cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25378/janelia.22675078.v2
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of A431 epithelial cells (aic_desmosome-3)

description: <strong>Sample: </strong>Cultured A431 (ATCC CRL-1555) cells stably expressing Desmoplakin-eGFP (Addgene #32227) and mApple-VAPB, stained with MitoView650 <strong>Sample Description: </strong>The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction. <strong>Protocol: </strong>High pressure freezing, freeze-substitution resin embedding with 2% OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12. <strong>Contributions: </strong>Sample prepared by Jesse Aaron and Satya Khuon (AIC Janelia), staining and resin embedding by Nirmala Iyer (HHMI/Janelia), trimming and imaging by Jesse Aaron and Satya Khoun (AIC Janelia), post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia), manual segmentations by COSEM Project Team (HHMI/Janelia) and Kowalczyk Lab (Pennsylvania State College of Medicine), and automated segmentations by COSEM Project Team. <strong>Acquisition ID:</strong> aic_desmosome-3 <strong>Voxel size (nm):</strong> 4 x 4 x 4 (X, Y, Z) <strong>Data dimensions (µm): </strong> 14.9 x 12.9 x 48.4 (X, Y, Z) <strong>Imaging start date:</strong> 2021-03-18 <strong>Dataset URL (Redirect): </strong>https://data.janelia.org/ve6M8 <strong>Visualization Website</strong>: https://openorganelle.janelia.org/datasets/aic_desmosome-3 <strong>Publications:</strong> "Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle" by Bharathan et al., 2022 <strong>DOI: </strong>https://doi.org/10.1101/2022.07.07.499185 <strong>Imaging duration (days): 8</strong> <strong>Landing energy (eV):</strong> 700 <strong>Imaging current (nA):</strong> .25 <strong>Scanning speed (MHz):</strong> 0.200
DOI: 10.25378/janelia.22675078.v1
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of A431 epithelial cells (aic_desmosome-3)

description: <strong>Sample: </strong>Cultured A431 (ATCC CRL-1555) cells stably expressing Desmoplakin-eGFP (Addgene #32227) and mApple-VAPB, stained with MitoView650 <strong>Sample Description: </strong>The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction. <strong>Protocol: </strong>High pressure freezing, freeze-substitution resin embedding with 2% OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12. <strong>Contributions: </strong>Sample prepared by Jesse Aaron and Satya Khuon (AIC Janelia), staining and resin embedding by Nirmala Iyer (HHMI/Janelia), trimming and imaging by Jesse Aaron and Satya Khoun (AIC Janelia), post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia), manual segmentations by COSEM Project Team (HHMI/Janelia) and Kowalczyk Lab (Pennsylvania State College of Medicine), and automated segmentations by COSEM Project Team. <strong>Acquisition ID:</strong> aic_desmosome-3 <strong>Voxel size (nm):</strong> 4 x 4 x 4 (X, Y, Z) <strong>Data dimensions (µm): </strong>14.9 x 48.4 x 12.9 (X, Y, Z) <strong>Imaging start date:</strong> 2021-03-18 <strong>Dataset URL (Redirect): </strong>https://data.janelia.org/ve6M8 <strong>Visualization Website</strong>: https://openorganelle.janelia.org/datasets/aic_desmosome-3 <strong>Publications:</strong> "Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle" by Bharathan et al., 2022 <strong>DOI: </strong>https://doi.org/10.1101/2022.07.07.499185 <strong>Imaging duration (days): 8</strong> <strong>Landing energy (eV):</strong> 700 <strong>Imaging current (nA):</strong> .25 <strong>Scanning speed (MHz):</strong> 0.200
DOI: 10.25378/janelia.22677058
title: Refined, automatic organelle segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of A431 epithelial cells (aic_desmosome-3)

