cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.971450
title: Carbon isotopic composition of dissolved inorganic carbon (δ13C-DIC) at IODP Site 370-C0023, Nankai Trough subduction zone

description: This dataset includes the carbon isotopic composition of dissolved inorganic carbon (δ13C-DIC) of sediment cores that were retrieved from Site C0023 (Hole A) during International Ocean Discovery Program (IODP) Expedition 370 in the Nankai Trough offshore Japan in the Pacific Ocean (Drilling vessel Chikyu). Site C0023 was established on 17 September 2016. Coring terminated on 3 November 2016.
description: The carbon isotopic composition of DIC (δ13C-DIC) was determined via isotopic ratio monitoring-gas chromatography mass spectrometry (irm-GC-C-MS; Thermo Finnigan Delta Plus XP isotope-ratio mass spectrometer (IRMS) connected to TRACE GC Ultra gas chromatograph) according to Ijiri et al. (2012) at the Kochi Institute for Core Sample Research, JAMSTEC, Japan. The δ13C-DIC values are expressed relative to VPDB (Vienna Pee Dee Belemnite). The standard deviation from repeated carbon isotope analysis of the laboratory standard (NaHCO3 solution) was &lt;0.2‰.
DOI: 10.6075/j03r0s65
title: CIL:41579, Cricetulus griseus, epithelial cell. In Cell Image Library

description: CHO cells at metaphase were treated with 50% D2O, fixed with glutaraldehyde, embedded in epoxy resin and 0.5 micrometer 'thick' sections stained with uranyl acetate and lead citrate for HVEM observation.
See also:
H. Ris 1981 Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96
H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
description: High voltage (1MeV) transmission electron microscopy image of a 0.5 micrometer section through a Chinese hamster ovary cell at metaphase showing a chromatid pair, with kinetochores at the centromere. The image was taken with a specimen tilt of 53 degrees and is one of a group of 5 tilts from 73 degrees to 33 degrees at 10 degree intervals. Pairs of images provide oblique stereo views of the chromosome.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; lead salt
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0g73cpv
title: CIL:35479, Homo sapiens, hepatocyte. In Cell Image Library

description: Fluorescence image of tripolar mitosis in a liver cancer cell line. Normally, dividing cells form a single metaphase plate of paired chromosomes which are pulled apart by opposing microtubule spindles. This Z series obtained using a laser scanning confocal microscope shows abnormal division by three sets of spindles.
 This image group includes other z-series and a 3D surface representation.
description: HuH-7 cells are an immortalized cultured cell line derived from hepatic carcinoma. Cells were grown on 1.5 glass coverslips, fixed with formaldehyde and glutareldehyde, extracted, and labeled for fluorescence microscopy with commercial antibodies to alpha- or beta-tubulin and propidium iodide. The coverslip was mounted on a slide in PBS and glycerol with n-propyl gallate as an antifading agent. Imaging was performed with a BioRad MRC 600 laser scanning confocal microscope with a Kr/Ar laser with lines at 488 and 568 nm. The microscope was a fixed tube length Nikon Diaphot with 60X N.A. 1.4 phase 3 optics. Z series was collected at 0.2 um step sizes. The original XY spatial scale has been lost.
description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Fluorescein (FITC); propidium iodide
Processing history: unprocessed raw data
Data qualification: Processed
DOI: 10.1594/pangaea.905681
title: OA and ripples metabolism data
DOI: 10.6075/j0vx0gbs
title: CIL:36917, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: This is IMAGE #3 (day 3) of a time lapse series contained with in this image group. It shows a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47.
 
 The images were acquired daily over 3 days and show dendritic arbor development and morphological plasticity of the dendritic arbor with branch additions and retractions.
 
 The cell was transfected with in vivo electroporation of plasmid DNA encoding eYFP ~24 hours before the first image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
DOI: 10.6075/j0rj4jbd
title: CIL:37072, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: This is IMAGE #1 of a group of neurons from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. This neuron cluster is part of an image group. The cells were imaged daily over 2 days and the images show the development of the dendritic arbors of the neurons. IMAGE #2 is another view of this same image group.
 
 The cells were transfected with in vivo electroporation of plasmid DNA encoding eGFP ~24 hours before the image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
DOI: 10.6075/j0qn66kw
title: CIL:37042, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: This is IMAGE #4 (time point: 4 hours)of an image group. It shows a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. In the series, z-stacks of this neuron were acquired at a 2 hour interval for 8 hours. Afterward, a second time lapse series was acquired at a 60 second interval for 10 minutes. This time series shows dendritic arbor development and morphological plasticity of the dendritic arbor with branch additions and retractions. The cell was transfected with in vivo electroporation of plasmid DNA encoding eGFP ~24 hours before the image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
DOI: 10.6075/j0w095rv
title: CIL:36868, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: This is IMAGE #3 (20 minutes) of a time lapse series contained with in this image group. It shows neurons from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47.
 
