cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20449327
title: Annona_procb_ESM_Table S3.xlsx from Evolution of the nitric oxide synthase family in vertebrates and novel insights in gill development

description: Nitric oxide (NO) is an ancestral key signalling molecule essential for life and has enormous versatility in biological systems, including cardiovascular homeostasis, neurotransmission and immunity. Although our knowledge of NO synthases (Nos), the enzymes that synthesize NO <i>in vivo</i>, is substantial, the origin of a large and diversified repertoire of <i>nos</i> gene orthologues in fishes with respect to tetrapods remains a puzzle. The recent identification of <i>nos3</i> in the ray-finned fish spotted gar, which was considered lost in this lineage, changed this perspective. This finding prompted us to explore <i>nos</i> gene evolution, surveying vertebrate species representing key evolutionary nodes. This study provides noteworthy findings: first, <i>nos2</i> experienced several lineage-specific gene duplications and losses. Second, <i>nos3</i> was found to be lost independently in two different teleost lineages, Elopomorpha and Clupeocephala. Third, the expression of at least one <i>nos</i> paralogue in the gills of developing shark, bichir, sturgeon, and gar, but not in lamprey, suggests that <i>nos</i> expression in this organ may have arisen in the last common ancestor of gnathostomes. These results provide a framework for continuing research on <i>nos</i> genes’ roles, highlighting subfunctionalization and reciprocal loss of function that occurred in different lineages during vertebrate genome duplications.
DOI: 10.6084/m9.figshare.20449327.v1
title: Annona_procb_ESM_Table S3.xlsx from Evolution of the nitric oxide synthase family in vertebrates and novel insights in gill development

description: Nitric oxide (NO) is an ancestral key signalling molecule essential for life and has enormous versatility in biological systems, including cardiovascular homeostasis, neurotransmission and immunity. Although our knowledge of NO synthases (Nos), the enzymes that synthesize NO <i>in vivo</i>, is substantial, the origin of a large and diversified repertoire of <i>nos</i> gene orthologues in fishes with respect to tetrapods remains a puzzle. The recent identification of <i>nos3</i> in the ray-finned fish spotted gar, which was considered lost in this lineage, changed this perspective. This finding prompted us to explore <i>nos</i> gene evolution, surveying vertebrate species representing key evolutionary nodes. This study provides noteworthy findings: first, <i>nos2</i> experienced several lineage-specific gene duplications and losses. Second, <i>nos3</i> was found to be lost independently in two different teleost lineages, Elopomorpha and Clupeocephala. Third, the expression of at least one <i>nos</i> paralogue in the gills of developing shark, bichir, sturgeon, and gar, but not in lamprey, suggests that <i>nos</i> expression in this organ may have arisen in the last common ancestor of gnathostomes. These results provide a framework for continuing research on <i>nos</i> genes’ roles, highlighting subfunctionalization and reciprocal loss of function that occurred in different lineages during vertebrate genome duplications.
DOI: 10.6084/m9.figshare.20449330
title: Annona_procb_ESM_Table S2.xlsx from Evolution of the nitric oxide synthase family in vertebrates and novel insights in gill development

description: Nitric oxide (NO) is an ancestral key signalling molecule essential for life and has enormous versatility in biological systems, including cardiovascular homeostasis, neurotransmission and immunity. Although our knowledge of NO synthases (Nos), the enzymes that synthesize NO <i>in vivo</i>, is substantial, the origin of a large and diversified repertoire of <i>nos</i> gene orthologues in fishes with respect to tetrapods remains a puzzle. The recent identification of <i>nos3</i> in the ray-finned fish spotted gar, which was considered lost in this lineage, changed this perspective. This finding prompted us to explore <i>nos</i> gene evolution, surveying vertebrate species representing key evolutionary nodes. This study provides noteworthy findings: first, <i>nos2</i> experienced several lineage-specific gene duplications and losses. Second, <i>nos3</i> was found to be lost independently in two different teleost lineages, Elopomorpha and Clupeocephala. Third, the expression of at least one <i>nos</i> paralogue in the gills of developing shark, bichir, sturgeon, and gar, but not in lamprey, suggests that <i>nos</i> expression in this organ may have arisen in the last common ancestor of gnathostomes. These results provide a framework for continuing research on <i>nos</i> genes’ roles, highlighting subfunctionalization and reciprocal loss of function that occurred in different lineages during vertebrate genome duplications.
DOI: 10.6084/m9.figshare.20449330.v1
title: Annona_procb_ESM_Table S2.xlsx from Evolution of the nitric oxide synthase family in vertebrates and novel insights in gill development

