cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc24h3tl
title: CCDC 1980739: Experimental Crystal Structure Determination

description: Related Article: Hana Stepankova, Marcin Swiatkowski, Rafal Kruszynski, Pavel Svec, Hana Michalkova, Vendula Smolikova, Andrea Ridoskova, Zbynek Splichal, Petr Michalek, Lukas Richtera, Pavel Kopel, Vojtech Adam, Zbynek Heger, Simona Rex|2021|Int. J. Nanomed.|16|4431|doi:10.2147/IJN.S304902
DOI: 10.48372/f92003b2-5f5d-4719-ab5a-e1c88cc0f3fc
title: Phytoplankton data from the coastal marine area of Salento peninsula, Apulia, Italy.

description: This dataset provides a broad perspective and information on taxonomic and morphological (shape and size)structure of phytoplankton communities, along coastal marine area of Salento peninsula (Adriatic and Ionian sea).
DOI: 10.48372/727f4327-41dc-4def-82ee-ff58b0d4bddc
title: Phytoplankton data collected in an impacted marine coastal area located in South Adriatic Sea from 2014 to 2017.

description: This dataset provides broad information on taxonomic and morphological (shape, linear dimensions, biovolume, cell abundance, cell size) structure of phytoplankton communities, in an impacted marine coastal area. The study was conducted in order to understand the role of anthropogenic pollution on phytoplankton community. For this reason, 3 different areas, along a pollution gradient, were considering. Data were collected at different spatial and temporal scales, in marine ecosystems, located in South Adriatic Sea, close to an industrial area and a marine protected area, in Brindisi, along Salento Peninsula (Puglia region, Italy).
DOI: 10.5281/zenodo.5513771
title: Processing single-cell RNA-seq of human hematopoietic stem/progenitor cells using SingCellaR

description: 1. cellranger_output.zip : Zipped files for cellranger output 2. Code.zip: This contains the code for Step2-7 3. Human_genesets.zip: This includes the geneset signatures (.gmt) files we used in the protocol and original study (Roy et al, 2021) 4. Human_HSPC_All.SingCellaR.rdata: The SingCellaR objects generated in Step 4 on a local computer 5. meta.data.txt: meta data includes the donor and batch information
DOI: 10.15468/3pfnn8
title: Pilosella hoppeana subsp. sicula Di Grist., Gottschl. & Raimondo (Asteraceae), a new endemic subspecies from Sicily (Italy)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Gristina, Emilio Di, Gottschlich, Günter, Raimondo, Francesco Maria (2016): Pilosella hoppeana subsp. sicula Di Grist., Gottschl. & Raimondo (Asteraceae), a new endemic subspecies from Sicily (Italy). Candollea 71 (1): 7-12, DOI: 10.15553/c2016v711a2
DOI: 10.6084/m9.figshare.15031998
title: JRC2018VncU_JRC2018VncF_h5

description: Transformations between JRC 2018 Female Ventral Nerve Cord template and the JRC 2018 Unisex Ventral Nerve Cord template.<br>This transformation operates in units of microns. Therefore, any point coordinates must be converted to micron units before applying this transformation.
DOI: 10.6084/m9.figshare.15031998.v1
title: JRC2018VncU_JRC2018VncF_h5

description: Transformations between JRC 2018 Female Ventral Nerve Cord template and the JRC 2018 Unisex Ventral Nerve Cord template.<br>This transformation operates in units of microns. Therefore, any point coordinates must be converted to micron units before applying this transformation.
DOI: 10.6084/m9.figshare.15029547
title: JRC2018VncM_JRC2018VncU_h5

description: Transformation between JRC 2018 Male Ventral Nerve Cord template and the JRC 2018 Unisex Ventral Nerve Cord template.<br>This transformation operates in units of microns. Therefore, any point coordinates must be converted to micron units before applying this transformation.
DOI: 10.6084/m9.figshare.15029547.v1
title: JRC2018VncM_JRC2018VncU_h5

