cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4979148
title: Stem cell hierarchies and developmental origins of rhabdomyosarcoma

description: Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma of childhood and is comprised of two major molecular subtypes. Despite sharing features with skeletal muscle, the conservation of underlying cellular hierarchy with human muscle development and the identification of molecularly-defined tumor-propagating cells have not been reported. Using single-cell RNA sequencing of patient-derived RMS, DNA-barcode cell fate mapping, and antibody enrichment and functional stem cell assays using <em>in vitro</em> culture and mouse xenografts, we have uncovered tumor cell hierarchies in Fusion-negative (FN-) RMS that are shared with normal human muscle development. We also identified common developmental stages at which tumor cells become arrested. FN-RMS resemble early muscle found in embryonic and larval development, while fusion-positive (FP-)RMS express a highly specific developmental gene program found in muscle cells transiting from embryonic to fetal development at 7-7.75 weeks of age. FP-RMS also have neural-pathway enriched cell states, suggesting less-rigid adherence to muscle development hierarchies in this disease. Finally, we identify a molecularly-defined tumor-propagating cell in FN-RMS that shares remarkable similarity to the newly described bi-potent, muscle mesenchyme stem/progenitor cell that makes both muscle and osteogenic cells.
description: The compressed datasets contain all the single-cell RNA-seq and lineage tracing data in the manuscript "Stem cell hierarchies and developmental origins of rhabdomyosarcoma". After uncompressing, the root directory contains all the clustering annotation information and rhabdomyosarcoa gene modules. For each folder, there is the filtered count matrix output by Cell Ranger, and normalized and filtered Seurat RDS data. The scripts to analyze the datasets are available on GitHub https://github.com/qinqian/rms_analysis.
DOI: 10.5281/zenodo.5749799
title: PEMA databases

description: In this repo, the CREST and the RDPTClassifier oriented databases unsed in PEMA will be versioned. Training the CREST algorithm for the PR2 database output files have been added
DOI: 10.5281/zenodo.5749908
title: Random numbers

description: This is a collection of ten datasets, each containing ten iid zero-mean, unit-variance random numbers. These are used in an example of the showyourwork open source scientific article workflow.<br><br>Created using showyourwork from this GitHub repo using the following command:<br><br><pre><code class="language-bash">cd src/figures && python src/data/run_simulation.py</code></pre><br>
DOI: 10.5281/zenodo.5017851
title: Molecular Dynamics Simulation of MC-congeners in complex with PPP1 - Replicate 3

description: This data sets contains Molecular Dynamics (MD) Simulation files and analysis. Microcystin (MC) congeners were simulated in solvent (water) and in complex with protein phosphatase 1 (PPP1). MD Simulation was repeated for three times. This data is replicate 3 and related data sets are available. Please cite the original publication when using all or part of the data: S. Jaeger-Honz, J. Nitschke, S. Altaner, K. Klein, D. R. Dietrich, F. Schreiber: Investigation of microcystin conformation and binding towards PPP1 by molecular dynamics simulation. <em>Chemico-Biological Interactions</em>, 2021
description: Terms of use: These data are provided "as is", without any warranties of any kind. The data are provided under the Creative Commons Attribution 4.0 International license.
DOI: 10.5281/zenodo.5017850
title: Molecular Dynamics Simulation of MC-congeners in complex with PPP1 - Replicate 3

description: This data sets contains Molecular Dynamics (MD) Simulation files and analysis. Microcystin (MC) congeners were simulated in solvent (water) and in complex with protein phosphatase 1 (PPP1). MD Simulation was repeated for three times. This data is replicate 3 and related data sets are available. Please cite the original publication when using all or part of the data: S. Jaeger-Honz, J. Nitschke, S. Altaner, K. Klein, D. R. Dietrich, F. Schreiber: Investigation of microcystin conformation and binding towards PPP1 by molecular dynamics simulation. <em>Chemico-Biological Interactions</em>, 2021
description: Terms of use: These data are provided "as is", without any warranties of any kind. The data are provided under the Creative Commons Attribution 4.0 International license.
DOI: 10.6084/m9.figshare.17113504
title: Table S3 from Resilience of cold-water coral holobionts to thermal stress

description: List of the most abundant ASVs associated to L. pertusa and M. oculata
DOI: 10.5281/zenodo.5017839
title: Molecular Dynamics Simulation of MC-congeners in complex with PPP1 - Replicate 2

