cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0zs2wvs
title: CIL:57368. In Cell Image Library

description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Ebola virus Huh7 infected cells 22 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
DOI: 10.6075/j03f4q02
title: CIL:57371. In Cell Image Library

description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Ebola virus Huh7 infected cells 22 hours post infection, anti-nucleocapsid immuno-golg labelling.
DOI: 10.6084/m9.figshare.30499770
title: Antibiotic resistance and first comprehensive genomic characteristics of <i>Salmonella</i> Gallinarum isolated from poultry in Morocco

description: Fowl typhoid, caused by <i>Salmonella enterica</i> subspecies <i>enterica</i> serovar Gallinarum biovar Gallinarum (SG), is a critical disease listed by the World Organization for Animal Health (WOAH) that causes substantial economic losses in the global poultry industry. In this study, 23 SG strains were isolated from poultry in Morocco showing typical lesions of fowl typhoid, including splenomegaly and hepatomegaly with necrotic foci and peritonitis. The isolates were biochemically identified and tested for phenotypic antibiotic susceptibility. Whole genome sequencing (WGS) was used for studying the genetic characteristics of isolated strains and to determine the virulence and antibiotic-resistance markers. Antibiotic susceptibility testing revealed that 13 (56.5%) isolates were resistant to flumequine with eight (34.8%) and 9 (39.1%) isolates having intermediate resistance to tetracycline and colistin, respectively. WGS revealed 26 resistance genes, coding mainly for efflux pumps and beta-lactamase, including <i>aac</i>(6’)-<i>Iaa</i>, aac(3)-IIa and <i>bla</i><sub>TEM-1a</sub>. Virulence profiling identified 107 genes and multiple <i>Salmonella</i> pathogenicity islands (SPIs), while mobile genetic elements analysis detected the IncI1-(α) plasmid in two strains, previously unreported in avian SG. Phylogenomic analysis showed that the isolated strains in this study were closely related to SG strains in the NCBI database, with eight strains phylogenetically linked to the SG9R vaccinal strain. Single Nucleotide Polymorphism (SNP) analysis, using the parental SG9 vaccine strain as a reference, revealed a low number of variants in these eight strains, suggesting reversion to virulence. These findings enhance understanding of SG’s genomic features, aiding improved management of fowl typhoid, vaccine programme development and reduction of antibiotic resistance in poultry. Identified 26 antibiotic resistance genes, including novel plasmid IncI1-(α) never described in <i>Salmonella</i> Gallinarum.Revealed 107 virulence genes and multiple complete SPIs like SPI-1 and SPI-2.SNP analysis suggested reversion to virulence in eight vaccine-related strains. Identified 26 antibiotic resistance genes, including novel plasmid IncI1-(α) never described in <i>Salmonella</i> Gallinarum. Revealed 107 virulence genes and multiple complete SPIs like SPI-1 and SPI-2. SNP analysis suggested reversion to virulence in eight vaccine-related strains.
DOI: 10.6084/m9.figshare.30499770.v1
title: Antibiotic resistance and first comprehensive genomic characteristics of <i>Salmonella</i> Gallinarum isolated from poultry in Morocco