description: Transformation between JRC 2018 Male Ventral Nerve Cord template and the JRC 2018 Unisex Ventral Nerve Cord template.<br>This transformation operates in units of microns. Therefore, any point coordinates must be converted to micron units before applying this transformation.
DOI: 10.6084/m9.figshare.13827530
title: Stochastic Photometric Variability of WR Stars - Online Material

description: De-trended photometric data of 50 Wolf-Rayet stars with 122 datasets ; 7 from BRITE-Constellation satellites, 6 from MOST and 109 from TESS. The TESS datasets are separated between the three time-sampling cadences of the telescope. We also include images in .eps format of these light-curves, as well as images in .eps format of all the periodograms of the stars in our sample fitted with the semi-Lorentzian model described in the article.
DOI: 10.48372/9cd2907f-8f44-4df6-9070-6b21e1991b94
title: An individual-based dataset of carbon and nitrogen isotopic data of Callinectes sapidus in invaded Mediterranean waters.

description: The dataset includes 360 records with 236 carbon and nitrogen isotopic signatures of Callinectes sapidus and 224 isotopic data of potential prey gathered from five countries and 12 locations between 2014 and 2019.
DOI: 10.48759/alouette
title: Alouette
DOI: 10.5522/04/14892822
title: Th17 cell master transcription factor RORC2 regulates HIV-1 gene expression and viral outgrowth

description: Source data files for Figures 1 to 7 and Supporting Information Figures 1 to 10. Methodological details are provided in the original paper and supplementary Methods<br>
DOI: 10.5281/zenodo.5644945
title: SynActJ: Easy-to-use automated analysis of synaptic activity

description: Neuronal synapses are highly dynamic communication hubs that mediate chemical neurotransmission via the exocytic fusion and subsequent endocytic recycling of neurotransmitter-containing synaptic vesicles (SVs). Functional imaging tools allow for the direct visualization of synaptic activity by detecting action potentials, pre- or postsynaptic calcium influx, SV exo- and endocytosis, and glutamate release. Fluorescent organic dyes or synapse-targeted genetic molecular reporters, such as calcium, voltage or neurotransmitter sensors and synapto-pHluorins reveal synaptic activity by undergoing rapid changes in their fluorescence intensity upon neuronal activity on timescales of milliseconds to seconds, which typically are recorded by fast and sensitive widefield live cell microscopy. The analysis of the resulting time-lapse movies in the past has been performed by either manually picking individual structures, custom scripts that have not been made widely available to the scientific community, or advanced software toolboxes that are complicated to use. For the precise, unbiased and reproducible measurement of synaptic activity, it is key that the research community has access to bio-image analysis tools that are easy-to-apply and allow the automated detection of fluorescent intensity changes in active synapses. Here we present SynActJ (<strong>Syn</strong>aptic <strong>Act</strong>ivity in Image<strong>J</strong>), an easy-to-use fully open-source workflow that enables automated image and data analysis of synaptic activity. The workflow consists of a Fiji plugin performing the automated image analysis of active synapses in time-lapse movies via an interactive seeded watershed segmentation that can be easily adjusted and applied to a dataset in batch mode. The extracted intensity traces of each synaptic bouton are automatically processed, analyzed, and plotted using a R Shiny workflow. We validate the workflow on time-lapse images of stimulated synapses expressing the presynaptic pH reporter Synaptophysin-pHluorin or a synapse-targeted calcium sensor, Synaptophysin-RGECO. We compare the automatic workflow to manual analysis and compute calcium-influx and SV exo-/ endocytosis kinetics and other parameters for synaptic vesicle recycling under different conditions. We predict SynActJ to become an important tool for the analysis of synaptic activity and synapse properties.
DOI: 10.5281/zenodo.5507359
title: SynActJ: Easy-to-use automated analysis of synaptic activity

