cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5682711
title: SMDemoBioref: Data from the University of Florida Stan Mayfield Demonstration Biorefinery

description: This dataset includes previously unpublished information collected during the operation of the University of Florida Stan Mayfield Demonstration Biorefinery. <strong>Terms of Use:</strong> These data are provided as is, without any warranties of any kind. A bibliographic citation should be included in the References section of publications and other media to acknowledge the authors of this dataset. Proper citations include the authors, title, publisher, and Digital Object Identifier (DOI) and will allow the products to be discovered and re-used by others.
DOI: 10.6084/m9.figshare.21790031.v2
title: All_29b_DEG.xls

description: Differentially expressed genes (DEG), raw sequence, fpkm, and read count data determined from global RNA-seq data between porcine granulosa cells treated with a miR-29b knockdown (siRNA), miR-29b mimic, or scrambled sequence negative control.
DOI: 10.6084/m9.figshare.21790043.v2
title: fpkm_genename.xls

description: Raw fpkm data for genes detected via global RNA-seq in porcine granulosa cells treated with miR-29b mimic, miR-29b knockdown (siRNA), or a scrambled sequence negative control.
DOI: 10.6084/m9.figshare.21790052.v2
title: miR-29b_RNA-seq_all.fa

description: Sequences for all genes detected via global RNA-seq in porcine granulosa cells treated with miR-29b mimic, miR-29b knockdown (siRNA), or a scrambled sequence negative control.
DOI: 10.6084/m9.figshare.21790031.v1
title: All_29b_DEG.xls

description: Differentially expressed genes (DEG) determined from global RNA-seq data between porcine granulosa cells treated with a miR-29b knockdown (siRNA), miR-29b mimic, or scrambled sequence negative control.
DOI: 10.6084/m9.figshare.21790043.v1
title: fpkm_genename.xls

description: Raw fpkm data for genes detected via global RNA-seq in porcine granulosa cells treated with miR-29b mimic, miR-29b knockdown (siRNA), or a scrambled sequence negative control.
DOI: 10.6084/m9.figshare.21790052.v1
title: miR-29b_RNA-seq_all.fa

description: Sequences for all genes detected via global RNA-seq in porcine granulosa cells treated with miR-29b mimic, miR-29b knockdown (siRNA), or a scrambled sequence negative control.
DOI: 10.6084/m9.figshare.21790040.v2
title: readcount_genename.xls

description: Raw read counts for all genes detected via global RNA-seq in porcine granulosa cells treated with a miR-29b mimic, miR-29b knockdown (siRNA), or scrambled sequence negative control.
DOI: 10.6084/m9.figshare.21790040.v1
title: readcount_genename.xls

description: Raw read counts for all genes detected via global RNA-seq in porcine granulosa cells treated with a miR-29b mimic, miR-29b knockdown (siRNA), or scrambled sequence negative control.
DOI: 10.5281/zenodo.7495407
title: MIREN survey of plant species in mountains

description: These data consist of plant species records observed between 2007 and 2019 and used in publications listed on the MIREN website. These are records of vascular plant species along mountain roads, the sampling strategy is explained in the accompanying protocol. The data include plant species records and their locations, and the native/non-native status of the species within the region. The names have been verified through a series of checks in available databases. The cover and abundance metrics are described in the protocol, but note cover was not estimated in the surveys in 2007. Note: this second version (v2) of the data set published Dec 31st 2022, it includes more regions and repeated measure of the same plots. Please contact miren.data@gmail.com with questions.
description: These data are of records of plant species recorded during the MIREN survey. This is the second version of the data and includes all records from the first version and new and repeated observations. These data was used in the papers linked below.
DOI: 10.26207/cxkz-fh78
title: Investigating the role of coral calcification as a source or sink of carbon
DOI: 10.18434/mds2-2515
title: SDNist v1.3: Temporal Map Challenge Environment
DOI: 10.5281/zenodo.7495177
title: Test

