cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11889153
title: Proteome database of Enterobacter hormaechei ATCC 49162

description: <i>Enterobacter hormaechei</i> is a clinically significant Gram-negative bacterium able to survive under anaerobic conditions. This work sought to provide fundamental information of this bacterium by parsing the UniProt proteome file of <i>E. hormaechei</i> ATCC 49162 using an in-house MATLAB proteome analysis software. The resulting proteome database comprises protein name, amino acid sequence, number of residues, molecular weight and nucleotide sequence. Overall, the database should provide clues to the molecular players partaking in pathogenesis processes as well as help guide efforts to characterize the functional consequence of gene deletions in loss-of-function studies.<br><br>
DOI: 10.6084/m9.figshare.11889153.v1
title: Proteome database of Enterobacter hormaechei ATCC 49162

description: <i>Enterobacter hormaechei</i> is a clinically significant Gram-negative bacterium able to survive under anaerobic conditions. This work sought to provide fundamental information of this bacterium by parsing the UniProt proteome file of <i>E. hormaechei</i> ATCC 49162 using an in-house MATLAB proteome analysis software. The resulting proteome database comprises protein name, amino acid sequence, number of residues, molecular weight and nucleotide sequence. Overall, the database should provide clues to the molecular players partaking in pathogenesis processes as well as help guide efforts to characterize the functional consequence of gene deletions in loss-of-function studies.<br><br>
DOI: 10.6084/m9.figshare.11889087
title: H3K27ac Peak Calls for 22 Cell Lines

description: Peaks were called using macs2 (non-default parameters: -q 0.01). All peak calls have been provided in narrowPeak format.
DOI: 10.6084/m9.figshare.11889087.v1
title: H3K27ac Peak Calls for 22 Cell Lines

description: Peaks were called using macs2 (non-default parameters: -q 0.01). All peak calls have been provided in narrowPeak format.
DOI: 10.6084/m9.figshare.11889063
title: VTT High Q Resonators supplementary data

description: This repository contains raw experimental data presented in B. Zhang et al, "Compact multi-million Q resonators and 100 MHz passband filter bank in a thick-SOI photonics platform," submitted to Optics Letters (2020)<br>
DOI: 10.6084/m9.figshare.11889063.v1
title: VTT High Q Resonators supplementary data

description: Supplementary data for paper "Compact multi-million Q resonators and 100 MHz passband filter bank in a thick-SOI photonics platform"<br>
DOI: 10.6084/m9.figshare.11889063.v2
title: VTT High Q Resonators supplementary data

description: This repository contains raw experimental data presented in B. Zhang et al, "Compact multi-million Q resonators and 100 MHz passband filter bank in a thick-SOI photonics platform," submitted to Optics Letters (2020)<br>
DOI: 10.6084/m9.figshare.11889024
title: RahmaniPeruaniRomanczuk_PLoS_Comp_Biol_2020.zip

description: Data from an individual-based model generated by numerical integration of the underlying stochastic equations of motion. Individual agents moving with constant speed, interact with k nearest objects in their surrounding. Elements of the k nearest object set can be either other agents (social cues) or distraction sites (local environmental cues), which for simplicity are referred to as obstacles. If an agent has an obstacle within its k nearest objects and it is within its repulsion distance, the agent turns away. Otherwise, the agent coordinates its motion with other agents through an alignment interaction. A small fraction of agents has additional private information about a global direction of motion and biases its motion accordingly. This data set contains all data required to generate figures of the linked manuscript. For details on the mathematical model, see corresponding Materials and Methods section in the manuscript.<br><br>Data was obtained from numerical simulations of the individual-based model by solving the stochastic differential equations of motion using custom made simulation code written in C++. Data contains depending on the file/figure:<br>individual coordinates of agents in 2D (x,y,vx,vy) or coordinates of (stationary) obstacles (x,y);<br>average quantities for individual runs for different parameter values (migration accuracy, obstacle avoidance, etc).<br>2D histogram data for the 2D probability density of in and out degrees of the interaction network.<br>See linked manuscript for the definition of the average quantities.<br><br>See included README.txt for additional information of the data contained in individual files. In addition two IPython notebooks are provided which contains additional processing steps and information for generation of corresponding plots (as in the linked manuscript).
DOI: 10.6084/m9.figshare.11889024.v1
title: RahmaniPeruaniRomanczuk_PLoS_Comp_Biol_2020.zip

