cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25378/janelia.5613169.v1
title: ShuTu: an Open-Source Software for Neuron Reconstruction rat dente gyrus granule cell 63X

description: ShuTu (Chinese for "dendrite") is a software platform for semi-automated reconstruction of neuronal morphology. It is designed for neurons stained following patch-clamp recording and biocytin filling/staining. With an additional preprocessing step, it can also handle fluorescence images from confocal stacks.Even when there is only a single neuron in the imaged volume, automated reconstruction is tricky, because of background. Thus, ShuTu was developed to facilitate a two-step process: automated reconstruction, followed by manual correction. The software uses sophisticated algorithms to perform the automated reconstruction, as well as a convenient user interface to facilitate efficient completion of the reconstruction via manual annotation.<br>Here we provide images of a rat dente gyrus granule cell for evaluting the software and practing reconstruction. The cell was filled and imaged by Ching-Lung Hsu at the Spruston Lab at Janelia. Two resolutions are provided, 63X and 100X. For quick evaluation, use this file 63X. <br>
DOI: 10.25378/janelia.5613184
title: ShuTu: Rat dentate gyrus granule cell 100X (compressed)

description: Here we provide images of a rat dentate gyrus granule cell (100X) for practicing reconstruction using the ShuTu software platform. The cell was filled and imaged by Ching-Lung Hsu in the Spruston Lab. Two resolutions are provided, 63X and 100X. For more accurate reconstruction, use 100X.Currently this compressed file is set up only for Ubuntu. Due to agressive compression, the sharpness of the images is somewhat reduced. To decompress, first install OpenJPEG then decompress the images using the following commands:sudo sh installOpenJpegForCompression.shpython decompressToTiff.py ~/granuleCellCompressShuTu (Chinese for "dendrite") is a software platform for semi-automated reconstruction of neuronal morphology. It is designed for neurons stained following patch-clamp recording and biocytin filling/staining. With an additional preprocessing step, it can also handle fluorescence images from confocal stacks.
Even when there is only a single neuron in the imaged volume, automated reconstruction is tricky, because of background. Thus, ShuTu was developed to facilitate a two-step process: automated reconstruction, followed by manual correction. The software uses sophisticated algorithms to perform the automated reconstruction, as well as a convenient user interface to facilitate efficient completion of the reconstruction via manual annotation.
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DOI: 10.25378/janelia.5613190
title: ShuTu: Rat dentate gyrus granule cell 100X

description: Here we provide images of a rat dentate gyrus granule cell (100X) for practicing reconstruction using the ShuTu software platform. The cell was filled and imaged by Ching-Lung Hsu in the Spruston Lab. Two resolutions are provided, 63X and 100X. For more accurate reconstruction, use this 100X fileset.<br>ShuTu (Chinese for "dendrite") is a software platform for semi-automated reconstruction of neuronal morphology. It is designed for neurons stained following patch-clamp recording and biocytin filling/staining. With an additional preprocessing step, it can also handle fluorescence images from confocal stacks.
Even when there is only a single neuron in the imaged volume, automated reconstruction is tricky, because of background. Thus, ShuTu was developed to facilitate a two-step process: automated reconstruction, followed by manual correction. The software uses sophisticated algorithms to perform the automated reconstruction, as well as a convenient user interface to facilitate efficient completion of the reconstruction via manual annotation.
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DOI: 10.6084/m9.figshare.5615365
title: Genome survey sequencing of Dracaena cambodiana

description: Dragon’s blood from the genus <i>Dracaena</i>
is<b> </b>used as a renowned traditional
medicine in various cultures worldwide. As
an important original plant in tropical and subtropical areas, <i>D. cambodiana</i> remains poorly described at
a genomic level, which impede research
on the mechanism of dragon’s blood formation. This is the <i>Dracaena cambodiana</i> genome assembly via survey sequencing.
DOI: 10.6084/m9.figshare.5615365.v2
title: Genome survey sequencing of Dracaena cambodiana

description: Dragon’s blood from the genus <i>Dracaena</i>
is<b> </b>used as a renowned traditional
medicine in various cultures worldwide. As
an important original plant in tropical and subtropical areas, <i>D. cambodiana</i> remains poorly described at
a genomic level, which impede research
on the mechanism of dragon’s blood formation. This is the <i>Dracaena cambodiana</i> genome assembly via survey sequencing.
DOI: 10.6084/m9.figshare.5615365.v1
title: Genome survey sequencing of Dracaena cambodiana

