cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14608002.v4
title: Homozygous MTAP deletion in primary human glioblastoma is not associated with elevation of methylthioadenosine

description: Dataset supporting Barekatain et al. Nature Communications. Article titled: Homozygous <i>MTAP</i> deletion in primary human glioblastoma is not associated with elevation of methylthioadenosine.
DOI: 10.6084/m9.figshare.14459535.v2
title: Data and scripts in Huang et al, "Comparative genomic analysis reveals metabolic flexibility of Woesearchaeota and a tendency toward an independent lifestyle"

description: This compressed file includes six folders: 1_single_protein_trees_of_orthologs: Alignments and treefiles used in the "Selection of orthologs for phylogenetic analysis of Woesearchaeota". 2_phylogenetic_trees_Woese&Pace: Alignments and treefiles of 152 MAGs for phylogenetic analysis based on 15 ribosomal proteins and the top-50% ranked orthologs 3_16S_rRNA_gene: Alignments and treefiles used in the 16S rRNA gene phylogenetic analysis 4_individual_protein_trees: Alignment and treefiles used in the phylogenetic analysis in fig.4, suppl. fig7-8, suppl. fig10-23 and suppl. fig25-42 5_protein_families_52_MAGs: The file includes alignment and treefile of phylogenetic analysis of 52 MAGs, ALE reconciliation results and protein families files 6_scripts Python scripts used in phylogenetic analysis and R scripts used in ecological analysis
DOI: 10.5281/zenodo.4897994
title: Example kidney segmentation data acquired on a Philips scanner

description: Example kidney segmentation data acquired on a Philips scanner
DOI: 10.5281/zenodo.4897993
title: Example kidney segmentation data acquired on a Philips scanner

description: Example kidney segmentation data acquired on a Philips scanner
DOI: 10.5517/ccdc.csd.cc20sjx8
title: CCDC 1870630: Experimental Crystal Structure Determination

description: Related Article: Irina A. Lutsenko, Mikhail A. Kiskin, Yulia V. Nelyubina, Nikolay N. Efimov, Yurii V. Maksimov, Vladimir K. Imshennik, Ekaterina M. Zueva, Alexander S. Goloveshkin, Andrey V. Khoroshilov, Eva Rentschler, Aleksey A. Sidorov, Igor L. Eremenko|2019|Polyhedron|159|426|doi:10.1016/j.poly.2018.12.018
DOI: 10.5517/ccdc.csd.cc24jfhm
title: CCDC 1982000: Experimental Crystal Structure Determination

description: Related Article: Ming Bai, Jing-Jie Chen, Wei Xu, Shu-Hui Dong, Qing-Bo Liu, Bin Lin, Xiao-Xiao Huang, Guo-Dong Yao, Shao-Jiang Song|2020|Eur.J.Med.Chem.|198|112362|doi:10.1016/j.ejmech.2020.112362
DOI: 10.5517/ccdc.csd.cc24jfjn
title: CCDC 1982001: Experimental Crystal Structure Determination

description: Related Article: Ming Bai, Jing-Jie Chen, Wei Xu, Shu-Hui Dong, Qing-Bo Liu, Bin Lin, Xiao-Xiao Huang, Guo-Dong Yao, Shao-Jiang Song|2020|Eur.J.Med.Chem.|198|112362|doi:10.1016/j.ejmech.2020.112362
DOI: 10.5517/ccdc.csd.cc24jfkp
title: CCDC 1982002: Experimental Crystal Structure Determination

description: Related Article: Ming Bai, Jing-Jie Chen, Wei Xu, Shu-Hui Dong, Qing-Bo Liu, Bin Lin, Xiao-Xiao Huang, Guo-Dong Yao, Shao-Jiang Song|2020|Eur.J.Med.Chem.|198|112362|doi:10.1016/j.ejmech.2020.112362
DOI: 10.6084/m9.figshare.13633943.v4
title: Copy number variants in Nubian ibex

description: Copy number variants detected in Nubian genome using read depth and split read method.
DOI: 10.6084/m9.figshare.13633943
title: Copy number variants in Nubian ibex

description: Copy number variants detected in Nubian genome using read depth and split read method.
DOI: 10.6084/m9.figshare.13633943.v6
title: Copy number variants in Nubian ibex

