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1,294 results for “reactions”
Data from: Latitudinal variation in norms of reaction of phenology in the greater duckweed Spirodela polyrhiza
<p>Variable environments may result in the evolution of adaptive phenotypic plasticity when cues reliably indicate an appropriate phenotype-environment match. Although adaptive plasticity is well established for phenological traits expressed across environments, local differentiation in norms of reaction is less well studied. The switch from the production of regular fronds to overwintering "turions" in the greater duckweed <i>Spirodela polyrhiza</i> is vital to fitness and is expressed as a norm of reaction induced by falling temperatures associated with the onset of winter. However, the optimal norm of reaction to temperature is expected to differ across latitudes. Here, we test the hypothesis that a gradient in the length and predictability of growing seasons across latitudes results in the evolution of reaction norms characterized by earlier turion production at higher latitudes. We test this by collecting <i>S. polyrhiza</i> from replicate populations across seven latitudes from Ontario to Florida, and then assessing differentiation in thermal reaction norms of turion production along a common temperature gradient. As predicted, northern populations produce turions at lower birth order and earlier; a significant latitude-by-temperature interaction suggests that reaction norm differentiation has occurred. Our results provide evidence of differentiation in reaction norms across latitudes in a phenological trait, and we discuss how the adaptive significance of this plasticity might be further tested.</p>
Application of spectral library prediction for parallel reaction monitoring of viral peptides_DDA_data
<p><strong>Project description: </strong></p> <p>A major part of the analysis of parallel reaction monitoring (PRM) data is the comparison of observed fragment ion intensities to a library spectrum. Classically, these libraries are generated by data-dependent acquisition (DDA). Here we test Prosit, a published deep neural network algorithm, for its applicability in predicting spectral libraries for PRM. For this purpose, we targeted 1,529 precursors derived from synthetic viral peptides and analyzed the data with Prosit and DDA-derived libraries. Additionally, we used a spectral library predicted by Prosit and a DDA library to identify SARS-CoV-2 peptides from a simulated oropharyngeal swab.</p> <p> </p> <p><strong>Sample processing protocol:</strong></p> <p>A total of 1,569 crude synthetic viral peptides were ordered in six pools from JPT (Berlin, Germany). Synthetic peptides were separated on a 200 cm μPAC™ column (PharmaFluidics) by using an EASY-nLC1200 system (Thermo Fisher Scientific) equipped with a μPAC™ trapping column (PharmaFluidics). The flow rate was set to 300 nL/min and a stepped linear 160 min gradient was applied: 3-10% B in 22 min, 10-33%B in 95 min, 33-49% B in 23 min, 49-80% B in 10 min and 80% B for 10 min. Solvent A was 0.1% (v/v) formic acid (FA) in water, solvent B consisted of 80% (v/v) acetonitrile in 0.1% (v/v) FA. The column temperature was set to 50 °C. The Q Exactive Plus (Thermo Fisher Scientific) operated in Full MS/dd-MS2 or unscheduled PRM mode. For MS/dd-MS2 the following parameters were used. MS1 resolution was 70.000 with an AGC target of 3x10<sup>6</sup>, max. injection time of 20 ms and a scan range of 300-1650 m/z. MS2 resolution was 17.500 with an AGC target of 10<sup>5</sup>, max. injection time of 50 ms and an isolation window of 2 m/z. The analysis parameters in PRM mode were set as follows. MS1 parameters were identical to DDA. MS2 resolution was 17.500 with an AGC target of 10<sup>6</sup>, max. injection time of 55 ms and an isolation window of 1.4 m/z.