cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc26mrj4
title: CCDC 2044776: Experimental Crystal Structure Determination

description: Related Article: Lamya H. Al-Wahaibi, Sai Ramya Sree Bysani, Samar S. Tawfik, Mohammed S. M. Abdelbaky, Santiago Garcia-Granda, Ali A. El-Emam, M. Judith Percino, Subbiah Thamotharan|2021|Cryst.Growth Des.|21|3234|doi:10.1021/acs.cgd.0c01583
DOI: 10.5517/ccdc.csd.cc2575yk
title: CCDC 2002908: Experimental Crystal Structure Determination

description: Related Article: Pinku Sarma, Pranay Sharma, Antonio Frontera, Miquel Barcelo-Oliver, Akalesh K. Verma, Trinayan Barthakur, Manjit K. Bhattacharyya|2021|Inorg.Chim.Acta|525|120461|doi:10.1016/j.ica.2021.120461
DOI: 10.5281/zenodo.4514928
title: emobpy: application for the German case

description: emobpy is a tool developed to generate electric vehicle time-series based on empirical data. This dataset is provided as an exemplary implementation of emobpy by taking into account the german mobility statistics. The dataset consists of four different time-series: vehicle mobility, driving electricity consumption, grid availability and grid electricity demand. We deliver the time-series in two time-resolutions—an hourly time-resolution resulting from aggregating the 15-minutes time-series. The 15-minutes time-resolution is the original form that emobpy generates the time-series. Two hundred electric vehicle have been simulated over a year of time-horizon. For more details, please, consult the following link: https://arxiv.org/abs/2005.02765v2
DOI: 10.5281/zenodo.3931663
title: emobpy: application for the German case

description: emobpy is a tool developed to generate electric vehicle time-series based on empirical data. This dataset is provided as an exemplary implementation of emobpy by taking into account the german mobility statistics. The dataset consists of four different time-series: vehicle mobility, driving electricity consumption, grid availability and grid electricity demand. We deliver the time-series in two time-resolutions—an hourly time-resolution resulting from aggregating the 15-minutes time-series. The 15-minutes time-resolution is the original form that emobpy generates the time-series. Two hundred electric vehicle have been simulated over a year of time-horizon. For more details, please, consult the following link: https://arxiv.org/abs/2005.02765v2
DOI: 10.6084/m9.figshare.14721264
title: taxonomy-and-betadiversity.R

description: taxonomy-and-betadiversity.R script
DOI: 10.6084/m9.figshare.14721264.v1
title: taxonomy-and-betadiversity.R

description: taxonomy-and-betadiversity.R script
DOI: 10.5281/zenodo.4895412
title: 3DED/microED datasets of biotin (Glacios/Ceta-D)

description: 3DED/microED data collected from 11 crystals of biotin (Sigma-Aldrich 14400) using a Thermo Fisher Scientific Glacios microscope equipped with a Ceta-D Camera. An image of the grid square with the crystal used for data collection marked is included in each folder. Data collection settings: 200kV, microprobe, gun lens 4, spot size 11, 30 µm C2 aperture. Illuminated area was ~3.3 µm and a 40 µm SA aperture was used. Camera length calibrated from Al powder is 838.5 mm. Data acquired using EPU-D (v1.5) with following settings: 2x binning, 0.5 °/s, 2s exposure, rolling shutter, noise reduction mode enabled. MRC format images can be processed with DIALS using the FormatMRC dxtbx format (distributed with DIALS from version 3.5 onwards), use goniometer.axes=1,0,0.
DOI: 10.5281/zenodo.4895411
title: 3DED/microED datasets of biotin (Glacios/Ceta-D)