description: Copy number variants detected in Nubian genome using read depth and split read method.
DOI: 10.6084/m9.figshare.13633943.v5
title: Copy number variants in Nubian ibex

description: Copy number variants detected in Nubian genome using read depth and split read method.
DOI: 10.5519/qd.7frhjite
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (25 records)
DOI: 10.21227/402w-8s89
title: Files to build autosampler

description: Automation of fluid manipulation is needed to increase throughput and reproducibility of experiments while reducing the time spent by researchers on performing repetitive tasks. Current solutions are however bulky and expensive, and hence not suited to enable automation in academic laboratories. This work therefore reports a low cost, modular and programmable analytical platform comprising of 3D printed autosampler and peristaltic pump with footprints of 248 mm by 243 mm and 104 mm by 112 mm, respectively. The autosampler consisted of four samples probes/needles that can be driven independently to any of the available solution vials placed along the circumference of a circle. The 3D printed autosampler developed in this work can access higher number of solution vials independently and is lower cost, but accommodates fewer number of total solution vials, than commercial devices. The autosampler and peristaltic pump were applied to determine (1) refractive index sensitivity, (2) porosity, and (3) sensing capability of leaky waveguides (LWs) where the read-out instrument was also 3D printed. We demonstrated that the automation of fluids enabled by the analytical platform improved the accuracy of results by separating the effect of temperature drifts from analyte solutions from the output of LWs. This work shows that 3D printed instrumentation can provide results comparable with standard laboratory versions at much lower cost, making it ideal for use in resource-limited settings, and with the possibility of customization as experimental needs change.
DOI: 10.6073/pasta/1aea37d5e5a449c7523684587f758b6c
title: Chemical characteristics of snow in the ablation zone of Canada Glacier in the McMurdo Dry Valleys, Antarctica during the 2016-2017 austral summer

description: This data package contains chemical characteristics of snow in the ablation zone of Canada Glacier, located in Taylor Valley, McMurdo Dry Valleys, Antarctica during the 2016-17 austral summer. Specifically, snow samples were collected from the ablation zones of Canada and Commonwealth Glaciers to characterize the chemistry of recent snowfall in the ablation zones of these glaciers. Samples were collected in triplicate near mass balance stakes on the same date ice cores were collected as part of a larger study characterizing the spatial and temporal geochemical evolution of glacial meltwater. A subset of snow samples collected from Canada Glacier have been analyzed and are included here. This package may be amended in the future if analysis of the remaining samples from both Canada and Commonwealth Glaciers occurs.
DOI: 10.6073/pasta/ea75e039fb7b6314e1c555c9ff8a5009
title: Chemical characteristics of supraglacial stream water on Canada Glacier, McMurdo Dry Valleys, Antarctica during the 2015-2016 austral summer

description: This data package contains chemical characteristics of water samples collected along four supraglacial streams on Canada Glacier, located in Taylor Valley, McMurdo Dry Valleys, Antarctica. Samples were collected during the 2015-16 and 2016-17 austral summers in order to characterize the spatial and temporal evolution of glacial meltwater as it travels over and off Canada Glacier. Samples from the 2015-16 austral summer have been fully analyzed and those data are included here. Samples from the 2016-17 austral summer have been stored frozen since collection and have not been analyzed. This package may be amended in the future if analysis of the 2016-17 samples occurs.
DOI: 10.6073/pasta/5e285dcbc8dfdf6816805c620510de05
title: Chemical characteristics of terminal waterfalls along the Canada and Suess Glaciers in the McMurdo Dry Valleys, Antarctica in January of 2018 and 2019

description: This data package contains chemical and other relevant characteristics for several waterfalls situated along the terminus of two glaciers in Taylor Valley, located in the McMurdo Dry Valleys region of Antarctica, during the 2017-18 and 2018-19 austral summers. Specifically, water samples were collected from terminal waterfalls along Canada and Seuss Glaciers as part of a larger study characterizing the geochemical evolution of glacier ice to meltwater. Samples were collected from just above the base of each waterfall and processed using similar protocols developed and used by the McMurdo Dry Valleys Long Term Ecological Research program.
DOI: 10.6084/m9.figshare.14143757.v1
title: Pan-transcriptomic profiling reveals novel transcripts, isomorphs and non-coding RNAs in endemic pathogenic fungus Talaromyces marneffei

