cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8117566
title: Armed conflict avalanches and Voronoi grids for Africa

description: This description outlines the dataset associated with the research paper "Discovering the Mesoscale for Chains of Conflict," published in PNAS Nexus (click here to view the article). Please cite this paper if you use our dataset. The dataset is divided into two main folders: "voronoi_grids": This folder contains 100 realizations of Voronoi tessellations over the African continent. These tessellations were generated during the research process detailed in the aforementioned paper. "avalanches": The "avalanches" folder comprises conflict avalanches derived from each of the realizations of the Voronoi tessellations. These avalanches were generated using the technique described in the research paper. Reading avalanches from the pickle files: The avalanches are stored in pickle files, and the following Python code can be used to read them: <pre><code class="language-python">import dill as pickle # Temporal scale. Choose one of the following values: 2, 4, 8, 16, 32, 64, 128, 256, 512 time = 32 # Spatial scale. Choose one of the following values: 20, 28, 40, 57, 80, 113, 160, 226, 320, 453, 640, 905, 1280 dx = 453 # Voronoi grid index. Choose from 0 to 99 gridix = 3 file_path = f"avalanches/battles/gridix_{gridix}/te/te_ava_{str(time)}_{str(dx)}.p" with open(file_path, "rb") as f: ava = pickle.load(f) ava_event = ava["ava_event"]</code></pre> The extracted avalanches are in "event form," represented as a list of lists, where each element corresponds to the index of an individual conflict event in the ACLED dataset. Each sublist represents an avalanche. The total number of avalanches at the given temporal and spatial scale can be determined by the length of <code>ava_event</code> (<code>len(ava_event)</code>). ACLED Dataset: Due to copyright issues, we are providing a filtered version of the ACLED dataset that we used in our study. To obtain the full version of the ACLED dataset containing all the information regarding each conflict event, please refer to the final bullet point of the manual installation instructions of our python pacakge arcolanche.
DOI: 10.34740/kaggle/dsv/6229378
title: Reddit r/Ukraine Dataset
DOI: 10.5281/zenodo.8202450
title: Datasets for phylogeny-guided analysis of pseudogenes in Pseudomonas aeruginosa

description: In the study entitled "A large-scale phylogeny-guided analysis of pseudogenes in <em>Pseudomonas aeruginosa</em> bacterium" we analyzed the genomic data of 4699 strains of the bacterium <em>Pseudomonas aeruginosa P. aeruginosa)</em> as they exhibit high variability in the number of annotated pseudogenes. In particular, we looked for correlations between the number of pseudogenes and other genomic- and meta- features of the strains. We identified orthologous genes and pseudogenes and compared cluster size distributions and length homogeneity within clusters. We mapped and examined orthology relationships between genes and pseudogenes. We generated a phylogenetic tree of the strains and found that phylogenetically related strains are more homogeneous in the number of pseudogenes and share a significant amount of pseudogenes. Finally, we dived into clusters of orthologues genes and pseudogenes and quantified their phylogenetic neighborhood, classifying pseudogenes into evolutionary preserved pseudogenes, misannotated pseudogenes, or pseudogenes formed by failed horizontal transfer events. This in-depth study provides important insights that can be incorporated into pseudogene annotation pipelines in the future.<br> <br> We provide the following files: protein_seq.zip: A fasta file containing 28,948,105 protein sequences of coding genes across all strains. pseudo_seq.zip: A fasta file containing 86,273 DNA sequences of pseudogenes across all strains. protein_clustering_output.zip: Clustering of protein sequences with CD-HIT clustering algorithm and the following parameters: similarity threshold of 70%, word size of 5, and the slow mode version. pseudo_clustering_output.zip: Clustering of pseudogene sequences with CD-HIT-EST clustering algorithm and the following parameters: similarity threshold of 80\%, word size of 5, and the slow mode version.
DOI: 10.5281/zenodo.8202449
title: Datasets for phylogeny-guided analysis of pseudogenes in Pseudomonas aeruginosa