description: Add here
DOI: 10.5281/zenodo.7495176
title: Test

description: Add here
DOI: 10.5281/zenodo.7457333
title: Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death

description: This dataset accompanies the article entitled <em>Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death</em>, published in ACS Cent. Sci. (https://doi.org/10.1021/acscentsci.2c01078). <strong>subboxes_overview.xlsx: </strong>This spreadsheet contains information about the protein composition of each sub-box. <strong>BOX_GEOMETRIES.zip: </strong>Starting structures (saved in Gromos87 .gro format) used for the production runs of the all-atom sub-boxes. <strong>PROTEIN_COM_MSD.zip: </strong>Text files containing the mean square displacements (MSDs) of the centers of mass (COMs) of individual proteins, as obtained from the production runs of the all-atom sub-boxes. The time is shown in picoseconds while the MSD values are given in nm<sup>2</sup>. For each sub-box, the protein numbering corresponds to the subboxes_overview.xlsx spreadsheet. <strong>CHAIN_COM_MSD.zip: </strong>Text files containing the mean square displacements (MSDs) of the centers of mass (COMs) of individual polypeptide chains, as obtained from the production runs of the all-atom sub-boxes. The time is shown in picoseconds while the MSD values are given in nm<sup>2</sup>. For each sub-box, the chain numbering corresponds to the subboxes_overview.xlsx spreadsheet. <strong>CHAIN_ROTACF.zip: </strong>Text files containing the rotational autocorrelation functions for individual polypeptide chains, as obtained from the production runs of the all-atom sub-boxes. The time is shown in picoseconds; the autocorrelation functions were calculated using a second-order Legendre polynomial. For each sub-box, the chain numbering corresponds to the subboxes_overview.xlsx spreadsheet.
DOI: 10.5281/zenodo.7457332
title: Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death

description: This dataset accompanies the article entitled <em>Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death</em>, published in ACS Cent. Sci. (https://doi.org/10.1021/acscentsci.2c01078). <strong>subboxes_overview.xlsx: </strong>This spreadsheet contains information about the protein composition of each sub-box. <strong>BOX_GEOMETRIES.zip: </strong>Starting structures (saved in Gromos87 .gro format) used for the production runs of the all-atom sub-boxes. <strong>PROTEIN_COM_MSD.zip: </strong>Text files containing the mean square displacements (MSDs) of the centers of mass (COMs) of individual proteins, as obtained from the production runs of the all-atom sub-boxes. The time is shown in picoseconds while the MSD values are given in nm<sup>2</sup>. For each sub-box, the protein numbering corresponds to the subboxes_overview.xlsx spreadsheet. <strong>CHAIN_COM_MSD.zip: </strong>Text files containing the mean square displacements (MSDs) of the centers of mass (COMs) of individual polypeptide chains, as obtained from the production runs of the all-atom sub-boxes. The time is shown in picoseconds while the MSD values are given in nm<sup>2</sup>. For each sub-box, the chain numbering corresponds to the subboxes_overview.xlsx spreadsheet. <strong>CHAIN_ROTACF.zip: </strong>Text files containing the rotational autocorrelation functions for individual polypeptide chains, as obtained from the production runs of the all-atom sub-boxes. The time is shown in picoseconds; the autocorrelation functions were calculated using a second-order Legendre polynomial. For each sub-box, the chain numbering corresponds to the subboxes_overview.xlsx spreadsheet.
DOI: 10.6084/m9.figshare.21764123
title: Usability of pulse oximeters used by community health and primary care workers as screening tools for severe illness in children under five in low resource settings - Data Set

description: These data sets contain all observational and survey data used for the analysis in a study on pulse oximeter usability in community health and primary care settings.
DOI: 10.6084/m9.figshare.21764123.v1
title: Usability of pulse oximeters used by community health and primary care workers as screening tools for severe illness in children under five in low resource settings - Data Set

