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.
1,723
datasets available to search
ShareScore release 0.7.1
Dataset results
1,723 results for “Reactivity”
Reward biases spontaneous neural reactivation during sleep
Open the record for dataset details and reuse information.
Dataset of "Elucidation of factors shaping reactivity of 5'-deoxyadenosyl – a prominent organic radical in biology"
<p>This study investigates the factors modulating the reactivity of 5'-deoxyadenosyl (5'dAdo•) radical, a potent hydrogen atom abstractor, present in the active sites of radical SAM enzymes, but otherwise undergoing a rapid self-decay in aqueous solution. Here, we compare hydrogen atom abstraction (HAA) reactions between native substrates of radical SAM enzymes and 5'dAdo• in aqueous solution and in two enzymatic microenvironments and reveal that HAA efficiency of 5'dAdo• depends on (i) formation of 5'dAdo• in a pre-ordered complex with a substrate, which attenuates the unfavorable effect of substrate:5'dAdo• complex formation, (ii) hindering the conformational change associated with self-decay by performing the reaction in a tight cavity. The enzymatic cavity, however, does not have a strong effect on the HAA activity of 5'dAdo•. We performed an analysis of HAA performed by 5'dAdo• based on the three-component thermodynamic model incorporating the diagonal effect of the free energy of reaction, and the off-diagonal effect of asynchronicity and frustration. The study is based on the straightforward relationship between the off-diagonal thermodynamic effects and the electronic-structure descriptor – the redistribution of charge between the reactants during the reaction. It allows to access HAA-competent redox and acidobasic properties of 5'dAdo• that are otherwise unavailable due to its instability upon one-electron reduction and protonation. The results show that all reactions feature a favourable thermodynamic driving force and tunneling, the latter of which lowers systematically barriers by ~2 kcal mol-1. In addition, most of the reaction experience a favourable off-diagonal thermodynamic contribution. In HAA reactions, 5'dAdo• acts as a weak oxidant as well as a base, also 5'dAdo•-promoted HAA reactions proceed with quite low degree of asynchronicity of proton and electron transfer. Finally, the study elucidates the crucial and dual role of asynchronicity. It directly lowers the barrier as a part of the off-diagonal thermodynamic contribution, but also indirectly increases the non-thermodynamic part of the barrier by controlling the adiabatic coupling between proton and electron transfer. The latter signals that the reaction proceeds as a hydrogen atom transfer rather than a proton-coupled electron transfer.</p>
Supplementary data (CC BY-NC-SA 4.0): A reactive neural network framework for water-loaded acidic zeolites
<p><strong>Content (Creative Commons Attribution Non Commercial Share Alike 4.0 International):</strong></p><p>This dataset provides supplementary data to "A reactive neural network framework for water-loaded acidic zeolites". It contains trained Neural Network Potentials (NNP and ΔNNP model), scripts, and all energy and force data used in this work at the (Δ)NNP, ReaxFF, and DFT (SCAN+D3(BJ) and ωB97X-D3(BJ)) level. Energy and forces are stored as ASE trajectory files (traj), readable by the <a href="https://wiki.fysik.dtu.dk/ase/index.html">Atomic Simulation Environment </a>(ASE). In addition, this repository contains the generated training database with DFT (SCAN+D3(BJ)) energies and forces as SchNetPack1.0 database (SiAlOH.db) file readable by ASE and <a href="https://github.com/atomistic-machine-learning/schnetpack/tree/schnetpack1.0">SchNetPack version 1.0</a>.