cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26180/21715979
title: Aspirin in Reducing Events in the Elderly eXTension (ASPREE-XT)

description: ASPREE (ASPirin in Reducing Events in the Elderly) was a joint US/Australian randomized clinical trial aiming to determine whether low-dose aspirin increases healthy life-span, defined as survival free of dementia and disability. ASPREE began in 2010 and completed recruitment in 2014. It was a randomized, double-blind, placebo controlled, primary prevention trial of daily 100 mg of aspirin in older people free of cardiovascular disease, dementia and physical disability in the United States (US) and Australia with a period of follow-up averaging 4.5 years. ASPREE's primary outcome was duration of survival free of dementia and persistent physical disability and had secondary outcomes encompassing the major health issues related to aging. The trial involving 19,114 persons aged 70 and above (65 years and above for US minorities) is distinctive for its large size, methodological rigor and high participant retention rate in both countries. ASPREE-XT is a post-treatment, longitudinal observational follow-up study of ASPREE participants that began in January 2018. This enables the monitoring of possible legacy effects of aspirin treatment, primarily on cancer incidence, metastases and mortality. In addition, the large well-characterized cohort with extended follow-up and a range of health outcomes provides a unique opportunity to study health and resilience in older individuals.
DOI: 10.6084/m9.figshare.22735724
title: Dataset Questionnaire.xlsx

description: This project contains the following underlying data : Questionnaire based on collection of socio-economic, knowledge, attitude and presence of influencing factors, following Singh<sup>1</sup> and modified based on recent literature on proper medical sharps disposal recommended by the Centers for Disease Control and Prevention (CDC), American Diabetes Association (ADA) and National Health Service (NHS) United Kingdom (UK). Twelve questions were translated into Bahasa Indonesia and conducted with 30 subjects to validate and assess the reliability of the questions. For each question, dichotomous scoring was applied, where one mark was awarded for a correct response and zero for an incorrect response. A score of zero indicated the poorest practice, while a score of 12 demonstrated the best practice.
DOI: 10.6084/m9.figshare.22736141.v1
title: Nano17 F/T sensor data of the Hemidactylus frenatus geckos

description: This is the raw force data for the hfren data set we used for our publication.
DOI: 10.6084/m9.figshare.22736141
title: Nano17 F/T sensor data of the Hemidactylus frenatus geckos

description: This is the raw force data for the hfren data set we used for our publication.
DOI: 10.6084/m9.figshare.21669860.v1
title: Supplementary information and data for "A quantitative evaluation of the impacts of human land modification on raptors globally"

description: Raptors are threatened by anthropogenic land modifications, but targeted assessment of these impacts is lacking. We provide the first global quantitative evaluation of the impacts of human-modified land on raptors. We found that 66.4% of raptors were impacted negatively by at least one kind of human-modified land, while 44.6% benefitted from at least one human-modified landscape. Settlements had the largest negative effect (83.2%) on raptor occupancy, followed by pasture (58.7%) and cropland (48.8%). The impacts of anthropogenic land modification proved species-specific and spatially heterogeneous, and largely dependent on the species’ trophic niche. Large raptors are more vulnerable to land modification than smaller species; raptors that prefer dense habitats and species with smaller ranges are more likely to be negatively impacted by human-modified land. Our study provides much-needed information for raptor conservation highlighting the need to increase habitat heterogeneity in human-dominated landscapes.
DOI: 10.6084/m9.figshare.22736030
title: Dataset: The Impact of Altitude Training on NCAA Division I Female Swimmers’ Performance

description: This dataset contains the data used in the paper: "The Impact of Altitude Training on NCAA Division I Female Swimmers’ Performance" being submitted to the International Journal of Performance Analysis in Sport.
DOI: 10.5281/zenodo.7888122
title: XP Project from DGX_part1-30

description: back up 22Feb2022 from DGX machine
DOI: 10.5281/zenodo.7888121
title: XP Project from DGX_part1-30

description: back up 22Feb2022 from DGX machine
DOI: 10.6084/m9.figshare.22735811
title: The oxygen concentration data in Forest Canopy of 2020 in Beijing Gongqing Forestry Farm

description: we provide the data of oxygen concentration in the canopy of a 160-hectare forest in Beijing, and give a convenient equation for calculating the carbon sequestration and carbon sink according to the changes of 15 days oxygen concentration.
DOI: 10.6084/m9.figshare.22735811.v1
title: The oxygen concentration data in Forest Canopy of 2020 in Beijing Gongqing Forestry Farm

