cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/g6bcw-sp373
title: Coxiella_burnetii_ wtACCMD_pH4d5

description: Coxiella burnetii Nine Mile phase II clone 4 (NMIIC4) strain. Wild-type cells day-5 culture. Cells grown in acidic media ACCMD and pH 4.75
description: <strong>Tilt Series Date:</strong> 2017-10-17</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Coxiella burnetii</p>
<strong>Strain:</strong> Nine Mile phase II clone 4</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Robert Heinzen. Data collected and processed by Debnath Ghosal and Mohammed Kaplan using Caltech tomography pipeline.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in Robert Heinzen's lab @NIAID and ~50 ul cells were sent to us.</p>
<strong>Sample Preparation:</strong> Refer to Heinzen lab. Freezing: 100% humidity, 4µl sample, Blot force 6, blot time 4 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-17-13/rawdata/</p>Cb_d5pH4_201710170007.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-17-13/rawdata/Cb_d5pH4_201710170007.mrc"
        > <i class="download icon"></i> Download </a></p>

        Cb_d5pH4_201710170007_full.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-17-13/3dimage_89194/Cb_d5pH4_201710170007_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.25582/data.2024-04.3096471/2562081
title: Data for EMSL Project 60257 from April 2024
DOI: 10.25582/data.2024-04.3096481/2562082
title: Data for EMSL Project 60257 from April 2024
DOI: 10.25582/data.2024-04.3096525/2562083
title: Data for EMSL Project 60257 from April 2024
DOI: 10.25582/data.2024-04.3096526/2562084
title: Data for EMSL Project 60257 from April 2024
DOI: 10.25582/data.2024-04.3096527/2562085
title: Data for EMSL Project 60257 from April 2024
DOI: 10.25582/data.2024-04.3096535/2562086
title: Data for EMSL Project 60257 from April 2024
DOI: 10.5281/zenodo.17651617
title: Trace gas data from the Munnar CZO
DOI: 10.5281/zenodo.17651618
title: Trace gas data from the Munnar CZO
DOI: 10.5281/zenodo.17650599
title: Labelled training data for gesture recognition in smart plush companions

description: The dataset contains labelled training data that was collected using plush smart companions with integrated capacitive sensors.

Each row contains 15 integer values defined as follows:










Parameter’s number in the sequence 









Description of the parameter 











1 









Cumulative signal, based on all the capacitive sensors 











2 









Cumulative signal, based on the capacitive sensors placed inside extremities 











3 









Signal from the capacitive sensor in the ears 











4 









Signal from the capacitive sensor in the head 











5 









Signal from the capacitive sensor in the neck 











6 









Signal from the proximity capacitive sensor 











7 









Signal from the capacitive sensor in the nose 











8 









Signal from the capacitive sensor in the tail 











9 









Signal from the capacitive sensor in the back 











10 









Signal from the capacitive sensor in the belly 











11 









X component of the accelerometer signal 











12 









Y component of the accelerometer signal 











13 









Z component of the accelerometer signal 











14 









Timestamp of the data frame, obtained from the MCU’s clock 











15 









Delay in ms from the previous measurement
DOI: 10.5281/zenodo.17650600
title: Labelled training data for gesture recognition in smart plush companions

description: The dataset contains labelled training data that was collected using plush smart companions with integrated capacitive sensors.

Each row contains 15 integer values defined as follows:










Parameter’s number in the sequence 









Description of the parameter 











1 









Cumulative signal, based on all the capacitive sensors 











2 









Cumulative signal, based on the capacitive sensors placed inside extremities 











3 









Signal from the capacitive sensor in the ears 











4 









Signal from the capacitive sensor in the head 











5 









Signal from the capacitive sensor in the neck 











6 









Signal from the proximity capacitive sensor 











7 









Signal from the capacitive sensor in the nose 











8 









Signal from the capacitive sensor in the tail 











9 









Signal from the capacitive sensor in the back 











10 









Signal from the capacitive sensor in the belly 











11 









X component of the accelerometer signal 











12 









Y component of the accelerometer signal 











13 









Z component of the accelerometer signal 











14 









Timestamp of the data frame, obtained from the MCU’s clock 











15 









Delay in ms from the previous measurement
DOI: 10.17182/hepdata.153302.v1/t28
title: "Figure_005-c-005" of "Measurement of the dineutrino system kinematic variables in dileptonic top quark pair production in proton-proton collisions at$\sqrt{s}$ = 13 TeV"