</p><ol><li>"aimd_simulations.zip" - VASP INCAR file, XDATCAR and traj file for 10 ps AIMD run (Supplementary Figure 6) and NNP level (re-)calculated energies/forces ("aimd_nnp_recalc.traj")</li><li>"biased_dynamics.zip" - VASP/Plumed input and output files for DFT (SCAN+D3(BJ)) and NNP level biased dynamics including traj files (Supplementary Figure 12)</li><li>"database_input.zip" - structure (cif) files of the initial structures used for database generation (Supplementary Table 1)</li><li>"delta_nnp.zip" - (pytorch) ΔNNP model (compatible with <a href="https://github.com/atomistic-machine-learning/schnetpack/tree/schnetpack1.0">SchNetPack version 1.0</a>) together with example scripts </li><li>"error_stats.zip" - traj files of all generalization tests (Figure 1 and Supplementary Figure 4) storing energies/forces at the SCAN+D3(BJ), ReaxFF, and NNP level as well as traj files with ΔNNP and ωB97X-D3(BJ) energies/forces for a subset taken from biased dynamics runs (Supplementary Figure 11)</li><li>"md_simulations.zip" - NNP level MD trajectories of all generalization test (Figure 1 and Supplementary Figure 4) runs including an example script for an MD run</li><li>"neb_calculations.zip" - traj files and example scripts for NEB calculations at the (Δ)NNP along with the corresponding DFT energy/force data (SCAN+D3(BJ) and ωB97X-D3(BJ))</li><li>"nnps.zip" - (pytorch) NNP model files (compatible with <a href="https://github.com/atomistic-machine-learning/schnetpack/tree/schnetpack1.0">SchNetPack version 1.0</a>)</li><li>"silica_database.zip" - output files of the single-point (SP) and optimization test runs (Supplementary Figure 1) of pure silica structures together with an example structure optimization script </li><li>"SiAlOH.db" - DFT (SCAN+D3(BJ)) training database as SchNetPack1.0 database file readable by ASE and <a href="https://github.com/atomistic-machine-learning/schnetpack/tree/schnetpack1.0">SchNetPack version 1.0</a></li></ol>
Sensitivity enhancement using chemically reactive gas cluster ion beams in secondary ion mass spectrometry (SIMS)
<p>We report for the first time on significant molecular secondary ion yield increases by modifying the chemistry of a water cluster primary ion beam. This was demonstrated using 70 keV ion beams of 0.15 eV/amu. For the neutral drug Bezafibrate, secondary ion yield enhancements ×5-10 were observed when replacing the Ar carrier gas in a water gas cluster ion beam (GCIB) source with a mixture containing 12% CO2 and 2% O2 in Ar. For the cationic drug Ranitidine the ion yield enhancements using the CO2-containing carrier gas were up to ×20-50 in positive mode and ×2-4 in negative mode. The extent of molecular fragmentation was very similar from both cluster beams. We conclude that additional chemically reactive species are present in the impact zone using the (H2O/CO2)n projectile which promote the formation of secondary ions of both polarity through projectile impact-induced chemical reactions. This methodology can be applied to further extend the capabilities of high-resolution 3-dimensional mass spectral imaging using reactive GCIB-SIMS.</p>
Dataset of 'HIV infection is associated with compromised tumor microenvironment adaptive immune reactivity in Hodgkin Lymphoma'
<p><span><span>§<span> </span></span></span><strong><span>:</span></strong><span>The data were generated using the i) GeoMx Digital Spatial Profiler (DSP) platform developed by Nanostring Technologies. GeoMx analysis utilizes <em>in situ </em>RNA hybridization with Whole Atlas Transcriptome probe (Nanostring) and ii) HTG platform (Immune Response kit) Our dataset comprises samples from donors categorized as HLposHIVnegEBVneg, HLposHIVposEBVpos, or HLposHIVnegEBVpos (HL: Hodgkin Lymphoma). Regions of interest (ROI) were spatially profiled to capture distinct molecular signatures associated with these donor categories.</span></p>
Growth of hexagonal boron nitride from molten nickel solutions: a reactive molecular dynamics study
