cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7115822
title: Collection of Extracted Data as part of the Publication "(Why) Do Taint Analyzers Fail in Practice? A Critical Literature Review"

description: This document provides an extensive list of the data extraction process for the systematic literature review. This anonymous version is review-friendly for double-blinded peer reviews.
DOI: 10.6084/m9.figshare.19228611.v4
title: Supplementary Material for: Three-dimensional interactive graphical model of the hindlimb muscles of the rat

description: Many questions in human movement sciences are addressed by exploiting the advantages of animal models. However, a 3D model of the musculoskeletal system of the frequently used rat model that includes a sufficient level of detail does not exist. Therefore, the aim of the present work was to develop an freely accessible 3D model of the rat hindlimb. Using the anatomical data of the Wistar rat (Mus norveqicus albinus) published by Green [Greene, 1935], a 3D representation of 34 muscles of the hindlimb was drawn. Two models were created, one using muscle like appearances and one using different colors. Each muscle can be viewed separately or within the context of its synergistic and antagonistic muscles. This model can serve to train new students before starting their experiments, but also for producing illustrations of experimental conditions or results. Further development of the model will be needed to equip it with the same advanced functionalities of some of the human anatomy atlases.
DOI: 10.5517/ccdc.csd.cc2d2w7m
title: CCDC 2207300: Experimental Crystal Structure Determination

description: Related Article: Ravishanker Kovi, Jayaraman Kannapan, Ananda Babu Thirunavakarasu, Gaurav Yadav, Veerabhadra Rao Bobbili, Shivnath Sahebrao Patil, Sanjay F. Thakor|2018|U.S.Patents|||
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: 10.6084/m9.figshare.21214082
title: Optimized Cysteine structure

description: Gaussian input and output files
DOI: 10.5281/zenodo.7115823
title: Habituation to onsets is controlled by spatially selective distractor expectation

description: Dataset pertaining to the paper "Habituation to onsets is controlled by spatially selective distractor expectation", to appear in the Journal of Experimental Psychology: HPP. The root folder contain a txt file named "AADescription.txt", which contains a detailed explanation of the dataset.
DOI: 10.5281/zenodo.7114487
title: Application of machine learning to improve appropriateness of treatment in an orthopaedic setting of personalized medicine

description: Raw Data
DOI: 10.5281/zenodo.7114486
title: Application of machine learning to improve appropriateness of treatment in an orthopaedic setting of personalized medicine

description: Raw Data
DOI: 10.5255/ukda-sn-855966
title: Drugs and (Dis)order Key Informant Interviews in Kachin State Myanmar, 2019

description: Collection of 194 face-to-face semi-structured interviews with interviewees in Kachin State, northern Myanmar, carried out as part of the GCRF Drugs and (dis)order project. Interviews were carried out in the second year of the project to gather in-depth evidence on key research themes selected based on emerging findings from the 2018 interviews. Interviews focused on the themes (1) drugs and processes of political and economic change, (2) drugs and social change and the impact on families, and (3) responses to drugs and the impact of drug interventions.
DOI: 10.6084/m9.figshare.21203015.v1
title: Vector Data

description: Dataset associated with meta-analysis.
DOI: 10.6084/m9.figshare.21203015
title: Vector Data

description: Draft dataset associated with meta-analysis study.
DOI: 10.6084/m9.figshare.21203015.v2
title: Vector Data

description: Draft dataset associated with meta-analysis study.
DOI: 10.6084/m9.figshare.21214205
title: Ab initio B3LYP/6-31+G* charges, dipole and energies for CH3SH quantum center (protonated and deprotonated)

description: Gaussian output files
DOI: 10.34740/kaggle/dsv/4255270
title: YouTube Daily
DOI: 10.17864/1947.000421
title: Material specific dataset covering information for decorated Iron Age artefacts

description: This dataset includes recorded information for five material types: ceramic pottery, antler/bone combs, stone, wood, and metal. This information has been accumulated into four Access databases [Pottery, Antler/Bone, Stone/Wood, and Metal]. Stone and Wood have been combined into one database for recording due to the number of examples compared to the other material sources. All four of these databases include information covering General Information [site name, type of site, county, regional zone, period of occupation], Context [previous artefact number, location on site, date of object], Material [general material, form type, inclusions, colour, condition], Decoration [general typology, location on object, direction on decoration, general decoration, motifs], Decorative Techniques, and Reference Information. This information was collected from object descriptions and illustrations within site reports and previous literature. In order to avoid any overlap, all of the artefacts were re-labelled based on the material and order in which they have been recorded within my database. My final database includes a Reference Database. This database includes a list of all materials covered within my previous Access databases, their current artefact numbers, and a citation of their original sources. This dataset was created to determine the visual qualities of different artefacts based on their material associations; their similarities, differences, and connections to form, function, and decoration. In turn, these databases were used within my PhD thesis to highlight the potential social connections between different groups and regions within southern Britain during the Iron Age.
DOI: 10.6084/m9.figshare.21214316
title: structure of TRX-TXNIP - from 4LL1 pdb file

