cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10497766
title: Cut&RUN ACLY Control Primary mouse hepatocytes

description: Pre-processed CUT&RUN files for ACLY and GCN5 were normalized to effective genome size.For each file, background signal was calculated in heterochromatin regions using negativeATAC-seq signal mask, and subsequently removed from the overall coverage. CUT&RUNcoverage heatmaps and profiles around the TSS of expressed genes were produced usingcomputeMatrix, plotHeatmap functions from deepTools v3.5.2 package51. The list of expressedgenes was inferred from the mouse primary hepatocyte RNA-seq data using variancestabilizing transformation of the expression matrix and selecting genes with values > 0 for allreplicates. Peak calling on each replicate was performed using MACS252 v.2.2.7.1, and theconsensus overlapping peaks between all replicates were considered as reproducible for thecorresponding dataset. Number of overlapping peaks between conditions was calculated in Rwith subsetByOverlaps (GenomicRanges v.1.54.1)57, and nearest genes were annotated topeaks using biomaRt.For the correlation of ChIP peaks with gene expression, all expressed genes derived fromRNA-seq data were divided into 4 equal groups based on their expression levels (quartiles (Q)1 to 4). Promoter regions of those genes (± 1kb TSS) were extracted using the Rsubreadv.2.16.0)59 package, and the CUT&RUN signal was quantified with multiBigwigSummary fromdeepTools package
DOI: 10.5281/zenodo.10593259
title: ПОЛИТИЧЕСКАЯ КУЛЬТУРА-ФАКТОР ПОЛИТИЧЕСКОГО РАЗВИТИЕ
DOI: 10.5281/zenodo.10593260
title: ПОЛИТИЧЕСКАЯ КУЛЬТУРА-ФАКТОР ПОЛИТИЧЕСКОГО РАЗВИТИЕ
DOI: 10.6084/m9.figshare.25111781
title: Data: Pilfering personalities: effects of small mammal personality on cache pilferage

description: These data and code accompany the paper: "Humphreys & Mortelliti, 2024. Pilfering personalities: effects of small mammal personality on cache pilferage." These data can be used to replicate all main analyses in the paper. These data are not intended for use in other publications. Please contact the authors if you would like to collaborate on a project using these data or if additional comments or questions arise: Brigit Humphreys (brigit.humphreys@maine.edu)Alessio Mortelliti (alessio.mortelliti@maine.edu)
DOI: 10.5281/zenodo.10592878
title: Dataset related to article: Harmonizing Genetic Testing for Parkinson's Disease: Results of the PARKNET Multicentric Study

description: Sanger sequencing (.abi) or NGS files (.vcf) showing detected positive variants.
DOI: 10.18159/kir-ebi23
title: Kiruna region earthquakes, blasts and mining induced events

description: Data set of 189 earthquakes, 221 mining induced events from the Kiruna mine and 221 blasts from the Kiruna mine, recorded by seismic stations of the Swedish National Seismic Network (SNSN) and neighbouring countries. The earthquakes are mostly located to the west of Kiruna town, along the Pärvie post-glacial fault. The data contains event information (origin time, latitude, longitude, depth magnitude), waveform data, station information and instrument response information.
DOI: 10.6084/m9.figshare.23737227
title: Simulation data

description: The dataset contains the results of the simulations for the paper "Polyadic Opinion Formation: The Adaptive<br>
Voter Model on a Hypergraph". 
<br>
To recreate the figures in the paper, extract the contents of the archives into the `AdaptiveHypergraphs/data` folder. 
<br>
The folder structure of every dataset is as follows:
<br>
run_timestamp_tag
| batch_001
| | run_001
| | run_002
| | ...
| | input_params.json
<br>
Here, the batch folders like "batch_001" contain the results of all simulations executed with the same parameters, and the run folders like "run_001" contain the results of a single execution of a simulation. The file input_params.json contains the input parameters of the batch. 
<br>
The run folders like "run_001" contain the time evolution of various observables of the system, each in a separate csv file. For example, the evolution of the number of active hyperedges of size 3 is saved in the file "active_hyperedge_count_3.csv". The csv file contains three columns: the id of the measurement, the time stamp and the value of the observable.
DOI: 10.6084/m9.figshare.23737227.v1
title: Simulation data

