cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22280632.v1
title: Supplemental Materials for: A standardized quantitative analysis strategy for stable isotope probing metagenomics

description: <strong>Table S1. </strong><em>E. coli</em> AFE (%) in each treatment condition. <strong>Table S2. </strong>Characteristics of pre-centrifugation spike-ins. To produce distinct distribution patterns along the density gradient, some spike-ins were artificially enriched with 13C through PCR by adjusting the ratio of unlabeled dNTPs and uniformly-labeled 13C dNTPs. Theoretical AFE values are reported based on the ratio of labeled dNTPs, but actual AFE values were not experimentally confirmed. <strong>Table S3. </strong>Comparison of various abundance estimation strategies. All results were derived from the qSIP analysis method. Sensitivity and specificity were averaged across the seven treatment conditions. <strong>Table S4. </strong>Average total coverage across all fractions for <em>E. coli</em> in different treatment conditions after subsampling from 100% to 0.001% of the original <em>E. coli </em>sequence reads. <strong>Table S5.</strong> Comparison of MW-HR-SIP and qSIP methods for detecting isotopic labeling of <em>E. coli</em> at different levels of total genome coverage across the density gradient. ‘True’ indicates <em>E. coli</em> was correctly identified to be isotopically labeled (true positive), and ‘false’ indicates <em>E. coli</em> was incorrectly identified as unlabeled (false negative). NA corresponds to the failure of the MW-HR-SIP algorithm with that dataset. <strong>Table S6.</strong> The impact of genome coverage levels on detecting isotope incorporation using the qSIP model. <strong>Table S7.</strong> Comparison of MAGs retained and the number of false positives detected using the qSIP method after applying different minimum genome coverage thresholds. MAGs were retained if their average total coverage in the unlabeled controls exceeded the coverage threshold. <em>E. coli </em>was the only true positive and had a coverage of 1029X, thus no false negatives were detected using the coverage thresholds below. <strong>Table S8.</strong> Comparison of specificity, sensitivity, and balanced accuracy of the qSIP method after applying minimum AFE thresholds. To be identified as isotopically labeled, the lower 95% CI interval of a genome’s estimated AFE must be greater than the minimum AFE threshold. <strong>Table S9. </strong>Comparison of false positives MAGs identified by the MW-HR-SIP, qSIP, and ΔBD methods. Names of the false positive MAGs are listed in each column. <strong>Table S10. </strong>Comparison of <em>E. coli</em> AFE confidence intervals estimated using qSIP alone, qSIP after first applying MW-HR-SIP, and qSIP after first applying ΔBD method to identify a subset of putatively labeled MAGs. Condition B (“20pct_20ng”) was removed as it <em>E coli </em>was never identified as an isotope incorporator in this condition.
DOI: 10.5517/ccdc.csd.cc2bh59b
title: CCDC 2159531: Experimental Crystal Structure Determination

description: Related Article: Hui Shen, Xiongkai Tang, Qingyuan Wu, Yuhao Zhang, Chuxin Ma, Zhen Xu, Boon K. Teo, Nanfeng Zheng|2022|ACS Nanosci. Au|2|520|doi:10.1021/acsnanoscienceau.2c00026
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fb3fb
title: CCDC 2244041: Experimental Crystal Structure Determination

description: Related Article: Rabina Pradhan, Laxmi Tiwari, Vincent M. Groner, Caleb Leach, Kyle Lusk, Nathan S. Harrison, Kenneth A. Cornell, Kristopher V. Waynant|2023|J.Inorg.Biochem.|246|112294|doi:10.1016/j.jinorgbio.2023.112294
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fcz82
title: CCDC 2245834: Experimental Crystal Structure Determination

description: Related Article: Shivam Pandey, Rahul K. Shukla, Chandra M. R. Volla|2023|Org.Lett.|25|4694|doi:10.1021/acs.orglett.3c01571
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fftwl
title: CCDC 2247620: Experimental Crystal Structure Determination

description: Related Article: Jianyu Wei, Fahime Bigdeli, Ling-Xiao Wang, Lin-Lin Hou, Akram Panjehpour, Yue Ma, Kang-Zhou Wang, Ali Morsali, Kuan-Guan Liu|2023|Inorg.Chem.|62|10185|doi:10.1021/acs.inorgchem.3c00811
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fm5js
title: CCDC 2252755: Experimental Crystal Structure Determination

