cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11820027
title: The RNA-dependent RNA polymerase of enterovirus A71 associates with ribosomal proteins and positively regulates protein translation

description: Enteroviruses, which may cause neurological complications, have become a public health threat worldwide in recent years. Interactions between cellular proteins and enteroviral proteins could interfere with cellular biological processes to facilitate viral replication in infected cells. Enteroviral RNA-dependent RNA polymerase (RdRP), known as 3D protein, mainly functions as a replicase for viral RNA synthesis in infected cells. However, the 3D protein encoded by enterovirus A71 (EV-A71) could also interact with several cellular proteins to regulate cellular events and responses during infection. To globally investigate the functions of the EV-A71 3D protein in regulating biological processes in host cells, we performed immunoprecipitation coupled with liquid chromatography−tandem mass spectrometry (LC-MS/MS) to identify host proteins that may associate with the 3D protein. We found that the 3D protein interacts with factors involved in translation-related biological processes, including ribosomal proteins. In addition, polysome profiling analysis showed that the 3D protein cosediments with small and large subunits of ribosomes. We further discovered that the EV-A71 3D protein could enhance EV-A71 internal ribosome entry site (IRES)-dependent translation as well as cap-dependent translation. Collectively, this research demonstrated that the RNA polymerase encoded by EV-A71 could join a functional ribosomal complex and positively regulate viral and host translation.
DOI: 10.6084/m9.figshare.11820027.v1
title: The RNA-dependent RNA polymerase of enterovirus A71 associates with ribosomal proteins and positively regulates protein translation

description: Enteroviruses, which may cause neurological complications, have become a public health threat worldwide in recent years. Interactions between cellular proteins and enteroviral proteins could interfere with cellular biological processes to facilitate viral replication in infected cells. Enteroviral RNA-dependent RNA polymerase (RdRP), known as 3D protein, mainly functions as a replicase for viral RNA synthesis in infected cells. However, the 3D protein encoded by enterovirus A71 (EV-A71) could also interact with several cellular proteins to regulate cellular events and responses during infection. To globally investigate the functions of the EV-A71 3D protein in regulating biological processes in host cells, we performed immunoprecipitation coupled with liquid chromatography−tandem mass spectrometry (LC-MS/MS) to identify host proteins that may associate with the 3D protein. We found that the 3D protein interacts with factors involved in translation-related biological processes, including ribosomal proteins. In addition, polysome profiling analysis showed that the 3D protein cosediments with small and large subunits of ribosomes. We further discovered that the EV-A71 3D protein could enhance EV-A71 internal ribosome entry site (IRES)-dependent translation as well as cap-dependent translation. Collectively, this research demonstrated that the RNA polymerase encoded by EV-A71 could join a functional ribosomal complex and positively regulate viral and host translation.
DOI: 10.6084/m9.figshare.11819982
title: OCT_OCTA.mat

description: Rat retina structural and angiographic volumes acquired by visible-light OCT
DOI: 10.6084/m9.figshare.11819868.v1
title: CI build prediction with Evolutionary Search

description: We provide the collected dataset for 10 Travis CI projects as well as all the data needed for replicating the validation:1. script for ML2. online validation test/train sets3. Failure rate in each problem instance4. All the results for the validation
DOI: 10.6084/m9.figshare.11819781
title: new_pullreq

description: This is the dataset for pull-based development, together with MSR 2020 data track paper
DOI: 10.6084/m9.figshare.11819781.v1
title: new_pullreq

description: This is the dataset for pull-based development, together with MSR 2020 data track paper
DOI: 10.6084/m9.figshare.11819868.v2
title: CI build prediction with Evolutionary Search

description: We provide the collected dataset for 10 Travis CI projects as well as all the data needed for replicating the validation:1. script for ML2. online validation test/train sets3. Failure rate in each problem instance4. All the results for the validation
DOI: 10.6084/m9.figshare.11819868.v3
title: CI build prediction with Evolutionary Search

description: We provide the collected dataset for 10 Travis CI projects as well as all the data needed for replicating the validation:1. script for ML2. online validation test/train sets3. Failure rate in each problem instance4. All the results for the validation
DOI: 10.6084/m9.figshare.11819655
title: Cloacal Swab Microbiota

description: The dataset includes sequence data and metadata files for a study comparing cecal versus cloacal microbiota from chicken.
DOI: 10.6084/m9.figshare.11819448
title: Run results for NASA’s Meteoroid Engineering Model where meteoroids are striking the asteroid Bennu.