description: The observed (black markers) and simulated two-dimensional distribution of $p_{\mathrm{T,DNN}}^\text{miss}$ and $\text{min}[\Delta\phi(\vec{p}_{\text{T, DNN}}^{\text{miss}},\vec{p}_{\text{T}}^{\ell})]$ for the azimuthal angle range 1.08&lt;$\phi$&lt;2.14 is shown. Events from all data-taking periods and all channels are combined. The hatched (grey) areas indicate the systematic (total) uncertainty in the simulation. The lower panel of each plot shows the ratio of observed data to the expectation from MC simulation in each bin. The last bin includes all events above the plotted range.
description: Abstract: Differential top quark pair production cross sections are measured in the dilepton final states $\mathrm{e}^{+}\mathrm{e}^{-}$, $\mu^{+}\mu^{-}$, and $\mathrm{e}^{\pm}\mu^{\mp}$, as a function of kinematic variables of the system of two neutrinos: the transverse momentum $p_{\text{T}}^{\nu\nu}$ of the dineutrino system, the minimum distance in azimuthal angle between $\vec{p}_{\text{T}}^{\nu\nu}$ and leptons, and in two dimensions in bins of both observables. The measurements are performed using CERN LHC proton-proton collisions at $\sqrt{s} = 13\,$TeV, recorded by the CMS detector between 2016 and 2018, corresponding to an integrated luminosity of 138 fb$^{-1}$. The measured cross sections are unfolded to the particle level using an unregularized least squares method. The obtained results are found to be in agreement with the latest theory predictions and Monte Carlo simulations.
DOI: 10.17182/hepdata.165888.v1/t15
title: "Vector portal limits, $c\tau=10$mm" of "Search for low-mass hidden-valley dark showers with non-prompt muon pairs in proton-proton collisions at $\sqrt{s}$ = 13 TeV"

description: Upper limits at 95% CL on the branching fraction $\mathcal{B}\left(\textrm{H}\rightarrow\psi\overline{\psi}\right)$ as a function of the $\tilde{\omega}$ meson mass for $c\tau=10~\textrm{mm}$ in the vector portal model. It is assumed that $m_{\tilde{\omega}}=\tilde{\Lambda}=m_{\tilde{\eta}}$, where $m_{\tilde{\omega}}$, $\tilde{\Lambda}$, and $m_{\tilde{\eta}}$ are parameters of the dark sector: the mass of the spin-one meson, confinement scale, and the mass of the spin-zero meson, respectively. The grey bands correspond to mass regions of known SM resonances, which are masked in the search.
description: A search for signatures of a dark analog to quantum chromodynamics is performed. The analysis targets long-lived dark mesons that decay into standard-model particles, with a high branching fraction of the dark mesons decaying into muons. The dark mesons are formed by the hadronisation of dark partons, which are produced by a decay of the Higgs boson. The search is performed using a data set corresponding to an integrated luminosity of $41.6~\textrm{fb}^{-1}$, which was collected in proton-proton collisions at $\sqrt{s}=13~\textrm{TeV}$ by the CMS experiment at the CERN LHC in 2018 using non-prompt muon triggers. The search is based on resonant muon pair signatures. Machine-learning techniques are employed in the analysis, utilising boosted decision trees to discriminate between signal and background. No significant excess is observed above the standard model expectation. Upper limits on the branching fraction of the Higgs boson decaying to dark partons are determined to be as low as $10^{-4}$ at 95% confidence level, surpassing and extending the existing limits on models with dark $\tilde{\omega}$ mesons for mean proper decay lengths of less than $500~\textrm{mm}$ and for $\tilde{\omega}$ masses down to $0.3~\textrm{GeV}$. First limits are set for extended dark-shower models with two dark flavours that contain dark photons, probing their masses down to $0.33~\textrm{GeV}$.
DOI: 10.15468/dl.tr4ks3
title: Occurrence Download

description: A dataset containing 8318 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Misgurnus fossilis",
 "HasCoordinate is true"
 ]
}

 The dataset includes 8318 records from 108 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045468-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uc2bfp
title: Occurrence Download

description: A dataset containing 5862 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Material sample, Specimen, Fossil)",
 "OccurrenceStatus is Present",
 "TaxonKey is Boa"
 ]
}

 The dataset includes 5862 records from 197 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045465-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.82250/3003512
title: Saccharomycopsis sp. strain UFMG-CM-Y6632 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence

description: Three yeast isolates were obtained from soil and rotting wood samples collected in an Amazonian rainforest biome in Brazil. Comparison of the intergenic spacer 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genus Saccharomycopsis. A tree inferred from the D1/D2 sequences placed the novel species near a subclade containing Saccharomycopsis lassenensis, Saccharomycopsis fermentans, Saccharomycopsis javanensis, Saccharomycopsis babjevae, Saccharomycopsis schoenii and Saccharomycopsis oosterbeekiorum, but with low bootstrap support. In terms of sequence divergence, the novel species had the highest identity in the D1/D2 domains with Saccharomycopsis capsularis, from which it differed by 36 substitutions. In contrast, a phylogenomic analysis based on 1061 single-copy orthologs for a smaller set of Saccharomycopsis species whose whole genome sequences are available indicated that the novel species represented by strain UFMG-CM-Y6991 is phylogenetically closer to Saccharomycopsis fodiens and Saccharomycopsis sp. TF2021a (=Saccharomycopsis phalluae). The novel yeast is homothallic and produces asci with one spheroidal ascospore with an equatorial or subequatorial ledge. The name Saccharomycopsis praedatoria sp. nov. is proposed to accommodate the novel species. The holotype of Saccharomycopsis praedatoria is CBS 16589(T). The MycoBank number is MB849369. S. praedatoria was able to kill cells of Saccharomyces cerevisiae by means of penetration with infection pegs, a trait common to most species of Saccharomycopsis.
DOI: 10.82250/3003513
title: Saccharomycopsis sp. isolate UFMG-CM-Y6632 large subunit ribosomal RNA gene, partial sequence

