cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0xw4jbd
title: CIL: 52204, Homo sapiens. In Cell Image Library

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: 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: 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/j0x066sw
title: CIL: 54545, Homo sapiens, HeLa. In Cell Image Library

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.
description: TK 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.
DOI: 10.6075/j0805302
title: CIL:57492. 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-VP40 immuno-golg labelling.
DOI: 10.6075/j0cr5tr4
title: CIL:57491. In Cell Image Library

description: Ebola virus Huh7 infected cells 22 hours post infection, anti-VP40 immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
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.
DOI: 10.6075/j0m9092r
title: CIL:57495. 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-VP40 immuno-golg labelling.
DOI: 10.6075/j0qz2bb0
title: CIL:57489. In Cell Image Library

description: Ebola virus Huh7 infected cells 22 hours post infection, anti-VP40 immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
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.
DOI: 10.6075/j0rj4j6m
title: CIL: 53803. In Cell Image Library

description: Visualization methods: confocal microscopy
description: NDK 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: 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: 10.15468/dl.m2hsw4
title: Occurrence Download

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

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009501-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9799c5
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Rubus lambertianus"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009500-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e66m3m
title: Occurrence Download

description: A dataset containing 2780 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "TaxonKey is Narcissus pseudonarcissus"
 ]
}

 The dataset includes 2780 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009503-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15151/esrf-es-2234936577
title: CHRONOS (continuation)

description: The CHRONOS BAG at ESRF is a specialized access mode designed for long-term in situ synchrotron experiments. Its mission is to capture slow processes in real time by enabling continuous X-ray imaging over extended periods. The principle relies on automated, scheduled scans that allow researchers to track dynamic changes in materials under controlled conditions with implications for numerous scientific and industrial fields. In geosciences, it enhances our understanding of fault mechanics, fluid-rock interactions, and carbon sequestration. In material science, it provides insights into creep, fatigue, and phase changes. By bridging timescales and automating data collection, CHRONOS advances synchrotron techniques and opens new possibilities for studying time-dependent natural and manufactured systems.
DOI: 10.15468/dl.95b9vv
title: Occurrence Download

description: A dataset containing 2634 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((106.76196 6.12132,124.75506 23.51861,123.80179 38.29441,114.55238 43.71916,97.32814 44.02369,97.10241 31.10675,95.27903 20.5084,106.76196 6.12132))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Diospyros kaki"
 ]
}

 The dataset includes 2634 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009502-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17491497
title: Living Labs as catalysts for experiential learning in law enforcement training: Insights from the TENACITy project.

description: Information sheets, consent form, etc for "Living Labs as catalysts for experiential learning in law enforcement training: Insights from the TENACITy project."
DOI: 10.5281/zenodo.17491498
title: Living Labs as catalysts for experiential learning in law enforcement training: Insights from the TENACITy project.

description: Information sheets, consent form, etc for "Living Labs as catalysts for experiential learning in law enforcement training: Insights from the TENACITy project."
DOI: 10.34740/kaggle/ds/3535804
title: Music Caption Dataset
DOI: 10.5517/ccdc.csd.cc241n3z
title: CCDC 1967790: Experimental Crystal Structure Determination

description: Related Article: Hironori Yamaguchi, Taiki Okita, Yoshiki Iwasaki, Yohei Kono, Nao Uemoto,
Yuko Hosokoshi, Takanori Kida, Takashi Kawakami, Akira Matsuo, Masayuki Hagiwara|2020|Scientific Reports|10|9193|doi:10.1038/s41598-020-66336-8
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.24396/ordar-205
title: Ne–Ar–N data for six fragments of the CI chondrite Oued Chebeika 002

description: This dataset accompanies the paper “H–N budgets and isotopic signatures of Oued Chebeika 002 and CI reservoir heterogeneity” by Yves Marrocchi, Evelyn Füri, Laurent Zimmermann, and Laurette Piani, submitted to Geochemical Perspectives Letters.
DOI: 10.15468/dl.e3pmv2
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Euphorbia micractina"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009505-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17482379
title: Supported data for manuscript "Assessing the Applicability of the wflow_sbm Model with seamless parameter maps in Small and Medium-Sized River Catchments in China"
DOI: 10.57710/alba-es-20250340081
title: Cell uptake and biomineralization pathway of nMBG in MSCs cells investigated combining cryo-soft X-ray tomography with XANES at the Ca L2,3 edges