</p> <p>Potential SARS-CoV-2 target peptides belonging to the N protein were identified by DDA of SARS-CoV-2 infected Calu-3 cells. Peptides were diluted in 0.1% TFA (0.2 µg/µL) and 5 µL were separated on a 50 cm μPAC™ column (PharmaFluidics) using an EASY-nLC1200 system (Thermo Fisher Scientific). The flow rate was set to 800 nL/min and a stepped 30 min gradient was applied: 6-11% B in 2:58 min, 11-30% B in 17:10 min, 30-35% B in 2:41 min, 35-47% B in 3:11 min, 47-80% B for 0:10 min, 80% B for 1:50 min, 80-0% B in 0:10 min and 100% A for 1:50 min. Solvent A was 0.1% (v/v) formic acid (FA) in water, solvent B consisted of 80% (v/v) acetonitrile in 0.1% (v/v) FA. The column temperature was set to 50 °C. The Q Exactive HF (Thermo Fisher Scientific) operated in Full MS/dd-MS2 (Top20) using the following parameters. MS1 resolution was 60.000 with an AGC target of 3x10<sup>6</sup>, max. injection time of 20 ms and a scan range of 300-1650 m/z. MS2 resolution was 17.500 with an AGC target of 10<sup>5</sup>, max. injection time of 50 ms and an isolation window of 2 m/z.</p> <p> </p> <p>To simulate a SARS-CoV-2 positive patient sample, we spiked cell-culture derived virus in a negative oropharyngeal swab and targeted the N protein by PRM. LC parameters were identical to DDA analysis of SARS-CoV-2 infected Calu-3 cells. The PRM parameters of the The Q Exactive HF (Thermo Fisher Scientific) were set as follows. MS1 parameters were identical to DDA. MS2 resolution was 45.000 with an AGC target of 10<sup>6</sup>, max. injection time of 100 ms and an isolation window of 1.4 m/z.</p> <p> </p> <p> </p> <p><strong>Data processing protocol:</strong></p> <p>DDA Raw files were searched with MaxQuant against the respective virus database (UniProt) with a peptide FDR of 1%. Detailed MaxQuant parameters can be found in the parameters.txt files of the according results. MaxQuant .msms output files were used to generate spectral libraries with BiblioSpec implemented in the Skyline environment using a cut-off score of 0.95. Peptide identification of PRM runs was done in Skyline using the top 6 fragment ions of the DDA spectral library or according Prosit derived library (Prosit_2020_intensity_model).</p>
Application of spectral library prediction for parallel reaction monitoring of viral peptides_PRM_NCE_data
<p><strong>Project description: </strong></p> <p>A major part of the analysis of parallel reaction monitoring (PRM) data is the comparison of observed fragment ion intensities to a library spectrum. Classically, these libraries are generated by data-dependent acquisition (DDA). Here we test Prosit, a published deep neural network algorithm, for its applicability in predicting spectral libraries for PRM. For this purpose, we targeted 1,529 precursors derived from synthetic viral peptides and analyzed the data with Prosit and DDA-derived libraries. Additionally, we used a spectral library predicted by Prosit and a DDA library to identify SARS-CoV-2 peptides from a simulated oropharyngeal swab.</p> <p> </p> <p><strong>Sample processing protocol:</strong></p> <p>A total of 1,569 crude synthetic viral peptides were ordered in six pools from JPT (Berlin, Germany). Synthetic peptides were separated on a 200 cm μPAC™ column (PharmaFluidics) by using an EASY-nLC1200 system (Thermo Fisher Scientific) equipped with a μPAC™ trapping column (PharmaFluidics). The flow rate was set to 300 nL/min and a stepped linear 160 min gradient was applied: 3-10% B in 22 min, 10-33%B in 95 min, 33-49% B in 23 min, 49-80% B in 10 min and 80% B for 10 min. Solvent A was 0.1% (v/v) formic acid (FA) in water, solvent B consisted of 80% (v/v) acetonitrile in 0.1% (v/v) FA. The column temperature was set to 50 °C. The Q Exactive Plus (Thermo Fisher Scientific) operated in Full MS/dd-MS2 or unscheduled PRM mode. For MS/dd-MS2 the following parameters were used. MS1 resolution was 70.000 with an AGC target of 3x10<sup>6</sup>, max. injection time of 20 ms and a scan range of 300-1650 m/z. MS2 resolution was 17.500 with an AGC target of 10<sup>5</sup>, max. injection time of 50 ms and an isolation window of 2 m/z. The analysis parameters in PRM mode were set as follows. MS1 parameters were identical to DDA. MS2 resolution was 17.500 with an AGC target of 10<sup>6</sup>, max. injection time of 55 ms and an isolation window of 1.4 m/z.