description: pdb structure from 4LL1 pdb file (https://www.rcsb.org/structure/4LL1)
DOI: 10.6084/m9.figshare.21214316.v1
title: structure of TRX-TXNIP - from 4LL1 pdb file

description: pdb structure from 4LL1 pdb file (https://www.rcsb.org/structure/4LL1)
DOI: 10.5258/soton/d2364
title: Dataset supporting the publication "Mean flow of turbulent boundary layers over porous substrates"

description: This dataset supports the following publication: L. B. Esteban, E. Rodriguez-Lopez, M. A. Ferreira and B. Ganapathisubramani, "Mean flow of turbulent boundary layers over porous substrates", Phys. Rev. Fluids, 2022 DOI: 10.1103/PhysRevFluids.00.004600 This dataset contains .mat files which has all the mean velocity profiles as well as the information on other scaling quantities such as skin-friction velocity, boundary layer thickness, kinematic viscosity and free stream velocity to obtain the different plots presented in the paper. The data is presented in three different .mat files, one for each of the three different porous/permeable substrates examined in the study. Measurements of turbulent boundary layer flow over all three porous substrates (10PPI, 45PPI and 90PPI) with two different thicknesses (3mm and 15 mm) have been performed using hot-wire anemometry and skin-friction drag-balance. The data presented provides profiles of mean velocity obtained using hot-wire measurements for the three cases at three different freestream velocities (10 m/s, 18 m/s and 26 m/s). The specifics of the data is self-evident upon using the data from the three different mat files.
DOI: 10.6084/m9.figshare.20510598.v1
title: SLaP mapper analysis of Blastocrithidia

description: SLaP mapper (http://www.stevekellylab.com/software/slap) analysis of identified trans-splicing and polyadenylation sites in Blastocrithidia nonstop genome, using regular transcriptome library and 3'-enriched RNA library. Also, the analyses made in the same method with a regular transcriptome library are provided for Novymonas esmeraldas and Blechomonas ayalai as a reference.
DOI: 10.6084/m9.figshare.20510598
title: SLaP mapper analysis of Blastocrithidia nonstop

description: SLaP mapper (http://www.stevekellylab.com/software/slap) analysis of identified trans-splicing and polyadenylation sites in Blastocrithidia nonstop genome, using regular transcriptome library and 3'-enriched RNA library. Also, the analyses made in the same method with a regular transcriptome library are provided for Novymonas esmeraldas and Blechomonas ayalai as a reference.
DOI: 10.6084/m9.figshare.20510598.v2
title: SLaP mapper analysis of Blastocrithidia

description: SLaP mapper (http://www.stevekellylab.com/software/slap) analysis of identified trans-splicing and polyadenylation sites in Blastocrithidia nonstop genome, using regular transcriptome library and 3'-enriched RNA library. Also, the analyses made in the same method with a regular transcriptome library are provided for Novymonas esmeraldas and Blechomonas ayalai as a reference.
DOI: 10.6084/m9.figshare.21214385
title: Cuenca_DB_2022

description: Excel database with the geographic coordinates and dendrological information of the trees taken as samples for their datation. The area at issue is located in the surroundings of the Toba Water Reservoir in Cuenca, Spain
DOI: 10.6084/m9.figshare.21214385.v1
title: Cuenca_DB_2022

description: Excel database with the geographic coordinates and dendrological information of the trees taken as samples for their datation. The area at issue is located in the surroundings of the Toba Water Reservoir in Cuenca, Spain
DOI: 10.6084/m9.figshare.20749387
title: Frantova et al_Supplement Material.pdf

description: The file contains supplement material for the article - <strong>Different Drought Tolerance Strategy of Wheat Varieties in Spike Architecture</strong>.
DOI: 10.6084/m9.figshare.20749387.v1
title: Frantova et al_Supplement Material.pdf