description: we provide the data of oxygen concentration in the canopy of a 160-hectare forest in Beijing, and give a convenient equation for calculating the carbon sequestration and carbon sink according to the changes of 15 days oxygen concentration.
DOI: 10.5517/ccdc.csd.cc207d5v
title: CCDC 1854146: Experimental Crystal Structure Determination

description: Related Article: Jin Hyoung Jo, Hyun-Chul Kim, Seong Huh, Youngmee Kim, Do Nam Lee|2019|Dalton Trans.|48|8084|doi:10.1039/C9DT00791A
description: Related Article: Do Nam Lee, Yeong Rim Kim, Youngmee Kim, Bong Joo Park, Su Jung Lee, Sung-Jin Kim, Jae Ho Shin|2022|ACS Appl. Bio Mater.|5|4301|doi:10.1021/acsabm.2c00501
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.cc25jt2m
title: CCDC 2012150: Experimental Crystal Structure Determination

description: Related Article: Do Nam Lee, Yeong Rim Kim, Youngmee Kim, Bong Joo Park, Su Jung Lee, Sung-Jin Kim, Jae Ho Shin|2022|ACS Appl. Bio Mater.|5|4301|doi:10.1021/acsabm.2c00501
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: 10.15151/esrf-es-1059317768
title: Joint-Structural Biology Group (JSBG) BAG proposal for ID29 beamline

description: The aim of the JSBG BAG proposal for ID29 beamline is to develop new methods for time-resolved serial crystallography experiments at 4th generation source and to study time dependent structural conformation of biological macromolecules that are studies at the ESRF-EMBL-GR Joint Structural Biology Group. Method developments include the study of radiation damage at high flux densities and with partially polychromatic beam (1% and 0.3%), the implementation and development of various sample delivery methods - high viscosity, GDVN, mixing injectors, microfluidics and fixed targets and the integration of software for large amount of SSX data reduction, data-acquisition software for JungFrau 4M detector, and new GPU-based algorithms for SSX data analysis and various data collection strategies for SSX experiments. Biological systems include the study of photoactivable proteins, dynamics/inhibitor mechanisms of non-photoactivable proteins by using photo-cage compounds and enzymatic systems.
DOI: 10.5281/zenodo.7889143
title: XP Project from DGX_part31-34

description: XP Project from DGX back up from 22Feb2022_part31-34
DOI: 10.5281/zenodo.7889142
title: XP Project from DGX_part31-34

description: XP Project from DGX back up from 22Feb2022_part31-34
DOI: 10.6084/m9.figshare.21696728
title: Optimisation method for automatic selection of rate constants of global reaction mechanisms

description: Optimisation approach to automate selection of global reaction mechanisms rate constants is proposed and studied. The objective of optimisation is to find reaction rate constants minimising deviation of some flame characteristics (e.g. laminar burning velocity, ignition delay time, etc.) calculated by global mechanism from their reference values known from experiments or computed by detailed mechanisms. Examples of one, two and four step mechanisms optimisation with respect to laminar burning velocity and concentration distributions in counterflow diffusion flame are given. Computer codes implementing optimisation algorithm for these examples are also afforded and can be modified and used for reaction constants selection in various applications. Uniqueness of singlecriteria and multicriteria optimisation solutions is studied numerically by computations with different initial guesses and by direct evaluation of the objective functions. Particularly, it is found that for considered global mechanisms the minimum value of objective function is reached in some subdomain of the parametric space. This means that any values of rate parameters from this subdomain results in almost the same deviations of chosen flame characteristic from its reference value.
DOI: 10.6084/m9.figshare.21696728.v1
title: Optimisation method for automatic selection of rate constants of global reaction mechanisms

description: Optimisation approach to automate selection of global reaction mechanisms rate constants is proposed and studied. The objective of optimisation is to find reaction rate constants minimising deviation of some flame characteristics (e.g. laminar burning velocity, ignition delay time, etc.) calculated by global mechanism from their reference values known from experiments or computed by detailed mechanisms. Examples of one, two and four step mechanisms optimisation with respect to laminar burning velocity and concentration distributions in counterflow diffusion flame are given. Computer codes implementing optimisation algorithm for these examples are also afforded and can be modified and used for reaction constants selection in various applications. Uniqueness of singlecriteria and multicriteria optimisation solutions is studied numerically by computations with different initial guesses and by direct evaluation of the objective functions. Particularly, it is found that for considered global mechanisms the minimum value of objective function is reached in some subdomain of the parametric space. This means that any values of rate parameters from this subdomain results in almost the same deviations of chosen flame characteristic from its reference value.
DOI: 10.6084/m9.figshare.21901545.v2
title: dataset1_p53

