cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10124173
title: Data and results of the example used in the SI-Hg D1 protocol for the SI-traceable calibration of elemental mercury (Hg0) gas generators used in the field

description: During the SI-Hg project a metrological traceable protocol for the calibration of mercury gas generators used in the field was developed and validated. The SI-Hg calibration protocol specifies the procedures for establishing traceability to the SI units for the quantitative output of elemental mercury generators that are employed in regulatory applications for emission monitoring or testing. This protocol provides methods for

the experimental procedures to compare the output of elemental mercury gas generators
the data processing for determination of mercury concentration and the expanded uncertainty of the mercury concentration obtained from the elemental mercury gas generator.
In the protocol examples are given to explain the data processing, determining the mercury concentration and corresponding uncertainty. In this repository the raw data and results used for the example calculated with the data processing script can be found.
DOI: 10.5281/zenodo.5760217
title: MICrONS: Machine Intelligence from Cortical Networks

description: A ground truth dataset for 3D neuron segmentation from electron microscopy (EM) images of mouse visual cortex, created for IARPA's Machine Intelligence from Cortical Networks (MICrONS) program. For more information, please visit our MICrONS explorer website.


 


Citation


Functional connectomics spanning multiple areas of mouse visual cortex
MICrONs Consortium et al.
bioRxiv 2021.07.28.454025; doi: https://doi.org/10.1101/2021.07.28.454025


 


Data Format Specification


Volumes and annotations are stored in a single HDF5 file with the following datasets:



	
volumes: are stored in row-major format, i.e., with dimensions (z, y, x). Every volume has an attribute resolution that specifies the voxel size in nm.

	

		
image
		
segmentation
		
mitochondria (optional)
		
synapse (optional): annotation for postsynaptic densities (PSDs)
		
fold (optional): annotation for folds (a kind of image defect) in images
		
mask: valid/invalid voxels are represented as 1s/0s respectively.
	
	
	
annotations: are incomplete, meaning that each volume may or may not contain proper annotations.
	

		
object_ids (optional): small unidentified objects or intracellular organelles that are oversegmented, which may require special handling.
		
myelin_ids (optional)
		
blood_vessel_ids (optional)
		
soma_ids (optional)
		
nucleus_ids (optional)
DOI: 10.5281/zenodo.5760218
title: MICrONS: Machine Intelligence from Cortical Networks

description: A ground truth dataset for 3D neuron segmentation from electron microscopy (EM) images of mouse visual cortex, created for IARPA's Machine Intelligence from Cortical Networks (MICrONS) program. For more information, please visit our MICrONS explorer website.


 


Citation


Functional connectomics spanning multiple areas of mouse visual cortex
MICrONs Consortium et al.
bioRxiv 2021.07.28.454025; doi: https://doi.org/10.1101/2021.07.28.454025


 


Data Format Specification


Volumes and annotations are stored in a single HDF5 file with the following datasets:



	
volumes: are stored in row-major format, i.e., with dimensions (z, y, x). Every volume has an attribute resolution that specifies the voxel size in nm.

	

		
image
		
segmentation
		
mitochondria (optional)
		
synapse (optional): annotation for postsynaptic densities (PSDs)
		
fold (optional): annotation for folds (a kind of image defect) in images
		
mask: valid/invalid voxels are represented as 1s/0s respectively.
	
	
	
annotations: are incomplete, meaning that each volume may or may not contain proper annotations.
	

		
object_ids (optional): small unidentified objects or intracellular organelles that are oversegmented, which may require special handling.
		
