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1,111 results for “nanoparticles”
Altered nanoparticle uptake by lung carcinoma cells when stimulated with epidermal growth factor
<p>This dataset provides the raw data supporting the paper "Altered nanoparticle uptake by lung carcinoma cells when stimulated with epidermal growth factor". The focus of the study was to investigate the uptake of two different sizes of silica NPs and gold NPs in lung epithelial cells A549 in the presence of epidermal growth factor (EGF). </p> <p>The data set includes:</p> <ul> <li>Screening for EGF receptor using western blot and confocal microscopy (Figure 1 and Figure S1)</li> <li>Investigating expression of RAC1/CDC42 proteins upon EGF stimulation using Western blot (Figure 2)</li> <li>Investigating expression of RAC1 gene upon EGF stimulation using RT-qPCR (Figure S2)</li> <li>Evaluating uptake of endocytic markers upon EGF stimulation using confocal laser scanning microscopy (Figure 3, Figure S4) and flow cytometry (Figure 3)</li> <li>Nanoparticle characterization using TEM (Figure 4, Figure S6) and UV-Vis (Figure S5, Figure S6)</li> <li>Evaluating silica nanoparticle uptake upon EGF stimulation using confocal laser scanning microscopy (Figure 5, Figure S8) and flow cytometry (Figure 5)</li> <li>Evaluating gold nanoparticle uptake upon EGF stimulation using dark-field microscopy and ICP-AES (Figure 6)</li> <li>Investigating expression of c-MYC gene upon EGF stimulation using RT-qPCR (Figure 6)</li> <li>Cell viability results, analysed via lactate dehydrogenase assay (Figure S3) and MTS assay (Figure S9)</li> <li>Raw integrated density data from dark-field images (Figure S9)</li> </ul>
Iron nanoparticle database
<p>This is a database of Fe nanoparticles generated with a GAP interatomic potential for iron [1]. The files are provided in ASE's extended XYZ format. For each nanoparticle, <em>convex_hull.xyz</em> includes the energies as computed with:</p> <ul> <li>PAW-PBE DFT [1,2]</li> <li>our GAP [3]</li> <li>the GAP by Dragoni et al. [4]</li> <li>the EAM by Mendelevet al. [5]</li> <li>the EAM by Finnis and Sinclair et al. [6]</li> </ul> <p>The movie <em>surface.mp4</em> shows the fractions of surface sites resembling surface motifs from pristine crystal surfaces more than the others, for each particle from <em>convex_hull.xyz</em>. Similarity is measured by comparing SOAP descriptors [7] of the surface environments with those from the reference structures.</p> <p>More details can be found in this arXiv preprint:</p> <blockquote> <p>Searching for iron nanoparticles with a general-purpose Gaussian approximation potential</p> <p>Richard Jana, Miguel A. Caro</p> <p>https://doi.org/10.1103/PhysRevB.107.245421</p> </blockquote> <p>The authors are grateful to the Academy of Finland for financial support under projects #321713 (R. J. & M.A. C.) and #330488 (M.A. C.), and CSC -- IT Center for Science as well as Aalto University's Science-IT Project for computational resources.</p>
Potential of Mean Force (PMFs) for Zerovalent Iron (Fe (100-110-111)) NanoParticles
<p>The data is potential of mean force for three fcc configurations of zero valent iron, (100), (110) and (111) nano particles interacting with side chain analugos of 22 different amino acids that are the building blocks of the proteins. We used adaptive Well-Tempered Metadynamics method to calculate the adsorption free energies that has previously been described for measuring the adsorption of the biomolecules for TiO2 and Ag. GROMACS and plumed softwares were used to carry out the simulations and the CHARMM-GUI/Nanomaterial Modeler was used create the iron slabs. </p> <p>The system was solvated using the original form of TIP3 water model . It was then neutralized by NaCl regarding the charge of the whole system. In the MD calculation the energy of the system has been minimized by Verlet particle-based cut-off scheme using charge groups and steepest gradient method for 1000 steps. The system was equilibrated under constant pressure, particles and temperature (300 K) condition (NPT) using Berendsen weak coupling or 1.0 ns. The component of the pressure tensor were set to 1.0 bar. The thermostat and the barostat for the relaxation time was 1.0 ps. The system underwent another more unbiased equilibrations for 10 ns in the NVT ensemble conditions. The Nose-Hoover thermostat’s relaxation time constant for the NVT ensemble was 5 ps. The cut-off distance was set to 1.0 nm for the VdW short range interactions. In the metadynamics biased simulation, the Surface Separation Distance (SSD) describes the reaction coordinates. This SSD measures the minimum distance of the center-of-mass (COMs) of the SCA Rmol and the surface atoms ri along the z coordinate.</p>
Photonic crystals with rainbow colors by centrifugation-assisted assembly of colloidal lignin nanoparticles