description: These data sets contain all observational and survey data used for the analysis in a study on pulse oximeter usability in community health and primary care settings.
DOI: 10.6084/m9.figshare.21788816.v1
title: Photoperiod_inlfuence_carbon_assimilation.xlsx

description: <strong>Experimental values</strong> <br> Photoperiod influence on : biomass productivity carbon dioxide fixation rate in the biomass carbon dioxide fixation rate in the supernatant pH evolution in the supernatant Nitrate evolution in the supernatant <br>
DOI: 10.6084/m9.figshare.21799604.v1
title: Data of Evelien Va Hoeymissen for manuscript "Gain-of-function variants in the ion channel gene TRPM3 underlie a spectrum of neurodevelopmental disorders"

description: Raw data for figures
DOI: 10.6084/m9.figshare.21788816
title: Photoperiod_inlfuence_carbon_assimilation.xlsx

description: <strong>Experimental values</strong> <br> Photoperiod influence on : biomass productivity carbon dioxide fixation rate in the biomass carbon dioxide fixation rate in the supernatant pH evolution in the supernatant Nitrate evolution in the supernatant <br>
DOI: 10.6084/m9.figshare.21788816.v3
title: Photoperiod_inlfuence_carbon_assimilation.xlsx

description: <strong>Experimental values</strong> <br> Photoperiod influence on : biomass productivity carbon dioxide fixation rate in the biomass carbon dioxide fixation rate in the supernatant pH evolution in the supernatant Nitrate evolution in the supernatant <br>
DOI: 10.6084/m9.figshare.21788816.v2
title: Photoperiod_inlfuence_carbon_assimilation.xlsx

description: <strong>Experimental values</strong> <br> Photoperiod influence on : biomass productivity carbon dioxide fixation rate in the biomass carbon dioxide fixation rate in the supernatant pH evolution in the supernatant Nitrate evolution in the supernatant <br>
DOI: 10.21227/1tn1-w054
title: Network data for major mobile Operator in UK from the county of Nottinghamshire

description: The data set contain network survey statistics from the county of Nottinghamshire for four major UK mobile operators. The data are collected from September 2022 till December 2022 and contain both 4G-LTE and 5G-NSA network information and their corresponding GPS location.
DOI: 10.6084/m9.figshare.20560821
title: Data and code for manuscript comparing genetic analyses in the CC, CC-RIX, and DO

description: This project includes data and code used to generate results for manuscript comparing heritability estimation and QTL mapping power in related mouse multiparental populations: Collaborative Cross (CC), their F1s (CC-RIX), and Diversity Outbred (DO) population.
DOI: 10.6084/m9.figshare.20560821.v3
title: Data and code for manuscript comparing genetic analyses in the CC, CC-RIX, and DO

description: This project includes data and code used to generate results for manuscript comparing heritability estimation and QTL mapping power in related mouse multiparental populations: Collaborative Cross (CC), their F1s (CC-RIX), and Diversity Outbred (DO) population.
DOI: 10.6084/m9.figshare.20560821.v2
title: Data and code for manuscript comparing genetic analyses in the CC, CC-RIX, and DO

description: This project includes data and code used to generate results for manuscript comparing heritability estimation and QTL mapping power in related mouse multiparental populations: Collaborative Cross (CC), their F1s (CC-RIX), and Diversity Outbred (DO) population.
DOI: 10.6084/m9.figshare.21335010
title: p-distances Proctoporus titans

description: Genetic distances (uncorrected p-distances) estimated from 462 bp of the non-coding 16S rRNA mitochondrial fragment between <em>Proctopours titans</em>, related taxa of the genus <em>Proctoporus</em>, and related genera of the family Gymnophthalmidae.
DOI: 10.6084/m9.figshare.3761562.v2441
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.20728327
title: Data from "Breakdown of Nernst-Einstein Relation in Carbon Nanotube Porins"