description: 3DED/microED data collected from 11 crystals of biotin (Sigma-Aldrich 14400) using a Thermo Fisher Scientific Glacios microscope equipped with a Ceta-D Camera. An image of the grid square with the crystal used for data collection marked is included in each folder. Data collection settings: 200kV, microprobe, gun lens 4, spot size 11, 30 µm C2 aperture. Illuminated area was ~3.3 µm and a 40 µm SA aperture was used. Camera length calibrated from Al powder is 838.5 mm. Data acquired using EPU-D (v1.5) with following settings: 2x binning, 0.5 °/s, 2s exposure, rolling shutter, noise reduction mode enabled. MRC format images can be processed with DIALS using the FormatMRC dxtbx format (distributed with DIALS from version 3.5 onwards), use goniometer.axes=1,0,0.
DOI: 10.5281/zenodo.4893549
title: The distribution of Meteoric Smoke Dust from the Whole Atmosphere Community Climate Model (WACCM) simulation

description: We have carried out the three-dimensional (3D) simulation of meteoric dust using the Whole Atmosphere Community Climate Model (WACCM) coupled to a sectional aerosol microphysics mode based upon the Community Aerosol and Radiation Model for Atmospheres (CARMA). The model is nudged with the available MERRA2 reanalysis dataset from 2007 to 2020. The horizontal resolution used here is 1.9° (in latitude) × 2.5° (in longitude) with 88 vertical levels (1000−5.96×10<sup>−6</sup> hPa) using a hybrid <em>σ</em>-pressure vertical coordinate. The meteoric dust has 28 size bins with radii between 0.34 nm and 1.76 μm., assuming We assume spherical particles and a dust particle bulk density of 2.0 g cm<sup>−3</sup>. The netcdf files uploaded here are the modelled daily meteoric dust volume density from 1 Jan 2007 to end of December 2019 (filename: MSP8ton_4MARK_smokevd_yyyy.nc, where yyyy is the year from 2007 to 2019, note MSP8ton_4MARK_smokevd_2020.nc can not be uploaded here due to the zenodo disk limitation, please contact Dr Wuhu Feng (w.feng@leeds.ac.uk) for it) and the monthly mean meteoric dust in mass mixing ratio (filename: MSP8ton_4MARK_smoke_2007_2020.nc). The data is used in: Mark E. Hervig, John Maurice Campbell Plane, David E. Siskind, Wuhu Feng, Charles Bardeen, Scott Martin Bailey, Meteoric smoke and meteor influx from global SOFIE observations, J. Geophys. Res., in review, 2021.
DOI: 10.5281/zenodo.4893548
title: The distribution of Meteoric Smoke Dust from the Whole Atmosphere Community Climate Model (WACCM) simulation

description: We have carried out the three-dimensional (3D) simulation of meteoric dust using the Whole Atmosphere Community Climate Model (WACCM) coupled to a sectional aerosol microphysics mode based upon the Community Aerosol and Radiation Model for Atmospheres (CARMA). The model is nudged with the available MERRA2 reanalysis dataset from 2007 to 2020. The horizontal resolution used here is 1.9° (in latitude) × 2.5° (in longitude) with 88 vertical levels (1000−5.96×10<sup>−6</sup> hPa) using a hybrid <em>σ</em>-pressure vertical coordinate. The meteoric dust has 28 size bins with radii between 0.34 nm and 1.76 μm., assuming We assume spherical particles and a dust particle bulk density of 2.0 g cm<sup>−3</sup>. The netcdf files uploaded here are the modelled daily meteoric dust volume density from 1 Jan 2007 to end of December 2019 (filename: MSP8ton_4MARK_smokevd_yyyy.nc, where yyyy is the year from 2007 to 2019, note MSP8ton_4MARK_smokevd_2020.nc can not be uploaded here due to the zenodo disk limitation, please contact Dr Wuhu Feng (w.feng@leeds.ac.uk) for it) and the monthly mean meteoric dust in mass mixing ratio (filename: MSP8ton_4MARK_smoke_2007_2020.nc). The data is used in: Mark E. Hervig, John Maurice Campbell Plane, David E. Siskind, Wuhu Feng, Charles Bardeen, Scott Martin Bailey, Meteoric smoke and meteor influx from global SOFIE observations, J. Geophys. Res., in review, 2021.
DOI: 10.17632/3w897jc4dd.1
title: Data for: Do Particle Verbs Share a Representation with their Root Verbs? Evidence from Structural Priming
DOI: 10.17632/4k3m38c5xt.1
title: Data for: Across the Stolen Ponds: The Political Geography of Social Welfare in Rural Eastern India