description: The file contains supplement material for the article - <strong>Different Drought Tolerance Strategy of Wheat Varieties in Spike Architecture</strong>.
DOI: 10.6084/m9.figshare.20254659
title: Anticodon stem length analysis in GtRNAdb

description: This dataset shows the length in nucleotide pairs of anticodon stem of tRNAs available in GtRNAdb.
DOI: 10.6084/m9.figshare.20254659.v2
title: Anticodon stem length analysis in GtRNAdb

description: This dataset shows the length in nucleotide pairs of anticodon stem of tRNAs available in GtRNAdb.
DOI: 10.6084/m9.figshare.20254659.v1
title: Anticodon stem length analysis in GtRNAdb

description: This dataset shows the length in nucleotide pairs of anticodon stem of tRNAs available in GtRNAdb.
DOI: 10.5281/zenodo.4266379
title: Dataset related to article "CCR5 and ACKR2 show distinct constitutive and agonist-induced signaling properties"

description: This record contains raw data related to article "CCR5 and ACKR2 show distinct constitutive and agonist-induced signaling properties" ACKR2 is an atypical chemokine receptor structurally uncoupled from G proteins and unable to activate those signaling pathways used by conventional chemokine receptors to promote cell migration. Nevertheless, ACKR2 regulates inflammation and immune responses by shaping chemokine gradients in tissues by means scavenging inflammatory chemokines. To investigate the signaling pathways downstream ACKR2, a quantitative SILAC-based phosphoproteomic analysis was carried out in an inducible cell model expressing ACKR2 or its conventional counterpart CCR5, stimulated or not with the common agonist CCL3L1. A comparative analysis of the phosphoproteomes revealed unique constitutive and agonist-dependent phosphorylation signatures. ACKR2-responsive phosphosites were enriched for pathways involving mTOR signaling networks, which resulted unrelated to receptor scavenger properties. In conclusion, mapping of phosphorylation events indicated that conventional and atypical chemokine receptors differ for both constitutive and agonist-dependent signaling properties, and revealed that ACKR2 expression influences the mTOR pathway, suggesting its potential role in the regulation of cell metabolism
DOI: 10.5281/zenodo.7115932
title: Dataset related to article "Phosphoproteomic mapping of CCR5 and ACKR2 signaling properties"

description: This record contains raw data related to article "Phosphoproteomic mapping of CCR5 and ACKR2 signaling properties" ACKR2 is an atypical chemokine receptor structurally uncoupled from G proteins and unable to activate those signaling pathways used by conventional chemokine receptors to promote cell migration. Nevertheless, ACKR2 regulates inflammation and immune responses by shaping chemokine gradients in tissues by means scavenging inflammatory chemokines. To investigate the signaling pathways downstream ACKR2, a quantitative SILAC-based phosphoproteomic analysis coupled to systems biology approaches based on network analysis was carried out in a HEK293 cell model expressing ACKR2 or its conventional counterpart CCR5, stimulated or not with the common agonist CCL3L1 for short (3 min) and long (30 min) time points. As expected, many of the identified proteins are known to participate in conventional signal transduction pathways and in the regulation of cytoskeleton dynamics. However, our analyses revealed unique phosphorylation and network signatures, suggesting roles for ACKR2 other than its scavenger activity. In conclusion, mapping of phosphorylation events at holistic level indicated that conventional and atypical chemokine receptors differ for signaling properties and provide an unprecedented level of detail of chemokine receptor signaling aimed at identifying potential targets for regulation of ACKR2 and CCR5 function.
DOI: 10.5281/zenodo.4266378
title: Dataset related to article "Phosphoproteomic mapping of CCR5 and ACKR2 signaling properties"

description: This record contains raw data related to article "Phosphoproteomic mapping of CCR5 and ACKR2 signaling properties" ACKR2 is an atypical chemokine receptor structurally uncoupled from G proteins and unable to activate those signaling pathways used by conventional chemokine receptors to promote cell migration. Nevertheless, ACKR2 regulates inflammation and immune responses by shaping chemokine gradients in tissues by means scavenging inflammatory chemokines. To investigate the signaling pathways downstream ACKR2, a quantitative SILAC-based phosphoproteomic analysis coupled to systems biology approaches based on network analysis was carried out in a HEK293 cell model expressing ACKR2 or its conventional counterpart CCR5, stimulated or not with the common agonist CCL3L1 for short (3 min) and long (30 min) time points. As expected, many of the identified proteins are known to participate in conventional signal transduction pathways and in the regulation of cytoskeleton dynamics. However, our analyses revealed unique phosphorylation and network signatures, suggesting roles for ACKR2 other than its scavenger activity. In conclusion, mapping of phosphorylation events at holistic level indicated that conventional and atypical chemokine receptors differ for signaling properties and provide an unprecedented level of detail of chemokine receptor signaling aimed at identifying potential targets for regulation of ACKR2 and CCR5 function.
DOI: 10.6084/m9.figshare.20105417
title: MS analysis of B. nonstop proteins

