cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ph510/5
title: Force Field Parameters

description: These are MD trajectories to accompany the paper: "Lipid Binding and Force Transduction in MscL: A Continuum-Molecular Approach" by Juan M. Vanegas and Marino Arroyo. PLoS ONE 2014. All trajectories were generated with GROMACS version 4.5.5 (www.gromacs.org). All trajectoories can be read and analyzed by the standard GROMACS utilities. Trajectories (.xtc) can also be visualized by common molecular graphics programs such as UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) or VMD (http://www.ks.uiuc.edu/Research/vmd/). Topology files in text (.top) and binary (.tpr) form are included, as well as simulation parameters (.mdp). In some cases text files (.xvg) including coordinate information are also included. The file MscL_Equilibration.tar.gz contains the trajectory corresponding to the 500 ns equilibration period of the MscL Channel embedded in the POPE bilayer. The file Local_Stress_and_Traction.tar.gz contains the trajectories for the tensionless and tensioned simulations, as well as the files needed to visualize the traction on the surface of the protein. The stress tensor was calculated with a custom version of GROMACS (http://www.lacan.upc.edu/LocalStressFromMD) and the files can be visualized with the program ParaView. The file Arrhenius_Bell_unbinding.tar.gz contains the steered MD simulation trajectories used to estimate the strength of lipid binding to the MscL protein. The file Channel_Actuation.tar.gz contains the steered MD simulation trajectories used to actuate the MscL channel by pulling on protein-bound lipids. Finally, the file force_field_parameters.tar.gz contains the parameters used in all of the simulations. We used the G43A1-S3 lipid parameters in combination with the G54A7 protein parameters.
DOI: 10.5061/dryad.j8776/1
title: CytB+RAG1+R35

description: Alignment file (nexus format). Matrix contains the molecular markers CytB, RAG1 and R35. All sequences were downloaded from GenBank. Outgroups are excluded.
DOI: 10.5061/dryad.j8776/2
title: CytB+RAG1+R35-inc-outgroups

description: Alignment file (nexus format). Matrix contains the molecular markers CytB, RAG1 and R35. All sequences were downloaded from GenBank.
DOI: 10.5061/dryad.j8776/3
title: BEAST.xml

description: Input file for divergence time analysis using BEAST.
DOI: 10.5061/dryad.j8776/4
title: mcmctree._sequence_file

description: Sequence input file for divergence time analysis using MCMCTREE.
DOI: 10.5061/dryad.j8776/5
title: mcmctree._tree_file._uniform_priors

description: Input tree for divergence time analysis in MCMCTREE. Includes minimum and maximum constraints on each node.
DOI: 10.5061/dryad.j8776/6
title: mcmctree.usedata1 control file

description: Input control file for divergence time analysis in MCMCTREE.
DOI: 10.5061/dryad.j8776/7
title: mcmctree._tree_file._minimum_bounds

description: Input tree for divergence time analysis in MCMCTREE. Includes minimum constraints only on each node.
DOI: 10.5061/dryad.j8776/8
title: mcmctree.usedata2 control file

description: Input control file for divergence time analysis in MCMCTREE, using the approximate likelihood method.
DOI: 10.5061/dryad.c574h/1
title: Combined Nuclear and Chloroplast Matrix

description: This matrix was used to construct the tree presented in Figure 1. The data partitioning scheme is the following:     Nuclear = 1-14246     Chloroplast = 14247-19949
DOI: 10.5061/dryad.c574h/2
title: Maximum Likelihood Tree from combined matrix

description: This is the tree (figure 1) resulting from the raxml analysis.
DOI: 10.5061/dryad.c574h/3
title: Chloroplast Orthologs

description: Results for Chloroplast genome orthology search
DOI: 10.5061/dryad.c574h/4
title: Nuclear Orthologs

description: Results for Nuclear genome orthology search
DOI: 10.5061/dryad.c574h/5
title: Matrix for Community Phylo Test

description: Concatenated data used to generate the PhyloTest tree. These data were used to test models of phylogenetic community structure in picante.
DOI: 10.5061/dryad.c574h/6
title: Phylo Test Tree

description: Resulting maximum likelihood tree from phylotest matrix. These data were used to test models of phylogenetic community structure in picante.
DOI: 10.5061/dryad.kt2g7/1
title: Results flume tank experiment