<p>Source data (CSV files) associated with the publication titled <strong>Photonic crystals with rainbow colors by </strong><strong>centrifugation-assisted assembly </strong><strong>of colloidal lignin nanoparticles</strong>.</p>
LungVis1.0: Active learning AI-powered 3D imaging ecosystem for spatial profiling of lung geometry and pulmonary nanoparticle delivery
<p>The imaging dataset was obtained by light sheet fluorescence microscopy on tissue cleared murine lungs. It includes whole lung autofluorence image, particle fluorescence image, and artifical intelligence nnU-Net generated lung airway segments. The dataset provides 78 healthy murine lung strucutre and airway geometry for C57BL/6 mice and offers comprehensive delivery features including qualitative and quantitative analysis on the temporal and spatial inter- and intra-acinar deposition patterns and NP regional dosimetry for four commonly-used routes of pulmonary delivery,namely intranasal liquid aspiration, intratracheal liquid instillation, ventilator-assisted and nose-only aerosol inhalation.</p> <p>Raw LSFM imaging data collection was carried out between 2017-2021, the AI code and generated airway segmention were performed in 2021-2022, the whole datasets were then compiled in 2023. </p> <p>Please ensure to cite our paper for any reuse or reanalysis. Yang, L., Liu, Q., Kumar, P. <em>et al.</em> LungVis 1.0: an automatic AI-powered 3D imaging ecosystem unveils spatial profiling of nanoparticle delivery and acinar migration of lung macrophages. <em>Nat Commun</em> <strong>15</strong>, 10138 (2024). https://doi.org/10.1038/s41467-024-54267-1</p> <p>For any inquiries, please feel free to contact us at lin.yang@helmholtz-munich.de </p>
BCC-Cu nanoparticles: from a transient to a stable allotrope by tuning size and reaction conditions
<p>Open data for "BCC-Cu nanoparticles: from a transient to a stable allotrope by tuning size and reaction conditions"</p>
DATASET: Protein Binding Leads to Reduced Stability and Solvated Disorder in the Polystyrene Nanoparticle Corona
<p>This dataset contains the DLS, CD, fluorescence, ITC, TEM, and ANS raw data used for the manuscript.</p>
The functions of cholera toxin subunit B as a modulator of silica nanoparticle endocytosis
<p>The gastrointestinal tract is the main target of orally ingested nanoparticles (NPs) and at 9 the same time exposed to noxious substances, such as bacterial components. We investigated the 10 interaction of 59 nm silica (SiO2) NPs with differentiated Caco-2 intestinal epithelial cells in the pres-11 ence of cholera toxin subunit B (CTxB) and compared the effects to J774A.1 macrophages. CTxB can 12 affect cellular functions and modulate endocytosis via binding to the monosialoganglioside (GM1) 13 receptor, expressed on both cell lines. After stimulating macrophages with CTxB, we observed no-14 table changes in the membrane structure but not in Caco-2 cells and no secretion of the pro-inflam-15 matory cytokine TNF-α was detected. Cells were then exposed to 59 nm SiO2 NPs and CtxB sequen-16 tially and simultaneously, resulting in a high NPs uptake in J774A.1 cells but no uptake in Caco-2 17 cells was detected. Flow cytometry analysis revealed that exposure of J774A.1 cells to CTxB resulted 18 in a significant reduction in the uptake of SiO2 NPs. In contrast, the uptake of NPs by highly selective 19 Caco-2 cells remained unaffected following CTxB exposure. Based on colocalization studies, CTxB 20 and NPs might enter cells via shared endocytic pathways, followed by their sorting into different 21 intracellular compartments. Our findings provide new insights into the CTxB function to modulate 22 SiO2 NPs uptake in phagocytic but not in differentiated intestine cells.</p>
Increased uptake of silica nanoparticles in inflamed macrophages but not upon co-exposure to micron-sized particles
<p>Silica nanoparticles (NPs) are widely used in various industrial and biomedical applications. Little is known about the cellular uptake of co-exposed silica particles, as can be expected in our daily life. In addition, an inflamed microenvironment might affect a NP’s uptake and a cell’s physiological response. Herein, prestimulated mouse J774A.1 macrophages with bacterial lipopolysaccharide were post-exposed to micron- and nanosized silica particles, either alone or together, i.e., simultaneously or sequentially, for different time points. The results indicated a morphological change and increased expression of tumor necrosis factor alpha in lipopolysaccharide prestimulated cells, suggesting a M1-polarization phenotype. Confocal laser scanning microscopy revealed the intracellular accumulation and uptake of both particle types for all exposure conditions. A flow cytometry analysis showed an increased particle uptake in lipopolysaccharide prestimulated macrophages. However, no differences were observed in particle uptakes between single- and co-exposure conditions. We did not observe any colocalization between the two silica (SiO<sub>2</sub>) particles. However, there was a positive colocalization between lysosomes and nanosized silica but only a few colocalized events with micro-sized silica particles. This suggests differential intracellular localizations of silica particles in macrophages and a possible activation of distinct endocytic pathways. The results demonstrate that the cellular uptake of NPs is modulated in inflamed macrophages but not in the presence of micron-sized particles.</p>
