cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7105318
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: 10.34740/kaggle/ds/2507471
title: Work Life Balance of IT Employees during COVID-19
DOI: 10.6084/m9.figshare.18251876
title: Extended Data 1: tRNAs of Blastocrithidia nonstop

description: Transfer RNAs (tRNAs) were predicted by tRNAScan-SE v2.0.5 (Chan and Lowe 2019) and Aragorn (Laslett and Canback 2014).
DOI: 10.6084/m9.figshare.18251876.v2
title: Extended Data 1: tRNAs of Blastocrithidia nonstop

description: Transfer RNAs (tRNAs) were predicted by tRNAScan-SE v2.0.5 (Chan and Lowe 2019) and Aragorn (Laslett and Canback 2014).
DOI: 10.6084/m9.figshare.18251876.v1
title: Extended Data 1: tRNAs of Blastocrithidia nonstop

description: Transfer RNAs (tRNAs) were predicted by tRNAScan-SE v2.0.5 (Chan and Lowe 2019) and Aragorn (Laslett and Canback 2014).
DOI: 10.6084/m9.figshare.17934200
title: Extended Data 3: tRNAseq analysis of Blastocrithidia nonstop

description: <b>Individual alignments corresponding to each identified tRNA species in Blastocrithidia nonstop.</b><br>For tRNA sequencing, Illumina sequencing of cDNA of cytosolic RNA fraction corresponding to tRNAs was used. Cytosolic RNA fraction was obtained as described previously (Paris et al. 2021) and submitted to Arraystar, Inc. (Rockville, MD, USA) for tRNA sequencing analysis. Before the sequencing experiment, the integrity and quantity control of each RNA sample using agarose gel electrophoresis and the NanodropTM instrument was performed. For tRNA isolation over 2μg total RNA was resolved on urea-polyacrylamide gels and recovered within a size window of 60-100 nt for tRNA followed by coupled nucleotide demethylation and Hydro-tRNAseq method to further improve the efficiency of tRNA-seq library preparation, containing the following treatments: a) m1A and m3C demethylation of purified tRNA; b) limited alkaline hydrolysis of demethylated tRNA by carbonate buffer; c) calf intestinal phosphatase (CIP) dephosphorylation and then T4 polynucleotide kinase (T4 PNK) re-phosphorylation of the partially hydrolyzed tRNA fragments. Fragments of ∼19-35nt for partially hydrolyzed and re-phosphorylated tRNA were converted to small RNA sequencing libraries using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® kit.The libraries were qualified and absolutely quantified using Agilent BioAnalyzer 2100. For tRNA sequencing on Illumina NextSeq 500 instrument, the sequencing type was 50-bp single-read.The Illumina sequencing yielded 7,912,517 reads with length of 50 nt. The reads were adapter- and quality-trimmed and mapped on the B. nonstop genome assembly to filter out low-quality and contaminating sequences. The 77 % of the trimmed reads that were successfully aligned on the assembly were used for further analysis.Firstly, vsearch v2.5.2 (Rognes et al., 2016) was used to cluster identical reads. 22,436 read clusters were obtained. To identify the origin of the sequences, clusters were aligned to B. nonstop tRNA and rRNA gene database using blastn from BLAST v.2.3.0+ (here and later in the text) (Camacho et al., 2009). The clusters together with their best BLAST hit (i.e., corresponding tRNA) were split into individual fasta files, and each dataset was aligned using MAFFT with “ --localpair --op 10 --ep 0 --maxiterate 1000” parameters. Each of the resulting alignments was manually analysed in Aliview (Larsson, 2014).<br>
DOI: 10.6084/m9.figshare.17934200.v1
title: Extended Data 3: tRNAseq analysis of Blastocrithidia nonstop

