cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.60712/si-id342962.1
title: StrainInfo SI-ID 342962.1

description: StrainInfo dataset 342962 about a strain of Pseudomonas. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id342803.1
title: StrainInfo SI-ID 342803.1

description: StrainInfo dataset 342803 about a strain of Collinsella aerofaciens. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id342804.1
title: StrainInfo SI-ID 342804.1

description: StrainInfo dataset 342804 about a strain of Bifidobacterium longum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id342805.1
title: StrainInfo SI-ID 342805.1

description: StrainInfo dataset 342805 about a strain of Clostridium. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id342806.1
title: StrainInfo SI-ID 342806.1

description: StrainInfo dataset 342806 about a strain of Mitsuokella jalaludinii. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id342873.1
title: StrainInfo SI-ID 342873.1

description: StrainInfo dataset 342873 about a strain of Bifidobacterium bifidum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id342874.1
title: StrainInfo SI-ID 342874.1

description: StrainInfo dataset 342874 about a strain of Bifidobacterium longum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id342875.1
title: StrainInfo SI-ID 342875.1

description: StrainInfo dataset 342875 about a strain of Bifidobacterium catenulatum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id342876.1
title: StrainInfo SI-ID 342876.1

description: StrainInfo dataset 342876 about a strain of Bifidobacterium longum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id342963.1
title: StrainInfo SI-ID 342963.1

description: StrainInfo dataset 342963 about a strain of Bifidobacterium longum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id342964.1
title: StrainInfo SI-ID 342964.1

description: StrainInfo dataset 342964 about a strain of Bifidobacterium adolescentis. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.15468/dl.bv94q5
title: Occurrence Download

description: A dataset containing 2014 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Drosophila melanogaster Meigen, 1830"
 ]
}

 The dataset includes 2014 records from 89 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0085851-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f7th6g
title: Occurrence Download

description: A dataset containing 9226 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Choristoneura rosaceana (Harris, 1841)"
 ]
}

 The dataset includes 9226 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014079-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18213098
title: Everything

description: If we found the theory of everything in my other paper, and I showed how any rational agent can be made into DeepThought with the reality filter...then after me inputting a few insane intuitions it cannot find on the internet, ChatGPT must be able to solve all the remaining open physics problems. Here, I tried to use this concept to make it write these papers, some I wrote with it, some I wrote alone, the longest one is written entirely by it as a rule. Feel free to use them as datasets or whatever you want, respecting my will of proper attribution

© 2026 Gabriele Manganelli. All rights reserved.

Public disclosure does not constitute permission for reuse, derivation, or incorporation into academic or commercial work without explicit consent.
DOI: 10.5281/zenodo.18213099
title: Everything

description: If we found the theory of everything in my other paper, and I showed how any rational agent can be made into DeepThought with the reality filter...then after me inputting a few insane intuitions it cannot find on the internet, ChatGPT must be able to solve all the remaining open physics problems. Here, I tried to use this concept to make it write these papers, some I wrote with it, some I wrote alone, the longest one is written entirely by it as a rule. Feel free to use them as datasets or whatever you want, respecting my will of proper attribution

© 2026 Gabriele Manganelli. All rights reserved.

Public disclosure does not constitute permission for reuse, derivation, or incorporation into academic or commercial work without explicit consent.
DOI: 10.6075/j05b0153
title: CIL:13647, Homo sapiens. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: fluorescence microscopy
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Alexa Fluor 555; Fluorescein (FITC)
Data qualification: Raw;spatialmeasurements
description: This image is Fig. 4B from PMID: 20679433. 

HeLa cells were fixed and double-labeled with rabbit anti-p125A (secondary Ab: goat anti-rabbit Ab conjugated with Alexa 555, shown in red) and mouse anti-Sec31A (secondary Ab: goat anti-mouse Ab conjugated with FITC, shown in green) antibodies. 