myelin_ids (optional)
		
blood_vessel_ids (optional)
		
soma_ids (optional)
		
nucleus_ids (optional)
DOI: 10.34740/kaggle/dsv/7080031
title: Survey about current Instability in Pakistan
DOI: 10.22029/jlupub-273
title: Data for "Genome-wide scan for selective sweeps identifies novel loci associated with resistance to mastitis in German Holstein cattle"

description: The data include the materials for the research article "Genome-wide scan for selective sweeps identifies novel loci associated with resistance to mastitis". The aim of this study was to identify the genomic regions associated with mastitis, using the genotypes from the national project of Holstein dairy cattle in Germany. The samples were genotyped with Bovine 50K SNP chip. Based on random residual effects of the mastitis diagnoses, 133 healthy and sick samples from 13290 genotyped dairy cows were selected, respectively. Selection signatures between cows in healthy and sick groups were detected using XP-EHH statistic. Detailed analyses and methods can be found in the article. The data used in this study are presented in the following three files: PhenoMast.txt: Mastitis records of the 13276 genotyped cows. First row includes column names, i.e., cow ID, herd, year-season, mastitis diagnoses. GenoHealth.txt: Genotypes of the 133 healthy cows. First column is cow ID and following 45613 columns are genotypes of the 133 cows (one SNP marker per column). GenoSick.txt: Genotypes from the 133 sick cows. First column is cow ID and following 45613 columns are genotypes of the 133 cows (one SNP marker per column).
DOI: 10.5281/zenodo.10212327
title: GIS bestanden inventaris mottekastelen

description: GIS bestanden (.geojson) met de inventaris van mottekastelen in Vlaanderen, opgemaakt binnen het kader van het project "Syntheseonderzoek Archeologie – Is het gras groener aan de andere kant van de heuvel? De studie van mottekastelen vanuit landschappelijk en beheersmatig perspectief".
De geïnventariseerde sites werden geografische gelokaliseerd en aangeduid als puntlocaties. De sites die werden gedetecteerd via luchtfotografie zijn ingetekend als polygonen. 
Het onderzoeksrapport is gepubliceerd als:
Herremans D. (red.), Cruz F., Storme A., Verhegge J., Allemeersch L., De Smedt P., Stichelbaut B.,  Rozek J., Vergauwe R., Van de Velde S., Van Parys V. & Laloo P. 2023: Is het gras groener aan de andere kant van de heuvel? De studie van mottekastelen vanuit landschappelijk en beheersmatig perspectief. SYNTAR 17, Brussel. doi: https://doi.org/10.55465/EVMA9277.
 (subsidie agentschap Onroerend Erfgoed)
DOI: 10.6084/m9.figshare.9784379.v2
title: China provincial energy inventory, 2016-2017

description: The dataset provides China provincial energy inventory from 2016-2017.Raw data are collect from China energy statistical yearbooks 2017-2018.
DOI: 10.6084/m9.figshare.9784388.v3
title: China provincial CO2 emission inventory (reference approach), 2016-2017

description: The dataset provides China provincial CO2 emission inventory (reference approach) from 2016-2017.The emissions include CO2 from fossil fuel combustion and cement process.
DOI: 10.6084/m9.figshare.3761562.v1312
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.25386/genetics.10247969.v3
title: Supplemental Material for Bhardwaj, Pandey, and Babu, 2020

description: Supplemental files and movies. <br>
DOI: 10.25387/g3.10287660
title: Supplemental Material for Liu et al., 2020

description: Table S1: Primers used in RT-qPCR, Table S2: E-value and top 10 species distributions, Table S3: Unigenes assigned to 25 function categories, Table S4: DEGs with stage-specific up expression in E14 vs. E18, E18 vs. E28, and E14 vs. E28, Table S5: DEGs with stage-specific down expression in E14 vs. E18, E18 vs. E28, and E14 vs. E28, Table S6: DEGs in E14 vs. E18 were assigned to three major GO categories, Table S7: DEGs in E14 vs. E28 were assigned to three major GO categories. Table S8: DEGs in E18 vs. E28 were assigned to three major GO categories, Table S9: Expression of DEGs between the different species by the values of RPKM and Count.
DOI: 10.25387/g3.10287660.v1
title: Supplemental Material for Liu et al., 2020