description: Related Article: Jia-yuan Li, Shi-fei Wu, Ya-ling An, Chang-liang Yao, Shuai Yao, Yong Huang, Wen-long Wei, Jian-qing Zhang, Qi-rui Bi, Hua Qu, De-an Guo|2023|Phytochemistry|213|113768|doi:10.1016/j.phytochem.2023.113768
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fnsvr
title: CCDC 2254315: Experimental Crystal Structure Determination

description: Related Article: Dmitri I. Fomenkov, Roman A. Budekhin, Vera A. Vil’, Alexander O. Terent’ev|2023|Org.Lett.|25|4672|doi:10.1021/acs.orglett.3c01477
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25345/c5n58cw87
title: MassIVE MSV000092374 - High-Field Asymmetric Waveform Ion Mobility Spectrometry Based Analysis of Cyclin-Dependent Kinase Substrate
title: Phosphoproteomics analysis of flavopiridol treatment using FAIMS, Eclipse, Exploris
DOI: 10.17043/zinke-2023-mesocosm-azores-1
title: Measurements of bioaerosols, bacteria and ionic composition in sea spray aerosols from mesocosm experiments in the Azores
DOI: 10.5281/zenodo.8125492
title: Studies of ALMA counterparts of SDSS quasars

description: <strong>Studies of ALMA counterparts of SDSS quasars</strong> Using a sample of 112 quasars from the 14th Data Release of the Sloan Digital Sky Survey (SDSS) within the Atacama Large Millimetre/submillimetre Array (ALMA) footprint, we explore the spectral properties of the high ionisation, broad emission \Civ. Specifically, we investigate the differences between the objects in the sample with submillimetre (submm) counterparts and those without them. We carried out a three-Gaussian fitting to model the C IV emission line in order to analyse relevant spectral properties of the total and individual components. We found a blueshift excess in the objects with submm counterparts with respect to those without submm counterparts, besides a stronger correlation between the blueshift and the line width in the former sample. Considering these findings within the context of an accretion disk wind model, these are indications of stronger outflows occurring in the quasars with submm counterparts. Furthermore, the objects in our sample had bolometric luminosity (Lbol &gt;10^45 erg/s), indicating the potential for outflow feedback. We observe large blueshifts in high accretion rates objects, suggesting the presence of strong disk winds requiring L/LEdd &gt; 0.1 and Mbh &gt; 10^8 Mo. The individual components analysis showed that, in our sample, the C IV emission line can be decomposed into a narrow core (NC) with no significant shift from the line centre, a low blueshift broad component (BC) consistent with disk wind models and a redshifted very broad component (VBC). The subsample with submm counterparts exhibited higher BC widths, further supporting the presence of stronger outflows.
DOI: 10.5281/zenodo.8125493
title: Studies of ALMA counterparts of SDSS quasars

description: Spectral properties of SDSS quasars with and without ALMA Submm counterparts
DOI: 10.5281/zenodo.8125527
title: Studies of ALMA counterparts of SDSS quasars

description: <strong>Studies of ALMA counterparts of SDSS quasars</strong> Using a sample of 112 quasars from the 14th Data Release of the Sloan Digital Sky Survey (SDSS) within the Atacama Large Millimetre/submillimetre Array (ALMA) footprint, we explore the spectral properties of the high ionisation, broad emission \Civ. Specifically, we investigate the differences between the objects in the sample with submillimetre (submm) counterparts and those without them. We carried out a three-Gaussian fitting to model the C IV emission line in order to analyse relevant spectral properties of the total and individual components. We found a blueshift excess in the objects with submm counterparts with respect to those without submm counterparts, besides a stronger correlation between the blueshift and the line width in the former sample. Considering these findings within the context of an accretion disk wind model, these are indications of stronger outflows occurring in the quasars with submm counterparts. Furthermore, the objects in our sample had bolometric luminosity (Lbol &gt;10^45 erg/s), indicating the potential for outflow feedback. We observe large blueshifts in high accretion rates objects, suggesting the presence of strong disk winds requiring L/LEdd &gt; 0.1 and Mbh &gt; 10^8 Mo. The individual components analysis showed that, in our sample, the C IV emission line can be decomposed into a narrow core (NC) with no significant shift from the line centre, a low blueshift broad component (BC) consistent with disk wind models and a redshifted very broad component (VBC). The subsample with submm counterparts exhibited higher BC widths, further supporting the presence of stronger outflows.
DOI: 10.3886/e112969v1-140002
title: Replication data for: The Determinants and Welfare Implications of US Workers' Diverging Location Choices by Skill: 1980-2000

