cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0d50kqb
title: CIL:13113, Paramecium multimicronucleatum, 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; 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; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: A high resolution micrograph of the Contractile Vacuole Complex membrane system to determine what happens to the CV during systole we observed the CV in a living cell and then fixed the cell as soon as the CV had opened to the outside. It was apparent that the CV membrane does not flatten into an empty sac but the CV membrane undergoes rapid tubule formation and collapses as a continuous mat of tubules that maintains its connection to the microtubular ribbons. These tubules are a uniform 40nm in diameter. TEM taken on 6/9/96 by R. Allen with Zeiss 10A operating at 80kV. Neg. 19,800X. Adapted with permission from the J. Exp. Biol. 200:1737-1744, 1997. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. 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/).
DOI: 10.6075/j0br8rbr
title: CIL:13112, Paramecium multimicronucleatum, 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; 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; Print from negative scanned for Photoshop.
Data qualification: Processed
description: Collecting canal of the contractile vacuole complex. Normally the collecting canal is expanded when the CV is in systole. In this micrograph the collecting canal is empty so that its two sides are flattened against each other. Presumably the CV is in diastole (filling phase). The ribbon of microtubules is split into 10 groups of two tubules each so the ribbon has 18 to 20 microtubules at this level. The smooth spongiome is connected to the collecting canal and bundles of decorated spongiome form the peripheral layer of the radial arm. The decorations consist of 2 closely set globular units forming a helix around the tubule. In this micrograph the globular units are outlined with more electron dense material so it appears there are 3 threads making up a helix. TEM taken on 12/9/70 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 24,000X. Bar = 0.2µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. An unprocessed, high resolution version of this image (CIL:13096) is in the library and available for quantitative analysis. 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/).
DOI: 10.6075/j08k77sn
title: CIL:13129, Paramecium multimicronucleatum, 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; 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; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: A high resolution image of the changes in the membrane complexes of the Contractile Vacuole Complex. This image illustrates the changes in the CVC caused by cell division and microinjecting mAbs specific for an antigen of the V-ATPase holoenzyme into a P. multimicronucleatum cell. Each condition causes the disappearance of the decorated tubules from the radial arms. In this micrograph the cell was injected with 86 µg/ml of serum containing the DS-1 mAb for the A4 antigen and lightly fixed 45 min later. It is observed that the bundles of decorated tubules had started to round into vesicles, several tubules forming one vesicle. By extrapolation, during bundle formation several decorated tubules apparently arise from each vesicle which accounts for the bundles of tubules emptying into a common duct. The common duct opens into the smooth spongiome. We believe that the V-ATPases have probably lost their functional integrity when the tubules vesiculate as the tubules close to the vesicles in this micrograph no longer have helical decorations. TEM taken on 3/30/93 by M. Ishida with Zeiss 10A operating at 80kV. Neg. 19,800X. Adapted with permission from the J. Cell Sci. 108:693-702, 1993. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. 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/).
DOI: 10.6075/j0z89bh5
title: CIL:13128, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: High resolution image of quick-freeze deep-etch of the P-face of the contractile vacuole. This face has many IMPs that are presumably transmembrane proteins many of which have been pulled free of the leaflet. There are also pits in this leaflet which represent the IMPs that remain with the opposite leaflet. Although we have found no mechano-sensitive or voltage-gated channels in the CVC (Sugino et al., J. Exp. Biol. 208:3957-3969, 2005) it is clear that proton pumps are present in the decorated tubules and that protons are exchanged for other ions such as calcium, potassium and sodium as these ions can accumulate in the CV against a concentration gradient from the cytosol. Some of the IMPs may function as ion exchange channels. What caused the large holes is not known. The texture of the luminal contents resembles the CV content and indicates the membrane is indeed that of the contractile vacuole. TEM taken on 5/27/92 by R. Allen with Zeiss 10A operating at 80kV. Neg. 31,500X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0wm1c2j
