cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8191583
title: Molecular dynamics simulation data 1: Structure of the connexin-43 gap junction channel in a putative closed state

description: Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) https://doi.org/10.7554/eLife.87616.2 The dataset includes: 1. The starting coordinates, topology, MD inputs 2. Production run gromacs trajectories for the Cx43 gap junction channel
description: {"references": ["Qi, Acosta-Gutierrez et al. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) https://doi.org/10.7554/eLife.87616.2"]}
DOI: 10.35077/add-vat
title: TasteBMN_spGAL4_proboscis_posterior: Posterior proboscis confocal imaging of fly driver line TasteBMN_spGAL4 expressing mCD8::GFP, stained using anti GFP antibodies (green channel) - Autofluorescence from the proboscis cuticle is in the red channel

description: Confocal z-stacks (.tiff stacks) of transgenic driver lines that express in mechanosensory neurons innervating specific bristle populations on the Drosophila melanogaster head. The neurons that are targeted by each driver line were labeled by expressing mCD8::GFP under control of the UAS or LexAop promotors, and then stained using anti-GFP antibodies (green channel). Autofluorescence from the head cuticle is in the red channel. The processed images are published in Figure 3 and Figure 3 – figure supplement 1 of the manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”. The confocal stacks used to produce these images are organized based on the driver line used in each figure panel.
description: A full protocol describing this work is available in the associated manuscript at manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”.
description: Autofluorescence from the proboscis cuticle is in the red channel DATASET METADATA: title:'TasteBMN_spGAL4_proboscis_posterior: Posterior proboscis confocal imaging of fly driver line TasteBMN_spGAL4 expressing mCD8::GFP, stained using anti GFP antibodies (green channel) - Autofluorescence from the proboscis cuticle is in the red channel', GeneralModality:'other', Technique:'other', Other:'GAL4 and LexA expression' SPECIMEN METADATA: LocalID:'TasteBMN_spGAL4_proboscis_posterior', Species:'Fruit fly', NCBITaxonomy:'NCBI:txid7227', Age:'5 to 8', Ageunit:'Days', Sex:'Male', Genotype:'w; VT023783_AD (attP40)/+; R11D02_DBD (attP2)/20XUAS-IVS- mCD8::GFP (attP2)', OrganName:'Peripheral (i.e. bristle mechanosensory neurons)', SampleLocalID:'20210320_11D02_DBD_VT023783_AD_20x_GFP_head_3', Locations:'Head peripheral nervous system (i.e. bristle mechanosensory neurons)' INSTRUMENT METADATA: MicroscopeType:'Confocal', MicroscopeManufacturerAndModel:'Zeiss LSM 800 Axio Imager.Z2', ObjectiveName:'Zeiss 20x objective (Plan-Apochromat 20x/0.8)', ObjectiveNA:'0.8', ObjectiveMagnification:'20x' IMAGE METADATA: xAxis:'left-to-right', yAxis:'left-to-right', zAxis:'left-to-right', Number:'1,2,red,green', displayColor:'(1.0, 0.0, 0.0),(0.0, 1.0, 0.0)', stepSizeX:'0.6239', stepSizeY:'0.6239'
DOI: 10.5281/zenodo.8193132
title: Molecular dynamics simulation data 3: Structure of the connexin-43 gap junction channel in a putative closed state

description: Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) https://doi.org/10.7554/eLife.87616.2 The dataset includes: Production run gromacs trajectories for the Cx43 gap junction channel (500 mV)
description: {"references": ["Qi, Acosta-Gutierrez et al. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) https://doi.org/10.7554/eLife.87616.2"]}
DOI: 10.35077/add-vex
title: InOc_Fly_1: Whole brain confocal imaging of fly driver line dBMN-spGAL4 crossed with UAS-MCFO-3 responder for labeling individual neurons (single channel shown).