description: The dataset contains the results of the simulations for the paper "Polyadic Opinion Formation: The Adaptive<br>
Voter Model on a Hypergraph". 
<br>
To recreate the figures in the paper, extract the contents of the archives into the `AdaptiveHypergraphs/data` folder. 
<br>
The folder structure of every dataset is as follows:
<br>
run__
| batch_001
| | run_001
| | run_002
| | ...
| | input_params.json
<br>
Here, the batch folders like "batch_001" contain the results of all simulations executed with the same parameters, and the run folders like "run_001" contain the results of a single execution of a simulation. The file input_params.json contains the input parameters of the batch. 
<br>
The run folders like "run_001" contain the time evolution of various observables of the system, each in a separate csv file. For example, the evolution of the number of active hyperedges of size 3 is saved in the file "active_hyperedge_count_3.csv". The csv file contains three columns: the id of the measurement, the time stamp and the value of the observable.
DOI: 10.6084/m9.figshare.23737227.v2
title: Simulation data

description: The dataset contains the results of the simulations for the paper "Polyadic Opinion Formation: The Adaptive<br>
Voter Model on a Hypergraph". 
<br>
To recreate the figures in the paper, extract the contents of the archives into the `AdaptiveHypergraphs/data` folder. 
<br>
The folder structure of every dataset is as follows:
<br>
run_timestamp_tag
| batch_001
| | run_001
| | run_002
| | ...
| | input_params.json
<br>
Here, the batch folders like "batch_001" contain the results of all simulations executed with the same parameters, and the run folders like "run_001" contain the results of a single execution of a simulation. The file input_params.json contains the input parameters of the batch. 
<br>
The run folders like "run_001" contain the time evolution of various observables of the system, each in a separate csv file. For example, the evolution of the number of active hyperedges of size 3 is saved in the file "active_hyperedge_count_3.csv". The csv file contains three columns: the id of the measurement, the time stamp and the value of the observable.
DOI: 10.5281/zenodo.10593294
title: СТРАТЕГИЯ РАЗВИТИЯ В ГОСУДАРСТВЕННОМ И ОБЩЕСТВЕННОМ СТРОИТЕЛЬСТВЕC
DOI: 10.5281/zenodo.10593295
title: СТРАТЕГИЯ РАЗВИТИЯ В ГОСУДАРСТВЕННОМ И ОБЩЕСТВЕННОМ СТРОИТЕЛЬСТВЕC
DOI: 10.5281/zenodo.10592877
title: Dataset related to article: Harmonizing Genetic Testing for Parkinson's Disease: Results of the PARKNET Multicentric Study

description: Sanger sequencing (.abi) or NGS files (.vcf) showing detected positive variants.
DOI: 10.6084/m9.figshare.25112261
title: Supplementary Material for: Bronchial Cryo-Denervation for Severe Asthma：A Pilot Study