description: From 1980 to 2000, the rise in the US college/high school graduate wage gap coincided with increased geographic sorting as college graduates concentrated in high wage, high rent cities. This paper estimates a structural spatial equilibrium model to determine causes and welfare consequences of this increased skill sorting. While local labor demand changes fundamentally caused the increased skill sorting, it was further fueled by endogenous increases in amenities within higher skill cities. Changes in cities' wages, rents, and endogenous amenities increased inequality between high school and college graduates by more than suggested by the increase in the college wage gap alone. (JEL D31, I26, J24, J31, J61, R23)
DOI: 10.6073/pasta/17eb4c7ab390c366782131d68022fabe
title: Sacramento-San Joaquin Bay-Delta Continuous (15 Minute) water quality monitoring data collected by the Continuous Environmental Monitoring Program, DWR, 2005- ongoing.

description: The Continuous Environmental Monitoring Program (CEMP) plays an instrumental role in overseeing real-time water quality in the Sacramento-San Joaquin Delta (the Delta) and Suisun Bay. The program harnesses wireless telemetry to transmit crucial data to the California Data Exchange Center (CDEC), making high-resolution environmental data pertaining to the Delta and Suisun Bay publicly accessible. The extensive dataset captures information at 15-minute intervals from 15 monitoring stations, utilizing YSI 6600 and YSI EXO sondes to obtain standalone water quality measurements. This extensive dataset informs the operations of the California State Water Project, ensuring it adheres to mandated water quality standards set by Water Right Decision 1641. This data compilation incorporates all information since the transition to YSI multiparameter sondes in 2005. It is important to note that the commencement dates and subsequent upgrades vary between stations, leading to slight discrepancies in the dataset's date ranges. Since its inception in the mid-1980s, CEMP has progressively expanded its monitoring capabilities, consistently augmenting the number of monitoring locations and the array of water quality parameters assessed. Its commitment to utilizing the most advanced water quality monitoring technology reaffirms its position as an environmental monitoring leader in the Delta and Suisun Bay. Today, the program oversees 15 water quality stations that reliably capture data every 15 minutes, each day of the year, transmitting this data in real-time. The core tenents of CEMP: • to obtain consistent and accurate data in real-time at established monitoring stations • to provide data necessary to achieve compliance with salinity, flow, and dissolved oxygen standards • to perform data analyses for further understanding of estuarine ecology • to report information to other government agencies, as well as the public, for the purpose of management and conservation of the upper San Francisco Estuary (SFE). • to provide continuous water quality monitoring expertise for other groups within DWR and sister agencies for the benefit of ecological studies throughout the San Francisco- Sacramento Estuary
DOI: 10.57833/cidacs/a5jahb
title: Índice Brasileiro de Privação (IBP) Municipal

description: Dados do Índice Brasileiro de Privação (IBP) calculado para os municípios brasileiros. Representa uma medida de privação material ou, de um modo mais geral, níveis de posição socioeconômica. Este índice foi calculado utilizando informações de renda, educação e condições de moradia a partir dos dados do Censo Demográfico 2010. Desenvolvido por pesquisadores do Centro de Integração de Dados e Conhecimentos para Saúde (Cidacs/Fiocruz Bahia) e da Universidade de Glasgow-Escócia, dentro do projeto Social Policy & Health Inequalities (SPHI), financiado pela agência de fomento do Reino Unido National Institute for the Health Research (NIHR).
DOI: 10.5281/zenodo.8125599
title: Dataset: Recruitment responses of shade-tolerant and heliophilous trees in human-degraded areas: the necessity of knowing the recruitment autecology of species for making reforestation decisions