description: Nitric oxide (NO) is an ancestral key signalling molecule essential for life and has enormous versatility in biological systems, including cardiovascular homeostasis, neurotransmission and immunity. Although our knowledge of NO synthases (Nos), the enzymes that synthesize NO <i>in vivo</i>, is substantial, the origin of a large and diversified repertoire of <i>nos</i> gene orthologues in fishes with respect to tetrapods remains a puzzle. The recent identification of <i>nos3</i> in the ray-finned fish spotted gar, which was considered lost in this lineage, changed this perspective. This finding prompted us to explore <i>nos</i> gene evolution, surveying vertebrate species representing key evolutionary nodes. This study provides noteworthy findings: first, <i>nos2</i> experienced several lineage-specific gene duplications and losses. Second, <i>nos3</i> was found to be lost independently in two different teleost lineages, Elopomorpha and Clupeocephala. Third, the expression of at least one <i>nos</i> paralogue in the gills of developing shark, bichir, sturgeon, and gar, but not in lamprey, suggests that <i>nos</i> expression in this organ may have arisen in the last common ancestor of gnathostomes. These results provide a framework for continuing research on <i>nos</i> genes’ roles, highlighting subfunctionalization and reciprocal loss of function that occurred in different lineages during vertebrate genome duplications.
DOI: 10.6084/m9.figshare.20449333
title: Annona_procb_ESM_File S1_tree_alignment.fas from Evolution of the nitric oxide synthase family in vertebrates and novel insights in gill development

description: Nitric oxide (NO) is an ancestral key signalling molecule essential for life and has enormous versatility in biological systems, including cardiovascular homeostasis, neurotransmission and immunity. Although our knowledge of NO synthases (Nos), the enzymes that synthesize NO <i>in vivo</i>, is substantial, the origin of a large and diversified repertoire of <i>nos</i> gene orthologues in fishes with respect to tetrapods remains a puzzle. The recent identification of <i>nos3</i> in the ray-finned fish spotted gar, which was considered lost in this lineage, changed this perspective. This finding prompted us to explore <i>nos</i> gene evolution, surveying vertebrate species representing key evolutionary nodes. This study provides noteworthy findings: first, <i>nos2</i> experienced several lineage-specific gene duplications and losses. Second, <i>nos3</i> was found to be lost independently in two different teleost lineages, Elopomorpha and Clupeocephala. Third, the expression of at least one <i>nos</i> paralogue in the gills of developing shark, bichir, sturgeon, and gar, but not in lamprey, suggests that <i>nos</i> expression in this organ may have arisen in the last common ancestor of gnathostomes. These results provide a framework for continuing research on <i>nos</i> genes’ roles, highlighting subfunctionalization and reciprocal loss of function that occurred in different lineages during vertebrate genome duplications.
DOI: 10.6084/m9.figshare.20449333.v1
title: Annona_procb_ESM_File S1_tree_alignment.fas from Evolution of the nitric oxide synthase family in vertebrates and novel insights in gill development

