cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7604131
title: Intrusive and Non-Intrusive Uncertainty Quantification Methodologies for Pyrolysis Modeling

description: This repository contains python scripts and results for uncertainty analysis of Arrhenius equation with kinetic parameters as uncertain. The data set contains folders for each PMMA variant (1,2 and 3) used for uncertainty quantification (UQ) and 'Misc' folder containing miscellaneous files and scripts used in the study. 


Each PMMA variant folder has further sub-folders for the UQ methods implemented:



	
Intrusive polynomial chaos (IPC)
	
Monte Carlo (MC)
	
Non-intrusive polynomial chaos (NIPC)



Additionally convergence and comparison for the UQ methods is available in sub-folders of the same name respectively.


The python file 'UoWu_noLatex.mplstyle' for plotting style used by us is attached to ease the rerunning of the scripts.
DOI: 10.6084/m9.figshare.24581710.v1
title: Data from reduction of wing area affects estimated stress in the primary flight muscles of chickens

description: Raw data including muscle mass, physiological cross-sectional area and estimated muscle stress of the supracoracoideus
DOI: 10.5281/zenodo.10203362
title: Data Management Plan (DMP)
DOI: 10.5281/zenodo.10203361
title: Data Management Plan (DMP)
DOI: 10.5281/zenodo.10203360
title: Test_KY
DOI: 10.5281/zenodo.10203359
title: Test_KY_new_version
DOI: 10.5281/zenodo.10203370
title: Test_KY
DOI: 10.5281/zenodo.10203379
title: Test_KY_new_version
DOI: 10.6084/m9.figshare.24631077
title: U-Pb zircon data from samples and standard in well 6206

description: Constraints on the continental weathering feedback on carbon-cycle perturbations on northern Pangea during the end Triassic extinction (ETE) are sparse. Here, we use hyperspectral core imaging (HSI) applied to conglomeratic beds offshore central Norway which shows that enhanced degassing of basalt flows from the Central Atlantic magmatic province (CAMP) was concurrent with intense continental transformation during the ETE. We use well-constrained mercury pulses emitted in gaseous form during volcanism, and subsequently deposited in near-coastal sediments, to identify the ETE. Parallel to mercury pulses, HSI derived smectite was immediately replaced by kaolinite at the extinction level corroborating increased radiogenic run-off from the hinterland as inferred from osmium isotopes. Our new results suggest that, parallel with CAMP activity and with atmospheric carbon dioxide (<i>p</i>CO<sub>2</sub>) up to four times the pre-extinction level, continental weathering instantaneously intensified, providing novel empirical knowledge that can be integrated in carbon-cycle models to underpin future warming assessments.
DOI: 10.6084/m9.figshare.24631077.v1
title: U-Pb zircon data from samples and standard in well 6206

description: Constraints on the continental weathering feedback on carbon-cycle perturbations on northern Pangea during the end Triassic extinction (ETE) are sparse. Here, we use hyperspectral core imaging (HSI) applied to conglomeratic beds offshore central Norway which shows that enhanced degassing of basalt flows from the Central Atlantic magmatic province (CAMP) was concurrent with intense continental transformation during the ETE. We use well-constrained mercury pulses emitted in gaseous form during volcanism, and subsequently deposited in near-coastal sediments, to identify the ETE. Parallel to mercury pulses, HSI derived smectite was immediately replaced by kaolinite at the extinction level corroborating increased radiogenic run-off from the hinterland as inferred from osmium isotopes. Our new results suggest that, parallel with CAMP activity and with atmospheric carbon dioxide (<i>p</i>CO<sub>2</sub>) up to four times the pre-extinction level, continental weathering instantaneously intensified, providing novel empirical knowledge that can be integrated in carbon-cycle models to underpin future warming assessments.
DOI: 10.14272/ggyqdmhuvmiefm-uhfffaoysa-n/chmo0000480
title: electron ionisation mass spectrometry (EI-MS) (4-tritylaniline;hydrochloride)
title: InChI=1S/C25H21N.ClH/c26-24-18-16-23(17-19-24)25(20-10-4-1-5-11-20,21-12-6-2-7-13-21)22-14-8-3-9-15-22;/h1-19H,26H2;1H