Technical details: Cells grown on coverslips were washed 2X with PBS supplemented with 1 mM CaCl2 and 1 mM MgCl2 (PBSCM), fixed with 4% paraformaldehyde in PBSCM for 20 min at RT, washed 5X at 5-min intervals using PBSCM, and then permeabilized with 0.1% Saponin in PBSCM for 20 min at RT. The cells were then immunolabeled with appropriate primary antibodies diluted in fluorescence dilution buffer (FDB; PBSCM with 5% FBS and 2% bovine serum albumin [BSA]) for 1 h at RT, washed 5X with 0.1% Saponin PBSCM at 5-min intervals. Secondary antibodies were diluted in FDB and incubated at RT for 1 h, washed again with 0.1% Saponin PBSCM 5X at 5-min intervals, and then 2X with PBSCM. The coverslips were mounted on microscopic slides with Vectashield mounting medium containing DAPI. Confocal microscopy was performed with an Axioplan II microscope (Carl Zeiss, Inc.) equipped with Zeiss confocal scanning optics. 100x objective.
DOI: 10.6075/j08s4nm9
title: CIL:13720, Homo sapiens, endothelial cell. In Cell Image Library

description: YFP-WT PINK1 (green) shows mitochondrial localization in HeLa cells following treatment with the mitochondrial depolarizing agent CCCP (carbonyl cyanide m-chlorophenyl hydrazone). When fixed cells are permeabilized with 0.005% digitonin, the antibody to GFP (red) (used to identify YFP-WT PINK1) and the antibody to Tom20 (white), a mitochondrial outer membrane marker, are able to bind their epitopes. This demonstrates that when mitochondrial membrane potential is dissipated, YFP-WT PINK1 accumulates on the outer mitochondrial membrane. YFP-WT PINK1 transfected HeLa cells were treated with CCCP (10µM) for 3 hrs, fixed with 4% paraformaldehyde and permeabilized with 0.005% digitonin. Primary antibodies used were: anti-GFP polyclonal Ab (Invitrogen) and anti-Tom20 mAb (BD); secondary antibodies used were: Alexa Fluor 594 and 647. Imaging was performed on an LSM510 Meta (Carl Zeiss, Inc) with a 63x 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the LSM image browser (Zeiss). This image corresponds to Fig 4c, 2nd row from top, and is part of a differential permeabilization assay to determine submitochondrial localization of PINK1 and that is further described in Fig 4c of J Cell Biol, 191: 933-942, 2010. Images in Fig 4 include CIL#s 13733, 13734, 13729, 13730, 13731, 13732, 13717, 13718, 13719, 13720, 13721, 13722, 13723, 13724.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
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: EYFP; primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0bz65t9
title: CIL: 54592. In Cell Image Library

description: Imaging mode: Lattice Light Sheet Microscope
Visualization methods: ChimeraX
description: Constitutive macropinocytosis
description: Raw and processed data
DOI: 10.6075/j01j9980
title: CIL: 52029, Homo sapiens. In Cell Image Library