description: <strong>Sample: </strong>Cultured A431 (ATCC CRL-1555) cells stably expressing Desmoplakin-eGFP (Addgene #32227) and mApple-VAPB, stained with MitoView650 <strong>Sample Description: </strong>The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction. <strong>Protocol: </strong>High pressure freezing, freeze-substitution resin embedding with 2% OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12. <strong>Contributions: </strong>Sample prepared by Jesse Aaron and Satya Khuon (AIC Janelia), staining and resin embedding by Nirmala Iyer (HHMI/Janelia), trimming and imaging by Jesse Aaron and Satya Khoun (AIC Janelia), post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia), manual segmentations by COSEM Project Team (HHMI/Janelia) and Kowalczyk Lab (Pennsylvania State College of Medicine), and automated segmentations by COSEM Project Team. <strong>Acquisition ID:</strong> aic_desmosome-3 <strong>Voxel size (nm):</strong> 4 x 4 x 4 (X, Y, Z) <strong>Data dimensions (µm): </strong> 14.9 x 12.9 x 48.4 (X, Y, Z) <strong>Imaging start date:</strong> 2021-03-18 <strong>Dataset URL (Redirect): </strong>https://data.janelia.org/VoDT2 <strong>EM DOI: </strong>https://doi.org/10.25378/janelia.22675078 <strong>Visualization Website</strong>: https://openorganelle.janelia.org/datasets/aic_desmosome-3 <strong>Publications:</strong> "Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle" by Bharathan et al., 2022 <strong>Imaging duration (days): 8</strong> <strong>Landing energy (eV):</strong> 700 <strong>Imaging current (nA):</strong> .25 <strong>Scanning speed (MHz):</strong> 0.200
DOI: 10.25378/janelia.22677058.v2
title: Refined, automatic organelle segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of A431 epithelial cells (aic_desmosome-3)

description: <strong>Sample: </strong>Cultured A431 (ATCC CRL-1555) cells stably expressing Desmoplakin-eGFP (Addgene #32227) and mApple-VAPB, stained with MitoView650 <strong>Sample Description: </strong>The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction. <strong>Protocol: </strong>High pressure freezing, freeze-substitution resin embedding with 2% OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12. <strong>Contributions: </strong>Sample prepared by Jesse Aaron and Satya Khuon (AIC Janelia), staining and resin embedding by Nirmala Iyer (HHMI/Janelia), trimming and imaging by Jesse Aaron and Satya Khoun (AIC Janelia), post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia), manual segmentations by COSEM Project Team (HHMI/Janelia) and Kowalczyk Lab (Pennsylvania State College of Medicine), and automated segmentations by COSEM Project Team. <strong>Acquisition ID:</strong> aic_desmosome-3 <strong>Voxel size (nm):</strong> 4 x 4 x 4 (X, Y, Z) <strong>Data dimensions (µm): </strong> 14.9 x 12.9 x 48.4 (X, Y, Z) <strong>Imaging start date:</strong> 2021-03-18 <strong>Dataset URL (Redirect): </strong>https://data.janelia.org/VoDT2 <strong>EM DOI: </strong>https://doi.org/10.25378/janelia.22675078 <strong>Visualization Website</strong>: https://openorganelle.janelia.org/datasets/aic_desmosome-3 <strong>Publications:</strong> "Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle" by Bharathan et al., 2022 <strong>Imaging duration (days): 8</strong> <strong>Landing energy (eV):</strong> 700 <strong>Imaging current (nA):</strong> .25 <strong>Scanning speed (MHz):</strong> 0.200
DOI: 10.25378/janelia.22677058.v1
title: Refined, automatic organelle segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of A431 epithelial cells (aic_desmosome-3)

description: <strong>Sample: </strong>Cultured A431 (ATCC CRL-1555) cells stably expressing Desmoplakin-eGFP (Addgene #32227) and mApple-VAPB, stained with MitoView650 <strong>Sample Description: </strong>The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction. <strong>Protocol: </strong>High pressure freezing, freeze-substitution resin embedding with 2% OsO₄ 0.1% UA 3% H₂O in acetone; resin embedding in Eponate 12. <strong>Contributions: </strong>Sample prepared by Jesse Aaron and Satya Khuon (AIC Janelia), staining and resin embedding by Nirmala Iyer (HHMI/Janelia), trimming and imaging by Jesse Aaron and Satya Khoun (AIC Janelia), post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia), manual segmentations by COSEM Project Team (HHMI/Janelia) and Kowalczyk Lab (Pennsylvania State College of Medicine), and automated segmentations by COSEM Project Team. <strong>Acquisition ID:</strong> aic_desmosome-3 <strong>Voxel size (nm):</strong> 4 x 4 x 4 (X, Y, Z) <strong>Data dimensions (µm): </strong> 14.9 x 12.9 x 48.4 (X, Y, Z) <strong>Imaging start date:</strong> 2021-03-18 <strong>Dataset URL (Redirect): </strong>https://data.janelia.org/VoDT2 <strong>EM DOI: </strong>https://doi.org/10.25378/janelia.22675078 <strong>Visualization Website</strong>: https://openorganelle.janelia.org/datasets/aic_desmosome-3 <strong>Publications:</strong> "Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle" by Bharathan et al., 2022 <strong>Imaging duration (days): 8</strong> <strong>Landing energy (eV):</strong> 700 <strong>Imaging current (nA):</strong> .25 <strong>Scanning speed (MHz):</strong> 0.200
DOI: 10.34740/kaggle/dsv/5755836
title: US Weather Events (2016 - 2022)
DOI: 10.5517/ccdc.csd.cc24cnfm
title: CCDC 1977410: Experimental Crystal Structure Determination