description: Dragon’s blood from the genus <i>Dracaena</i>
is<b> </b>used as a renowned traditional
medicine in various cultures worldwide. As
an important original plant in tropical and subtropical areas, <i>D. cambodiana</i> remains poorly described at
a genomic level, which impede research
on the mechanism of dragon’s blood formation. This is the <i>Dracaena cambodiana</i> genome assembly via survey sequencing.
DOI: 10.4225/03/5a1254b6c6b0b
title: Petrophysical data for Tasmania and Victoria

description: Magnetic Susceptibility values from David Moore's PhD thesis for King Island, Western Tasmania and Victoria.
DOI: 10.6084/m9.figshare.5616637
title: PlosOne Dataset

description: PlosOne article dataset used in our journal article "Understanding disciplinary vocabularies using a
full-text enabled domain-independent term extraction approach"
DOI: 10.6084/m9.figshare.5616637.v2
title: PlosOne Dataset

description: PlosOne article dataset used in our journal article "Understanding disciplinary vocabularies using a
full-text enabled domain-independent term extraction approach"
DOI: 10.6084/m9.figshare.5616637.v1
title: PlosOne Dataset

description: PlosOne article dataset used in our journal article "Understanding disciplinary vocabularies using a
full-text enabled domain-independent term extraction approach"
DOI: 10.6084/m9.figshare.5619313
title: Mouse ­Behavior Data for Static Authentication

description: The data consist of mouse dynamics information from 56 subjects, each of who accomplish a fixed mouse ­operating pattern 200 times.
DOI: 10.6084/m9.figshare.5619328
title: Mouse ­Behavior Data for Continuous Authentication

description: The data consist of mouse dynamics information from 28 subjects who each accomplished at least 30 data sessions. Each session consists of about thirty minutes of a user’s mouse activity data (around 3000 mouse operations).
DOI: 10.6084/m9.figshare.5619688.v1
title: Comprehensive assessment of shockwave intensity: Transcriptomic biomarker discovery for primary blast-induced mild traumatic brain injury using the mammalian hair follicle

description: <i>Objective</i>: Primary blast-induced mild traumatic brain injury (mTBI) is an injury experienced during modern warfare due to exposure to the pressure waves produced by the detonation of explosives. With virtually no apparent physical damage or symptoms presented, there is a need for more objective and accessible mTBI biomarkers posing minimal invasiveness risk. <i>Methods</i>: We measured the transcriptomic sensitivity of the hair follicles in relation to the severity of primary blast-derived TBI. An Advanced Blast Simulator system was used to expose male rats to single pulse shock waves (intensities ranging from 15 to 30 psi) in a head-only fashion. Gene differential expression (DE) and gene set (GS) analyses were conducted in the rat whisker hair follicles and the whole blood samples. <i>Results</i>: While shared cellular function, themes were found across the exposure groups, some gene sets under such themes were unique to the exposure conditions. Intensity-specific pathway enrichment patterns within shared GS themes were also identified. Furthermore, while exhibited shared pathways, the blood transcriptome showed substantially fewer enriched gene sets compared with the hair follicles across all exposure conditions. <i>Conclusions</i>: Accordingly, we demonstrate the potential of mammalian hair follicles serving as an additional source for biomarker discovery and for diagnosing mTBI with high accessibility.
DOI: 10.6084/m9.figshare.5620408
title: The finite element simulation data of epidermis layer of the paw pad

description: The fileset contains two 3D PDFs of the models in solid works which based on the paw pad of canine, 35 animations of the simulations and results of simulations.
DOI: 10.6084/m9.figshare.5620408.v1
title: The finite element simulation data of epidermis layer of the paw pad

description: The fileset contains two 3D PDFs of the models in solid works which based on the paw pad of canine, 35 animations of the simulations and results of simulations.
DOI: 10.25378/janelia.5620687
title: ShuTu: Mouse CA3 pyramidal neuron I 100X Parts 1 - 4