description: Mesoporous bioactive glass nanoparticles (nMBG) represent a promising material for bone regeneration; however, their intracellular behaviour remains poorly understood. The bioactivity of nMBG is influenced by both the Si/Ca ratio and their mesoporous structure, which impact ion release, cellular internalization, and osteogenic differentiation. In a previous study, we investigated nMBG compositions Si100, Si90Ca10, and Si60Ca40 (w/w) and observed that excess calcium destabilizes the silica network, thereby altering osteogenic potential. Notably, only specific calcium levels were found to enhance the differentiation of human mesenchymal stem cells (hMSCs). This proposal at ALBA aims to elucidate the effects of Si/Ca composition on nMBG internalization, subcellular localization, and intracellular mineralization, providing valuable insights for bone tissue engineering. To achieve a deeper understanding of nMBG performance in hMSCs, we propose to analyze frozen-hydrated MSCs in contact with nMBG at various time points using a combination of cryosoft X-ray tomography and XANES microscopy. The primary objective is to characterize the uptake, localization, and calcium phosphate mineral deposition at the Ca L2,3 edges with nanoscale spatial resolution and nano-TXM within hMSCs during their differentiation into osteoblasts. This investigation will demonstrate the ability of nMBG to induce the formation of a bone-like mineral phase in biologically relevant fluids.
DOI: 10.57710/alba-es-2024078921
title: Glycoproteins and flavoenzymes: mechanism studies and biotechnological application

description: Our main interests are the understanding of how glycosyltransferases (GTs), glycosylhydrolases, transglycosylases (TGs) and carbohydrate binding proteins bind to its ligands and catalyze chemical reactions as potential drug targets to treat diseases. We work with the following enzymes: a) Gas2, Gel4, Phr1 and Phr2, TGs involved in remodelling of the cell wall and drug targets for Aspergilosis, Candidiasis and Cryptococcosis; b) ppGalNAc transferases (ppGalNAcTs) thattransfer GalNAc into mucins and are relevant in lung diseases, osteoporosis and some type of cancers; c) mucinases, that hydrolyzes mucins; d) NGTs from bacteria, in particular, NleB from Gram-negative and NGTs from Haemophilus influenza and Actinobacillus pleuropneumoniae. These bacteria require these activities to promote infection in their respective hosts; e) FUT8, a fucosyltransferase that fucosylates the innermost GlcNAc of N-glycans, is a drug target for cancer; f) anti-Tn and anti-STn antibodies such as 5E5, G2D11 and mutants and chimeras of G2D11. These antibodies are anti-cancer molecules and likely useful to diagnose cancer; g) core 3 synthases and ST6GalNAcI, that glycosylate the Tn antigen. The overexpression of the latter enzyme is intricately related with the development of cancer. On the other hand, flavoproteins catalyze redox reactions in cells, and those produced by pathogens could become potential targets since many of them play a role in defending against host-induced stress conditions. Our goal is to increase the use of all of these proteins in biotechnological and therapeutic applications by understanding their mechanisms. In addition, we are studying other systems like symbiotic globins from plants that exhibit new functions and also ferric regulators and transcription factors that interact with DNA
DOI: 10.25549/usctheses-ouc11399m6go
title: Identifying Novel Therapeutic Strategies against Antibiotic Resistant Pathogens using Bicarbonate Supplemented Media
DOI: 10.17028/rd.lboro.30498848
title: Supplementary information files for "A comprehensive framework for model evaluation and refinement using MBDoE estimability and structural identifiability: application to a crystallization process"