title: CIL:13120, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: Quick-freeze deep-etch image of two decorated tubules with helically wound subunits on their cytosolic surfaces. Each step in a helical turn appears to be formed of three dyads lying side by side across the row. Each dyad appears to be independent with the other two dyads at each step. Thus each helical row apparently consists of a long series of three dyads lying end to end rather than two rows of subunits. This accounts for the three lines per helix observed in some studies (McKanna, J. Ultrastruct. Res. 54:1-10, 1976. Following the tubules downward in this picture the fracture exposes the inside of one tubule and IMPs exposed here may represent the luminal transmembrane extensions of their much larger heads that appear on the cytosolic surface of the tubule. Additionally, a filled collecting canal lies near the decorated tubules with its P-fracture face exposed that is studded with IMPs. A row of indentations leading to openings to the smooth spongiome and holes in a second row are visible. IMPs appear to have different diameters on this P-face and some are organized into rows. The content of the collecting canal lumen has a uniquely etched pattern distinguishing it from other vacuoles and the cytosol. Adapted with permission from the Journal of Cell Science. TEM taken on 6/22/88 by C. Schroeder with Zeiss 10A operating at 60kV. Neg. 31,500X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0np23m9
title: CIL:1312, Paramecium tetraurelia, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in vitreous ice embedment; microtome-sectioned tissue; monoclonal antibody
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: intrinsic mass distribution; stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; gold
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: High resolution image of the surface pattern of P. tetraurelia in a region with two basal bodies in each cortical unit. This is a thin-frozen section labeled with immunogold showing the location of b-tubulin. The gold lies over the microtubules of the x-sectioned basal bodies and ciliary axonemes. It also labels tangentially sectioned transverse and postciliary microtubules. Neither the infraciliary lattice, the less obvious striated bands or the kinetodesmal fibers are labeled with anti-b-tubulin. TEM taken on 7/8/96 by R. Allen with Zeiss 10A operating at 80kV. Neg. 12,000X. Cells were lightly fixed with 0.25% glutaraldehyde and infiltrated with 2.3M sucrose before being frozen in liquid nitrogen and thin sectioned at a temperature of –100°C at approximately 75nm thickness. Frozen sections from these preparations were then thawed, washed, and exposed to a monoclonal primary antibody that was raised in mice or rabbit/goat and to colloidal gold-complexed goat-anti-mouse/rabbit secondary antibodies. Further details of preparation are detailed in Methods Cell Biol. 2010;96:143-73. The raw film was scanned with a Nikon Coolscan 9000ED. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0r78czt
title: CIL:13121, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High resolution image of when the antigen was visualized with immunogold using DS-1 on thin-frozen sections the antigen could be seen to be present on the periphery of the decorated tubules. The collecting canal and smooth spongiome were not labeled with this mAb. Please see the paper for details. TEM taken on 3/22/86 by R. Allen with Zeiss 10A operating at 80kV. Neg. 12,000X. Adapted with permission from J. Cell Sci. Cells were lightly fixed with 0.25% glutaraldehyde and infiltrated with 2.3M sucrose before being frozen in liquid nitrogen and thin sectioned at a temperature of –100°C at approximately 75nm thickness. Frozen sections from these preparations were then thawed, washed, and exposed to a monoclonal primary antibody that was raised in mice or rabbit/goat and to colloidal gold-complexed goat-anti-mouse/rabbit secondary antibodies. Further details of preparation are outlined in Methods Cell Biol. 2010;96:143-73. The raw film was scanned with a Nikon Coolscan 9000ED. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; tissue in vitreous ice embedment; microtome-sectioned tissue; monoclonal antibody
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: intrinsic mass distribution; stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; gold
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0h70dk3
title: CIL:13123, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in vitreous ice embedment; microtome-sectioned tissue; monoclonal antibody
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: intrinsic mass distribution; stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; gold
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: High resolution micrograph that shows the pegs on the surface of the decorated tubules that are negatively stained by the uranyl acetate dissolved in the methylcellulose solution used to give support to the frozen then thawed section. This section was labeled by a polyclonal antibody to the V-ATPase of Dictyostelium which cross-reacts with the V-ATPase in Paramecium. TEM taken on 2/28/92 by R. Allen with Zeiss 10A operating at 80kV. Neg. 31,500X. Adapted with permission from J. Cell Sci. Cells were lightly fixed with 0.25% glutaraldehyde and infiltrated with 2.3M sucrose before being frozen in liquid nitrogen and thin sectioned at a temperature of –100°C at approximately 75nm thickness. Frozen sections from these preparations were then thawed, washed, and exposed to a monoclonal primary antibody that was raised in mice or rabbit/goat and to colloidal gold-complexed goat-anti-mouse/rabbit secondary antibodies. Further details of preparation are outlined in Methods Cell Biol. 2010;96:143-73. The raw film was scanned with a Nikon Coolscan 9000ED. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.5281/zenodo.10303827
title: Outputs of the "Passenger demand mobility model" developed for South Asia