description: Introduction
Targeting the parasympathetic nervous system innervating airway with pharmacologic products has been proved to improve the clinical outcomes of severe asthma. Bronchial cryo-denervation (BCD) is a novel non-pharmacologic treatment for severe asthma using an endobronchial cryo-balloon administered via bronchoscopy to denervate parasympathetic pulmonary nerves. Preclinical studies have demonstrated that BCD signiﬁcantly disrupted vagal innervation to the lung.
Methods
A total of 15 patients with severe asthma were enrolled in this prospective, single-center pilot study. Patients underwent bifurcated BCD treatment at 30-day interval after baseline assessment. Follow-up through 12 months included assessment of adverse event, technical feasibility, and changes in pulmonary function, asthma control questionaire-7 (ACQ-7) and asthma control test (ACT). 
Results
BCD was performed in all 15 severe asthma patients, with technical feasibility of 96.7%. There were no device-related and 2 procedure-related serious adverse events through 12 months, which resolved without sequelae. The most frequent nonserious procedure-related adverse event was increased cough in 60% (9 of 15) patients. Pulmonary function remained unchanged and significant improvements from baseline of ACQ-7 (mean, -1.19, p=0.0032) and ACT (mean, 3.18, p=0.0011) scores were observed since the first month's follow-up after a single lung airway treatment, with similar trends till the end of 12-month follow-up.
Conclusion
This study provides the first clinical evidence of the safety, feasibility, and initial efficacy of BCD in patients with severe asthma.
DOI: 10.5281/zenodo.10593307
title: DEVELOPMENT OF FOREIGN CULTURAL COOPERATION OF THE REPUBLIC OF KARAKALPAKSTAN
DOI: 10.5281/zenodo.10593308
title: DEVELOPMENT OF FOREIGN CULTURAL COOPERATION OF THE REPUBLIC OF KARAKALPAKSTAN
DOI: 10.5281/zenodo.10593278
title: ДУХОВНОСТЬ, СИСТЕМА НАУКИ И ОБРАЗОВАНИЯ - ФАКТОР ОБЩЕСТВЕННОГО РАЗВИТИЯ
DOI: 10.5281/zenodo.10593279
title: ДУХОВНОСТЬ, СИСТЕМА НАУКИ И ОБРАЗОВАНИЯ - ФАКТОР ОБЩЕСТВЕННОГО РАЗВИТИЯ
DOI: 10.5281/zenodo.10593322
title: KONSTITUCIYALIQ BАQLАW INSTITUTINIŃ QÁLIPLЕSIW TАRIYХI
DOI: 10.5281/zenodo.10593323
title: KONSTITUCIYALIQ BАQLАW INSTITUTINIŃ QÁLIPLЕSIW TАRIYХI
DOI: 10.5281/zenodo.10593021
title: Similarity Relationships Evaluator Data Benchmark

description: This dataset provides a subgraph extracted from the OpenAIRE Graph and disambiguated through the FDup framework to train models for the similarity relationships evaluation.
DOI: 10.5281/zenodo.10593022
title: Similarity Relationships Evaluator Data Benchmark

description: This dataset provides a subgraph extracted from the OpenAIRE Graph and disambiguated through the FDup framework to train models for the similarity relationships evaluation.
DOI: 10.5281/zenodo.10593228
title: Kirov UFSIN News Crawl Pt.6

description: WARC files produced by a webcrawl of Kirov UFSIN news online resource. WARC reader is necessary to view files.
DOI: 10.5281/zenodo.10593229
title: Kirov UFSIN News Crawl Pt.6

description: WARC files produced by a webcrawl of Kirov UFSIN news online resource. WARC reader is necessary to view files.
DOI: 10.5281/zenodo.10590385
title: Research data for the article "Charge of a Transmembrane Peptide Alters Its Interaction with Lipid Membranes" by Thakur et al. Colloids and Surfaces B: Biointerfaces, 2024

description: Research data for the publication Thakur, G.C.N., Uday, A., Cebecauer, M., Roos, W.H., Cwiklik, L., Hof, M., Jurkiewicz, P., and Melcrová, A. Charge of a Transmembrane Peptide Alters Its Interaction with Lipid Membranes. Colloids and Surfaces B: Biointerfaces, 2024. https://doi.org/10.1016/j.colsurfb.2024.113765

The data set contains experimental and simulation data on the study of transmembrane peptides WALP-KD and WALP-KK4+ and their interaction with model lipid membranes. Experimental and simulation details can be found in the Materials and Methods section of the mentioned article. 

The data set contains:



Files starting with "Figure..." contain source data used for the generation of the figures in the mentioned article.

Atomic Force Microscopy images are in the raw format as collected on JPK Nano Wizard Ultra Speed AFM.