description: Three yeast isolates were obtained from soil and rotting wood samples collected in an Amazonian rainforest biome in Brazil. Comparison of the intergenic spacer 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genus Saccharomycopsis. A tree inferred from the D1/D2 sequences placed the novel species near a subclade containing Saccharomycopsis lassenensis, Saccharomycopsis fermentans, Saccharomycopsis javanensis, Saccharomycopsis babjevae, Saccharomycopsis schoenii and Saccharomycopsis oosterbeekiorum, but with low bootstrap support. In terms of sequence divergence, the novel species had the highest identity in the D1/D2 domains with Saccharomycopsis capsularis, from which it differed by 36 substitutions. In contrast, a phylogenomic analysis based on 1061 single-copy orthologs for a smaller set of Saccharomycopsis species whose whole genome sequences are available indicated that the novel species represented by strain UFMG-CM-Y6991 is phylogenetically closer to Saccharomycopsis fodiens and Saccharomycopsis sp. TF2021a (=Saccharomycopsis phalluae). The novel yeast is homothallic and produces asci with one spheroidal ascospore with an equatorial or subequatorial ledge. The name Saccharomycopsis praedatoria sp. nov. is proposed to accommodate the novel species. The holotype of Saccharomycopsis praedatoria is CBS 16589(T). The MycoBank number is MB849369. S. praedatoria was able to kill cells of Saccharomyces cerevisiae by means of penetration with infection pegs, a trait common to most species of Saccharomycopsis.
DOI: 10.82250/3003514
title: Saccharomycopsis sp. KB-2023a isolate UFMG-CM-Y6991, whole genome shotgun sequencing project

description: Three yeast isolates were obtained from soil and rotting wood samples collected in an Amazonian rainforest biome in Brazil. Comparison of the intergenic spacer 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genus Saccharomycopsis. A tree inferred from the D1/D2 sequences placed the novel species near a subclade containing Saccharomycopsis lassenensis, Saccharomycopsis fermentans, Saccharomycopsis javanensis, Saccharomycopsis babjevae, Saccharomycopsis schoenii and Saccharomycopsis oosterbeekiorum, but with low bootstrap support. In terms of sequence divergence, the novel species had the highest identity in the D1/D2 domains with Saccharomycopsis capsularis, from which it differed by 36 substitutions. In contrast, a phylogenomic analysis based on 1061 single-copy orthologs for a smaller set of Saccharomycopsis species whose whole genome sequences are available indicated that the novel species represented by strain UFMG-CM-Y6991 is phylogenetically closer to Saccharomycopsis fodiens and Saccharomycopsis sp. TF2021a (=Saccharomycopsis phalluae). The novel yeast is homothallic and produces asci with one spheroidal ascospore with an equatorial or subequatorial ledge. The name Saccharomycopsis praedatoria sp. nov. is proposed to accommodate the novel species. The holotype of Saccharomycopsis praedatoria is CBS 16589(T). The MycoBank number is MB849369. S. praedatoria was able to kill cells of Saccharomyces cerevisiae by means of penetration with infection pegs, a trait common to most species of Saccharomycopsis.
DOI: 10.82250/3003515
title: SRX13165144: yHMH446_Pichia_sp_nov_plate33_SPADES

description: A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446(T) (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.
DOI: 10.82250/3003510
title: Functional and genomic diversity of the sorghum phyllosphere microbiome

description: A collection of 47 bacteria isolated from the mucilage of aerial roots of energy sorghum is available at the Great Lakes Bioenergy Research Center, Michigan State University, Michigan, USA. We enriched bacteria with putative plant-beneficial phenotypes and included information on phenotypic diversity, taxonomy, and whole genome sequences.
DOI: 10.82250/3003516
title: Pichia sp. yHMH446, whole genome shotgun sequencing project

description: A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446(T) (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.
DOI: 10.82250/3003517
title: Pichia sp. strain yHMH446 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence

description: A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446(T) (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.
DOI: 10.82250/3003518
title: Pichia sp. strain yHMH446 internal transcribed spacer 2 and large subunit ribosomal RNA gene, partial sequence

description: A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446(T) (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.
DOI: 10.82250/3003520
title: Budding yeasts in the subphylum Saccharomycotina Genome sequencing and assembly

description: Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial reads from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.