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7 results for “UV-vis spectra”
Experimental data for "Deep Learning Methods for Colloidal Silver Nanoparticle Concentration and Size Distribution Determination from UV-Vis Extinction Spectra"
<p>Testing data (experimental data) for neural networks published in preprint https://doi.org/10.48550/arXiv.2404.10891</p> <p>The UV-VIS-NIR spectral data was also used in the dissertation of Nadzeya Khinevch, titled "Two-dimensional structures of nanoparticles for elements of surface-enhanced Raman scattering substrates".</p> <p>Emails of the corresponding authors:</p> <p>Tomas Klinavičius tomas.klinavicius@ktu.lt</p> <p>Tomas Tamulevičius tomas.tamulevicius@ktu.lt</p>
Time series of in situ Uv-Vis absorbance spectra and high-frequency predictions of total and soluble Fe and Mn concentrations measured at multiple depths in Falling Creek Reservoir (Vinton, VA, USA) in 2020 and 2021
High-frequency measurements of light absorbance were collected at multiple depths in Falling Creek Reservoir (FCR; Vinton, VA, USA) using a s::can Spectrolyser UV-Visible spectrophotometer coupled with a multiplexor pumping system. The system pumps water samples from individual depths into a flow-through cuvette where the UV-vis absorbance spectra of the sample are measured by the spectrophotometer. The system used in our study collected measurements of light absorbance every 2.5 nm wavelengths from 200 nm to 732.5 nm (optical path length of 10 mm) approximately at an hourly time step for seven monitoring depths in the reservoir. Data was collected during two periods; the first deployment (16 October to 9 November 2020) was to observe changes in Fe and Mn concentrations before, during, and after reservoir fall turnover and the second deployment (26 May to 21 June 2021) was to observe the effects of engineered hypolimnetic oxygenation on Fe and Mn concentrations. Partial least squares regression models were developed to generate predictions of total and soluble Fe and Mn concentrations based on the correlation between absorbance spectra and sampling data.
Gold Nanoparticles Synthesized in the Presence of Peptides - UV-Vis Spectra, Fluorescence, USAXS, Electron Microscopy
<p>Content Summary:</p> <ul> <li>Data from experiments in which gold nanoparticles were synthesized in the presence of peptides using a liquid-handling robot. Samples were analyzed using UV-Vis spectroscopy, fluorescence emission, USAXS, TEM, and SEM. </li> <li>Notebooks for loading and plotting data</li> <li>Code for synthesizing samples using an OT2 Opentrons liquid-handling robot.</li> </ul> <p>README:</p> <p><strong>/Data</strong></p> <p>Contains all UV-Vis, electron microscopy, fluorescence, and SAXS data for gold nanoparticles synthesized in the presence of peptides and HEPES.</p> <p><strong>/Data/2021_12_30_Prepared_UV_Vis_Data</strong></p> <p>The primary portion of the experimental dataset. UV-Vis spectroscopy data collected on a Biotek Epoch 2 microplate spectrophotometer 24 hours after samples were synthesized using a liquid handling robot (Opentrons OT2). The <strong>4x4x4_SI.csv </strong>file is the compilation of all sample information:</p> <ul> <li>Concentrations (M) of peptide, HAuCl4, and HEPES</li> <li>UID – unique ID based on date of synthesis, sample position, and peptide which was used to synthesize the sample.</li> <li>Peptide names: Z2: RMRMKMK; MZ2: myristoylated - RMRMKMK; MZ2R: myristoylated - KMKMRMR; PZ2: palmitoylated – RMRMKMK; Z2M6I: RMRMKIK; Z2M246I: RIRIKIK; AG3: AYSSGAPPMPPF.</li> </ul> <p>Each sample’s UID is a key to match with UV-Vis measurement result stored in the {<strong>UID}.txt </strong>files. Each of these files contains the wavelength, absorbance, and absorbance after subtraction of a water measurement.</p> <p><strong>/Data/2022_02_13_AuPeptide_Kinetics</strong></p> <p><strong>Measurement_Data.xlsx</strong> and <strong>Measurement_Times.xlsx </strong>contain UV-Vis spectra at several time points for each well measured, and the time corresponding to each time step, respectively. See <strong>/Notebooks/UV_Vis_Kinetics.ipynb</strong> for data plotting and sample concentration information.</p> <p><strong>/Data/ElectronMicroscopy</strong></p> <p>Scanning electron microscopy and transmission electron microscopy results of gold nanoparticles formed from the reduction of HAuCl4 in the presence or absence of different peptides.</p> <p>Fig A, B, C, D, E/F were prepared in the presence of Z2, Z2M6I, Z2M246I, no peptide, and MZ2R, respectively.