description: Data from an individual-based model generated by numerical integration of the underlying stochastic equations of motion. Individual agents moving with constant speed, interact with k nearest objects in their surrounding. Elements of the k nearest object set can be either other agents (social cues) or distraction sites (local environmental cues), which for simplicity are referred to as obstacles. If an agent has an obstacle within its k nearest objects and it is within its repulsion distance, the agent turns away. Otherwise, the agent coordinates its motion with other agents through an alignment interaction. A small fraction of agents has additional private information about a global direction of motion and biases its motion accordingly. This data set contains all data required to generate figures of the linked manuscript. For details on the mathematical model, see corresponding Materials and Methods section in the manuscript.<br><br>Data was obtained from numerical simulations of the individual-based model by solving the stochastic differential equations of motion using custom made simulation code written in C++. Data contains depending on the file/figure:<br>individual coordinates of agents in 2D (x,y,vx,vy) or coordinates of (stationary) obstacles (x,y);<br>average quantities for individual runs for different parameter values (migration accuracy, obstacle avoidance, etc).<br>2D histogram data for the 2D probability density of in and out degrees of the interaction network.<br>See linked manuscript for the definition of the average quantities.<br><br>See included README.txt for additional information of the data contained in individual files. In addition two IPython notebooks are provided which contains additional processing steps and information for generation of corresponding plots (as in the linked manuscript).
DOI: 10.6084/m9.figshare.11889015
title: Data File 2_Candidatus Afipia apatlaquensis.OGRI.pdf

description: <b>Overall genome relatedness index for “<i>Candidatus</i> Afipia apatlaquensis” sp. nov., strain IBT-C3 with close phylogenetic neighbors</b>
DOI: 10.6084/m9.figshare.11889018
title: Data File 4_Candidatus Afipia apatlaquensis-Description and Features.pdf

description: <i>Description of </i>“<i>Candidatus </i>Afipia apatlaquensis”<i> </i>sp. nov.,<i> and Genomic features</i><br><i></i><i></i>
DOI: 10.6084/m9.figshare.11889012
title: Data File 3_Enzymes.pdf

description: <b>Potentially relevant enzymes for textile dyes degradation encoded in “<i>Candidatus </i>Afipia apatlaquensis<i>”</i> sp. nov., genome</b><br><b></b>
DOI: 10.6084/m9.figshare.11889018.v1
title: Data File 3_Description and Features.pdf

description: <i>Description of </i>“<i>Candidatus </i>Afipia apatlaquensis”<i> </i>sp. nov.,<i> and Genomic features</i><br><i></i><i></i>
DOI: 10.6084/m9.figshare.11889012.v2
title: Data File 3_Enzymes.pdf

description: <b>Potentially relevant enzymes for textile dyes degradation encoded in “<i>Candidatus </i>Afipia apatlaquensis<i>”</i> sp. nov., genome</b><br><b></b>
DOI: 10.6084/m9.figshare.11889015.v1
title: Data File 1_OGRI.pdf

description: <b>Overall genome relatedness index for “<i>Candidatus</i> Afipia apatlaquensis” sp. nov., strain IBT-C3 with close phylogenetic neighbors</b>
DOI: 10.6084/m9.figshare.11889012.v1
title: Data File 2_Enzymes.pdf