 The images were acquired with ~10 minute intervals and show morphological plasticity of the dendritic arbor with branch additions and retractions.
 
 These cells were transfected ~24 hours earlier with in vivo electroporation of plasmid DNA encoding eYFP. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
 
 Images were acquired a 0, 10, 20, 30, and 50 minutes. After 60 minutes, the animal was placed in a 50 microMolar anisomycin solution for ~4 hours. A second time lapse series (10 minute interval for 60 minutes) was then acquired.
description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.15468/dl.5638p2
title: Occurrence Download

description: A dataset containing 1315 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((70.37956 -34.62742,183.62044 -34.62742,183.62044 10.62742,70.37956 10.62742,70.37956 -34.62742))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Uromys caudimaculatus"
 ]
}

 The dataset includes 1315 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009195-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j06m35z8
title: CIL:9700, Coleps hirtus, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: film; Print from negative scanned for Photoshop.
description: Some tubules near a contractile vacuole which appear to be decorated with pegs similar to the spongiome of the CV of Paramecium. In Paramecium these pegs are known to be V-type proton pumps (V-ATPases). Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. TEM taken on 3/2/69 by R. Allen with Philips 300. Neg. 12,500X. Bar = 0.5µm. A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. A high resolution image (CIL:9253) is available for quantitative analysis. Additional information is available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j06w9980
title: CIL:9702, Coleps hirtus, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Section through the cytopharynx of Coleps showing the corrugated lips containing lamellae surrounding the atrium of the buccal cavity. Rods composed of hexagonally packed microtubules that support the buccal cavity are seen in the cytoplasm. At the periphery an algal endosymbiont enclosed within a membrane is observed. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. TEM taken on 3/24/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,800X. Bar = 0.5µm. A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. A high resolution image (CIL:2869) is available for quantitative analysis.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: unprocessed raw data; film; Printed and scanned for Photoshop
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j00g3j92
title: CIL:9717, Coleps hirtus, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A longitudinal section of somatic cilia of Coleps showing the axoneme, basal body, and attached fibrous and microtubular elements. Adjacent digestive vacuoles and cortical cytoplasm evident with typical ciliate tubular mitochondrial cristae. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. TEM taken on 5/24/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,800X. Bar = 0.5µm. A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. A high resolution image (CIL:2870) is available for quantitative analysis.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j0b8578p
title: CIL:9705, Euplotes sp., cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A high resolution image of the cilia of a membranelle of the AZM (adoral zone of membranelles) have well defined doublets, singlets and dynein arms as well as spokes. Euplotes has a plasma membrane which covers a very flat and electron opaque alveolar sac. The alveolar sac membrane appears less opaque than the alveolar content. The septum between alveoli forms a slight bulge in the cell surface. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. TEM taken on 7/29/67 by R. Allen with Philips 200 operating at 60kV. Neg. 28,000X. The raw negative was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Additional information is available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0862fkr
title: CIL:9704, Euplotes sp., cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: A high resolution image of a dikinetid of Euplotes shows the transverse microtubular ribbon as well as a postciliary ribbon extending from the posterior basal body. Vesicles containing electron opaque bodies are typically found next to basal bodies. A peroxisome is also present. In this section a pattern of cross-hatched microtubules lies immediately under the cell surface membranes. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. TEM taken on 8/3/67 by R. Allen with Philips 200 operating at 60kV. Neg. 19,200X. The raw negative was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Additional information is available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j06w9963
title: CIL:9806, Euplotes sp., cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A high resolution image of an individual cirrus of Euplotes with 91 cilia/basal body complexes. The transition from basal body to cilium can be followed from right to left in each row. Small vesicles, many containing electron opaque granules, surround the base of the cirrus. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. TEM taken on 7/24/67 by R. Allen with Philips 200 operating at 60kV. Neg. 12,400X. The raw negative was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Additional information is available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0zs2vnp
title: CIL:9720, Coleps hirtus, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print from negative scanned to Photoshop.
Data qualification: Processed;spatialmeasurements
description: This image of a cortical monokinetid shows the basal body as well as postciliary and transverse microtubular ribbons. Slender endosomal vesicles accumulate near the bottom of a parasomal sac which is located out of the plane of section, and a round mucocyst lies adjacent to the basal body. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. TEM taken on 5/25/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,500X. The negative was printed to paper and the image was scanned with a flatbed scanner and 0.5µm bar added in Photoshop. This digitized image is available for qualitative analysis. A raw, unprocessed, high resolution version of this image (CIL:9016) is in the library and available for quantitative analysis.
Additional information available at (http://www5.pbrc.hawaii.edu/allen/).