description: The Raw Data set details out the political composition of the 46 village councils, NREGS expenditure and registration patterns between 2013-2018.
DOI: 10.5281/zenodo.4895667
title: CoVaxxy Tweet IDs data set

description: A collection of Tweet IDs related to Covid-19 Vaccines, gathered from Twitter since Jan 4, 2021. Please see https://arxiv.org/abs/2101.07694 for more information.
DOI: 10.5281/zenodo.4895677
title: Standard curves and table of genes implicated in nEPS Production by H desertis G11

description: Standard curves and table of genes implicated in nEPS production by H. desertis G11
DOI: 10.5281/zenodo.4895676
title: Standard curves and table of genes implicated in nEPS Production by H desertis G11

description: Standard curves and table of genes implicated in nEPS production by H. desertis G11
DOI: 10.5281/zenodo.4895682
title: Dynamics of the tongue of ionizations during the geomagnetic storm on September 7, 2015

description: The simulation from TIEGCM used in the manuscript entitled "Dynamics of the tongue of ionizations during the geomagnetic storm on September 7, 2015".
DOI: 10.5281/zenodo.4895681
title: Dynamics of the tongue of ionizations during the geomagnetic storm on September 7, 2015

description: The simulation from TIEGCM used in the manuscript entitled "Dynamics of the tongue of ionizations during the geomagnetic storm on September 7, 2015".
DOI: 10.5281/zenodo.4895679
title: Dataset for Super.FELT

description: Dataset for Super.FELT (https://github.com/DMCB-GIST/Super.FELT)
DOI: 10.5281/zenodo.4635707
title: Dataset for Super.FELT

description: Dataset for Super.FELT (https://github.com/DMCB-GIST/Super.FELT)
DOI: 10.25345/c5h24c
title: MassIVE MSV000087564 - Salivary glands from Aedes aegypti infected with DENV, ZIKV, and CHIKV
title: Aedes aegypti mosquitoes were orally infected with DENV, ZIKV or CHIKV virus, and once virus infection reached salivary gland tissues, these glands were dissected out and i-TRAQ performed to identify differentially expressed proteins during virus infection.
DOI: 10.6084/m9.figshare.14227028.v2
title: Strategy for balancing the preservation of area, shape, and topology during polygon-to-raster conversion

description: We proposed a balanced strategy for decreasing multiple types of rasterization errors to preserve the spatial attributes of the area, shape, and topology during polygon-to-raster conversion. Starting with the outcome of the conventional rasterization algorithm, the proposed strategy first attempts to reassign as few raster cells as possible to compensate for the loss in the shape attributes. The strategy then corrects the topological changes according to the real topologies of vector polygons. Finally, the areas in the raster regions are coordinated with those of the corresponding polygons to preserve the area attributes. <br>
DOI: 10.6084/m9.figshare.14221811
title: landcolormap.mat

description: landcolormap
DOI: 10.6084/m9.figshare.14221811.v2
title: landcolormap.mat

description: landcolormap
DOI: 10.6084/m9.figshare.14221811.v1
title: landcolormap.mat

description: landcolormap
DOI: 10.5281/zenodo.4604144
title: OKI2018_I69 assembly and annotation of the genome of an individual Oikopleura dioica from Okinawa