DATASET: Exploring the Residue-Level Interactions between the R2ab Protein and Polystyrene Nanoparticles
<p>This file contains the raw hydrogen-deuterium exchange data used in the manuscript. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD044469. 202308</p>
Influence of protein corona on cytotoxicity of metal oxide nanoparticles against human keratinocyte cell line (HaCaT)
<p>The model identified, among the factors determining the cytotoxic properties of metal oxide nanoparticles against HaCaT cell lines, a number of variables related to the processes occurring on the surface of nanoparticles in a biological medium, including the ability to form protein corona.</p> <p>The selected descriptors describe both the electronic structure of the metal oxides that are the components of the nanoparticles, i.e. the ionization potential (IP_ActivM_SM_#1, IP_ActivM_SM_#2) and the initial nanoforms, i.e. the particle size (Primary size) and the percentage content of the metal oxide which is the main component of the nanoparticle (Purity_#1) ; characterize nanoparticles in the medium, i.e. the isoelectric point (PZZP_#2), stability (Stability), potential for dissolution (Dissolution), generation of reactive oxygen species (ROS production) and protein adsorption (Protein adsorption). The listed descriptors reflect the features that are discussed in the literature as potentially related to the toxic effect of nanoparticles.</p>
Identification of factors determining the process of aggregation/agglomeration of metal oxide nanoparticles in a biological medium
<p>The model allows to identify factors determining the process of aggregation/agglomeration of metal oxide nanoparticles in a biological medium and to verify the importance of ion adsorption and protein adsorption in this process. </p> <p>Model confirms the significant effect of protein adsorption on the hydrodynamic diameter of metal oxide particles in the biological medium, and does not confirm the significant effect of ion adsorption in this process. It’s an example of modeling the properties of nanoparticles, where apart from the descriptors describing the structure of nanoparticles, there are also parameters characterizing the medium.</p>
The influence of the properties of inorganic solvents on the hydrodynamic diameter of TiO2 nanoparticles
<p>In this model the property of a nanomaterial is predicted not on the basis of descriptors characterizing the chemical composition of nanoparticles or physical properties of the initial nanoforms, but on the basis of descriptors describing the dispersion medium (pH, IP, D3_HeteroNonMetals) and the property of nanoparticles dependent on it (Potential ζ). </p> <p>The observed small size of the hydrodynamic diameter of TiO2 in solvents of strong acids and bases compared to other solvents may indicate stronger repulsive interactions between nanoparticles than in the case of other systems. Moreover, in the case of salt solutions, the observed large size of the hydrodynamic diameter of TiO2 may be the result of a thicker electrical layer surrounding the particles in the dispersion system.</p>
Solvent Engineered Synthesis of SnO Nanoparticles for High-Performance Anodes
<p>Batteries are the most abundant form of electrochemical energy storage. Lithium and sodium ion batteries account for a significant portion of the battery market, but high-performance electrochemically active materials still need to be discovered and optimized for these technologies. Recently, tin(II) oxide (SnO) has emerged as a highly-promising battery electrode. In this work, we present a facile synthesis method to produce SnO nanoparticles whose size and shape can be tailored by changing the solvent nature. We study the complex relationship between wet chemistry synthesis conditions and resulting nanoparticle morphology. Furthermore, high-level electronic structure theory, including dispersion corrections to account for van der Waals forces, are employed to augment our understanding of the underlying chemical mechanisms. The electronic vacuum alignment and surface energies are determined, allowing the prediction of the thermodynamically-favoured crystal shape (Wulff construction) and surface-weighted work function. Finally, the synthesized nanomaterials were tested as Li-ion battery anodes, demonstrating significantly enhanced electrochemical performance for morphologies obtained from specific synthesis conditions. </p> <p>Open-access publication in npj 2D Mater & Appl <a href="https://rdcu.be/cgdWZ">here</a>.</p>
