cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.4228/zalf-8m35-s7sy
title: Soil profile 'BDF_22'

description: null
DOI: 10.4228/zalf-d70x-c2sb
title: Soil profile 'BDF_19'

description: null
DOI: 10.4228/zalf-515j-g789
title: Soil profile 'BDF_18'

description: null
DOI: 10.15468/dl.db9a5j
title: Occurrence Download

description: A dataset containing 310 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Year is 1991,2010",
 "OccurrenceStatus is Present",
 "BasisOfRecord is Specimen",
 "TaxonKey is Artocarpus altilis (Parkinson) Fosberg"
 ]
}

 The dataset includes 310 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004394-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25934/pr00008832.1
title: Available datapackage for study 'A Phase III Randomised, Double-blind Trial to Evaluate Efficacy and Safety of Once Daily Empagliflozin 10 mg Compared to Placebo, in Patients With Chronic Heart Failure With Reduced Ejection Fraction (HFrEF)'

description: The aim of the study is to investigate the safety and efficacy of empagliflozin versus placebo on top of guideline-directed medical therapy in patients with heart failure with reduced ejection fraction.
DOI: 10.5281/zenodo.14617308
title: Data from: Future expansion of upper forest-grassland ecotone under land-use and climate change in the Eastern Alps

description: Across Alpine landscapes, a combination of land-use abandonment and climate change is driving forest expansion and promoting the upward migration of trees on grasslands. Yet, it remains unclear how rapidly the upper forest-grassland ecotone will shift and how tree species composition will change, both in terms of species proportions and along elevational gradients. Our aim is to investigate the future forest expansion in a landscape in the Eastern Alps under potential grassland abandonment, climate change, natural disturbances (wind and bark beetle), and forest management. We used the iLand forest landscape model to simulate long-term dynamics (2020-2200) under different scenarios. We coupled model outputs with the concave hull algorithm to identify potential changes in the forest-grassland ecotone, tracking tree species expansion and quantifying elevation and compositional shifts. Under a potential abandonment of alpine grasslands, forest will likely expand rapidly within the 21st century regardless climate warming. This because the current upper forest-grassland ecotone is mainly constrained by land use rather than climate. Our simulations also showed that ecotone shifts will be more pronounced on S-facing slopes, while climate change will affect more future tree species composition and forest stocking at higher elevations. Our outcomes provide useful insights on future dynamics of the upper forest ecotone by using a forest landscape model and by integrating not only species migration and climate but also other factors such as disturbances and management. Our results could provide useful information for designing landscape management strategies in rapidly changing Alpine mountain valleys.
description: The folder contains the files used to simulate the Stubai landscape in the iLand model and can be used to reproduce the simulation experiment. The model is freely available and can be downloaded here.
DOI: 10.5281/zenodo.14617309
title: Data from: Future expansion of upper forest-grassland ecotone under land-use and climate change in the Eastern Alps

description: Across Alpine landscapes, a combination of land-use abandonment and climate change is driving forest expansion and promoting the upward migration of trees on grasslands. Yet, it remains unclear how rapidly the upper forest-grassland ecotone will shift and how tree species composition will change, both in terms of species proportions and along elevational gradients. Our aim is to investigate the future forest expansion in a landscape in the Eastern Alps under potential grassland abandonment, climate change, natural disturbances (wind and bark beetle), and forest management. We used the iLand forest landscape model to simulate long-term dynamics (2020-2200) under different scenarios. We coupled model outputs with the concave hull algorithm to identify potential changes in the forest-grassland ecotone, tracking tree species expansion and quantifying elevation and compositional shifts. Under a potential abandonment of alpine grasslands, forest will likely expand rapidly within the 21st century regardless climate warming. This because the current upper forest-grassland ecotone is mainly constrained by land use rather than climate. Our simulations also showed that ecotone shifts will be more pronounced on S-facing slopes, while climate change will affect more future tree species composition and forest stocking at higher elevations. Our outcomes provide useful insights on future dynamics of the upper forest ecotone by using a forest landscape model and by integrating not only species migration and climate but also other factors such as disturbances and management. Our results could provide useful information for designing landscape management strategies in rapidly changing Alpine mountain valleys.
description: The folder contains the files used to simulate the Stubai landscape in the iLand model and can be used to reproduce the simulation experiment. The model is freely available and can be downloaded here.
DOI: 10.5281/zenodo.14177700
title: MD Simulation of AtALMT9 TMD Using Martini3 and charmm36 Force Field