description: Here we provide images of the mouse CA3 pyramidal neuron I (100X) for practicing reconstruction using the ShuTu software platform. The cell was filled and imaged by David Hunt in the Spruston Lab. This is the neuron discussed as the main example in the paper. Due to large sizes of the images files, the data for some neurons are split into multiple parts. After downloading and decompressing, the parts should be combined into one directory.ShuTu (Chinese for "dendrite") is a software platform for semi-automated reconstruction of neuronal morphology. It is designed for neurons stained following patch-clamp recording and biocytin filling/staining. With an additional preprocessing step, it can also handle fluorescence images from confocal stacks.
Even when there is only a single neuron in the imaged volume, automated reconstruction is tricky, because of background. Thus, ShuTu was developed to facilitate a two-step process: automated reconstruction, followed by manual correction. The software uses sophisticated algorithms to perform the automated reconstruction, as well as a convenient user interface to facilitate efficient completion of the reconstruction via manual annotation.<br><br>
DOI: 10.6084/m9.figshare.5621041.v1
title: Lipopolysaccharide mediates hepatic stellate cell activation by regulating autophagy and retinoic acid signaling

description: Bacterial translocation and lipopolysaccharide (LPS) leakage occur at a very early stage of liver fibrosis in animal models. We studied the role of LPS in hepatic stellate cell (HSC) activation and the underlying mechanisms in vitro and in vivo. Herein, we demonstrated that LPS treatment led to a dramatic increase in autophagosome formation and autophagic flux in LX-2 cells and HSCs, which was mediated through the AKT-MTOR and AMPK-ULK1 pathway. LPS significantly decreased the lipid content, including the lipid droplet (LD) number and lipid staining area in HSCs; pretreatment with macroautophagy/autophagy inhibitors or silencing ATG5 attenuated this decrease. Furthermore, lipophagy was induced by LPS through the autophagy-lysosomal pathway in LX-2 cells and HSCs. Additionally, LPS-induced autophagy further reduced retinoic acid (RA) signaling, as demonstrated by a decrease in the intracellular RA level and <i>Rar</i> target genes, resulting in the downregulation of <i>Bambi</i> and promoting the sensitization of the HSC's fibrosis response to TGFB. Compared with CCl<sub>4</sub> injection alone, CCl<sub>4</sub> plus LPS injection exaggerated liver fibrosis in mice, as demonstrated by increased <i>Col1a1</i> (collagen, type I, α 1), <i>Acta2, Tgfb</i> and <i>Timp1</i> mRNA expression, ACTA2/α-SMA and COL1A1 protein expression, and Sirius Red staining area, which could be attenuated by injection of an autophagy inhibitor. LPS also reduced lipid content in HSCs in vivo, with this change being attenuated by chloroquine (CQ) administration. In conclusion, LPS-induced autophagy resulted in LD loss, RA signaling dysfunction, and downregulation of the TGFB pseudoreceptor <i>Bambi</i>, thus sensitizing HSCs to TGFB signaling.
DOI: 10.6084/m9.figshare.5621041
title: Lipopolysaccharide mediates hepatic stellate cell activation by regulating autophagy and retinoic acid signaling

description: Bacterial translocation and lipopolysaccharide (LPS) leakage occur at a very early stage of liver fibrosis in animal models. We studied the role of LPS in hepatic stellate cell (HSC) activation and the underlying mechanisms in vitro and in vivo. Herein, we demonstrated that LPS treatment led to a dramatic increase in autophagosome formation and autophagic flux in LX-2 cells and HSCs, which was mediated through the AKT-MTOR and AMPK-ULK1 pathway. LPS significantly decreased the lipid content, including the lipid droplet (LD) number and lipid staining area in HSCs; pretreatment with macroautophagy/autophagy inhibitors or silencing ATG5 attenuated this decrease. Furthermore, lipophagy was induced by LPS through the autophagy-lysosomal pathway in LX-2 cells and HSCs. Additionally, LPS-induced autophagy further reduced retinoic acid (RA) signaling, as demonstrated by a decrease in the intracellular RA level and <i>Rar</i> target genes, resulting in the downregulation of <i>Bambi</i> and promoting the sensitization of the HSC's fibrosis response to TGFB. Compared with CCl<sub>4</sub> injection alone, CCl<sub>4</sub> plus LPS injection exaggerated liver fibrosis in mice, as demonstrated by increased <i>Col1a1</i> (collagen, type I, α 1), <i>Acta2, Tgfb</i> and <i>Timp1</i> mRNA expression, ACTA2/α-SMA and COL1A1 protein expression, and Sirius Red staining area, which could be attenuated by injection of an autophagy inhibitor. LPS also reduced lipid content in HSCs in vivo, with this change being attenuated by chloroquine (CQ) administration. In conclusion, LPS-induced autophagy resulted in LD loss, RA signaling dysfunction, and downregulation of the TGFB pseudoreceptor <i>Bambi</i>, thus sensitizing HSCs to TGFB signaling.
DOI: 10.25378/janelia.5623510
title: ShuTu: Mouse CA3 pyramidal neuron II 100X Parts 1 - 4