description: Related Article: Yashiro Rojas, Evana Halaka, Mary Hanna, Alex Sidoti, Jehan Joma, Mina Mikhael, Roger A. Lalancette, Ivan Bernal |2020|Adv. Chem. Res.|2|1|doi:10.21926/acr.2003008
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.cc2d8wm6
title: CCDC 2213078: Experimental Crystal Structure Determination

description: Related Article: Qiang-Qiang Jia, Meng-Meng Lun, Gele Teri, Li-Yan Xie, Da-Wei Fu, Qiang Guo|2023|Inorg.Chem.|62|7186|doi:10.1021/acs.inorgchem.2c04267
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.7963448
title: supplementary atherial of article Pleistocene aquatic refuges support the east-west breakage of the Neotropical catfish Trichomycterinae (Siluriformes: Trichomycteridae) and high diversity in the Magdalena, Guiana, and Paraná-Paraguay basins

description: Figure S1. Phylogenetic tree original of Trichomycterinae based on 566 cytochrome b sequences (405 haplotypes) with 999bp. Bayesian Inference with values above each branch correspond to the branch consistency index (BPP); Figure S2. Phylogenetic tree original of Trichomycterinae based on 566 cytochrome b sequences (405 haplotypes) with 999bp. Bayesian Inference with values above each branch correspond to age for clades, as well as the margin of error demonstrated in node bars; Figure S3. Phylogenetic tree original of Trichomycterinae based on 566 cytochrome b sequences (405 haplotypes) with 999bp. Maximum Likelihood with values above each branch correspond to the branch consistency index (ML bootstrap); Table S1: Sequences used in the present study with their respective locations, references, haplotypes, and clades according to the phylogenetic tree in figure 2; Table S2: Type locality of the species nominally allocated to Trichomycterus and of the type species of the nine genera of Trichomycterinae. Type species in asterisk.; Table S3A: Table with percentages of K2P pairwise genetic distances between the subclades of Trichomycterus sensu stricto. Values in diagonal (below, dark grey) correspond to the genetic distance between clades by category. Values above (above, blue) refer to the respective standard errors. Bold values on the diagonal refer to the intraclade distance (1 to 31, as referenced in Table S1 and S3C); Table S3B: Genetic divergence range, by category, and occurrence within subclades. genera and subfamily; Table S3C: List of Alphabetical clade code and respective genus/species and numerical subclade code with respective species.
DOI: 10.5281/zenodo.7963447
title: supplementary atherial of article Pleistocene aquatic refuges support the east-west breakage of the Neotropical catfish Trichomycterinae (Siluriformes: Trichomycteridae) and high diversity in the Magdalena, Guiana, and Paraná-Paraguay basins

description: Figure S1. Phylogenetic tree original of Trichomycterinae based on 566 cytochrome b sequences (405 haplotypes) with 999bp. Bayesian Inference with values above each branch correspond to the branch consistency index (BPP); Figure S2. Phylogenetic tree original of Trichomycterinae based on 566 cytochrome b sequences (405 haplotypes) with 999bp. Bayesian Inference with values above each branch correspond to age for clades, as well as the margin of error demonstrated in node bars; Figure S3. Phylogenetic tree original of Trichomycterinae based on 566 cytochrome b sequences (405 haplotypes) with 999bp. Maximum Likelihood with values above each branch correspond to the branch consistency index (ML bootstrap); Table S1: Sequences used in the present study with their respective locations, references, haplotypes, and clades according to the phylogenetic tree in figure 2; Table S2: Type locality of the species nominally allocated to Trichomycterus and of the type species of the nine genera of Trichomycterinae. Type species in asterisk.; Table S3A: Table with percentages of K2P pairwise genetic distances between the subclades of Trichomycterus sensu stricto. Values in diagonal (below, dark grey) correspond to the genetic distance between clades by category. Values above (above, blue) refer to the respective standard errors. Bold values on the diagonal refer to the intraclade distance (1 to 31, as referenced in Table S1 and S3C); Table S3B: Genetic divergence range, by category, and occurrence within subclades. genera and subfamily; Table S3C: List of Alphabetical clade code and respective genus/species and numerical subclade code with respective species.
DOI: 10.21227/hpch-xv71
title: Dataset for lossless compression testing on already compressed data