</p> <p>Potential SARS-CoV-2 target peptides belonging to the N protein were identified by DDA of SARS-CoV-2 infected Calu-3 cells. Peptides were diluted in 0.1% TFA (0.2 µg/µL) and 5 µL were separated on a 50 cm μPAC™ column (PharmaFluidics) using an EASY-nLC1200 system (Thermo Fisher Scientific). The flow rate was set to 800 nL/min and a stepped 30 min gradient was applied: 6-11% B in 2:58 min, 11-30% B in 17:10 min, 30-35% B in 2:41 min, 35-47% B in 3:11 min, 47-80% B for 0:10 min, 80% B for 1:50 min, 80-0% B in 0:10 min and 100% A for 1:50 min. Solvent A was 0.1% (v/v) formic acid (FA) in water, solvent B consisted of 80% (v/v) acetonitrile in 0.1% (v/v) FA. The column temperature was set to 50 °C. The Q Exactive HF (Thermo Fisher Scientific) operated in Full MS/dd-MS2 (Top20) using the following parameters. MS1 resolution was 60.000 with an AGC target of 3x10<sup>6</sup>, max. injection time of 20 ms and a scan range of 300-1650 m/z. MS2 resolution was 17.500 with an AGC target of 10<sup>5</sup>, max. injection time of 50 ms and an isolation window of 2 m/z.</p> <p> </p> <p>To simulate a SARS-CoV-2 positive patient sample, we spiked cell-culture derived virus in a negative oropharyngeal swab and targeted the N protein by PRM. LC parameters were identical to DDA analysis of SARS-CoV-2 infected Calu-3 cells. The PRM parameters of the The Q Exactive HF (Thermo Fisher Scientific) were set as follows. MS1 parameters were identical to DDA. MS2 resolution was 45.000 with an AGC target of 10<sup>6</sup>, max. injection time of 100 ms and an isolation window of 1.4 m/z.</p> <p> </p> <p> </p> <p><strong>Data processing protocol:</strong></p> <p>DDA Raw files were searched with MaxQuant against the respective virus database (UniProt) with a peptide FDR of 1%. Detailed MaxQuant parameters can be found in the parameters.txt files of the according results. MaxQuant .msms output files were used to generate spectral libraries with BiblioSpec implemented in the Skyline environment using a cut-off score of 0.95. Peptide identification of PRM runs was done in Skyline using the top 6 fragment ions of the DDA spectral library or according Prosit derived library (Prosit_2020_intensity_model).</p>
Synthesis of Vinylene-Linked Two-Dimensional Conjugated Pol-ymers via the Horner-Wadsworth-Emmons Reaction
<p>DFTB+ // mio-0-1 optimised structures of 2D-PPQV1 and 2D-PPQV2. "Layer mismatch" structures were optimized with fixed unit cells.</p>
Raw data accompanying: Ground reaction forces in monitor lizards (Varanidae) and the scaling of locomotion in sprawling tetrapods
<p>Geometric scaling predicts a major challenge for legged, terrestrial locomotion.<b> </b>Locomotor support requirements scale identically with body mass (α M<sup>1</sup>), while force generation capacity should scale α M<sup>2/3</sup> as it depends on muscle cross-sectional area. Mammals compensate with more upright limb postures at larger sizes, but it remains unknown how sprawling tetrapods deal with this challenge. Varanid lizards are an ideal group to address this question because they cover an enormous body size range while maintaining a similar bent-limb posture and body proportions. This study reports the scaling of ground reaction forces and duty factor for varanid lizards ranging from 7 g 37 kg. Impulses (force x time) scaled roughly as predicted by the inverted pendulum model (α M<sup>0.99-1.34</sup>) while peak forces (α M<sup>0.73-1.00</sup>) scaled higher than expected. Duty factor scaled α M<sup>0.04 </sup>and was higher for the hindlimb than the forelimb. The proportion of vertical impulse to total impulse increased with body size, and impulses decreased while peak forces increased with speed. These results provide valuable data into how locomotor forces vary with body size and suggest how other, extinct, sprawling tetrapods may have dealt with the biomechanical challenges associated with generating sufficient locomotor forces at larger body sizes.</p>