description: Confocal z-stacks (.tiff stacks) of single labeled mechanosensory neurons that innervate specific bristle populations on the Drosophila melanogaster head. The bristle mechanosensory neurons (BMNs) were stochastically labeled using driver lines that express in specific subsets of BMNs and the multicolor flipout reagent (Nern et al., 2015). The processed images of the BMNs are published in Figure 4 and Figure 4 – figure supplements 6-8 of the manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”. The confocal stacks used to produce these images are organized based on the specific bristle labelled (e.g. InOc or Taste bristles) and the individual fly that was tested (e.g. Fly_1 and Fly_2).
description: A full protocol describing this work is available in the associated manuscript at manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”.
description: DATASET METADATA: title:'InOc_Fly_1: Whole brain confocal imaging of fly driver line dBMN-spGAL4 crossed with UAS-MCFO-3 responder for labeling individual neurons (single channel shown).', GeneralModality:'other', Technique:'other', Other:'Stochastic labelling' SPECIMEN METADATA: LocalID:'InOc_Fly_1', Species:'Fruit fly', NCBITaxonomy:'NCBI:txid7227', Age:'9 to 12', Ageunit:'Days', Sex:'Male', Genotype:'w, R57C10-FLPG5.PEST (su(Hw)attP8); VT019023_AD (attP40)/+; VT050279_DBD (attP2)/10xUAS(FRT.stop)myr::smGdP-HA (VK00005), 10xUAS(FRT.stop)myr::smGdP-V5-THS-10xUAS(FRT.stop)myr::smGdP-FLAG (su(Hw)attP1)', OrganName:'Brain', SampleLocalID:'C3_20220127_VT050279_DBD_VT019023_AD_MCFO_L_20x_brain_1', Locations:'Subesophageal zone (SEZ)' INSTRUMENT METADATA: MicroscopeType:'Confocal', MicroscopeManufacturerAndModel:'Zeiss LSM 800 Axio Imager.Z2', ObjectiveName:'Zeiss 20x objective (Plan-Apochromat 20x/0.8)', ObjectiveNA:'0.8', ObjectiveMagnification:'20x' IMAGE METADATA: xAxis:'left-to-right', yAxis:'left-to-right', zAxis:'left-to-right', Number:'1,blue', displayColor:'(0.0, 0.0, 1.0)', stepSizeX:'0.6239', stepSizeY:'0.6239'
DOI: 10.35077/add-vow
title: InOc_Fly_2: Whole brain confocal imaging of fly driver line dBMN-spGAL4 crossed with UAS-MCFO-3 responder for labeling individual neurons (single channel shown).

description: Confocal z-stacks (.tiff stacks) of single labeled mechanosensory neurons that innervate specific bristle populations on the Drosophila melanogaster head. The bristle mechanosensory neurons (BMNs) were stochastically labeled using driver lines that express in specific subsets of BMNs and the multicolor flipout reagent (Nern et al., 2015). The processed images of the BMNs are published in Figure 4 and Figure 4 – figure supplements 6-8 of the manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”. The confocal stacks used to produce these images are organized based on the specific bristle labelled (e.g. InOc or Taste bristles) and the individual fly that was tested (e.g. Fly_1 and Fly_2).
description: A full protocol describing this work is available in the associated manuscript at manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”.
description: DATASET METADATA: title:'InOc_Fly_2: Whole brain confocal imaging of fly driver line dBMN-spGAL4 crossed with UAS-MCFO-3 responder for labeling individual neurons (single channel shown).', GeneralModality:'other', Technique:'other', Other:'Stochastic labelling' SPECIMEN METADATA: LocalID:'InOc_Fly_2', Species:'Fruit fly', NCBITaxonomy:'NCBI:txid7227', Age:'9 to 12', Ageunit:'Days', Sex:'Male', Genotype:'w, R57C10-FLPG5.PEST (su(Hw)attP8); VT019023_AD (attP40)/+; VT050279_DBD (attP2)/10xUAS(FRT.stop)myr::smGdP-HA (VK00005), 10xUAS(FRT.stop)myr::smGdP-V5-THS-10xUAS(FRT.stop)myr::smGdP-FLAG (su(Hw)attP1)', OrganName:'Brain', SampleLocalID:'C1_20220127_VT050279_DBD_VT019023_AD_MCFO_L_20x_brain_4_rotated', Locations:'Subesophageal zone (SEZ)' INSTRUMENT METADATA: MicroscopeType:'Confocal', MicroscopeManufacturerAndModel:'Zeiss LSM 800 Axio Imager.Z2', ObjectiveName:'Zeiss 20x objective (Plan-Apochromat 20x/0.8)', ObjectiveNA:'0.8', ObjectiveMagnification:'20x' IMAGE METADATA: xAxis:'left-to-right', yAxis:'left-to-right', zAxis:'left-to-right', Number:'1,red', displayColor:'(1.0, 0.0, 0.0)', stepSizeX:'0.6239', stepSizeY:'0.6239'
DOI: 10.6084/m9.figshare.23800728
title: BPD scores.xlsx