description: Seed retrieval data of feeding trials with eight individual mallards in the five experimental treatments. This file reports individual mallard, date of feeding trial, experimental treatment (0=resting, 1=floating, 2-4=swimming at increasing speed), swimming speed (m/s), retention time (hours after feeding), seed species name, number of seeds retrieved per hour and seed size (length in mm).
DOI: 10.5061/dryad.22p7m.2
title: Data from: Lessons learned from microsatellite development for non-model organisms using 454 pyrosequencing
DOI: 10.5061/dryad.22p7m.2/1.1
title: Schoebel et al. R-script

description: R script to use with MSATCOMMANDER output files for microsatellite mining.
DOI: 10.5061/dryad.22p7m.2/2.1
title: Schoebel et al. supplementary materials

description: Online supplementary material
DOI: 10.25919/0cma-0t40
title: ForestTrav Data Set

description: A data set containing labeled and voxelized point cloud data. The data set combines hand-labeled data (HL) and data labeled through robot experience (LfE).
DOI: 10.17632/tnxh2mf7cz.1
title: Sepsis

description: Sepsis patients from the Mimic-iv database
DOI: 10.17632/832pbjkzc9.1
title: Data for:  Enhancing Understanding of Niche Indicators and CSR Strategies of Woody Plants in Remnant Forests: Exploring the Impact of Surrounding Spatiotemporal Urban Expansion

description: This data set contains all data used for analyzing the influences of temporal and spatial characteristics of urbanization on niche indicators and CSR strategies of woody plants in urban remnant forests in Guiyang, China. It includes urban expansion indicators surrounding remnant patches, niche indicators for woody plants and CSR strategies for woody plants.
DOI: 10.17632/832pbjkzc9.2
title: Data for:  Enhancing Understanding of Niche Indicators and CSR Strategies of Woody Plants in Remnant Forests: Exploring the Impact of Surrounding Spatiotemporal Urban Expansion

description: This data set contains all data used for analyzing the influences of temporal and spatial characteristics of urbanization on niche indicators and CSR strategies of woody plants in urban remnant forests in Guiyang, China. It includes urban expansion indicators surrounding remnant patches, niche indicators for woody plants and CSR strategies for woody plants.
DOI: 10.17632/r6rhrffcv3.1
title: Synthetic near-source acceleration waveforms for the 2018 Hokkaido Eastern Iburi earthquake

description: Synthetic near-source acceleration waveforms for the 2018 Hokkaido Eastern Iburi earthquake (Matlab MAT-file: Synthetic_Acceleration_Waveform_Dataset.mat). Seismic ground motions in the near-source area are spatially evaluated by combining the ground motion model and the phase characteristics extracted from downhole records. Detailed workflow can be found in the attached documents.
DOI: 10.17632/r6rhrffcv3.2
title: Synthetic near-source acceleration waveforms for the 2018 Hokkaido Eastern Iburi earthquake

description: Synthetic near-source acceleration waveforms for the 2018 Hokkaido Eastern Iburi earthquake (Matlab MAT-file: Synthetic_Acceleration_Waveform_Dataset.mat). Seismic ground motions in the near-source area are spatially evaluated by combining the ground motion model and the phase characteristics extracted from downhole records. Detailed workflow can be found in the attached documents.
DOI: 10.17632/2m3r9csbmd.1
title: Cross-Sectional Analysis of Marginal Expenditures Associated with Melanoma Care in the United States

description: Supplemental file for the manuscript titled "Cross-Sectional Analysis of Marginal Expenditures Associated with Melanoma Care in the United States" is provided here for review purposes and benefit of readers
DOI: 10.17632/2m3r9csbmd.2
title: Marginal Healthcare Expenditures for Melanoma Care in the United States: A Cross-sectional Study

description: Supplemental file for the manuscript titled "Cross-Sectional Analysis of Marginal Expenditures Associated with Melanoma Care in the United States" is provided here for review purposes and benefit of readers
DOI: 10.17632/2xkfkcsxx8.1
title: Full framework for a structured ethical review to assess potential adverse outcomes of wastewater-based testing efforts. Specific categories originated from either Marx 1997 [*] or Hrudey et al., 2021 [†].