DFT Calculated xyz and log Files in Support of "Reaction Mechanism of Pd-catalyzed "CO-free" Carbonylation Reaction Uncovered by In situ Spectroscopy: The Formyl Mechanism"
<p>Theoretically calculated xyz and log files for hydrogen, carbon monoxide, carbon dioxide, methane, methanol, methyl formate, butene, methyl pentanoate and multiple Pd-dtbpx complexes (dtbpx = 1,2-Bis(di-<em>tert</em>-butylphosphino)xylene) which catalyze the addition of HCOOMe/CO onto butene to form methyl pentanoate.</p> <p>All quantum chemical simulations were performed using the Gaussian16 software. The ground state equilibrium structures and electronic properties were obtained at the density functional (DFT) level of theory utilizing the B3LYP XC functional.The def2-SVP basis set as well as the respective core potentials were applied for all atoms. A subsequent vibrational analysis was carried out for each optimized ground state structure to verify that a minimum on the potential energy (hyper‑)surface (PES) was obtained. All calculations were performed including D3 dispersion correction with Becke-Johnson damping.</p> <p>An analogous computational setup was applied for the optimization of transition states (TSs), while an initial guess in the vicinity of the saddle point was at first obtained via the Nudged Elastic Band (NEB) method as implemented in pysisyphus with xtb.<sup> </sup>Thereafter, the TSs were obtained in Gaussian16 via the Berny algorithm, followed by a vibrational analysis to verify that a first-order saddle point on the PES was obtained.</p>
Adaptation to hand-tapping affects sensory processing of numerosity directly: evidence from reaction times and confidence
<p>Each file contains a matrix called “MatriceRisultati”. Each row of the matrix “MatriceRisultati” is a trial. </p> <p>The columns contain the following information:</p> <ul> <li>1<sup>st</sup>: Number of trial</li> <li>2<sup>nd</sup>: Test numerosity</li> <li>3<sup>rd</sup>: Subject response on numerosity </li> <li>4<sup>th</sup>: Subject response on their confidence level</li> <li>5<sup>th</sup>: Response time</li> <li>6<sup>th</sup>: 0 if the test numerosity< 16; 1 if the test numerosity> 16</li> </ul>
Diapause is not selected as a bet-hedging strategy in insects: a meta-analysis of reaction norm shapes
<p>Many organisms escape from lethal climatological conditions by entering a resistant resting stage called diapause, and it is essential that this strategy remains optimally timed with seasonal change. Climate change therefore exerts selection pressure on phenology, which is expected to cause the evolution of mean diapause timing, but also phenotypic plasticity and bet-hedging strategies. Especially the latter as a strategy to cope with unpredictability is so far little considered in the context of climate change, and it is unknown whether it can readily evolve.</p> <p>Contemporary patterns of phenological strategies across a geographic range may provide information about their evolvability. We thus extracted 458 diapause reaction norms from 60 studies. First, we correlated mean diapause timing with mean winter onset. Then we partitioned the reaction norm variance into a temporal component (phenotypic plasticity) and among-offspring variance (diversified bet-hedging) and correlated this variance composition with predictability of winter onset. Contrary to our expectation, mean diapause timing correlated only weakly with mean winter onset, as populations at high latitudes failed to track early onsets. Variance among offspring was also limited and correlated only weakly with environmental predictability, indicating little scope for bet-hedging. We conclude that constraints may limit the evolution of phenology in a rapidly changing climate.</p>
Development of predictive models of the kinetics of a hydrogen abstraction reaction combining quantum-mechanical calculations and experimental data