description: Datasets of BPD-ASD scores, demographics, and sub-component analysis from BPD-ASD score for 10 BPD patients before and after closure.
DOI: 10.6084/m9.figshare.23800728.v1
title: BPD scores.xlsx

description: Dataset of BPD-ASD scores for 10 BPD patients before and after closure.
DOI: 10.6084/m9.figshare.23800728.v2
title: BPD scores.xlsx

description: Datasets of BPD-ASD scores, demographics, and sub-component analysis from BPD-ASD score for 10 BPD patients before and after closure.
DOI: 10.25387/g3.22809347
title: Supplemental Material for Simon et al., 2023

description: Table S1. Accession numbers of 78 cat genome sequences. Table S2. This table contains private sequence variants in the sequenced kitten affected with EDS. Private variants were obtained by filtering all variants that were present at least once in the 48 control genomes. Table S3. List of sampled cats including genotype. Table S4. Results of the parentage testing using an ISAG approved microsatellite panel.
DOI: 10.25345/c5804xv97
title: MassIVE Reanalysis RMSV000000695.1 - Markdown files to analyze Zebrafish data with TPP, NPARC, SCAM and MSstatsTMT statistical models
title: NPARC, TPP, SCAM and MSstatsTMT vignettes to reanalyze thermal profiling dataset.
DOI: 10.48324/dandi.000579/0.230728.1727
title: Two-photon calcium imaging of mouse posterior cortical areas during dynamic navigation decisions (Tseng et al., 2022, Neuron)

description: This is the dataset for Tseng et al, "Shared and specialized coding across posterior cortical areas for dynamic navigation decisions" in Neuron (2022). The dataset contains calcium activity of >200,000 neurons recorded from 6 different cortical areas in mouse posterior cortex L2/3 and L5 using two-photon imaging, including V1 and secondary visual areas, retrosplenial cortex (RSC) and posterior parietal cortex (PPC), while the mice were performing a flexible decision-making task based on rule-switching during virtual navigation. There are total 300 behavior + imaging sessions collected from 8 mice. The neurons in each experiment have been registered into the Allen Institute Mouse Common Coordinate Framework (CCF) based on widefield retinotopy. In addition, these neurons contain fluorescent labels of retroAAV injected in one of the two sets of projection targets: an anterior part of anterior cingulate cortex/secondary motor cortex (ACC/M2) and striatum, or a posterior part of ACC/M2 and orbitofrontal cortex (OFC).   