description: Neuronal synapses are highly dynamic communication hubs that mediate chemical neurotransmission via the exocytic fusion and subsequent endocytic recycling of neurotransmitter-containing synaptic vesicles (SVs). Functional imaging tools allow for the direct visualization of synaptic activity by detecting action potentials, pre- or postsynaptic calcium influx, SV exo- and endocytosis, and glutamate release. Fluorescent organic dyes or synapse-targeted genetic molecular reporters, such as calcium, voltage or neurotransmitter sensors and synapto-pHluorins reveal synaptic activity by undergoing rapid changes in their fluorescence intensity upon neuronal activity on timescales of milliseconds to seconds, which typically are recorded by fast and sensitive widefield live cell microscopy. The analysis of the resulting time-lapse movies in the past has been performed by either manually picking individual structures, custom scripts that have not been made widely available to the scientific community, or advanced software toolboxes that are complicated to use. For the precise, unbiased and reproducible measurement of synaptic activity, it is key that the research community has access to bio-image analysis tools that are easy-to-apply and allow the automated detection of fluorescent intensity changes in active synapses. Here we present SynActJ (<strong>Syn</strong>aptic <strong>Act</strong>ivity in Image<strong>J</strong>), an easy-to-use fully open-source workflow that enables automated image and data analysis of synaptic activity. The workflow consists of a Fiji plugin performing the automated image analysis of active synapses in time-lapse movies via an interactive seeded watershed segmentation that can be easily adjusted and applied to a dataset in batch mode. The extracted intensity traces of each synaptic bouton are automatically processed, analyzed, and plotted using a R Shiny workflow. We validate the workflow on time-lapse images of stimulated synapses expressing the presynaptic pH reporter Synaptophysin-pHluorin or a synapse-targeted calcium sensor, Synaptophysin-RGECO. We compare the automatic workflow to manual analysis and compute calcium-influx and SV exo-/ endocytosis kinetics and other parameters for synaptic vesicle recycling under different conditions. We predict SynActJ to become an important tool for the analysis of synaptic activity and synapse properties.
DOI: 10.48372/bf44cfa0-3eeb-4175-a657-2d1a094a1a6d
title: Macrozoobenthos data collected in the hydrographic basin of Flumini Mannu - Cixerri, Sardinia, Italy, during the years 1992-1993.

description: The dataset contains taxonomic and body size data of the benthic macroinvertebrate communities collected in the hydrographic basin of Flumini Mannu - Cixerri (Sardinia, Italy) during the years 1992-1993. Sampling sites were located along two main basins Flumini Mannu and Cixerri, and other smaller coastal basins. Data refer to 98 taxa and 14566 individuals.
DOI: 10.5281/zenodo.5526715
title: Data from: Improving the Effectiveness of the Solid-Solution-Strengthening Elements Mo, Re, Ru and W in Single-Crystalline Nickel-Based Superalloys

description: This dataset is the basis for the journal article "Improving the Effectiveness of the Solid-Solution-Strengthening Elements Mo, Re, Ru and W in Single-Crystalline Nickel-Based Superalloys" (doi.org/10.3390/met11111707). Differential Scanning Calorimetry (DSC), Electron-Probe Mirco-Analysis (EPMA equipped with WDS detectors), Compression Creep and CalPhaD calculation data are included in this dataset. In the resulting article the partitioning and solid solution strengthening behavior of the elements Mo, Re, Ru, and W are investigated in three different alloy collections: "Reference" alloys: ERBO/1 (based on the commercial alloy CMSX-4), ERBO/13 (optimized alloy: doi.org/10.1088/0965-0393/23/3/035004) and ERBO/15 (optimized alloy: doi.org/10.1002/9781119075646.ch4) "Model" alloys: ERBO/17, ERBO/18, ERBO/19 and ERBO/32 - experimental SX Nickel-Based superalloys to investigate the influence of Ti and Ta on the partitioning behavior of W "Experimental" alloys: EXP10, EXP11, EXP12, EXP13, EXP14, EXP15, EXP16, EXP17, EXP18 - general investigation of the behavior of Mo, Re, Ru and W, in terms of partitioning and thermophysical properties. _________ CalPhaD data: short meta data file included in the respective subdirectory DSC data: Meta data as header in each file EPMA data: For each alloy a directory includes a general meta data file "0.cnd", an element specific meta data file "*.cnd" and the actual mapping data of each element "*.txt" (element name is listed in the corresponding specific meta data file). All element compositions are given in wt.-% in the mapping data .txt files. Exceptions: "COMPO" maps represent the total amount of detector counts; The values correspond to counts if the mapping .txt files contain non-float (e.g. integer) values (usually this means that there is very little or none of that element present and should therefore not be quantified to a wt.-% value). Creep: short meta data file included in the respective subdirectory
DOI: 10.5281/zenodo.5526714
title: Data from: Improving the Effectiveness of the Solid-Solution-Strengthening Elements Mo, Re, Ru and W in Single-Crystalline Nickel-Based Superalloys