description: dataset1_p53
DOI: 10.5281/zenodo.7428686
title: Images for 8BVO Titin I110-I111 FnIII tandem from the MIR region (I/A5-I/A6)

description: Images for 8BVO Titin I110-I111 FnIII tandem from the MIR region (I/A5-I/A6)
DOI: 10.5281/zenodo.7428685
title: Images for 8BVO Titin I110-I111 FnIII tandem from the MIR region (I/A5-I/A6)

description: Images for 8BVO Titin I110-I111 FnIII tandem from the MIR region (I/A5-I/A6)
DOI: 10.5281/zenodo.7413948
title: Example Dataset from BioMAX, MAX IV Laboratory

description: Dataset collected at BioMAX beamline, MAX IV Labortory, Sweden, of thaumatin. Data collection parameters: Data collected: 30 November 2022 Wavelength: 0.9763 Å (12.7 keV) Beamline: BioMAX, MAX IV Laboratory Detector: DECTRIS EIGER 16M File format: HDF5 in EIGER Nexus format Number of frames: 1800 Oscillation per frame: 0.1°, 180° total Resolution at detector corners: 2 Å Estimated flux: 1.68e11 ph/s Beamline parameters: <strong>Synchrotron Name</strong> MAX IV <strong>Focusing Optics</strong> K-B Mirror <strong>Detector Type</strong> Hybrid Pixel Counting Detector <strong>Beamline name</strong> BioMAX <strong>Monochromator<br> Type</strong> Si(111) <strong>Detector Model </strong> EIGER 16M <strong>Synchrotron Current</strong> 297.0 mA <strong>Beam Shape</strong> ellipse <strong>Detector Manufacturer</strong> DECTRIS <strong>Undulator type</strong> <strong>Beam size at sample Horiz/vert (µm)</strong> 50/50 <strong>Detector pixel size (um)</strong> 75 <strong>Undulator gap</strong> 5.04 mm <strong>Beam divergence<br> Horiz/vert (µrad)</strong> 6/104 <strong>Beam polarization</strong> 0.99 Crystals of thaumatin were grown from solutions of thaumatin (20-50 mg/mL) in NaK-tartrate (1.0 M), HEPES pH 7 (100 µM), and 25% glycerol.
DOI: 10.5281/zenodo.7352800
title: Unmerged reflections from XFEL thermolysin experiment in DIALS and mmCIF format

description: Unmerged reflections from an XFEL dataset collected on thermolysin crystals in Feb 2013, as part of LCLS experiment L785. Raw CSPAD images were processed using cctbx.xfel/DIALS as described in cxi.db entry 81, which includes integrated intensities for each image. These intensities were then scaled and post-refined by the program cctbx.xfel.merge, then saved as unmerged data in DIALS format. This is a work in progress. Full processing details and an unmerged mmCIF file will be provided here in a new version of this dataset.
DOI: 10.5281/zenodo.7352801
title: Unmerged reflections from XFEL thermolysin experiment in DIALS and mmCIF format

description: Unmerged reflections from an XFEL dataset collected on thermolysin crystals in Feb 2013, as part of LCLS experiment L785. Raw CSPAD images were processed using cctbx.xfel/DIALS as described in cxi.db entry 81, which includes integrated intensities for each image. These intensities were then scaled and post-refined by the program cctbx.xfel.merge, then saved as unmerged data in DIALS format. This is a work in progress. Full processing details and an unmerged mmCIF file will be provided here in a new version of this dataset.
DOI: 10.5281/zenodo.4033810
title: Binder H33 - diffraction images for PDB record 8BDU

description: Binder H33 - diffraction data.
DOI: 10.5281/zenodo.4018708
title: Binder J61 - diffraction images for PDB record 7AVC

description: Raw diffraction images for DoBi scaffold variant J61 based on PIH1D1 N-terminal domain - PDB code 7AVC. Primary publication:<br> P.N. Pham, M. Huličiak, L. Biedermannová, J. Černý, T. Charnavets, G. Fuertes, Š. Herynek, L. Kolářová, P. Kolenko, J. Pavlíček, J. Zahradník, P. Mikulecký, B. Schneider. (2021). Protein Binder (ProBi) as a New Classs of Structurally Robust Non-Antibody Protein Scaffold for Directed Evolution. <em>Viruses</em>, <strong>13(2)</strong>, 190.
DOI: 10.5281/zenodo.4018707
title: Binder J61 - diffraction images for PDB record 7AVC

