Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
1,805
datasets available to search
ShareScore release 0.9.0
Dataset results
1,805 results for “molecule”
Radiation Damage in Small Molecule Crystallography - Experiment 8
<p>Eighth data set in a series of experiments investigating the effect of radiation damage to a small molecule crystal structure.</p> <p>Sample: catena-(bis(m2-Glycyl-histidinato-N,N',O)-nickel(II) heptahydrate)</p> <p>sum formula: C16H36N8NiO13</p> <p>Wavelength: 0.6889 Angstrom</p> <p>Temperature: 120 K</p> <p>Flux: 8.42•109<sup> </sup>ph/s</p> <p>Crystal size: 0.050 x 0.010 x 0.010 mm</p> <p>Calculated dose (DWD) per scan: 0.60 MGy</p>
Radiation damage in small molecule crystallography - experiment 1
<p>First data set in a series of experiments investigating the effect of radiation damage to a small molecule crystal structure.</p> <p>Sample: catena-(bis(m2-Glycyl-histidinato-N,N',O)-nickel(II) heptahydrate)</p> <p>sum formula: C16H36N8NiO13</p> <p>Wavelength: 0.6889 Angstrom</p> <p>Temperature: 100 K</p> <p>Flux: 8.8•10<sup>9 </sup>ph/s</p> <p>Crystal size: 0.050 x 0.010 x 0.010 mm</p> <p>Calculated dose (DWD) per scan: 0.63 MGy</p>
Radiation Damage in Small Molecule Crystallography - Experiment 4
<p>Fourth data set in a series of experiments investigating the effect of radiation damage to a small molecule crystal structure.</p> <p>Sample: catena-(bis(m2-Glycyl-histidinato-N,N',O)-nickel(II) heptahydrate)</p> <p>sum formula: C16H36N8NiO13</p> <p>Wavelength: 0.6889 Angstrom</p> <p>Temperature: 100K</p> <p>Flux: 8.162•10<sup>9 </sup>ph/s</p> <p>Calculated dose (average DWD) per scan: 0.57 MGy</p>
Radiation Damage in Small Molecule Crystallography - Experiment 2
<p>Second data set in a series of experiments investigating the effect of radiation damage to a small molecule crystal structure.</p> <p>Sample: catena-(bis(m2-Glycyl-histidinato-N,N',O)-nickel(II) heptahydrate)</p> <p>sum formula: C16H36N8NiO13</p> <p>Wavelength: 0.6889 Angstrom</p> <p>Temperature: 100 K</p> <p>Flux: 1.73•10<sup>10 </sup>ph/s</p> <p>Crystal size: 0.050 x 0.010 x 0.010 mm</p> <p>Calculated dose (average DWD) per scan: 1.27 MGy</p>
Benchmarking Smartphone Fluorescence-Based Microscopy with DNA Origami Nanobeads: Reducing the Gap toward Single-Molecule Sensitivity
<p>Smartphone-based fluorescence microscopy has been rapidly developing over the last few years, enabling point-of-need detection of cells, bacteria, viruses, and biomarkers. These mobile microscopy devices are cost-effective, field-portable, and easy to use, and benefit from economies of scale. Recent developments in smartphone camera technology have improved their performance, getting closer to that of lab microscopes. Here, we report the use of DNA origami nanobeads with predefined numbers of fluorophores to quantify the sensitivity of a smartphone-based fluorescence microscope in terms of the minimum number of detectable molecules per diffraction-limited spot. With the brightness of a single dye molecule as a reference, we compare the performance of color and monochrome sensors embedded in state-of-the-art smartphones. Our results show that the monochrome sensor of a smartphone can achieve better sensitivity, with a detection limit of ∼10 fluorophores per spot. The use of DNA origami nanobeads to quantify the minimum number of detectable molecules of a sensor is broadly applicable to evaluate the sensitivity of various optical instruments.</p>
Systematic assessment of burst impurity in confocal-based single-molecule fluorescence detection using Brownian motion simulations - photon timetag simulation files
<p>Attached are the photon timestamp and channels simulated for different 3D diffusing molecules simulations at different conditions (simulation was performed by PyBroMo).</p> <p>Each of the files has, in its name, a code. The meaning of the codes are as following:</p> <pre>f32445 - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 90 micron^2/s - 60 second simulation using a numerical PSF model </pre> <pre>a01f8f - 15 molecules at a concentration of 31 pM, with a diffusion coefficient of 90 micron^2/s - 60 second simulation using a numerical PSF model</pre> <pre>9ff667 - 15 molecules at a concentration of 15.5 pM, with a diffusion coefficient of 90 micron^2/s - 60 second simulation using a numerical PSF model</pre> <pre>71154a - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 22.5 micron^2/s - 60 second simulation using a numerical PSF model</pre> <pre>ad926d - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 5.625 micron^2/s - 60 second simulation