description: In the study entitled "A large-scale phylogeny-guided analysis of pseudogenes in <em>Pseudomonas aeruginosa</em> bacterium" we analyzed the genomic data of 4699 strains of the bacterium <em>Pseudomonas aeruginosa P. aeruginosa)</em> as they exhibit high variability in the number of annotated pseudogenes. In particular, we looked for correlations between the number of pseudogenes and other genomic- and meta- features of the strains. We identified orthologous genes and pseudogenes and compared cluster size distributions and length homogeneity within clusters. We mapped and examined orthology relationships between genes and pseudogenes. We generated a phylogenetic tree of the strains and found that phylogenetically related strains are more homogeneous in the number of pseudogenes and share a significant amount of pseudogenes. Finally, we dived into clusters of orthologues genes and pseudogenes and quantified their phylogenetic neighborhood, classifying pseudogenes into evolutionary preserved pseudogenes, misannotated pseudogenes, or pseudogenes formed by failed horizontal transfer events. This in-depth study provides important insights that can be incorporated into pseudogene annotation pipelines in the future.<br> <br> We provide the following files: protein_seq.zip: A fasta file containing 28,948,105 protein sequences of coding genes across all strains. pseudo_seq.zip: A fasta file containing 86,273 DNA sequences of pseudogenes across all strains. protein_clustering_output.zip: Clustering of protein sequences with CD-HIT clustering algorithm and the following parameters: similarity threshold of 70%, word size of 5, and the slow mode version. pseudo_clustering_output.zip: Clustering of pseudogene sequences with CD-HIT-EST clustering algorithm and the following parameters: similarity threshold of 80\%, word size of 5, and the slow mode version.
DOI: 10.6084/m9.figshare.23816625
title: scRNAseq gene expression matrices for "Immunophenotypic correlates of sustained MRD negativity in patients with multiple myeloma"

description: Single-cell gene expression matrices were prepared using the Chromium Single Cell 5’ Gene Expression and V(D)J Enrichment Kit for Human T and B Cells v1.0 (10X Genomics). Please refer to the manuscript supplementary data for barcoded V(D)J sequences. Each sample is represented by a compressed directory containing three files: matrix.mtx, features.tsv, and barcodes.tsv. The directory is named according to the numeric patient identifier followed by the time point. "Baseline" is before lenalidomide maintenance and "FollowUp" is approximately one year after lenalidomide maintenance. The same data files are also available through CReSCENT (https://crescent.cloud), CRES-P31.
DOI: 10.5281/zenodo.8205815
title: Modified IEEE 123-bus MG system

description: Modified IEEE 123-bus MG system for paper "Piece-wise Linear Function Based Continuous ADP Algorithm for Multiple Battery Energy Storage Lifespan Benefit Ensurance in Real-Time Schedule"
DOI: 10.5281/zenodo.8205814
title: Modified IEEE 123-bus MG system

description: Modified IEEE 123-bus MG system for paper "Piece-wise Linear Function Based Continuous ADP Algorithm for Multiple Battery Energy Storage Lifespan Benefit Ensurance in Real-Time Schedule"
DOI: 10.5281/zenodo.7787165
title: Replication package of: 'Perceived Fairness and Consequences of Affirmative Action Policies'

description: Replication package for: Schildberg-Hörisch, H., Schwarz, M., Trieu, C., and Willrodt, J. (2023). “Perceived Fairness and Consequences of Affirmative Action Policies”, Economic Journal, conditionally accepted.
DOI: 10.5281/zenodo.7787166
title: Replication package of: 'Perceived Fairness and Consequences of Affirmative Action Policies'

description: Replication package for: Schildberg-Hörisch, H., Schwarz, M., Trieu, C., and Willrodt, J. (2023). “Perceived Fairness and Consequences of Affirmative Action Policies”, Economic Journal, conditionally accepted.
DOI: 10.5281/zenodo.8122676
title: Replication package for: "Persuadable or Dissuadable Altruists? The Impact of Information of Recipient Characteristics on Giving"

description: ""
DOI: 10.5281/zenodo.8122677
title: Replication package for: "Persuadable or Dissuadable Altruists? The Impact of Information of Recipient Characteristics on Giving"