description: This data sets contains Molecular Dynamics (MD) Simulation files and analysis. Microcystin (MC) congeners were simulated in solvent (water) and in complex with protein phosphatase 1 (PPP1). MD Simulation was repeated for three times. This data is replicate 2 and related data sets are available. Please cite the original publication when using all or part of the data: S. Jaeger-Honz, J. Nitschke, S. Altaner, K. Klein, D. R. Dietrich, F. Schreiber: Investigation of microcystin conformation and binding towards PPP1 by molecular dynamics simulation. <em>Chemico-Biological Interactions</em>, 2021
description: Terms of use: These data are provided "as is", without any warranties of any kind. The data are provided under the Creative Commons Attribution 4.0 International license.
DOI: 10.5281/zenodo.5017838
title: Molecular Dynamics Simulation of MC-congeners in complex with PPP1 - Replicate 2

description: This data sets contains Molecular Dynamics (MD) Simulation files and analysis. Microcystin (MC) congeners were simulated in solvent (water) and in complex with protein phosphatase 1 (PPP1). MD Simulation was repeated for three times. This data is replicate 2 and related data sets are available. Please cite the original publication when using all or part of the data: S. Jaeger-Honz, J. Nitschke, S. Altaner, K. Klein, D. R. Dietrich, F. Schreiber: Investigation of microcystin conformation and binding towards PPP1 by molecular dynamics simulation. <em>Chemico-Biological Interactions</em>, 2021
description: Terms of use: These data are provided "as is", without any warranties of any kind. The data are provided under the Creative Commons Attribution 4.0 International license.
DOI: 10.5281/zenodo.5017745
title: Molecular Dynamics Simulation of MC-congeners in complex with PPP1 - Replicate 1

description: This data sets contains Molecular Dynamics (MD) Simulation files and analysis. Microcystin (MC) congeners were simulated in solvent (water) and in complex with protein phosphatase 1 (PPP1). MD Simulation was repeated for three times. This data is replicate 1 and related data sets are available. Please cite the original publication when using all or part of the data: S. Jaeger-Honz, J. Nitschke, S. Altaner, K. Klein, D. R. Dietrich, F. Schreiber: Investigation of microcystin conformation and binding towards PPP1 by molecular dynamics simulation. <em>Chemico-Biological Interactions</em>, 2021
description: Terms of use: These data are provided "as is", without any warranties of any kind. The data are provided under the Creative Commons Attribution 4.0 International license.
DOI: 10.5281/zenodo.5017744
title: Molecular Dynamics Simulation of MC-congeners in complex with PPP1 - Replicate 1

description: This data sets contains Molecular Dynamics (MD) Simulation files and analysis. Microcystin (MC) congeners were simulated in solvent (water) and in complex with protein phosphatase 1 (PPP1). MD Simulation was repeated for three times. This data is replicate 1 and related data sets are available. Please cite the original publication when using all or part of the data: S. Jaeger-Honz, J. Nitschke, S. Altaner, K. Klein, D. R. Dietrich, F. Schreiber: Investigation of microcystin conformation and binding towards PPP1 by molecular dynamics simulation. <em>Chemico-Biological Interactions</em>, 2021
description: Terms of use: These data are provided "as is", without any warranties of any kind. The data are provided under the Creative Commons Attribution 4.0 International license.
DOI: 10.6084/m9.figshare.17109143.v1
title: Data for ''Lake salinization drives consistent losses of zooplankton abundance and diversity across coordinated mesocosm experiments''

description: NOTE:<br>-This data set includes taxon-specific trait information only.<br>-body length = mm ; body mass = mg (see Appendix/Metadata of the paper for additional info)<br>-Environmental and abundance data reported in this paper can be found here: https://doi.org/10.5683/SP3/BIDMCI-Contact info: mphebert4@gmail.com<br><br>ABSTRACT:<br>Human-induced salinization increasingly threatens inland waters; yet we know little about the multifaceted response of lake communities to salt contamination. By conducting a coordinated experiment of lake salinization across 16 sites in North America and Europe, we quantified the response of zooplankton abundance and (taxonomic and functional) community structure to a broad gradient of environmentally relevant chloride concentrations, ranging from 4 to ca.1400 mgCl/L. We found that crustaceans were distinctly more sensitive to elevated chloride than rotifers; yet rotifers did not show compensatory abundance increases in response to crustacean declines. For crustaceans, our among-lake comparisons indicate: (1) highly consistent decreases in abundance and taxon richness with salinity; (2) widespread chloride sensitivity across major taxonomic groups (Cladocera, Cyclopoida, and Calanoida); and (3) weaker loss of functional than taxonomic diversity. Overall, our study demonstrates that aggregate properties of zooplankton communities can be affected at chloride concentrations relevant to anthropogenic salinization in lakes.<br>
DOI: 10.5281/zenodo.5713457
title: Dataset for article "Nonlinear Response of Asian Summer Monsoon Precipitation to Emission Reductions in South and East Asia"