description: A chromosome-scale assembly of the <em>Oikopleura dioica</em> genome from Okinawa, Japan. The contig assembly was generated with long-read Nanopore data using Canu pipeline v1.8, and polished with short Illumina MiSeq reads using Pilon v1.22. Both Nanopore and Illumina data were generated from DNA of a single <em>O. dioica </em>male. Hi-C chromosomal conformation capture data was used to order and orient the contigs into scaffolds using Juicer v1.6 and 3D de novo assembly (3D-DNA) pipelines. The OKI2018_I69_1.0 assembly comprises 19 scaffolds with an N50 of 16.2 Mbp (OKI2018_I69_1.0.fa). The total assembly length is 64.3 Mbp. The five longest scaffolds represent autosomal chromosomes (chr 1 and chr 2), and sex chromosomes split into pseudo-autosomal region (PAR) and X-specific (XSR) or Y-specific (YSR) regions. One of the smaller scaffolds represent a draft assembly of mitochondrial genome (chrUn_12). The rest of scaffolds are highly repetitive and were marked as unplaced. The OKI2018_I69_1.0 assembly was annotated with AUGUSTUS v3.3 and MAKER v3.01.03 pipelines. Gene predictions from these software were refined and merged using EvidenceModeler v1.1.1. To predict UTRs and alternative isoforms, the EVM models were updated using two round of PASA pipeline, resulting in 18,485 transcript models distributed among 16,936 protein-coding genes (OKI2018_I69_1.0.gene_models.gff3).
description: The genome is now published in BMC genomics (Bliznina et al., 2021) and deposited to ENA (BioProject ID PRJEB40135) .
DOI: 10.5281/zenodo.4023776
title: OKI2018_I69 assembly and annotation of the genome of an individual Oikopleura dioica from Okinawa

description: A chromosome-scale assembly of the <em>Oikopleura dioica</em> genome from Okinawa, Japan. The contig assembly was generated with long-read Nanopore data using Canu pipeline v1.8, and polished with short Illumina MiSeq reads using Pilon v1.22. Both Nanopore and Illumina data were generated from DNA of a single <em>O. dioica </em>male. Hi-C chromosomal conformation capture data was used to order and orient the contigs into scaffolds using Juicer v1.6 and 3D de novo assembly (3D-DNA) pipelines. The OKI2018_I69_1.0 assembly comprises 19 scaffolds with an N50 of 16.2 Mbp (OKI2018_I69_1.0.fa). The total assembly length is 64.3 Mbp. The five longest scaffolds represent autosomal chromosomes (chr 1 and chr 2), and sex chromosomes split into pseudo-autosomal region (PAR) and X-specific (XSR) or Y-specific (YSR) regions. One of the smaller scaffolds represent a draft assembly of mitochondrial genome (chrUn_12). The rest of scaffolds are highly repetitive and were marked as unplaced. The OKI2018_I69_1.0 assembly was annotated with AUGUSTUS v3.3 and MAKER v3.01.03 pipelines. Gene predictions from these software were refined and merged using EvidenceModeler v1.1.1. To predict UTRs and alternative isoforms, the EVM models were updated using two round of PASA pipeline, resulting in 18,485 transcript models distributed among 16,936 protein-coding genes (OKI2018_I69_1.0.gene_models.gff3).
description: The genome is now published in BMC genomics (Bliznina et al., 2021) and deposited to ENA (BioProject ID PRJEB40135) .
DOI: 10.5066/p9wtwcpg
title: Model Archive Summary for acoustic derived suspended-sediment concentration at 14144700 Columbia River at Vancouver, WA

description: Model archive summary describing the development of an acoustic derived suspended sediment time series computation model. The model archive summary describes the methods and techniques used to develop the model for the Columbia River at Vancouver site - USGS site ID# 14144700. The time series suspended sediment data will help determine the suspended sediment concentration at the site in real-time enabling science entities, managers, and others, track the movement of sediment in the Columbia River.
DOI: 10.34740/kaggle/dsv/2297863
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.25345/c5c80p
title: MassIVE MSV000087565 - Fruit and leaf metabolomics of 12 Neotropical Piper spp
title: Interactions between plants and leaf herbivores have long been implicated as the major driver of plant secondary metabolite diversity. However, other plant-animal interactions, such as those between fruits and frugivores, may also be involved in phytochemical diversification. Using 12 species of Piper, we conducted untargeted metabolomics and molecular networking with extracts of fruits and leaves. We evaluated organ-specific secondary metabolite composition and compared multiple dimensions of phytochemical diversity across organs, including richness, structural complexity, and variability across samples at multiple scales within and across species.
DOI: 10.5281/zenodo.4895729
title: SAPS-EEJ longitudinal responses