description: Nitric oxide (NO) is an ancestral key signalling molecule essential for life and has enormous versatility in biological systems, including cardiovascular homeostasis, neurotransmission and immunity. Although our knowledge of NO synthases (Nos), the enzymes that synthesize NO <i>in vivo</i>, is substantial, the origin of a large and diversified repertoire of <i>nos</i> gene orthologues in fishes with respect to tetrapods remains a puzzle. The recent identification of <i>nos3</i> in the ray-finned fish spotted gar, which was considered lost in this lineage, changed this perspective. This finding prompted us to explore <i>nos</i> gene evolution, surveying vertebrate species representing key evolutionary nodes. This study provides noteworthy findings: first, <i>nos2</i> experienced several lineage-specific gene duplications and losses. Second, <i>nos3</i> was found to be lost independently in two different teleost lineages, Elopomorpha and Clupeocephala. Third, the expression of at least one <i>nos</i> paralogue in the gills of developing shark, bichir, sturgeon, and gar, but not in lamprey, suggests that <i>nos</i> expression in this organ may have arisen in the last common ancestor of gnathostomes. These results provide a framework for continuing research on <i>nos</i> genes’ roles, highlighting subfunctionalization and reciprocal loss of function that occurred in different lineages during vertebrate genome duplications.
DOI: 10.34740/kaggle/dsv/4044411
title: COVID Vaccination in World (updated daily)
DOI: 10.5517/ccdc.csd.cc27gzxm
title: CCDC 2069991: Experimental Crystal Structure Determination

description: Related Article: Kehan Zhou, Dongjie Wang, Guodong Ju, Zefeng Deng, Pengcheng Huang, Zhibin Huang, Bao Li, Yingsheng Zhao|2022|Org.Lett.|24|5568|doi:10.1021/acs.orglett.2c02104
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.cc28t2z5
title: CCDC 2109487: Experimental Crystal Structure Determination

description: Related Article: Wenzhong Li, Ran Shi, Xuesi Zhang, Sen Chen, Yu Wang, Mengqi Wang, Bin Yang, Jiazhu Li, Xin-Ming Xu|2022|J.Org.Chem.|87|9769|doi:10.1021/acs.joc.2c00829
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.cc28x4y9
title: CCDC 2112431: Experimental Crystal Structure Determination

description: Related Article: Na Gao, Xiaoyu Liu, Xu Yuan, Bingwei Hu, Peiyun Jiang, Jun Lin, Yi Jin|2022|J.Org.Chem.|87|10298|doi:10.1021/acs.joc.2c01330
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.cc28x4zb
title: CCDC 2112432: Experimental Crystal Structure Determination

description: Related Article: Na Gao, Xiaoyu Liu, Xu Yuan, Bingwei Hu, Peiyun Jiang, Jun Lin, Yi Jin|2022|J.Org.Chem.|87|10298|doi:10.1021/acs.joc.2c01330
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.cc29lpwh
title: CCDC 2133137: Experimental Crystal Structure Determination

description: Related Article: Ethan Chi Ho Wen, Peter H. Jacobse, Jingwei Jiang, Ziyi Wang, Ryan D. McCurdy, Steven G. Louie, Michael F. Crommie, Felix R. Fischer|2022|J.Am.Chem.Soc.|144|13696|doi:10.1021/jacs.2c04432
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.cc2bl3z1
title: CCDC 2162373: Experimental Crystal Structure Determination

description: Related Article: Akanksha M. Pandey, Shankhajit Mondal, Boopathy Gnanaprakasam|2022|J.Org.Chem.|87|9926|doi:10.1021/acs.joc.2c00941
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.cc2bl403
title: CCDC 2162374: Experimental Crystal Structure Determination

description: Related Article: Akanksha M. Pandey, Shankhajit Mondal, Boopathy Gnanaprakasam|2022|J.Org.Chem.|87|9926|doi:10.1021/acs.joc.2c00941
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.cc2brlc2
title: CCDC 2167624: Experimental Crystal Structure Determination