description: This manuscript describes a pan-transcriptomic profile of <i>Talaromyces marneffei</i> performed with the aid of an RNA-seq-based approach, aimed at characterizing the general transcriptome in this human pathogenic fungus, responsible for talaromycosis. Results confirm that ~58.28% of the genes currently annotated in the T. marneffei genome are, in fact, transcribed in vivo and that ~23.6% of them may display alternative isomorphs. Moreover, we identified 585 transcripts that do not match any gene currently mapped in the genome, represented by 7,358 coding transcripts and 211 non-coding RNAs (ncRNAs), including 102 long-non-coding RNAs (lncRNAs).
DOI: 10.34863/g4wa-0j57
title: Dataset: Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose

description: Dataset includes raw data (matlab mat format, filename: rawdata_1x_crop.mat), expected reconstruction of raw data (png format, filename: pty_crop_phase.png), and analysis codes used.  Utilizes the ptychography reconstruction toolkit, PtychoShelves developed at Paul Scherrer Institut, Switzerland [https://www.psi.ch/en/sls/csaxs].
DOI: 10.5281/zenodo.4898071
title: Paper supplements demo csv

description: A small demo csv file
DOI: 10.5281/zenodo.4898070
title: Paper supplements demo csv

description: A small demo csv file
DOI: 10.34863/083j-x818
title: Dataset: Utilizing complex oxide substrates to control 2 carrier concentration in large-area monolayer 3 MoS2 films
DOI: 10.34863/a2jw-kh18
title: Dataset: Adsorption-controlled growth of Ga2O3 by suboxide molecular-beam epitaxy
DOI: 10.6084/m9.figshare.13651454
title: Bermuda aerosol, gas, and wet deposition composition dataset

description: Monthly mean concentrations of sulfate, chloride, and sodium in aerosol and wet deposition samples collected at Fort Prospect in Bermuda (32.30N, 64.77W). <br><br>Added data on 3 June 2021 include hourly data for NO, NO2, NOx, and PM2.5, in addition to daily data for PM10. <br>
DOI: 10.6084/m9.figshare.13651454.v1
title: Bermuda aerosol and wet deposition composition dataset

description: Monthly mean concentrations of sulfate, chloride, and sodium in aerosol and wet deposition samples collected at Fort Prospect in Bermuda (32.30N, 64.77W)<br>
DOI: 10.34863/pvfm-0y37
title: Dataset: Epitaxial stannate pyrochlore thin films: Limitations of cation stoichiometry and electron doping
DOI: 10.6084/m9.figshare.12198471
title: Meta-Analysis Results for Any MSDP

description: Results from our meta-analysis of maternal smoking during pregnancy and placental DNA methylation; models were adjusted for maternal age, parity, education, putative cellular heterogeneity, and residual bias. This file includes the following:CPG_ID = Name of the CpG site,Meta_BETA = Difference in DNA methylation (proportion between 0.0 and 1.0) between placental tissue exposed to any smoking during pregnancy versus no smoking during pregnancy,Meta_ZVAL = Test-statistics for regression coefficients,Meta_PVAL = Raw p-values,Meta_CI_lb = Lower bound of 95% confidence intervals,Meta_CI_ub = Upper bound of 95% confidence intervals,Meta_I2 = I-squared for the meta-analysis test of heterogeneity,Meta_Het_PVAL = p-values for the meta-analysis test of heterogeneity.<br>
DOI: 10.6084/m9.figshare.12198504
title: Meta-Analysis Results for Sustained MSDP

description: Results from our meta-analysis of maternal smoking during pregnancy and placental DNA methylation; models were adjusted for maternal age, parity, education, putative cellular heterogeneity, and residual bias. This file includes the following:CPG_ID = Name of the CpG site,Meta_BETA = Difference in DNA methylation (proportion between 0.0 and 1.0) between placental tissue exposed to sustained smoking throughout pregnancy versus no smoking during pregnancy,Meta_ZVAL = Test-statistics for regression coefficients,Meta_PVAL = Raw p-values,Meta_CI_lb = Lower bound of 95% confidence intervals,Meta_CI_ub = Upper bound of 95% confidence intervals,Meta_I2 = I-squared for the meta-analysis test of heterogeneity,Meta_Het_PVAL = p-values for the meta-analysis test of heterogeneity.
DOI: 10.34863/gbra-0060
title: Dataset: Electron Ptychography of 2D Materials to Deep Sub-Ångström Resolution