description: This ethical review table is associated with the publication Bowes et al., "Structured Ethical Review for Wastewater-Based Testing to Support Public Health" 2023. Environmental Science and Technology https://doi.org/10.1021/acs.est.3c04529. Any usage or reproduction of this work must cite the originating manuscript.
DOI: 10.57841/casdc.0001937
title: ATP改性UHMWPE水润滑轴承材料的摩擦学特性研究
DOI: 10.17632/ghgw5wg3sf.1
title: IMPACT OF SENSE OF COHERENCE ON ORAL HEALTH, ORAL HEALTH RELATED BEHAVIOURS & ORAL HEALTH RELATED QUALITY OF LIFE AMONG AN ADOLESCENT POPULATION 

description: this data is the data of a PhD thesis
DOI: 10.5281/zenodo.8278416
title: Anaerobic Methane Oxidation is Quantitatively Important in Deeper Peat Layers of Boreal Peatlands: Evidence from in situ Stable Isotopes Depth Profiles, Anaerobic Incubations, and Microbial Communities

description: Dataset contains complete result of laboratory anaerobic incubations with peat samples from 3 West Siberian peatlands. Before the incubation, the peat samples were thoroughly mixed to ensure homogeneity. Aliquots (140 ± 1 g) were mixed with distilled water at a ratio of 1:2 by weight, and then placed into sterile 500 ml glass bottles, flushed with pure argon (99.9999%, Voessen, Russia) for 5 min to remove any oxygen and sealed with butyl rubber septa to maintain anaerobic conditions. The bottles were kept at +5°C for 1 day to allow the equilibration between the peat and the headspace. Then bottles were again thoroughly flushed with argon for 5 min, sealed, and an additional 5 ml of argon was added to prevent air diffusion into the bottle headspace. The incubation was performed in two different ways: i) unamended control, and ii) amended with 10 ml of CH<sub>3</sub>F to inhibit acetotrophic methanogenesis. Peat samples from the depths of 15-20 and 40-50 cm were incubated at 15° and 10°C, respectively, for a period of 60 days, whereas deeper peat samples were incubated at 5°С, representing the temperature of the deeper peat layers of Mukhrino bog during the snow-free period for 150 days. Gas (1 mL for Н<sub>2</sub>, CH<sub>4</sub> and CO<sub>2</sub> concentration, 1 mL for stable isotope compositions) and liquid (1 mL for organic acids) samples were taken for analysis every two weeks after manually shaking the bottles for approximately 5 s to equilibrate the gaseous and aqueous phases. At the end of the incubation, methane headspace concentrations ranged from 1 to 3 % for deeper samples. The incubations with and without CH<sub>3</sub>F addition were carried out in three replicates for samples from Mukhrino bog and in two replicates for Chistoe and Lempino bogs. Net methane and CO<sub>2</sub> production were calculated from the gas concentrations, the volume of the gas space, and the water volume using the ideal gas law. Gas solubility was calculated using Henry’s law. The reported net methane and CO<sub>2</sub> production are the averages of 2-3 replicates. See further details in a paper with the same title and the first author.
DOI: 10.5281/zenodo.8278415
title: Anaerobic Methane Oxidation is Quantitatively Important in Deeper Peat Layers of Boreal Peatlands: Evidence from in situ Stable Isotopes Depth Profiles, Anaerobic Incubations, and Microbial Communities

description: Dataset contains complete result of laboratory anaerobic incubations with peat samples from 3 West Siberian peatlands. Before the incubation, the peat samples were thoroughly mixed to ensure homogeneity. Aliquots (140 ± 1 g) were mixed with distilled water at a ratio of 1:2 by weight, and then placed into sterile 500 ml glass bottles, flushed with pure argon (99.9999%, Voessen, Russia) for 5 min to remove any oxygen and sealed with butyl rubber septa to maintain anaerobic conditions. The bottles were kept at +5°C for 1 day to allow the equilibration between the peat and the headspace. Then bottles were again thoroughly flushed with argon for 5 min, sealed, and an additional 5 ml of argon was added to prevent air diffusion into the bottle headspace. The incubation was performed in two different ways: i) unamended control, and ii) amended with 10 ml of CH<sub>3</sub>F to inhibit acetotrophic methanogenesis. Peat samples from the depths of 15-20 and 40-50 cm were incubated at 15° and 10°C, respectively, for a period of 60 days, whereas deeper peat samples were incubated at 5°С, representing the temperature of the deeper peat layers of Mukhrino bog during the snow-free period for 150 days. Gas (1 mL for Н<sub>2</sub>, CH<sub>4</sub> and CO<sub>2</sub> concentration, 1 mL for stable isotope compositions) and liquid (1 mL for organic acids) samples were taken for analysis every two weeks after manually shaking the bottles for approximately 5 s to equilibrate the gaseous and aqueous phases. At the end of the incubation, methane headspace concentrations ranged from 1 to 3 % for deeper samples. The incubations with and without CH<sub>3</sub>F addition were carried out in three replicates for samples from Mukhrino bog and in two replicates for Chistoe and Lempino bogs. Net methane and CO<sub>2</sub> production were calculated from the gas concentrations, the volume of the gas space, and the water volume using the ideal gas law. Gas solubility was calculated using Henry’s law. The reported net methane and CO<sub>2</sub> production are the averages of 2-3 replicates. See further details in a paper with the same title and the first author.
DOI: 10.6084/m9.figshare.23935683
title: <b>A lightweight </b><b>spatiotemporal graph dilated convolutional network</b>