description: Table S1: Primers used in RT-qPCR, Table S2: E-value and top 10 species distributions, Table S3: Unigenes assigned to 25 function categories, Table S4: DEGs with stage-specific up expression in E14 vs. E18, E18 vs. E28, and E14 vs. E28, Table S5: DEGs with stage-specific down expression in E14 vs. E18, E18 vs. E28, and E14 vs. E28, Table S6: DEGs in E14 vs. E18 were assigned to three major GO categories, Table S7: DEGs in E14 vs. E28 were assigned to three major GO categories. Table S8: DEGs in E18 vs. E28 were assigned to three major GO categories, Table S9: Expression of DEGs between the different species by the values of RPKM and Count.
DOI: 10.25387/g3.10565996
title: Supplemental Material for Schmidt et al., 2020

description: File_S1-T1 contains a list of strains and sequences of barcodes introduced into each strain. File_S1-T2 contains a primer list. File_S1-T3 contains complete sequence of the 150 bp barcode element inserted into each strain. File_S1-T4 provides the absorbance of individual cultures prior to pooling. File_S1-T5 and File_S1-T6 contains a summary of experimental conditions. File_S1-T7 provides the results of all pair-wise comparisons (log2 fold-change) and associated statistics. File_S2 includes all supplementary figures including absorbance and sugar utilization data for all experiments discussed in the manuscript. File_S3 provides the code used in pair wise comparison of strain performance. All raw count data is provided in File_S4.
DOI: 10.25387/g3.10565996.v1
title: Supplemental Material for Schmidt et al., 2020

description: File_S1-T1 contains a list of strains and sequences of barcodes introduced into each strain. File_S1-T2 contains a primer list. File_S1-T3 contains complete sequence of the 150 bp barcode element inserted into each strain. File_S1-T4 provides the absorbance of individual cultures prior to pooling. File_S1-T5 and File_S1-T6 contains a summary of experimental conditions. File_S1-T7 provides the results of all pair-wise comparisons (log2 fold-change) and associated statistics. File_S2 includes all supplementary figures including absorbance and sugar utilization data for all experiments discussed in the manuscript. File_S3 provides the code used in pair wise comparison of strain performance. All raw count data is provided in File_S4.
DOI: 10.25387/g3.9879566
title: Supplemental Material for Faure et al., 2020

description: Table S1: P. oligandrum predicted proteins.Table S2: P. oligandrum predicted secreted proteins Table S3: REVIGO analysis table of the GO term occurrence related to the biological process axe of the putative secreted proteins.Table S4: REVIGO analysis table of the GO term occurrence related to the molecular function axe of the putative secreted proteins.Table S5: The 490 predicted proteins with annotated CAZY domain.Table S6: P. oligandrum 156 predicted secreted proteins with a peptidase GO annotation.Table S7: P. oligandrum 303 putative Small Secreted Proteins (SSP) Table S8: P. oligandrum 27 putative Crinkler (CRN) effectors.
DOI: 10.25405/data.ncl.11302853
title: Endogenous Nanoparticles Strain Perovskite Host Lattice Providing Oxygen Capacity and Driving Oxygen Exchange and CH4 Conversion to Syngas

description: Particles dispersed on the surface of oxide supports have enabled a wealth of applications in electro- photo- and heterogeneous catalysis. Dispersing nanoparticles within the bulk of oxides is, however, synthetically much more challenging and therefore less explored, but could open new dimensions to control material properties analogous to substitutional doping of ions in crystal lattices. Here we demonstrate such a concept allowing extensive, controlled growth of metallic nanoparticles, at nanoscale proximity, within a perovskite oxide lattice as well as on its surface. By employing operando techniques, we show that in the emergent nanostructure, the endogenous nanoparticles and the perovskite lattice become reciprocally strained and seamlessly connected, enabling enhanced oxygen exchange. Additionally, even deeply embedded nanoparticles can reversibly exchange oxygen with a methane stream, driving its redox conversion to syngas with remarkable selectivity and long term cyclability while surface particles are present. These results not only exemplify the means to create extensive, self-strained nanoarchitectures with enhanced oxygen transport and storage capabilities, but also demonstrate that deeply submerged, redox-active nanoparticles could be entirely accessible to reaction environments, driving redox transformations and thus offering intriguing new alternatives to design materials underpinning several energy conversion technologies.
DOI: 10.25387/g3.9879566.v1
title: Supplemental Material for Faure et al., 2020