description: Raw input data (Matlab mat format, sample_data_mos2.dat)
DOI: 10.5519/qd.3ihzudbr
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (37 records)
DOI: 10.5281/zenodo.4898011
title: Human aortic endothelial cell ground truth dataset

description: Ground truth dataset of human aortic endothelial cells expressing Laconic (GFP channel) and stained with Hoechst (nuclei).
DOI: 10.5519/qd.5ictd3nq
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (133 records)
DOI: 10.5281/zenodo.4628273
title: Characterizing the X-ray Emission of Intermediate-Mass Pre-Main-Sequence Stars

description: Probabilistic H-R Diagrams (pHRD) and X-ray spectral results for sources in the IMPS Paper (abstract below). phrds.zip (uncompressed size ~ 30 MB): Contains flip through PS (postscript) of the pHRDs for each source. The PS are separated by disk status (disky/diskless) and IR classification (AB, IMPS, TTS, and Unc). MIR names are used. XRay_spectra_and_lightcurves.zip (uncompressed size ~50 MB): Contains PS of binned best X-ray spectral fit (binned for display purposes), sequenced light curve, and stacked light curve for each source. X-ray names are used. spectra.ps: A compilation of the binned X-ray spectral fits for our entire sample as a flip through PS Paper Abstract: We use X-ray and infrared observations to study the properties of three classes of young stars in the Carina Nebula: intermediate-mass \edit1{(2--5~M$_\odot$)} pre-main sequence stars (IMPS\edit1{; i.e. intermediate-mass T Tauri stars}), late-B and A stars on the zero-age main sequence (AB), and lower-mass T Tauri stars (TTS). We divide our sources among these three sub-classifications and further identify disk-bearing young stellar objects versus diskless sources with no detectable infrared (IR) excess emission using IR (1--8 $\mu$m) spectral energy distribution modeling. We then perform X-ray spectral fitting to determine the hydrogen absorbing column density ($N_{\rm H}$), absorption-corrected X-ray luminosity ($L_{\rm X}$), and coronal plasma temperature ($kT$) for each source. We find that the X-ray spectra of both IMPS and TTS are characterized by similar $kT$ and $N_{\rm H}$, and on average $L_{\rm X}$/$L_{\rm bol} \sim4\times10^{-4}$. IMPS are systematically more luminous in X-rays (by $\sim$0.3 dex) than all other sub-classifications, with median $L_{\rm X} = 2.5\times10^{31}$ erg s$^{-1}$, while AB stars of similar masses have X-ray emission consistent with TTS companions. These lines of evidence converge on a magneto-coronal flaring source for IMPS X-ray emission, a scaled-up version of the TTS emission mechanism. IMPS therefore provide powerful probes of isochronal ages for the first $\sim$10 Myr in the evolution of a massive stellar population, because their intrinsic, coronal X-ray emission decays rapidly after they commence evolving along radiative tracks. We suggest that the most luminous (in both X-rays and IR) IMPS could be used to place empirical constraints on the location of the intermediate-mass stellar birth line.
DOI: 10.5281/zenodo.4628272
title: Characterizing the X-ray Emission of Intermediate-Mass Pre-Main-Sequence Stars