description: This repository contains the files associated with the following article: Johanna Croce, Ernesto I. Badano, Andrés Tálamo. Recruitment responses of shade-tolerant and heliophilous trees in human-degraded areas: the necessity of knowing the recruitment autecology of species for making reforestation decisions Submitted to <em>Land Degradation & Development</em>. The first Microsoft Excel file (Dataset 01 - Microclimate.xlsx) contains two sheets with the microclimatic data (average, maximum and minimum soil temperatures, and volumetric soil water content) measured in Cerro Chachapoyas and Cerro Fachacano. These measurements were performed on three plots of each trearment, including shrub-protected treatment with high shade, shrub-protected treatment with medium shade, sunny treatment with high herbaceous cover, sunny treatment with medium herbaceous cover and controls. The second Microsoft Excel file (Dataset 02 -Plant responses.xlsx Dataset 02 - Plant responses.xlsx) contains three sheets with the data used to estimate the seedling emergence rates, plant survival rates and net aboveground growth rates of the tree species, including <em>Anadenanthera colubrina</em> and <em>Ceiba chodatii</em> in Cerro Chachapoyas, and <em>Jacaranda mimosifolia</em> in Cerro Fachacano.
description: This study was supported The Rufford Foundation, project "Fires in mountain dry forests: importance of plant-plant interaction in the post-fire regeneration"
DOI: 10.5281/zenodo.8125598
title: Dataset: Recruitment responses of shade-tolerant and heliophilous trees in human-degraded areas: the necessity of knowing the recruitment autecology of species for making reforestation decisions

description: This repository contains the files associated with the following article: Johanna Croce, Ernesto I. Badano, Andrés Tálamo. Recruitment responses of shade-tolerant and heliophilous trees in human-degraded areas: the necessity of knowing the recruitment autecology of species for making reforestation decisions Submitted to <em>Land Degradation & Development</em>. The first Microsoft Excel file (Dataset 01 - Microclimate.xlsx) contains two sheets with the microclimatic data (average, maximum and minimum soil temperatures, and volumetric soil water content) measured in Cerro Chachapoyas and Cerro Fachacano. These measurements were performed on three plots of each trearment, including shrub-protected treatment with high shade, shrub-protected treatment with medium shade, sunny treatment with high herbaceous cover, sunny treatment with medium herbaceous cover and controls. The second Microsoft Excel file (Dataset 02 -Plant responses.xlsx Dataset 02 - Plant responses.xlsx) contains three sheets with the data used to estimate the seedling emergence rates, plant survival rates and net aboveground growth rates of the tree species, including <em>Anadenanthera colubrina</em> and <em>Ceiba chodatii</em> in Cerro Chachapoyas, and <em>Jacaranda mimosifolia</em> in Cerro Fachacano.
description: This study was supported The Rufford Foundation, project "Fires in mountain dry forests: importance of plant-plant interaction in the post-fire regeneration"
DOI: 10.5281/zenodo.7837922
title: Magellan/M2FS and MMT/Hectochelle Spectroscopy of Dwarf Galaxies and Faint Star Clusters within the Galactic Halo

description: m2fs_HiRes_catalog_public.fits: public catalog of measurements derived from spectroscopic observations of individual targets with the Magellan/M2FS spectrograph in HiRes configuration m2fs_MedRes_catalog_public.fits: public catalog of measurements derived from spectroscopic observations of individual targets with the Magellen/M2FS spectrograph in MedRes configuration hecto_catalog_public.fits: public catalog of measurements derived from spectroscopic observations of individual targets with the MMT/Hectochelle spectrograph fits_files.tar.gz: Supplementary data products, including all sky-subtracted spectra from individual targets and best-fitting model spectra. template_spectra.tar.gz: synthetic template spectra (columns are wavelength in air (Angstroms), normalized flux)
DOI: 10.5281/zenodo.7837921
title: Magellan/M2FS and MMT/Hectochelle Spectroscopy of Dwarf Galaxies and Faint Star Clusters within the Galactic Halo

description: m2fs_HiRes_catalog_public.fits: public catalog of measurements derived from spectroscopic observations of individual targets with the Magellan/M2FS spectrograph in HiRes configuration m2fs_MedRes_catalog_public.fits: public catalog of measurements derived from spectroscopic observations of individual targets with the Magellen/M2FS spectrograph in MedRes configuration hecto_catalog_public.fits: public catalog of measurements derived from spectroscopic observations of individual targets with the MMT/Hectochelle spectrograph fits_files.tar.gz: Supplementary data products, including all sky-subtracted spectra from individual targets and best-fitting model spectra. template_spectra.tar.gz: synthetic template spectra (columns are wavelength in air (Angstroms), normalized flux)
DOI: 10.5281/zenodo.8123244
title: Leukemia data by T.R. Golub et al.