description: <b>Individual alignments corresponding to each identified tRNA species in Blastocrithidia nonstop.</b><br>For tRNA sequencing, Illumina sequencing of cDNA of cytosolic RNA fraction corresponding to tRNAs was used. Cytosolic RNA fraction was obtained as described previously (Paris et al. 2021) and submitted to Arraystar, Inc. (Rockville, MD, USA) for tRNA sequencing analysis. Before the sequencing experiment, the integrity and quantity control of each RNA sample using agarose gel electrophoresis and the NanodropTM instrument was performed. For tRNA isolation over 2μg total RNA was resolved on urea-polyacrylamide gels and recovered within a size window of 60-100 nt for tRNA followed by coupled nucleotide demethylation and Hydro-tRNAseq method to further improve the efficiency of tRNA-seq library preparation, containing the following treatments: a) m1A and m3C demethylation of purified tRNA; b) limited alkaline hydrolysis of demethylated tRNA by carbonate buffer; c) calf intestinal phosphatase (CIP) dephosphorylation and then T4 polynucleotide kinase (T4 PNK) re-phosphorylation of the partially hydrolyzed tRNA fragments. Fragments of ∼19-35nt for partially hydrolyzed and re-phosphorylated tRNA were converted to small RNA sequencing libraries using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® kit.The libraries were qualified and absolutely quantified using Agilent BioAnalyzer 2100. For tRNA sequencing on Illumina NextSeq 500 instrument, the sequencing type was 50-bp single-read.The Illumina sequencing yielded 7,912,517 reads with length of 50 nt. The reads were adapter- and quality-trimmed and mapped on the B. nonstop genome assembly to filter out low-quality and contaminating sequences. The 77 % of the trimmed reads that were successfully aligned on the assembly were used for further analysis.Firstly, vsearch v2.5.2 (Rognes et al., 2016) was used to cluster identical reads. 22,436 read clusters were obtained. To identify the origin of the sequences, clusters were aligned to B. nonstop tRNA and rRNA gene database using blastn from BLAST v.2.3.0+ (here and later in the text) (Camacho et al., 2009). The clusters together with their best BLAST hit (i.e., corresponding tRNA) were split into individual fasta files, and each dataset was aligned using MAFFT with “ --localpair --op 10 --ep 0 --maxiterate 1000” parameters. Each of the resulting alignments was manually analysed in Aliview (Larsson, 2014).<br>
DOI: 10.15129/59c261cb-cdb7-4888-acfb-860e717c5149
title: Data for: "Mixing and flow-induced nanoprecipitation for morphology control of silk fibroin self-assembly"

description: Semi-batch and micro-mixers are promising platforms for nanoprecipitation of aqueous silk fibroin with aqueous-miscible solvents under conditions of polymer flow. Although the shear rates experienced by regenerated silk feeds and the aqueous–organic mixing time are critical for process scalability, their influence on the properties of the resulting assemblies remains poorly understood. Here, we implement low and high shear semi-batch systems and low and high shear micro-mixer systems to investigate the roles of shear and mixing in nanoprecipitation of the silk biopolymer. This work facilitates the modulation of silk nanoparticle shape and aids the transition of sustainable silk nanomedicines from lab to pilot-scale technology. All equipment, software and measurements are detailed in the Readme file. Raw and processed data pertaining to each figure and table are documented in the respective zipped folders. This dataset has been corrected as follows: 1. Copy errors in the zeta potential data for the semi-batch system in Figure 4, Figure S3 (Folder: Figure4_FigureS3_Conc_Shear.zip) at 0 rpm and 400 rpm have been corrected in the files contained within the sub-folders named Raw Data, Statistics, and Images. Copy error in the PDI data for the semi-batch system in Figure 4, Figure S3 (Folder: Figure4_FigureS3_Conc_Shear.zip) at 0 rpm has been corrected in the file contained within the sub-folder named Raw Data. 2. Copy errors in the SEM images for the semi-batch system in Figure 5 (Folder: Figure5_SEM.zip) have been corrected in the files contained within the sub-folder Images. (Sept 2022)
DOI: 10.25625/nok6nn/4tbdpi
title: LAI_A02.tab

description: :unav
DOI: 10.25625/nok6nn/5hnh3n
title: Below Canopy Surface temperature_A02.tab

