cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.15223014
title: Supplement: Long-read sequencing reveals rapid evolution of immunity- and cancer-related genes in bats

description: This dataset includes supplementary tables and data for the manuscript "Long-read sequencing reveals rapid evolution of immunity- and cancer-related genes in bats". Captions for supplementary tables are included in the file and captions for the supplementary data are listed below.<br><b>Supplementary Data</b><br><b>Data S1.</b> Positive selection analysis of orthogroups in bats (order Chiroptera). All orthogroup clusters generated by Orthofinder are shown, including multicopy orthogroups and lineage-specific orthogroups, but only single-copy orthogroups were analysed for positive selection. Gene annotations are based on biomaRt data for the human protein, or, when not available, the protein of mouse or another mammal. Published p-values for the same genes were extracted based on publicly available data from eight studies. Branch-site likelihood ratio test p-values are shown for aBSREL and PAML M2a tests for the bat lineage as well as for Artibeus jamaicensis (Ajamaicensis) and Pteronotus mesoamericanus (Pmesoericanus). Uncorrected p-values are shown as well as p-values adjusted with FDR for multiple tested branches and for multiple tested branches and genes.<br><b>Data S2.</b> Gene-associated microindels detected in five or more bats from a Cactus multiple alignment of six bats with human, mouse and pig. The bats included in the alignment were D. rotundus, A. jamaicensis, P. mesoamericanus, P. discolor, M. myotis and R. ferrumequinum. Only indels occurring within coding sequences, within 1 kilobase of coding sequence or within the core promotor (based on human core promoters downloaded from https://epd.epfl.ch//index.php) were included. Coordinates are based on the human hg38 assembly and coordinates of aligned sequence from A. jamaicensis and P. mesoamericanus are also provided.<br><b>Data S3. </b>Coding sequences and RAxML phylogenies for the type I interferon, interferon-induced transmembrane and PRDM9 orthogroups.<br><b>Data S4.</b> Unfiltered PRANK alignments of all single-copy orthologs where positive selection was detected on the branch leading to the bat most recent common ancestor.<br>
DOI: 10.6084/m9.figshare.15223014.v2
title: Supplement: Long-read sequencing reveals rapid evolution of immunity- and cancer-related genes in bats

description: This dataset includes supplementary tables and data for the manuscript "Long-read sequencing reveals rapid evolution of immunity- and cancer-related genes in bats". Captions for supplementary tables are included in the file and captions for the supplementary data are listed below.<br><b>Supplementary Data</b><br><b>Data S1.</b> Positive selection analysis of orthogroups in bats (order Chiroptera). All orthogroup clusters generated by Orthofinder are shown, including multicopy orthogroups and lineage-specific orthogroups, but only single-copy orthogroups were analysed for positive selection. Gene annotations are based on biomaRt data for the human protein, or, when not available, the protein of mouse or another mammal. Published p-values for the same genes were extracted based on publicly available data from eight studies. Branch-site likelihood ratio test p-values are shown for aBSREL and PAML M2a tests for the bat lineage as well as for Artibeus jamaicensis (Ajamaicensis) and Pteronotus mesoamericanus (Pmesoericanus). Uncorrected p-values are shown as well as p-values adjusted with FDR for multiple tested branches and for multiple tested branches and genes.<br><b>Data S2.</b> Gene-associated microindels detected in five or more bats from a Cactus multiple alignment of six bats with human, mouse and pig. The bats included in the alignment were D. rotundus, A. jamaicensis, P. mesoamericanus, P. discolor, M. myotis and R. ferrumequinum. Only indels occurring within coding sequences, within 1 kilobase of coding sequence or within the core promotor (based on human core promoters downloaded from https://epd.epfl.ch//index.php) were included. Coordinates are based on the human hg38 assembly and coordinates of aligned sequence from A. jamaicensis and P. mesoamericanus are also provided.<br><b>Data S3. </b>Coding sequences and RAxML phylogenies for the type I interferon, interferon-induced transmembrane and PRDM9 orthogroups.<br><b>Data S4.</b> Unfiltered PRANK alignments of all single-copy orthologs where positive selection was detected on the branch leading to the bat most recent common ancestor.<br>
DOI: 10.6084/m9.figshare.21676952
title: Impact of HSUVs elicitation and T-Y models on treatment recommendation