Please see the related paper for more details: https://doi.org/10.1016/j.neuron.2022.05.012

Additional resources:

- Jupyter notebook for a tutorial to read and extract information from these NWB files: https://github.com/sytseng/Notebook_for_Dandiset_000579

- NWB extension code for custom lab meta data (required for reading NWB files): https://github.com/sytseng/ndx-harvey-swac 

- Code and tutorials for fitting GLM to neural activity in Tensorflow 2: https://github.com/sytseng/GLM_Tensorflow_2
DOI: 10.6084/m9.figshare.23792208.v3
title: Underlying data

description: This is the underlying data for the article entitled "L2 Acquisition of <i>Wh-</i>interrogatives at the Syntax-discourse Interface: Interface Hypothesis again", by Mohammed Shormani
DOI: 10.6084/m9.figshare.23792382.v2
title: Example of participants' responses (AVG)

description: This is the underlying data for the article entitled "L2 Acquisition of <i>Wh-</i>interrogatives at the Syntax-discourse Interface: Interface Hypothesis again", by Mohammed Shormani
DOI: 10.6084/m9.figshare.23792277.v1
title: Example of participants' responses (IMG)

description: This is the underlying data for the article entitled "L2 Acquisition of <i>Wh-</i>interrogatives at the Syntax-discourse Interface: Interface Hypothesis again", by Mohammed Shormani
DOI: 10.6084/m9.figshare.23802213
title: Preferences and Perceptions of Self-Hypnosis for Sleep in Aging Adults

description: Data from a cross sectional survey of aging adults perceptions and preferences for self-hypnosis for sleep.
DOI: 10.6084/m9.figshare.23792385.v2
title: Underlying data- Example of participants' responses (NSG)

description: This is the underlying data for the article entitled "L2 Acquisition of <i>Wh-</i>interrogatives at the Syntax-discourse Interface: Interface Hypothesis again", by Mohammed Shormani
DOI: 10.6084/m9.figshare.23792382.v3
title: Underlying data- Example of participants' responses (AVG)

description: This is the underlying data for the article entitled "L2 Acquisition of <i>Wh-</i>interrogatives at the Syntax-discourse Interface: Interface Hypothesis again", by Mohammed Shormani
DOI: 10.6084/m9.figshare.23792277.v2
title: Underlying data-Example of participants' responses (IMG)

description: This is the underlying data for the article entitled "L2 Acquisition of <i>Wh-</i>interrogatives at the Syntax-discourse Interface: Interface Hypothesis again", by Mohammed Shormani
DOI: 10.5281/zenodo.8193166
title: Supporting data for manuscript: "Global-scale evaluation of coastal ocean alkalinity enhancement in a fully-coupled Earth system model"

description: Supporting data for manuscript: "Global-scale evaluation of coastal<br> ocean alkalinity enhancement in a fully-coupled Earth system model" Authors: Julien Palmieri and Andrew Yool Institute: National Oceanography Centre, European Way, Southampton<br> SO14 3ZH, UK This repository consists of four main sets of files: 1. Matlab scripts used for analysis, figure plotting and table<br> preparation Filenames of the format: Figure_??.m 2. Raw netCDF output files from UKESM1 for six model experiments Filenames of the format: medusa_c*.nc 3. BGCVal processed timeseries shelve files Filenames of the format: u-c*.shelve.txt 4. CMM2 processed timeseries netCDF files Filenames of the format: c*_global.nc File sets 2-4 are read and processed by script files in file set 1<br>
DOI: 10.5281/zenodo.8193165
title: Supporting data for manuscript: "Global-scale evaluation of coastal ocean alkalinity enhancement in a fully-coupled Earth system model"

description: Supporting data for manuscript: "Global-scale evaluation of coastal<br> ocean alkalinity enhancement in a fully-coupled Earth system model" Authors: Julien Palmieri and Andrew Yool Institute: National Oceanography Centre, European Way, Southampton<br> SO14 3ZH, UK This repository consists of four main sets of files: 1. Matlab scripts used for analysis, figure plotting and table<br> preparation Filenames of the format: Figure_??.m 2. Raw netCDF output files from UKESM1 for six model experiments Filenames of the format: medusa_c*.nc 3. BGCVal processed timeseries shelve files Filenames of the format: u-c*.shelve.txt 4. CMM2 processed timeseries netCDF files Filenames of the format: c*_global.nc File sets 2-4 are read and processed by script files in file set 1<br>
DOI: 10.6084/m9.figshare.23802273
title: Article Hafida Zerigui Acide Gallique.rar