description: <b>Potentially relevant enzymes for textile dyes degradation encoded in “<i>Candidatus </i>Afipia apatlaquensis<i>”</i> sp. nov., genome</b><br><b></b>
DOI: 10.6084/m9.figshare.11889015.v2
title: Data File 2_OGRI.pdf

description: <b>Overall genome relatedness index for “<i>Candidatus</i> Afipia apatlaquensis” sp. nov., strain IBT-C3 with close phylogenetic neighbors</b>
DOI: 10.6084/m9.figshare.11889018.v2
title: Data File 4_Description and Features.pdf

description: <i>Description of </i>“<i>Candidatus </i>Afipia apatlaquensis”<i> </i>sp. nov.,<i> and Genomic features</i><br><i></i><i></i>
DOI: 10.6084/m9.figshare.11888952
title: U-shaped response Unifies views on temperature dependency of stoichiometric requirements

description: GRr : Daphnia magna Growth rate versus dietary treatment and temperature<br>CP : Daphnia magna CP versus dietary treatment and temperature<br>TER model last version : R script to predict model component and TER with each parameters varying independently<br>TER sensibilité model : Model sensitivity test testing the TER shape when each parametrs is selected randomly
DOI: 10.6084/m9.figshare.11888952.v1
title: U-shaped response Unifies views on temperature dependency of stoichiometric requirements

description: GRr : Daphnia magna Growth rate versus dietary treatment and temperature<br>CP : Daphnia magna CP versus dietary treatment and temperature<br>TER model last version : R script to predict model component and TER with each parameters varying independently<br>TER sensibilité model : Model sensitivity test testing the TER shape when each parametrs is selected randomly
DOI: 10.6084/m9.figshare.11888916
title: Brazilian Transparency Portal Contracts and Procurements Crawled from the public API

description: This is a crawl of the Web API provided by the Brazilian Federal Government for open budget data under the transparency portal (http://www.portaltransparencia.gov.br).<br>The datasets included in this crawl are the procurement (licitações), contracts (contratos) and government organizations (Organizações SIAFI). An introduction to the APIs is provided (http://www.portaltransparencia.gov.br/api-de-dados) and there is a swagger documentation available at http://www.transparencia.gov.br/swagger-ui.html.<br>Two additional undocumented APIs were also crawled:<br>- (/criterios/contratos/fornecedor/autocomplete) Surrogate IDs from CNPJ (a fiscal organization identifier);- (/pessoa-juridica/{id}/participante-licitacao/resultado) Participation of contractors in procurements (contractors are identified by their surrogate ID, not their CNPJ).<br>These undocumented APIs where only crawled for contractors that had contracts with organization number 26246 (Federal University of Santa Catarina).<br><br>The crawl includes data up to January 31st, 2020. The aforementioned datasets are updated monthly. <br><br>Software used to perform this crawl can be found at https://bitbucket.org/alexishuf/compsac-2020-experiments. This crawl-all.sh script does the full crawl (this requires 4 hours or more). More details of the crawling procedures can be found in the EXPERIMENTS.md file.<br>
DOI: 10.6084/m9.figshare.11888916.v1
title: Brazilian Transparency Portal Contracts and Procurements Crawled from the public API

description: This is a crawl of the Web API provided by the Brazilian Federal Government for open budget data under the transparency portal (http://www.portaltransparencia.gov.br).<br>The datasets included in this crawl are the procurement (licitações), contracts (contratos) and government organizations (Organizações SIAFI). An introduction to the APIs is provided (http://www.portaltransparencia.gov.br/api-de-dados) and there is a swagger documentation available at http://www.transparencia.gov.br/swagger-ui.html.<br>Two additional undocumented APIs were also crawled:<br>- (/criterios/contratos/fornecedor/autocomplete) Surrogate IDs from CNPJ (a fiscal organization identifier);- (/pessoa-juridica/{id}/participante-licitacao/resultado) Participation of contractors in procurements (contractors are identified by their surrogate ID, not their CNPJ).<br>These undocumented APIs where only crawled for contractors that had contracts with organization number 26246 (Federal University of Santa Catarina).<br><br>The crawl includes data up to January 31st, 2020. The aforementioned datasets are updated monthly. <br><br>Software used to perform this crawl can be found at https://bitbucket.org/alexishuf/compsac-2020-experiments. This crawl-all.sh script does the full crawl (this requires 4 hours or more). More details of the crawling procedures can be found in the EXPERIMENTS.md file.<br>
DOI: 10.6084/m9.figshare.11888883
title: D_guttifera_ DEG_list.xlsx