description: Probabilistic H-R Diagrams (pHRD) and X-ray spectral results for sources in the IMPS Paper (abstract below). phrds.zip (uncompressed size ~ 30 MB): Contains flip through PS (postscript) of the pHRDs for each source. The PS are separated by disk status (disky/diskless) and IR classification (AB, IMPS, TTS, and Unc). MIR names are used. XRay_spectra_and_lightcurves.zip (uncompressed size ~50 MB): Contains PS of binned best X-ray spectral fit (binned for display purposes), sequenced light curve, and stacked light curve for each source. X-ray names are used. spectra.ps: A compilation of the binned X-ray spectral fits for our entire sample as a flip through PS Paper Abstract: We use X-ray and infrared observations to study the properties of three classes of young stars in the Carina Nebula: intermediate-mass \edit1{(2--5~M$_\odot$)} pre-main sequence stars (IMPS\edit1{; i.e. intermediate-mass T Tauri stars}), late-B and A stars on the zero-age main sequence (AB), and lower-mass T Tauri stars (TTS). We divide our sources among these three sub-classifications and further identify disk-bearing young stellar objects versus diskless sources with no detectable infrared (IR) excess emission using IR (1--8 $\mu$m) spectral energy distribution modeling. We then perform X-ray spectral fitting to determine the hydrogen absorbing column density ($N_{\rm H}$), absorption-corrected X-ray luminosity ($L_{\rm X}$), and coronal plasma temperature ($kT$) for each source. We find that the X-ray spectra of both IMPS and TTS are characterized by similar $kT$ and $N_{\rm H}$, and on average $L_{\rm X}$/$L_{\rm bol} \sim4\times10^{-4}$. IMPS are systematically more luminous in X-rays (by $\sim$0.3 dex) than all other sub-classifications, with median $L_{\rm X} = 2.5\times10^{31}$ erg s$^{-1}$, while AB stars of similar masses have X-ray emission consistent with TTS companions. These lines of evidence converge on a magneto-coronal flaring source for IMPS X-ray emission, a scaled-up version of the TTS emission mechanism. IMPS therefore provide powerful probes of isochronal ages for the first $\sim$10 Myr in the evolution of a massive stellar population, because their intrinsic, coronal X-ray emission decays rapidly after they commence evolving along radiative tracks. We suggest that the most luminous (in both X-rays and IR) IMPS could be used to place empirical constraints on the location of the intermediate-mass stellar birth line.
DOI: 10.5066/p9giq9zn
title: Surveyed peak-stage elevations, coordinates, and indicator data of strandlines from large floods on the Colorado River in Grand Canyon National Park, Arizona

description: These data provide a comprehensive survey of peak-stage indicators along the Colorado River corridor between river mile (RM) 0 and RM 87 (see Figure 1 in the associated USGS-SIR). In 2008, the locations of peak-stage indicators in three short reaches downstream from RM 87 were measured using a handheld GPS unit (see Appendix 1 in the associated USGS-SIR). Total-station measurements were made using an established network of survey control that references the 2011 realization of NAD83 (NAD83 (2011)) (Kaplinski and others, 2017). The measurements were projected into the State Plane Coordinate System of 1983, Arizona central zone (FIPS zone 0202). Vertical positions are provided in both NAD83 ellipsoid heights and in NAVD88 orthometric elevations modeled from GEOID12b.
DOI: 10.5281/zenodo.4898134
title: Human aortic endothelial cell ground truth dataset

description: Ground truth dataset of human aortic endothelial cells expressing Laconic (GFP channel) and stained with Hoechst (nuclei).
DOI: 10.5281/zenodo.4897882
title: Human aortic endothelial cell ground truth dataset

description: Ground truth dataset of human aortic endothelial cells expressing Laconic (GFP channel) and stained with Hoechst (nuclei).
DOI: 10.25386/genetics.14721033
title: Supplementary Material for Mural et al., 2021

description: Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate pleiotropy. Here we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome wide association studies conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35-43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations.
DOI: 10.25386/genetics.14721033.v1
title: Supplementary Material for Mural et al., 2021

description: Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate pleiotropy. Here we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome wide association studies conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35-43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations.
DOI: 10.5281/zenodo.4898181
title: 1D (time) and 2D (time and vertical coordinate) data for the cases DIU-500m, RCE-500m and DIU2RCE-500m.

description: Timeseries for the case of 500m horizontal resolution.
DOI: 10.5281/zenodo.4897939
title: Data and code for "Birds breathe at an aerodynamic resonance"

description: The repository contains data and scripts that support the analysis in a paper under consideration for publication.
DOI: 10.5281/zenodo.4897938
title: Data and code for "Birds breathe at an aerodynamic resonance"

description: The repository contains data and scripts that support the analysis in a paper under consideration for publication.