cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15131/shef.data.7058078
title: Data for the assessment of the effect of repositioning in in vivo loading studies with Digital Volume Correlation

description: Link to the data used in:<br>Giorgi, M., Dall'Ara, E. (2018)<i><br></i><i>Variability in strain distribution in the mice tibia loading model: preliminary study using digital volume correlation.</i> Medical Engineering and Physics 2018<br>The images and data are too large to be uploaded in ORDA, so please contact e.dallara@sheffield.ac.uk or the Project Management Office at: pmo@insigneo.org if you are interested in working on the files.<br>Only an example of a dataset has been uploaded.In the B-03-a folder the preloaded image (Scan1_crop.dcm) has been registered with three different files "Scan2_cop.dcm" that represent:01_Scan2_preload_REGwith_Scan1_load: registration between the second preloaded image and the first loaded image<br>01_Scan2_preload_REGwith_Scan2: registration between the second preloaded image and the repeated image in the loaded configuration<br>01_Scan2_preload_REGwith_Repositioning: registration between the second preloaded image and the image of the loaded specimen taken after repositioning<br><br>In the folder C-03-a-02-Nodes the results from the deformable registration are reported for each registration for Node Spacing of 50. Registrations have been done with ShIRT followed by the voxel detection algorithms as described in the paper.<br>"output_map.txt" reports the coordinates of the nodes of the grid and the computed displacements"results.txt" reports the principal strains in each node <br>The whole dataset is stored in the University of Sheffield file-store at the link:https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP7/Mario_Giorgi/DVC_Tibia_Precision_Study/
DOI: 10.15131/shef.data.7058078.v1
title: Data for the assessment of the effect of repositioning in in vivo loading studies with Digital Volume Correlation

description: Link to the data used in:<br>Giorgi, M., Dall'Ara, E. (2018)<i><br></i><i>Variability in strain distribution in the mice tibia loading model: preliminary study using digital volume correlation.</i> Medical Engineering and Physics 2018<br>The images and data are too large to be uploaded in ORDA, so please contact e.dallara@sheffield.ac.uk or the Project Management Office at: pmo@insigneo.org if you are interested in working on the files.<br>Only an example of a dataset has been uploaded.In the B-03-a folder the preloaded image (Scan1_crop.dcm) has been registered with three different files "Scan2_cop.dcm" that represent:01_Scan2_preload_REGwith_Scan1_load: registration between the second preloaded image and the first loaded image<br>01_Scan2_preload_REGwith_Scan2: registration between the second preloaded image and the repeated image in the loaded configuration<br>01_Scan2_preload_REGwith_Repositioning: registration between the second preloaded image and the image of the loaded specimen taken after repositioning<br><br>In the folder C-03-a-02-Nodes the results from the deformable registration are reported for each registration for Node Spacing of 50. Registrations have been done with ShIRT followed by the voxel detection algorithms as described in the paper.<br>"output_map.txt" reports the coordinates of the nodes of the grid and the computed displacements"results.txt" reports the principal strains in each node <br>The whole dataset is stored in the University of Sheffield file-store at the link:https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP7/Mario_Giorgi/DVC_Tibia_Precision_Study/
DOI: 10.15468/pv3x2t
title: Two new species of the genus Trilacuna from Chongqing Municipality, China (Araneae, Oonopidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Wang, Ying, Tong, Yanfeng, Bian, Dongju, Li, Shuqiang (2021): Two new species of the genus Trilacuna from Chongqing Municipality, China (Araneae, Oonopidae). Zootaxa 4927 (3): 431-443, DOI: https://doi.org/10.11646/zootaxa.4927.3.6
DOI: 10.6084/m9.figshare.14074622
title: S1 Master chart.xlsx

description: Comparison of scapular morphology in degenerative and traumatic rotator cuff tears<b>.</b>
DOI: 10.6084/m9.figshare.14074622.v1
title: S1 Master chart.xlsx

description: Comparison of scapular morphology in degenerative and traumatic rotator cuff tears<b>.</b>
DOI: 10.5281/zenodo.4546264
title: TROVE Benchmarks

description: This is a set of sample inputs and outputs for the software TROVE and is intended for use as a regression test.
description: {"references": ["S. N. Yurchenko, W. Thiel, and P. Jensen, Theoretical ROVibrational Energies (TROVE): A robust numerical approach to the calculation of rovibrational energies for polyatomic molecules, J. Mol. Spectrosc. 245, 126 (2007) https://doi.org/10.1016/j.jms.2007.07.009", "A. Yachmenev and S. N. Yurchenko, Automatic differentiation method for numerical construction of the rotational-vibrational Hamiltonian as a power series in the curvilinear internal coordinates using the Eckart frame, J. Chem. Phys. 143, 014105 (2015). https://doi.org/10.1063/1.4923039", "S. N. Yurchenko, A. Yachmenev, and R. I. Ovsyannikov, Symmetry adapted ro-vibrational basis functions for variational nuclear motion: TROVE approach, J. Chem. Theory Comput. 13, 4368 (2017). https://doi.org/10.1021/acs.jctc.7b00506"]}
DOI: 10.5281/zenodo.4546263
title: TROVE Benchmarks