description: Fowl typhoid, caused by <i>Salmonella enterica</i> subspecies <i>enterica</i> serovar Gallinarum biovar Gallinarum (SG), is a critical disease listed by the World Organization for Animal Health (WOAH) that causes substantial economic losses in the global poultry industry. In this study, 23 SG strains were isolated from poultry in Morocco showing typical lesions of fowl typhoid, including splenomegaly and hepatomegaly with necrotic foci and peritonitis. The isolates were biochemically identified and tested for phenotypic antibiotic susceptibility. Whole genome sequencing (WGS) was used for studying the genetic characteristics of isolated strains and to determine the virulence and antibiotic-resistance markers. Antibiotic susceptibility testing revealed that 13 (56.5%) isolates were resistant to flumequine with eight (34.8%) and 9 (39.1%) isolates having intermediate resistance to tetracycline and colistin, respectively. WGS revealed 26 resistance genes, coding mainly for efflux pumps and beta-lactamase, including <i>aac</i>(6’)-<i>Iaa</i>, aac(3)-IIa and <i>bla</i><sub>TEM-1a</sub>. Virulence profiling identified 107 genes and multiple <i>Salmonella</i> pathogenicity islands (SPIs), while mobile genetic elements analysis detected the IncI1-(α) plasmid in two strains, previously unreported in avian SG. Phylogenomic analysis showed that the isolated strains in this study were closely related to SG strains in the NCBI database, with eight strains phylogenetically linked to the SG9R vaccinal strain. Single Nucleotide Polymorphism (SNP) analysis, using the parental SG9 vaccine strain as a reference, revealed a low number of variants in these eight strains, suggesting reversion to virulence. These findings enhance understanding of SG’s genomic features, aiding improved management of fowl typhoid, vaccine programme development and reduction of antibiotic resistance in poultry. Identified 26 antibiotic resistance genes, including novel plasmid IncI1-(α) never described in <i>Salmonella</i> Gallinarum.Revealed 107 virulence genes and multiple complete SPIs like SPI-1 and SPI-2.SNP analysis suggested reversion to virulence in eight vaccine-related strains. Identified 26 antibiotic resistance genes, including novel plasmid IncI1-(α) never described in <i>Salmonella</i> Gallinarum. Revealed 107 virulence genes and multiple complete SPIs like SPI-1 and SPI-2. SNP analysis suggested reversion to virulence in eight vaccine-related strains.
DOI: 10.5281/zenodo.17492473
title: Global warming enhances nitrogen-limitation in a temperate reservoir system under consistent external load.

description: Data belonging to AGU:Water Resources Research submission:

Global warming and continued external loading increase nitrogen limitation in a temperate reservoir system.

Climate change impacts hydrology, geochemistry, and biology of lakes and reservoirs worldwide, also affecting surface water concentrations of the essential nutrients nitrogen (N) and phosphorus (P). Few studies have illustrated climate change’s impact on nutrient processing due to compounded effects of both climate change and catchment inputs. In this study, we have evaluated monitoring data from the years 2000 to 2019 in the Franconian Lake District (FLD), which consists of one shallow (hypertrophic) and three deep reservoirs (meso- to eutrophic), interconnected by a transfer canal. The cascade configuration and consistent external load buffer catchment variations, making nutrient trends attributable to internal processing. Mass balances were set up and statistical analyses were conducted for trends in stratification, hypolimnetic anoxia and nutrient concentrations. Warming significantly increased water temperature (+0.35-1.0°C decade−1 ), stratification (+7-18 days decade−1), and hypolimnetic anoxia (+15-35 days decade−1). TP increased in deep reservoirs (+0.006-0.01 mg-P L−1 decade−1 ) and TN decreased in all reservoirs (−0.2-0.4 mg-N L−1 decade−1 ). The increased rates of NO3-loss could be related to enhanced denitrification rates and earlier algal uptake. Increased TP-concentrations were attributable to increased sediment P-release, induced by prolonged stratification and hypolimnetic anoxia. Primarily, the decrease in TN drove a strong decrease in TN:TP-ratio (-4 to -15 mol:mol decade−1), triggering a biogeochemical regime shift towards N-limitation, associated with proliferation of harmful algae blooms. The identified impacts emphasizes the need to consider the potential disruptive effects of intensifying climate change on the health and restoration efforts for temperate, eutrophic lakes worldwide.
DOI: 10.6075/j09z958z
title: CIL:57228, Ebola virus - Mayinga, Zaire, 1976, Huh7. In Cell Image Library

description: Pixel size: 83.92 Å; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Ebola virus Huh7 infected cells 14 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
DOI: 10.6075/j0t15417
title: CIL:57229, Ebola virus - Mayinga, Zaire, 1976, Huh7. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Pixel size: 83.92 Å; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Ebola virus Huh7 infected cells 14 hours post infection, anti-nucleocapsid immuno-golg labelling.
DOI: 10.6075/j0fq9x09
title: CIL:57216, Ebola virus - Mayinga, Zaire, 1976, Huh7. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Ebola virus Huh7 infected cells 14 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Pixel size: 83.92 Å; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
DOI: 10.6075/j090245w
title: CIL:57230, Ebola virus - Mayinga, Zaire, 1976, Huh7. In Cell Image Library