description: dataset for electron ionisation mass spectrometry (EI-MS) MS (FAB, 3-NBA), m/z (%): 336 (14) [M-Cl]+, 335 (48) [M-H-Cl]+, 259 (20), 258 (100), 180 (21), 165 (17). HRMS–FAB (m/z): [M-Cl]+ calcd for C25H22N 336.1747; found 336.1748.
DOI: 10.14272/ggyqdmhuvmiefm-uhfffaoysa-n/chmo0000563
title: fast-atom bombardment mass spectrometry (FABMS) (4-tritylaniline;hydrochloride)
title: InChI=1S/C25H21N.ClH/c26-24-18-16-23(17-19-24)25(20-10-4-1-5-11-20,21-12-6-2-7-13-21)22-14-8-3-9-15-22;/h1-19H,26H2;1H

description: dataset for fast-atom bombardment mass spectrometry (FABMS) MS (FAB, 3-NBA), m/z (%): 337 (28), 336 (100) [M-Cl]+, 335 (36), 258 (34), 243 (17), 165 (12), 154 (29), 138 (11), 137 (17), 136 (23).
DOI: 10.14272/ggyqdmhuvmiefm-uhfffaoysa-n.3
title: 4-Tritylaniline hydrochloride
title: InChI=1S/C25H21N.ClH/c26-24-18-16-23(17-19-24)25(20-10-4-1-5-11-20,21-12-6-2-7-13-21)22-14-8-3-9-15-22;/h1-19H,26H2;1H

description: This is a physical chemical entity[CHEBI_24431] associated with a molecule[CHEBI_25367]. The molecule[CHEBI_25367] can be described by the following structural desciptors[cheminf_000085]: InChI descriptor[cheminf_000113]: InChI=1S/C25H21N.ClH/c26-24-18-16-23(17-19-24)25(20-10-4-1-5-11-20,21-12-6-2-7-13-21)22-14-8-3-9-15-22;/h1-19H,26H2;1H, and canonical SMILES descriptor[cheminf_000007]: [NH3+]c1ccc(cc1)C(c1ccccc1)(c1ccccc1)c1ccccc1.[Cl-], and by the IUPAC name[cheminf_000107]: 4-tritylaniline;hydrochloride. The physical chemical entity[CHEBI_24431] has a component solvent[CHEBI_46787] which is described by the canonical SMILES descriptor[cheminf_000007]: The physical chemical entity[CHEBI_24431] has the following Sample ID as registered in the research data repository chemotion (www.chemotion-repository.net, https://doi.org/10.25504/FAIRsharing.iagXcR): CRS-32758 The physical chemical entity[CHEBI_24431] can be described by the physical descriptors [CHEMINF_000025]: Melting point descriptor[CHEMINF_000256]: Boiling point descriptor[CHEMINF_000257]: Refractive index descriptor[CHEMINF_000253]: The physical chemical entity[CHEBI_24431] can be further described by the following assays[OBI:0000070][CHMO:0001133]: CHMO:0000630 | infrared absorption spectroscopy (IR) CHMO:0000563 | fast-atom bombardment mass spectrometry (FABMS) CHMO:0000480 | electron ionisation mass spectrometry (EI-MS) CHMO:0000593 | 1H nuclear magnetic resonance spectroscopy (1H NMR) The physical chemical entity[CHEBI_24431] was deposited to the Molecule Archive of the Karlsruhe Insitute of Technology (KIT) with the following Sample ID: Used ontologies: CHEBI - Chemical Entities of Biological Interest CHEMINF - chemical information ontology (information entities about chemical entities) CHMO - Chemical Methods Ontology OBI - Ontology for Biomedical Investigations
DOI: 10.14272/ggyqdmhuvmiefm-uhfffaoysa-n/chmo0000630.2
title: infrared absorption spectroscopy (IR) (4-tritylaniline;hydrochloride)
title: InChI=1S/C25H21N.ClH/c26-24-18-16-23(17-19-24)25(20-10-4-1-5-11-20,21-12-6-2-7-13-21)22-14-8-3-9-15-22;/h1-19H,26H2;1H