<p>The files contain the electronic structure calculations for all the levels of theory tested in this work.</p>
Synthesis of Ti3AuC2, Ti3Au2C2 and Ti3IrC2 by noble-metal substitution reaction in Ti3SiC2 for high-temperature-stable ohmic contacts to SiC
<p>Repository data for paper "Synthesis of Ti<sub>3</sub>AuC<sub>2</sub>, Ti<sub>3</sub>Au<sub>2</sub>C<sub>2</sub> and Ti<sub>3</sub>IrC<sub>2</sub> by noble-metal substitution reaction in Ti<sub>3</sub>SiC<sub>2</sub> for high-temperature-stable ohmic contacts to SiC".</p> <p>Detailed information:</p> <p>Data from calculations include relaxed structures, electronic band-structure (selected compounds), electronic density of states and crystal overlap Hamilton population (selected compounds). In addition, spin-orbit coupling used for selected compounds. Data fro each compound are found in separate zip files. Scripts used to extract data are found in tools.zip.</p> <p>EDX-mapping:<br> Fig1d.xlsx</p> <p>XRD data:<br> Fig1h.xlsx, Fig2g.xlsx, FigS3.xlsx, FigS7a.xlsx</p> <p>I/V-measurements:<br> Fig4c.xlsx, FigS7b.xlsx, FigS13.xlsx</p> <p>Electrical resistance:<br> FigS5.xlsx, FigS14.xlsx</p>
Data and code to accompany the manuscript Phillipsite and Al-tobermorite mineral cements produced through low-temperature water-rock reactions in Roman marine concrete, American Mineralogist
<p>EPMA data and code used to produce figures in the publication.</p>
Real time, in-situ deuteriding of uranium encapsulated in grout; effects of temperature on the uranium-deuterium reaction
<p>To accurately predict the initiation and evolution of uranium hydride potentially present in nuclear waste containers, studies of simulated conditions are required. Here, for the first time, the uranium-deuterium reaction was examined in-situ, in real time, whilst within grouted media. A deuterium gas control rig and stainless steel-quartz glass reaction cell were configured on a synchrotron beam line to collect X-ray diffraction and X-ray tomography data. It was found that deuteride formation, and thus hydride formation, was limited by the uranium and grout thermal conductivities and deuteride initiation only commenced above a threshold temperature. Strong adherence between uranium oxide and grout was also observed.</p>
Kinetics of the redox reactions in STEAP1 and STEAP2
<p>The data repository includes the kinetic data of the redox reactions in STEAP1 and STEAP2, which are presented in "Mechanism of stepwise electron transfer in six-transmembrane epithelial antigen of the prostate (STEAP) 1 and 2" by Kehan Chen, Lie Wang, Jiemin Shen, Ah-lim Tsai, Ming Zhou and Gang Wu. The data include: 1) the reduction of ferric STEAP1 by reduced FADH2 and ferrous STEAP2; 2) the reduction of ferric STEAP1 by cytochrome b5 reductase; 3) the reduction of ferric STEAP2 with NADPH; and 4) the oxidation of ferrous STEAP1 and STEAP2 by ferric.NTA.</p>
Lanthanum modulated reaction pacemakers on a single catalytic nanoparticle - Database
<p><strong>Supplementary Data to the associated "Nature Communications" article (doi: 10.1038/s41467-023-43026-3) containing the FEM measurements and timeseries simulated by the microkinetic modelling.</strong></p><p>FEM measurements of the oscillating hydrogen oxidation reaction on Rh at T = 453 K at constant pressures of pH2 = 5.0 x 10-6 and pO2 = 4.4 x 10-6 mbar on a clean Rh tip (Data 1) and Lanthanum modulated surface (Data 2).</p>
Elucidating the reaction mechanism of SO2 with Cu-CHA catalysts for NH3-SCR by X-ray absorption spectroscopy
<p>Dataset related to the article with the same title and authors:</p><p>https://pubs.rsc.org/en/content/articlelanding/2023/SC/D3SC03924B#fn1</p><p>dat files corresponding to the spectra reported in the article. See the article for the description of the procedures and of high and load loading catalysts</p><p> </p><p> </p>
Output from paper: The s process in massive stars, a benchmark for neutron capture reaction rates
