cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6387455
title: Analysis of the synthesis of benzamide derivatives through the application of the catalyst diatomite earth under ultrasound irradation

description: This dataset consists of 27 figures relating to an experiment which demonstrates a new, green method for the preparation of a solid acid catalyst to provide active sites for the synthesis of benzamides under ultrasound irradiation. <br>The reaction was performed through the direct condensation of benzoic acids and amines under ultrasonic irradiation in the presence of Lewis acidic ionic liquid, immobilised on diatomite earth (diatomite earth@IL/ZrCl4). The prepared catalyst was found to provide active sites for the synthesis of benzamides.<br><br>The figures included in this dataset provide the results of 1H-NMR (hydrogen-1 nuclear magnetic resonance), 13 C-NMR (Carbon-13 nuclear magnetic resonance) and mass spectrometry (MS) analysis of the resultant samples.<br><br>The data are in the form of a single PDF file which can be accessed with any proprietary or open source PDF viewer.<br>
DOI: 10.6084/m9.figshare.6387455.v1
title: Analysis of the synthesis of benzamide derivatives through the application of the catalyst diatomite earth under ultrasound irradation

description: This dataset consists of 27 figures relating to an experiment which demonstrates a new, green method for the preparation of a solid acid catalyst to provide active sites for the synthesis of benzamides under ultrasound irradiation. <br>The reaction was performed through the direct condensation of benzoic acids and amines under ultrasonic irradiation in the presence of Lewis acidic ionic liquid, immobilised on diatomite earth (diatomite earth@IL/ZrCl4). The prepared catalyst was found to provide active sites for the synthesis of benzamides.<br><br>The figures included in this dataset provide the results of 1H-NMR (hydrogen-1 nuclear magnetic resonance), 13 C-NMR (Carbon-13 nuclear magnetic resonance) and mass spectrometry (MS) analysis of the resultant samples.<br><br>The data are in the form of a single PDF file which can be accessed with any proprietary or open source PDF viewer.<br>
DOI: 10.6084/m9.figshare.6387392
title: Pellet vs. intraoral voltammetry

description: This data set originates from an experiment in rats using fast-scan cyclic voltammetry to record dopamine release during a behavioural task in which rats experienced either: sucrose pellets, intraoral delivery of sucrose, or cues that predicted delivery of sucrose rewards. Matlab analysis code is available at https://github.com/mccutcheonlab/pellet-vs-intraoral. The .zip archive 'Raw data and snipped trials' includes separate folders for each rat (pvixx) where each folder includes: aa_Raw data - original voltammetry data (collected in TarHeel. 120s files with accompanying text files that contain timings of the TTLs. TTL descriptions are included on the Github site that is linked to. bb_Chemometrics - voltammetry data and other files needed for chemometric analysis 01 to 05 - these folders contain 20s voltammetry data files 'snipped' from raw data and aligned to TTLs of interest (e.g. pellet cue, infusion cue etc.). These folders also contain the dopamine concentration and noise files extracted using the chemometrics function in CV_Analysis. The second .zip archive, 'Extracted Matlab data', includes matrices containing dopamine concentrations for each trial type, as described in the linked Github site. These files will enable all Matlab analysis scripts - except the ones that assembled these matrices - to be run. These matrices consist of baseline-subtracted dopamine concentration data sampled at 10 Hz in 20 second trials aligned to either cue onset or, when cues were not present, to reward delivery. Voltammetry data are contained in the 's' matrix/variable and metadata, relating to each file, are contained in the 'x' matrix.<br>
DOI: 10.6084/m9.figshare.6387392.v1
title: Pellet vs. intraoral voltammetry