description: ""
DOI: 10.5281/zenodo.8205847
title: test upload for anonymous review supplemental material

description: test upload for anonymous review
DOI: 10.5281/zenodo.8205848
title: test upload for anonymous review supplemental material

description: test upload for anonymous review
DOI: 10.5517/ccdc.csd.cc28rg1k
title: CCDC 2107908: Experimental Crystal Structure Determination

description: Related Article: Xu Zhang, Jin-Yun Wang, Liang-Jin Xu, Xu-Yuan Jin, Xin Yang, Li-Yi Zhang, Zhong-Ning Chen|2022|CCS Chem.|4|3832|doi:10.31635/ccschem.022.202101675
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: 10.5517/ccdc.csd.cc28sfvc
title: CCDC 2108863: Experimental Crystal Structure Determination

description: Related Article: Mariana Darii, Annabel Mikosch, Jan van Leusen, Victor Ch. Kravtsov, Elena G. Dvornina, Steliana T. Clapco, Alexandra Ciloci, Paul Kögerler, Svetlana G. Baca|2022|RSC Advances|12|29034|doi:10.1039/D2RA04868J
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: 10.5517/ccdc.csd.cc28sfwd
title: CCDC 2108864: Experimental Crystal Structure Determination

description: Related Article: Mariana Darii, Annabel Mikosch, Jan van Leusen, Victor Ch. Kravtsov, Elena G. Dvornina, Steliana T. Clapco, Alexandra Ciloci, Paul Kögerler, Svetlana G. Baca|2022|RSC Advances|12|29034|doi:10.1039/D2RA04868J
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: 10.5517/ccdc.csd.cc28sfxf
title: CCDC 2108865: Experimental Crystal Structure Determination

description: Related Article: Mariana Darii, Annabel Mikosch, Jan van Leusen, Victor Ch. Kravtsov, Elena G. Dvornina, Steliana T. Clapco, Alexandra Ciloci, Paul Kögerler, Svetlana G. Baca|2022|RSC Advances|12|29034|doi:10.1039/D2RA04868J
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: 10.5517/ccdc.csd.cc2fnn1t
title: CCDC 2254166: Experimental Crystal Structure Determination

description: Related Article: Si-Yue Zhang, Zhi-Cheng Zhang, Tie Zhang, Hao-Fei Ni, Zhi-Xu Zhang, Da-Wei Fu, Hai-Feng Lu|2023|Dalton Trans.|52|10415|doi:10.1039/D3DT01574B
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: 10.5517/ccdc.csd.cc2fnn3w
title: CCDC 2254168: Experimental Crystal Structure Determination

description: Related Article: Si-Yue Zhang, Zhi-Cheng Zhang, Tie Zhang, Hao-Fei Ni, Zhi-Xu Zhang, Da-Wei Fu, Hai-Feng Lu|2023|Dalton Trans.|52|10415|doi:10.1039/D3DT01574B
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: 10.5517/ccdc.csd.cc2fnn5y
title: CCDC 2254170: Experimental Crystal Structure Determination

description: Related Article: Si-Yue Zhang, Zhi-Cheng Zhang, Tie Zhang, Hao-Fei Ni, Zhi-Xu Zhang, Da-Wei Fu, Hai-Feng Lu|2023|Dalton Trans.|52|10415|doi:10.1039/D3DT01574B
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: 10.5517/ccdc.csd.cc2fnn6z
title: CCDC 2254171: Experimental Crystal Structure Determination

description: Related Article: Si-Yue Zhang, Zhi-Cheng Zhang, Tie Zhang, Hao-Fei Ni, Zhi-Xu Zhang, Da-Wei Fu, Hai-Feng Lu|2023|Dalton Trans.|52|10415|doi:10.1039/D3DT01574B
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: 10.5517/ccdc.csd.cc2gkqzr
title: CCDC 2281165: Experimental Crystal Structure Determination

description: Related Article: Polina Lapido, Doron RUDIK|2023|U.S.Patents|||
description: Related Article: Polina Lapido, Doron Rudik|2021|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: 10.5519/qd.tp9sadsr
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (220 records)
DOI: 10.6084/m9.figshare.23798184
title: Data supplement for 'The medial septum controls hippocampal supra-theta oscillations'.