description: This dataset contains the MD simulation data associated with the article:

"Structural basis for malate-driven, pore lipid-regulated activation of the Arabidopsis vacuolar anion channel ALMT9"

(Not published yet)

 

Folder

AA : All-atom simulation files.

CG : Coarse-grained simulation files.

toppar : parameter files.

 

File Description

conf.pdb : Initial structure of the simulation.

all.fit.10ns.now.zen.xtc  : trajectory file without water. 

now.pdb : coordinate file of corresponding trajectory.

topol.top : GROMACS topology file.
DOI: 10.5281/zenodo.14177701
title: MD Simulation of AtALMT9 TMD Using Martini3 and charmm36 Force Field

description: This dataset contains the MD simulation data associated with the article:

"Structural basis for malate-driven, pore lipid-regulated activation of the Arabidopsis vacuolar anion channel ALMT9"

(Not published yet)

 

Folder

AA : All-atom simulation files.

CG : Coarse-grained simulation files.

toppar : parameter files.

 

File Description

conf.pdb : Initial structure of the simulation.

all.fit.10ns.now.zen.xtc  : trajectory file without water. 

now.pdb : coordinate file of corresponding trajectory.

topol.top : GROMACS topology file.
DOI: 10.71724/7517-0813
title: Nanostructured copper - defects density, passive layers chemical composition, antibacterial properties SONATA BIS 11 2021/42/E/ST5/00118

description: <p>The study presents a database of X-ray photoelectron spectroscopy (XPS) measurements results, Doppler broadening variable energy positron annihilation spectroscopy (DB-VEPAS) measurements results, variable energy positron annihilation lifetime spectroscopy (VEPALS) measurements results, and luminous intensity measurements results  (after adhesion tests using <em>S. aureus</em>) for annealed and high-pressure torsion (HPT) processed copper. </p><p><br />XPS spectra have been collected using Microlab 350 spectrometer, Thermo Electron.  A non-monochromatic X-ray source (Al Kα) with an energy of 1486.6 eV for the most intense line and a power of 300 W was used for XPS measurements. Spectra were obtained with a 100 eV pass energy for the survey scan and 40 eV pass energy for narrow regions (high-resolution spectra).</p><p><br />DB-VEPAS measurements have been conducted at the apparatus for in-situ defect analysis (AIDA) of slow positron beamline (SPONSOR) in HZDR, Germany. Positrons were accelerated and implanted with defined kinetic energies into samples in the positron implantation energy range of Ep &#61; 0.05-35 keV. VEPALS measurements were conducted at the Mono-energetic Positron Source (MePS) beamline at HZDR, Germany using a CrBr<sub>3 </sub>scintillator detector coupled to a Hamamatsu R13089-100 photomultiplier (PMT) tube and a processing unit the SPDevices ADQ14DC-2X digitizer. The time resolution function was in the range of 0.250 ns. All spectra contained at least 1·10<sup>7</sup> counts.</p><p><br />The areas of the image occupied by fluorescent light (indicating the presence of bacteria) have been calculated using the ImageJ program. The luminous intensity was calculated as the surface fraction of pixels above a certain intensity level.<br /><br /></p>
DOI: 10.15468/dl.s5nndc
title: Occurrence Download

description: A dataset containing 97 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rubus idaeus L.",
 "Geometry POLYGON((-4.57907617500001 39.884719509, -4.57907617500001 41.165844755, -3.05298331400002 41.165844755, -3.05298331400002 39.884719509, -4.57907617500001 39.884719509))"
 ]
}

