cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11874291.v1
title: Data in "Large-scale integration of artificial atoms in hybrid photonic circuits"

description: <b>Datasets </b><br><b>Manuscript:</b> Large-scale integration of artificial atoms in hybrid photonic circuits<br><b>Authors:</b> Noel H. Wan*, Tsung-Ju Lu**, Kevin C. Chen, Michael P. Walsh, Matthew E. Trusheim, Lorenzo De Santis, Eric A. Bersin, Isaac B. Harris, Sara L. Mouradian, Ian R. Christen, Edward S. Bielejec, and Dirk Englund***<br>*noelwan@mit.edu**tsungjul@mit.edu***englund@mit.edu<br><br>______________________________________________<b><br></b><b>Data: Experiment</b><br><b><br></b>Figure 3: https://figshare.com/s/e6930cd950711bbcc477Figure 4: https://figshare.com/s/d6ce61e336a135fc8cebFigure 5 & Extended Data Fig 6: https://figshare.com/s/d4259b9376dc0222cf86Extended Data Fig 4: https://figshare.com/s/02ff5993922dadec7a2b<br>Extended Data Fig 7: https://figshare.com/s/01dc1c0aa8b3289df154<br>Extended Data Fig 8: https://figshare.com/s/fcf126addbe10624bb14<br>Extended Data Fig 9: https://figshare.com/s/162698a8d1f857264826<br>Extended Data Table 1: https://figshare.com/s/683bf55a952d0caccea5<br><br>______________________________________________<br><br><b>Data: Simulation <br><br></b>Extended Data Fig 3: https://figshare.com/s/607a8c1eae618e7bc5e9<br><br><br><br>
DOI: 10.6084/m9.figshare.11874198
title: The transcriptional landscape of Venezuelan equine encephalitis virus infection

description: U87 human cells were infected with GFP+ Venezuelan Equine Encephalitis Virus (VEEV) strain TC-83 with 3 MOIs (0.1, 1, 3) and harvested at 6 time points (0.5 - 24 hours post infection). viscRNA-Seq was performed as in Zanini F, Pu SY, et al. eLife (2018).<br>The file is a zip archive containing two files:- counts table with the gene expression of human genes, VEEVGFP, ERCC spike-in RNA controls, and other features from the aligner (e.g. unmapped reads). The counts are unnormalized, raw read pair numbers.- cell_metadata table with the following columns: - coverage: total number of uniquely mapped human reads - VEEV_counts: total number of viral reads - plate: microtiter plate each cell was sorted into (to spot batch effects) - well: the well within each plate each cell was sorted into - time [h]: time post infection - vRNA_5' [cpm]: viral reads in bases 1-1700 of the viral genome, normalized by human coverage per million reads - vRNA_3' [cpm]: viral reads in bases 7501+ of the viral genome, normalized by human coverage per million reads
DOI: 10.6084/m9.figshare.11874222
title: test

description: testing
DOI: 10.6084/m9.figshare.11874222.v1
title: test

description: testing
DOI: 10.6084/m9.figshare.11874198.v2
title: The transcriptional landscape of Venezuelan equine encephalitis virus infection

description: U87 human cells were infected with GFP+ Venezuelan Equine Encephalitis Virus (VEEV) strain TC-83 with 3 MOIs (0.1, 1, 3) and harvested at 6 time points (0.5 - 24 hours post infection). viscRNA-Seq was performed as in Zanini F, Pu SY, et al. eLife (2018).<br>The file is a zip archive containing two files:- counts table with the gene expression of human genes, VEEVGFP, ERCC spike-in RNA controls, and other features from the aligner (e.g. unmapped reads). The counts are unnormalized, raw read pair numbers.- cell_metadata table with the following columns: - coverage: total number of uniquely mapped human reads - VEEV_counts: total number of viral reads - plate: microtiter plate each cell was sorted into (to spot batch effects) - well: the well within each plate each cell was sorted into - time [h]: time post infection - vRNA_5' [cpm]: viral reads in bases 1-1700 of the viral genome, normalized by human coverage per million reads - vRNA_3' [cpm]: viral reads in bases 7501+ of the viral genome, normalized by human coverage per million reads
DOI: 10.6084/m9.figshare.11874198.v1
title: Untitled Item