description: Below canopy surface temperature
DOI: 10.25625/nok6nn/q9cjzb
title: Below Canopy Surface temperature_A02.tab

description: Below Canopy Surface Temperature
DOI: 10.25625/nok6nn
title: Landscape Assessment (A02) Leaf Area Index (LAI)

description: :unav
DOI: 10.25625/nok6nn/cquev3
title: Below Canopy Surface temperature_A02.tab

description: Below Canopy Surface Temperature
DOI: 10.5283/epub.52944
title: aPKC knockout
DOI: 10.5283/epub.52947
title: Baz knockout in all neurons
DOI: 10.5283/epub.52948
title: FoxP cond knockout
DOI: 10.5283/epub.52949
title: GMR11F02-GAL4 x Cas9gFoxP
DOI: 10.5281/zenodo.5906867
title: Exploring the conformational space within phase transfer catalysts: computational methods benchmarking - Supporting information

description: Supporting information for Exploring the conformational space within phase transfer catalysts: computational methods benchmarking. In this study, a complete exploration of the conformational space within phase transfer catalysts by means of computational methods benchmarking is presented. For this particular research work, only the most applied conformational analysis approaches have been chosen to characterise different Cinchona alkaloid-based phase transfer catalysts. This particular benchmarking study aims to rigorously compare the performance of different conformational methods, determining the strengths of each method and to provide recommendations regarding suitable choices of methods for an analysis. <strong> </strong>
DOI: 10.5281/zenodo.6565941
title: Exploring the conformational space within phase transfer catalysts: computational methods benchmarking - Supporting information

description: Supporting information for Exploring the conformational space within phase transfer catalysts: computational methods benchmarking. In this study, a complete exploration of the conformational space within phase transfer catalysts by means of computational methods benchmarking is presented. For this particular research work, only the most applied conformational analysis approaches have been chosen to characterise different Cinchona alkaloid-based phase transfer catalysts. This particular benchmarking study aims to rigorously compare the performance of different conformational methods, determining the strengths of each method and to provide recommendations regarding suitable choices of methods for an analysis. <strong> </strong>
DOI: 10.5281/zenodo.6574373
title: Exploring the conformational space within phase transfer catalysts: computational methods benchmarking - Supporting information

description: Supporting information for Exploring the conformational space within phase transfer catalysts: computational methods benchmarking. In this study, a complete exploration of the conformational space within phase transfer catalysts by means of computational methods benchmarking is presented. For this particular research work, only the most applied conformational analysis approaches have been chosen to characterise different Cinchona alkaloid-based phase transfer catalysts. This particular benchmarking study aims to rigorously compare the performance of different conformational methods, determining the strengths of each method and to provide recommendations regarding suitable choices of methods for an analysis. <strong> </strong>
DOI: 10.5281/zenodo.5906866
title: Efficiency and suitability when exploring the conformational space of phase transfer catalysts - Supporting information

description: Supporting information for Efficiency and suitability when exploring the conformational space of phase transfer catalysts. In this study, a complete exploration of the conformational space within phase transfer catalysts by means of computational methods benchmarking is presented. For this particular research work, only the most applied conformational analysis approaches have been chosen to characterise different Cinchona alkaloid-based phase transfer catalysts. This particular benchmarking study aims to rigorously compare the performance of different conformational methods, determining the strengths of each method and to provide recommendations regarding suitable choices of methods for an analysis. <strong> </strong>
DOI: 10.5281/zenodo.6574414
title: Exploring the conformational space within phase transfer catalysts: computational methods benchmarking - Supporting information

description: Supporting information for Exploring the conformational space within phase transfer catalysts: computational methods benchmarking. In this study, a complete exploration of the conformational space within phase transfer catalysts by means of computational methods benchmarking is presented. For this particular research work, only the most applied conformational analysis approaches have been chosen to characterise different Cinchona alkaloid-based phase transfer catalysts. This particular benchmarking study aims to rigorously compare the performance of different conformational methods, determining the strengths of each method and to provide recommendations regarding suitable choices of methods for an analysis. <strong> </strong>
DOI: 10.5281/zenodo.6906824
title: Exploring the conformational space within phase transfer catalysts: computational methods benchmarking - Supporting information