description: This dataset contains simultaneous hippocampal CA1 and medial septal electrophysiological recordings from rodents acquired with silicon probe implants. Further methodological details are available in Király et al 2023.'The medial septum controls hippocampal supra-theta oscillations'. The dataset consist of anesthetized rat (13 session from 5 rats), anesthetized mouse (5 session from 5 mice) and awake chronic mouse recordings (31 session from 6 mice). Each folder refers to the identifier of an animal containing separate folders for each session recorded from the animal. The folder of each session contains separate files for the action potential times (in ms) of each identified septal single unit resulting from spike sorting. Hippocampal local field potential recordings are downsampled at 1000 Hz. Mouse folders contain a recording from the str. radiatum layer of the hippocampus; rat folders contain all 32 channels of a hippocampal linear probe recording. When available, spatial position and speed as a function of time are also provided in awake mouse sessions.
DOI: 10.6084/m9.figshare.23816610
title: Data

description: We investigated the role and mechanism of IL-27 in the live attenuated Streptococcus pneumoniae vaccine SPY1 by using IL-27Rα-deficient mice and wild mice.
DOI: 10.6084/m9.figshare.23816610.v1
title: Data

description: We investigated the role and mechanism of IL-27 in the live attenuated Streptococcus pneumoniae vaccine SPY1 by using IL-27Rα-deficient mice and wild mice.
DOI: 10.6084/m9.figshare.23816793
title: Supplement_1.xlsx

description: Supplement file 3 for Geochimica et Cosmochimica Acta submission entitled "Complex zoning in the nakhlite and chassignite martian meteorites reveals multi-stage petrogenesis and undercooling during crystallization".
DOI: 10.6084/m9.figshare.20424942
title: Augmentation of telemedicine post-operative follow-up after oculofacial plastic surgery with a self-guided patient tool

description: This study evaluates a web-based tool designed to augment telemedicine post-operative visits after periocular surgery. Adult, English-speaking patients undergoing periocular surgery with telemedicine follow-up were studied prospectively in this interventional case series. Participants submitted visual acuity measurements and photographs via a web-based tool prior to routine telemedicine post-operative visits. An after-visit survey assessed patient perceptions. Surgeons rated photographs and live video for quality and blurriness; external raters also evaluated photographs. Images were analyzed for facial centration, resolution, and algorithmically detected blur. Complications were recorded and graded for severity and relation to telemedicine. Seventy-nine patients were recruited. Surgeons requested an in-person assessment for six patients (7.6%) due to inadequate evaluation by telemedicine. Surgeons rated patient-provided photographs to be of higher quality than live video at the time of the post-operative visit (p &lt; 0.001). Image blur and resolution had moderate and weak correlation with photograph quality, respectively. A photograph blur detection algorithm demonstrated sensitivity of 85.5% and specificity of 75.1%. One patient experienced a wound dehiscence with a possible relationship to inadequate evaluation during telemedicine follow-up. Patients rated the telemedicine experience and their comfort with the structure of the visit highly. Augmented telemedicine follow-up after oculofacial plastic surgery is associated with high patient satisfaction, rare conversion to clinic evaluation, and few related post-operative complications. Automated detection of image resolution and blur may play a role in screening photographs for subsequent iterations of the web-based tool.
DOI: 10.6084/m9.figshare.20424942.v1
title: Augmentation of telemedicine post-operative follow-up after oculofacial plastic surgery with a self-guided patient tool

