in "KsgA facilitates ribosomal small subunit maturation by proofreading a key structural lesion"
DOI: 10.25380/iastate.23284496.v1
title: Mammalian orthoreovirus and HER2+ breast cancer

description: Investigation into mammalian orthoreovirus infection in HER2+ breast cancer cells. This contains the datasets of the raw data from replication and viability assays as well as raw figures of western blot analysis of HER2, Akt, pAkt-Thr, pAkt-Ser and 4E-BP1.
DOI: 10.25380/iastate.23284496
title: Mammalian orthoreovirus and HER2+ breast cancer

description: Investigation into mammalian orthoreovirus infection in HER2+ breast cancer cells. This contains the datasets of the raw data from replication and viability assays as well as raw figures of western blot analysis of HER2, Akt, pAkt-Thr, pAkt-Ser and 4E-BP1.
DOI: 10.5281/zenodo.7998809
title: WRF model configuration and data used for the NHESS manuscript "Heat wave characteristics: evaluation of regional climate model performances for Germany"

description: The file contains: the namelist.input document with the description of the WRF model configuration used in Warscher et al. (2019) WRF simulation outputs from the reanalysis run: daily values of maximum temperature for the time period 1980-2009 from the innermost (5 km grid resolution) and second innermost (15 km) domain; from both domains the same section, relevant for the study, was taken; the data was bilineraily interpolated to 12.5 km horizontal grid resolution to match the EUR-11 CORDEX format
DOI: 10.5281/zenodo.7998808
title: WRF model configuration and data used for the NHESS manuscript "Heat wave characteristics: evaluation of regional climate model performances for Germany"

description: The file contains: the namelist.input document with the description of the WRF model configuration used in Warscher et al. (2019) WRF simulation outputs from the reanalysis run: daily values of maximum temperature for the time period 1980-2009 from the innermost (5 km grid resolution) and second innermost (15 km) domain; from both domains the same section, relevant for the study, was taken; the data was bilineraily interpolated to 12.5 km horizontal grid resolution to match the EUR-11 CORDEX format
DOI: 10.6084/m9.figshare.23285267
title: HajjTweet_v2_Arb.xlsx

description: Tweets related to Hajj, Umrah, Pilgrims
DOI: 10.6084/m9.figshare.23285267.v1
title: HajjTweet_v2_Arb.xlsx

description: Tweets related to Hajj, Umrah, Pilgrims
DOI: 10.15156/bio/sh3377235.08fu
title: SH3377235.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh548212.07fu
title: SH548212.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh548213.07fu
title: SH548213.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh548214.07fu
title: SH548214.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3377236.08fu
title: SH3377236.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3377237.08fu
title: SH3377237.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh548215.07fu
title: SH548215.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.