description: U87 human cells were infected with GFP+ Venezuelan Equine Encephalitis Virus (VEEV) strain TC-83 with 3 MOIs (0.1, 1, 3) and harvested at 6 time points (0.5 - 24 hours post infection). viscRNA-Seq was performed as in Zanini F, Pu SY, et al. eLife (2018).<br>The file is a zip archive containing two files:- counts table with the gene expression of human genes, VEEVGFP, ERCC spike-in RNA controls, and other features from the aligner (e.g. unmapped reads). The counts are unnormalized, raw read pair numbers.- cell_metadata table with the following columns: - coverage: total number of uniquely mapped human reads - VEEV_counts: total number of viral reads - plate: microtiter plate each cell was sorted into (to spot batch effects) - well: the well within each plate each cell was sorted into - time [h]: time post infection - vRNA_5' [cpm]: viral reads in bases 1-1700 of the viral genome, normalized by human coverage per million reads - vRNA_3' [cpm]: viral reads in bases 7501+ of the viral genome, normalized by human coverage per million reads
DOI: 10.6084/m9.figshare.11874159
title: Increasing the species diversity in the <i>Aspergillus</i> section <i>Nidulantes</i>: Six novel species mainly from the indoor environment

description: <i>Aspergillus</i> section <i>Nidulantes</i> encompasses almost 80 homothallic and anamorphic species, mostly isolated from soil, plant material, or the indoor environment. Some species are clinically relevant or produce mycotoxins. This study reevaluated the species boundaries within several clades of section <i>Nidulantes</i>. Five data sets were assembled, each containing presumptive new species and their closest relatives, and phylogenetic and phenotypic analyses were performed. We tested the hypotheses that the newly isolated or reexamined strains constitute separate species (splitting approach) or should be treated as part of broadly defined species (lumping approach). Four DNA sequence loci were amplified, internal transcribed spacer (ITS) and large subunit (LSU) regions of the rDNA and partial sequences of the β-tubulin (<i>benA</i>), calmodulin (<i>CaM</i>), and RNA polymerase II second largest subunit (<i>RPB2</i>) genes. The latter three loci were used for the phylogenetic analysis and served as input for single-locus (GMYC, bGMYC, PTP, and bPTP) and multilocus (STACEY and BP&P) species delimitation analyses. The phenotypic analysis comprised macro- and micromorphology (including scanning electron microscopy) and comparison of cardinal growth temperatures. The phylogenetic analysis supported the splitting hypothesis in all cases, and based on the combined approach, we propose six new species, four that are homothallic and two anamorphic. Four new species were isolated from the indoor environment (Jamaica, Trinidad and Tobago, USA), one originated from soil (Australia), and one from a kangaroo rat cheek pouch (USA).
DOI: 10.6084/m9.figshare.11874159.v1
title: Increasing the species diversity in the <i>Aspergillus</i> section <i>Nidulantes</i>: Six novel species mainly from the indoor environment