description: Adjusting elicited health utilities after the fact can adversely affect shared decision making.
DOI: 10.6084/m9.figshare.21676952.v1
title: Impact of HSUVs elicitation and T-Y models on treatment recommendation

description: Adjusting elicited health utilities after the fact can adversely affect shared decision making.
DOI: 10.25921/97qd-z260
title: ES60 Water Column Sonar Data Collected During AI14AP
DOI: 10.6084/m9.figshare.21651911
title: Elicited and adjusted HSUVs using T-Y models

description: Adjusting elicited health utilities after the fact can adversely affect shared decision making.
DOI: 10.6084/m9.figshare.21651911.v1
title: Elicited and adjusted HSUVs using T-Y models

description: Adjusting elicited health utilities after the fact can adversely affect shared decision making.
DOI: 10.25430/researchdata.cab.unipd.it.00000784
title: Diagrammi stratigrafici Scavo Cossar (Mura, domus Tito Macro)

description: La documentazione rappresenta la descrizione delle sequenze di scavo secondo la forma del diagramma di Harris. Lo scavo è stato condotto tra il 2009 e il 2015 presso l'area dei fondi Cossar di Aquileia.
DOI: 10.5281/zenodo.7401787
title: Clipped pentaloop files used for identification and characterization of RNA pentaloop sequence families

description: This dataset includes the pentaloop structures that were clipped from PDB structures and used in the structural analysis described in Identification and Characterization of RNA Pentaloop Sequence Families
DOI: 10.5281/zenodo.7401786
title: Clipped pentaloop files used for identification and characterization of RNA pentaloop sequence families

description: This dataset includes the pentaloop structures that were clipped from PDB structures and used in the structural analysis described in Identification and Characterization of RNA Pentaloop Sequence Families
DOI: 10.26093/cds/vizier.19120049
title: Clumps identified in z&lt;0.06 SDSS Stripe 82 sample

description: VizieR online Data Catalogue associated with article published in journal Astronomical Journal (AAS) with title 'Investigating clumpy galaxies in the Sloan Digital Sky Survey Stripe 82 using the Galaxy Zoo.' (bibcode: 2021ApJ...912...49M)
DOI: 10.26093/cds/vizier.19120081
title: Kepler and XMM LCs of 3 KIC stars with flares

description: VizieR online Data Catalogue associated with article published in journal Astronomical Journal (AAS) with title 'Stellar superflares observed simultaneously with Kepler and XMM-Newton.' (bibcode: 2021ApJ...912...81K)
DOI: 10.26093/cds/vizier.22620012
title: Kepler P&lt;2d close binaries

description: VizieR online Data Catalogue associated with article published in journal Astronomical Journal (AAS) with title 'A Bayesian analysis of physical parameters for 783 Kepler close binaries: extreme-mass-ratio systems and a new mass ratio versus period lower limit.' (bibcode: 2022ApJS..262...12K)
DOI: 10.25934/pr00007577.0
title: Available IPD datapackage for study 'A Multicenter, Long-Term Extension Study of 104 Weeks, Including a Double-Blind, Placebo-Controlled 40-Week Randomized Withdrawal-Retreatment Period, to Evaluate the Maintenance of Treatment Effect of Ixekizumab (LY2439821) in Patients With Axial Spondyloarthritis'

description: The purpose of this study is to evaluate, in participants having achieved a state of sustained remission, if the ixekizumab treatment groups are superior to the placebo group in maintaining response during the randomized withdrawal-retreatment period in participants with axial spondyloarthritis.
DOI: 10.5517/ccdc.csd.cc2c9js0
title: CCDC 2183912: Experimental Crystal Structure Determination

description: Related Article: Yu-Li Wu, Guo-Liang Hou, Hai-Xia Cui, Lei Chen, Yu-Long An, Hui-Di Zhou, Jian-Min Chen|2022|CSD Communication|||
description: Related Article: Yu-Li Wu, Guo-Liang Hou, Hai-Xia Cui, Lei Chen, Hui-Di Zhou, Jian-Min Chen|2022|New J.Chem.|46|22509|doi:10.1039/D2NJ04869H
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.cc2c9jw3
title: CCDC 2183915: Experimental Crystal Structure Determination