Force-indentation curves from the force measurements by JPK Nano Wizard Ultra Speed AFM in the *.txt format. These curves were used for the analysis of the mechanical properties of the membranes with and without the transmembrane peptides.

Line profiles (cross-sections) over the height of the supported membranes and the surrounding support. Extracted from the height images measured on JPK Nano Wizard Ultra Speed AFM.

Molecular Dynamic simulation data - configuration files, trajectories, density profiles of chosen parts of the membrane alongside the membrane axis. These files are in respective directories for all simulated systems: POPC 100%, POPC/POPS 80/20 mol%, and both with the addition of 3 mol% peptide WALP-KD or WALP-KK4+.
DOI: 10.5281/zenodo.10590386
title: Research data for the article "Charge of a Transmembrane Peptide Alters Its Interaction with Lipid Membranes" by Thakur et al. Colloids and Surfaces B: Biointerfaces, 2024

description: Research data for the publication Thakur, G.C.N., Uday, A., Cebecauer, M., Roos, W.H., Cwiklik, L., Hof, M., Jurkiewicz, P., and Melcrová, A. Charge of a Transmembrane Peptide Alters Its Interaction with Lipid Membranes. Colloids and Surfaces B: Biointerfaces, 2024. https://doi.org/10.1016/j.colsurfb.2024.113765

The data set contains experimental and simulation data on the study of transmembrane peptides WALP-KD and WALP-KK4+ and their interaction with model lipid membranes. Experimental and simulation details can be found in the Materials and Methods section of the mentioned article. 

The data set contains:



Files starting with "Figure..." contain source data used for the generation of the figures in the mentioned article.

Atomic Force Microscopy images are in the raw format as collected on JPK Nano Wizard Ultra Speed AFM.

Force-indentation curves from the force measurements by JPK Nano Wizard Ultra Speed AFM in the *.txt format. These curves were used for the analysis of the mechanical properties of the membranes with and without the transmembrane peptides.

Line profiles (cross-sections) over the height of the supported membranes and the surrounding support. Extracted from the height images measured on JPK Nano Wizard Ultra Speed AFM.

Molecular Dynamic simulation data - configuration files, trajectories, density profiles of chosen parts of the membrane alongside the membrane axis. These files are in respective directories for all simulated systems: POPC 100%, POPC/POPS 80/20 mol%, and both with the addition of 3 mol% peptide WALP-KD or WALP-KK4+.
DOI: 10.12751/g-node.t74vi9
title: Dissociable contributions of basolateral amygdala and ventrolateral orbitofrontal cortex to flexible learning under uncertainty

description: This file provides source data for Figures appearing in Aguirre, C. G., Woo, J. H., Romero-Sosa, J. L., Rivera, Z. M., Tejada, A. N., Munier, J. J., Perez, J., Goldfarb, M., Das, K., Gomez, M., Ye, T., Pannu, J., Evans, K., O'Neill, P. R., Spigelman, I., Soltani, A., & Izquierdo, A. (2023). Dissociable Contributions of Basolateral
Amygdala and Ventrolateral Orbitofrontal Cortex to Flexible Learning Under
Uncertainty. Journal of Neuroscience. https://doi.org/10.1523/JNEUROSCI.0622-23.2023
description: IsSupplementTo: Aguirre, C. G., Woo, J. H., Romero-Sosa, J. L., Rivera, Z. M., Tejada, A. N., Munier, J. J., Perez, J., Goldfarb, M., Das, K., Gomez, M., Ye, T., Pannu, J., Evans, K., O'Neill, P. R., Spigelman, I., Soltani, A., & Izquierdo, A. (2023). Dissociable contributions of basolateral amygdala and ventrolateral orbitofrontal cortex to flexible learning under uncertainty. Preprint of a study based on the data. (https://doi.org/10.1101/2023.04.03.535471)
description: IsSupplementTo: Aguirre, C. G., Woo, J. H., Romero-Sosa, J. L., Rivera, Z. M., Tejada, A. N., Munier, J. J., Perez, J., Goldfarb, M., Das, K., Gomez, M., Ye, T., Pannu, J., Evans, K., O'Neill, P. R., Spigelman, I., Soltani, A., & Izquierdo, A. (2023). Dissociable Contributions of Basolateral
Amygdala and Ventrolateral Orbitofrontal Cortex to Flexible Learning Under
Uncertainty. Journal of Neuroscience. (https://doi.org/10.1523/JNEUROSCI.0622-23.2023)
DOI: 10.5281/zenodo.10497769
title: Cut&RUN ACLY BA Primary mouse hepatocytes

