cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28157091.v1
title: Impact of basalt application on soil chemical properties and elemental uptake by paddy rice through enhanced rock weathering

description: Enhanced Rock Weathering (ERW) is a negative emission technology in which crushed rock powder is applied to cropland to sequestrate carbon by enhancing chemical weathering of silicate minerals. It is a co-benefit approach to promote crop growth by supplying elements (silicon (Si), calcium (Ca), magnesium (Mg), etc.) from weathering rock as well. In this study, we cultivated paddy rice for 99 days in a pot experiment with Gray Lowland soil (pH = 6.19) with six application rates of basalt equivalent to 0, 5, 10, 20, 50, 100 t ha<sup>−1</sup>. We investigated the change of soil chemical properties and elemental uptake in rice. Then, we calculated the release of Si, Ca, Mg, potassium (K), and sodium (Na) from the basalt, and carbon balance between before planting and after harvest in the whole system including soil and plant. The application of the basalt increased the total amount of soil available Si and exchangeable Mg and Na in the pot as well as the uptake of Si and Na in rice (<i>p</i> &lt; 0.05). There was no significant difference in arsenic, cadmium, chromium, copper, and nickel concentrations in rice grain among the application rates of the basalt. The release of Si, Mg, and Na from the basalt increased corresponding to the application rate of the basalt, suggesting that the applied basalt was weathered during cultivation, though increased carbon sequestration by the basalt weathering was not detected in 99 days of this experiment. We clearly demonstrated that basalt powder got weathered and released Si, Mg, and Na in paddy field condition and additional Si enhanced paddy rice growth.
DOI: 10.15468/dl.fnczma
title: Occurrence Download

description: A dataset containing 2918 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((-75.09704 4.54567,-74.92303 4.54567,-74.92303 4.65155,-75.09704 4.65155,-75.09704 4.54567))"
 ]
}

 The dataset includes 2918 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042669-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mk8c49
title: Occurrence Download

description: A dataset containing 3778 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aegilops speltoides Tausch"
 ]
}

 The dataset includes 3778 records from 96 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020509-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6apgjy
title: Occurrence Download

description: A dataset containing 8017 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Bombus frigidus Smith, 1854"
 ]
}

 The dataset includes 8017 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0194226-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7g3f6k
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lactuca ramosissima (Benth.) Baker & S.Moore, 1879",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 30 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0181848-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hqmr7g
title: Occurrence Download

description: A dataset containing 228 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "GadmGid is BRA.13.338_2",
 "TaxonKey is Aves",
 "Year 1992-2022"
 ]
}

 The dataset includes 228 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0212864-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k85fph
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Boana atlantica (Caramaschi & Velosa, 1996)"
 ]
}

 The dataset includes 73 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0194248-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9a8st7
title: Occurrence Download

description: A dataset containing 6699 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Tinamiformes, Apterygiformes, Rheiformes, Struthioniformes, Dromaiidae, Casuariidae, Aepyornithidae, Dinornithidae, Lithornithidae)"
 ]
}

 The dataset includes 6699 records from 118 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0212855-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60933/prdr/rwjucx/azkjam
title: SRR23252442.sra

description: Treatment: Adipogenic differentiation
DOI: 10.15468/dl.58meym
title: Occurrence Download

description: A dataset containing 121967 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "Country is one of (United States of America, United States Minor Outlying Islands, American Samoa, Micronesia (Federated States of), Guam, Marshall Islands, Northern Mariana Islands, Puerto Rico, Palau, Virgin Islands (U.S.))",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Plethodon cinereus (Green, 1818))"
 ]
}

 The dataset includes 121967 records from 84 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0181834-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3nd6ea
title: Occurrence Download

description: A dataset containing 18155 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Spain",
 "IucnRedListCategory is EN",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 18155 records from 284 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0242085-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r5vnbj
title: Occurrence Download

description: A dataset containing 15416072 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Passer domesticus (Linnaeus, 1758)"
 ]
}

 The dataset includes 15416072 records from 2750 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0227961-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j01v5d8t
title: CIL:39521, Saccharomyces cerevisiae. In Cell Image Library

description: The images were acquired using a 60x 1.42 NA objective lens on Delta Vision system equipped with CoolSNAP_HQ2 / HQ2-ICX285. Please see the microscopy section in the referenced manuscript for details for image analysis.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cdc20, a cell-cycle regulated activator of anaphase-promoting complex/cyclosome (APC/C) required for metaphase/anaphase transition; directs ubiquitination of mitotic cyclins, Pds1p, and other anaphase inhibitors; potential Cdc28p substrate novel protein thought to be involved in cell cycle regulation.These phase,gfp z-series images are part of an image group that ranges from CIL:39521-39525. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0mk6bt2
title: CIL:35144, Mus musculus, macrophage. In Cell Image Library

description: Phase contrast microscopy of living bone marrow derived macrophages. These cells are highly motile and the snapshot catches lamella and ruffles where the cells are protruding and phase dense organelles inside the volumes of the cells.
description: Cells were extracted from a mouse femur and plated in a coverslip bottom well (MatTek) in standard culture media. The Olympus IX 71 microscope had a simple heated stage. Cells were imaged with a 60X N.A. 1.4 phase 3 planapo objective with a Cooke Sensicam QE operated by IP Lab software running on a Dell Windows XP computer.