description: dataset for infrared absorption spectroscopy (IR) IR (ATR, ṽ) = 3366 (vw), 3271 (w), 3030 (vw), 2968 (w), 2785 (w), 2597 (w), 1594 (w), 1528 (vw), 1507 (m), 1490 (m), 1441 (w), 1421 (w), 1215 (w), 1184 (w), 1163 (w), 1082 (w), 1050 (w), 1034 (w), 1021 (w), 887 (w), 820 (w), 766 (w), 748 (vs), 724 (w), 700 (vs), 681 (w), 657 (w), 643 (w), 630 (vs), 619 (w), 584 (w), 541 (w), 518 (m), 497 (m), 483 (m), 418 (w), 375 (m) cm–1.
DOI: 10.14272/ggyqdmhuvmiefm-uhfffaoysa-n/chmo0000593
title: 1H nuclear magnetic resonance spectroscopy (1H NMR) (4-tritylaniline;hydrochloride)
title: InChI=1S/C25H21N.ClH/c26-24-18-16-23(17-19-24)25(20-10-4-1-5-11-20,21-12-6-2-7-13-21)22-14-8-3-9-15-22;/h1-19H,26H2;1H

description: dataset for 1H nuclear magnetic resonance spectroscopy (1H NMR) 1H NMR (400 MHz, DMSO-d6 [2.50 ppm], ppm) δ = 7.30–7.26 (m, 6H), 7.20–7.18 (m, 3H), 7.13–7.12 (m, 6H), 6.92–6.90 (m, 2H), 6.74–6.72 (m, 2H). Missing signals: Amine signals (3H) not visible in the spectrum. Impurities: unknown impurities at 7.16 , 6.82, 6.80 ppm.
DOI: 10.57745/y3yvhu
title: Table Trees.txt

description: :unav
DOI: 10.57745/muloqz
title: Table Tree Rings.txt

description: :unav
DOI: 10.6084/m9.figshare.24631095
title: Supplementary Material for: Co-culture device for in vitro high throughput analysis of cancer associated fibroblast and cancer cell interactions

description: Abstract Introduction Cancers in general, and specifically lung cancer, continue to have low patient survival rates when the patient is at an advanced stage when diagnosed. It appears that the local environment, especially fibroblasts and their signaling molecules, tends to induce metastasis, increase cancer cell resistance to treatment, and aid in tumor growth rates. Since 3-D models quickly become too complex and/or expensive, and therefore rarely leave the lab they are developed in, it is interesting to develop a 2-D model that more closely mimics the clustered tumor formation and bulk interaction with a surrounding fibroblast environment. Methods In the present study, we utilize an off-the-shelf stereolithography 3-D printer, standard use well plates, magnets, and metallic beads to create a customizable 2-D co-culture system capable of being analyzed quantitatively with staining and qualitatively with standard fluorescent/brightfield microscopy to determine cancer-fibroblast interactions while also being able to test chemotherapeutic drugs in a high-throughput manner with standard 96-well plates. Results Comparisons from monoculture and co-culture growth rates shows that the presence of fibroblasts allows for significantly increased growth rates for H460 cancer. Additionally, viability of cancer cells can be quantified with simple cell staining methods and morphology and cell-cell interactions can be observed and studied. Discussion The high throughput model demonstrates that boundary condition changes can be observed between cancer cells and fibroblasts based upon the different chemotherapeutics that have been administered.
DOI: 10.6084/m9.figshare.24631095.v1
title: Supplementary Material for: Co-culture device for in vitro high throughput analysis of cancer associated fibroblast and cancer cell interactions

description: Abstract Introduction Cancers in general, and specifically lung cancer, continue to have low patient survival rates when the patient is at an advanced stage when diagnosed. It appears that the local environment, especially fibroblasts and their signaling molecules, tends to induce metastasis, increase cancer cell resistance to treatment, and aid in tumor growth rates. Since 3-D models quickly become too complex and/or expensive, and therefore rarely leave the lab they are developed in, it is interesting to develop a 2-D model that more closely mimics the clustered tumor formation and bulk interaction with a surrounding fibroblast environment. Methods In the present study, we utilize an off-the-shelf stereolithography 3-D printer, standard use well plates, magnets, and metallic beads to create a customizable 2-D co-culture system capable of being analyzed quantitatively with staining and qualitatively with standard fluorescent/brightfield microscopy to determine cancer-fibroblast interactions while also being able to test chemotherapeutic drugs in a high-throughput manner with standard 96-well plates. Results Comparisons from monoculture and co-culture growth rates shows that the presence of fibroblasts allows for significantly increased growth rates for H460 cancer. Additionally, viability of cancer cells can be quantified with simple cell staining methods and morphology and cell-cell interactions can be observed and studied. Discussion The high throughput model demonstrates that boundary condition changes can be observed between cancer cells and fibroblasts based upon the different chemotherapeutics that have been administered.
DOI: 10.5281/zenodo.10183318
title: UAV Aerial videos and paper Original images