description: Runs results for NASA’s Meteoroid Engineering Model where meteoroids are striking the asteroid Bennu.
DOI: 10.6084/m9.figshare.11819448.v1
title: Run results for NASA’s Meteoroid Engineering Model where meteoroids are striking the asteroid Bennu.

description: Runs results for NASA’s Meteoroid Engineering Model where meteoroids are striking the asteroid Bennu.
DOI: 10.6084/m9.figshare.11819388
title: Analyzed results of Pinch Model

description: CSV file of the Analyzed Results of the Pinch model. Each row represents results for a unique simulation.<br>Columns: <b>Run.number</b>: unique number associated with a specific simulation<b>Wo</b>: Womersley number (Wo, input parameter)<b>Comp</b>: Compression ratio (CR, input parameter)<b>Freq</b>: Compression frequency (f, input parameter)<b>iposn</b>: parameter associated with holding wave speed constant<b>Sim Time</b>: total simulation time (in seconds) run for the simulation. Different simulation times were required because of variations in compression frequency.<b>Q:</b> Volume flow rate (Q, performance output)<b>UpperUmavg</b>: average flow speed across upper region of racetrack (Uavg)<b>UpperUmpeak</b>: peak flow speed across upper region of racetrack (Upeak)<b>ConnectUmavg</b>: average flow speed across connect region of racetrack (Uavg)<b>ConnectUmpeak</b>: peak flow speed across connect region of racetrack (Upeak)<b>AortaUmavg</b>: average flow speed across aorta region of racetrack (Uavg)<b>AortaUmpeak</b>: peak flow speed across aorta region of racetrack (Upeak)<b>VenaUmavg</b>: average flow speed across vena cava region of racetrack (Uavg)<b>VenaUmpeak</b>: peak flow speed across vena cava region of racetrack (Upeak)<b>AortaP</b>: average pressure across the aorta region of the racetrack (Pout)<b>VenaP</b>: average pressure across the vena cava region of the racetrack (Pin)<b>DeltaPmax</b>: maximum pressure change across the contracting region of the tube (delta P)<b>COT</b>: Cost of transport (COT) for the simulation<b>Work</b>: work done on the tube for the simulation<br><br>
DOI: 10.6084/m9.figshare.11819439
title: Analyzed results of Sine-wave model

description: CSV file of the Analyzed Results of the Sine-wave model. Each row represents results for a unique simulation.<br>Columns:<b>Run.number</b>: unique number associated with a specific simulation<b>Wo</b>: Womersley number (Wo, input parameter)<b>Comp</b>: Compression ratio (CR, input parameter)<b>Freq</b>: Compression frequency (f, input parameter)<b>iposn</b>: parameter associated with holding wave speed constant<b>Sim Time</b>: total simulation time (in seconds) run for the simulation. Different simulation times were required because of variations in compression frequency.<b>Q</b>: Volume flow rate (Q, performance output)<b>UpperUmavg</b>: average flow speed across upper region of racetrack (Uavg)<b>UpperUmpeak</b>: peak flow speed across upper region of racetrack (Upeak)<b>ConnectUmavg</b>: average flow speed across connect region of racetrack (Uavg)<b>ConnectUmpeak</b>: peak flow speed across connect region of racetrack (Upeak)<b>AortaUmavg</b>: average flow speed across aorta region of racetrack (Uavg)<b>AortaUmpeak</b>: peak flow speed across aorta region of racetrack (Upeak)<b>VenaUmavg</b>: average flow speed across vena cava region of racetrack (Uavg)<b>VenaUmpeak</b>: peak flow speed across vena cava region of racetrack (Upeak)<b>AortaP</b>: average pressure across the aorta region of the racetrack (Pout)<b>VenaP</b>: average pressure across the vena cava region of the racetrack (Pin)<b>DeltaPmax</b>: maximum pressure change across the contracting region of the tube (delta P)<b>COT</b>: Cost of transport (COT) for the simulation<b>Work</b>: work done on the tube for the simulation
DOI: 10.6084/m9.figshare.11819361
title: PL2SS.3

description: Data from simulation PL2SS.3 from Almeida & Nemmen 2020.
DOI: 10.6084/m9.figshare.11819388.v1
title: Analyzed results of Pinch Model