description: Pre-processed CUT&RUN files for ACLY and GCN5 were normalized to effective genome size.For each file, background signal was calculated in heterochromatin regions using negativeATAC-seq signal mask, and subsequently removed from the overall coverage. CUT&RUNcoverage heatmaps and profiles around the TSS of expressed genes were produced usingcomputeMatrix, plotHeatmap functions from deepTools v3.5.2 package51. The list of expressedgenes was inferred from the mouse primary hepatocyte RNA-seq data using variancestabilizing transformation of the expression matrix and selecting genes with values > 0 for allreplicates. Peak calling on each replicate was performed using MACS252 v.2.2.7.1, and theconsensus overlapping peaks between all replicates were considered as reproducible for thecorresponding dataset. Number of overlapping peaks between conditions was calculated in Rwith subsetByOverlaps (GenomicRanges v.1.54.1)57, and nearest genes were annotated topeaks using biomaRt.For the correlation of ChIP peaks with gene expression, all expressed genes derived fromRNA-seq data were divided into 4 equal groups based on their expression levels (quartiles (Q)1 to 4). Promoter regions of those genes (± 1kb TSS) were extracted using the Rsubreadv.2.16.0)59 package, and the CUT&RUN signal was quantified with multiBigwigSummary fromdeepTools package
DOI: 10.5281/zenodo.10497770
title: Cut&RUN ACLY BA Primary mouse hepatocytes

description: Pre-processed CUT&RUN files for ACLY and GCN5 were normalized to effective genome size.For each file, background signal was calculated in heterochromatin regions using negativeATAC-seq signal mask, and subsequently removed from the overall coverage. CUT&RUNcoverage heatmaps and profiles around the TSS of expressed genes were produced usingcomputeMatrix, plotHeatmap functions from deepTools v3.5.2 package51. The list of expressedgenes was inferred from the mouse primary hepatocyte RNA-seq data using variancestabilizing transformation of the expression matrix and selecting genes with values > 0 for allreplicates. Peak calling on each replicate was performed using MACS252 v.2.2.7.1, and theconsensus overlapping peaks between all replicates were considered as reproducible for thecorresponding dataset. Number of overlapping peaks between conditions was calculated in Rwith subsetByOverlaps (GenomicRanges v.1.54.1)57, and nearest genes were annotated topeaks using biomaRt.For the correlation of ChIP peaks with gene expression, all expressed genes derived fromRNA-seq data were divided into 4 equal groups based on their expression levels (quartiles (Q)1 to 4). Promoter regions of those genes (± 1kb TSS) were extracted using the Rsubreadv.2.16.0)59 package, and the CUT&RUN signal was quantified with multiBigwigSummary fromdeepTools package
DOI: 10.5281/zenodo.10593351
title: IMMERSE Dataset Catalogue
DOI: 10.5281/zenodo.10593352
title: IMMERSE Dataset Catalogue
DOI: 10.5281/zenodo.8199733
title: Dataset associated to "Quantifying the effect of competition on the functional assembly of bryophyte and lichen communities: A process-based model analysis"