description: This is a set of sample inputs and outputs for the software TROVE and is intended for use as a regression test.
description: {"references": ["S. N. Yurchenko, W. Thiel, and P. Jensen, Theoretical ROVibrational Energies (TROVE): A robust numerical approach to the calculation of rovibrational energies for polyatomic molecules, J. Mol. Spectrosc. 245, 126 (2007) https://doi.org/10.1016/j.jms.2007.07.009", "A. Yachmenev and S. N. Yurchenko, Automatic differentiation method for numerical construction of the rotational-vibrational Hamiltonian as a power series in the curvilinear internal coordinates using the Eckart frame, J. Chem. Phys. 143, 014105 (2015). https://doi.org/10.1063/1.4923039", "S. N. Yurchenko, A. Yachmenev, and R. I. Ovsyannikov, Symmetry adapted ro-vibrational basis functions for variational nuclear motion: TROVE approach, J. Chem. Theory Comput. 13, 4368 (2017). https://doi.org/10.1021/acs.jctc.7b00506"]}
DOI: 10.5281/zenodo.4550846
title: Data for paper publication 'Extreme 2019-2020 Australian wildfires substantially perturbed Earth's radiation budget'

description: This repository contains data from the aerosol-climate simulations performed with the ECHAM6.3-HAM2.3 model and aerosol lidar profles, as presented in the paper publication by Heinold et al.: Extreme 2019-2020 Australian wildfires substantially perturbed Earth’s radiation budget, submitted to Nature Geoscience. For details, please refer to the enclosed data description (README) file.
DOI: 10.5281/zenodo.4545789
title: Ha Noi dataset for DATAbASE

description: VOC and CO mixing ratios (in ppb) measured @ Le Hong Phong Political School in Hanoi (21°0'24" N, 105°49'4"E) on the roof of seven-story building (~ 30 m from ground) VOCs were measured every hour by a thermo-desorption dual-chanel gas chromatograph coupled to FID detectors (DC-GC-FID). The duration of the air sampling is 10 min. The local time corresponds to hourly average concentrations. CO measurements were perfomed every 3 minutes using a TA 3000 CO analyzer supplied by AMETEK Reference papers : Dominutti et al 2021 in prep, Duong Huu et al 2021 in prep
DOI: 10.5281/zenodo.4545775
title: Athens dataset for DATAbASE

description: VOC (in μg m-3), NOx and CO (both in ppb) were measured at the Thissio Monitoring Station (37°58'12'' Ν 23°43'12'' Ε, 105 m a.s.l) in Athens, Greece. VOC were measured every 30 minutes by two automatic GC-FIDs and they were averaged to 1 hour. NOx and CO were measured on a 1-min basis using Horiba 360 Series Gas Analyzers, the concentrations were averaged to 1 hour.
DOI: 10.5281/zenodo.4545774
title: Athens dataset for DATAbASE

description: VOC (in μg m-3), NOx and CO (both in ppb) were measured at the Thissio Monitoring Station (37°58'12'' Ν 23°43'12'' Ε, 105 m a.s.l) in Athens, Greece. VOC were measured every 30 minutes by two automatic GC-FIDs and they were averaged to 1 hour. NOx and CO were measured on a 1-min basis using Horiba 360 Series Gas Analyzers, the concentrations were averaged to 1 hour.
DOI: 10.5281/zenodo.4544397
title: São Paulo dataset at two tunnels for DATAbASE

description: VOC mixing ratios measured @ two traffic tunnels in the Metropolitan Area of São Paulo (MASP), Brazil Samplings @ Jânio Quadros Tunnel (-46° 41' 36.28" W, -23° 35' 15.81 S") carried out during November 4 - 13, 2018 Samplings @ Rodoanel Tunnel (-46° 47' 43.85 W", -23° 27' 38.94 S") carried out during October 26 - November 3, 2018 VOC were collected using sampling canisters and measured by GC-FID. Samples were collected at a constant flow rate (~ 2ml/min) for approximately 8 hours. <br> <br> Contact: thiago.nogueira@iag.usp.br or pamela.dominutti@gmail.com This work was financially supported by the project “Chemical and toxicological SOurce PROfiling of particulate matter in urban air (SOPRO)”, POCI-01-0145-FEDER-029574, funded by FEDER, through Compete 2020 - Programa Operacional Competitividade e Internacionalização (POCI), by national funds (OE), through FCT/MCTES, and by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, São Paulo Research Foundation; Grants no. 18/07848-9).
DOI: 10.15131/shef.data.7043279
title: Analysis scripts for "Competitive species interactions constrain abiotic adaptation in a bacterial soil community"