description: The simulation data used in our manuscript.
DOI: 10.5281/zenodo.4895728
title: SAPS-EEJ longitudinal responses

description: The simulation data used in our manuscript.
DOI: 10.6084/m9.figshare.14221940
title: data in Tokara Strait

description: data used in Tokara Strait<br>
DOI: 10.6084/m9.figshare.14221940.v1
title: data in Tokara Strait

description: data used in Tokara Strait<br>
DOI: 10.5281/zenodo.4895643
title: Multi-Object Datasets

description: Multi-Object Datasets (https://github.com/deepmind/multi_object_datasets) post-processed for easy replication of the training and evaluation of the ICML'21 paper "Efficient Iterative Amortized Inference for Learning Symmetric and Disentangled Multi-Object Representations".<br> Datasets for CLEVR6, Multi-dSprites, and Tetrominoes are in the .h5 format and split by training and test. Images and masks are provided for each. CLEVR6 also contains the ground truth latent factors for disentanglement evaluation. Unzip the provided zip file in the desired location.
DOI: 10.5281/zenodo.4895642
title: Multi-Object Datasets

description: Multi-Object Datasets (https://github.com/deepmind/multi_object_datasets) post-processed for easy replication of the training and evaluation of the ICML'21 paper "Efficient Iterative Amortized Inference for Learning Symmetric and Disentangled Multi-Object Representations".<br> Datasets for CLEVR6, Multi-dSprites, and Tetrominoes are in the .h5 format and split by training and test. Images and masks are provided for each. CLEVR6 also contains the ground truth latent factors for disentanglement evaluation. Unzip the provided zip file in the desired location.
DOI: 10.6084/m9.figshare.14721570.v1
title: Supplementary data for parameter optimization from An integrated platform to facilitate the calculation, validation and visualization of optical flow velocities in biological images

description: Table containing the ranks and mean end point errors of all the sets of parameters tested during parameter optimization for Farneback, PyrLK and PIV.
DOI: 10.6084/m9.figshare.14721570
title: Supplementary data for parameter optimization from An integrated platform to facilitate the calculation, validation and visualization of optical flow velocities in biological images

description: Table containing the ranks and mean end point errors of all the sets of parameters tested during parameter optimization for Farneback, PyrLK and PIV.
DOI: 10.26182/2ewa-pd24
title: Amborella pangenome and supplementary tables v4
DOI: 10.25345/c57k0j
title: MassIVE MSV000087566 - Microscaled Proteogenomic Methods for Precision Oncology
title: &lt;p&gt;Shankha Satpathy, Eric J. Jaehnig, et al., &lt;a href="https://www.nature.com/articles/s41467-020-14381-2" target="_blank"&gt;Nature Communications volume 11, Article number: 532 (2020)&lt;/a&gt;&lt;/p&gt;&lt;p&gt;Cancer proteogenomics promises new insights into cancer biology and treatment efficacy by integrating genomics, transcriptomics and protein profiling including modifications by mass spectrometry (MS). A critical limitation is sample input requirements that exceed many sources of clinically important material. Here we report a proteogenomics approach for core biopsies using tissue-sparing specimen processing and microscaled proteomics. As a demonstration, we analyze core needle biopsies from ERBB2 positive breast cancers before and 48-72 h after initiating neoadjuvant trastuzumab-based chemotherapy. We show greater suppression of ERBB2 protein and both ERBB2 and mTOR target phosphosite levels in cases associated with pathological complete response, and identify potential causes of treatment resistance including the absence of ERBB2 amplification, insufficient ERBB2 activity for therapeutic sensitivity despite ERBB2 amplification, and candidate resistance mechanisms including androgen receptor signaling, mucin overexpression and an inactive immune microenvironment. The clinical utility and discovery potential of proteogenomics at biopsy-scale warrants further investigation.&lt;br&gt;&lt;br&gt;&lt;em&gt;Genomic Data&lt;/em&gt; for samples in the Microscaled Proteogenomic Methods Publication are available from the NIH Database of Genotypes and Phenotypes (dbGaP), Study Accession: phs001907.v1.p1, &lt;a href="https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001907.v1.p1" target="_blank"&gt;here&lt;/a&gt;&lt;/p&gt;
DOI: 10.6084/m9.figshare.14722292.v1
title: Additional file 1 of Association between electronic cigarette use and tobacco cigarette smoking initiation in adolescents: a systematic review and meta-analysis