description: CSV file of the Analyzed Results of the Pinch model. Each row represents results for a unique simulation.<br>Columns: <b>Run.number</b>: unique number associated with a specific simulation<b>Wo</b>: Womersley number (Wo, input parameter)<b>Comp</b>: Compression ratio (CR, input parameter)<b>Freq</b>: Compression frequency (f, input parameter)<b>iposn</b>: parameter associated with holding wave speed constant<b>Sim Time</b>: total simulation time (in seconds) run for the simulation. Different simulation times were required because of variations in compression frequency.<b>Q:</b> Volume flow rate (Q, performance output)<b>UpperUmavg</b>: average flow speed across upper region of racetrack (Uavg)<b>UpperUmpeak</b>: peak flow speed across upper region of racetrack (Upeak)<b>ConnectUmavg</b>: average flow speed across connect region of racetrack (Uavg)<b>ConnectUmpeak</b>: peak flow speed across connect region of racetrack (Upeak)<b>AortaUmavg</b>: average flow speed across aorta region of racetrack (Uavg)<b>AortaUmpeak</b>: peak flow speed across aorta region of racetrack (Upeak)<b>VenaUmavg</b>: average flow speed across vena cava region of racetrack (Uavg)<b>VenaUmpeak</b>: peak flow speed across vena cava region of racetrack (Upeak)<b>AortaP</b>: average pressure across the aorta region of the racetrack (Pout)<b>VenaP</b>: average pressure across the vena cava region of the racetrack (Pin)<b>DeltaPmax</b>: maximum pressure change across the contracting region of the tube (delta P)<b>COT</b>: Cost of transport (COT) for the simulation<b>Work</b>: work done on the tube for the simulation<br><br>
DOI: 10.6084/m9.figshare.11819361.v1
title: PL2SS.3

description: Data from simulation PL2SS.3 from Almeida & Nemmen 2020.
DOI: 10.6084/m9.figshare.11819328
title: Lagrangian Data (pinch model) Simulations 1-500

description: Lagrangian data for the pinch model simulations 1-500.
DOI: 10.6084/m9.figshare.11819331
title: Lagrangian Data (Sine-wave model) Simulations 1-500

description: Lagrangian Data (Sine-wave model) Simulations 1-500
DOI: 10.6084/m9.figshare.11819328.v1
title: Lagrangian Data (pinch model)

description: Lagrangian data for the pinch model.
DOI: 10.6084/m9.figshare.11819328.v2
title: Lagrangian Data (pinch model) Simulations 1-500

description: Lagrangian data for the pinch model simulations 1-500.
DOI: 10.6084/m9.figshare.11819274
title: Additional Examples

description: The collection contains two sets of examples: 1. examplary RDF datasets, demontrating generation of semantic models for the analyses described in Results/Exemplary analyses section with 'SemLMM' R package, 2. exemplary SPARQL queries, implementing the use cases discussed in Results/Exemplary queries section.
DOI: 10.6084/m9.figshare.11819274.v1
title: Additional Examples

description: The collection contains two sets of examples: 1. examplary RDF datasets, demontrating generation of semantic models for the analyses described in Results/Exemplary analyses section with 'SemLMM' R package, 2. exemplary SPARQL queries, implementing the use cases discussed in Results/Exemplary queries section.
DOI: 10.6084/m9.figshare.11819277
title: Supplementary Tables for "Brachylaima spp. (Trematoda) parasitizing Cornu aspersum (Gastropoda) in France with potential risk for human consumption."

description: 2 files (xlsx for data extraction, pdf for archiving) each containing 3 genetic identity matrices<br><br>Table 1: Percentages of identity between the 28S sequences used in the present study. Values were estimated based on aligned sequences using the SeqinR package (Charif and Lobry 2007, doi:10.1007/978-3-540-35306-5_10) <br><br>Table 2: Percentages of identity between the COI sequences used in the present study. Values were estimated based on aligned sequences using the SeqinR package (Charif and Lobry 2007, doi:10.1007/978-3-540-35306-5_10) <br><br>Table 3: Percentages of identity between the COI+28S supergene alignment sequences used in the present study. GenBank accession numbers refer respectively to 28S and COI sequences. Values were estimated based on aligned sequences using the SeqinR package (Charif and Lobry 2007, doi:10.1007/978-3-540-35306-5_10) <br>
DOI: 10.6084/m9.figshare.11819277.v1
title: Supplementary Tables for "Brachylaima spp. (Trematoda) parasitizing Cornu aspersum (Gastropoda) in France with potential risk for human consumption."