description: green synthesis of a brand-new, all-natural diester based on gallic acid and polyethylene glycol. This di-gallate is created in a single step without the use of a solvent (solid-solid reaction). This reaction has a potential yield of up to 90%. The bathochromic shift of the absorption bands from 277 nm to 295 nm in the UV-VIS spectra was caused by the addition of PEG to gallic acid. To confirm the structure of this di-gallate, Fourier-transform infrared (FTIR) spectroscopy, proton and carbon nuclear magnetic resonance (<sup>1</sup>H and <sup>13</sup>C NMR), the thermal stability identified by thermogravimetric analysis (TGA), X-ray diffraction (XRD), and scanning electron microscopy (SEM) were all used to thoroughly analyze the manufactured product.
DOI: 10.6084/m9.figshare.23802273.v1
title: Article Hafida Zerigui Acide Gallique.rar

description: green synthesis of a brand-new, all-natural diester based on gallic acid and polyethylene glycol. This di-gallate is created in a single step without the use of a solvent (solid-solid reaction). This reaction has a potential yield of up to 90%. The bathochromic shift of the absorption bands from 277 nm to 295 nm in the UV-VIS spectra was caused by the addition of PEG to gallic acid. To confirm the structure of this di-gallate, Fourier-transform infrared (FTIR) spectroscopy, proton and carbon nuclear magnetic resonance (<sup>1</sup>H and <sup>13</sup>C NMR), the thermal stability identified by thermogravimetric analysis (TGA), X-ray diffraction (XRD), and scanning electron microscopy (SEM) were all used to thoroughly analyze the manufactured product.
DOI: 10.34740/kaggle/dsv/6211501
title: DDoS Evaluation Dataset (CIC-DDoS2019)
DOI: 10.6084/m9.figshare.23802291
title: <b>The Dynamics of Science-Industry Knowledge Transfer During the Emergence of Deep Learning</b>

description: We consider the dynamics of science-industry knowledge transfer during the 30-year emergence of deep learning. Deep learning constituted a paradigm shift in artificial intelligence and has been identified as the only true breakthrough in the 70-year history of the field. Using patent-to-paper citations as an indicator of knowledge transfer, we examine the factors that affect the likelihood that private technology developers absorb and build upon the research of pioneer scientists Geoffrey Hinton, Yoshua Bengio, and Yann LeCun. The data are 18,009 AI patent families. (2023-05-28)
DOI: 10.6084/m9.figshare.23802291.v1
title: <b>The Dynamics of Science-Industry Knowledge Transfer During the Emergence of Deep Learning</b>

description: We consider the dynamics of science-industry knowledge transfer during the 30-year emergence of deep learning. Deep learning constituted a paradigm shift in artificial intelligence and has been identified as the only true breakthrough in the 70-year history of the field. Using patent-to-paper citations as an indicator of knowledge transfer, we examine the factors that affect the likelihood that private technology developers absorb and build upon the research of pioneer scientists Geoffrey Hinton, Yoshua Bengio, and Yann LeCun. The data are 18,009 AI patent families. (2023-05-28)
DOI: 10.15784/601706
title: Gerlache Strait Krill Demographics
DOI: 10.5281/zenodo.8192482
title: Data for investigation of cell-type-specific expression and regulation in Setbp1 (p.S858R) atypical SGS male mice