description: •Mascot error tolerant (Mascot server) search and dependent peptides search (MaxQuant) has been done •Mascot •2nd replicate search used only •takes into account <strong>whole protein sequences of identified proteins </strong>and searches them with relaxed search conditions like semispecific enzyme specificity, all modifications etc. •MaxQuant •all replicates were used •takes into account <strong>identified peptides </strong>and searches them with all set modifications •search results filtering •Mascot: ion score &gt;20 •8652 peptide spectrum matches used after the filtration •MaxQuant: PEP &lt;0.05 (i.e., local FDR 5%), peptide length difference = 0 •25961 peptide features (3D peaks in the LC-MS profile) used after the filtration
DOI: 10.6084/m9.figshare.20105417.v1
title: MS analysis of B. nonstop proteins

description: •Mascot error tolerant (Mascot server) search and dependent peptides search (MaxQuant) has been done •Mascot •2nd replicate search used only •takes into account <strong>whole protein sequences of identified proteins </strong>and searches them with relaxed search conditions like semispecific enzyme specificity, all modifications etc. •MaxQuant •all replicates were used •takes into account <strong>identified peptides </strong>and searches them with all set modifications •search results filtering •Mascot: ion score &gt;20 •8652 peptide spectrum matches used after the filtration •MaxQuant: PEP &lt;0.05 (i.e., local FDR 5%), peptide length difference = 0 •25961 peptide features (3D peaks in the LC-MS profile) used after the filtration
DOI: 10.6084/m9.figshare.20101949
title: Analysis of 3'UTRs in B. nonstop

description: To identify the 3'UTRs, we assembled the transcripts de novo using Trinity (https://doi.org/10.1038/nprot.2013.084) with both standard and 3'enriched transcriptomic reads. Then we mapped transcripts back to the genome using BLAST and chose those transcripts that were identical to the genome but had one or more of A at the 3' end of the transcript and analysed them using custom Python scripts.
DOI: 10.6084/m9.figshare.20101949.v7
title: Analysis of 3'UTRs in B. nonstop

description: To identify the 3'UTRs, we assembled the transcripts de novo using Trinity (https://doi.org/10.1038/nprot.2013.084) with both standard and 3'enriched transcriptomic reads. Then we mapped transcripts back to the genome using BLAST and chose those transcripts that were identical to the genome but had one or more of A at the 3' end of the transcript and analysed them using custom Python scripts.
DOI: 10.6084/m9.figshare.20101949.v6
title: Analysis of 3'UTRs in B. nonstop

description: To identify the 3'UTRs, we assembled the transcripts de novo using Trinity (https://doi.org/10.1038/nprot.2013.084) with both standard and 3'enriched transcriptomic reads. Then we mapped transcripts back to the genome using BLAST and chose those transcripts that were identical to the genome but had one or more of A at the 3' end of the transcript and analysed them using custom Python scripts.
DOI: 10.6084/m9.figshare.20101922
title: Analysis of eRF1, UPF1/2 and tRNAs in ciliate genomes

description: <strong>Analysis of genetic code, eRF1 and presence of UPF proteins in ciliates.</strong> Genomes and transcriptomes of ciliates were retrieved from NCBI and EukProt. Schematic phylogenetic tree is based on 18S phylogenetic analyses performed previously (Boscaro et al. 2018, Lian et al. 2020, Tsai et al. 2022). Major ciliate clades are depicted next to species names. Dataset shows the kind of data used for particular species as explained above the figure. Genetic code was retrieved from NCBI Taxonomy database (https://www.ncbi.nlm.nih.gov/taxonomy) and/or from a previous study (Swart et al. 2016). In genomic datasets, all tRNAs were predicted by Aragorn (Laslett and Canback 2004) with default settings. Presence of stop-codon recognizing tRNAs is marked by “+”, while their absence by “-“; unknown presence in other datasets is marked by “?”. eRF1 and UPF proteins were identified by BLAST 2.11.0+ (Altschul et al 1990), number indicates the count of homologues.
DOI: 10.6084/m9.figshare.20101922.v3
title: Analysis of eRF1, UPF1/2 and tRNAs in ciliate genomes