description: 2 files (xlsx for data extraction, pdf for archiving) each containing 3 genetic identity matrices<br><br>Table 1: Percentages of identity between the 28S sequences used in the present study. Values were estimated based on aligned sequences using the SeqinR package (Charif and Lobry 2007, doi:10.1007/978-3-540-35306-5_10) <br><br>Table 2: Percentages of identity between the COI sequences used in the present study. Values were estimated based on aligned sequences using the SeqinR package (Charif and Lobry 2007, doi:10.1007/978-3-540-35306-5_10) <br><br>Table 3: Percentages of identity between the COI+28S supergene alignment sequences used in the present study. GenBank accession numbers refer respectively to 28S and COI sequences. Values were estimated based on aligned sequences using the SeqinR package (Charif and Lobry 2007, doi:10.1007/978-3-540-35306-5_10) <br>
DOI: 10.23645/epacomptox.11819265
title: Profiling the ToxCast Library With a Pluripotent Human (H9) Stem Cell Line-Based Biomarker Assay for Developmental Toxicity

description: Supplemental files for paper titled "Profiling the ToxCast Library With a Pluripotent Human (H9) Stem Cell Line-Based Biomarker Assay for Developmental Toxicity."
DOI: 10.6084/m9.figshare.11819313.v1
title: Viz Dump Data Simulations (Sine-wave model)

description: Viz Dump Data Simulations (Sine-wave model) 1-5
DOI: 10.23645/epacomptox.11819265.v1
title: Profiling the ToxCast Library With a Pluripotent Human (H9) Stem Cell Line-Based Biomarker Assay for Developmental Toxicity

description: Supplemental files for paper titled "Profiling the ToxCast Library With a Pluripotent Human (H9) Stem Cell Line-Based Biomarker Assay for Developmental Toxicity."
DOI: 10.6084/m9.figshare.11818977
title: PL2SS.1

description: Data from simulation PL2SS.1 from Almeida & Nemmen 2020.
DOI: 10.6084/m9.figshare.11818977.v1
title: PL2SS.1

description: Data from simulation PL2SS.1 from Almeida & Nemmen 2020.
DOI: 10.6084/m9.figshare.11819313.v4
title: Viz Dump Data Simulations (Sine-wave model) Simulations 1-500

description: Viz Dump Data Simulations (Sine-wave model) 1-500
DOI: 10.6084/m9.figshare.11819313.v5
title: Viz Dump Data Simulations (Sine-wave model) Simulations 1-500

description: Viz Dump Data Simulations (Sine-wave model) 1-500
DOI: 10.6084/m9.figshare.11816748
title: Metadata record for: Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods

description: This dataset contains key characteristics about the data described in the Data Descriptor Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.11816733
title: Cattle and Yak Raw Data.zip

description: This data set contribute to relevant information about physiology and Genetics of Yak and Cattle. <br><br>
DOI: 10.6084/m9.figshare.11816733.v1
title: Cattle and Yak Raw Data.zip

description: This data set contribute to relevant information about physiology and Genetics of Yak and Cattle. <br><br>
DOI: 10.6084/m9.figshare.11816748.v2
title: Metadata record for: Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods

description: This dataset contains key characteristics about the data described in the Data Descriptor Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.11816748.v1
title: Metadata record for: Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods

description: This dataset contains key characteristics about the data described in the Data Descriptor Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.11819313
title: Viz Dump Data Simulations (Sine-wave model) Simulations 1-500

description: Viz Dump Data Simulations (Sine-wave model) 1-500
DOI: 10.6084/m9.figshare.11816577
title: 3D_mapping_data.zip from Three-dimensional digital mapping of ecosystems: a new era in spatial ecology

description: Ecological processes occur over multiple spatial, temporal and thematic scales in three-dimensional (3D) ecosystems. Characterizing and monitoring change in 3D structure at multiple scales is challenging within the practical constraints of conventional ecological tools. Remote sensing from satellites and crewed aircraft has revolutionized broad-scale spatial ecology, but fine-scale patterns and processes operating at sub-metre resolution have remained understudied over continuous extents. We introduce two high-resolution remote sensing tools for rapid and accurate 3D mapping in ecology—terrestrial laser scanning and structure-from-motion photogrammetry. These technologies are likely to become standard sampling tools for mapping and monitoring 3D ecosystem structure across currently under-sampled scales. We present practical guidance in the use of the tools and address barriers to widespread adoption, including testing the accuracy of structure-from-motion models for ecologists. We aim to highlight a new era in spatial ecology that uses high-resolution remote sensing to interrogate 3D digital ecosystems.
DOI: 10.6084/m9.figshare.11816565
title: Supplemental Tables