description: This study evaluates a web-based tool designed to augment telemedicine post-operative visits after periocular surgery. Adult, English-speaking patients undergoing periocular surgery with telemedicine follow-up were studied prospectively in this interventional case series. Participants submitted visual acuity measurements and photographs via a web-based tool prior to routine telemedicine post-operative visits. An after-visit survey assessed patient perceptions. Surgeons rated photographs and live video for quality and blurriness; external raters also evaluated photographs. Images were analyzed for facial centration, resolution, and algorithmically detected blur. Complications were recorded and graded for severity and relation to telemedicine. Seventy-nine patients were recruited. Surgeons requested an in-person assessment for six patients (7.6%) due to inadequate evaluation by telemedicine. Surgeons rated patient-provided photographs to be of higher quality than live video at the time of the post-operative visit (p &lt; 0.001). Image blur and resolution had moderate and weak correlation with photograph quality, respectively. A photograph blur detection algorithm demonstrated sensitivity of 85.5% and specificity of 75.1%. One patient experienced a wound dehiscence with a possible relationship to inadequate evaluation during telemedicine follow-up. Patients rated the telemedicine experience and their comfort with the structure of the visit highly. Augmented telemedicine follow-up after oculofacial plastic surgery is associated with high patient satisfaction, rare conversion to clinic evaluation, and few related post-operative complications. Automated detection of image resolution and blur may play a role in screening photographs for subsequent iterations of the web-based tool.
DOI: 10.6084/m9.figshare.23675334
title: Convallaria Photon Counting Dataset (Conv-PC)

description: Data was recorded from a Convallaria majalis rhizome section sample slide at a Leica TCS SP8 TPE DIVE with FALCON and the HC PL IRAPO 25x dipping objective. We used 850 nm excitation at 1% laser power, HyD-RLD detector, emission range of 600 – 650 nm, pixel size 0.6 x 0.6 µm, an 8 MHz resonant scanner and 4x averaging.We imaged 5 fields of view (FOVs), each containing 512x512x2048 voxels (xyt). Four FOVs were used as training data for supervised denoising, and the fifth FOV was used as test data.We used a time binning of 4, resulting in datasets of 512x512x512 voxels, and named these low-SNR raw data 'trainingData.tif' and 'testData.tif' respectively.Furthermore, we summed these 512 frames to produce the high SNR ('ground truth') version and named it 'trainingDataGT.tif' and 'testDataGT.tif'.Each frame of the raw data contains a significant amount of image noise. All voxel values correspond to photon counts.
DOI: 10.6084/m9.figshare.23675334.v1
title: Convallaria Photon Counting Dataset (Conv-PC)

description: Data was recorded from a Convallaria majalis rhizome section sample slide at a Leica TCS SP8 TPE DIVE with FALCON and the HC PL IRAPO 25x dipping objective. We used 850 nm excitation at 1% laser power, HyD-RLD detector, emission range of 600 – 650 nm, pixel size 0.6 x 0.6 µm, an 8 MHz resonant scanner and 4x averaging.We imaged 5 fields of view (FOVs), each containing 512x512x2048 voxels (xyt). Four FOVs were used as training data for supervised denoising, and the fifth FOV was used as test data.We used a time binning of 4, resulting in datasets of 512x512x512 voxels, and named these low-SNR raw data 'trainingData.tif' and 'testData.tif' respectively.Furthermore, we summed these 512 frames to produce the high SNR ('ground truth') version and named it 'trainingDataGT.tif' and 'testDataGT.tif'.Each frame of the raw data contains a significant amount of image noise. All voxel values correspond to photon counts.
DOI: 10.5519/qd.g671ii87
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (179 records)
DOI: 10.25494/p6/when_where_and_how_kelp_restoration_guidebook
title: When, where and how? A guide to kelp restoration in California using spatio-temporal models of kelp dynamics. California. Biological and environmental predictors of kelp density. Site classification for kelp restoration (2004-2021)

description: Biological and environmental predictors of kelp density. Data includes information on kelp density from in situ surveys from Reef Check and PISCO long-term monitoring programs (2006-2021 and 2004-2021 respectively). Biological predictors were also obtained from in situ surveys while environmental predictors were obtained or derived from remote sensing products. Seafloor terrain bathymetry data was obtained from Multibeam Bathymetry surveys and other environmental predictors from satellite imagery. These datasets were used to identify the best predictors of the density of two kelp species in California: the bull kelp, Nereocystis luetkeana, and the giant kelp, Macrocystis pyrifera.
DOI: 10.25494/p6/kelp_predictors_all_ca
title: (:unkn)
DOI: 10.25494/p6/site_classification_kelp_restoration_all_ca
title: (:unkn)