description: This dataset comprises outputs and intermediate calculations of the passenger mobility demand model developed for South Asian regions. The dataset includes the following: 



'Total_PDT.zip' folder contains files of the type total_pdt_scename_j_m.csv:



 These CSV files are the model output that contain passenger distance travelled (PDT) by mode in each area type and distance category for daily travel; and PDT by mode for long distance travel in different scenarios (scen_name), type of urbanisation (j), and mode share trajectory (m).

scename- This refers to the scenarios considered which are as follows - 'Base', 'NP', 'BP', 'TOD and 'TECH'

j- This refers to the type of urbanisation trajectories considered and are defined as follows:



1  -  Urbanisation_type_trajectory_1.csv

2  -  Urbanisation_type_trajectory_2.csv



m- This refers to the mode share trajectories considered in this study and are defined as follows:



1- Business as Usual (BaU)

2- Car-oriented future (COF)

3- Sustainable future (SF)








Trip rates calculated for SSP 2- trip_rate_2.csv
DOI: 10.5281/zenodo.17492238
title: Outputs of the "Passenger demand mobility model" developed for South Asia

description: This dataset comprises outputs and intermediate calculations of the passenger mobility demand model developed for South Asian regions. The dataset includes the following: 



'Total_PDT.zip' folder contains files of the type total_pdt_scename_j_m.csv:



 These CSV files are the model output that contain passenger distance travelled (PDT) by mode in each area type and distance category for daily travel; and PDT by mode for long distance travel in different scenarios (scen_name), type of urbanisation (j), and mode share trajectory (m).

scename- This refers to the scenarios considered which are as follows - 'Base', 'NP', 'BP', 'TOD and 'TECH'

j- This refers to the type of urbanisation trajectories considered and are defined as follows:



1  -  Urbanisation_type_trajectory_1.csv

2  -  Urbanisation_type_trajectory_2.csv



m- This refers to the mode share trajectories considered in this study and are defined as follows:



1- Business as Usual (BaU)

2- Car-oriented future (COF)

3- Sustainable future (SF)








Trip rates calculated for SSP 2- trip_rate_2.csv
DOI: 10.6075/j01v5d41
title: CIL:13122, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High resolution electron micrograph of a thin frozen section treated with a clone of the mAb (D40-2) used to show the A4 antigen on decorated tubules. The immunogold lies along the outer margin of these tubules for the most part. Mitochondria are not labeled. TEM taken on 2/10/93 by R. Allen with Zeiss 10A operating at 80kV. Neg. 19,800X. Cells were lightly fixed with 0.25% glutaraldehyde and infiltrated with 2.3M sucrose before being frozen in liquid nitrogen and thin sectioned at a temperature of –100°C at approximately 75nm thickness. Frozen sections from these preparations were then thawed, washed, and exposed to a monoclonal primary antibody that was raised in mice or rabbit/goat and to colloidal gold-complexed goat-anti-mouse/rabbit secondary antibodies. Further details of preparation are outlined in Methods Cell Biol. 2010;96:143-73. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; tissue in vitreous ice embedment; microtome-sectioned tissue; monoclonal antibody
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: intrinsic mass distribution; stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; gold
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0hd7ts4
title: CIL:13135, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The somatic basal bodies along the sides of the cytoproct ridge have bundles of microtubules extending into the endoplasm from near their proximal ends. These bundles make contact with the spent vacuole and aid its movement to the cytoproct. The plasma membrane and alveolar sacs were ruptured in this cell during preparation for electron microscopy. TEM taken on 6/13/79 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 10,000X. Bar = 0.5µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. An unprocessed, high resolution version of this image (CIL:12350) is in the library and available for quantitative analysis. 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; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.6075/j0p26xb8
title: CIL:13126, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: High resolution view of the E-face of the fractured collecting canal of the contractile vacuole showing its association with microtubular ribbons and with the smooth spongiome. The E-fracture face of the smooth spongiome is highly pitted like that of the collecting canal. Thin filaments lie between the microtubules and the collecting canal membrane. TEM taken on 7/19/88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 40,500X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).