description: The dataset is associated with the article 'Quantifying the effect of competition on the functional assembly of bryophyte and lichen communities: A process-based model analysis' by Yunyao Ma*, Maaike Y. Bader, Imke Petersen and Philipp Porada published in Journal of Ecology. The dataset includes all data and Rscripts to reproduce the findings of the article, as well as the source code of LiBry model applied in this study.
DOI: 10.5281/zenodo.8199734
title: Dataset associated to "Quantifying the effect of competition on the functional assembly of bryophyte and lichen communities: A process-based model analysis"

description: The dataset is associated with the article 'Quantifying the effect of competition on the functional assembly of bryophyte and lichen communities: A process-based model analysis' by Yunyao Ma*, Maaike Y. Bader, Imke Petersen and Philipp Porada published in Journal of Ecology. The dataset includes all data and Rscripts to reproduce the findings of the article, as well as the source code of LiBry model applied in this study.
DOI: 10.5517/ccdc.csd.cc21dsx5
title: CCDC 1889137: Experimental Crystal Structure Determination

description: Related Article: Tuǧba Aycan|2021|CSD Communication|||
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: 10.5281/zenodo.10497775
title: Cut&RUN GCN5 Control Primary mouse hepatocytes

description: Pre-processed CUT&RUN files for ACLY and GCN5 were normalized to effective genome size.For each file, background signal was calculated in heterochromatin regions using negativeATAC-seq signal mask, and subsequently removed from the overall coverage. CUT&RUNcoverage heatmaps and profiles around the TSS of expressed genes were produced usingcomputeMatrix, plotHeatmap functions from deepTools v3.5.2 package51. The list of expressedgenes was inferred from the mouse primary hepatocyte RNA-seq data using variancestabilizing transformation of the expression matrix and selecting genes with values > 0 for allreplicates. Peak calling on each replicate was performed using MACS252 v.2.2.7.1, and theconsensus overlapping peaks between all replicates were considered as reproducible for thecorresponding dataset. Number of overlapping peaks between conditions was calculated in Rwith subsetByOverlaps (GenomicRanges v.1.54.1)57, and nearest genes were annotated topeaks using biomaRt.For the correlation of ChIP peaks with gene expression, all expressed genes derived fromRNA-seq data were divided into 4 equal groups based on their expression levels (quartiles (Q)1 to 4). Promoter regions of those genes (± 1kb TSS) were extracted using the Rsubreadv.2.16.0)59 package, and the CUT&RUN signal was quantified with multiBigwigSummary fromdeepTools package
DOI: 10.5281/zenodo.10497776
title: Cut&RUN GCN5 Control Primary mouse hepatocytes

description: Pre-processed CUT&RUN files for ACLY and GCN5 were normalized to effective genome size.For each file, background signal was calculated in heterochromatin regions using negativeATAC-seq signal mask, and subsequently removed from the overall coverage. CUT&RUNcoverage heatmaps and profiles around the TSS of expressed genes were produced usingcomputeMatrix, plotHeatmap functions from deepTools v3.5.2 package51. The list of expressedgenes was inferred from the mouse primary hepatocyte RNA-seq data using variancestabilizing transformation of the expression matrix and selecting genes with values > 0 for allreplicates. Peak calling on each replicate was performed using MACS252 v.2.2.7.1, and theconsensus overlapping peaks between all replicates were considered as reproducible for thecorresponding dataset. Number of overlapping peaks between conditions was calculated in Rwith subsetByOverlaps (GenomicRanges v.1.54.1)57, and nearest genes were annotated topeaks using biomaRt.For the correlation of ChIP peaks with gene expression, all expressed genes derived fromRNA-seq data were divided into 4 equal groups based on their expression levels (quartiles (Q)1 to 4). Promoter regions of those genes (± 1kb TSS) were extracted using the Rsubreadv.2.16.0)59 package, and the CUT&RUN signal was quantified with multiBigwigSummary fromdeepTools package
DOI: 10.5517/ccdc.csd.cc21wd1d
title: CCDC 1903153: Experimental Crystal Structure Determination

description: Related Article: Danim Lim, Jaewook Kim|2023|CSD Communication|||
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.