description: Raw diffraction images for DoBi scaffold variant J61 based on PIH1D1 N-terminal domain - PDB code 7AVC. Primary publication:<br> P.N. Pham, M. Huličiak, L. Biedermannová, J. Černý, T. Charnavets, G. Fuertes, Š. Herynek, L. Kolářová, P. Kolenko, J. Pavlíček, J. Zahradník, P. Mikulecký, B. Schneider. (2021). Protein Binder (ProBi) as a New Classs of Structurally Robust Non-Antibody Protein Scaffold for Directed Evolution. <em>Viruses</em>, <strong>13(2)</strong>, 190.
DOI: 10.5281/zenodo.7002446
title: X-ray diffraction images recorded for Aumonier et al., (2022) Slow protein dynamics probed by time-resolved oscillation crystallography at room temperature, IUCrJ

description: The present repository contains diffraction images corresponding to 27 distinct datasets collected at room temperature on the ESRF beamline ID30A-3 using an Eiger X 4M detector. Datasets have been uploaded with their original names to maintain the metadata integrity. The two following tables match the original names with those attributed in the supplementary table S1 of Aumonier et al., IUCrJ (2022) (https://doi.org/10.1107/S2052252522009150). Data set name on Zenodo X06_01 X12_05 X07_02_ X06_08 X14_06 X13_03 X08_06 X11_05 X13_05 X06_02 X11_01 X08_01 X14_01 X13_01 X06_03 Data set in Aumonier et al. 2022 Dark PS2 PS2 PS3 PS4 PS5 PS6 PS7 R<sub>2”</sub> R<sub>3”</sub> R<sub>7”</sub> R<sub>10”</sub> R<sub>13”</sub> R<sub>21”</sub> R<sub>35”</sub> Data set on Zenodo X08_02 X11_02 X12_02 X14_02 X13_04 X13_02 X12_06 X06_09 X09_04 X12_04 X06_07 X13_07 Data set in Aumonier et al. 2022 R<sub>51”</sub> R<sub>62”</sub> R<sub>62”</sub> R<sub>67”</sub> R<sub>72”</sub> R<sub>80”</sub> R<sub>90”</sub> R<sub>130”</sub> R<sub>166”</sub> R<sub>258”</sub> R<sub>630”</sub> R<sub>1620”</sub> One dataset consists of a master file, four data files and two metadata files.
DOI: 10.5281/zenodo.7002447
title: X-ray diffraction images recorded for Aumonier et al., (2022) Slow protein dynamics probed by time-resolved oscillation crystallography at room temperature, IUCrJ

description: The present repository contains diffraction images corresponding to 27 distinct datasets collected at room temperature on the ESRF beamline ID30A-3 using an Eiger X 4M detector. Datasets have been uploaded with their original names to maintain the metadata integrity. The two following tables match the original names with those attributed in the supplementary table S1 of Aumonier et al., IUCrJ (2022) (https://doi.org/10.1107/S2052252522009150). Data set name on Zenodo X06_01 X12_05 X07_02_ X06_08 X14_06 X13_03 X08_06 X11_05 X13_05 X06_02 X11_01 X08_01 X14_01 X13_01 X06_03 Data set in Aumonier et al. 2022 Dark PS2 PS2 PS3 PS4 PS5 PS6 PS7 R<sub>2”</sub> R<sub>3”</sub> R<sub>7”</sub> R<sub>10”</sub> R<sub>13”</sub> R<sub>21”</sub> R<sub>35”</sub> Data set on Zenodo X08_02 X11_02 X12_02 X14_02 X13_04 X13_02 X12_06 X06_09 X09_04 X12_04 X06_07 X13_07 Data set in Aumonier et al. 2022 R<sub>51”</sub> R<sub>62”</sub> R<sub>62”</sub> R<sub>67”</sub> R<sub>72”</sub> R<sub>80”</sub> R<sub>90”</sub> R<sub>130”</sub> R<sub>166”</sub> R<sub>258”</sub> R<sub>630”</sub> R<sub>1620”</sub> One dataset consists of a master file, four data files and two metadata files.
DOI: 10.5281/zenodo.4063577
title: Long-term triaxial test of Passwang Marl, Z-orientation