<p>Authors: Amin Ahmadisharaf and Jeffrey Comer</p> <p><br>Publication: Amin Ahmadisharaf, Bin Liu, James H. Edgar, and Jeffrey Comer (2025) Growth of Hexagonal Boron Nitride from Molten Nickel Solutions: A Reactive Molecular Dynamics Study. ACS Applied Materials & Interfaces. <a href="https://doi.org/10.1021/acsami.4c16991">doi.org/10.1021/acsami.4c16991</a></p> <p>Funding: Department of Energy Office of Science, grant DE-SC0021264, <a>https://pamspublic.science.energy.gov/WebPAMSExternal/Interface/Common/ViewPublicAbstract.aspx?rv=5e6ffff5-0daa-47e8-a3d0-20f594b7bfb8&rtc=24&PRoleId=10</a></p> <p>**************************************</p> <p>This data set for the manuscript entitled "Growth of Hexagonal Boron Nitride from Molten Nickel Solutions: A Reactive Molecular Dynamics Study" includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software LAMMPS, as well as the output of the simulations. The files are organized into directories corresponding to the figures of the main text. They include force field parameter files (in ReaxFF format), LAMMPS configuration files (*.in), ReaxFF control files (*.control), LAMMPS log files (*.log), and LAMMPS output including restart files (in binary LAMMPS format) and trajectories in dcd format (downsampled to 12.5 or 25 ps per frame) and also PDB and PSF files are useful for visualization with VMD. Analysis is performed by python and shell scripts (Bash-compatible) that call VMD Tcl scripts or python scripts. These scripts and their output are also included.</p> <p>The species analysis is performed by the VMD Tcl script "Figure3/analysis/count_hBN_species_NNB_BN.tcl" using the parameters given in "Figure3/analysis/doCount.sh".</p> <p>The directory contents are as follows.</p> <p>--------------------------------------------------------------<br>Figure-1: Parallel tempering simulations of the boron-nickel system and calculation of the boron concentration along the z-dimension of the nickel slab.</p> <p>The analysis of the boron concentration profile is performed by the VMD Tcl scripts calcRatioZRef.tcl and calcConcZRef.tcl using the parameters given in "Figure1/analysis/step3_conc_profile.sh". Also, the reorganization of the parallel tempering trajectories into frames at a single temperature is performed by the VMD Tcl script extractReplicaFrames.tcl based on "Figure1/analysis/step1_sort_frames.sh".</p> <p><br>--------------------------------------------------------------<br>Figure-2: Simulation of hBN sheet growth at 1750 K and calculation of largest cluster.</p> <p><br>--------------------------------------------------------------<br>Figure-3: Simulations of different boron-to-nickel ratios at varying nitrogen pressures at 1750 K and the calculation of the largest hBN cluster formed under different scenarios. The suffixes "liu", "long_liu", and "low_liu" correspond to pressures of 100.0, 50.0, and 25.0 atm respectively.</p> <p>The analysis of hBN clusters is performed by the VMD Tcl script "Figure3/analysis/" using the parameters given in "Figure3/analysis/doCount.sh". The related simulations files and outputs for panel A in this figure are located in Figure 5 directory.</p> <p><br>--------------------------------------------------------------<br>Figure-4: Recognition and counting the different boron-nitrogen motifs in the simulation was performed in Figure 2.</p> <p>The related simulations files and outputs for panel B and C in this figure are located in Figure 5 directory.</p> <p><br>--------------------------------------------------------------<br>Figure-5: Simulation of the temperature effect on hBN growth, and recognition and counting of the different boron-nitrogen motifs at 1750, 1800, 1900, 2000, 2200, and 2700 K.. </p> <p><br>--------------------------------------------------------------<br>Figure-6: Recognition of existing motifs for nitrogen atoms in the growth path of hBN and calculation of the probabilities of transitions between different motifs across all nitrogen atoms.</p> <p>The related simulations files and outputs for all panels in this figure are located in Figure 5 directory.</p> <p><br>--------------------------------------------------------------<br>Figure-7: Comparing the ReaxFF and ab initio simulations of small B-N motifs(B--N--B and B--N) in a nickel slab and calculation of bond lengths and angle values.</p> <p><br>--------------------------------------------------------------<br>Figure-8: Diffusion simulations of four different systems at 1800 K: nickel with a single B atom, nickel with a single N atom, nickel with a free B-N-B molecule, and nickel with a small hBN sheet and Mean Squared Displacement (MSD) values were calculated and compared to assess the surface mobility of the different particles.</p> <p> </p>