description: Full dataset from the manuscript, including data from all main text, extended data, and supplementary materials sections. <br> Abstract: For over 100 years, the Nernst-Einstein relation has provided a universal link between a charged particle electrophoretic mobility and its diffusion coefficient. Here, we report experimental measurements of diffusive and electrophoretically-driven K<sup>+</sup> ion transport in narrow pores of 0.8 nm diameter single-wall carbon nanotubes (CNTs), which indicate that the Nernst-Einstein relation breaks down by over three orders of magnitude in these channels. To explain these findings, we carried out all-atomistic molecular dynamics simulations using polarizable force fields that showed that the K<sup>+</sup> ion diffusion in the narrow pore of the CNT in the presence of a single file water chain was at least three orders of magnitude slower than the K<sup>+</sup> ion diffusion in bulk solution. Intriguingly, the simulations also revealed a novel mechanism for electrophoretic transport of K<sup>+</sup> ions where the single file water chain disintegrated in the presence of applied electric fields, forming distinct ion-water clusters, which then traversed the CNT at significantly higher velocities. Finally, we demonstrate that although the individual ion-water clusters still obey the Nernst-Einstein relation, the overall relation breaks down because of two distinct ion transport mechanisms for concentration gradient-driven versus electric field-driven ion flows in these channels.
DOI: 10.15482/usda.adc/1528381
title: Data and code from: Buffered peptone water formulation does not influence growth of pESI positive Salmonella serovar Infantis

description: This repository contains all data and code required to reproduce the growth curve-fitting analysis from the manuscript:
McMillan, E. A., M. E. Berrang, Q. D. Read, S. Ramasetti, A. K. Richards, N. W. Shariat, and J. G. Frye. Buffered peptone water formulation does not influence growth of pESI positive Salmonella serovar Infantis. Journal of Food Protection, accepted.
citation will be updated upon publication
Manuscript abstract
Salmonella enterica is a major cause of human foodborne illness and is often attributed to poultry food sources. S. enterica serovar Infantis, specifically those carrying the pESI plasmid, has become a frequently isolated serotype from poultry meat samples at processing and has caused numerous recent human infections. In 2016, the USDA Food Safety and Inspection Service changed the official sampling method for raw poultry products from BPW to using neutralizing BPW (nBPW) as the rinsing agent in order to prevent residual antimicrobial effects from acidifying and oxidizing processing aids. This change was contemporaneous to the emergence of pESI-positive ser. Infantis as a prevalent serovar in poultry, prompting some to question if nBPW could be selecting for this prevalent serovar. We performed two experiments: a comparison of ser. Infantis growth in BPW versus nBPW, and a simulation of regulatory sampling methods. We found that when inoculated into both broths, ser. Infantis initially grows slightly slower in nBPW than in BPW but little difference was seen in abundance after six hours of growth. Additionally, use of nBPW to simulate poultry rinse sample and overnight cold shipping to a regulatory lab did not affect survival or subsequent growth of ser. Infantis in BPW. We concluded that the change in USDA-FSIS methodology to include nBPW in sampling procedures has likely not affected the emergence of S. ser. Infantis as a prevalent serovar in chicken and turkey meat product samples.
Contents
All necessary data are in a single comma-separated file, Sal_Infantis_growth_curve_data_EAM.csv. All R code is in a single RMarkdown document, salmonella_growth_curve_fitting.Rmd. The RMarkdown contains code to read and process the data, produce exploratory plots, fit the model, do all hoc calculations with the posterior output, and produce figures and tables from the manuscript.
Software versions
This was run on Windows 10, R version 4.1.2. Models were fit using CmdStan version 2.28.2, with brms version 2.17.0, cmdstanr version 0.4.0, emmeans version 1.7.3, and tidybayes version 3.0.2.
Program information
National Program: Food Safety (108)
Project Plan Number: 6040-32000-085-000-D
DOI: 10.25919/bv6k-1p60
title: Parkes observations for project P1170 semester 2022OCTS_20