description: <i>Aspergillus</i> section <i>Nidulantes</i> encompasses almost 80 homothallic and anamorphic species, mostly isolated from soil, plant material, or the indoor environment. Some species are clinically relevant or produce mycotoxins. This study reevaluated the species boundaries within several clades of section <i>Nidulantes</i>. Five data sets were assembled, each containing presumptive new species and their closest relatives, and phylogenetic and phenotypic analyses were performed. We tested the hypotheses that the newly isolated or reexamined strains constitute separate species (splitting approach) or should be treated as part of broadly defined species (lumping approach). Four DNA sequence loci were amplified, internal transcribed spacer (ITS) and large subunit (LSU) regions of the rDNA and partial sequences of the β-tubulin (<i>benA</i>), calmodulin (<i>CaM</i>), and RNA polymerase II second largest subunit (<i>RPB2</i>) genes. The latter three loci were used for the phylogenetic analysis and served as input for single-locus (GMYC, bGMYC, PTP, and bPTP) and multilocus (STACEY and BP&P) species delimitation analyses. The phenotypic analysis comprised macro- and micromorphology (including scanning electron microscopy) and comparison of cardinal growth temperatures. The phylogenetic analysis supported the splitting hypothesis in all cases, and based on the combined approach, we propose six new species, four that are homothallic and two anamorphic. Four new species were isolated from the indoor environment (Jamaica, Trinidad and Tobago, USA), one originated from soil (Australia), and one from a kangaroo rat cheek pouch (USA).
DOI: 10.6084/m9.figshare.11874150
title: New species and reports of <i>Cuphophyllus</i> from northern North America compared with related Eurasian species

description: This study describes four gray or brown species of <i>Cuphophyllus</i> (Hygrophoraceae, Agaricales), two of them new species, restricted to arctic-alpine and northern boreal zones of North America, and relates them morphologically and phylogenetically using multigene and nuc rDNA internal transcribed spacer ITS1-5.8S-ITS (ITS barcode) analyses to their similar, known counterparts. <i>Cuphophyllus cinerellus</i>, epitypified here, is shown to be a pan-palearctic species with sequence-confirmed collections from Fennoscandia and easternmost Asia. Occupying a similar habitat in the Nearctic is its sister species, the morphologically similar but novel <i>C. esteriae</i>, so far known only from eastern North America, including Greenland. Sister to the <i>C. cinerellus</i>–<i>C. esteriae</i> lineage, and known only from boreal raised <i>Sphagnum</i> bogs in Newfoundland, is a new medium-sized light cinereous brown species, <i>C. lamarum</i>. It has a yellow stipe but is phylogenetically distant from the yellow-stiped European <i>C. flavipes</i> and its North American sister species, <i>Hygrophorus pseudopallidus</i>. As cryptic speciation was discovered within <i>C. flavipes</i>, we lecto- and epitypify the name and transfer <i>H. pseudopallidus</i> to <i>Cuphophyllus</i> based on ITS analysis of the holotype. We also transfer the small European <i>Hygrocybe comosa</i> to <i>Cuphophyllus</i> based on morphology. <i>Cuphophyllus hygrocyboides</i> is reported from North America with the first sequence-confirmed collections from arctic-alpine British Columbia and Greenland. In addition, sequencing the holotype of <i>C. subviolaceus</i> identifies it as the sister species to the putative <i>C. lacmus</i>. Both species seem to have an intercontinental distribution. In total, we add new sequences to GenBank from 37 <i>Cuphophyllus</i> collections, including the holotypes of <i>C. hygrocyboides</i> and <i>C. subviolaceus</i>, the two new epitypes, and the two novel species.
DOI: 10.6084/m9.figshare.11874150.v1
title: New species and reports of <i>Cuphophyllus</i> from northern North America compared with related Eurasian species