description: Additional file 1: We present all additional information in one excel file (supplementary excel file) and within the file each tab is a single appendix. Appendix 1. (or Table 1) presents the Medline literature search strategy. Appendix 2. presents the study PRISMA flow chart. Appendix 3. presents the quality assessment tool and results. Appendix 4. presents characteristics of included studies. Appendix 5. presents primary research AOR for ever e-cigarette and cigarette use among adolescents in the selected longitudinal cohort studies. Appendix 6. presents primary studies ever use of e-cigarettes and cigarettes among adolescents in the selected longitudinal cohort studies using statistical measures such as adjusted relative risk, estimates, or standardised coefficient. Appendix 7. presents AORs for different frequencies of e-cigarette and cigarette use among adolescents in the selected longitudinal cohort studies. Appendix 8. presents adjusted relative risk for different frequencies of e-cigarette and cigarette use. Appendix 9. presents the feasibility assessment for meta-analysis and Appendix 10. presents the results of the meta-analysis, sensitivity analysis, and subgroup analysis.
DOI: 10.6084/m9.figshare.14722229.v1
title: Additional file 5 of Holobiont nitrogen control and its potential for eutrophication resistance in an obligate photosymbiotic jellyfish

description: Additional file 4: R-scripts employed to analyse the bacterial microbiome.
DOI: 10.6084/m9.figshare.14722226.v1
title: Additional file 4 of Holobiont nitrogen control and its potential for eutrophication resistance in an obligate photosymbiotic jellyfish

description: Additional file 3: Table S2. ASV abundance table detailing ASV numbers over samples, including taxonomy and representative sequences. Number of ASVs 303, of which 7 are contaminants (marked with *), core microbiome members in bold, 'symbiome' members underlined for symbiotic samples and 'apobiome' members underlined for aposymbiotic samples. Table S3. Detailed stable isotope measurements of Cassiopea xamachana and its associated Symbiodiniaceae in symbiotic-light (SymL), symbiotic-dark (SymD), aposymbiotic-light (ApoL) treatments and upon heterotrophic feeding. Table S4. Stable isotope analysis enrichment statistics. Table S5. Stable isotope labelling of Isochrysis galbana and Artemia salina. 13C and 15N enriched Isochrysis galbana algae were employed to label Artemia salina as a heterotrophic food source for C. xamachana. Table S6. OTU abundance table detailing OTU numbers over samples, including taxonomy and representative sequences. Number of OTUs 697, of which 9 are contaminants (marked with *), core microbiome members in bold, 'symbiome' members underlined for symbiotic samples and 'apobiome' members underlined for aposymbiotic samples. Table S7. Closest blastn hits considered for presumably important OTUs (including core microbiome, symbiome, and apobiome; assessed June 2020). Table S8. Closest complete genomes of the 20 most abundant ASVs based on an NCBI blastn search (assessed November 2020). Considered gene homologs are related to nitrogen cycling and transport.
DOI: 10.6084/m9.figshare.14722197.v1
title: Additional file 9 of Evaluating implementation of the Transparency and Openness Promotion (TOP) guidelines: the TRUST process for rating journal policies, procedures, and practices

description: Additional file 9.
DOI: 10.6084/m9.figshare.14722185.v1
title: Additional file 5 of Evaluating implementation of the Transparency and Openness Promotion (TOP) guidelines: the TRUST process for rating journal policies, procedures, and practices

description: Additional file 5.
DOI: 10.6084/m9.figshare.14722088.v1
title: Additional file 4 of Comprehensive analysis of LncRNAs expression profiles in an in vitro model of steatosis treated with Exendin-4

description: Additional file 4: Table S4. lncRNAs (50) downregulated in steatotic cells and upregulated in Exendin-4-treated steatotic cells.