description: We request 15.5 hours of observations with the Parkes UWL receiver to search for giant pulses (GPs) in all seven pulsars in the Southern sky which are known to exhibit this phenomenon. The UWL receiver is particularly well-suited to such a study, since some GPs from known emitters have been found to be very narrow-band and so the observed emission rate is likely to be highly frequency-dependent. Additionally, the wide bandwidth allows one to detect spectral structures such as the 'banding' effect recently observed in GPs from some pulsars, similar to that observed in the spectra of fast radio bursts. These observations should provide a wealth of information about the underlying GP emission mechanism, and a stringent test of current theories.
DOI: 10.5517/ccdc.csd.cc2cjzrn
title: CCDC 2191072: Experimental Crystal Structure Determination

description: Related Article: Sudip Bhunia, Rosa M. Gomila, Antonio Frontera, Shouvik Chattopadhyay|2023|Inorg.Chim.Acta|547|121324|doi:10.1016/j.ica.2022.121324
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.cc2cjzsp
title: CCDC 2191073: Experimental Crystal Structure Determination

description: Related Article: Sudip Bhunia, Rosa M. Gomila, Antonio Frontera, Shouvik Chattopadhyay|2023|Inorg.Chim.Acta|547|121324|doi:10.1016/j.ica.2022.121324
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.cc2cz0hw
title: CCDC 2203588: Experimental Crystal Structure Determination

description: Related Article: Sudip Bhunia, Shouvik Chattopadhyay|2022|Results in Chemistry|5|100701|doi:10.1016/j.rechem.2022.100701
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.cc2cz0jx
title: CCDC 2203589: Experimental Crystal Structure Determination

description: Related Article: Sudip Bhunia, Shouvik Chattopadhyay|2022|Results in Chemistry|5|100701|doi:10.1016/j.rechem.2022.100701
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.cc2d3n17
title: CCDC 2208038: Experimental Crystal Structure Determination

description: Related Article: Ming Bai, Wei Xu, Xin Zhang, Qian Li, Ning-Ning Du, De-Feng Liu, Guo-Dong Yao, Bin Lin, Shao-Jiang Song, Xiao-Xiao Huang|2022|Phytochemistry|206|113562|doi:10.1016/j.phytochem.2022.113562
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.cc2d3n39
title: CCDC 2208040: Experimental Crystal Structure Determination

description: Related Article: Ming Bai, Wei Xu, Xin Zhang, Qian Li, Ning-Ning Du, De-Feng Liu, Guo-Dong Yao, Bin Lin, Shao-Jiang Song, Xiao-Xiao Huang|2022|Phytochemistry|206|113562|doi:10.1016/j.phytochem.2022.113562
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.cc2d3n5c
title: CCDC 2208042: Experimental Crystal Structure Determination

description: Related Article: Ming Bai, Wei Xu, Xin Zhang, Qian Li, Ning-Ning Du, De-Feng Liu, Guo-Dong Yao, Bin Lin, Shao-Jiang Song, Xiao-Xiao Huang|2022|Phytochemistry|206|113562|doi:10.1016/j.phytochem.2022.113562
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.cc2d3n6d
title: CCDC 2208043: Experimental Crystal Structure Determination

description: Related Article: Ming Bai, Wei Xu, Xin Zhang, Qian Li, Ning-Ning Du, De-Feng Liu, Guo-Dong Yao, Bin Lin, Shao-Jiang Song, Xiao-Xiao Huang|2022|Phytochemistry|206|113562|doi:10.1016/j.phytochem.2022.113562
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.cc2d3n7f
title: CCDC 2208044: Experimental Crystal Structure Determination

description: Related Article: Ming Bai, Wei Xu, Xin Zhang, Qian Li, Ning-Ning Du, De-Feng Liu, Guo-Dong Yao, Bin Lin, Shao-Jiang Song, Xiao-Xiao Huang|2022|Phytochemistry|206|113562|doi:10.1016/j.phytochem.2022.113562
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.