description: Related Article: Yu-Li Wu, Guo-Liang Hou, Hai-Xia Cui, Lei Chen, Yu-Long An, Hui-Di Zhou, Jian-Min Chen|2022|CSD Communication|||
description: Related Article: Yu-Li Wu, Guo-Liang Hou, Hai-Xia Cui, Lei Chen, Hui-Di Zhou, Jian-Min Chen|2022|New J.Chem.|46|22509|doi:10.1039/D2NJ04869H
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.cc2df8lq
title: CCDC 2217293: Experimental Crystal Structure Determination

description: Related Article: Farhana Hasan, Isiah M. Warner, Frank R. Fronczek|2022|CSD Communication|||
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.cc2dfjm0
title: CCDC 2217542: Experimental Crystal Structure Determination

description: Related Article: W. Clegg, J.D. Kennedy, T.R. Spalding, Faridoon|2022|CSD Communication|||
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.cc2dfjn1
title: CCDC 2217543: Experimental Crystal Structure Determination

description: Related Article: W. Clegg, J.D. Kennedy, S.L. Shea|2022|CSD Communication|||
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.cc2dfjr4
title: CCDC 2217546: Experimental Crystal Structure Determination

description: Related Article: W. Clegg, J.D. Kennedy, P.K. Dosangh, J. Bould, T. Jelinek, N.P. Rath|2022|CSD Communication|||
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.cc2dfjs5
title: CCDC 2217547: Experimental Crystal Structure Determination

description: Related Article: W. Clegg, J.D. Kennedy, M.J. Carr|2022|CSD Communication|||
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.cc2dgsnb
title: CCDC 2218752: Experimental Crystal Structure Determination

description: Related Article: Constantin G. Daniliuc, Ulrich Blaschke, Roland Fröhlich, Gerhard Erker|2022|CSD Communication|||
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.cc2dgv3v
title: CCDC 2218797: Experimental Crystal Structure Determination

description: Related Article: Constantin G. Daniliuc, Christian Strauch, Roland Fröhlich, Gerhard Erker|2022|CSD Communication|||
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.cc2dgyys
title: CCDC 2218916: Experimental Crystal Structure Determination

description: Related Article: James E. Hines III, Zechariah Myles, Garrick Breaux, Frank R. Fronczek, Rao M. Uppu|2022|CSD Communication|||
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: 10.5281/zenodo.5794251
title: Simulation Input Data for "Molecular simulation of lignin-related aromatic compound permeation through Gram-negative bacterial outer membranes"

description: This is the reduced data behind an upcoming manuscript investigating permeability across the outer membranes of Gram-negative bacteria. The data is taken directly from the directory structure that contains both the simulation and analysis, with excluded trajectory files and intermediate products to fit within the zenodo upload limit. The tar command used to generate this tarball was: <pre><code class="language-bash">tar --exclude="*BAK" --exclude="*dcd" --exclude="*xsc" --exclude="*vel" --exclude="*coor" --exclude="*csv" --exclude="*old" --exclude="*log" --exclude="*state" --exclude="*watpos/*npz" --exclude="*new*png" --exclude="*frame*png" --exclude="*ppm" --exclude="*mp4" --exclude="*bayesdata*npy" --exclude="*run.npy" -zcvf OM.tgz OuterMembrane</code></pre> Within the OuterMembrane directory, there are 3 primary subdirectories. <strong>Build </strong>contains the scripts and files to build the simulation systems, including the CHARMM-GUI output <strong>Equilibrium</strong> contains the equilibrium simulation inputs and the analysis scripts (subdirectory <strong>Analysis</strong>) <strong>REUS2</strong>, which has the replica exchange inputs and essential output. It also contains an <strong>Analysis</strong> subdirectory that carries out the analysis within the text.
description: This work was authored in part by Alliance for Sustainable Energy, LLC, the manager and operator of the National Renewable Energy Laboratory for the U.S. Department of Energy (DOE) under Contract No. DE-AC36-08GO28308. JVV, MFC, and GTB acknowledge funding from the U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Bioenergy Technologies Office. GTB also acknowledges funding from the Center for Bioenergy Innovation, which is a U.S. DOE Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725. This project made use of the high performance computing resources provided by the NREL Computational Sciences Center, which is supported by the DOE Office of EERE under Contract No. DE-AC36-08GO28308.
DOI: 10.5281/zenodo.5794252
title: Simulation Input Data for "Molecular simulation of lignin-related aromatic compound permeation through Gram-negative bacterial outer membranes"