description: (wg) in the data set means <i>wingless</i> overexpression.
DOI: 10.6084/m9.figshare.11888898
title: Genes differentially expressed in the pigmentation areas of Drosophila guttifera.

description: This data set is obtained from transcriptome analysis of <i>Drosophila guttifera</i>. This species has plka-dotted pigmentation pattern on its wings. We identified upregulated or downregulated differentially expressed genes (DEGs) in the pigmentation area around a campaniform sensilla (cs), a tip of a wing vein (vt). We also identified upregulated or downregulated DEGs in the area where <i>wingless</i> gene is overexpressed (wg).
DOI: 10.6084/m9.figshare.11888778
title: siRNA Example Dataset – QuantEscape

description: QuantEscape is a MATLAB App and toolkit for quantification of endosomal escape and damage from live-cell fluorescence microscopy images.<br><br>The file contains fluorescence microscopy images of HeLa cells expressing the membrane damage sensor galectin-9, incubated with cholesterol-conjugated siRNA. Images are provided as an example dataset for demonstration of the QuantEscape quantification tools for endosomal escape and damage.<br><b><i>Dataset description</i></b><b>Channel 1 (c1): </b>YFP-galectin-9<b>Channel 2 (c2):</b> DY547-siRNA<b><i>x</i> Dimension:</b> 512 px<b><i>y</i> Dimension:</b> 512 px<b><i>z</i> Dimension:</b> 10 planes<b><i>t</i> Dimension:</b> 500 frames (<i>dt</i> = 3.2 s)<b>Image format:</b> 16-bit tif<br>
DOI: 10.6084/m9.figshare.11888778.v1
title: siRNA Example Dataset – QuantEscape

description: QuantEscape is a MATLAB App and toolkit for quantification of endosomal escape and damage from live-cell fluorescence microscopy images.<br><br>The file contains fluorescence microscopy images of HeLa cells expressing the membrane damage sensor galectin-9, incubated with cholesterol-conjugated siRNA. Images are provided as an example dataset for demonstration of the QuantEscape quantification tools for endosomal escape and damage.<br><b><i>Dataset description</i></b><b>Channel 1 (c1): </b>YFP-galectin-9<b>Channel 2 (c2):</b> DY547-siRNA<b><i>x</i> Dimension:</b> 512 px<b><i>y</i> Dimension:</b> 512 px<b><i>z</i> Dimension:</b> 10 planes<b><i>t</i> Dimension:</b> 500 frames (<i>dt</i> = 3.2 s)<b>Image format:</b> 16-bit tif<br>
DOI: 10.6084/m9.figshare.11888760
title: SAXS data from "Kjaergaard et al. (2010) Conformational selection in the molten globule state of the nuclear coactivator binding domain of CBP. PNAS 107(28):12535-40"

description: SAXS data of the "nuclear coactivator binding domain" (NCBD) from CREB binding protein "CBP" in various concentrations of urea and TMAO. Detailed conditions in paper.<br>
DOI: 10.6084/m9.figshare.11888760.v1
title: SAXS data from "Kjaergaard et al. (2010) Conformational selection in the molten globule state of the nuclear coactivator binding domain of CBP. PNAS 107(28):12535-40"