description: This dataset is the basis for the journal article "Improving the Effectiveness of the Solid-Solution-Strengthening Elements Mo, Re, Ru and W in Single-Crystalline Nickel-Based Superalloys" (doi.org/10.3390/met11111707). Differential Scanning Calorimetry (DSC), Electron-Probe Mirco-Analysis (EPMA equipped with WDS detectors), Compression Creep and CalPhaD calculation data are included in this dataset. In the resulting article the partitioning and solid solution strengthening behavior of the elements Mo, Re, Ru, and W are investigated in three different alloy collections: "Reference" alloys: ERBO/1 (based on the commercial alloy CMSX-4), ERBO/13 (optimized alloy: doi.org/10.1088/0965-0393/23/3/035004) and ERBO/15 (optimized alloy: doi.org/10.1002/9781119075646.ch4) "Model" alloys: ERBO/17, ERBO/18, ERBO/19 and ERBO/32 - experimental SX Nickel-Based superalloys to investigate the influence of Ti and Ta on the partitioning behavior of W "Experimental" alloys: EXP10, EXP11, EXP12, EXP13, EXP14, EXP15, EXP16, EXP17, EXP18 - general investigation of the behavior of Mo, Re, Ru and W, in terms of partitioning and thermophysical properties. _________ CalPhaD data: short meta data file included in the respective subdirectory DSC data: Meta data as header in each file EPMA data: For each alloy a directory includes a general meta data file "0.cnd", an element specific meta data file "*.cnd" and the actual mapping data of each element "*.txt" (element name is listed in the corresponding specific meta data file). All element compositions are given in wt.-% in the mapping data .txt files. Exceptions: "COMPO" maps represent the total amount of detector counts; The values correspond to counts if the mapping .txt files contain non-float (e.g. integer) values (usually this means that there is very little or none of that element present and should therefore not be quantified to a wt.-% value). Creep: short meta data file included in the respective subdirectory
DOI: 10.48372/b6fad39f-0e6c-4c68-a352-5b4f33dff6e3
title: Macrozoobenthos data collected in the abandoned mining area of Ingurtosu-Montevecchio, Sardinia, Italy during the years 1993-1994.

description: The dataset contains taxonomic and body size data of the benthic macroinvertebrate communities collected in the abandoned mining area of Ingurtosu-Montevecchio (Sardinia, Italy) during the years 1993-1994. Sampling sites were located along two main streams Rio Roia Cani-Piscinas and Rio Naracauli, and outside the mining area. Data refer to 34 taxa and 2033 individuals.
DOI: 10.25345/c5np22
title: MassIVE MSV000088372 - Smoke Inhalation and NIST SRM Lipidomics
title: LC-IMS-CID-MS lipidomics of BALF and plasma from severe smoke inhalation and NIST SRM 1950.
DOI: 10.5281/zenodo.5682588
title: Dataset for "Reinforcement Learning reveals fundamental limits on the mixing of active particles"