description: This is the processed data, the original data is from exprSets for golub leukemia data. Used in the paper "Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring" by T.R. Golub et al.; this is the version after data preprocessing (code from a reproduction of the original paper), with 3051 predictors.
description: {"references": ["Golub, Todd R., et al. \"Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.\" science 286.5439 (1999): 531-537.", "Golub T (2023). golubEsets: exprSets for golub leukemia data. R package version 1.42.0."]}
DOI: 10.5281/zenodo.8123245
title: Leukemia data by T.R. Golub et al.

description: This is the processed data, the original data is from exprSets for golub leukemia data. Used in the paper "Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring" by T.R. Golub et al.; this is the version after data preprocessing (code from a reproduction of the original paper), with 3051 predictors.
description: {"references": ["Golub, Todd R., et al. \"Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.\" science 286.5439 (1999): 531-537.", "Golub T (2023). golubEsets: exprSets for golub leukemia data. R package version 1.42.0."]}
DOI: 10.22003/xfel.eu-data-900319-00
title: LPD commissioning and calibration
DOI: 10.22003/xfel.eu-data-900320-00
title: FXE commissioning
DOI: 10.22003/xfel.eu-data-900321-00
title: FXE HELIOS
DOI: 10.22003/xfel.eu-data-900326-00
title: Small area detector test
DOI: 10.22003/xfel.eu-data-900331-00
title: SASE3 Photon Beam Measurements
DOI: 10.22003/xfel.eu-data-900348-00
title: SASE1 Photon Beam Measurements
DOI: 10.22003/xfel.eu-data-900350-00
title: SASE2 Photon Beam Measurements
DOI: 10.22003/xfel.eu-data-900354-00
title: SXP Commissioning
DOI: 10.6084/m9.figshare.23646456
title: Missouri Raster Data

description: Rasters assocaited with elevation (from the National elevation dataset), slope (created from the elevation dataset using ArcGIS), a Shannon diversity index as a metric of landscape fragmentation (created from the forest/shrub layer using Fragstats), distance to all roads (created in ArcGIS using a road TIGER shapefile), distance to forest/shrubs (created using NLCD 2016 data), human population density (created using data from the US Census Bureau). All rasters are at a 90m resolution.
DOI: 10.6084/m9.figshare.20485716
title: Pymatgen PatchedPhaseDiagrams

description: Patched phase diagram covering a large number of chemical systems (all the ones in Materials Project and WBM dataset put together) as well as the ComputedStructureEntry queried from MPRester to generate it. <br> PPDs were generated in this file: https://github.com/janosh/dielectric-frontier/blob/314fb478/diel_frontier/patched_phase_diagram/combine_mp_wbm_ppd.py <br> Load e.g. the Jan 2022 MP+WBM PPD using <br> ```py import gzip<br> import io<br> import pickle<br> from urllib.request import urlopen<br> <br> # 2022-01-25-ppd-mp+wbm.pkl.gz (235 MB)<br> ppd_pickle_url = "https://figshare.com/ndownloader/files/36669624"<br> zipped_file = urlopen(ppd_pickle_url)<br> ppd_mp_wbm = pickle.load(io.BytesIO(gzip.decompress(zipped_file.read()))) ```
DOI: 10.6084/m9.figshare.20485716.v1
title: Pymatgen PatchedPhaseDiagrams

description: Patched phase diagram covering a large number of chemical systems (all the ones in Materials Project and WBM dataset put together) as well as the ComputedStructureEntry queried from MPRester to generate it. <br> PPDs were generated in this file: https://github.com/janosh/dielectric-frontier/blob/314fb478/diel_frontier/patched_phase_diagram/combine_mp_wbm_ppd.py