description: <b>Codes and Data</b>
DOI: 10.6084/m9.figshare.23935683.v1
title: <b>A lightweight </b><b>spatiotemporal graph dilated convolutional network</b>

description: <b>Codes and Data</b>
DOI: 10.17632/hxhkphgmtt.1
title: China annual rapeseed maps at 30 m spatial resolution from 2000 to 2022

description: Format: .tif
Spatial resolution: 30 m
Temporal resolution: Yearly (2000-2022)
Coordinate system: WGS 1984 UTM Zone 48N
DOI: 10.17632/zrc982rvjm.1
title: MeLB Raw DNA Methylation Data; Herrgott et al., 2023

description: Raw cfDNA methylation data associated with 234 liquid biopsy serum and plasma collections from meningioma (MNG; n=93) and non-MNG (Other CNS diseases, glioma, pituitary tumors; n = 141) are located in folder 'LB IDATs'.   Raw cfDNA methylation data associated with tumor tissue collections from meningioma (MNG; n=31) are located in folder 'Tissue IDATs'. Additional generated random forest machine learning classifiers (d-MeLB & p-MeLB) and associated R-based syntax used for preprocessing of samples and application of classifiers are provided (MeLB_Script.R). Also, source syntax which guides the application of a random forest classifier (d-MeLB) is also included (dMeLB_MasterSyntax.R).
DOI: 10.17632/zrc982rvjm.2
title: MeLB Raw DNA Methylation Data; Herrgott et al., 2023

description: Raw cfDNA methylation data associated with 234 liquid biopsy serum and plasma collections from meningioma (MNG; n=93) and non-MNG (Other CNS diseases, glioma, pituitary tumors; n = 141) are located in folder 'LB IDATs'.   Raw DNA methylation data associated with tumor tissue collections from meningioma (MNG; n=88) are located in folder 'Tissue IDATs'. Additional generated random forest machine learning classifiers (d-MeLB & p-MeLB) are provided (Classifiers.zip).
DOI: 10.17632/fypp6xhkjy.1
title: Colorectal cancer organoid-stroma biobank allows subtype-specific assessment of individualized therapy responses

description: 2 Tab-delimited Text files contain the raw luminescence data of the drug treatment experiments:

Drug_sensitivity_all_lines.txt:
Sensitivity of patient-derived tumor organoids to 5-FU, Oxaliplatin, SN-38 and Gefitinib in mono- and coculture with auto- or heterologous CAFs.

Chemogenomic_coculture_screen.txt:
Sensitivity of patient-derived tumor organoids to chemogenomic drug library. Experiments were performed in presence of CAFs and in presence or absence of a sub-lethal concentration of Gefitinib.
DOI: 10.57841/casdc.0001938
title: 自然环境条件下轮轨接触黏着特性研究进展
DOI: 10.4121/1bbc3a27-c9b0-462e-9991-22b63d723605
title: Dataset underlying the publication: “Do I See What You See?”—Differentiation of Stakeholders in Assessing Heritage Significance of Neighbourhood Attributes

description: This dataset is underlying the analysis of interview data, about the heritage assessment of neighbourhood attributes. It shows on what scale levels different participants mention attributes, and what type of attributes they mention. It includes individual reports (per participant) and group overviews (per stakeholder group).
DOI: 10.4121/1bbc3a27-c9b0-462e-9991-22b63d723605.v1
title: Dataset underlying the publication: “Do I See What You See?”—Differentiation of Stakeholders in Assessing Heritage Significance of Neighbourhood Attributes