description: SAXS data of the "nuclear coactivator binding domain" (NCBD) from CREB binding protein "CBP" in various concentrations of urea and TMAO. Detailed conditions in paper.<br>
DOI: 10.6084/m9.figshare.11888769
title: The impact of horse age, sex and number of riders on horse performance in British Eventing horse trials

description: The data is publicly accessible on the British Eventing website (https://www.britisheventing.com/compete/fixtures-and-results). The master dataset includes scores from all horses competing between 2008 and 2018. The age at which a horse competed is calculated using the year of birth of the horse, and the year of the competition. To create dA, the lowest position for each horse is selected for each class in which they competed. To create dB, the lowest score for each individual horse/rider combination is selected. Both dA and dB are split into the major classes of British Eventing competition.
DOI: 10.6084/m9.figshare.11888745
title: SAXS data from "Kjaergaard et. al. (2010) Temperature‐dependent structural changes in intrinsically disordered proteins: Formation of α‒helices or loss of polyproline II? Protein Science 19(8):1555-1564

description: The raw SAXS data used in the paper "Kjaergaard et. al. (2010) Temperature‐dependent structural changes in intrinsically disordered proteins: Formation of α‒helices or loss of polyproline II? Protein Science 19(8):1555-1564". Recorded at EMBL Hamburg June 2009.<br>
DOI: 10.6084/m9.figshare.11888733
title: Simulated zero-crossing wave period (3-hourly, 1850.01-2014.12) from FIO-ESM v2.0 historical experiment r1i1p1f1

description: Simulated zero-crossing wave period (3-hourly, 1850.01-2014.12) from FIO-ESM v2.0 historical experiment r1i1p1f1, which is branch from Jan 1, 301 of piControl experiment. The grid, named gx1v6, is the displaced pole (the North Pole displaced to the Greenland) grid with 1.1 degree in longitude and 0.27-0.54 degree in latitude.
DOI: 10.6084/m9.figshare.11888745.v1
title: SAXS data from "Kjaergaard et. al. (2010) Temperature‐dependent structural changes in intrinsically disordered proteins: Formation of α‒helices or loss of polyproline II? Protein Science 19(8):1555-1564

description: The raw SAXS data used in the paper "Kjaergaard et. al. (2010) Temperature‐dependent structural changes in intrinsically disordered proteins: Formation of α‒helices or loss of polyproline II? Protein Science 19(8):1555-1564". Recorded at EMBL Hamburg June 2009.<br>
DOI: 10.6084/m9.figshare.11888724
title: Bangaram coral 18O data.txt

description: The stable oxygen isotope data of <i>Porites</i> coral from Bangaram Island, Lakshadweep is obtained from Ahmad et al., 2010. The data has been interpolated to monthly values using QAnalySeries software.
DOI: 10.6084/m9.figshare.11888733.v1
title: Simulated zero-crossing wave period (3-hourly, 1850.01-2014.12) from FIO-ESM v2.0 historical experiment r1i1p1f1

description: Simulated zero-crossing wave period (3-hourly, 1850.01-2014.12) from FIO-ESM v2.0 historical experiment r1i1p1f1, which is branch from Jan 1, 301 of piControl experiment. The grid, named gx1v6, is the displaced pole (the North Pole displaced to the Greenland) grid with 1.1 degree in longitude and 0.27-0.54 degree in latitude.
DOI: 10.6084/m9.figshare.11888718
title: Footedness predicts escape performance in a passerine bird_data

description: Datasets of Footedness predicts escape performance in a passerine bird.
DOI: 10.6084/m9.figshare.11888724.v1
title: Bangaram coral 18O data.txt

description: The stable oxygen isotope data of <i>Porites</i> coral from Bangaram Island, Lakshadweep is obtained from Ahmad et al., 2010. The data has been interpolated to monthly values using QAnalySeries software.
DOI: 10.6084/m9.figshare.11888586
title: Additional file 1 of Rodents as intermediate hosts of cestode parasites of mammalian carnivores and birds of prey in Poland, with the first data on the life-cycle of Mesocestoides melesi