description: This record contains sample R analysis scripts associated with 'Competitive species interactions constrain abiotic adaptation in a bacterial soil community' by J. P. J. Hall et al. (2018). The data used in these analyses is presented in the Supplementary Tables published as an Excel workbook in the manuscript. For ease of analysis, .csv versions of these tables are provided in another ORDA record (doi: 10.15131/shef.data.7088906).<br>Full details of the experiments and their interpretation can be found in the open access paper, published in Evolution Letters (see References below). <br><br>Briefly, <i>Pseudomonas fluorescens</i> SBW25 carrying the mercury resistance plasmid pQBR57 were cultured in soil microcosms in the presence or absence of a competitor, <i>Pseudomonas putida</i> KT2440, and with or without mercury. After ~440 generations, clones were re-isolated and their fitness relative to the ancestral strain was measured. Clones from single-species treatments had increased relative fitness compared with those from co-culture. Investigation of the resequenced genomes showed parallel mutations occurring to the <i>actP</i> gene, but only in clones which had evolved without <i>P. putida</i>. Subsequent experiments show that <i>actP</i> disruption is associated with increased growth, but only where <i>P. putida</i> is absent.<br>1_CompetitionsAnalysis.R: example code describing analyses presented in Figure 1, showing relative fitness of evolved clones.<br>2_MutationsAnalysis.R: example code describing analyses presented in Figure 2, showing parallel mutations in evolved clones.<br>4_GrowthAnalysis.R: example code describing analyses presented in Figure 4, showing growth of clones with mutated and non-mutated <i>actP</i> in the presence and absence of <i>P. putida</i>.<br>S3_PopulationsAnalysis.R: example code describing analyses presented in Figure S3, showing population densities of <i>P. fluorescens</i> during evolution experiment.<br>S4_AcetateGrowth.R: example code describing analyses presented in Figure S4, showing growth of <i>P. fluorescens</i> in minimal media with glycerol or acetate as carbon sources.<br>S5A_DiscDiffusion.R: example code describing analyses presented in Figure S5A, showing inhibition of evolved <i>P. fluorescens</i> by tellurite. <br>S5B_TellMIC.R: example code describing analyses presented in Figure S5B, showing inhibition of evolved <i>P. fluorescens</i> by tellurite. <br><br>
DOI: 10.15131/shef.data.7043279.v2
title: Analysis scripts for "Competitive species interactions constrain abiotic adaptation in a bacterial soil community"

description: This record contains sample R analysis scripts associated with 'Competitive species interactions constrain abiotic adaptation in a bacterial soil community' by J. P. J. Hall et al. (2018). The data used in these analyses is presented in the Supplementary Tables published as an Excel workbook in the manuscript. For ease of analysis, .csv versions of these tables are provided in another ORDA record (doi: 10.15131/shef.data.7088906).<br>Full details of the experiments and their interpretation can be found in the open access paper, published in Evolution Letters (see References below). <br><br>Briefly, <i>Pseudomonas fluorescens</i> SBW25 carrying the mercury resistance plasmid pQBR57 were cultured in soil microcosms in the presence or absence of a competitor, <i>Pseudomonas putida</i> KT2440, and with or without mercury. After ~440 generations, clones were re-isolated and their fitness relative to the ancestral strain was measured. Clones from single-species treatments had increased relative fitness compared with those from co-culture. Investigation of the resequenced genomes showed parallel mutations occurring to the <i>actP</i> gene, but only in clones which had evolved without <i>P. putida</i>. Subsequent experiments show that <i>actP</i> disruption is associated with increased growth, but only where <i>P. putida</i> is absent.<br>1_CompetitionsAnalysis.R: example code describing analyses presented in Figure 1, showing relative fitness of evolved clones.<br>2_MutationsAnalysis.R: example code describing analyses presented in Figure 2, showing parallel mutations in evolved clones.<br>4_GrowthAnalysis.R: example code describing analyses presented in Figure 4, showing growth of clones with mutated and non-mutated <i>actP</i> in the presence and absence of <i>P. putida</i>.<br>S3_PopulationsAnalysis.R: example code describing analyses presented in Figure S3, showing population densities of <i>P. fluorescens</i> during evolution experiment.<br>S4_AcetateGrowth.R: example code describing analyses presented in Figure S4, showing growth of <i>P. fluorescens</i> in minimal media with glycerol or acetate as carbon sources.<br>S5A_DiscDiffusion.R: example code describing analyses presented in Figure S5A, showing inhibition of evolved <i>P. fluorescens</i> by tellurite. <br>S5B_TellMIC.R: example code describing analyses presented in Figure S5B, showing inhibition of evolved <i>P. fluorescens</i> by tellurite. <br><br>
DOI: 10.5281/zenodo.4544266
title: São Paulo dataset at IAG for DATAbASE