description: Open access data set for manuscript "Reinforcement Learning reveals fundamental limits on the mixing of active particles" currently (2021) in preparation.
description: We acknowledge funding through the Foundational Questions Institute and Fetzer Franklin Fund through FQXi 1816, the Packard Foundation (2019-69662), and the Heritage medical research institute. We acknowledge additional funding through the SFP SURF program.
DOI: 10.5281/zenodo.4749678
title: Dataset for "Reinforcement Learning reveals fundamental limits on the mixing of active particles"

description: Open access data set for manuscript "Reinforcement Learning reveals fundamental limits on the mixing of active particles" currently (2021) in preparation.
description: We acknowledge funding through the Foundational Questions Institute and Fetzer Franklin Fund through FQXi 1816, the Packard Foundation (2019-69662), and the Heritage medical research institute. We acknowledge additional funding through the SFP SURF program.
DOI: 10.48372/00e80756-a78f-4c1e-a710-234152fde59b
title: Macrozoobenthos data of the Pula river, Sardinia, Italy.

description: The dataset contains taxonomic data of the macroinvertebrates community of Pula River (Sardinia, Italy). Data refer to 232 taxa and 29213 individuals.
DOI: 10.5281/zenodo.5682753
title: msd-errors - Data for the LLZO figure

description: Results of the diffusion analysis of the LLZO simulations.<br><br>Created using showyourwork from this GitHub repo.
DOI: 10.6084/m9.figshare.16867488
title: Critical review on PFOA, kidney cancer, and testicular cancer

description: Critical review on PFOA, kidney cancer, and testicular cancer
DOI: 10.6084/m9.figshare.16867488.v1
title: Critical review on PFOA, kidney cancer, and testicular cancer

description: Critical review on PFOA, kidney cancer, and testicular cancer
DOI: 10.18742/16974823
title: Latin lexical semantic annotation

description: This dataset is a collection of lexical annotation of the corpus occurrences 40 Latin lemmas. The corpus instances are from LatinISE and the process is described in Schlechtweg et al. (2020, 2021).<br>The annotation was coordinated by Barbara McGillivray, and done by Annie Burman, Daria Kondakova, Francesca Dell'Oro, Helena Bermudez Sabel, Hugo Burgess, Paola Marongiu, and Rozalia Dobos. The pre-annotation was coordinated and designed by Barbara McGillivray and done by Manuel Márquez Cruz.<br><b>References</b><b><br></b>McGillivray, B. and Kilgarriff, A. (2013). Tools for historical corpus research, and a corpus of Latin. In Paul Bennett, Martin Durrell, Silke Scheible, Richard J. Whitt (eds.), New Methods in Historical Corpus Linguistics. Tübingen: Narr<br><br>Barbara McGillivray, Dominik Schlechtweg, Haim Dubossarsky, Nina Tahmasebi, & Simon Hengchen. (2021). DWUG LA: Diachronic Word Usage Graphs for Latin [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5255228<br><br>Schlechtweg, D., McGillivray, B., Hengchen, S., Dubossarsky, H., Tahmasebi, N. (2020). SemEval-2020 Task 1: Unsupervised Lexical Semantic Change Detection. In <i>Proceedings of the Fourteenth Workshop on Semantic Evaluation, 2020.</i> International Committee for Computational Linguistics. DOI: 10.18653/v1/2020.semeval-1.1<br>Schlechtweg, D., Tahmasebi, N., Hengchen, S., Dubossarsky, H., McGillivray, B. (2021). DWUG: A large Resource of Diachronic Word Usage Graphs in Four Languages. In <i>Proceedings of EMNLP 2021.</i>
DOI: 10.18742/16974823.v1
title: Latin lexical semantic annotation