description: The original image file contains 13 videos and original image data captured by drones in the air.
DOI: 10.5281/zenodo.10183317
title: UAV Aerial videos and paper Original images

description: The original image file contains 13 videos and original image data captured by drones in the air.
DOI: 10.6084/m9.figshare.24625413
title: Query results and Code Book for SLR on Smart City Challenges

description: Study on Smart City Challenges
DOI: 10.5281/zenodo.10203391
title: [Supplementary material] Machine Learning-driven Testing of Web APIs

description: This is the supplementary material of the paper entitled "Machine Learning-driven Testing of Web APIs".
DOI: 10.5281/zenodo.10203392
title: [Supplementary material] Machine Learning-driven Testing of Web APIs

description: This is the supplementary material of the paper entitled "Machine Learning-driven Testing of Web APIs".
DOI: 10.5281/zenodo.10171187
title: Expanding the chemical space using a Chemical Reaction Knowledge Graph

description: This contains:

the reaction graph dataset used to train the link prediction model
Homepage: https://github.com/MolecularAI/reaction-graph-link-prediction
DOI: 10.5281/zenodo.10171188
title: Expanding the chemical space using a Chemical Reaction Knowledge Graph

description: This contains:

the reaction graph dataset used to train the link prediction model
Homepage: https://github.com/MolecularAI/reaction-graph-link-prediction
DOI: 10.5281/zenodo.10118868
title: Italian Nuts2 Sex Ratio - Workshop Biodemography - Example

description: This is a sample dataset for the Biodemography Workshop. Within this dataset, input files related to demographic statistics will be considered, specifically population by gender and by Nuts2 in Italy, as well as shapefiles for map creation. The variables to be analyzed include the ratio between male and female, and vice versa. The final output consists of two maps. The data source is Istat, which provides these with a CC BY license:
1-https://demo.istat.it/app/?i=POS&l=it
2-https://www.istat.it/it/archivio/222527
To conduct the analysis, the open-source software R-Studio was used. The data management methodology will also be outlined in a Data Management Plan, written using Overleaf, in which we will provide more detailed information.
DOI: 10.5281/zenodo.10118869
title: Italian Nuts2 Sex Ratio - Workshop Biodemography - Example

description: This is a sample dataset for the Biodemography Workshop. Within this dataset, input files related to demographic statistics will be considered, specifically population by gender and by Nuts2 in Italy, as well as shapefiles for map creation. The variables to be analyzed include the ratio between male and female, and vice versa. The final output consists of two maps. The data source is Istat, which provides these with a CC BY license:
1-https://demo.istat.it/app/?i=POS&l=it
2-https://www.istat.it/it/archivio/222527
To conduct the analysis, the open-source software R-Studio was used. The data management methodology will also be outlined in a Data Management Plan, written using Overleaf, in which we will provide more detailed information.
DOI: 10.6084/m9.figshare.24631174
title: Rapid loading and deformation of soft sediments during emplacement of a Lava Delta in the Vøring Basin, Mid-Norwegian Margin

description: Egg-box dimension measurements.
DOI: 10.6084/m9.figshare.24631174.v1
title: Rapid loading and deformation of soft sediments during emplacement of a Lava Delta in the Vøring Basin, Mid-Norwegian Margin

description: Egg-box dimension measurements.
DOI: 10.4121/6e5f65f6-530f-438d-8e43-3593e259aaba
title: Data underlying the publication: Hydrological consequences of controlled drainage with subirrigation