description: Related Article: Tao Jin, Lukas Kunze, Stefanie Breimaier, Michael Bolte, Hans-Wolfram Lerner, Frieder Jäkle, Rainer F. Winter, Markus Braun, Jan-Michael Mewes, Matthias Wagner|2022|J.Am.Chem.Soc.|144|13704|doi:10.1021/jacs.2c04516
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.cc2brld3
title: CCDC 2167625: Experimental Crystal Structure Determination

description: Related Article: Tao Jin, Lukas Kunze, Stefanie Breimaier, Michael Bolte, Hans-Wolfram Lerner, Frieder Jäkle, Rainer F. Winter, Markus Braun, Jan-Michael Mewes, Matthias Wagner|2022|J.Am.Chem.Soc.|144|13704|doi:10.1021/jacs.2c04516
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.cc2brlf4
title: CCDC 2167626: Experimental Crystal Structure Determination

description: Related Article: Tao Jin, Lukas Kunze, Stefanie Breimaier, Michael Bolte, Hans-Wolfram Lerner, Frieder Jäkle, Rainer F. Winter, Markus Braun, Jan-Michael Mewes, Matthias Wagner|2022|J.Am.Chem.Soc.|144|13704|doi:10.1021/jacs.2c04516
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.cc2bsf6s
title: CCDC 2168425: Experimental Crystal Structure Determination

description: Related Article: Sujitra Tunsrichon, Kittipong Chainok, Vinich Promarak, Phattananawee Nalaoh, Sujittra Youngme, Jaursup Boonmak|2022|Inorg.Chem.|61|11734|doi:10.1021/acs.inorgchem.2c01421
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.cc2c3tlx
title: CCDC 2178419: Experimental Crystal Structure Determination

description: Related Article: Yan Li, Deguang Liu, Lei Wan, Jun-Yang Zhang, Xi Lu, Yao Fu|2022|J.Am.Chem.Soc.|144|13961|doi:10.1021/jacs.2c06279
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: 10.6084/m9.figshare.20449344.v1
title: S3 Table. Bivariate analysis of socio-demographic and economic factors among type 2 diabetic patients at Public hospitals in Hadiya Zone, Southern Ethiopia, 2019.

description: Bivariate analysis of socio-demographic and economic factors among type 2 diabetic patients at Public hospitals in Hadiya Zone, Southern Ethiopia, 2019.
DOI: 10.6084/m9.figshare.20449344
title: S3 Table. Bivariate analysis of socio-demographic and economic factors among type 2 diabetic patients at Public hospitals in Hadiya Zone, Southern Ethiopia, 2019.

description: Bivariate analysis of socio-demographic and economic factors among type 2 diabetic patients at Public hospitals in Hadiya Zone, Southern Ethiopia, 2019.
DOI: 10.25345/c5ks8r
title: MassIVE MSV000083869 - Molecular characterization of the brain peri-infarct region after post-stroke MANF administration
title: Shotgun proteomics analysis of brain peri-infarct region from rats subjected to ischemic stroke and treated with AAV-MANF or a control AAV-eGFP, compared to each other and to rats subjected to a sham operation.
DOI: 10.5281/zenodo.3234370
title: Supplementary data: Computational analysis of mechanical stress in colonic diverticulosis

description: The data set contains code, source data, and derivatives data for the results presented in our research paper titled "Computational analysis of mechanical stress in colonic diverticulosis". The "code" contains Abaqus (SIMULIA, Providence, RI) files for the simulations presented in the paper (tested with Abaqus version 6.13) and jupyter notebooks developed to analyze simulation results. The "sourcedata" folder contains Excel files with parameters used for the simulations as well as data directly extracted from the simulation results. The "derivatives" folder contains secondary data calculated based on the files from "sourcedata". The README document included in the dataset contains a more detailed description of the files and folders.
DOI: 10.5281/zenodo.3234371
title: Supplementary data: Computational analysis of mechanical stress in colonic diverticulosis

description: The data set contains code, source data, and derivatives data for the results presented in our research paper titled "Computational analysis of mechanical stress in colonic diverticulosis".