description: Additional file 1: Table S1. Similarity (%) between selected 12S rDNA sequences of Mesocestoides generated in the present study and sequences of Mesocestoides spp. from the GenBank database. Table S2. Similarity (%) between selected 18S rDNA sequences of Mesocestoides generated in the present study and sequences of Mesocestoides spp. from the GenBank database. Table S3. Similarity (%) between selected cox1 sequences of Mesocestoides generated in the present study and sequences of Mesocestoides spp. from the GenBank database.
DOI: 10.6084/m9.figshare.11888586.v1
title: Additional file 1 of Rodents as intermediate hosts of cestode parasites of mammalian carnivores and birds of prey in Poland, with the first data on the life-cycle of Mesocestoides melesi

description: Additional file 1: Table S1. Similarity (%) between selected 12S rDNA sequences of Mesocestoides generated in the present study and sequences of Mesocestoides spp. from the GenBank database. Table S2. Similarity (%) between selected 18S rDNA sequences of Mesocestoides generated in the present study and sequences of Mesocestoides spp. from the GenBank database. Table S3. Similarity (%) between selected cox1 sequences of Mesocestoides generated in the present study and sequences of Mesocestoides spp. from the GenBank database.
DOI: 10.6084/m9.figshare.11888562
title: Additional file 3 of Risk factors for poor treatment outcomes of 2266 multidrug-resistant tuberculosis cases in Ho Chi Minh City: a retrospective study

description: Additional file 3. Dataset of drug-susceptibility testing results.
DOI: 10.6084/m9.figshare.11888556
title: Additional file 2 of Risk factors for poor treatment outcomes of 2266 multidrug-resistant tuberculosis cases in Ho Chi Minh City: a retrospective study

description: Additional file 2. Dataset of 2266 MDR-TB patients.
DOI: 10.6084/m9.figshare.11888556.v1
title: Additional file 2 of Risk factors for poor treatment outcomes of 2266 multidrug-resistant tuberculosis cases in Ho Chi Minh City: a retrospective study

description: Additional file 2. Dataset of 2266 MDR-TB patients.
DOI: 10.6084/m9.figshare.11888562.v1
title: Additional file 3 of Risk factors for poor treatment outcomes of 2266 multidrug-resistant tuberculosis cases in Ho Chi Minh City: a retrospective study

description: Additional file 3. Dataset of drug-susceptibility testing results.
DOI: 10.6084/m9.figshare.11888451
title: Additional file 1 of Successful control of an extended-spectrum beta-lactamase-producing Klebsiella pneumoniae ST307 outbreak in a neonatal intensive care unit

description: Additional file 1. Case report form and raw data of Klebsiella pneumoniae outbreak, hand hygiene monitoring, and active surveillance cultures.
DOI: 10.6084/m9.figshare.11888451.v1
title: Additional file 1 of Successful control of an extended-spectrum beta-lactamase-producing Klebsiella pneumoniae ST307 outbreak in a neonatal intensive care unit

description: Additional file 1. Case report form and raw data of Klebsiella pneumoniae outbreak, hand hygiene monitoring, and active surveillance cultures.
DOI: 10.6084/m9.figshare.11888367
title: Additional file 9 of Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions

description: Additional file 9: Table S3. Inheritance error rates for pMEIs in YRI families.
DOI: 10.6084/m9.figshare.11888367.v1
title: Additional file 9 of Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions

description: Additional file 9: Table S3. Inheritance error rates for pMEIs in YRI families.
DOI: 10.6084/m9.figshare.11888358
title: Additional file 8 of Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions

description: Additional file 8: Table S2. Candidate de novo pMEIs in YRI families.
DOI: 10.6084/m9.figshare.11888349
title: Additional file 7 of Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions

description: Additional file 7: Table S1. Number of passed filter reads for YRI samples.