description: This data set originates from an experiment in rats using fast-scan cyclic voltammetry to record dopamine release during a behavioural task in which rats experienced either: sucrose pellets, intraoral delivery of sucrose, or cues that predicted delivery of sucrose rewards. Matlab analysis code is available at https://github.com/mccutcheonlab/pellet-vs-intraoral. The .zip archive 'Raw data and snipped trials' includes separate folders for each rat (pvixx) where each folder includes: aa_Raw data - original voltammetry data (collected in TarHeel. 120s files with accompanying text files that contain timings of the TTLs. TTL descriptions are included on the Github site that is linked to. bb_Chemometrics - voltammetry data and other files needed for chemometric analysis 01 to 05 - these folders contain 20s voltammetry data files 'snipped' from raw data and aligned to TTLs of interest (e.g. pellet cue, infusion cue etc.). These folders also contain the dopamine concentration and noise files extracted using the chemometrics function in CV_Analysis. The second .zip archive, 'Extracted Matlab data', includes matrices containing dopamine concentrations for each trial type, as described in the linked Github site. These files will enable all Matlab analysis scripts - except the ones that assembled these matrices - to be run. These matrices consist of baseline-subtracted dopamine concentration data sampled at 10 Hz in 20 second trials aligned to either cue onset or, when cues were not present, to reward delivery. Voltammetry data are contained in the 's' matrix/variable and metadata, relating to each file, are contained in the 'x' matrix.<br>
DOI: 10.6084/m9.figshare.6387338
title: piciformes_TEs

description: Files associated with DOI:10.1093/gbe/evy105<br>MELT vcf files - vcf files in a zip repository, each file is output of a MELT analysis for one of four CR1 elements and a specific sensitivity setting (specifics in manuscript, and in file names) these output have not been filtered (procedure described in manuscript)<br>SNP vcf file - output of GATK genotyping for six individuals (after filtering for use in analyses)<br>custom repeat consensus sequences - used for MELT analyses (dryobates_consensus.fasta)<br>REPdenovo repeat identification - output filtered fasta file of REPdenovo analyses identifying repeat elements from kmer searches
DOI: 10.6084/m9.figshare.6387338.v1
title: piciformes_TEs

description: Files associated with DOI:10.1093/gbe/evy105<br>MELT vcf files - vcf files in a zip repository, each file is output of a MELT analysis for one of four CR1 elements and a specific sensitivity setting (specifics in manuscript, and in file names) these output have not been filtered (procedure described in manuscript)<br>SNP vcf file - output of GATK genotyping for six individuals (after filtering for use in analyses)<br>custom repeat consensus sequences - used for MELT analyses (dryobates_consensus.fasta)<br>REPdenovo repeat identification - output filtered fasta file of REPdenovo analyses identifying repeat elements from kmer searches
DOI: 10.6084/m9.figshare.6387251
title: Data Repository.xlsx

description: Radiation therapy data for patients with meningioma receiving hypofractionated stereotactic radiosurgery with definitive intent at a single instittion from 2013-2017
DOI: 10.6084/m9.figshare.6387251.v2
title: Data Repository.xlsx

description: Radiation therapy data for patients with meningioma receiving hypofractionated stereotactic radiosurgery with definitive intent at a single instittion from 2013-2017
DOI: 10.6084/m9.figshare.6387251.v1
title: Data Repository.xlsx

description: Radiation therapy data for patients with meningioma receiving hypofractionated stereotactic radiosurgery with definitive intent at a single instittion from 2013-2017
DOI: 10.6084/m9.figshare.6384572
title: Values obtained for each replicate of matrix effects and recovery samples (lung tissue, plasma and culture medium) (pdf)

description: Demonstrated all values obtained for each replicate of matrix effects and recovery samples (lung tissue, plasma and culture medium). In these experiments the analytes corresponded to internal standards (deutered compounds) for eliminate the interference of matrix endogenous metabolites. The individual values were used to determine the average (n = 6) of matrix effect and recovery of the extraction method.
DOI: 10.6084/m9.figshare.6384572.v1
title: Values obtained for each replicate of matrix effects and recovery samples (lung tissue, plasma and culture medium) (pdf)

description: Demonstrated all values obtained for each replicate of matrix effects and recovery samples (lung tissue, plasma and culture medium). In these experiments the analytes corresponded to internal standards (deutered compounds) for eliminate the interference of matrix endogenous metabolites. The individual values were used to determine the average (n = 6) of matrix effect and recovery of the extraction method.
DOI: 10.6084/m9.figshare.6384566
title: Values obtained for each replicate of quality control (HQC, MQC and LQC) assay (pdf)

description: Presented all values obtained for each replicate of quality control (HQC, MQC and LQC) assay. The individual values from quality control assay were used to determine the average (n = 5) of precision and accuracy of the MRMHR method.
DOI: 10.6084/m9.figshare.6384566.v1
title: Values obtained for each replicate of quality control (HQC, MQC and LQC) assay (pdf)