Compound I Formation and Reactivity in Dimeric Chlorite Dismutase: Impact of pH and the Dynamics of the Catalytic Arginine
<ul> <li><strong>Data type</strong>: spectroscopic measurements (UV-visible, ECD, EPR), enzyme activity measurements, mass spectrometry, spectroelectrochemistry and data analysis.</li> <li>Files are in<strong> .DTA, .DSC, .xlsx, .m, .mat, .BSW, .csv, .txt, .dsx, .pdf, .uds </strong>formats</li> <li>Information on <strong>origin of the data</strong>: <ul> <li>EPR spectroscopic measurements in <strong>DTA </strong>and<strong> DSC</strong> formats</li> <li>EPR spectroscopic simulation and analyses in <strong>m </strong>and<strong> mat</strong> format</li> <li>Analysis of Rapid Freeze-Quench calibration curve is in <strong>xlsx</strong> format</li> <li>UV-vis spectroscopic measurements in <strong>csv, xlsx, txt, uds and dsx</strong> format</li> <li>ECD measurements in <strong>csv, xlsx and dsx</strong> format</li> <li>Enzyme activity data in <strong>csv and xlsx</strong> format</li> <li>Mass spectrometry data in <strong>pdf and xlsx</strong> format</li> <li>Spectroelectrochemistry data in <strong>BSW</strong> and <strong>xlsx</strong> format</li> </ul> </li> <li>The data are <strong>generated</strong> by: <ul> <li>UV−vis spectra were recorded using a Cary 60 UV–vis spectrophotometer (Agilent) and a U-3900 spectrophotometer (Hitachi, Mannheim, Germany).</li> <li>Electronic circular dichroism spectroscopy was performed using Chirascan (Applied Photophysics, Leatherhead, UK).</li> <li>Rapid Freeze-Quench of EPR sample was performed with the use of a device from BioLogic (Grenoble, France), consisting of an SFM-2000 stopped-flow unit and an MPS-70 controller unit, combined with a freeze-quench sample collector adapted for EPR tubes. The ejected volumes and flow rate were controlled by the BioLogic BIOKINE software, v. 4.72.</li> <li>X-Band CW-EPR experiments were performed on X-band ELEXSYS E580 spectrometer (Bruker BioSpin GmbH) operating at a microwave frequency of ∼9.4 GHz and equipped with a standard TE102 cavity and a liquid He cryostat (Oxford Inc.)</li> <li>Enzyme activity was measured polarographically following the release of O<sub>2</sub> by using a Clark-type oxygen electrode (Oxygraph Plus; Hansatech Instruments, Norfolk, UK).</li> <li>Stopped-flow spectroscopy measurements were performed with a SX-18MV or Pi-star from Applied Photophysics using either a diode array detector or a monochromator and photomultiplier detector.</li> <li>Mass spectrometry analysis was performed with an ion-trap mass spectrometer (amaZon speed ETD, Bruker) equipped with the standard ESI source in positive ion, DDA mode (i.e., switching to MSMS mode for eluting peaks).</li> <li>All spectroelectrochemistry experiments were conducted in a homemade OTTLE (optical transparent thin-layer spectroelectrochemical) cell. In detail, the three-electrode configuration consisted of a gold minigrid working electrode (Buckbee-Mears, Chicago, IL), a homemade Ag/AgCl/KCl<sub>sat</sub> microreference electrode separated from the working solution by a Vycor set, and a platinum wire as the counter electrode. UV−vis spectra were recorded using a Varian Cary C50 spectrophotometer.</li> </ul> </li> </ul> <p> </p> <p> </p> <ul> <li>If the dataset includes multiple files that relate to each other: <ul> <li>Files in <strong>PARACAT_WP3_20230302_01_EPR </strong>folder includes EPR spectroscopic measurements and computer simulations/analyses, original data are in <strong>DTA/DSC</strong> formats; files in <strong>m</strong> format were used to process the data.