description: VOC mixing ratios (in ppb) measured @ the University of the Sao Paulo campus - IAG 17 m above the ground (23°33'33.6" S, 46°44'0.3" W) in Sao Paulo - Brazil NOx mixing ratios (in ppb) and CO mixing ratios (in ppm) obtained online from the Environmental Agency of Sao Paulo State (CETESB), station IPEN-Cidade Universitaria located 800m far from the VOC sampling point (23°33'58.96"S 46°44'15.57"W) VOC were measured every hour by a Thermo-Desorption dual-Gas Chromatography coupled to FID detectors (TD-GC-FID). The duration of the air sampling is 40 min. The Local time corresponds to the start of the sampling Reference papers : Dominutti et al 2016, Dominutti et al 2020<br>
DOI: 10.5281/zenodo.3942084
title: ODP Leg 105, Hole 647A - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: ODP Leg 105: Labrador Sea and Baffin Bay
DOI: 10.5281/zenodo.3942083
title: ODP Leg 105, Hole 647A - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: ODP Leg 105: Labrador Sea and Baffin Bay
DOI: 10.5281/zenodo.3942088
title: ODP Leg 107, Hole 652A - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: ODP Leg 107: Tyrrhenian Sea
DOI: 10.5281/zenodo.3942087
title: ODP Leg 107, Hole 652A - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: ODP Leg 107: Tyrrhenian Sea
DOI: 10.5281/zenodo.3942090
title: ODP Leg 107, Hole 655B - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: ODP Leg 107: Tyrrhenian Sea
DOI: 10.5281/zenodo.3942089
title: ODP Leg 107, Hole 655B - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: ODP Leg 107: Tyrrhenian Sea
DOI: 10.5258/soton/d1742
title: Dataset for Detection of sub-atomic movement in nanostructures

description: Research data supports the paper: T. Liu, J. Y. Ou, K. F. MacDonald, and N. I. Zheludev, Detection of sub-atomic movement in nanostructures. Nanoscale Advances
DOI: 10.5066/p9zspa9d
title: Model of groundwater flow, gas migration, and reactive transport in the Virgin River Basin, SW Utah

description: To better understand the possible risks posed to shallow groundwater resources by geologic carbon sequestration (GCS), a multi-scale numerical modeling approach was invoked using the TOUGHREACT code from Lawrence Berkeley National Laboratory. The code solves coupled equations representing conservation of mass and energy on a finite difference grid to simulate multiphase, multicomponent, non-isothermal heat and mass transport in porous media. Two different two-dimensional cross-section modeling domains were constructed to improve understanding of groundwater flow and contaminant transport processes at a field site in soutwestern Utah. The site represents a natural analogue for leakage from a GCS site because water with elevated concentrations of salt and CO2 are migrating upward into a shallow aquifer system. The first modeling domain was designed to improve understanding of long-term hydrological leakage and conservative transport processes at the regional scale, while the second was designed to investigate site-scale reactive transport processes that could occur if the leaking fluids, or those with higher carbon dioxide (CO2) concentrations, were to interact with a potential source of contamination along their flow path toward the ground surface. Lead (Pb+2) was used as an example heavy metal contaminant and was incorporated into a region of iron oxide representing concretion zones that are common in the geographic area. Results indicate that the initial state of potential heavy metal contaminant (i.e., sorbed onto the surface of the iron oxide or in an oxide mineral assemblage as PbO, litharge), exerts strong control on the amount of contamination that may occur, and that precipitation readily sequesters mobilized Pb+2. This USGS data release contains all of the input and output files for the simulations described in the associated journal article. Descriptions of the data in each subdirectory are given to facilitate understanding of this model archive. File descriptions are provided for select files to provide additional information that may be of use for understanding this model archive. Support is provided for correcting errors in the data release and clarification of the modeling conducted by the U.S. Geological Survey. Users are encouraged to review the complete journal article (See 'Related External Resources' section below) to understand the purpose, report construction, and limitations of this model.
DOI: 10.5281/zenodo.3942080
title: ODP Leg 105, Hole 645E - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: ODP Leg 105: Labrador Sea and Baffin Bay
DOI: 10.5281/zenodo.3942079
title: ODP Leg 105, Hole 645E - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: ODP Leg 105: Labrador Sea and Baffin Bay
DOI: 10.5281/zenodo.3942191
title: ODP Leg 110, Hole 672A - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: ODP Leg 110: Lesser Antilles
DOI: 10.5281/zenodo.3942190
title: ODP Leg 110, Hole 672A - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: ODP Leg 110: Lesser Antilles
DOI: 10.5281/zenodo.3942193
title: ODP Leg 110, Hole 676A - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: ODP Leg 110: Lesser Antilles