description: Supplementary files for article "A comprehensive framework for model evaluation and refinement using MBDoE estimability and structural identifiability: application to a crystallization process"<br><br>This paper presents a novel framework for the systematic evaluation, discrimination, and calibration of mathematical models. A diverse set of model candidates is first constructed to capture a broad range of underlying physical and kinetic phenomena. Structural identifiability analysis is then employed to determine whether unique parameter estimates can be derived from ideal, noise-free data, enabling early-stage model screening. A single model is then selected based on arigorous model discrimination criterion. To calibrate and refine the selected model, parameter estimability analysis is integrated with Model-Based Design of Experiments (MBDoE), ensuring optimal sampling strategies, data-rich experiments, and reduced prediction uncertainty. To maximize the effectiveness of MBDoE, a novel temperature cycling protocol is introduced, enabling a single, well-designed, information-rich experiment that minimizes experimental effort. This methodology is demonstrated through a cooling crystallization case study using paracetamol. The results show that the proposed framework significantly enhances model discrimination, parameter precision, and estimability resulting in amodel with superior predictive performance, as proven by the additional post-MBDoE validation experiment operated under different conditions and designed independently from the MBDoE framework. The proposed framework bridges the gaps between the different modeling pillars, reduces experimental efforts, and lays the foundation for more effective modeling and optimal design of experiments for the crystallization systems and beyond.<br><br>© The Author(s), CC BY-NC-ND 4.0
DOI: 10.17028/rd.lboro.30498848.v1
title: Supplementary information files for "A comprehensive framework for model evaluation and refinement using MBDoE estimability and structural identifiability: application to a crystallization process"

description: Supplementary files for article "A comprehensive framework for model evaluation and refinement using MBDoE estimability and structural identifiability: application to a crystallization process"<br><br>This paper presents a novel framework for the systematic evaluation, discrimination, and calibration of mathematical models. A diverse set of model candidates is first constructed to capture a broad range of underlying physical and kinetic phenomena. Structural identifiability analysis is then employed to determine whether unique parameter estimates can be derived from ideal, noise-free data, enabling early-stage model screening. A single model is then selected based on arigorous model discrimination criterion. To calibrate and refine the selected model, parameter estimability analysis is integrated with Model-Based Design of Experiments (MBDoE), ensuring optimal sampling strategies, data-rich experiments, and reduced prediction uncertainty. To maximize the effectiveness of MBDoE, a novel temperature cycling protocol is introduced, enabling a single, well-designed, information-rich experiment that minimizes experimental effort. This methodology is demonstrated through a cooling crystallization case study using paracetamol. The results show that the proposed framework significantly enhances model discrimination, parameter precision, and estimability resulting in amodel with superior predictive performance, as proven by the additional post-MBDoE validation experiment operated under different conditions and designed independently from the MBDoE framework. The proposed framework bridges the gaps between the different modeling pillars, reduces experimental efforts, and lays the foundation for more effective modeling and optimal design of experiments for the crystallization systems and beyond.<br><br>© The Author(s), CC BY-NC-ND 4.0
DOI: 10.15468/w2pwfk
title: Recent additional records of the little-known mydas fly, Nemomydas gruenbergi (Hermann, 1914) (Diptera, Mydidae) from Iriomote Island, southern Japan, with the first documentation of mating and oviposition

description: This dataset contains occurrence records and voucher specimen information of Nemomydas gruenbergi (Hermann, 1914) (Diptera, Mydidae) collected from northern Iriomote Island, Yaeyama Islands, Japan. The data were obtained during summer field surveys and include both direct observations and preserved specimens. These records represent newly confirmed occurrences of the species from northern Iriomote, extending its known distribution in Japan. Notably, this dataset also includes photographic documentation of a mating pair and oviposition behavior, providing valuable biological information for this rarely recorded fly in East Asia.
DOI: 10.5281/zenodo.17491476
title: GAS M-Enn-Mrp association table
DOI: 10.5281/zenodo.17491475
title: GAS M-Enn-Mrp association table
DOI: 10.6075/j08s4nr3
title: CIL:11196, Rattus, Homo sapiens, intestinal epithelial cell, Sertoli cell. In Cell Image Library

description: Upper panel shows a typical zonula occludens of rat intestinal epithelium, prepared using freeze fracture techniques. A network of intersecting strands on the P-face, and a complementary pattern of grooves on the E-face of this freeze fracture image. The lower panel includes a portion of a Sertoli junction from human testis consisting of a large number of parallel rows of complementary grooves of intramembranous particles which adhere preferentially to the E-face. Fig. 70 micrograph (upper) contributed by J.P. Revel; fig. 71 (lower) from Suzuki and Nagano, Cell Tissue Res. 166: 37 (1976), reprinted with permission in Chapter 3 (Junctional Specializations) 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/j0kh0mkz
title: CIL:1118, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 4 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data