description: Ebola virus Huh7 infected cells 14 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Pixel size: 83.92 Å; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
DOI: 10.6075/j0668dk0
title: CIL:57235, Ebola virus - Mayinga, Zaire, 1976, Huh7. In Cell Image Library

description: Pixel size: 83.92 Å; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Ebola virus Huh7 infected cells 14 hours post infection, anti-nucleocapsid immuno-golg labelling.
DOI: 10.15468/dl.v5u7tw
title: Occurrence Download

description: A dataset containing 2120 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((72.69386 5.15859,158.26886 -19.61312,147.17169 52.28231,119.76499 59.19356,92.00081 42.51123,70.79042 40.12803,61.37681 29.16536,72.69386 5.15859))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Androsace umbellata"
 ]
}

 The dataset includes 2120 records from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009633-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0cr5s53
title: CIL:10929, Felis catus, epithelial cell, enterocyte. In Cell Image Library

description: This electron micrograph shows a region of the brush border of the cat intestine. Tufted and branched polysaccharide filaments, each a few nanometers thick, extend from the microvilli to make up the glycocalyx, or surface coat, on the surface of plasma membrane of these epithelial cells. This image, courtesy of Susumu Ito is Figure 16 from Chapter 1 (The Cell Surface) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: crosslinking-fixative fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Data qualification: Processed
DOI: 10.6084/m9.figshare.30499700
title: Example dataset for testing IonStats tool.

description: This dataset is a small test set for users to try IonStats tool: https://github.com/ykoski/ionstats
DOI: 10.6084/m9.figshare.30499700.v1
title: Example dataset for testing IonStats tool.

description: This dataset is a small test set for users to try IonStats tool: https://github.com/ykoski/ionstats
DOI: 10.6075/j07943f9
title: CIL:11016, Batrachoseps attenuatus, myelocyte. In Cell Image Library

description: Transmission electron micrograph of a dividing myelocyte from the slender salamander Batrachoseps attenuatus showing mitotic chromosomes at late prophase.
description: Figure 126 from Chapter 4 (Nucleus) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the corresponding chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: tissue in plastic embedment; osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM); detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Processing history: Image extracted from .pdf file of 'The Cell'
Data qualification: Processed
DOI: 10.6075/j0b27t35
title: CIL:11014, Ovis aries, Cricetulus griseus, spermatogonium. In Cell Image Library

description: Figures 124 (upper) and 125 (lower from Chapter 4 (Nucleus) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: tissue in plastic embedment; osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM); detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Processing history: Image extracted from .pdf file of 'The Cell'
Data qualification: Processed
description: Transmission electron micrographs showing chromosomes in dividing spermatogonia during metaphase in tissue from ram testis (upper panel) and as they begin to separate during early anaphase in tissue from the Chinese hamster (lower panel).
DOI: 10.6075/j0hm5777
title: CIL:10900, unidentified monkey, epithelial cell. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Data qualification: Processed
description: With the freeze-fracture technique, tissue is rapidly frozen and cracked to shear along zones of weakness. Cleavage of membranes occurs along the hydrophobic interior of the lipid bilayer to reveal views of a "p-face" (the outwardly-facing inner half of the membrane) and an "e-face" (the inwardly-facing outer half of the membrane), and a metallic replica is made of the fractured surface.
description: This electron micrograph shows the E-fracture face (above) and P-fracture face (below) of the membrane of adjacent epithelial cells from the ciliary epithelium of the monkey eye. Intramembranous particles, representing integral membrane proteins, appear as bumpy projections, and are prominent in this image with high density on the p-face, but also can be detected on the e-face. This image, contributed by Giuseppina Raviola, is Figure 4 from Chapter 1 (The Cell Surface) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j09p30gj
title: CIL:10898, Cavia porcellus, Sertoli cell. In Cell Image Library

description: Freeze-fracture preparation of the plasma membrane from an unspecialized area composed of Sertoli cells of the guinea pig testis. With the freeze-fracture technique, tissue is rapidly frozen and cracked to shear along zones of weakness. Cleavage of membranes occurs along the hydrophobic interior of the lipid bilayer to reveal views of a "p-face" (the outwardly-facing inner half of the membrane) and an "e-face" (the inwardly-facing outer half of the membrane), and a metallic replica is made of the fractured surface. Intramembranous particles, representing integral membrane proteins, appear as bumpy projections, and are prominent on the p-face, but also can be detected on the e-face. The particles on the p-face range in size from 6 - 9 nm. Figure 3 from Chapter 1 (The Cell Surface) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Data qualification: Processed
DOI: 10.6075/j0542mdz
title: CIL:10989, Anura, Insecta, erythrocyte, spermatid. In Cell Image Library