description: This study describes four gray or brown species of <i>Cuphophyllus</i> (Hygrophoraceae, Agaricales), two of them new species, restricted to arctic-alpine and northern boreal zones of North America, and relates them morphologically and phylogenetically using multigene and nuc rDNA internal transcribed spacer ITS1-5.8S-ITS (ITS barcode) analyses to their similar, known counterparts. <i>Cuphophyllus cinerellus</i>, epitypified here, is shown to be a pan-palearctic species with sequence-confirmed collections from Fennoscandia and easternmost Asia. Occupying a similar habitat in the Nearctic is its sister species, the morphologically similar but novel <i>C. esteriae</i>, so far known only from eastern North America, including Greenland. Sister to the <i>C. cinerellus</i>–<i>C. esteriae</i> lineage, and known only from boreal raised <i>Sphagnum</i> bogs in Newfoundland, is a new medium-sized light cinereous brown species, <i>C. lamarum</i>. It has a yellow stipe but is phylogenetically distant from the yellow-stiped European <i>C. flavipes</i> and its North American sister species, <i>Hygrophorus pseudopallidus</i>. As cryptic speciation was discovered within <i>C. flavipes</i>, we lecto- and epitypify the name and transfer <i>H. pseudopallidus</i> to <i>Cuphophyllus</i> based on ITS analysis of the holotype. We also transfer the small European <i>Hygrocybe comosa</i> to <i>Cuphophyllus</i> based on morphology. <i>Cuphophyllus hygrocyboides</i> is reported from North America with the first sequence-confirmed collections from arctic-alpine British Columbia and Greenland. In addition, sequencing the holotype of <i>C. subviolaceus</i> identifies it as the sister species to the putative <i>C. lacmus</i>. Both species seem to have an intercontinental distribution. In total, we add new sequences to GenBank from 37 <i>Cuphophyllus</i> collections, including the holotypes of <i>C. hygrocyboides</i> and <i>C. subviolaceus</i>, the two new epitypes, and the two novel species.
DOI: 10.6084/m9.figshare.11873967
title: CGA and Python code for procedurally modeling forest in CityEngine

description: This code reads a tree database that contains species, height, diameter, spatial contagion and outputs 3D models in CityEngine.
DOI: 10.6084/m9.figshare.11873937
title: Transcriptome resources for Erysimum species

description: We present here a set of assembled unigenes, their predicted coding sequences and proteins, and the annotation of these unigenes for several <i>Erysimum</i> species (Brassicaceae): <i>Erysimum bastetanum</i> (populations: Ebt01, Ebt12, Ebt13, Ebt22), <i>E. mediohispanicum</i> (populations: Em21, Em39, Em71), <i>E. nevadense</i> (populations: En05,En10, En12), <i>E. popovii</i> (Ep16, Ep20, Ep27), <i>E. baeticum</i> (populations: Ebb07, Ebb10, Ebb12), <i>E. fitzii</i> (population Ef01), and <i>E. lagascae</i> (population Ela07).<br>
DOI: 10.6084/m9.figshare.11873937.v1
title: Transcriptome resources for Erysimum species

description: We present here a set of assembled unigenes, their predicted coding sequences and proteins, and the annotation of these unigenes for several <i>Erysimum</i> species (Brassicaceae): <i>Erysimum bastetanum</i> (populations: Ebt01, Ebt12, Ebt13, Ebt22), <i>E. mediohispanicum</i> (populations: Em21, Em39, Em71), <i>E. nevadense</i> (populations: En05,En10, En12), <i>E. popovii</i> (Ep16, Ep20, Ep27), <i>E. baeticum</i> (populations: Ebb07, Ebb10, Ebb12), <i>E. fitzii</i> (population Ef01), and <i>E. lagascae</i> (population Ela07).<br>
DOI: 10.6084/m9.figshare.11873883
title: LANDIS-II Input data and code

description: This dataset contains the data and code for the following: (1) forecast forest change using the LANDIS-II modeling framework, (2) convert LANDIS-II output into variables and formatting necessary for 3D modeling.<br><br><br>
DOI: 10.6084/m9.figshare.11873967.v3
title: CGA code for procedurally modeling forest in CityEngine

description: This code reads a tree database that contains species, height, diameter, spatial contagion and outputs 3D models in CityEngine.
DOI: 10.6084/m9.figshare.11873874
title: Relative efficiencies of simple and complex substitution models in estimating divergence times in phylogenomics

description: The archive contains the empirical and simulated data used in the Tao et al. 2020. Relative efficiencies of simple and complex substitution models in estimating divergence times in phylogenomics. <i>MBE</i>. All the alignments are derived from published studies (see Table 1 in Tao et al. 2020). So, if you want to use the datasets or results provided here, please cite the original source publication and Tao et al.'s article.<br><br>
DOI: 10.6084/m9.figshare.11873883.v1
title: LANDIS-II Input data