description: Presented all values obtained for each replicate of quality control (HQC, MQC and LQC) assay. The individual values from quality control assay were used to determine the average (n = 5) of precision and accuracy of the MRMHR method.
DOI: 10.6084/m9.figshare.6384560
title: Linear regression equation, correlation coefficient (r2) and linear range of concentration for each analyte (pdf)

description: Showed the linear regression graphics. MS files were processed for each metabolite quantified in MRMHR method with mobile phase pH 5.8. The graphics describe the linear regression equation, correlation coefficient (r2) and linear range of concentration for each analyte assessed by means of 10-point standard curves prepared for five replicate samples. Also the retention time were described in this file.
DOI: 10.6084/m9.figshare.6384560.v1
title: Linear regression equation, correlation coefficient (r2) and linear range of concentration for each analyte (pdf)

description: Showed the linear regression graphics. MS files were processed for each metabolite quantified in MRMHR method with mobile phase pH 5.8. The graphics describe the linear regression equation, correlation coefficient (r2) and linear range of concentration for each analyte assessed by means of 10-point standard curves prepared for five replicate samples. Also the retention time were described in this file.
DOI: 10.6084/m9.figshare.6384548
title: Metabolite standard details (pdf)

description: Gives for each metabolite standard purchase from Cayman Chemical all details, such as molecular weight, molecular formula, CAS number and supplied solution, as well biological information, such as fatty acid precursor, biosynthetic pathway and chemical class. The file include Internal lipid standards used in for extraction control, matrix effect and recovery experiments, also standards for calibration curves in UHPLC-MS/MS and for quantitative calculation of lipid species.
DOI: 10.6084/m9.figshare.6384548.v1
title: Metabolite standard details (pdf)

description: Gives for each metabolite standard purchase from Cayman Chemical all details, such as molecular weight, molecular formula, CAS number and supplied solution, as well biological information, such as fatty acid precursor, biosynthetic pathway and chemical class. The file include Internal lipid standards used in for extraction control, matrix effect and recovery experiments, also standards for calibration curves in UHPLC-MS/MS and for quantitative calculation of lipid species.
DOI: 10.6084/m9.figshare.6384545
title: Metabolite standard details (docx)

description: Gives for each metabolite standard purchase from Cayman Chemical all details, such as molecular weight, molecular formula, CAS number and supplied solution, as well biological information, such as fatty acid precursor, biosynthetic pathway and chemical class. The file include Internal lipid standards used in for extraction control, matrix effect and recovery experiments, also standards for calibration curves in UHPLC-MS/MS and for quantitative calculation of lipid species.
DOI: 10.6084/m9.figshare.6384545.v1
title: Metabolite standard details (docx)

description: Gives for each metabolite standard purchase from Cayman Chemical all details, such as molecular weight, molecular formula, CAS number and supplied solution, as well biological information, such as fatty acid precursor, biosynthetic pathway and chemical class. The file include Internal lipid standards used in for extraction control, matrix effect and recovery experiments, also standards for calibration curves in UHPLC-MS/MS and for quantitative calculation of lipid species.
DOI: 10.6084/m9.figshare.6384413
title: OpenABL: A Domain-Specific Language for Parallel and Distributed Agent-Based Simulations

description: OpenABL is a domain-specific language for portable, high-performance, parallel agent modeling. <br>This code and data artifact includes the source code of the OpenABL programming language, as well as an overview document describing how to build OpenABL and its dependencies, and how to reproduce the results presented in the corresponding Euro-Par 2018 paper. <br>In particular, automated performance benchmarks of the Flame, FlameGPU, Mason and D-Mason toolkits across six sample applications from different fields can be performed by leveraging the OpenABL code generator. <br><br>OpenABL is designed as a portable, efficient and easy-to-use environment for agent-based modeling. It was developed as a tool to support OpenAB communities in addressing the requirement for portable solutions to reproduce simulations on different parallel implementations and hardware platforms. OpenABL was designed to compile to multiple backends targeting different computing architectures, including single CPUs,GPUs and clusters.<br>The dataset consists of a single .zip archive file containing:<b>/test</b><b> - </b>script files to execute test simulations<b> .exp </b>and <b>.abl</b><b>/src</b><b> - </b>source code files in C++ language <b>.cpp </b>and <b>.hpp </b>formats<b>/bench</b><b> - </b>benchmark files in Python language <b>.py </b>format<b>/deps - </b>Makefile for various simulation environments and libraries described in the related Euro-Par 2018 submission<b>/examples - </b>input <b>.abl</b> files for six experimental agent-based models from different domains described in the related Euro-Par 2018 publication<b>/asset</b><b> - </b>auxiliary library and build files used during code-generation, in bash script <b>.sh</b>, Java <b>.java </b>and C <b>.h</b> and <b>.c</b> formats<br>For further detail see the README and artifact overview files in this dataset and the related Euro-Par 2018 publication.
DOI: 10.6084/m9.figshare.6384413.v1
title: OpenABL: A Domain-Specific Language for Parallel and Distributed Agent-Based Simulations