description: The following dataset is used to test lossless compression algorithm on already compressed data, i.e. reduce data size even further without compromising its integrity. This Dataset has 1.000 “.txt” text files extracted from other Datasets and compressed in “.zip” format with a maximum size of 1 kB (Kilobyte), that is, 1.024 bytes. The largest Dataset file has 1670 characters including “text_zip (970).zip” spaces, and the smallest repository file has 14 characters with “text_zip (1).zip” spaces. The maximum compression of the Dataset file is 25.42%, file “text_zip (5).zip”, and a minimum of 1.53%, file “text_zip (972).zip”. The average compression of the entire repository is 8.16%. All dataset files have significant lossless compression.
DOI: 10.6084/m9.figshare.23108354
title: Data from Shi & Zhang et al, 'Vector-mediated viral exchange between crops and weedy plants'

description: Data underlying figures 1-7 in the paper 'Vector-mediated viral exchange between crops and weedy plants', with lead authors Xiao-bin Shi and Zhuo Zhang, submitted for publication in the Journal of Pest Science.<strong> </strong>
DOI: 10.5281/zenodo.7963513
title: Instances and Cutting schemes of CAOR-D-22-01050

description: Instances and Cutting schemes of CAOR-D-22-01050
DOI: 10.6084/m9.figshare.22561183
title: Identification and distribution of species of <i>Neofusicoccum</i> that cause blueberry stem blight in Chile

description: Stem blight is a destructive woody disease of blueberry (<i>Vaccinium corymbosum</i>) caused by several species of the family Botryosphaeriaceae. A field survey was conducted in the mayor blueberry production area of Chile, comprising latitudes 32°49ʹS to 40°55ʹS, to determine the occurrence and distribution of Botryosphaeriaceae in the region. Together, a multilocus analysis, morphological characterization, and phytopathogenicity testing were used to identify 51 <i>Neofusicoccum</i> isolates belonging to <i>N. nonquaesitum</i> (28 strains), <i>N. parvum</i> (22 strains), and <i>N. australe</i> (1 strain). Of these, <i>N. parvum</i> and <i>N. nonquaesitum</i> were the most commonly found, with <i>N. parvum</i> most frequent from latitude 37°40ʹS to the north and <i>N. nonquaesitum</i> predominantly located from the same latitude toward the south. Morphological traits of the isolates were consistent with the species identified by molecular techniques, despite the overlapping of conidial size of some isolates among species. Pathogenicity trials showed that the three species were pathogenic to blueberry plants and revealed that <i>N. parvum</i> and <i>N. nonquaesitum</i> were the most aggressive species, although variability in virulence was observed among isolates of <i>N. parvum</i> and <i>N. nonquaesitum</i>.
DOI: 10.6084/m9.figshare.22561183.v1
title: Identification and distribution of species of <i>Neofusicoccum</i> that cause blueberry stem blight in Chile

description: Stem blight is a destructive woody disease of blueberry (<i>Vaccinium corymbosum</i>) caused by several species of the family Botryosphaeriaceae. A field survey was conducted in the mayor blueberry production area of Chile, comprising latitudes 32°49ʹS to 40°55ʹS, to determine the occurrence and distribution of Botryosphaeriaceae in the region. Together, a multilocus analysis, morphological characterization, and phytopathogenicity testing were used to identify 51 <i>Neofusicoccum</i> isolates belonging to <i>N. nonquaesitum</i> (28 strains), <i>N. parvum</i> (22 strains), and <i>N. australe</i> (1 strain). Of these, <i>N. parvum</i> and <i>N. nonquaesitum</i> were the most commonly found, with <i>N. parvum</i> most frequent from latitude 37°40ʹS to the north and <i>N. nonquaesitum</i> predominantly located from the same latitude toward the south. Morphological traits of the isolates were consistent with the species identified by molecular techniques, despite the overlapping of conidial size of some isolates among species. Pathogenicity trials showed that the three species were pathogenic to blueberry plants and revealed that <i>N. parvum</i> and <i>N. nonquaesitum</i> were the most aggressive species, although variability in virulence was observed among isolates of <i>N. parvum</i> and <i>N. nonquaesitum</i>.