description: Table S1: P. oligandrum predicted proteins.Table S2: P. oligandrum predicted secreted proteins Table S3: REVIGO analysis table of the GO term occurrence related to the biological process axe of the putative secreted proteins.Table S4: REVIGO analysis table of the GO term occurrence related to the molecular function axe of the putative secreted proteins.Table S5: The 490 predicted proteins with annotated CAZY domain.Table S6: P. oligandrum 156 predicted secreted proteins with a peptidase GO annotation.Table S7: P. oligandrum 303 putative Small Secreted Proteins (SSP) Table S8: P. oligandrum 27 putative Crinkler (CRN) effectors.
DOI: 10.6084/m9.figshare.3761562.v1313
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.6084/m9.figshare.6808853.v9
title: Young adults make rational sexual decisions - to be deleted

description: The ZIP file contains all necessary codes (Matlab and R) and data for reproducing the results from the paper (Hatz, Park, McCarty, McCarthy, & Davis-Stober, submitted). It also includes the instruction and stimuli we used for the monetary gamble task from the paper.<br>The pdf file "readme.pdf" provides a step-by-step instruction for readers to reproduce the results.
DOI: 10.6084/m9.figshare.8192183.v2
title: New spiders (Araneae: Palpimanoidea) from the Jurassic Yanliao Biota of China

description: Several new spider specimens, belonging to the superfamily Palpimanoidea, are described from the Middle–Upper Jurassic Haifanggou Formation (early assemblage of the Yanliao Biota) of Inner Mongolia, China. Two new genera and species, and a new species in the genus <i>Sinaranea</i> Selden, Huang & Ren, 2008, are described. <i>Caestaranea jurassica</i> gen. et sp. nov. is described on the basis of several adult males, typified by boxing-glove shaped pedipalps, as well as females and juveniles. <i>Onychopalpus thomisoides</i> gen. et sp. nov. is the largest palpimanoid known, and its habitus resembles that of a crab spider (Thomisidae) in having large, laterigrade anterior legs with rows of macrosetae on the femora and a squat, rotund opisthosoma. However, the distinctive adult male pedipalp bears a pectinate claw, so the holotype specimen is a subadult male; the other specimens referred to this species are smaller juveniles. Three new specimens of <i>Sinaranea metaxyostraca</i> Selden, Huang & Ren, 2008, including two adult males, are described here, and the new species <i>S. brevicrus</i> sp. nov., which has shorter legs than the type species, is described from an adult male and an adult female. These new palpimanoids substantially increase the diversity of the superfamily in the Middle Jurassic, and the unusual <i>Onychopalpus</i> provides evidence for a different mode of life for these spiders. http://www.zoobank.org/urn:lsid:zoobank.org:pub:D7726F4B-349E-4C2B-960D-371C27A6B77F
DOI: 10.25412/iop.10324745
title: Field_data_Arndt.csv

description: This dataset represents field measuremtents made near Utiagvik Alaska between July 21 and July 29, 2018. Coordinates are in meters in UTM zone 4 NAD84 datum. All thaw depth and canopy height measurements are in cm. Soil moisture content is in % volume. Plant type counts are in % of the one square meter grid.
DOI: 10.25412/iop.10324745.v1
title: Field_data_Arndt.csv