description: OpenABL is a domain-specific language for portable, high-performance, parallel agent modeling. <br>This code and data artifact includes the source code of the OpenABL programming language, as well as an overview document describing how to build OpenABL and its dependencies, and how to reproduce the results presented in the corresponding Euro-Par 2018 paper. <br>In particular, automated performance benchmarks of the Flame, FlameGPU, Mason and D-Mason toolkits across six sample applications from different fields can be performed by leveraging the OpenABL code generator. <br><br>OpenABL is designed as a portable, efficient and easy-to-use environment for agent-based modeling. It was developed as a tool to support OpenAB communities in addressing the requirement for portable solutions to reproduce simulations on different parallel implementations and hardware platforms. OpenABL was designed to compile to multiple backends targeting different computing architectures, including single CPUs,GPUs and clusters.<br>The dataset consists of a single .zip archive file containing:<b>/test</b><b> - </b>script files to execute test simulations<b> .exp </b>and <b>.abl</b><b>/src</b><b> - </b>source code files in C++ language <b>.cpp </b>and <b>.hpp </b>formats<b>/bench</b><b> - </b>benchmark files in Python language <b>.py </b>format<b>/deps - </b>Makefile for various simulation environments and libraries described in the related Euro-Par 2018 submission<b>/examples - </b>input <b>.abl</b> files for six experimental agent-based models from different domains described in the related Euro-Par 2018 publication<b>/asset</b><b> - </b>auxiliary library and build files used during code-generation, in bash script <b>.sh</b>, Java <b>.java </b>and C <b>.h</b> and <b>.c</b> formats<br>For further detail see the README and artifact overview files in this dataset and the related Euro-Par 2018 publication.
DOI: 10.6084/m9.figshare.6384404.v1
title: Combination use of BMP2 and VEGF165 promotes osseointegration and stability of dental implants in irradiated bone

description: the data used in "Combination use of BMP2 and VEGF165 promotes osseointegration and stability of dental implants in irradiated bone"<br>
DOI: 10.17045/sthlmuni.6384200
title: LysM phylogeny including Datisca glomerata and Ceanothus thyrsiflorus

description: Phylogeny of LysM paralogs with sequences harvested from newly sequenced transcriptomes from <i>Datisca glomerata</i> and <i>Ceanothus thyrsiflorus</i> plus the following species as references: <i>Arabidopsis thaliana, Cicer arietinum, Cucurbita pepo, Fragaria vesca, Glycine max, Lotus japonicus, Manihot esculenta, Medicago trunculata, Morus notabilis, Oryza sativa, Prunus persica, Ricinus communis, Solanum lycopersicum, Sorghum bicolor, Theobroma cacao, Vigna radiata </i>and<i> Ziziphus jujuba</i>.<br>Sequences were collected with blastp searches against the RefSeq database subset by the above list of species, using presumed <i>D. glomerata </i>and<i> C. thyrsiflorus</i> orthologs.<br>Sequences were aligned with Clustal Omega (http://www.clustal.org/omega/; Sievers et al. 2014) and reliable alignment positions were selected with the BMGE algorithm (Criscuolo and Gribaldo 2010) using the BLOSUM62 substitution matrix. Sequences that were identical after BMGE, were discarded.<br>The tree was estimated with RAxML v. 8.2.4 (https://sco.h-its.org/exelixis/web/software/raxml/index.html; Stamatakis 2014) using the PROTGAMMAAUTO model and automatic bootstopping.<br>Files provided are:<br>1. The full alignment after BMGE selection of positions and removal of identical sequences: lysm.refseq_harvest_plus_selected.co.BLOSUM62.bmge.rx.red.phylip<br><br>2. The maximum likelihood tree labelled with bootstrap values in:a. newick format: lysm.refseq_harvest_plus_selected.co.BLOSUM62.bmge.rx.red.PROTGAMMAAUTO.raxml.besttree.newickb. Dendroscope (http://dendroscope.org/; Huson et al. 2007): lysm.refseq_harvest_plus_selected.co.BLOSUM62.bmge.rx.red.PROTGAMMAAUTO.raxml.bipartitions.nexml<br>
DOI: 10.17045/sthlmuni.6384200.v1
title: LysM phylogeny including Datisca glomerata and Ceanothus thyrsiflorus