The "code" contains Abaqus (SIMULIA, Providence, RI)  files for the simulations presented in the paper (tested with Abaqus version 6.13) and jupyter notebooks developed to analyze simulation results.

The "sourcedata" folder contains Excel files with parameters used for the simulations as well as data directly extracted from the simulation results.

The "derivatives" folder contains secondary data calculated based on the files from "sourcedata".
DOI: 10.17909/t9-4xvp-7s45
title: Photometric Catalogs from Hubble Frontier Fields ("HFFCATALOGS")

description: HFFCATALOGS presents multiwavelength photometric catalogs derived from HST, VLT, and Spitzer imaging, and catalogs of derived properties, for two Hubble Frontier Fields massive galaxy clusters, Abell 370 and RXC J2248.7−4431 (Bradac et al. 2019). These catalogs were developed by the ASTRODEEP team and used the ASTRODEEP pipeline. Photometric catalog columns include fluxes, magnitudes, and errors for HST WFC3 F160W, F140W, F125W, and F105W; ACS F814W, F606W, and F435W; Spitzer IRAC Channels 1 and 2, and VLT HAWK-I KS; as well as spectroscopic data compiled by Shipley et al. (2018). Property catalog columns include magnifications, photometric redshifts, errors, and goodness of fit, as well as derived stellar masses and star formation rates.
DOI: 10.18112/openneuro.ds001019.v1.0.0
title: navLearn
DOI: 10.17632/zcggnksyv3.2
title: Data for: Toward a numerical-simulation-based liquefaction hazard assessment for urban regions using high-performance computing

description: These two data files contain the simulation results described in the corresponding paper. See the discussion section for the warnings and restrictions about making use of the data.
DOI: 10.5281/zenodo.3234157
title: Analysis of Huntingtin BioID Datasets 2019/04/09

description: <strong>Project: </strong>Investigation of putative HTT interacting proteins

<strong>Experiment: </strong>Analysis of HTT BioID datasets 

<strong>Date completed:­ </strong>2019/04/09

<strong>Rationale: </strong>BioID technology employs a promiscuous biotin ligase (BirA) fused to the terminus of the target protein, huntingtin, allowing proximal proteins to be biotinylated and then subsequently identified through mass spectrometry experiments. This technique has not been applied to assess huntingtin interactors to date in the published literature, so will provide a novel methodology to characterize the huntingtin interactome. As huntingtin is a large protein molecule and the precise location of the N and C-termini remain unresolved due to their flexible nature, both N and C terminally BirA-tagged constructs for full-length huntingtin will be generated for overexpression as well as a truncated construct spanning amino acids 80-3100, the region of the protein resolved in the recent cryo-electron microscopy structure which omits the flexible termini. Huntingtin fusion proteins will be overexpressed in cells subjected to different ROS stresses as well as control conditions. Resultant cell lysates will be analysed through collaboration with Prof. Anne-Claude Gingras (Lunenfeld Tanenbaum Research Institute, University of Toronto). From this work, we hope to obtain a list of putative huntingtin interactors which will be compared to previously published findings and assessed for stable complex formation with huntingtin
description: Dr. Harding is the recipient of the Huntington's Disease Society of America Berman Topper Career Development Fellowship which funds and supports this research, in addition to generous funding from the CHDI Foundation and the Huntington Society of Canada. The SGC is a registered charity (number 1097737) that receives funds from AbbVie, Bayer Pharma AG, Boehringer Ingelheim, Canada Foundation for Innovation, Eshelman Institute for Innovation, Genome Canada through Ontario Genomics Institute [OGI-055], Innovative Medicines Initiative (EU/EFPIA) [ULTRA-DD grant no. 115766], Janssen, Merck KGaA, Darmstadt, Germany, MSD, Novartis Pharma AG, Ontario Ministry of Research, Innovation and Science (MRIS), Pfizer, São Paulo Research Foundation-FAPESP, Takeda, and Wellcome.