description: This dataset is underlying the analysis of interview data, about the heritage assessment of neighbourhood attributes. It shows on what scale levels different participants mention attributes, and what type of attributes they mention. It includes individual reports (per participant) and group overviews (per stakeholder group).
DOI: 10.5281/zenodo.8183014
title: Raw data for article "Iron-catalyzed synthesis of α-azido α-amino esters via the alkylazidation of alkenes"

description: Raw NMR, IR and MS data for the article "Iron-catalyzed synthesis of α-azido α-amino esters via alkylazidation of alkenes" published in <em>Org. Lett.</em> The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.
DOI: 10.5281/zenodo.8183015
title: Raw data for article "Iron-catalyzed synthesis of α-azido α-amino esters via the alkylazidation of alkenes"

description: Raw NMR, IR and MS data for the article "Iron-catalyzed synthesis of α-azido α-amino esters via alkylazidation of alkenes" published in <em>Org. Lett.</em> The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.
DOI: 10.4121/52bbc7e8-ecec-4a57-8c89-2b0bd3187b24
title: Dataset underlying the publication: Methods in assessing the values of architecture in residential neighbourhoods

description: This dataset presents the analysis of systematic literature review about methods in assessing the values of architecture in residential neighborhoods. The literature review is part of a PhD thesis and analyses scientific articles and categorises the topics they address.
DOI: 10.4121/52bbc7e8-ecec-4a57-8c89-2b0bd3187b24.v1
title: Dataset underlying the publication: Methods in assessing the values of architecture in residential neighbourhoods

description: This dataset presents the analysis of systematic literature review about methods in assessing the values of architecture in residential neighborhoods. The literature review is part of a PhD thesis and analyses scientific articles and categorises the topics they address.
DOI: 10.5281/zenodo.8210605
title: Dataset for the Literature Review in ANYMOS WP 5.1

description: Dataset for Literature Review in ANYMOS AP 5.1 <em>This work was supported by the German Federal Ministry of Education and Research (BMBF) grant number 16KISA086 (ANYMOS) and the NextGenerationEU project by the European Union (EU).</em>
DOI: 10.5281/zenodo.8210604
title: Dataset for the Literature Review in ANYMOS WP 5.1

description: Dataset for Literature Review in ANYMOS AP 5.1 <em>This work was supported by the German Federal Ministry of Education and Research (BMBF) grant number 16KISA086 (ANYMOS) and the NextGenerationEU project by the European Union (EU).</em>
DOI: 10.5517/ccdc.csd.cc24d0g1
title: CCDC 1977752: Experimental Crystal Structure Determination

description: Related Article: Guangfeng Jin|2020|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc23pt0n
title: CCDC 1957371: Experimental Crystal Structure Determination

description: Related Article: Martin Hejda, Daniel Duvinage, Enno Lork, Robert Jirásko, Antonín Lyčka, Stefan Mebs, Libor Dostál, Jens Beckmann|2020|Organometallics|39|1202|doi:10.1021/acs.organomet.0c00014
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.cc26cgnq
title: CCDC 2036813: Experimental Crystal Structure Determination

description: Related Article: Manman Zhou, Yizheng Bao, Shan Jin, Shuaishuai Wen, Shuang Chen, Manzhou Zhu|2021|Chem.Commun.|57|10383|doi:10.1039/D1CC04934H
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.cc28j20x
title: CCDC 2100808: Experimental Crystal Structure Determination

description: Related Article: Wei-Chieh Chang, Fritz Deufel, Thomas Weyhermüller, Christophe Farès, Christophe Werlé|2021|RSC Advances|11|37383|doi:10.1039/D1RA07126B
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.cc28j21y
title: CCDC 2100809: Experimental Crystal Structure Determination

description: Related Article: Wei-Chieh Chang, Fritz Deufel, Thomas Weyhermüller, Christophe Farès, Christophe Werlé|2021|RSC Advances|11|37383|doi:10.1039/D1RA07126B
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.cc297qx6
title: CCDC 2122598: Experimental Crystal Structure Determination

description: Related Article: Yohei Hattori, Ryota Kitajima, Ryota Matsuoka, Tetsuro Kusamoto, Hiroshi Nishihara, Kingo Uchida|2022|Chem.Commun.|58|2560|doi:10.1039/D1CC06555F
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.