description: Here we provide images of the mouse CA3 pyramidal neuron II (100X) for practicing reconstruction using the ShuTu software platform. The cell was imaged by David Hunt in the Spruston Lab. Due to large sizes of the images files, the data for some neurons are split into multiple parts. After downloading and decompressing, the parts should be combined into one directory.ShuTu (Chinese for "dendrite") is a software platform for semi-automated reconstruction of neuronal morphology. It is designed for neurons stained following patch-clamp recording and biocytin filling/staining. With an additional preprocessing step, it can also handle fluorescence images from confocal stacks.
Even when there is only a single neuron in the imaged volume, automated reconstruction is tricky, because of background. Thus, ShuTu was developed to facilitate a two-step process: automated reconstruction, followed by manual correction. The software uses sophisticated algorithms to perform the automated reconstruction, as well as a convenient user interface to facilitate efficient completion of the reconstruction via manual annotation.
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DOI: 10.25378/janelia.5623621
title: ShuTu: Mouse Purkinje cell confocal images 63X

description: Here we provide images of the mouse Purkinje cell (63X) for practicing reconstruction using the ShuTu software platform. The cell was imaged by David Hunt in the Spruston Lab. ShuTu (Chinese for "dendrite") is a software platform for semi-automated reconstruction of neuronal morphology. It is designed for neurons stained following patch-clamp recording and biocytin filling/staining. With an additional preprocessing step, it can also handle fluorescence images from confocal stacks.
Even when there is only a single neuron in the imaged volume, automated reconstruction is tricky, because of background. Thus, ShuTu was developed to facilitate a two-step process: automated reconstruction, followed by manual correction. The software uses sophisticated algorithms to perform the automated reconstruction, as well as a convenient user interface to facilitate efficient completion of the reconstruction via manual annotation.
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DOI: 10.25378/janelia.5623621.v1
title: ShuTu: an Open-Source Software for Neuron Reconstruction Mouse Purkinje Cell confocal images 63X

description: ShuTu (Chinese for "dendrite") is a software platform for semi-automated reconstruction of neuronal morphology. It is designed for neurons stained following patch-clamp recording and biocytin filling/staining. With an additional preprocessing step, it can also handle fluorescence images from confocal stacks.
Even when there is only a single neuron in the imaged volume, automated reconstruction is tricky, because of background. Thus, ShuTu was developed to facilitate a two-step process: automated reconstruction, followed by manual correction. The software uses sophisticated algorithms to perform the automated reconstruction, as well as a convenient user interface to facilitate efficient completion of the reconstruction via manual annotation.
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Here we provided the images and reconstructions of the neurons described in the paper.<br>Mouse Purkinje cell, confocal images, 63X (David Hunt).
DOI: 10.25378/janelia.5623636
title: ShuTu: Rat CA1 pyramidal neuron 63X (Parts 1 - 12)

description: Here we provide images of a rat CA1 pyramidal neuron (63X) for practicing reconstruction using the ShuTu software platform. The cell was imaged by Ching-Lung Hsu in the Spruston Lab. Due to large sizes of the images files, the data for some neurons are split into multiple parts. After downloading and decompressing, the parts should be combined into one directory.ShuTu (Chinese for "dendrite") is a software platform for semi-automated reconstruction of neuronal morphology. It is designed for neurons stained following patch-clamp recording and biocytin filling/staining. With an additional preprocessing step, it can also handle fluorescence images from confocal stacks.
Even when there is only a single neuron in the imaged volume, automated reconstruction is tricky, because of background. Thus, ShuTu was developed to facilitate a two-step process: automated reconstruction, followed by manual correction. The software uses sophisticated algorithms to perform the automated reconstruction, as well as a convenient user interface to facilitate efficient completion of the reconstruction via manual annotation.
DOI: 10.25378/janelia.5623636.v1
title: ShuTu: an Open-Source Software for Neuron Reconstruction Rat CA1 pyramidal neuron 63X (Parts 1 - 12)