description: Dataset and jupyter notebook relating to the journal article "Nonlinear Response of Asian Summer Monsoon Precipitation to Emission Reductions in South and East Asia". The published paper can be found at https://doi.org/10.1088/1748-9326/ac3b19 The dataset includes all model output. The jupyter notebook has all neccessary scripts for plotting the model output and reproducing figures from the article. In order to run the script please update the dataset path name and figure output path at the beginning of the notebook.
DOI: 10.5281/zenodo.4639422
title: Dataset for article "Nonlinear Response of Asian Summer Monsoon Precipitation to Emission Reductions in South and East Asia"

description: Dataset and jupyter notebook relating to the journal article "Nonlinear Response of Asian Summer Monsoon Precipitation to Emission Reductions in South and East Asia". The published paper can be found at https://doi.org/10.1088/1748-9326/ac3b19 The dataset includes all model output. The jupyter notebook has all neccessary scripts for plotting the model output and reproducing figures from the article. In order to run the script please update the dataset path name and figure output path at the beginning of the notebook.
DOI: 10.5258/soton/d2034
title: Culture Teaching Practices of Lower Secondary School ELT Teachers

description: Transcripts of classroom observations and interviews with 7 ELT teachers, eight focus group interviews with students, and interviews with two administrators and four management staff in one private school in Bangkok, Thailand. The data were collected for the PhD thesis in Modern Languages and Linguistics, University of Southampton, titled "Culture Teaching Practices of Lower Secondary School ELT Teachers from the Global English Perspective: A Qualitative Case Study in Thailand".
DOI: 10.5281/zenodo.5749788
title: Supplementary Data: A model-independent analysis of b→sμ+μ− transitions with GAMBIT's FlavBit

description: Supplementary Data A model-independent analysis of b→sμ+μ− transitions with GAMBIT's FlavBit The files in this record contain supplementary data including the samples and plotting scripts used for the results in Bhom. J et al. " A model-independent analysis of b→sμ+μ− transitions with GAMBIT's FlavBit." Samples have been created using GAMBIT and figures can be reproduced with pippi. This record contains: 2 hdf5 files containing the samples produced for this article. 2 pip files to create the figures from the samples, using pippi.
DOI: 10.5281/zenodo.5749787
title: Supplementary Data: A model-independent analysis of b→sμ+μ− transitions with GAMBIT's FlavBit

description: Supplementary Data A model-independent analysis of b→sμ+μ− transitions with GAMBIT's FlavBit The files in this record contain supplementary data including the samples and plotting scripts used for the results in Bhom. J et al. " A model-independent analysis of b→sμ+μ− transitions with GAMBIT's FlavBit." Samples have been created using GAMBIT and figures can be reproduced with pippi. This record contains: 2 hdf5 files containing the samples produced for this article. 2 pip files to create the figures from the samples, using pippi.
DOI: 10.5281/zenodo.5749922
title: Random numbers

description: This is a collection of ten datasets, each containing ten iid zero-mean, unit-variance random numbers. These are used in an example of the showyourwork open source scientific article workflow.<br><br>Created using showyourwork from this GitHub repo using the following command:<br><br><pre><code class="language-bash">cd src/figures && python src/data/run_simulation.py</code></pre><br>
DOI: 10.5281/zenodo.5720042
title: Dataset for "Mechanically robust supramolecular polymer co-assemblies"

description: Source data of the study reported in the publication entitled "Mechanically robust supramolecular polymer co-assemblies". The data should be considered together with the published manuscript and the supplementary information file.
DOI: 10.5281/zenodo.5720041
title: Dataset for "Mechanically robust supramolecular polymer co-assemblies"

description: Source data of the study reported in the publication entitled "Mechanically robust supramolecular polymer co-assemblies". The data should be considered together with the published manuscript and the supplementary information file.
DOI: 10.5281/zenodo.58985
title: Dense skeleton reconstructions of neurons in the larval zebrafish olfactory bulb