 The dataset includes 97 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004395-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4j87hm
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rubus lainzii H.E.Weber",
 "Geometry POLYGON((-4.57907617500001 39.884719509, -4.57907617500001 41.165844755, -3.05298331400002 41.165844755, -3.05298331400002 39.884719509, -4.57907617500001 39.884719509))"
 ]
}

 The dataset includes 56 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004397-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.knzrqn
title: Occurrence Download

description: A dataset containing 36690 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Calendula officinalis L."
 ]
}

 The dataset includes 36690 records from 707 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004396-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5t3qbp
title: Occurrence Download

description: A dataset containing 34325 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Estonia",
 "TaxonKey is Alces alces (Linnaeus, 1758)"
 ]
}

 The dataset includes 34325 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000000-250225085111116/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13682948
title: Calibration of non-local damage models from full-field measurements: application to discrete element fields.

description: The codes, datasets, and results from the manuscript  'Calibration of non-local damage models from full-field measurements: application to discrete element fields' are available here.

 

This repository is organized into four folders:



'Ideal Case' folder: This corresponds to Section ‘3. Application of the calibration method on a 1D ideal case' of the manuscript. In this folder, you will find the FreeFEM+ and Python scripts and a makefile to run them. These codes reproduce all the figures, as well as the complete dataset associated with Figures 1-7.

'Virtual Testing Machine' folder: This corresponds to Section 4, 'Introduction of a Virtual Testing Machine' of the manuscript. Here, you will find:



The data for Figure 9, contains the force vs. CMOD response for all sizes and geometries.

The data for Figure 10, contains the scores associated with this parametric identification.



'Green Functions' folder: This includes the FreeFEM++ code to solve the boundary value problem for obtaining Green's function of the Eikonal equation. The code is demonstrated with both a non-damaged case and a polynomial damage case. In the first case, Green’s function corresponds to the weighting functions of the Implicit Gradient method (Peerlings et al., 1996).

'Real Case' folder: This corresponds to Section 5, 'Application of the Proposed Calibration Procedure to Virtual Tests.' Here, you will find:



The complete 'Damage vs. Strain' Dataset was generated with the Virtual Testing Machine. Figures 12-15 correspond to this dataset, processed as explained in the manuscript.

The 'damage vs. damage driving variable' dataset for each characteristic length.  Figure 16 in the manuscript corresponds to this dataset.

The data for Figures 17 and 18, contain the evolution of the error with the characteristic length for different evolution laws.
DOI: 10.5281/zenodo.13682949
title: Calibration of non-local damage models from full-field measurements: application to discrete element fields.

description: The codes, datasets, and results from the manuscript  'Calibration of non-local damage models from full-field measurements: application to discrete element fields' are available here.

 

This repository is organized into four folders:



'Ideal Case' folder: This corresponds to Section ‘3. Application of the calibration method on a 1D ideal case' of the manuscript. In this folder, you will find the FreeFEM+ and Python scripts and a makefile to run them. These codes reproduce all the figures, as well as the complete dataset associated with Figures 1-5.

'Virtual Testing Machine' folder: This corresponds to Section 4, 'Introduction of a Virtual Testing Machine' of the manuscript. Here, you will find:



The data for Figure 7, contains the force vs. CMOD response for all sizes and geometries.

The data for Figure 8, contains the scores associated with this parametric identification.



'Green Functions' folder: This includes the FreeFEM++ code to solve the boundary value problem for obtaining Green's function of the Eikonal equation. The code is demonstrated with both a non-damaged case and a polynomial damage case. In the first case, Green’s function corresponds to the weighting functions of the Implicit Gradient method (Peerlings et al., 1996).