Dataset From: Structural and double layer forces between silica surfaces in suspensions of negatively charged nanoparticles
<p>The dataset for the publication "Structural and double layer forces between silica surfaces in suspensions of negatively charged nanoparticles". DOI: 10.1021/acs.langmuir.0c02917.</p> <p>Files containing data have .dat extension and are in text format</p>
Dataset and Jupyter worksheet interpreting the (results from) small- and wide-angle scattering data from a series of boehmite/epoxy nanocomposites. Accompanies the publication "Competition of nanoparticle-induced mobilization and immobilization effects on segmental dynamics of an epoxy-based nanocomposite"
<p>Dataset and Jupyter worksheet interpreting the (results from) small- and wide-angle scattering data from a series of boehmite/epoxy nanocomposites. Accompanies the publication "Competition of nanoparticle-induced mobilization and immobilization effects on segmental dynamics of an epoxy-based nanocomposite", by Paulina Szymoniak, Brian R. Pauw, Xintong Qu, and Andreas Schönhals.</p> <p>Datasets are in three-column ascii (processed and azimuthally averaged data) from a Xenocs NanoInXider SW instrument. Monte-Carlo analyses were performed using McSAS 1.3.1, other analyses are in the Python 3.7 worksheet. Graphics and result tables are output by the worksheet. </p>
Silver Nanoparticles Alter Cell Viability Ex Vivo and in Vitro and Induce Proinflammatory Effects in Human Lung Fibroblasts
<p>Dataset for data generated and presented in following article by Löfdahl et al in Nanomaterials 2020, 10, 1868. doi:10.3390/nano10091868</p>
BAM reference data: SEM raw data for the Particles Size Distribution of Al-coated titania nanoparticles (JRCNM62001a and JRCNM62002a)
<p>The SEM images are given in the TIF format.</p> <p>For further information please look at:</p> <p>- Radnik, J. Kersting, R., Hagenhoff, B., Bennet, F., Ciornii, D.; Nymark, P., Grafström R. and Hodoroaba, V.- D. <em>Nanomaterials </em><strong>2021</strong>, <em>11</em>, 639. https://doi.org/10.3390/nano11030639, and</p> <p>- Vasile-Dan Hodoroaba. (2021). BAM reference data: EDS raw data of Al-coated titania nanoparticles (JRCNM62001a and JRCNM62002a) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4986420</p> <p>- Radnik, Jörg. (2021). BAM reference data: XPS raw data of Al-coated titania nanoparticles (JRCNM62001a and JRCNM62002a) [Data set]. Nanomaterials. Zenodo. http://doi.org/10.5281/zenodo.4986068</p> <p>Measurement conditions:</p> <p>In the present work, a SEM of type Supra 40 (ZEISS, Oberkochen, Germany) with a Schottky field emitter and an InLens secondary electron detector was used at a 5 kV beam acceleration voltage.</p>
Topology and structure of Au144(SRNH3+)60 from "Atomistic Simulations of Functional Au144(SR)60 Gold Nanoparticles in Aqueous Environment"
<p>Positively charged monolayer-protected gold nanoparticles (AuNPs) structure and topology files for GROMACS used in DOI: 10.1021/jp301094m. The final structure of the simulation reported in DOI: 10.1021/jp301094m for the neutral case is provided.</p> <p>The gold nanoparticle contain a core of 144 Au atoms and 60 functionalized alkanethiol side groups (undecanyl chain, R = C11H22), each possessing a positively charged amonium terminal group.</p> <p>When using this structure do not forget to cite DOI: 10.1021/jp301094m. </p> <p>NOTE1: Different versions for the topology files are provided of both AuNPs. All versions were used for the publication. The changes only affect the core surface and therefore had no influence in the reported properties. Still we recommentd using the latest version: AU144SRNH360_v3.itp.</p> <p>NOTE2: The original simulations used GROMACS 4.0.5. The files should work, however, as well up to GROMACS 4.6.7.</p>
Topology and structure of Au144(SRCOO-)60 from "Atomistic Simulations of Functional Au144(SR)60 Gold Nanoparticles in Aqueous Environment"
<p>Negatively charged monolayer-protected gold nanoparticles (AuNPs) structure and topology files for GROMACS used in DOI: 10.1021/jp301094m. The final structure of the simulation reported in DOI: 10.1021/jp301094m for the neutral case is provided.</p> <p>The gold nanoparticle contain a core of 144 Au atoms and 60 functionalized alkanethiol side groups (undecanyl chain, R = C11H22), each possessing a negatively charged carboxylic terminal group.</p> <p>When using this structure do not forget to cite DOI: 10.1021/jp301094m. </p> <p>NOTE1: Different versions for the topology files are provided of both AuNPs. All versions were used for the publication. The changes only affect the core surface and therefore had no influence in the reported properties. Still we recommentd using the latest version: AU144SRCOO60_v2.itp.</p> <p>NOTE2: The original simulations used GROMACS 4.0.5. The files should work, however, as well up to GROMACS 4.6.7.</p>
ScienceDex guides
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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.