description: Final input files for LANDIS-II from Stacey Olson (MS student with Erica Smithwick)
DOI: 10.6084/m9.figshare.11873967.v4
title: CGA code for procedurally modeling forest in CityEngine

description: This code reads a tree database that contains species, height, diameter, spatial contagion and outputs 3D models in CityEngine.
DOI: 10.6084/m9.figshare.11873883.v2
title: LANDIS-II Input data and code

description: This dataset contains the data and code for the following: (1) forecast forest change using the LANDIS-II modeling framework, (2) convert LANDIS-II output into variables and formatting necessary for 3D modeling.<br><br><br>
DOI: 10.6084/m9.figshare.11873967.v5
title: CGA code for procedurally modeling forest in CityEngine

description: This code reads a tree database that contains species, height, diameter, spatial contagion and outputs 3D models in CityEngine.
DOI: 10.6084/m9.figshare.11873883.v3
title: LANDIS-II Input data and code

description: This dataset contains the data and code for the following: (1) forecast forest change using the LANDIS-II modeling framework, (2) convert LANDIS-II output into variables and formatting necessary for 3D modeling.<br><br><br>
DOI: 10.6084/m9.figshare.11873967.v6
title: CGA code for procedurally modeling forest in CityEngine

description: This code reads a tree database that contains species, height, diameter, spatial contagion and outputs 3D models in CityEngine.
DOI: 10.6084/m9.figshare.11873883.v4
title: LANDIS-II Input data and code

description: This dataset contains the data and code for the following: (1) forecast forest change using the LANDIS-II modeling framework, (2) convert LANDIS-II output into variables and formatting necessary for 3D modeling.<br><br><br>
DOI: 10.6084/m9.figshare.11873790
title: A multivocal literature review on developer experience

description: Dataset used in Master's Thesis titled <b>A multivocal literature review on developer experience</b> at Aalto University school of science
DOI: 10.6084/m9.figshare.11873754
title: Supplemental Table 4.xlsx

description: Supplemental tables containing coverage of all genes in metagenomic and metatranscriptomic data from the Coast Range Ophiolite Microbial Observatory.
DOI: 10.6084/m9.figshare.11873883.v5
title: LANDIS-II Input data and code

description: This dataset contains the data and code for the following: (1) forecast forest change using the LANDIS-II modeling framework, (2) convert LANDIS-II output into variables and formatting necessary for 3D modeling.<br><br><br>
DOI: 10.6084/m9.figshare.11873883.v6
title: LANDIS-II Input data and code

description: This dataset contains the data and code for the following: (1) forecast forest change using the LANDIS-II modeling framework, (2) convert LANDIS-II output into variables and formatting necessary for 3D modeling.<br><br><br>
DOI: 10.6084/m9.figshare.11873883.v7
title: LANDIS-II Input data and code

description: This dataset contains the data and code for the following: (1) forecast forest change using the LANDIS-II modeling framework, (2) convert LANDIS-II output into variables and formatting necessary for 3D modeling.<br><br><br>
DOI: 10.6084/m9.figshare.11872512
title: CuPCP-WAXS.zip

description: Pump-probe X-ray scattering data for [Cu4(PCP)3]+ measured at ID09 of ESRF <br>
DOI: 10.6084/m9.figshare.11872530
title: annotations on elifesciences.org

description: This dataset accompanies the conference contribution<br>"An Online Field Study on Scholarly Journal<br>Annotations" (Felix Lange, de Gruyter 2020, yet to be published), in which annotations on the journal plattform elifesciences.org are analysed. <br>File "flange_cohen_kappa" contains the content-type attributions made by two annotators. Annotator 2 is the author of the study, Annotator 1 is a student assistant that worked on a subset of the data presented in the publication.<br>On the basis of this attributions, the interrater reliability score (Cohen's kappa) was calculated (0.54). This data was created for test purposes. Minor differences (less than 5%) to the data used for the publication are possible, but not probable.<br>The content-types reffered to in the spreadsheet are Assertion/Contribution (1), Information Request (2), Unspecified Praise/Criticism (3), Unclear (4). The file contains snippets of the annotation texts to differentiate between annotations that are referenced by the same web url.The "dataset anno_data_export" represents the data used in the final, published version of the article. It is accompanied by a data description. Errors in the data caused during the export are possible, but not probable.<br>
DOI: 10.6084/m9.figshare.11872530.v1
title: content-types of annotations on elifesciences.org