description: Transmission electron micrographs. The upper panel shows a section through a frog nucleated erythrocyte. The nucleus is largely filled with heterochromatin which appears to have a fibro-granular structure when fixed with formaldehyde and osmium tetroxide. The lower panel shows the filamentous conformation of chromatin in an insect spermatid nucleus. Figure 119 (upper, courtesy of Hans Ris) and 120 (lower, courtesy of David Phillips) from Chapter 4 (Nucleus) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: tissue in plastic embedment; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM); detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Processing history: Image extracted from .pdf file of 'The Cell'
Data qualification: Processed
DOI: 10.6075/j0p849pm
title: CIL:10987, Unspecified, pancreatic acinar cell. In Cell Image Library

description: Preparation: tissue in plastic embedment; osmium tetroxide fixed tissue; glu
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM); detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Processing history: Image extracted from .pdf file of 'The Cell'
Data qualification: Processed
description: Transmission electron micrograph of glutaraldehyde fixed pancreatic acinar cell showing the characteristic features of nuclear chromatin with this preparative method. Darkly staining heterochromatin (here labeled 'chromatin') appears granular and concentrated at the nuclear periphery and nucleolus. Micrograph courtesy of Susumu Ito appears as Figure 118 from Chapter 4 (Nucleus) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the corresponding chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j00k27cw
title: CIL:10976, Myotis lucifugus, pancreatic acinar cell. In Cell Image Library

description: Preparation: tissue in plastic embedment; osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM); detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Processing history: Image extracted from .pdf file of 'The Cell'
Data qualification: Processed
description: Transmission electron micrograph of nucleus showing the characteristic features of glutaraldehyde fixation introduced as a primary fixative in 1962 and since used routinely. Chromatin appears differentiated into coarse, darkly stained heterochromatin that accumulates near the nuclear periphery and the nucleolus and less darkly staining euchromatin. In contrast, chromatin appears uniformly stained with osmium tetroxide as primary fixative (for example, see CIL image 10974, in this image group). Figure 113 from Chapter 4 (Nucleus) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the corresponding chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j0pv6j6v
title: CIL:10937, epithelial cell, enterocyte. In Cell Image Library

description: Preparation: crosslinking-fixative fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Data qualification: Processed
description: These two micrographs show the outer cell surface of the epithelial cell border in intestine (upper) and stomach (lower) tissue. This surface, called the glycocalyx, is composed of negatively charged acidic polysaccharides, which here, have been stained by binding a polycationic derivative of ferritin. High iron content causes electron scattering, and thus, regions to which the ferritin have bound appear dark in these images. These images, courtesy of Susumu Ito, are Figures 20 (upper) and 21 (lower) from Chapter 1 (The Cell Surface) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j0th8khv
title: CIL:10931, Myotis, epithelial cell, enterocyte. In Cell Image Library

description: Filaments extend from microvilli of the epithelial cells in the intestine of the bat, Moytis lucifugus in these two high magnification electron micrographs. These filaments, which are 2.5-5nm thick, and extend from 0.1 - 0.5µm beyond the microvilli, make up the glycocalyx that encompasses the brush border of the intestine. Filaments from each microvilli radiate and intermingle with those from adjacent microvilli to form a near-continuous network. Micrographs courtesy of Susumu Ito; upper panel was reprinted with permission from Fawcett, D. J. (1965) Histochem. Cytochem. 13: 75-95, and are figures 17 (upper) and 18 (lower) from Chapter 1 (The Cell Surface) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: crosslinking-fixative fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Data qualification: Processed
DOI: 10.3535/2l1-3bq-qqa
title: Donax vittatus (da Costa, 1778)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/406-mwp-wts
title: Campylaea planospira (Lamarck, 1822)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8qj-lfs-5hk
title: Petasina H. Beck, 1847

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/76j-rml-m01
title: Anadara pilula (Reeve, 1843)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.