description: Controlled drainage with subirrigation (CD-SI) could be a viable measure to i) retain, ii) recharge, and iii) discharge recharge fresh water in agricultural fields. Four field CD-SI pilots with varying geohydrological conditions in the sandy Pleistocene uplands in the Netherlands were monitored (minimum 5 years) to study the effects on groundwater level, soil moisture content and soil water potential. Measurements include time series of groundwater level, soil moisture content, ditch level and CD-SI crest level, pit levels, and water supply. Field data were used for dynamic modelling with the agro-hydrological model Soil-Water-Atmosphere-Plant (SWAP). Calibrated SWAP models were used to i) model CD-SI systems dynamically and ii) model the hydrological consequences of subirrigation. Field measurements on four experimental plots showed that the water supply by to CD-SI systems can be high (ranging between roughly 500 mm to 1000 mm in the field sites), but CD-SI systems are able to raises the groundwater level such that soil water availability for crops increases. Furthermore, this study showed that CD-SI systems alter the hydrological fluxes significantly. Comparison of the four experimental fields also showed that a resistance to downward flow is needed to reduce downward seepage losses. Excessive downward seepage, or drainage losses towards surface water, increase the required water supply. However, unnecessary ditch drainage losses can be avoided by adapting the surface water level to the groundwater level. The data of these field experiments are required to understand the real-world situation better, leading to better models in terms of schematization, processes modelled, and model parameter values. This study showed that field pilots varying in geohydrological conditions could be modelled acceptably well with using SWAP. Both the required water supply and the water level in the control pit of the CD-SI system were simulated dynamically, which is a key element in understanding the functioning of CD-SI systems. The process-based model results lead to insight in the water balance components, also those components that cannot be (easily) measured in the field, and for in (extreme dry or wet) meteorological conditions that were not part of the experimental periods. Based on this research a number of recommendations are given to improve the implementation and operation of CD-SI systems.
DOI: 10.4121/6e5f65f6-530f-438d-8e43-3593e259aaba.v3
title: Data underlying the publication: Hydrological consequences of controlled drainage with subirrigation

description: Controlled drainage with subirrigation (CD-SI) could be a viable measure to i) retain, ii) recharge, and iii) discharge recharge fresh water in agricultural fields. Four field CD-SI pilots with varying geohydrological conditions in the sandy Pleistocene uplands in the Netherlands were monitored (minimum 5 years) to study the effects on groundwater level, soil moisture content and soil water potential. Measurements include time series of groundwater level, soil moisture content, ditch level and CD-SI crest level, pit levels, and water supply. Field data were used for dynamic modelling with the agro-hydrological model Soil-Water-Atmosphere-Plant (SWAP). Calibrated SWAP models were used to i) model CD-SI systems dynamically and ii) model the hydrological consequences of subirrigation. Field measurements on four experimental plots showed that the water supply by to CD-SI systems can be high (ranging between roughly 500 mm to 1000 mm in the field sites), but CD-SI systems are able to raises the groundwater level such that soil water availability for crops increases. Furthermore, this study showed that CD-SI systems alter the hydrological fluxes significantly. Comparison of the four experimental fields also showed that a resistance to downward flow is needed to reduce downward seepage losses. Excessive downward seepage, or drainage losses towards surface water, increase the required water supply. However, unnecessary ditch drainage losses can be avoided by adapting the surface water level to the groundwater level. The data of these field experiments are required to understand the real-world situation better, leading to better models in terms of schematization, processes modelled, and model parameter values. This study showed that field pilots varying in geohydrological conditions could be modelled acceptably well with using SWAP. Both the required water supply and the water level in the control pit of the CD-SI system were simulated dynamically, which is a key element in understanding the functioning of CD-SI systems. The process-based model results lead to insight in the water balance components, also those components that cannot be (easily) measured in the field, and for in (extreme dry or wet) meteorological conditions that were not part of the experimental periods. Based on this research a number of recommendations are given to improve the implementation and operation of CD-SI systems.
DOI: 10.6084/m9.figshare.24591297
title: [<sup>15</sup>N]<i>Ab</i>HisG<sub>S</sub> Mass Spec Raw Data

description: Raw mass spec data for [<sup>15</sup>N]<i>Ab</i>HisG<sub>S</sub>.
DOI: 10.6084/m9.figshare.24591297.v1
title: [<sup>15</sup>N]<i>Ab</i>HisG<sub>S</sub> Mass Spec Raw Data

description: Raw mass spec data for [<sup>15</sup>N]<i>Ab</i>HisG<sub>S</sub>.
DOI: 10.6084/m9.figshare.24591324.v1
title: [<sup>13</sup>C,<sup>15</sup>N]R70A-<i>Ab</i>HisG<sub>S</sub> Mass Spec Raw Data