using a numerical PSF model</pre> <pre>1ab235 - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 90 micron^2/s - 180 second simulation using a numerical PSF model</pre> <pre>d00978 - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 5.625 micron^2/s - 180 second simulation using a numerical PSF model</pre> <p> </p> <pre>2469bb - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 90 micron^2/s - 60 second simulation using a Gaussian PSF model </pre> <pre>4be121 - 15 molecules at a concentration of 31 pM, with a diffusion coefficient of 90 micron^2/s - 60 second simulation using a Gaussian PSF model</pre> <pre>a7088f - 15 molecules at a concentration of 15.5 pM, with a diffusion coefficient of 90 micron^2/s - 60 second simulation using a Gaussian PSF model</pre> <pre>023983 - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 22.5 micron^2/s - 60 second simulation using a Gaussian PSF model</pre> <pre>653f61 - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 5.625 micron^2/s - 60 second simulation using a Gaussian PSF model</pre> <pre>4f06ee - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 90 micron^2/s - 180 second simulation using a Gaussian PSF model</pre> <pre>dec32c - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 5.625 micron^2/s - 180 second simulation using a Gaussian PSF model</pre> <p> </p> <pre>85b0a1 - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 90 micron^2/s , 10 of which belong to a sub-population with a mean FRET efficiency of 0.75, and the leftover 5 belong to another sub-populations with a mean FRET efficiency of 0.50 - 60 second simulation using a Numerical PSF model</pre> <pre>964ef3 - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 90 micron^2/s , 10 of which belong to a sub-population with a mean FRET efficiency of 0.75, and the leftover 5 belong to another sub-populations with a mean FRET efficiency of 0.50 - 180 second simulation using a Numerical PSF model</pre> <p> </p> <pre>f28f6e - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 90 micron^2/s , 10 of which belong to a sub-population with a mean FRET efficiency of 0.75, and the leftover 5 belong to another sub-populations with a mean FRET efficiency of 0.50 - 60 second simulation using a Gaussian PSF model</pre> <pre>c311dd - 15 molecules at a concentration of 62 pM, with a diffusion coefficient of 90 micron^2/s , 10 of which belong to a sub-population with a mean FRET efficiency of 0.75, and the leftover 5 belong to another sub-populations with a mean FRET efficiency of 0.50 - 180 second simulation using a Gaussian PSF model</pre>
Data for "Experimental investigation into the volatilities of highly oxygenated organic molecules (HOM)"
<p>The data used in the preparation of the manuscript "Experimental investigation into the volatilities of highly oxygenated organic molecules (HOM)". The data consists of the data in each of the figures, as well as the time series for measured ozone, alpha-pinene, NOx, NO, condensation sink, temperature, relative humidity, aerosol mass concentration for organics, sulfate and ammonium, as well as the high resolution fitted compounds and unit mass resolution sticks from the CI-APi-TOF.</p>
High-throughput Computational Screening of Hydrocarbon Molecules for Long-wavelength Infrared Imaging
<p>This repository contains datasets associated with the paper titled "High-throughput Computational Screening of Hydrocarbon Molecules for Long-wavelength Infrared Imaging," accepted at ACS Materials Letters Journal.</p> <p><strong>Contents:</strong></p> <ol> <li> <p><strong>Optimized XYZ Coordinates:</strong> The hydrocarbon molecules' XYZ coordinates, obtained using the B3LYP functional and the 6-31g(d,p) basis set in Gaussian 16 software, used to simulate the IR spectra (including transition energies and absorption intensities) of the molecules.</p> </li> <li> <p><strong>Broadened Molar Absorptivity IR Spectra:</strong> The dataset's IR spectra, broadened using a Lorentzian band shape with a gamma (half-width at half-height) value of 5 cm⁻¹. Molecules with imaginary frequencies have been excluded.</p> </li> <li> <p><strong>Related SMILES Strings:</strong> Contains SMILES strings for these hydrocarbons.</p> </li> <li> <p><strong>NUMBERS_SMILES.csv:</strong> Provides the associated SMILES string for each numerated XYZ coordinate.</p> </li> </ol> <p>For any inquiries, please contact Dr. Maliheh Shaban Tameh at malihe.shaban<a rel="noreferrer">@gmail.com</a></p>
3D super-resolution datasets associated with the paper "Whole-cell multi-target single-molecule super-resolution imaging in 3D with microfluidics and a single-objective tilted light sheet"