description: This data set describes a long-term (&gt; 3 yr) rock mechanics experiment of Psswang Marl using a triaxial apparatus. The sample is consolidated and fully saturated. The bedding orientation is 45° to the main axis of the sample (Z-orientation). Confining stress, axial stress and pore pressure are changed multiple times in order to investigate dilatancy, pressure diffusion coefficients and Young's modulus.
DOI: 10.5281/zenodo.4063576
title: Long-term triaxial test of Passwang Marl, Z-orientation

description: This data set describes a long-term (&gt; 3 yr) rock mechanics experiment of Psswang Marl using a triaxial apparatus. The sample is consolidated and fully saturated. The bedding orientation is 45° to the main axis of the sample (Z-orientation). Confining stress, axial stress and pore pressure are changed multiple times in order to investigate dilatancy, pressure diffusion coefficients and Young's modulus.
DOI: 10.6084/m9.figshare.22732706
title: Vertebrate chemoreceptor sequences

description: One fasta file for each chemoreceptor families and for each gene category. For each gene, the species name as well as the genome location and the number of exon is reported in the sequence header. Gene sequences were obtained following the procedures available on github (https://github.com/MaximePolicarpo/Vertebrate_Chemoreceptors_mining) <br>
DOI: 10.6084/m9.figshare.22736543
title: Vertebrate chemoreceptor alignments

description: One sequence alignment file (fasta) for each chemoreceptor family. Alignments were obtained following the procedure indicated in the manuscript : - First, a template alignment was produced using known chemoreceptor sequences from previous studies and outgroup sequence - Then, all complete chemoreceptor sequences were added to these alignments with mafft --add and the --keeplength option
DOI: 10.6084/m9.figshare.22736549.v1
title: PASTML results - Mammals diet preferences

description: We inferred the ancestral diet preference for all branches of the mammalian phylogeny with PastML98 using the Felsenstein81 model and the MPPA (marginal posterior probabilities approximation) prediction method. Diet preferences of each terminal branches were obtained on the MammalDiet database
DOI: 10.6084/m9.figshare.22736549
title: PASTML results - Mammals diet preferences

description: We inferred the ancestral diet preference for all branches of the mammalian phylogeny with PastML98 using the Felsenstein81 model and the MPPA (marginal posterior probabilities approximation) prediction method. Diet preferences of each terminal branches were obtained on the MammalDiet database
DOI: 10.6084/m9.figshare.22736555
title: Vertebrates species trees

description: Vertebrate complete phylogenetic tree (Vertebrate_consensus_tree_nodelabel.nwk) and the same tree but pruned retaining only species with at-least 80% complete BUSCO genes (BUSCO80_vertebrate_tree.nwk) or with at-least 90% complete BUSCO genes (BUSCO90_vertebrate_tree.nwk) <br>
DOI: 10.6084/m9.figshare.22736561.v1
title: Alternative topologies - Mammals - BUSCO80

description: For mammals : 50 concatenated alignments (.fa) (concatenation of 20 BUSCO genes) and calibrated phylogenetic tree computed from these alignments with IQ-TREE2
DOI: 10.6084/m9.figshare.22736561
title: Alternative topologies - Mammals - BUSCO80

description: For mammals : 50 concatenated alignments (.fa) (concatenation of 20 BUSCO genes) and calibrated phylogenetic tree computed from these alignments with IQ-TREE2
DOI: 10.6084/m9.figshare.22736567
title: Alternative topologies - Birds - BUSCO80

description: For birds : 50 concatenated alignments (.fa) (concatenation of 20 BUSCO genes) and calibrated phylogenetic tree computed from these alignments with IQ-TREE2
DOI: 10.6084/m9.figshare.22736567.v1
title: Alternative topologies - Birds - BUSCO80

description: For birds : 50 concatenated alignments (.fa) (concatenation of 20 BUSCO genes) and calibrated phylogenetic tree computed from these alignments with IQ-TREE2
DOI: 10.6084/m9.figshare.22736564
title: Dataset qol eathquake

description: Dataset qol earthquake
DOI: 10.6084/m9.figshare.22736576
title: Alternative topologies - Ray-finned fishes - BUSCO80

description: For ray-finned fishes : 50 concatenated alignments (.fa) (concatenation of 20 BUSCO genes) and calibrated phylogenetic tree computed from these alignments with IQ-TREE2
DOI: 10.6084/m9.figshare.22736576.v1
title: Alternative topologies - Ray-finned fishes - BUSCO80

description: For ray-finned fishes : 50 concatenated alignments (.fa) (concatenation of 20 BUSCO genes) and calibrated phylogenetic tree computed from these alignments with IQ-TREE2