description: This dataset represents field measuremtents made near Utiagvik Alaska between July 21 and July 29, 2018. Coordinates are in meters in UTM zone 4 NAD84 datum. All thaw depth and canopy height measurements are in cm. Soil moisture content is in % volume. Plant type counts are in % of the one square meter grid.
DOI: 10.25387/g3.11234654
title: Supplemental Material for Caraballo et al., 2020

description: <b>Supplementary Figure 1. </b>Branch-specific relaxation in <i>Caenorhabditis </i>UGGTs recognition (top) and catalytic (bottom) domains. Branches are color-coded according to the selection strength parameter k, inferred under the general descriptive RELAX model. Low k values (&lt;1) indicate purifying selection relaxation, whereas high k values (&gt;1) indicate selection intensification.<b>Supplementary Figure 2. </b>Branch-specific relaxation in vertebrate UGGTs recognition (left) and catalytic (right) domains. Branches are color-coded according to the selection strength parameter k, inferred under the general descriptive RELAX model. Low k values (&lt;1) indicate purifying selection relaxation, whereas high k values (&gt;1) indicate selection intensification. <b>Supplementary Figure 3 (in Additional File 5).</b> Expression of <i>Sp</i>UGGT, <i>Ce</i>-UGGT-a, <i>Ce</i>-UGGT-b and chimeric proteins in <i>alg6/gpt1- </i>cells. Microsomal proteins derived of <i>S.pombe alg6/gpt1 </i>transformed with pREP3X-<i>uggt</i>-b (lane1), pREP3X-<i>uggt</i>-a (lane 2), pREP3X-<i>gpt1+ </i>(lane 3), pREP3X-chimera I (<i>Ce</i>-N-term-<i>uggt</i>-a-C-term-<i>gpt1+c-myc</i>) (lane 4), pREP3X-chimera II (<i>Ce</i>-N-term-<i>uggt-b</i>-C-term<i> gpt1+</i>-<i>c-myc</i>) (lane 5) and pREP3X (lane 6) were analyzed in 8 % SDS PAGE and submitted to Western-blot analysis using a commercial anti c-Myc antibody. <b>Table S1 </b><b>(in Additional File 5)</b><b>.</b> Templates and primers used in the PCR amplification of the sequences encoding the N- and C-terminal domains of <i>S. pombe</i> UGGT, <i>Ce</i>-UGGT-a, and <i>Ce</i>-UGGT-b.<b> Table S2 </b><b>(in Additional File 5)</b><b>.</b> Templates and primers used in the PCR amplification of the full-length fragments encoding chimeric UGGTs <b> Table S3 </b><b>(in Additional File 5)</b><b>.</b> List of DNA primers used in this work<b>Additional File 1</b>. <b>(xls). </b>Species names, phyla, database and Accession Numbers of the 195 UGGT (and UGGT-like) sequences included in this study. The criteria for excluded sequences is detailed.<b> Additional File 2. (fas).</b> Unaligned 195 UGGT (and UGGT-like) protein sequences.<b> Additional File 3. (fas).</b> Alignment of 195 UGGT (and UGGT-like) protein sequences used for phylogenetic inference.<b> Additional File 4. (doc).</b> Aminoacidic positions corresponding to each UGGT domain taken as reference sequences. <b> Additional File 5. (doc).</b> Procedures performed in the construction of expression plasmids and list of primer sequences used in this study. Supplementary Figure S3. Western-blot analysis of the expression of the c-Myc labeled full length and chimeric proteins.<br>
DOI: 10.25387/g3.11234654.v1
title: Supplemental Material for Caraballo et al., 2020