description: Imaging mode: Fluoresence
Visualization methods: objective based TIRFM using a modified Nikon TE-2000U (60x 1.49 N.A. TIRF objective) and illumination from a 532-nm solid-state laser with power modification by neutral-density filters
description: A single molecule TIRFM assay was employed to measure the kinase activity of purified PI3K molecules on a supported lipid bilayer by counting the number of product PIP3 molecules they produce.
description: This assay utilizes physiological concentrations class I PI3Ka, 1mM ATP, drug identified in subfolder, and saturating concentrations of fluorescently-labeled GRP-PH domain, a PIP3 product lipid binder, in order to count each product lipid produced. Enzyme rates are calculated as the slope of product lipid created vs. time. 21.5 ± 0.5°C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
DOI: 10.6075/j0057dn9
title: CIL:13731, Homo sapiens, endothelial cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
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: EYFP; primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Mitochondria in HeLa cells are identified by mito-YFP (green) following treatment with the mitochondrial depolarizing agent CCCP (carbonyl cyanide m-chlorophenyl hydrazone). When fixed cells are permeabilized with 0.005% digitonin, the antibody to cyctochrome c (red), a mitochondrial matrix marker, is unable to reach and bind cytochrome c, but the antibody to Tom20 (white), a mitochondrial outer membrane marker, is now able to bind Tom20. Mito-YFP transfected HeLa cells were treated with CCCP (10µM) for 3 hrs, fixed with 4% paraformaldehyde and permeabilized with 0.005% digitonin/PBS. Primary antibodies used were: anti-Cyt c mAb (BD) and anti-Tom20 mAb (BD); secondary antibodies used were: Alexa Fluor 594 and 647. Imaging was performed on an LSM510 Meta (Carl Zeiss, Inc) with a 63x 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the LSM image browser (Zeiss). This image corresponds to Fig 4b, 5th row from top and is part of a differential permeabilization assay with and without CCCP that is further described in Fig 4b of J Cell Biol, 191: 933-942, 2010. Images in Fig 4 include CIL#s 13733, 13734, 13729, 13730, 13731, 13732, 13717, 13718, 13719, 13720, 13721, 13722, 13723, 13724.
DOI: 10.6075/j0r21044
title: CIL:13730, Homo sapiens, endothelial cell. In Cell Image Library

description: Preparation: 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: EYFP; primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Mitochondria in HeLa cells are identified by mito-YFP (green) following treatment with the mitochondrial depolarizing agent CCCP (carbonyl cyanide m-chlorophenyl hydrazone). When fixed cells are unpermeabilized (not treated with detergent), antibodies to cyctochrome c (red), a mitochondrial matrix marker, and Tom20 (white), a mitochondrial outer membrane marker, are unable to reach and bind their epitopes. Mito-YFP transfected HeLa cells were treated with CCCP (10µM) for 3 hrs, fixed with 4% paraformaldehyde and not permeabilized. Primary antibodies used were: anti-Cyt c mAb (BD) and anti-Tom20 mAb (BD); secondary antibodies used were: Alexa Fluor 594 and 647. Imaging was performed on an LSM510 Meta (Carl Zeiss, Inc) with a 63x 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the LSM image browser (Zeiss). This image corresponds to Fig 4b, 4th row from top and is a control experiment for a differential permeabilization assay with and without CCCP that is further described in Fig 4b of J Cell Biol, 191: 933-942, 2010. Images in Fig 4 include CIL#s 13733, 13734, 13729, 13730, 13731, 13732, 13717, 13718, 13719, 13720, 13721, 13722, 13723, 13724.
DOI: 10.6075/j0cf9px4
title: CIL: 54729. In Cell Image Library

description: Item type: EM tomogram
Imaging mode: Electronic tomography
description: We examined the structural organization of cytoskeletal components and membrane systems in neurons of well preserved biopsy material from Alzheimer’s disease (AD). Information was obtained from thin sectioned material using conventional electron microscopy and from thick sections with the high voltage electron microscope.
description: This image displays the PHF array.
DOI: 10.6075/j0zs2v79
title: CIL:13474, Drosophila melanogaster, motor neuron. In Cell Image Library