description: This is the reduced data behind an upcoming manuscript investigating permeability across the outer membranes of Gram-negative bacteria. The data is taken directly from the directory structure that contains both the simulation and analysis, with excluded trajectory files and intermediate products to fit within the zenodo upload limit. The tar command used to generate this tarball was: <pre><code class="language-bash">tar --exclude="*BAK" --exclude="*dcd" --exclude="*xsc" --exclude="*vel" --exclude="*coor" --exclude="*csv" --exclude="*old" --exclude="*log" --exclude="*state" --exclude="*watpos/*npz" --exclude="*new*png" --exclude="*frame*png" --exclude="*ppm" --exclude="*mp4" --exclude="*bayesdata*npy" --exclude="*run.npy" -zcvf OM.tgz OuterMembrane</code></pre> Within the OuterMembrane directory, there are 3 primary subdirectories. <strong>Build </strong>contains the scripts and files to build the simulation systems, including the CHARMM-GUI output <strong>Equilibrium</strong> contains the equilibrium simulation inputs and the analysis scripts (subdirectory <strong>Analysis</strong>) <strong>REUS2</strong>, which has the replica exchange inputs and essential output. It also contains an <strong>Analysis</strong> subdirectory that carries out the analysis within the text.
description: This work was authored in part by Alliance for Sustainable Energy, LLC, the manager and operator of the National Renewable Energy Laboratory for the U.S. Department of Energy (DOE) under Contract No. DE-AC36-08GO28308. JVV, MFC, and GTB acknowledge funding from the U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Bioenergy Technologies Office. GTB also acknowledges funding from the Center for Bioenergy Innovation, which is a U.S. DOE Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725. This project made use of the high performance computing resources provided by the NREL Computational Sciences Center, which is supported by the DOE Office of EERE under Contract No. DE-AC36-08GO28308.
DOI: 10.25921/6re2-mx67
title: ES60 Water Column Sonar Data Collected During EBS15AK
DOI: 10.6084/m9.figshare.21677165
title: probe_seed.hdf5

description: High-resolution Siemens star data using a 13.5 nm HHG source. The detector pixel size corresponds to 13.5 um and the detector-to-sample distance was roughly 30.5 mm.
DOI: 10.6084/m9.figshare.21677165.v1
title: probe_seed.hdf5

description: High-resolution Siemens star data using a 13.5 nm HHG source. The detector pixel size corresponds to 13.5 um and the detector-to-sample distance was roughly 30.5 mm.
DOI: 10.6084/m9.figshare.21579125
title: Maintaining social and emotional wellbeing among older adults during periods of increased social isolation: lessons from the COVID-19 pandemic

description: Older adults are vulnerable to isolation and poor emotional wellbeing during COVID-19, however, their access to appropriate supports is unknown. The aim of this study was to explore older adults’ experiences accessing social and emotional support during the COVID-19 pandemic in Australia. Ten older adults from Western Australia (Australia) aged 68 to 78 years participated in individual semi-structured interviews between December 2020 and January 2021. Responses were investigated using thematic analysis. Three key themes emerged: adaptability and self-sufficiency; informal support-seeking; and digital and online technologies. Older adults were adaptable to COVID-19 restrictions; however, some were anxious about reconnecting with their social networks once restrictions had eased. Older adults relied on their informal support networks to maintain their social and emotional wellbeing during lockdown. Digital platforms (e.g., Zoom, social media) enabled older adults to stay connected with others, yet some older people were unable or reluctant to use technology, leaving them vulnerable to social isolation. Older adults are resilient to the challenges of COVID-19. Informal supports and digital technologies are important to maintaining social and emotional wellbeing during lockdown. Local governments and community groups may benefit from increased funding to deliver services that promote social connectedness during times of crisis. <b>What is already known about this topic:</b> (1) Older adults are vulnerable to social isolation and poor mental health during COVID-19. (2) Older adults are less likely to seek and receive help for their emotional and social health than younger age groups. (3) Barriers to accessing appropriate supports include physical health problems, stigma, negative attitudes towards help-seeking and system-level factors. <b>What this topic adds:</b> (1) Older adults were able to adapt well to COVID-19 restrictions and relied on informal supports to maintain their wellbeing. (2) Older adults with limited social networks and poor access to and/or knowledge of digital technologies are at the greatest risk of social and emotional declines. (3) Telephone “warm” lines, volunteering opportunities, and programs to improve digital literacy may help to protect older adults’ social and emotional wellbeing during times of crises.