'Real Case' folder: This corresponds to Section 5, 'Application of the Proposed Calibration Procedure to Virtual Tests.' Here, you will find:



The complete 'Damage vs. Strain' Dataset was generated with the Virtual Testing Machine. Figures 10-13 correspond to this dataset, processed as explained in the manuscript.

The 'damage vs. damage driving variable' dataset for each characteristic length.  Figure 14 in the manuscript corresponds to this dataset.

The data for Figures 15 and 16, contain the evolution of the error with the characteristic length for different evolution laws.
DOI: 10.15468/dl.kkanj7
title: Occurrence Download

description: A dataset containing 95 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rumex suffruticosus Meisn.",
 "Geometry POLYGON((-4.57907617500001 39.884719509, -4.57907617500001 41.165844755, -3.05298331400002 41.165844755, -3.05298331400002 39.884719509, -4.57907617500001 39.884719509))"
 ]
}

 The dataset includes 95 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000001-250225085111116/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zdvgdv
title: Occurrence Download

description: A dataset containing 1244 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Myrica rubra A.Chev."
 ]
}

 The dataset includes 1244 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000003-250225085111116/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6nz3cq
title: Occurrence Download

description: A dataset containing 34323 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Estonia",
 "OccurrenceStatus is Present",
 "TaxonKey is Alces alces (Linnaeus, 1758)"
 ]
}

 The dataset includes 34323 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000002-250225085111116/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12798130
title: Datasets for triggered events

description: datasets for aseismic and seismic events dynamically triggered by the 2023 Turkey earthquake sequence including InSAR observations, geodetic model, detected seismicity catalogs and seismic stations
DOI: 10.5281/zenodo.13835397
title: Calibration of non-local damage models from full-field measurements: application to discrete element fields.

description: The codes, datasets, and results from the manuscript  'Calibration of non-local damage models from full-field measurements: application to discrete element fields' are available here.

 

This repository is organized into four folders:



'Ideal Case' folder: This corresponds to Section ‘3. Application of the calibration method on a 1D ideal case' of the manuscript. In this folder, you will find the FreeFEM+ and Python scripts and a makefile to run them. These codes reproduce all the figures, as well as the complete dataset associated with Figures 1-7.

'Virtual Testing Machine' folder: This corresponds to Section 4, 'Introduction of a Virtual Testing Machine' of the manuscript. Here, you will find:



The data for Figure 9, contains the force vs. CMOD response for all sizes and geometries.

The data for Figure 10, contains the scores associated with this parametric identification.



'Green Functions' folder: This includes the FreeFEM++ code to solve the boundary value problem for obtaining Green's function of the Eikonal equation. The code is demonstrated with both a non-damaged case and a polynomial damage case. In the first case, Green’s function corresponds to the weighting functions of the Implicit Gradient method (Peerlings et al., 1996).

'Real Case' folder: This corresponds to Section 5, 'Application of the Proposed Calibration Procedure to Virtual Tests.' Here, you will find:



The complete 'Damage vs. Strain' Dataset was generated with the Virtual Testing Machine. Figures 12-15 correspond to this dataset, processed as explained in the manuscript.

The 'damage vs. damage driving variable' dataset for each characteristic length.  Figure 16 in the manuscript corresponds to this dataset.

The data for Figures 17 and 18, contain the evolution of the error with the characteristic length for different evolution laws.
DOI: 10.5281/zenodo.6137082
title: Predicted and experimental chemical and ecotoxicological properties for the toxic unit based hazard assessment