</li> <li>Files in <strong>PARACAT_WP3_20230302_02_UVVIS </strong>folder includes sequential and non-sequential stopped flow data, measured with detection by photodiode array or monochromator (time traces): original data is in <strong>dsx and csv </strong>format<strong>, xlsx </strong>format contains processed data; conventional photometric data is originally in <strong>txt and uds </strong>format, <strong>xlsx </strong>format contains processed data</li> <li>Files in <strong>PARACAT_WP3_20230302_03_ECD</strong> folder contain ECD spectra: original data is in <strong>dsx and csv </strong>format<strong>, xlsx </strong>format contains processed data</li> <li>Files in <strong>PARACAT_WP3_20230302_04_Enzyme activity </strong>folder contain polarographically detected changes in dioxygen concentration, due to enzyme activity: original data is in <strong>csv </strong>format<strong>, xlsx </strong>format contains processed data</li> <li>Files in <strong>PARACAT_WP3_20230302_05_MassSpec </strong>folder contain mass spectrometry data for the MNP assay: original data is in <strong>pdf </strong>format<strong>, xlsx </strong>format contains processed data</li> <li>Files in <strong>PARACAT_WP3_20230302_06_Spectroelectrochemistry </strong>folder includes spectroelectrochemistry measurements and computer analyses, original data are in <strong>BSW</strong> formats; files in <strong>xlsx</strong> format were used to process the data.</li> </ul> </li> </ul> <p> </p> <p>NB. See the “READ ME” text file in each subfolder for more detailed information on files organization.</p> <p> </p> <ul> <li>Information on: <ul> <li><strong>Abbreviations:</strong> <ul> <li>, chlorite dismutase; <strong><em>C</em>Cld</strong>, chlorite dismutase from Cyanothece sp. PCC7425; <strong>CcP</strong>, cytochrome c peroxidase;<strong> DaCld</strong>, chlorite dismutase from <em>Dechloromonas aromatica</em>; <strong>E°′</strong>, standard reduction potential; <strong>ECD</strong>, electronic circular dichroism; <strong>EPR</strong>, electron paramagnetic resonance; <strong>HRP</strong>, horseradish peroxidase; <strong>LPO</strong>, lactoperoxidase; <strong>MNP</strong>, 2-methyl-2-nitrosopropane; <strong>MPO</strong>, myeloperoxidase; <strong>PAA</strong>, peracetic acid; <strong>RFQ</strong>, rapid freeze-quench.</li> </ul> </li> </ul> </li> </ul> <p> </p> <ul> <li><strong>Units of measurement</strong>: <ul> <li>Concentration: <strong>mM</strong> (millimolar), <strong>µM</strong> (micromolar), <strong>nM</strong> (nanomolar), <strong>mg/mL</strong> (milligrams per milliliter)</li> <li>Molecular mass: <strong>Da</strong> (Dalton)</li> <li>Absorptivity: <strong>M<sup>-1</sup></strong> <strong>cm<sup>-1</sup></strong></li> <li>Volume: <strong>mL</strong> (milliliters), <strong>µL </strong>(microliters), <strong>nL</strong> (nanoliters)</li> <li>Wavelength:<strong> nm</strong> (nanometers)</li> <li>Temperature:<strong> °C</strong> (Celsius degrees), <strong>K</strong> (Kelvin degrees)</li> <li>Time:<strong> ms</strong> (milliseconds), <strong>s</strong> (seconds), <strong>min</strong> (minutes), <strong>h</strong> (hours),</li> <li>Ellipticity: millidegrees</li> <li>Frequency: <strong>GHz</strong> (gigahertz), <strong>kHz</strong> (kilohertz)</li> <li>Power: <strong>mW</strong> (milliwatt)</li> <li>Magnetic field: <strong>mT</strong> (milliTesla)</li> <li>Reduction potential: <strong>mV </strong>(milliVolts)</li> </ul> </li> </ul>
Multiple-object tracking as atool for parametrically modulating memory reactivation
Open the record for dataset details and reuse information.
Increased brain reactivity to gambling unavailability is a marker of problem gambling
Open the record for dataset details and reuse information.
Model-based aversive learning in humans is supported by preferential task state reactivation
Open the record for dataset details and reuse information.