<p>3D single-molecule super-resolution datasets corresponding to reconstructions shown in <em>Whole-cell multi-target single-molecule super-resolution imaging in 3D with microfluidics and a single-objective tilted light sheet</em> by Saliba & Gagliano, Gustavsson et. al.</p>
Datasets and scripts for: Single-Molecule Dynamic Structural Biology with Vertically Arranged DNA on a Fluorescence Microscope
<p>The folder contains raw datasets (.ptu files) together with scripts and relevant results to reproduce the figures' plots of: "Single-Molecule Dynamic Structural Biology with Vertically Arranged DNA on a Fluorescence Microscope". </p>
Original data and code for "Wave-function engineering on superconducting substrates: Chiral Yu-Shiba-Rusinov molecules"
<p>We provide all experimental data and the code to simulate the tight-binding YSR patterns in the paper "Wave-function engineering on superconducting substrates: Chiral Yu-Shiba-Rusinov molecules"</p>
Datasets for: Fullerene-based Single Molecule Diodes with Huge Rectification Ratios: A DFT-NEGF Study
<p>Input files and main output files for the study "Fullerene-based Single Molecule Diodes with Huge Rectification Ratios: A DFT-NEGF Study"</p>
Linked collectors and determiners for: There's gold in them thar hills! Morphology and molecules delimit species in Xerochrysum (Asteraceae; Gnaphalieae) and reveal many new taxa.
Natural history specimen data linked to collectors and determiners held within, "There's gold in them thar hills! Morphology and molecules delimit species in Xerochrysum (Asteraceae; Gnaphalieae) and reveal many new taxa". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/95ab9cb9-571f-4639-983c-cd94719fb83b">https://bionomia.net/dataset/95ab9cb9-571f-4639-983c-cd94719fb83b</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/95ab9cb9-571f-4639-983c-cd94719fb83b">https://gbif.org/dataset/95ab9cb9-571f-4639-983c-cd94719fb83b</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Integrating museum collections and molecules reveals genus-level synonymy and new species in red devil spiders (Araneae, Dysderidae) from the Middle East and Central Asia.
Natural history specimen data linked to collectors and determiners held within, "Integrating museum collections and molecules reveals genus-level synonymy and new species in red devil spiders (Araneae, Dysderidae) from the Middle East and Central Asia". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/dec1718c-64e8-4411-865f-271d0e950fbe">https://bionomia.net/dataset/dec1718c-64e8-4411-865f-271d0e950fbe</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/dec1718c-64e8-4411-865f-271d0e950fbe">https://gbif.org/dataset/dec1718c-64e8-4411-865f-271d0e950fbe</a>. Formatted as a Frictionless Data package.
AstraZeneca ChromLogD and EPSA experimental measurements for Ro5 and bRo5 molecules
<p>These datasets contain a list of 234 and 245 within Rule of Five (Ro5) and beyond Rule of Five (bRo5) molecules that were measured in chromatographic LogD (ChromLogD) and experimental polar surface area (EPSA) experimental assays, respectively, at two AstraZeneca's Research and Development (R&D) sites in Gothenburg, Sweden and Cambridge, United Kingdom. For each molecule, its SMILES representation, molecular weight, ion class, and compound type (Ro5 or bRo5) are provided. Experimental measurements were performed in several replicates, for which a number of replicates, an averaged value, and standard deviation are provided for both R&D sites separately. In addition, the molecules are further characterized by the number of rings, number of rotable bonds, number of H-bond acceptors, number of H-bond donors, and number of Lipinski violations. If a molecule had at least two Lipinski rule violations, it would be labeled as bRo5, else it would be labeled as Ro5.</p>
Integrated Omics-Based Discovery of Novel Genes, Secondary Metabolites Clusters, and Small Molecules in Penicillium spp. with Disparate Fungal Isolates
