Find research datasets worth reusing

opencc-by-4.0Apr 2023View details →

Dataset for the paper "Oxygen reduction reaction activity in non-precious single atom (M-N/C) catalysts – contribution of metal and carbon/nitrogen framework-based sites", 2023, ACS Catalysis, DOI:10.1021/acscatal.3c00356

The data in this spreadsheet was used to produce the figures in the paper Authors:Mengjun Gong, Asad Mehmood, Basit Ali, Kyung-Wan Nam and Anthony Kucernak Title:Oxygen reduction reaction activity in non-precious single atom (M-N/C) catalysts – contribution of metal and carbon/nitrogen framework-based sites Journal:ACS Catalysis DOI:10.1021/acscatal.3c00356 Please cite the above reference if you wish to use this data DOI of data:10.5281/zenodo.7879881

opencc-by-4.0Apr 2023View details →

Dataset and code accompanying publication: "High gamma coherence between task-responsive sensory-motor cortical regions in a motor reaction-time task"

For questions, contact Peter Brunner, PhD (pbrunner@wustl.edu) Code written by Shashank Anand (sanand24@wustl.edu) and Hohyun Cho (hohyun@wustl.edu) This repository contains the processed data and MATLAB scripts (*.m) used to create the figures of this publication.  Custom dependences are included. EEGLAB and VERA must be downloaded separately.  Figure 4 is generated using the same code as Figure 3 (fig3.m), but by changing the frequency of the coherence analysis.

opencc-by-4.0Feb 2023View details →

Dataset: Dissecting reaction mechanisms and catalytic contributions in flavoprotein fumarate reductases

Dataset with all stationary points (in xyz file format) and videos of the reactions discussed in the work: Dissecting reaction mechanisms and catalytic contributions in flavoprotein fumarate reductases.

opencc-by-4.0May 2023View details →

Supporting data for "Conformational and state-specific effects in reactions of 2,3-dibromobutadiene with Coulomb-crystallized calcium ions"

Supporting data for "Conformational and state-specific effects in reactions of 2,3-dibromobutadiene with Coulomb-crystallized calcium ions”, Phys. Chem. Chem. Phys (2023), DOI: 10.1039/D3CP01416A

opencc-by-4.0May 2023View details →

Chemical reaction networks of glycolonitrile and glycolonitrile-H

Reaction networks of glycolonitrile (HOCH2CN) and HOCH2CHN radical obtained with the automated reaction discovery program <a href="https://rxnkin.usc.es/index.php/AutoMeKin">AutoMeKin</a>

opencc-by-4.0Jun 2023View details →

Supplementary data as part of the article "Comparing the reaction profiles of single-iron catalytic sites in enzymes and in reticular frameworks for methane-to-methanol oxidation" (https://doi.org/10.1016/j.xcrp.2023.101422)

Cartesian coordinates in the *.XYZ format for all the structures optimized at the M06-L/def2-TZVP in the reactivity study as part of the article "Comparing the reaction profiles of single-iron catalytic sites in enzymes and in reticular frameworks for methane-to-methanol oxidation" (<a href="https://doi.org/10.1016/j.xcrp.2023.101422">https://doi.org/10.1016/j.xcrp.2023.101422</a>)

opencc-by-4.0Jun 2023View details →

Open Data for publication Influence of the Time Scale on the Reaction Mechanism of CO Oxidation over a Au/TiO2 Catalyst

The file contains the origianl raw data for publication: Influence of the Time Scale on the Reaction Mechanism of CO Oxidation over a Au/TiO2 Catalyst, Angewandte Chemie, 2023 The data contains the IR spectra of the CO2 signal, the IR spectra at different temepratures (modulation experiments) and the IR spectra for different modulation periods at 50 deg C (modulation experiments), as described in the publication.