<p>Title: "The s process in massive stars, a benchmark for neutron capture reaction rates"; Authors: Marco Pignatari, Roberto Gallino, Rene Reifarth</p><p>------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------</p><p>Content: tar.gz package including a README file and two folders. The folders contain all the abundance plots associated to the work Pignatari, Gallino & Reifarth, 2023 The European Physical Journal A, Special Issue on: 'From reactors to stars' in honor of Franz Kaeppeler. </p>
USPTO Dataset for: Fast Chemical Reaction Condition Suggestion via Rule-Based Classification and Similarity Search
<p>USPTO database that is analyzed with Rxn-INSIGHT (<a href="https://github.com/mrodobbe/Rxn-INSIGHT">https://github.com/mrodobbe/Rxn-INSIGHT</a>).</p><p>This gzip file contains a very large Pandas DataFrame that can be loaded via pd.read_parquet('uspto_rxn_insight.gzip'). Because of the large size of the data, PyArrow version 13.0 must be used. </p><p>To use parquet in Pandas, install PyArrow and fastparquet using pip:</p><p>pip install pyarrow==13.0<br>pip install fastparquet</p>
Photoactivation of the Orange Carotenoid Protein Requires Two Light-Driven Reactions Mediated by a Metastable Monomeric Intermediate – Absorption Spectra and Global Analysis Results, Molecular Dynamics Simulations
<p>Time-resolved absorption and molecular dynamics trajectory datasets associated with: Rose, J. B.; Gascón, J. A.; Sutter, M.; Sheppard, D. I.; Kerfeld, C. A.; Beck, W. F. Photoactivation of the Orange Carotenoid Protein Requires Two Light-Driven Reactions Mediated by a Metastable Monomeric Intermediate. <i>Phys. Chem. Chem. Phys.</i> <strong>2023</strong>, DOI: 10.1039/d3cp04484j.</p>
Participation of electrochemically inserted protons in the hydrogen evolution reaction on tungsten oxides
<p>Understanding the mechanisms by which electrodes undergo the hydrogen evolution reaction (HER) is<br>necessary to design better materials for aqueous energy storage and conversion. Here, we investigate<br>the HER mechanism on tungsten oxide electrodes, which are stable in acidic electrolytes and can<br>undergo proton-insertion coupled electron transfer concomitant with the HER. Electrochemical<br>characterization showed that anhydrous and hydrated tungsten oxides undergo changes in HER activity<br>coincident with changes in proton composition, with activity in the order HxWO3*H2O>HxWO3 ><br>HxWO3*2H2O. We used operando X-ray diffraction and density functional theory to understand the<br>structural and electronic changes in the materials at high states of proton insertion, when the oxides are<br>most active towards the HER. H0.69WO3*H2O and H0.65WO3 have similar proton composition, structural<br>symmetry, and electronic properties at the onset of the HER, yet exhibit different activity. We<br>hypothesize that the electrochemically inserted protons can diffuse in hydrogen bronzes and participate<br>in the HER. This would render the oxide volume, and not just the surface, as a proton and electron<br>reservoir at high overpotentials. HER activity is highest in HxWO3*H2O, which optimizes both the degree<br>of proton insertion and solid-state proton transport kinetics. Our results highlight the interplay between<br>the HER and proton insertion-coupled electron transfer on transition metal oxides, many of which are<br>non-blocking electrodes towards protons.</p>
The second research task in the project entitled "Research on the electrodialytic recovery of selected hydrophilic ionic liquids from post-reaction solutions" - NCN project SONATA-17, grant no. 2021/43/D/ST8/02776.
<p><span>The second research task carried out under the project concerns study <span>on the fouling and stability of the ion-exchange membranes</span>. The information relates to research performing for the NCN project SONATA-17, grant no. </span><span>2021/43/D/ST8/02776</span><span>.</span></p>
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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.