description: ShuTu (Chinese for "dendrite") is a software platform for semi-automated reconstruction of neuronal morphology. It is designed for neurons stained following patch-clamp recording and biocytin filling/staining. With an additional preprocessing step, it can also handle fluorescence images from confocal stacks.
Even when there is only a single neuron in the imaged volume, automated reconstruction is tricky, because of background. Thus, ShuTu was developed to facilitate a two-step process: automated reconstruction, followed by manual correction. The software uses sophisticated algorithms to perform the automated reconstruction, as well as a convenient user interface to facilitate efficient completion of the reconstruction via manual annotation.
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Here we provided the images and reconstructions of the neurons described in the paper. Due to large sizes of the images files, the data for some neurons are split into multiple parts. After downloading and decompressing, the parts should be combined into one directory.<br>Rat CA1 pyramidal neuron, 63X (Ching-Lung Hsu).<br>
DOI: 10.25378/janelia.5623636.v2
title: ShuTu: Open-Source Software for Neuron Reconstruction Rat CA1 pyramidal neuron 63X (Parts 1 - 12)

description: ShuTu (Chinese for "dendrite") is a software platform for semi-automated reconstruction of neuronal morphology. It is designed for neurons stained following patch-clamp recording and biocytin filling/staining. With an additional preprocessing step, it can also handle fluorescence images from confocal stacks.
Even when there is only a single neuron in the imaged volume, automated reconstruction is tricky, because of background. Thus, ShuTu was developed to facilitate a two-step process: automated reconstruction, followed by manual correction. The software uses sophisticated algorithms to perform the automated reconstruction, as well as a convenient user interface to facilitate efficient completion of the reconstruction via manual annotation.
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Here we provided the images and reconstructions of the neurons described in the paper. Due to large sizes of the images files, the data for some neurons are split into multiple parts. After downloading and decompressing, the parts should be combined into one directory.<br>Rat CA1 pyramidal neuron, 63X (Ching-Lung Hsu).<br>
DOI: 10.6084/m9.figshare.3761562.v2892
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.6084/m9.figshare.5624824
title: Amorphous silica nanoparticles induce malignant transformation and tumorigenesis of human lung epithelial cells <i>via</i> P53 signaling

description: Rapid development and deployment of engineered nanomaterials, such as amorphous silica nanoparticles (SiNPs) in various commercial and biomedical applications have raised concerns about their potential adverse health effects, especially their chronic effects which have not been well addressed. In this study, human lung epithelial cells, BEAS-2B were continuously exposed to amorphous SiNPs, 5 μg/mL for 40 passages. We demonstrated here that prolonged exposure of BEAS-2B cells to amorphous SiNPs induced malignant transformation as indicated by enhanced cellular proliferation, anchorage-independent cell growth, and increased cell migration. The transformed cells induced tumorigenesis in nude mice. Furthermore, a comprehensive understanding of genome-wide transcriptional analysis was performed to clarify the molecular mechanisms based on microarray and bioinformatics analysis. Microarray data analysis demonstrated that chronic exposure of SiNPs affected expression of 821 genes, including 5 up-regulated and 816 down-regulated genes. Gene ontology and pathway analysis showed that SiNPs caused significant changes in gene expression patterns related to many important functions and pathways, mainly including response to cellular processes, oxidative stress, DNA damage, and cancer. In addition, Signal-net analysis indicated the most prominent significant role of tumor protein p53 in amorphous SiNPs-induced transformation. Further, data confirmed the inactivated p53 and aberrant p53 signaling under chronic amorphous SiNPs exposure. In summary, our data firstly demonstrated chronically low-dose amorphous SiNPs exposure resulted in malignant transformation of human lung epithelial cell <i>via</i> p53 signaling, which provides new <i>in vitro</i> evidence for the carcinogenicity of amorphous SiNPs.