description: Supplemental tables for manuscript. Include species list and gene mapping.
DOI: 10.6084/m9.figshare.11816538
title: Estimating genotyping error rates

description: We developed a method to infer genotyping error rates with pedigree analysis. We demonstrated this technique using genotype-phase information on a dataset from whole-genome sequencing of owl monkeys (<i>Aotus nancymaae</i>). The abbreviated counts for genotype-phase combinations in four pedigrees of owl monkeys are provided here as a set of tab separated text files.<br><br>Column names in each file are the genotypic-phase combinations for the five individuals in the pedigree. Genotypes are abbreviated by a single digit: 0, 1, and 2 for homozygous reference, heterozygous, and homozygous alternate respectively. These are ordered as: mother, father, focal individual, partner of focal, and child. Phases are abbreviated as M and F for mother and father respectively. There are four non-header rows in each file, ordered by increasing stringency of minimum genotype quality (GQ): no filter, 20, 40, 60.<br>
DOI: 10.6084/m9.figshare.11816538.v1
title: Estimating genotyping error rates

description: We developed a method to infer genotyping error rates with pedigree analysis. We demonstrated this technique using genotype-phase information on a dataset from whole-genome sequencing of owl monkeys (<i>Aotus nancymaae</i>). The abbreviated counts for genotype-phase combinations in four pedigrees of owl monkeys are provided here as a set of tab separated text files.<br><br>Column names in each file are the genotypic-phase combinations for the five individuals in the pedigree. Genotypes are abbreviated by a single digit: 0, 1, and 2 for homozygous reference, heterozygous, and homozygous alternate respectively. These are ordered as: mother, father, focal individual, partner of focal, and child. Phases are abbreviated as M and F for mother and father respectively. There are four non-header rows in each file, ordered by increasing stringency of minimum genotype quality (GQ): no filter, 20, 40, 60.<br>
DOI: 10.6084/m9.figshare.11816565.v1
title: Supplemental Tables

description: Supplemental tables for manuscript. Include species list and gene mapping.
DOI: 10.6084/m9.figshare.11816517
title: R5096_41348_cryo.HITS

description: Al alloys prepared by Ga-FIB at room temperature and cryogenic temperature
DOI: 10.6084/m9.figshare.11816532
title: Assemblies

description: Hybrid asseblies of 45 clinical Enterobacteriacae isolates from bloodstream infections of patients in Oxfordshire 2008-2018. NB bc prefixed files are assembled using data demultiplexed by Guppy with reads binned as unclassified additionally demultiplxed with DeepBinner. Assemblies prefixed BC are created from reads demultiplexed using Guppy only.
DOI: 10.6084/m9.figshare.11816517.v1
title: R5096_41348_cryo.HITS

description: Al alloys prepared by Ga-FIB at room temperature and cryogenic temperature
DOI: 10.6084/m9.figshare.11816577.v2
title: 3D_mapping_data.zip from Three-dimensional digital mapping of ecosystems: a new era in spatial ecology

description: Ecological processes occur over multiple spatial, temporal and thematic scales in three-dimensional (3D) ecosystems. Characterizing and monitoring change in 3D structure at multiple scales is challenging within the practical constraints of conventional ecological tools. Remote sensing from satellites and crewed aircraft has revolutionized broad-scale spatial ecology, but fine-scale patterns and processes operating at sub-metre resolution have remained understudied over continuous extents. We introduce two high-resolution remote sensing tools for rapid and accurate 3D mapping in ecology—terrestrial laser scanning and structure-from-motion photogrammetry. These technologies are likely to become standard sampling tools for mapping and monitoring 3D ecosystem structure across currently under-sampled scales. We present practical guidance in the use of the tools and address barriers to widespread adoption, including testing the accuracy of structure-from-motion models for ecologists. We aim to highlight a new era in spatial ecology that uses high-resolution remote sensing to interrogate 3D digital ecosystems.
DOI: 10.6084/m9.figshare.11816532.v2
title: Assemblies

description: Hybrid asseblies of 45 clinical Enterobacteriacae isolates from bloodstream infections of patients in Oxfordshire 2008-2018. NB bc prefixed files are assembled using data demultiplexed by Guppy with reads binned as unclassified additionally demultiplxed with DeepBinner. Assemblies prefixed BC are created from reads demultiplexed using Guppy only.