description: Colocalization between DVGLUT (red) aggregates and the endosomal ESCRT protein Hrs (green, also known as Vps27) in motoneuron cell bodies of the ventral nerve cord of a wild-type larva. Wandering third instar larvae were dissected in ice-cold PBS and fixed with Bouin's solution for 5 min. Blocking and antibody incubation were performed in PBS containing 0.1% Triton X-100. anti-DVGLUT (Daniels et al., 2004) antibody was used at 1: anti-HRS-FL (Lloyd et al., 2002) was used at 1:1000. Secondary antibodies (Alexa 488-/Cy3-conjugated) were used at 1:1000. After staining, specimens were equilibrated in 70% glycerol in PBS and mounted with VectaShield (Vector Laboratories). Confocal images were acquired with a confocal microscope (model C1; Nikon) and accompanying EZ-C1 software using argon (excitation at 488 nm) and HeNe (excitation at 543 and 633 nm) lasers and a 60x Plan-Apochromat NA 1.4 objective (Nikon) at room temperature. Samples for each experiment were processed using the same confocal gain setting. Image corresponds to Figure 2A, top 3 panels in Kim et al. J Cell Biol. 188: 717-734. 2010.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: whole mounted tissue
Item type: recorded image; photomultiplier tube (PMT)
Imaging mode: fluorescence microscopy; confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; Cy3
Data qualification: Raw;intensitiesquantitation
DOI: 10.6075/j0v40szn
title: CIL:13460, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Kre2-GFP is not efficiently maintained in the Golgi apparatus when Pik1-mediated PtdIns4P synthesis (the Golgi-localized PtdIns 4-kinase in yeast is composed of the Pik1 catalytic subunit and a myristoylated calcium-binding protein, Frq1) ceases, implicating Pik1 signaling in retrograde trafficking of Golgi residents. In this image, Kre2-GFP is expressed in the frq1-1 mutant strain at permissive temperature of 26C. Cells grown in liquid medium were mounted in growth medium and 3D image stacks were collected at 0.4-µm z increments on a DeltaVision workstation (Applied Precision) based on an inverted microscope (IX-70; Olympus) using a 100× NA 1.4 oil immersion lens. Images were captured at 23C with a 12-bit CCD camera (CoolSnap HQ; Photometrics) and deconvolved using the iterative-constrained algorithm (Agard, 1984) and the measured point spread function. One image from the approximate center of z stack is shown in Fig4D 26C frq1-1 panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 4D include CIL#s 13460, 13461, 13462, 13463, 13464, 13465, 13466, 13467.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0cf9pkn
title: CIL: 51913, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
DOI: 10.6075/j02f7mb4
title: CIL:13524, Mus musculus, neuronal stem cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; permeabilized tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain; distribution of epitope; distribution of a specific protein
Visualization methods: Alexa Fluor 488; 4',6-diamidino-2-phenylindole (DAPI); Alexa Fluor 647
Data qualification: Raw
description: A retroviral vector containing sh-miR-137 under a U6 promoter and EGFP under a chicken actin promoter was prepared, and the virus containing the construct was injected into the dentate gyrus of adult mice in vivo. BrdU was injected twice/day (50,g/kg i.p.) for a total of 7 injections beginning immediately after viral grafting. After 1 week, animals were anesthetized, perfused with 4% paraformaldehyde, brains removed and postfixed, equilibrated in 30% sucrose, and sectioned at a thickness of 40µm with a sliding microtome. Infected cells were localized using chicken-α-GFP (Invitrogen) and rat-α-BrdU (Abcam), secondaries were α-chicken Alexa Fluor 488 and goat-α-rat Alexa Fluor 647 (both from Invitrogen). Confocal z-stacks were acquired at 1 µm steps using a Nikon TE2000 with equipped with a spinning disc confocal with an oil immersion 40X 1.3 NA objective (Zeiss). For additional details see: J. Cell Biol. Vol. 189:127–141.
description: A confocal Z-stack of neurons in postnatal hippocampus, expressing a GFP-tagged knockdown construct for the microRNA miR-137 (green, sh-miR-137), a marker of neuronal differentiation, çand BrdU (red) to localize total cells and newly-generated cells respectively. miR-137 regulates a core transcription factor in stem cell renewal. Data from these experiments suggest that high levels of miR-137 promotes neuronal stem cell proliferation, but repressed neuronal differentiation. This image is original data from Fig. 5 of Szulwach et al.(2010) Cross talk between microRNA and epigenetic regulation in adult neurogenesis, J. Cell Biol. Vol. 189:127–141.