description: <b>Supplementary Figure 1. </b>Branch-specific relaxation in <i>Caenorhabditis </i>UGGTs recognition (top) and catalytic (bottom) domains. Branches are color-coded according to the selection strength parameter k, inferred under the general descriptive RELAX model. Low k values (&lt;1) indicate purifying selection relaxation, whereas high k values (&gt;1) indicate selection intensification.<b>Supplementary Figure 2. </b>Branch-specific relaxation in vertebrate UGGTs recognition (left) and catalytic (right) domains. Branches are color-coded according to the selection strength parameter k, inferred under the general descriptive RELAX model. Low k values (&lt;1) indicate purifying selection relaxation, whereas high k values (&gt;1) indicate selection intensification. <b>Supplementary Figure 3 (in Additional File 5).</b> Expression of <i>Sp</i>UGGT, <i>Ce</i>-UGGT-a, <i>Ce</i>-UGGT-b and chimeric proteins in <i>alg6/gpt1- </i>cells. Microsomal proteins derived of <i>S.pombe alg6/gpt1 </i>transformed with pREP3X-<i>uggt</i>-b (lane1), pREP3X-<i>uggt</i>-a (lane 2), pREP3X-<i>gpt1+ </i>(lane 3), pREP3X-chimera I (<i>Ce</i>-N-term-<i>uggt</i>-a-C-term-<i>gpt1+c-myc</i>) (lane 4), pREP3X-chimera II (<i>Ce</i>-N-term-<i>uggt-b</i>-C-term<i> gpt1+</i>-<i>c-myc</i>) (lane 5) and pREP3X (lane 6) were analyzed in 8 % SDS PAGE and submitted to Western-blot analysis using a commercial anti c-Myc antibody. <b>Table S1 </b><b>(in Additional File 5)</b><b>.</b> Templates and primers used in the PCR amplification of the sequences encoding the N- and C-terminal domains of <i>S. pombe</i> UGGT, <i>Ce</i>-UGGT-a, and <i>Ce</i>-UGGT-b.<b> Table S2 </b><b>(in Additional File 5)</b><b>.</b> Templates and primers used in the PCR amplification of the full-length fragments encoding chimeric UGGTs <b> Table S3 </b><b>(in Additional File 5)</b><b>.</b> List of DNA primers used in this work<b>Additional File 1</b>. <b>(xls). </b>Species names, phyla, database and Accession Numbers of the 195 UGGT (and UGGT-like) sequences included in this study. The criteria for excluded sequences is detailed.<b> Additional File 2. (fas).</b> Unaligned 195 UGGT (and UGGT-like) protein sequences.<b> Additional File 3. (fas).</b> Alignment of 195 UGGT (and UGGT-like) protein sequences used for phylogenetic inference.<b> Additional File 4. (doc).</b> Aminoacidic positions corresponding to each UGGT domain taken as reference sequences. <b> Additional File 5. (doc).</b> Procedures performed in the construction of expression plasmids and list of primer sequences used in this study. Supplementary Figure S3. Western-blot analysis of the expression of the c-Myc labeled full length and chimeric proteins.<br>
DOI: 10.25405/data.ncl.11309618
title: Raw data underpinning paper: Fabrication via stereolithography 3D printing and characterization of microfluidic PCR cartridges on a purpose-built infrared-mediated PCR thermocycler

description: Excel file contains raw data underpinning the paper Fabrication via stereolithography 3D printing and characterization of microfluidic PCR cartridges on a purpose-built infrared-mediated PCR thermocycler
DOI: 10.25405/data.ncl.11309618.v1
title: Raw data underpinning paper: Fabrication via stereolithography 3D printing and characterization of microfluidic PCR cartridges on a purpose-built infrared-mediated PCR thermocycler

description: Excel file contains raw data underpinning the paper Fabrication via stereolithography 3D printing and characterization of microfluidic PCR cartridges on a purpose-built infrared-mediated PCR thermocycler
DOI: 10.6084/m9.figshare.11317250.v1
title: table S1.pdf

description: Here we present surface seawater iodine isotopes data from the central English Channel in December 2010 as part of the 2010/2011 Antarctica two-ship expedition
DOI: 10.6084/m9.figshare.11320523
title: Improved estimates on global carbon stock and carbon pools in tidal wetlands

description: These datasets are carbon pools of global mangrove forests, including sediment organic and inorganic carbon, live and dead biomass carbon.