An Experimental Investigation of Reactive Melt Channelization in Partially Molten Rocks
<p>Mechanical, microstructural and chemical data from experiments on reactive melt migration. Each zip file contains all data from the specific experiment that were collected (optical images, scanning electron microscope images, microCT reconstructions, electron microprobe data). Master metadata table is provided with all details about the performed experiments. Experiment number corresponds to zip file number. Further information about the dataset is contained in the following publications:</p> <p>Matej Pec, Benjamin K. Holtzman, Mark Zimmerman, David L. Kohlstedt; (2015) Reaction infiltration instabilities in experiments on partially molten mantle rocks. <em><em>Geology</em></em> ; 43 (7): 575–578. doi: <a href="https://doi.org/10.1130/G36611.1">https://doi.org/10.1130/G36611.1</a></p> <p>Matej Pec, Benjamin K. Holtzman, Mark E. Zimmerman, David L. Kohlstedt, (2017) Reaction Infiltration Instabilities in Mantle Rocks: an Experimental Investigation, <em>Journal of Petrology</em>, Volume 58, Issue 5, May 2017, Pages 979–1003, <a href="https://doi.org/10.1093/petrology/egx043">https://doi.org/10.1093/petrology/egx043</a></p> <p>Matej Pec, Benjamin K. Holtzman, Mark E. Zimmerman, David L. Kohlstedt, (submitted) Influence of Lithology on Reactive Melt Flow Channelization: Infiltration Instabilities and Dikes, submitted to<em> Geochemistry, Geophysics, Geosystems</em></p>
Data from: Grand Theft Empathy? Evidence for the absence of effects of violent video games on empathy for pain and emotional reactivity to violence
<p><strong>Abstract:</strong></p><p>Influential accounts claim that violent video games (VVG) decrease players' emotional empathy by desensitizing them to both virtual and real-life violence. However, scientific evidence for this claim is inconclusive and controversially debated. To assess the causal effect of VVGs on the behavioral and neural correlates of empathy and emotional reactivity to violence, we conducted a prospective experimental study using functional magnetic resonance imaging (fMRI). We recruited eighty-nine male participants without prior VVG experience. Over the course of two weeks, participants played either a highly violent video game, or a non-violent version of the same game. Before and after this period, participants completed an fMRI experiment with paradigms measuring their empathy for pain and emotional reactivity to violent images. Applying a Bayesian analysis approach throughout enabled us to find substantial evidence for the absence of an effect of VVGs on the behavioral and neural correlates of empathy. Moreover, participants in the VVG group were not desensitized to images of real-world violence. These results imply that short and controlled exposure to VVGs does not numb empathy nor the responses to real-world violence. We discuss the implications of our findings regarding the potential and limitations of experimental research on the causal effects of VVGs. While VVGs might not have a discernible effect on the investigated subpopulation within our carefully controlled experimental setting, our results cannot preclude that effects could be found in special vulnerable subpopulations, or in settings with higher ecological validity.<br> </p><p><strong>Dataset:</strong><br>This dataset contains the fMRI data collected for the study in the BIDS-format (https://bids.neuroimaging.io/)</p><ul><li>functional neuroimaging (*_bold.nii.gz) data of 89 human participants, collected during two tasks:<ul><li>Empathy-for-Pain paradigm (Session 1 & 2)</li><li>Emotional Reactivity paradigm (Session 2)</li></ul></li><li>associated event files (*_events.tsv) containing event onsets, durations, and behavioral covariates</li><li>metadata</li></ul><p>FMRI bold timeseries are fully preprocessed, as described in the manuscript.</p><p>Additional data, such as behavioral data in a simpler format, can be accessed on https://osf.io/yx423/</p><p> </p>
Two-Electron Redox Reactivity of Thorium Supported by Redox-Active Tripodal Frameworks
<p>This upload contains raw data (NMR, X-Ray, UV, Electrochemistry and Elemental Analysis) files for the article</p>
Kinetic Study on the Reactivity of Azanone (HNO) toward Cyclic C-Nucleophiles