<p><em><span>Penicillium expansum</span></em><span> is a ubiquitous postharvest pathogen of pome fruit that causes blue mold decay of apple fruit while another member of the genus, <em>P. chrysogenum</em><span>,</span><em> </em>is a well-studied saprophyte used for antibiotic and small molecule production. While these two fungi have been investigated individually, the recent discovery of <em>P. chrysogenum </em>hindering <em>P. expansum</em> apple fruit infection has not been well studied. To shed light on this interaction between the two species, we conducted a comparative transcriptomic, metabolomic, and genomic study. Global transcriptional and metabolomic outputs were disparate between the species, nearly identical for the <em>P. chrysogenum </em>isolates, and different between <em>P. expansum </em>isolates. Further, the two <em>P. chrysogenum</em> genomes revealed secondary metabolite gene clusters that differed from <em>P. expansum</em>. This included the absence of an intact patulin gene cluster in <em>P. chrysogenum</em>, which corroborates the metabolomic data regarding the species’ inability to produce patulin. Additionally, <em>P. expansum </em>virulence gene homologues were identified in <em>P. chrysogenum </em>and were similarly transcriptionally regulated <em>in vitro</em>. Molecules with potential antimicrobial activity, and phytohormones like indole-3-acetic acid (IAA), were detected for the first time in <em>P. expansum</em> while pharmacological compounds like the well-studied antibiotic penicillin G were identified in <em>P. chrysogenum</em> culture supernatants. Our findings provide new omics-based resources that enable the study of small molecule production of interest, the potential of <em>Penicillium</em>-derived antimicrobials for postharvest decay control, and <em>P.</em> <em>expansum’s</em> metabolites roles in host-pathogen interactions. </span></p>
Novel integrative modeling of molecules and morphology across evolutionary timescales
<p>Evolutionary models account for either population or species-level processes, but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth-death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments, and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.</p>
Raw data for the article: Human Amnion Epithelial Cells Impair T Cell Proliferation: The Role of HLA-G and HLA-E Molecules
<p>The immunoprivilege status characteristic of human amnion epithelial cells (hAECs) has been recently highlighted in the context of xenogenic transplantation. However, the mechanism(s) involved in such regulatory functions have been so far only partially been clarified. Here, we have analyzed the expression of HLA-Ib molecules in isolated hAEC obtained from full term placentae. Moreover, we asked whether these molecules are involved in the immunoregulatory functions of hAEC. Human amnion-derived cells expressed surface HLA-G and HLA-F at high levels, whereas the commonly expressed HLA-E molecule has been measured at a very low level or null on freshly isolated cells. HLA-Ib molecules can be expressed as membrane-bound and soluble forms, and in all hAEC batches analyzed we measured high levels of sHLA-G and sHLA-E when hAEC were maintained in culture, and such a release was time-dependent. Moreover, HLA-G was present in extracellular vesicles (EVs) released by hAEC. hAEC suppressed T cell proliferation in vitro at different hAEC:T cell ratios, as previously reported. Moreover, inhibition of T cell proliferation was partially reverted by pretreating hAEC with anti-HLA-G, anti-HLA-E and anti-β2 microglobulin, thus suggesting that HLA-G and -E molecules are involved in hAEC-mediated suppression of T cell proliferation. Finally, either large-size EV (lsEV) or small-size EV (ssEV) derived from hAEC significantly modulated T-cell proliferation. In conclusion, we have here characterized one of the mechanism(s) underlying immunomodulatory functions of hAEC, related to the expression and release of HLA-Ib molecules.</p>
Figure 7 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record
Figure 7. Cartoon to depict consensus relationships among Charadriiformes ('shorebirds') along with the holotype specimen of Morsoravis sedile, a new and exceptionally well-preserved fossil from Palaeocene–Lower Eocene deposits in Jutland, Denmark (1–2; G. J. Dyke, M. van Tuinen & D. M. Waterhouse, unpubl. data). The tree is based on various sources; see text for details. Scale bar = 10 mm.
Figure 6 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record
Figure 6. Cartoon to depict consensus relationships among Galliformes ('landfowl') along with some selected fossil material (based on Dyke, 2003b and Dyke et al., 2003): A, hypothesis for the phylogenetic positions of the Lower Eocene (c. 55 Mya) taxa Gallinuloides and Paraortygoides; B, fossil elements of Paraortygoides from the Lower Eocene London Clay Formation of England (see Dyke & Gulas, 2002); C, holotype specimen of Gallinuloides wyomingensis from the Lower Eocene Green River Formation of Wyoming (North America) (Dyke, 2003b). Scale bar = 10 mm.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.