description: Phylogeny of LysM paralogs with sequences harvested from newly sequenced transcriptomes from <i>Datisca glomerata</i> and <i>Ceanothus thyrsiflorus</i> plus the following species as references: <i>Arabidopsis thaliana, Cicer arietinum, Cucurbita pepo, Fragaria vesca, Glycine max, Lotus japonicus, Manihot esculenta, Medicago trunculata, Morus notabilis, Oryza sativa, Prunus persica, Ricinus communis, Solanum lycopersicum, Sorghum bicolor, Theobroma cacao, Vigna radiata </i>and<i> Ziziphus jujuba</i>.<br>Sequences were collected with blastp searches against the RefSeq database subset by the above list of species, using presumed <i>D. glomerata </i>and<i> C. thyrsiflorus</i> orthologs.<br>Sequences were aligned with Clustal Omega (http://www.clustal.org/omega/; Sievers et al. 2014) and reliable alignment positions were selected with the BMGE algorithm (Criscuolo and Gribaldo 2010) using the BLOSUM62 substitution matrix. Sequences that were identical after BMGE, were discarded.<br>The tree was estimated with RAxML v. 8.2.4 (https://sco.h-its.org/exelixis/web/software/raxml/index.html; Stamatakis 2014) using the PROTGAMMAAUTO model and automatic bootstopping.<br>Files provided are:<br>1. The full alignment after BMGE selection of positions and removal of identical sequences: lysm.refseq_harvest_plus_selected.co.BLOSUM62.bmge.rx.red.phylip<br><br>2. The maximum likelihood tree labelled with bootstrap values in:a. newick format: lysm.refseq_harvest_plus_selected.co.BLOSUM62.bmge.rx.red.PROTGAMMAAUTO.raxml.besttree.newickb. Dendroscope (http://dendroscope.org/; Huson et al. 2007): lysm.refseq_harvest_plus_selected.co.BLOSUM62.bmge.rx.red.PROTGAMMAAUTO.raxml.bipartitions.nexml<br>
DOI: 10.6084/m9.figshare.6384164
title: Score-P measurement system code and event logs for Euro-Par 2018 paper: A Methodology for Performance Analysis of Applications Using Multi-layer I/O

description: This artifact contains the prototype implementation of a novel approach for recording I/O operations across multi-layer I/O interfaces and a case study using that approach, as described in the accompanying paper, "A Methodology for Performance Analysis of Applications Using Multi-layer I/O".<br>In order to fully utilise the high bandwidth offered by modern high-performance computing storage systems, and to handle increasingly large volumes of data, parallel I/O operations are often implemented through libraries such as HDF5, NetCDF and MPI I/O. In many cases, multiple libraries may operate concurrently within a given software stack. This concurrency and operations between libraries can impact upon each other. Given this, it is essential to be able to effectively monitor I/O operations across all libraries utilised by a given application.<br>Here, a prototype methodology for recording calls to I/O libraries on multiple layers of the software stack is presented. This methodology is implemented as an extension of Open Trace Format Version 2 (OTF2) and the Score-P measurement infrasctructure. The implementation is provided here in the tarball <b>scorep-4.0-io.tar.gz</b><b><br></b>In addition to the implementation, event logs generated by its test evaluation of the Met Office NERC Cloud model (MONC) simulator are provided. Therein, the I/O behavior of MONC using the Score-P implementation are provided. These logs, provided in the directory <b>monc_112n_14N_10T_small</b>, can be visualized in a tool such as Vampir.<br>Further instructions on recreating the analyses presented in the accompanying paper are provided in <b>artifact.pdf</b>.