description: Large-scale reconstructions of neuronal populations are critical for structural analyses of neuronal cell types and circuits. Dense reconstructions of neurons from image data require ultrastructural resolution throughout large volumes, which can be achieved by automated volumetric electron microscopy (EM) techniques. We used serial block face scanning EM (SBEM) and conductive sample embedding to acquire an image stack from an olfactory bulb (OB) of a zebrafish larva at a voxel resolution of 9.25 × 9.25 × 25 nm<sup>3</sup> (Wanner et al., 2016). Skeletons of 1,022 neurons, ~98% of all neurons in the OB, were reconstructed by manual tracing and efficient error correction procedures. An ergonomic software package, PyKNOSSOS, was created in Python for data browsing, neuron tracing, synapse annotation, and visualization. PyKNOSSOS is available for free download (https://github.com/adwanner/PyKNOSSOS). The reconstructions as provided for download here allow for detailed analyses of morphology, projections and subcellular features of different neuron types. The high density of reconstructions enables geometrical and topological analyses of the OB circuitry. Image data can be accessed and viewed through the neurodata web services (http://www.neurodata.io/wanner16). Raw data and reconstructions can be visualized in PyKNOSSOS. PyKNOSSOS: https://github.com/adwanner/PyKNOSSOS Wanner AA, Genoud C, Masudi T, Siksou L, Friedrich RW (2016) Dense EM-based reconstruction of the interglomerular projectome in the zebrafish olfactory bulb. Nat Neurosci 19:816-825.<br> http://www.nature.com/neuro/journal/v19/n6/full/nn.4290.html
description: {"references": ["Wanner AA, Genoud C, Masudi T, Siksou L, Friedrich RW (2016) Dense EM-based reconstruction of the interglomerular projectome in the zebrafish olfactory bulb. Nat Neurosci 19:816-825."]}
DOI: 10.5281/zenodo.5749927
title: Random numbers

description: This is a collection of ten datasets, each containing ten iid zero-mean, unit-variance random numbers. These are used in an example of the showyourwork open source scientific article workflow.<br><br>Created using showyourwork from this GitHub repo using the following command:<br><br><pre><code class="language-bash">cd src/figures && python src/data/run_simulation.py</code></pre><br>
DOI: 10.6073/pasta/1c57b6613111c9d05c0225de12fd1098
title: Relative percent cover and leaf nutrients was measured for plant species on Arctic LTER experimental plots in moist acidic and non-acid tundra, Arctic LTER Toolik Field Station, Alaska 2015

description: Relative percent cover was measured for plant species on Arctic LTER experimental plots at Toolik field station in moist acidic and non-acidic tundra in greenhouse and control plots. Leaf percent carbon, percent nitrogen and percent phosphorus were collected from dominant species in greenhouse and control plots on Arctic LTER experimental plots at Toolik field station in moist acidic, non-acidic tundra, wet sedge and shrub tundra
DOI: 10.6073/pasta/d4f567844673857239eec0cb61c6f543
title: Soil biogeochemical variables collected on the Arctic LTER experimental plots in moist acidic, moist non-acidic, wet shrub and shrub tundra, Arctic LTER Toolik Field Station, Alaska 2015

description: We investigated the effect of long-term warming on multiple soil and microbial carbon, nitrogen, and phosphorus pools, and microbial extracellular enzyme activities, with a particular focus on phosphorus, in Alaskan tundra plots underlain by permafrost
DOI: 10.5281/zenodo.5749926
title: Supplementary Table 1. Raw data of egg quality parameters for 990 egg samples with ATOL (Animal Trait Ontology for Livestock) descriptors, as function of hen age, pen no. and genotype in 15 replicates.

description: Data table of egg quality parameters
DOI: 10.5281/zenodo.5749925
title: Supplementary Table 1. Raw data of egg quality parameters for 990 egg samples with ATOL (Animal Trait Ontology for Livestock) descriptors, as function of hen age, pen no. and genotype in 15 replicates.