description: This dataset accompanies the conference contribution<br>"An Online Field Study on Scholarly Journal<br>Annotations" (Felix Lange, de Gruyter 2020, yet to be published), in which annotations on the journal plattform elifesciences.org are analysed. <br>It contains the content-type attributions made by two annotators. Annotator 2 is the author of the study, Annotator 1 is a student assistant that worked on a subset of the data presented in the publication.<br>On the basis of this attributions, the interrater reliability score (Cohen's kappa) was calculated (0.54).The content-types reffered to in the spreadsheet are Assertion/Contribution (1), Information Request (2), Unspecified Praise/Criticism (3), Unclear (4). The file contains snippets of the annotation texts to differentiate between annotations that are referenced by the same web url.<br>
DOI: 10.6084/m9.figshare.11872449
title: Proteomic Supplementary Tables S1-S5

description: Proteomic Supplementary Tables S1-S5
DOI: 10.25373/ctsnet.11872425.v1
title: Moving the Needle: A Guide to Solving the Global Cardiac Surgery Puzzle for Surgeons, Societies, Students, and Researchers

description: Six billion people worldwide lack access to safe, timely, and affordable cardiac surgical care when needed; this article provides an overview and call to action for all stakeholders to start with global cardiac surgery research in order to map the global disparities and hold countries accountable for the existing gaps in cardiac care.
DOI: 10.6084/m9.figshare.11872401
title: Metadata

description: Metadata of appliances
DOI: 10.6084/m9.figshare.11872401.v1
title: Metadata

description: Metadata of appliances
DOI: 10.6084/m9.figshare.11872449.v1
title: Proteomic Supplementary Tables S1-s5

description: Proteomic Supplementary Tables S1-S5
DOI: 10.6084/m9.figshare.11872383
title: Metadata record for: Harmonized global maps of above and belowground biomass carbon density in the year 2010

description: This dataset contains key characteristics about the data described in the Data Descriptor Harmonized global maps of above and belowground biomass carbon density in the year 2010. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> <br>
DOI: 10.6084/m9.figshare.11872383.v1
title: Metadata record for: Harmonized global maps of above and belowground biomass carbon density in the year 2010

description: This dataset contains key characteristics about the data described in the Data Descriptor Harmonized global maps of above and belowground biomass carbon density in the year 2010. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> <br>
DOI: 10.6084/m9.figshare.11872347
title: CuPCP-XAS.zip

description: Pump-sequential-probe data collected at SuperXAS beamline of SLS. Cu K-edge of [Cu4(PCP)3]+<br>
DOI: 10.6084/m9.figshare.11872392.v1
title: Motivation Chart Data

description: Motivation Chart Data. ClinicalTrials.gov Identifier: NCT03484637
DOI: 10.6084/m9.figshare.11872347.v1
title: CuPCP-XAS.zip

description: Pump-sequential-probe data collected at SuperXAS beamline of SLS. Cu K-edge of [Cu4(PCP)3]+<br>
DOI: 10.6084/m9.figshare.11872392.v2
title: Motivation Chart Data

description: Motivation Chart Data. ClinicalTrials.gov Identifier: NCT03484637
DOI: 10.6084/m9.figshare.11872392.v3
title: Motivation Chart Data

description: Motivation Chart Data. ClinicalTrials.gov Identifier: NCT03484637
DOI: 10.6084/m9.figshare.11872392.v4
title: Motivation Chart Data

description: Motivation Chart Data. ClinicalTrials.gov Identifier: NCT03484637