description: Supporting information for Exploring the conformational space within phase transfer catalysts: computational methods benchmarking. In this study, a complete exploration of the conformational space within phase transfer catalysts by means of computational methods benchmarking is presented. For this particular research work, only the most applied conformational analysis approaches have been chosen to characterise different Cinchona alkaloid-based phase transfer catalysts. This particular benchmarking study aims to rigorously compare the performance of different conformational methods, determining the strengths of each method and to provide recommendations regarding suitable choices of methods for an analysis. <strong> </strong>
DOI: 10.5281/zenodo.7116024
title: Efficiency and suitability when exploring the conformational space of phase transfer catalysts - Supporting information

description: Supporting information for Efficiency and suitability when exploring the conformational space of phase transfer catalysts. In this study, a complete exploration of the conformational space within phase transfer catalysts by means of computational methods benchmarking is presented. For this particular research work, only the most applied conformational analysis approaches have been chosen to characterise different Cinchona alkaloid-based phase transfer catalysts. This particular benchmarking study aims to rigorously compare the performance of different conformational methods, determining the strengths of each method and to provide recommendations regarding suitable choices of methods for an analysis. <strong> </strong>
DOI: 10.5283/epub.52950
title: GMR20A02 x tetoxE/Kir
DOI: 10.5281/zenodo.7101915
title: Efficiency and suitability when exploring the conformational space of phase transfer catalysts - Supporting information

description: Supporting information for Efficiency and suitability when exploring the conformational space of phase transfer catalysts. In this study, a complete exploration of the conformational space within phase transfer catalysts by means of computational methods benchmarking is presented. For this particular research work, only the most applied conformational analysis approaches have been chosen to characterise different Cinchona alkaloid-based phase transfer catalysts. This particular benchmarking study aims to rigorously compare the performance of different conformational methods, determining the strengths of each method and to provide recommendations regarding suitable choices of methods for an analysis. <strong> </strong>
DOI: 10.5281/zenodo.7037187
title: Demo data and models for: Automated speech detection in eco-acoustic data enables privacy protection and human disturbance quantification

description: Folder containing a <strong>demo dataset</strong> and the <strong>model weights</strong> resulting from the ecoVAD pipeline. The data contained in this folder allows for full reproducibility of the pipeline described on the ecoVAD GitHub repository. If you have any questions or issues with the dataset, please open an issue on the ecoVAD GitHub repository.
DOI: 10.5281/zenodo.7037186
title: Demo data and models for: Automated speech detection in eco-acoustic data enables privacy protection and human disturbance quantification

description: Folder containing a <strong>demo dataset</strong> and the <strong>model weights</strong> resulting from the ecoVAD pipeline. The data contained in this folder allows for full reproducibility of the pipeline described on the ecoVAD GitHub repository. If you have any questions or issues with the dataset, please open an issue on the ecoVAD GitHub repository.
DOI: 10.6084/m9.figshare.21214460
title: SFS-based admixture history reconstruction

description: Zipped folder containing all input files, site frequency spectra and accessory scripts for admixture history reconstruction using fastsimcoal2 in Nouhaud et al. (https://doi.org/10.1101/2022.01.16.476493). See README files for more information on the content of each folder.
DOI: 10.5281/zenodo.7116041
title: IEA 2020 TIMSS 2019 (Example items, highlighted Portugal) International Results in Mathematics and Science

description: IEA 2020 TIMSS 2019 (Example items, highlighted Portugal) International Results in Mathematics and Science Grades 4 and 8, Mathematics and Science
DOI: 10.5281/zenodo.7116040
title: IEA 2020 TIMSS 2019 (Example items, highlighted Portugal) International Results in Mathematics and Science