</p> <p><strong>/Data/Fluorescence</strong></p> <p>Pyrene fluorescence data collected in the presence of different concentrations of lipidated peptides (MZ2, MZ2R, and PZ2) for estimation of the peptide critical micelle concentration.</p> <p><strong>/Data/SAXS</strong></p> <p>SAXS data of a high concentration of MZ2 which was fit using a cylindrical model form factor. The evaluated model is also shared in this directory.</p> <p><strong>/Data/USAXS</strong></p> <p>Similarly to the UV-Vis data directory, the <strong>USAXS_SI.csv</strong> file contains sample information for all of the USAXS measurements. The <strong>dsm_rg.csv</strong> file contains the output of AUTORG evaluated on the desmeared data after subtraction of a flat background at high-q. <strong>/DSM_Nexus, DSM_sub_AUTORG, </strong>and <strong>SMR_Nexus</strong> contain the desmeared, desmeared with background subtraction, and smeared versions of the USAXS data, respectively.</p> <p><strong>/Notebooks</strong></p> <p>Notebooks for plotting the shared data and estimating the CMC from the fluorescence data. See <strong>/Notebooks/environment.yml</strong> for packages necessary to execute the notebooks here and in <strong>/Synthesis_Protocol</strong>. We recommend installing this environment by using:</p> <p>conda env create -f /environment.yml</p> <p>Refer to <a href="https://github.com/SasView/sasmodels">https://github.com/SasView/sasmodels</a> and the first cell of <strong>/Notebooks/USAXS.ipynb</strong> for specific instructions on how to complete installation of the sasmodels module (sasmodels will be installed by Pip if you correctly use the shared environment.yml file).</p> <p><strong>/Figures</strong></p> <p>Figures generated from <strong>/Notebooks</strong>.</p> <p><strong>/Synthesis_Protocol</strong></p> <p>Please read the instructions within <strong>/Synthesis_Procol/Example.ipynb</strong>. In short, this folder contains the code used to synthesize the samples in this dataset using an OT2 Opentrons liquid handling robot.</p> <p> </p>
CdSe Quantum Dots Sonochemically Synthesized in the Presence of Oleic Acid & Oleylamine at different concentrations- UV-Vis Spectra, Photoluminescence, SAXS
<p>Conntent Smmary: </p> <ul> <li>Data from experiments in which CdSe quantum dots and magic sized clusters were sonochemically synthesized in the presence of Oleic Acid and Oleylamine at different concentration. A total of 625 unique sample conditions were tested, in triplicates using an open-hardware sonochemical materials acceleration platform (Jubilee) and a liquid handling robot ( Opentrons)</li> <li>Notebooks for loading and plotting the data</li> </ul> <p>README: </p> <p><strong>/Spectral_Data</strong></p> <p>The primary portion of te experimental dataset. UV-Vis spectroscopy was collected on a Biotek Epoch 2 micropate spectrometer. The Photoluminescence data was collected on a Biotek Synergy H1 microplate spectrometer. Notebook to visualize the data can also be found in this folder. </p> <p>The<strong> "CdSe_sample_info.csv" </strong>contains all the sample information, including:</p> <ol> <li>Metal precursors and ligands concentration (M)</li> <li>Labware information- name, OT2 deck location, plate number</li> <li>Sample code- this is a combination of plate # and well position within the plate</li> </ol> <p>The "<strong>CdSe_Summary_Final.csv"</strong> contains all the sample information, along with the key parameters extracted from the UV-Vis and Photoluminescence data. These include, first peak position & peak intensity from both spectroscopic tecniques, particle diameter ( based on the UV-Vis peak position) for all 3 replicates. </p> <p>Finally,there are 3 notebooks to visualize the data in their spectral form, for both pre and post processing of the samples, as well as the notebook to recreate the scatterplot visualization of the summary parameters from the spectroscopic techniques implemented. </p> <p><strong>/Spectral_Data/Spectral_Data_Files</strong></p> <p>Folder containing all the raw data for the pre and post processing of the CdSe samples for UV-Vis spectroscopy and Photoluminescence spectroscopy. </p> <p><strong>/SAXS_Data</strong></p> <p>Folder containing all the data small-angle X-ray scattering data. This was collected on a Xenocs Xeuss 3.0 SAXS instrument. </p> <p>The "<strong>SAXS_Sample_Composition.csv" </strong> file contains the composition of precursors and ligands for the subset of samples tested using small-angle scattering. </p> <p>Notebooks to visualized the SAXS profiles obtained for all samples characterized, as well as their