This picture is one of a series that may be composed into a montage to see a large field of cells interacting while preserving the high magnification. Some of the pixels in this and the neighboring images are saturated.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j01v5d7c
title: CIL:711, Gallus gallus, nucleate erythrocyte. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons
Parameter imaged: electron density
Source of contrast: elastic scattering
Visualization methods: visualization of contiguous regions; uranyl salt
Processing history: unprocessed raw data
description: chicken erythrocyte nuclei were allowed to decondense in a low salt high pH buffer, fixed with HCOH, centrifuged onto a carbon coated EM grid, and stained with uranyl acetate. (Spreading technique of Oscar L Miller Jr).
 Beaded chains of nucleosomes separated by linker DNA are seen emanating from a central mass of less dispersed chromatin.
DOI: 10.6075/j0x63kkp
title: CIL:28750. In Cell Image Library

description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
description: One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of five subsets with increasing degree of clustering. Five subsets of 20 images each are provided. Each image contains 300 objects, but the objects overlap and cluster with overlap probability ranging from 0.0 to 0.6, and can be found with CIL 27833, 27853, 28754, 28734, and 28714, respectively. This image set has 0.45 probability overlap. The images were generated with the SIMCEP (http://www.cs.tut.fi/sgn/csb/simcep/tool.html) simulating platform for fluorescent cell population images (Lehmussola et al., IEEE T. Med. Imaging, 2007 and Lehmussola et al., P. IEEE, 2008). Ground truth for foreground/background segmentation are available as binary images as the second image in the tiff image stack. 
Recommended citation "We used the Synthetic 1 image set (Ruusuvuori et al., in Proc. of the 16th European Signal Processing Conference (EUSIPCO-2008), 2008), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
DOI: 10.6075/j0nc5ztc
title: CIL:39168, Paramecium caudatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: This micrograph shows that the discoidal vesicles meet the cytopharyngeal membrane edge-on where they fuse. Besides the ribbon of 12 microtubules abutting the membrane there is a second small ribbon of 2 or 3 microtubules lying against the cytopharyngeal membrane on the posterior side of each ribbon. This narrow ribbon does not curve away from the membrane but remains close to the membrane and its termination marks the boundary line between the cytopharynx and the nascent vacuole membrane. TEM taken on 7/27/73 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 12,750X. Published in J. Cell Biol. 63:904-922, 1974. Adapted with permission.
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used 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; microtome-sectioned tissue
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; uranyl salt; osmium tetroxide; lead salt
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.15468/dl.593ncc
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Cirsium souliei"
 ]
}

 The dataset includes 10 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009283-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j08p604w
title: CIL: 53368. In Cell Image Library

description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: CAMK family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j06d5sj1
title: CIL: 52604. In Cell Image Library

description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: One z layer of a z-stack at the given tile position
description: Tile x=2, y=1, z=12 from PS09_20676_2B_Myc_Terc
DOI: 10.6075/j0gm87bd
title: CIL:36171, Rattus, multipolar neuron. In Cell Image Library

description: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for MAP2 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a 20X objective (Fluotar, 0.5NA), Photometrics CoolSnap ES CCD camera and MetaMorph software. This color was generated using the MetaMorph "color combine" function.
description: Synapse development in cultured hippocampal neurons after 15 days in vitro. Neurons were immunostained for MAP2, a microtubule associated protein localized to dendrites (green) and the presynaptic vesicle protein Synapsin I (red) to show the density of presynaptic contacts along the dendritic arbor.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0jq10kn
title: CIL: 52784, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Tile x=1, y=1, z=3 from PS11_167511L_Myc_Terc
DOI: 10.15468/dl.4kdw4b
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Chondrilla laticoronata"
 ]
}

 The dataset includes 7 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009284-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0b857fx
title: CIL:39792, Tetrahymena pyriformis, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The contractile vacuole, an organelle used by many protists for osmoregulation of water and some ions, such as calcium, is connected to the cell surface in Tetrahymena usually by two ‚Äúpores," indentations of the plasma membrane. A spent food vacuole lies nearby. TEM taken on 1/8/74 by R. Wolf with Hitachi HU11A operating at 75kV. Neg. 17,500X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
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
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0qn66f3
title: CIL: 53778, Homo sapiens, HeLa. In Cell Image Library

description: CMGC family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Visualization methods: confocal microscopy
description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
DOI: 10.6075/j0zk5fkw
title: CIL:36553, Xenopus laevis, fertilized egg. In Cell Image Library

description: This image is part of a large data set of Xenopus laevis eggs imaged at various times post fertilization (the first number of the file name corresponds minutes, eg 30_2 is 30 min post fertilization). The embryos are stained for alpha-tubulin (green) using a directly labeled B-5-1-2 antibody and DNA (red).
description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: labeled primary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
DOI: 10.6075/j0hd7vhz
title: CIL: 54696, Bacteria E coli, MC1061. In Cell Image Library

description: Live cell bacterial imaging, expressing fluroescent protein in the cytoplasm.
description: sfGFP with TIR-STD site, scale bar 4 um.
description: Imaging mode: EPI on a Nikon TiE2 Hamamatsu ORCA Flash 4.0 sCMOS Camera and Nikon SR Apo TIRF 100x objective lens (NA 1.49)