description: IEA 2020 TIMSS 2019 (Example items, highlighted Portugal) International Results in Mathematics and Science Grades 4 and 8, Mathematics and Science
DOI: 10.5281/zenodo.7116045
title: IG receptor germline set for species: Mouse subgroup: AKR/J set_name: AKR/J IGKV

description: Germline Reference set published on the Open Germline Receptor Database (OGRDB)
DOI: 10.5281/zenodo.7116044
title: IG receptor germline set for species: Mouse subgroup: AKR/J set_name: AKR/J IGKV

description: Germline Reference set published on the Open Germline Receptor Database (OGRDB)
DOI: 10.5281/zenodo.7116047
title: IG receptor germline set for species: Mouse subgroup: AKR/J set_name: AKR/J IGLV

description: Germline Reference set published on the Open Germline Receptor Database (OGRDB)
DOI: 10.5281/zenodo.7116046
title: IG receptor germline set for species: Mouse subgroup: AKR/J set_name: AKR/J IGLV

description: Germline Reference set published on the Open Germline Receptor Database (OGRDB)
DOI: 10.5281/zenodo.7116049
title: IG receptor germline set for species: Mouse subgroup: BALB/c set_name: BALB/c IGH

description: Germline Reference set published on the Open Germline Receptor Database (OGRDB)
DOI: 10.5281/zenodo.7116048
title: IG receptor germline set for species: Mouse subgroup: BALB/c set_name: BALB/c IGH

description: Germline Reference set published on the Open Germline Receptor Database (OGRDB)
DOI: 10.5281/zenodo.7116063
title: IG receptor germline set for species: Mouse subgroup: BALB/c/ByJ set_name: BALB/cByJ IGKV

description: Germline Reference set published on the Open Germline Receptor Database (OGRDB)
DOI: 10.5281/zenodo.7116062
title: IG receptor germline set for species: Mouse subgroup: BALB/c/ByJ set_name: BALB/cByJ IGKV

description: Germline Reference set published on the Open Germline Receptor Database (OGRDB)
DOI: 10.5281/zenodo.7116067
title: IG receptor germline set for species: Mouse subgroup: C3H/HeJ set_name: C3H/HeJ IGKV

description: Germline Reference set published on the Open Germline Receptor Database (OGRDB)
DOI: 10.5281/zenodo.7116066
title: IG receptor germline set for species: Mouse subgroup: C3H/HeJ set_name: C3H/HeJ IGKV

description: Germline Reference set published on the Open Germline Receptor Database (OGRDB)
DOI: 10.6084/m9.figshare.21210566.v1
title: Excel files

description: This folder contains Excel files with measurments of shark bodies (metadata) and results from denticle detection and analysis.
DOI: 10.5281/zenodo.5718424
title: Spectroscopic ellipsometry mapping of PAAO (AJ-3-04-20 sample)

description: Spectroscopic ellipsometry measurement data obtained from the porous anodized aluminum oxide (PAAO). The sample was made by anodization of aluminum monocrystal in 0.3 mol/L oxalic acid at 40 V for 4 minutes and 8 seconds. The measurements were carried out at 20 × 20 locations covering all of the sample surface (approximately 4.8 × 4.8 mm<sup>2</sup>). The coordinates of each of 400 locations are available in "mapping_points.csv" file. All measurement data is also included in a single "AJ-3-04-20 Ellipsometry Mapping Measurements.rar" file. Ellipsometer: rotating compensator GES5-E (Semilab). Light source: 75 W xenon short arc lamp with 185-2000 nm wavelength spectrum. Detector: UV-Vis CCD with 0.8 nm resolution. Spectral range: approximately 230-960 nm. Light incidence angles: 50°, 55°, 60°, 65°, 70°, 75°. Light beam size: microspot (365 × 470 μm<sup>2</sup> at 75° angle of incidence). The same sample was also measured using the same spectroscopic ellipsometry method after being covered with gold nanoparticles. The data can be found here: https://doi.org/10.5281/zenodo.7115166
description: The research was carried out under postdoctoral project "Patterned hybrid multilayer films for optical sensors", No. 1.1.1.2/VIAA/4/20/615.