comparison with UV-Vis data can also be found in this folder. </p> <p><strong>/SAXS_Data/Reduced_Raw_Data</strong></p> <p>Folder containing the 1D data obtained from the reduction of the 2D dector data for each sample tested at three different dector distances ( 50, 370, and 900 nm). </p> <p><strong>/SAXS_Data/Processed_Data</strong></p> <p>Folder containing the final process SAXS data which includes merging of the data in the 3 tested instrumental configuration and subsequent background subtraction. </p> <p><strong>/SAXS_Data/McSAS_Fit_Data</strong></p> <p>Folder containing the results obtained form fitting the SAXS data from the diluted samples using the McSAS Python software. The fitting parameters used for the samples can be found in the <strong>"SAXS_Sample_McSAS_Fitting_Parameters.csv" </strong>file.</p> <p><strong>/SAXS_Data/UV-Vis_Data/ </strong></p> <p>Folder containing the UV-Vis data of the subset of samples characterized using SAXS. </p>
Gold Nanoparticles Synthesized in the Presence of Peptides - UV-Vis Spectra, Fluorescence, USAXS, Electron Microscopy; pre-publication version
<p>Content Summary:</p> <ul> <li>Data from experiments in which gold nanoparticles were synthesized in the presence of peptides using a liquid-handling robot. Samples were analyzed using UV-Vis spectroscopy, fluorescence emission, USAXS, TEM, and SEM. </li> <li>Notebooks for loading and plotting data</li> <li>Code for synthesizing samples using an OT2 Opentrons liquid-handling robot.</li> </ul> <p>README:</p> <blockquote> <p><strong>/Data</strong></p> <p>Contains all UV-Vis, electron microscopy, fluorescence, and SAXS data for gold nanoparticles synthesized in the presence of peptides and HEPES.</p> <p><strong>/Data/2021_12_30_Prepared_UV_Vis_Data</strong></p> <p>The primary portion of the experimental dataset. UV-Vis spectroscopy data collected on a Biotek Epoch 2 microplate spectrophotometer 24 hours after samples were synthesized using a liquid handling robot (Opentrons OT2). The <strong>4x4x4_SI.csv </strong>file is the compilation of all sample information:</p> <ul> <li>Concentrations (M) of peptide, HAuCl4, and HEPES</li> <li>UID – unique ID based on date of synthesis, sample position, and peptide which was used to synthesize the sample.</li> <li>Peptide names: Z2: RMRMKMK; MZ2: myristoylated - RMRMKMK; MZ2R: myristoylated - KMKMRMR; PZ2: palmitoylated – RMRMKMK; Z2M6I: RMRMKIK; Z2M246I: RIRIKIK; AG3: AYSSGAPPMPPF.</li> </ul> <p>Each sample’s UID is a key to match with UV-Vis measurement result stored in the {<strong>UID}.txt </strong>files. Each of these files contains the wavelength, absorbance, and absorbance after subtraction of a water measurement.</p> <p><strong>/Data/ElectronMicroscopy</strong></p> <p>Scanning electron microscopy and transmission electron microscopy results of gold nanoparticles formed from the reduction of HAuCl4 in the presence or absence of different peptides.</p> <p>Fig A, B, C, D, E/F were prepared in the presence of Z2, Z2M6I, Z2M246I, no peptide, and MZ2R, respectively.</p> <p><strong>/Data/Fluorescence</strong></p> <p>Pyrene fluorescence data collected in the presence of different concentrations of lipidated peptides (MZ2, MZ2R, and PZ2) for estimation of the peptide critical micelle concentration.</p> <p><strong>/Data/SAXS</strong></p> <p>SAXS data of a high concentration of MZ2 which was fit using a cylindrical model form factor. The evaluated model is also shared in this directory.</p> <p><strong>/Data/USAXS</strong></p> <p>Similarly to the UV-Vis data directory, the <strong>USAXS_SI.csv</strong> file contains sample information for all of the USAXS measurements. The <strong>dsm_rg.csv</strong> file contains the output of AUTORG evaluated on the desmeared data after subtraction of a flat background at high-q. <strong>/DSM_Nexus, DSM_sub_AUTORG, </strong>and <strong>SMR_Nexus</strong> contain the desmeared, desmeared with background subtraction, and smeared versions of the USAXS data, respectively.</p> <p><strong>/Notebooks</strong></p> <p>Notebooks for plotting the shared data and estimating the CMC from the fluorescence data. See <strong>/Notebooks/environment.yml</strong> for packages necessary to execute the notebooks here and in <strong>/Synthesis_Protocol</strong>. Refer to <a href="https://github.com/SasView/sasmodels">https://github.com/SasView/sasmodels</a> for specific instructions on how to install the sasmodels module.</p> <p><strong>/Figures</strong></p> <p>Figures generated from <strong>/Notebooks</strong>.</p> <p><strong>/Synthesis_Protocol</strong></p> <p>Please read the instructions within <strong>/Synthesis_Procol/Example.ipynb</strong>. In short, this folder contains the code used to synthesize the samples in this dataset using an OT2 Opentrons liquid handling robot.</p> <p> </p> </blockquote>