description: This dataset is a collection of lexical annotation of the corpus occurrences 40 Latin lemmas. The corpus instances are from LatinISE and the process is described in Schlechtweg et al. (2020, 2021).<br>The annotation was coordinated by Barbara McGillivray, and done by Annie Burman, Daria Kondakova, Francesca Dell'Oro, Helena Bermudez Sabel, Hugo Burgess, Paola Marongiu, and Rozalia Dobos. The pre-annotation was coordinated and designed by Barbara McGillivray and done by Manuel Márquez Cruz.<br><b>References</b><b><br></b>McGillivray, B. and Kilgarriff, A. (2013). Tools for historical corpus research, and a corpus of Latin. In Paul Bennett, Martin Durrell, Silke Scheible, Richard J. Whitt (eds.), New Methods in Historical Corpus Linguistics. Tübingen: Narr<br><br>Barbara McGillivray, Dominik Schlechtweg, Haim Dubossarsky, Nina Tahmasebi, & Simon Hengchen. (2021). DWUG LA: Diachronic Word Usage Graphs for Latin [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5255228<br><br>Schlechtweg, D., McGillivray, B., Hengchen, S., Dubossarsky, H., Tahmasebi, N. (2020). SemEval-2020 Task 1: Unsupervised Lexical Semantic Change Detection. In <i>Proceedings of the Fourteenth Workshop on Semantic Evaluation, 2020.</i> International Committee for Computational Linguistics. DOI: 10.18653/v1/2020.semeval-1.1<br>Schlechtweg, D., Tahmasebi, N., Hengchen, S., Dubossarsky, H., McGillivray, B. (2021). DWUG: A large Resource of Diachronic Word Usage Graphs in Four Languages. In <i>Proceedings of EMNLP 2021.</i>
DOI: 10.48372/9b425164-31e0-4f3a-b870-d851bea9398c
title: Macrozoobenthos data of the river Tirso, Sardinia, Italy.

description: The dataset contains abundance and body size data of benthic macroinvertebrates collected in the river Tirso (Sardinia, Italy) during the years 1998-1999. Data refer to 143 taxa and 48248 individuals.
DOI: 10.6084/m9.figshare.16435221
title: DRL-1

description: numerical raw data for DRL-1 manuscript<br>
DOI: 10.5281/zenodo.5676247
title: "Genome binning of viral entities from bulk metagenomics data" - CAMISIM simulated datasets and genomes

description: <strong>Genome binning of viral entities from bulk metagenomics data</strong> <strong>Authors</strong> <strong>Joachim Johansen1,2, Damian R. Plichta2, Jakob Nybo Nissen1,3, Marie Louise Jespersen1,4, Shiraz A. Shah5, Ling Deng6, Jakob Stokholm5,6, Hans Bisgaard5, Dennis Sandris Nielsen6, Søren Sørensen7, Simon Rasmussen1</strong> <strong>Affiliations</strong> 1 Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark 2 Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA 3 Statens Serum Institut, Viral & Microbial Special diagnostics, Copenhagen, Denmark 4 National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark 5 Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark 6 Section of Food Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark 7 Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark <strong>Methods description</strong> We compared the viral binning performance of VAMB and MetaBAT2 using the official CAMI consortium method to create assemblies and metagenome profiles. To this end we generated 3 different metagenome compositions with up to 308 reference genomes; one mixed with bacteria, plasmids and viruses to test binning in complex samples i.e. high diversity (1), one with only crass-like viruses to test binning with highly similar viruses i.e. high relatedness (2) and a set of small-viruses (&lt;6,000 bp) including members of the Microviridae family to address the bias of size (3). Bacterial genomes were gathered from NCBIs refseq genome repository 2021, plasmids from the PLSDB database (v. 2021_06_23) and viral genomes from the recent MGV database. Dataset A contained a mixture of bacteria (N=8), plasmids (N=20) and viruses (N=280) to test binning in complex samples, i.e. high diversity. Dataset B contained only crass-like viruses (N=80) to test binning with highly similar viruses i.e. high relatedness. Dataset C contained small-viruses (N=50, &lt;6,000 bp) of the Microviridae family to address the bias of size. Bacterial genomes were sampled from the Refseq genome repository 2021, plasmids from the PLSDB database and viral genomes from the recent MGV database (Nayfach, et al. Nature Microbiology 2021).