<p>1. Equipment</p> <p>UV-Vis absorption spectra were collected using an Agilent 8453 spectrophotometer equipped with a photodiode array detector and thermostated cell holder.</p> <p>2. Chemicals</p> <p>The Angeli’s salt stock solution was prepared in 1 mM NaOH. Its concentration was determined by measuring the absorbance at 248 nm (ε = 8.3 · 10<sup>3</sup> M<sup>−1</sup>cm<sup>−1</sup>). The solution was kept on ice. 1-(4-Methoxybenzyl)-2,4-piperidinedione, 2-acetyl-1,3-cyclohexanedione were purchased from Angene Chemical. 1,3-Cyclopentanedione, 2-methyl-1,3-cyclopentanedione, 1,3-cyclohexanedione, 2-methyl-1,3-cyclohexanedione, 1,3-cycloheptanedione, and 2,4-piperidinedione were purchased from Fluorochem, United Kingdom. All other chemicals (of the highest purity available) were sourced from Sigma-Aldrich Corp. All solutions were prepared using deionized water (Millipore Milli-Q system).</p> <p>3. Kinetic Experiments</p> <p>The HNO flux was determined from the rate of FlBA oxidation in aerated aqueous solution of Angeli’s salt, monitored at 490 nm. The initial concentration of Angeli’s salt was equal to 20 µM. Due to the scavenging of HNO by O<sub>2</sub> and other scavengers, the steady-state concentration of azanone is very low. The HNO dimerization was therefore negligible and was not taken into consideration. HNO released from Angeli’s salt reacts either with the HNO scavenger or with the molecular oxygen to form peroxynitrite, which was detected with the use of the FlBA probe (25 µM). Its reaction with ONOO<sup>–</sup> results in the formation of fluorescein. The formation of fluorescein was monitored spectrophotometrically by following the increase in its characteristic absorbance at 490 nm. The reaction mixtures contained Angeli’s salt (20 µM), the fluorescein-based monoborate probe FlBA (25 µM), phosphate buffer (50 mM, pH 7.4), dtpa (100 µM), and the HNO scavenger (at an appropriate concentration). In addition, each solution contained 5% (vol.) CH<sub>3</sub>CN. The rate constants were determined with the assumption that the concentration of molecular oxygen was equal to 225 µM. Each rate constant was determined in at least three independent experiments.</p> <p>The dataset contains ASCII files with UV-Vis spectra of the reaction mixtures recorded for an incubation time of 10 min. (see Artelska, A.; Rola, M.; Rostkowski, M.; Pięta, M.; Pięta, J.; Michalski, R.; Sikora, A.B. Kinetic Study on the Reactivity of Azanone (HNO) toward Cyclic C-Nucleophiles. Int. J. Mol. Sci. (2021), in press.).</p> <p>4. Computational Details</p> <p>Quantum mechanical calculations were performed in the Gaussian G09 suite of programs, Revision E01. Stationary points were found by geometry optimization algorithms with tight convergence criteria except for transition state structure in the reaction of HNO with 1-(4-methoxybenzyl)-2,4-piperidinedione, where default criteria had to be used due to lack of computation convergence. To verify the nature of stationary points, as well as to compute Gibbs free energies, respective frequencies were computed. In calculations, the presence of the water environment was described by the Gaussian default continuum solvation model (IEFPCM). Density functional theory (DFT) functional B2PLYP with Grimme’s D3 dispersion correction (B2PLYP-D3) combined with 6-311+(2df,2p) split valence basis set, was used. The theory level was selected based on the fact that double-hybrid DFT functionals perform well in describing chemical system properties as well as reaction energy barriers, especially when London dispersion corrections are employed.</p> <p>The file AtomicCoordinatesOfStationaryPoints.txt contains geometries of stationary points obtained at the B2PLYP-D3/6-311+(2df,2p) theory level used for Gibbs free energey calculations in computational studies (see Artelska, A.; Rola, M.; Rostkowski, M.; Pięta, M.; Pięta, J.; Michalski, R.; Sikora, A.B. Kinetic Study on the Reactivity of Azanone (HNO) toward Cyclic C-Nucleophiles. Int. J. Mol. Sci. (2021), in press.).</p>
Reactive nitrogen fluxes over peatland (Bourtanger Moor) and forest (Bavarian Forest National Park) using micrometeorological measurement techniques
<p>Within the framework of the research projects NITROSPHERE and FORESTFLUX, field campaigns were carried out to investigate the biosphere-atmosphere exchange of reactive nitrogen compounds. We applied novel fast-response instruments in eddy-covariance setups for continuous determination of surface ammonia (NH<sub>3</sub>) and total reactive nitrogen (<span class="math-tex">\(\Sigma\)</span>N<sub>r</sub>) fluxes using two different analytical devices. While high-frequency measurements of ammonia were measured with a quantum cascade laser absorption spectrometer (QCL), a custom-built converter called TRANC coupled to a chemiluminescence detector was used for the determination of total reactive nitrogen. High-resolution data of surface-atmosphere fluxes of reactive compounds are still scarce, but highly desired for testing and validating local inferential and larger scale models. We provide access to campaign data including concentrations, fluxes and ancillary measurements of meteorological data. Campaigns were conducted in natural (forest) and semi-natural (peatland) ecosystem types. The published datasets stress the importance of recent advancements in laser spectrometry and help improve our understanding of the temporal variability of surface-atmosphere exchange in different ecosystems, thereby providing validation opportunities for inferential models simulating the exchange of reactive nitrogen.</p>