UV-Vis absorbance data, molar extinction coefficients and circular dichroism spectra for the two cyanobacterial metabolites anabaenopeptin A and anabaenopeptin B
<p>Data for:</p> <p>"<span>The UV-Vis absorbance spectra, molar extinction coefficients and circular dichroism spectra as well as NMR and mass spectrometry spectra were determined for two prominent secondary metabolites from cyanobacteria, namely anabaenopeptin A and anabaenopeptin B. The compounds were extracted from the cyanobacterium </span><em><span>Planktothrix rubescens</span></em><span> CBT929 and purified by flash chromatography and HPLC. Exact amounts of isolated compounds were assessed by quantitative <sup>1</sup>H-NMR with internal calibrant ethyl 4-(dimethylamino)benzoate in DMSO-<em>d<sub>6</sub></em> at 298 K with a recycle delay (d1) of 120 s. UV-Vis absorbance spectra were recorded in methanol at room temperature. Molar extinction coefficients were determined at 278 nm as 4190 M<sup>-1</sup> cm<sup>-1</sup> and 2300 M<sup>-1</sup> cm<sup>-1</sup> in methanol for anabaenopeptin A and anabaenopeptin B, respectively. Circular dichroism spectra and secondary fragmentation mass spectra are also reported."</span></p>
UV-VIS Spectra Activated Droplet Sorting for Label-Free Chemical Identification and Collection in Droplets
<p>Data underlying the figures in the publication “UV-VIS Spectra Activated Droplet Sorting for Label-Free Chemical Identification and Collection in Droplets”, published in <em>Analytical Chemistry, </em><strong>2021</strong>.</p> <p>Table of contents:</p> <p><strong>1. Fig2_BSA_calibration_2000us</strong>; Excel file containing the BSA UV-VIS spectra corresponding to <em>Figure 2</em>. It demonstrates the calibration of the UV-VIS in-droplet measurement. Spectroscopy settings: 2000 us integration time and 200 nm to 800 nm wavelength range. Samples: PBS (control), 500 uM BSA, 250 uM BSA, 100 uM BSA, 50 uM BSA, and 10 uM BSA.</p> <p><strong>2. Fig3_Data</strong>; Excel file containing the UV-VIS time-lapse data for high-throughput droplet measurements used in all subfigures of <em>Figure 3</em>. <em>Fig3data.csv</em> is a semi-colon separated csv file for UV-VIS measurements collected over ~30 minutes. Saved wavelengths include 250, 280, 300, 311, 315, 400, 500, and 600 nm. An integration time for the spectrometer of 500 us was used.</p> <p><strong>3. Fig4_C_Postsorting and Fig4_C_Presorting</strong>; Overlaid bright field & fluorescent images of droplets containing E. coli expressing gfp microcolonies before and after droplet sorting.</p> <p><strong>4. Fig4ABD_Data</strong>; Zip. archive containing the experimental data for <em>Figure 4</em>. Interaction of polymersome-based melanosome mimics with HaCaT cells. (A) Cell proliferation assay showing the non-toxicity of different polymersomes encapsulating dopamine and Tyrosinase (dashed purple), L-DOPA and</p> <p><strong>5. Fig5A_Combined Data</strong>; Excel file containing the UV-VIS spectra for <em>Figure 5A</em>. Separate sheets contain spectra for the 3 conditions: empty droplet, mutant (ergothionase activity negative) droplets, and wild type (positive) droplets. UV-VIS range from 200 nm to 1000 nm.</p> <p><strong>6. Fig5B_Ergothionase assay_wild type mutant mix</strong>; Excel file containing the UV-VIS time-lapse data for high-throughput droplet measurements used in <em>Figure 5B</em>.</p> <p>“Fig5B_Ergothionase assay_wild type mutant mix.csv” is a semi-colon separated csv file. Wavelengths 280, 311, 400, and 600 nm are saved. An integration time of 2000 ms was used.</p> <p>“Fig5B_Ergothionase assay_wild type mutant mix_settings.conf” is a configuration file for the spectrophotometer used for this measurement. It describes all spectrometer settings used in the droplet sorting process.</p> <p><strong>7. Fig5C_Combined Data</strong>; Excel file containing the 311 nm absorbance data of <em>Figure 5C</em>; from droplets before and after droplet sorting. The data from both conditions are separated as sheets within the file. An integration time of 2000 ms was used for these measurements.</p> <p><strong>8. SI_Absorbance_by_Geometry</strong>; Excel file containing the data used in <em>Figure S1</em> to test different UV-VIS detection region geometries.</p>
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