description: <strong>Analysis of genetic code, eRF1 and presence of UPF proteins in ciliates.</strong> Genomes and transcriptomes of ciliates were retrieved from NCBI and EukProt. Schematic phylogenetic tree is based on 18S phylogenetic analyses performed previously (Boscaro et al. 2018, Lian et al. 2020, Tsai et al. 2022). Major ciliate clades are depicted next to species names. Dataset shows the kind of data used for particular species as explained above the figure. Genetic code was retrieved from NCBI Taxonomy database (https://www.ncbi.nlm.nih.gov/taxonomy) and/or from a previous study (Swart et al. 2016). In genomic datasets, all tRNAs were predicted by Aragorn (Laslett and Canback 2004) with default settings. Presence of stop-codon recognizing tRNAs is marked by “+”, while their absence by “-“; unknown presence in other datasets is marked by “?”. eRF1 and UPF proteins were identified by BLAST 2.11.0+ (Altschul et al 1990), number indicates the count of homologues.
DOI: 10.6084/m9.figshare.20101922.v2
title: Analysis of eRF1, UPF1/2 and tRNAs in ciliate genomes

description: <strong>Analysis of genetic code, eRF1 and presence of UPF proteins in ciliates.</strong> Genomes and transcriptomes of ciliates were retrieved from NCBI and EukProt. Schematic phylogenetic tree is based on 18S phylogenetic analyses performed previously (Boscaro et al. 2018, Lian et al. 2020, Tsai et al. 2022). Major ciliate clades are depicted next to species names. Dataset shows the kind of data used for particular species as explained above the figure. Genetic code was retrieved from NCBI Taxonomy database (https://www.ncbi.nlm.nih.gov/taxonomy) and/or from a previous study (Swart et al. 2016). In genomic datasets, all tRNAs were predicted by Aragorn (Laslett and Canback 2004) with default settings. Presence of stop-codon recognizing tRNAs is marked by “+”, while their absence by “-“; unknown presence in other datasets is marked by “?”. eRF1 and UPF proteins were identified by BLAST 2.11.0+ (Altschul et al 1990), number indicates the count of homologues.
DOI: 10.5281/zenodo.7113472
title: Re-Training Extension of the Benchmark for Automatic Glottis Segmentation (BAGLS-RT)

description: BAGLS-RT is an extension of the BAGLS dataset (DOI 10.5281/zenodo.3762320) intended for (re-)training glottis segmentation models.
DOI: 10.5281/zenodo.7113473
title: Re-Training Extension of the Benchmark for Automatic Glottis Segmentation (BAGLS-RT)

description: BAGLS-RT is an extension of the BAGLS dataset (DOI 10.5281/zenodo.3762320) intended for (re-)training glottis segmentation models.
DOI: 10.5281/zenodo.7100535
title: Biases in LWP adjustments, code and dataset

description: Code and source data to reproduce the figures in article: Antti Arola, Antti Lipponen, Pekka Kolmonen, Timo H. Virtanen, Nicolas Bellouin, Daniel P. Grosvenor, Edward Gryspeerdt, Johannes Quaas, and Harri Kokkola: Aerosol Effects on Clouds Are Concealed by Natural Cloud Heterogeneity and Satellite Retrieval Errors, submitted to Nature Communications, 2022.
description: The code consists of short Matlab scripts which are comprehensively commented and straightforward to use. A separate user guide or installation guide is not needed. Matlab is required for running the codes, but no toolboxes or other installation is required. The codes have been tested with Matlab version 2017b. Running the codes takes a few minutes at the most on a regular laptop. Input data and comprehensive output examples are provided.
DOI: 10.6084/m9.figshare.21214307.v1
title: Co_IP_MS_Ssr1238_SfGFP_05_2022

description: Raw file of the Co-IP-MS experiment from 05.2022 of Ssr1238 and SfGFP. Master Thesis Anna Miucci
DOI: 10.6084/m9.figshare.21214307.v2
title: Co_IP_MS_Ssr1238_SfGFP_05_2022

description: Raw file of the Co-IP-MS experiment from 05.2022 of Ssr1238 and SfGFP. Master Thesis Anna Miucci