Memory reactivation in slow wave sleep enhances relational learning
<p>EEG raw files in Brain Product format (3 files per participant). Sleep EEG recordings from healthy volunters under TMR stimulation. </p> <p>Two conditions: up-going slow oscillation stimulation / down-going oscillation stimulations</p> <p>Two type of sounds: experimental (they hear them before) and control (completely new)</p> <p>Triggers: 100-112 up experimental sounds / >112 up control sounds / 1-12 down experimetal sounds / 12-100 down control</p> <p>Please cite:</p> <p>"Memory reactivation in slow wave sleep enhances relational learning" ( https://doi.org/10.1101/2022.03.29.486197 )</p> <p> </p>
Dataset of "Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-infected Cells"
<p><strong>Detailed quantitative analysis of GFP expression in SAHA and TCR-treated cells & Computational analysis of bulk and single-cell RNA-Seq data.</strong></p> <p> </p> <p><em><strong>Detailed quantitative analysis of GFP expression in SAHA and TCR-treated cells.</strong></em></p> <p>Cells were prepared for single cell analysis at the Genome Technology Facility (GTF) of the University of Lausanne. Cells were loaded on Fluidigm C1 IFC plates (5-10 μm), with run ID smart33, smart34 and smart35, corresponding to untreated, SAHA- and TCR-treated conditions respectively. After single cell capture on the Fluidigm C1 IFC plate, each chamber was inspected visually by microscopy and pictures were captured with a Zeiss Axiovert 200 M fluorescence microscope equipped with a Roper Scientific CoolSnap HQ camera using a Plan-Neofluar 10X lens (smart34 run) or 20X lens (for smart35 run). For each capture chamber, pictures in bright field and FITC channel were taken with the MetaMorph 6.3 software. Picture analysis was then performed using ImageJ 1.50b software (open access software: website). Brightness and contrast were adjusted for qualitative assessment of the pictures.</p> <p><em><strong>Computational analysis of bulk and single-cell RNA-Seq data.</strong></em></p> <p>Upon bulk or single cell isolation, RNA extraction and library preparation was performed according to Illumina protocols. Bulk and single-cell RNA-Seq data analysis are detailed here.</p> <p> </p> <p>Linked to the paper published in Cell Reports (doi:10.1016/j.celrep.2018.03.102): </p> <p><strong>Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-infected Cells</strong></p> <p>Despite effective treatment, HIV can persist in latent reservoirs, which represent a major obstacle towards HIV eradication. Targeting and reactivating latent cells is challenging due to the heterogeneous nature of HIV infected cells. Here, we used a primary model of HIV latency and single-cell RNA sequencing to characterize transcriptional heterogeneity during HIV latency and reactivation. Our analysis identified transcriptional programs leading to successful reactivation of HIV expression.</p> <p> </p> <p> </p>
Reactive pressure infiltration of Cu-46at.pct. Si into carbon
<p>Raw data linked to the paper published in Acta Materialia :Reactive pressure infiltration of Cu-46at.pct. Si into carbon (DOI:h<a href="https://doi.org/10.1016/j.actamat.2019.07.010">ttps://doi.org/10.1016/j.actamat.2019.07.010</a>)</p>
Dataset of a multiphase flow and reactive transport benchmark for radioactive waste disposal
<p>The files include the full dataset (tables and figures) of the comparion the results of a multiphase flow and reactive transport<br>benchmark for radioactive waste disposal. The codes INVERSE-FADES-CORE V2, DuMuX , TOUGHREACT and<br>iCP were benchmarked with 6 test cases of increasing complexity, starting with conservative tracer transport under variably<br>unsaturated conditions and ending with water flow, gas diffusion, minerals and cation exchange.</p>
Data for paper "Parametric schedulability analysis of a launcher flight control system under reactivity constraints"
<p>This is the data set (models, sources and results) for the paper "Parametric schedulability analysis of a launcher flight control system under reactivity constraints" published in Informatica Fundamentae in 2021.</p>
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.