description: Data table of egg quality parameters
DOI: 10.6084/m9.figshare.8082524
title: The Entropy of the Angenent Torus is Approximately 1.85122

description: To study the singularities that appear in mean curvature flow, one must understand <i>self-shrinkers</i>, surfaces that shrink by dilations under mean curvature flow. The simplest examples of self-shrinkers are spheres and cylinders. In 1989, Angenent constructed the first nontrivial example of a self-shrinker, a torus. A key quantity in the study of the formation of singularities is the <i>entropy</i>, defined by Colding and Minicozzi based on work of Huisken. The values of the entropy of spheres and cylinders have explicit formulas, but there is no known formula for the entropy of the Angenent torus. In this work, we numerically estimate the entropy of the Angenent torus using the discrete Euler–Lagrange equations.
DOI: 10.6084/m9.figshare.8082524.v1
title: The Entropy of the Angenent Torus is Approximately 1.85122

description: To study the singularities that appear in mean curvature flow, one must understand <i>self-shrinkers</i>, surfaces that shrink by dilations under mean curvature flow. The simplest examples of self-shrinkers are spheres and cylinders. In 1989, Angenent constructed the first nontrivial example of a self-shrinker, a torus. A key quantity in the study of the formation of singularities is the <i>entropy</i>, defined by Colding and Minicozzi based on work of Huisken. The values of the entropy of spheres and cylinders have explicit formulas, but there is no known formula for the entropy of the Angenent torus. In this work, we numerically estimate the entropy of the Angenent torus using the discrete Euler–Lagrange equations.
DOI: 10.6073/pasta/3d368a11b0c200813e093010abc603d8
title: Soil enzyme activities and soil chemistry near and away from alder collected at sites along the Sagavanirktok River, BNZ LTER sites UP3a-c, and sites near BNZ LTER site WDI6, collected June and July 2019

description: This dataset contains the data and R code associated with Heslop et al. 2021 "Soil Enzymes Illustrate the Effects of Alder Nitrogen Fixation on Soil Carbon Processes in Arctic and Boreal Ecosystems" published in Ecosphere. Activities of acid phosphatase, beta-glucosidase, and phenoloxidase, as well as %N, C, P, and Mo, 15N and 13C natural abundance, resin extractable P, and SOM chemsitry using FTIR spectroscopy were measured for soils taken under alder (Alnus viridis ssp. fruticosa) canopies and 5 m away. Samples were collected in the Arctic at sites near Sagwon Bluffs and the Lupine-Sagavanirktok river confluence as well as in the boreal forest at BNZ LTER sites UP3a-c and at sites located near BNZ LTER site WDI6.
DOI: 10.5281/zenodo.5727081
title: Selective ligand removal to improve accessibility of active sites in hierarchical MOFs for heterogeneous photocatalysis

description: This file includes the source data for all experimental and theoretical data of the publication.
DOI: 10.5281/zenodo.5727080
title: Selective ligand removal to improve accessibility of active sites in hierarchical MOFs for heterogeneous photocatalysis

description: This file includes the source data for all experimental and theoretical data of the publication.
DOI: 10.5281/zenodo.5749821
title: Simple Physical Interactions Yield Social Self-Organization in Honeybees - datasets

description: Empirical data of the location of the bees in complex thermal environments in specific time intervals. For more details please refer to <br> <br> Szopek M, Stokanic V, Radspieler G and Schmickl T (2021) Simple Physical Interactions Yield Social Self-Organization in Honeybees. <em>Front. Phys.</em> 9:670317. doi: 10.3389/fphy.2021.670317 exp_1.csv contains the percentage of bees in the left, the center and the right evaluation zone in 1-minute intervals (runtime 30 min) for each of the 9 repetitions of Experiment 1 (static thermal environment with one global optimum at 36°C and a pessimum at 30°C). exp_2.csv contains the percentage of bees in the left, the center and the right evaluation zone in 1-minute intervals (runtime 30 min) for each of the 8 repetitions of Experiment 2 (static thermal environment with one global optimum at 36°C and one local optimum at 32°C). exp_3.csv contains the percentage of bees in the left, the center and the right evaluation zone in 1-minute intervals (runtime 30 min) for each of the 6 repetitions of Experiment 3 (static thermal environment with two equal optima of 36°C). exp_4.csv contains the percentage of bees in the left, the center and the right evaluation zone in 1-minute intervals (runtime 105 min) for each of the 17 repetitions of Experiment 4 (dynamic thermal environment). exp_5.csv contains the percentage of bees in the left, the center and the right evaluation zone at minute 30 for i) each of the 10 repetitions of Experiment 5 (static thermal environment with social stimulus) and ii) for each of the 8 repetitions of an experiment with the same thermal environment but without a social stimulus for comparison.