description: Raw data of the [<sup>13</sup>C,<sup>15</sup>N]-labelled R70A-<i>Ab</i>HisG<sub>S</sub> mutant.
DOI: 10.6084/m9.figshare.24591384
title: Unlabelled R70A-<i>Ab</i>HisG<sub>S </sub>Mass Spec Raw Data

description: Raw mass spec data for the unlabelled R70A-<i>Ab</i>HisG<sub>S</sub> mutant.
DOI: 10.6084/m9.figshare.24591384.v1
title: Unlabelled R70A-<i>Ab</i>HisG<sub>S </sub>Mass Spec Raw Data

description: Raw mass spec data for the unlabelled R70A-<i>Ab</i>HisG<sub>S</sub> mutant.
DOI: 10.6084/m9.figshare.24591399
title: [<sup>2</sup>H,<sup>15</sup>N]<i>Ab</i>HisG<sub>S</sub> Mass Spec Raw Data

description: Raw mass spec data for [<sup>2</sup>H,<sup>15</sup>N]<i>Ab</i>HisG<sub>S</sub>.
DOI: 10.6084/m9.figshare.24591399.v1
title: [<sup>2</sup>H,<sup>15</sup>N]<i>Ab</i>HisG<sub>S</sub> Mass Spec Raw Data

description: Raw mass spec data for [<sup>2</sup>H,<sup>15</sup>N]<i>Ab</i>HisG<sub>S</sub>.
DOI: 10.6084/m9.figshare.24591411
title: [<sup>2</sup>H,<sup>13</sup>C,<sup>15</sup>N]<i>Ab</i>HisG<sub>S</sub> Mass Spec Raw Data

description: Raw mass spec data for [<sup>2</sup>H,<sup>13</sup>C,<sup>15</sup>N]<i>Ab</i>HisG<sub>S</sub>.
DOI: 10.6084/m9.figshare.24591411.v1
title: [<sup>2</sup>H,<sup>13</sup>C,<sup>15</sup>N]<i>Ab</i>HisG<sub>S</sub> Mass Spec Raw Data

description: Raw mass spec data for [<sup>2</sup>H,<sup>13</sup>C,<sup>15</sup>N]<i>Ab</i>HisG<sub>S</sub>.
DOI: 10.6084/m9.figshare.24591258.v1
title: [<sup>13</sup>C,<sup>15</sup>N]<i>Ab</i>HisG<sub>S</sub> Mass Spec Raw Data

description: Raw mass spec data for [<sup>13</sup>C<sup>15</sup>N]<i>Ab</i>HisG<sub>S</sub>.
DOI: 10.6084/m9.figshare.24591267.v1
title: Unlabelled <i>Ab</i>HisG<sub>S</sub> Mass Spec Raw Data

description: Raw mass spec data of unlabelled <i>Ab</i>HisG<sub>S</sub> produced in M9 minimal medium using standard-OD<sub>600</sub> cell growth method.
DOI: 10.6084/m9.figshare.24591324
title: [<sup>13</sup>C,<sup>15</sup>N]R70A-<i>Ab</i>HisG<sub>S</sub> Mass Spec Raw Data

description: Raw data of the [<sup>13</sup>C,<sup>15</sup>N]-labelled R70A-<i>Ab</i>HisG<sub>S</sub> mutant.
DOI: 10.6084/m9.figshare.24560386
title: HisG_Short_uniprot_align

description: Output of HisG<sub>s</sub> sequence alignment.
DOI: 10.6084/m9.figshare.24581301
title: High OD<sub>600</sub> Unlabelled <i>Ab</i>HisG<sub>S</sub> Mass Spec

description: Mass Spec raw data of unlabelled <i>Ab</i>HisG<sub>S</sub> produced in M9 minimal medium using the high-OD cell growth protocol.
DOI: 10.6084/m9.figshare.24581301.v1
title: High OD<sub>600</sub> Unlabelled <i>Ab</i>HisG<sub>S</sub> Mass Spec

description: Mass Spec raw data of unlabelled <i>Ab</i>HisG<sub>S</sub> produced in M9 minimal medium using the high-OD cell growth protocol.