description: <strong>Description</strong> This dataset contains ecotoxicity data of 1585 chemicals of environmental concern (CECs) and chemical identifiers. The ecotoxicity data was retrieved from US EPA ECOTOX Knowlegdebase in ASCII file format and was aggregated for the ecotoxicity groups algae, crustaceans, and fish based on the ideas of Busch et al. 2016. The dataset includes the 5-percentile, the mean and the geomean of all retrieved ecotoxicity for each compound. Missing ecotoxicity data was estimated with ECOSAR 1.0 algorithms for green algae, daphnids, and fish using ChemProp 6.8. The main purpose of this dataset is the toxic unit (TU) based hazard assessment of environmental water samples. Chemical properties were estimated using OPERA 2.7, Instant JChem, and ACD Percepta 2015 based on QSAR-ready SMILES derived from OPERA 2.7. All data aggregated from EcoTox Knowledgebase (e.g., raw values, species, etc.) is available in the dataset in the detailed sheets. REcoTox, the processing script written in R is available on GitHub. <strong>CAUTION</strong> It needs to be emphasized that quantitative-structure activity relationship data is just an estimate, which does not necessarily reflect the real property and behaviour of a modelled compound. The calculated data needs to be reviewed in deep. Especially for non-polar or very polar compounds, the QSAR predictions might fail. If a compound ranks high in the TU ranking, it is required to search for literature or regulative data evidences to underpin the finding to avoid false positive prioritizations. <strong>RELEASE NOTE</strong> Version 210714_v1 was created with REcoTox version v0.1.0.
DOI: 10.6084/m9.figshare.25511386
title: The Potential Land-Use Impacts of Bio-Based Plastics and Plastic Alternatives

description: The zipped file contains results for the paper "The potential land-use impacts of bio-based plastics and plastic alternatives" published in <i>Nature Sustainability</i>. <b>DOI : </b>10.1038/s41893-024-01492-7Results are in the form of raster files, representing land-systems at the global level. The initial land-system map and modeled scenarios are included. The results from this study are calculated using these raster maps. For more details, please refer to the manuscript and manuscript supplementary information. Additionally, the land-use model utilized in this study requires land suitability maps, based on empirical relationships between land-system patters and suitability criteria, as calculated by a logistic regression. The regression results are presented in the accompanying excel sheet.
DOI: 10.6084/m9.figshare.28087742
title: Choi et al., (2024) Nat. Commun. <b>"Cortical Representations of Affective Pain Shape Empathic Fear in Male Mice"</b>

description: Codes and example datasets related to Choi et al., (2024) Nature CommunicationsSource Data related to Choi et al., (2024) Nature CommunicationsOriginal figures (Fig. 5, Fig. 6) related to Choi et al., (2024) Nature CommunicationsHere, using miniature endoscopic calcium imaging, we identify distinct and dynamic neural ensembles in the anterior cingulate cortex (ACC) that encode observational fear across both excitatory and inhibitory neurons in male mice. Notably, we find that the population dynamics encoding vicarious freezing information are conserved in ACC pyramidal neurons and are specifically represented by affective, rather than sensory, responses to direct pain experience. Furthermore, using circuit-specific imaging and optogenetic manipulations, we show that distinct populations of ACC neurons projecting to the periaqueductal gray (PAG), but not to the basolateral amygdala (BLA), selectively convey affective pain information and regulate observational fear.
DOI: 10.6084/m9.figshare.28246586
title: Supplementary Material for: DRUG-INDUCED LIVER INJURY ASSOCIATED WITH TURMERIC AND PIPERINE: A CASE AND REVIEW

description: Introduction: Turmeric is a common spice used in traditional Chinese and Ayurvedic medicine for a variety of purported health benefits. Recent concerns have arisen regarding turmeric-induced liver injury linked to formulations with enhanced bioavailability, often including piperine found in black pepper. Case presentation: We explore a case of a 40-year-old female with increasing fatigue, pruritus and dark urine following consumption of turmeric and black pepper “wellness shots” leading to a significant drug-induced liver injury. Conclusion: This case underscores the critical need to recognise herbal remedies, such as turmeric, as potential sources of hepatotoxicity. Despite a reputation of safety, limited regulation and testing of turmeric may mean potential adverse effects are under-recognised. Understanding the mechanisms behind turmeric and black pepper’s hepatotoxicity, including the role of potential genetic predispositions, requires further investigation for its safe use.
DOI: 10.17909/xpr9-e989
title: JWST PID3690 Data