description: <strong>processed.tar.gz, contains all files from the data directory associated with this projects and includes the following:</strong> <strong>setbp1_targets.csv</strong> : list of human SETP1 gene targets from ChIP-seq experiments converted to mouse and enriched for additional interactions from literature references (https://pubmed.ncbi.nlm.nih.gov/35685777/ and https://www.nature.com/articles/s41467-018-04462-8, <strong>seurat_objects/</strong> <strong>kidney_integrated_celltypes.Rdata </strong>: filtered and preprocessed seurat object with cell type assignments for input to SoupX processing <strong>kidney_integrated_celltypes_postSoup.Rdata</strong> : preprocessed and quality controlled seurat object with final cell type assignments after SoupX processing <strong>setbp1_cerebralintcelltypes.Rdata</strong> : preprocessed and quality controlled seurat object with final cell type assignments <strong>decoupleR_CollecTRI/</strong> <strong>mouse_prior_tri.csv</strong> : accessed May 2023, it is unclear how versioning or accessions are used so we provided the Mouse CollecTRI (https://github.com/saezlab/CollecTRI) used in this study to calculate cell-type-specific TF activity <strong>motif_inputs/</strong> <strong>Mus_motif_all.txt </strong>: TF-motif PANDA input for mm10 reference genome enriched for <strong>expression_inputs/</strong> : expression matrices for all cell types for both tissues and conditions (n = 50) used to construct cell-type-specific PANDA networks <strong>The below files are from the data/results directory of this associated project and include the following:</strong> <strong>alpaca.tar.gz</strong> : directory containing differential community analysis outputs from ALPACA <strong>seurat.tar.gz </strong>: directory containing SoupX intermediates, as well as the
DOI: 10.5281/zenodo.8192481
title: Data for investigation of cell-type-specific expression and regulation in Setbp1 (p.S858R) atypical SGS male mice

description: <strong>processed.tar.gz, contains all files from the data directory associated with this projects and includes the following:</strong> <strong>setbp1_targets.csv</strong> : list of human SETP1 gene targets from ChIP-seq experiments converted to mouse and enriched for additional interactions from literature references (https://pubmed.ncbi.nlm.nih.gov/35685777/ and https://www.nature.com/articles/s41467-018-04462-8, <strong>seurat_objects/</strong> <strong>kidney_integrated_celltypes.Rdata </strong>: filtered and preprocessed seurat object with cell type assignments for input to SoupX processing <strong>kidney_integrated_celltypes_postSoup.Rdata</strong> : preprocessed and quality controlled seurat object with final cell type assignments after SoupX processing <strong>setbp1_cerebralintcelltypes.Rdata</strong> : preprocessed and quality controlled seurat object with final cell type assignments <strong>decoupleR_CollecTRI/</strong> <strong>mouse_prior_tri.csv</strong> : accessed May 2023, it is unclear how versioning or accessions are used so we provided the Mouse CollecTRI (https://github.com/saezlab/CollecTRI) used in this study to calculate cell-type-specific TF activity <strong>motif_inputs/</strong> <strong>Mus_motif_all.txt </strong>: TF-motif PANDA input for mm10 reference genome enriched for <strong>expression_inputs/</strong> : expression matrices for all cell types for both tissues and conditions (n = 50) used to construct cell-type-specific PANDA networks <strong>The below files are from the data/results directory of this associated project and include the following:</strong> <strong>alpaca.tar.gz</strong> : directory containing differential community analysis outputs from ALPACA <strong>seurat.tar.gz </strong>: directory containing SoupX intermediates, as well as the
DOI: 10.15784/601707
title: Feeding Experiment - Krill Lipid Classes
DOI: 10.5281/zenodo.8193434
title: Muon000 and Muon002 raw and pressure temperature corrected data set

description: Data from Two detectors Muon000 and Muon002. Raw coincidence counts and pressure temperature corrected data set.
DOI: 10.5281/zenodo.8193435
title: Muon000 and Muon002 raw and pressure temperature corrected data set

description: Data from Two detectors Muon000 and Muon002. Raw coincidence counts and pressure temperature corrected data set.
DOI: 10.15784/601708
title: 2019 Krill Morphometrics
DOI: 10.15784/601709
title: 2019 Krill Carbon Content