opencc-by-4.0May 2023View details →

Benchmarking data on worker reactions to triggering events

1. Real-world Benchmarking Data The objective of this task was to determine if Virtual Reality-based captured behavioral data on responses to notifications are similar to what is expected in real-world settings. For this purpose, a real-world bench mark experiment was designed to capture participant response times to wearable watch alarms triggered upon simulated traffic near the mobile work zone on the experiment site in an urban setting. The proposed scope of data collection of the real-world study included the external environmental factors (e.g., site accessibility, weather). The key parameters of research are defined as reaction time to received alarms and the heart rate measures. Table 1 provides the list of parameters that were controlled and measured during the experiments. <table align="center"> <caption>Table 1. Key parameters measured and tracked during real-world experiments</caption> <tbody> <tr> <td> </td> <td>Variable name</td> <td>Descriptions</td> </tr> <tr> <td>Key parameters captured</td> <td>Reaction time</td> <td>The time that one takes from getting the haptic or sound alarm from a wearable alarm device, herein referring to the apple watch, to the point when the participant gives a response by stopping the alarm by pressing on the screen of the smartwatch</td> </tr> <tr> <td> </td> <td>Inter-beat interval (IBI, heart rate)</td> <td>The time interval between individual beats of the heart; the data is measured by using E4 application provided by Empatica</td> </tr> <tr> <td>External factors tracked</td> <td>Ambient noise</td> <td>The level of ambient noise in the area is a factor potentially influencing participants’ reactions and is considered in the experiment design</td> </tr> <tr> <td> </td> <td>Temperature</td> <td>Daytime temperature recorded at each experiment</td> </tr> <tr> <td> </td> <td>Number of pedestrians on site</td> <td>Number of participants counted during the time of the experiment to record on the varying factors in the external environment in real-world settings</td> </tr> </tbody> </table> In the experiment, each participant was asked to participate in the experiment three times. In each trial, data was recorded separately for each alarm sent to smartwatch from the administrator at triggering events (precisely, every time the remote-controlled toy car reaches the line 30 ft apart from the designated work area). Each alarm signal at each trial was recorded for all 31 participants to the experiment. Timestamps are automatically recorded in server in the events recorded in the format of Table 2:  <table align="center"> <caption>Table 2. Format of raw data stored in the server, starting in December 2022.</caption> <tbody> <tr> <td> </td> <td>Timestamp</td> <td>From</td> <td>Event</td> </tr> <tr> <td>0</td> <td>2022-12-08 13:37:53.101391      </td> <td>VR</td> <td>Received car approaching alert, mode=3, id=1000</td> </tr> <tr> <td>1</td> <td>2022-12-08 15:53:05.098288</td> <td>Watch</td> <td>Start Simulation</td> </tr> <tr> <td>2</td> <td>2022-12-08 15:53:07.437488   </td> <td>VR</td> <td>Received car approaching alert, mode=4, id=1004</td> </tr> <tr> <td>3</td> <td>2022-12-08 15:53:13.064067</td> <td>Watch</td> <td>Stop Simulation</td> </tr> <tr> <td>4</td> <td>2022-12-08 15:53:13.163635</td> <td>Watch</td> <td>Stop Simulation</td> </tr> <tr> <td>...</td> <td> </td> <td> </td> <td> </td> </tr> <tr> <td>2417</td> <td>2023-03-03 16:17:46.166644</td> <td>Watch</td> <td>1398</td> </tr> <tr> <td>2418</td> <td>2023-03-03 16:18:00.004425</td> <td>Watch</td> <td>1398</td> </tr> <tr> <td>2419</td> <td>2023-03-03 16:18.01.272071</td> <td>Watch</td> <td>1398</td> </tr> <tr> <td>2420</td> <td>2023-03-03 16:18:07.359187</td> <td>Watch</td> <td>Stop Simulation</td> </tr> <tr> <td>2421</td> <td>2023-03-03 16:18:07.388183 </td> <td>Watch</td> <td>Stop Simulation</td> </tr> </tbody> </table> Some intervals used different timestamps as benchmarks to calibrate on the vehicle speed and user response time to the alarm signals, which include the following cases:  1) At the beginning of each trial, vehicle travels 70 ft from start point to the 30 ft apart point, when the first alarm is signaled; given this travel distance, the travel time of the first trip the toy vehicle makes is calculated by subtracting tn_alarm1_sent from tn_start. 2) Similarly, user response times to all alarms are recorded by subtracting the timestamps when the alarm is received by participant from when the alarm is sent from the server. (tn_alarmn_sent - tn_alarmn_received)   2. Supplementary Data Ambient noise level data were collected using a noise meter, allowing to save noise level by seconds to multiple seconds (i.e., 5, 10, 30, 60 seconds). All noise data recorded were recorded in the interval of one second using the meter. The collected data was processed to match the certain timestamps collected for user response time data collected in the experiment to allow comparisons and correlation analysis to be performed later on, which include the following: 1) worker response; 2) sending of alarm signals; 3) start and stop of experiments. All data points were later modified using the rolling mean function of pandas python module to replace the missing data points by moving average method.

dryad32/100

Plasticity and the adaptive evolution of switchlike reaction norms under environmental change

Phenotypic plasticity is often posited as an avenue for adaptation to environmental change, whereby environmental influences on phenotypes could shift trait expression toward new optimal values. Conversely, plastic trait expression may inhibit adaptation to environmental change by reducing selective pressure on ill-adapted traits. While plastic responses are often assumed to be linear, non-linear phenotype-environment relationships are common, especially in thermally-sensitive traits. Here we examine non-linear plasticity in a trait with great ecological and evolutionary significance: sexual phenotype in species with environmental sex determination (ESD). In species with ESD development switches between male and female at an environmental threshold (the inflection point). The inflection point is a key trait for adaptive responses to changing environments and should evolve toward the new optimum in order to maintain evolutionarily stable sex ratios. We used an individual-based theoretical model to investigate how two forms of plasticity in the ESD reaction norm – the non-linear slope of the reaction norm and a linear shift in the inflection point – influence the evolution of the inflection point under climate warming. We found that steeper reaction norm slopes (high non-linear plasticity) promoted evolution toward new optimal phenotypes (higher inflection points). In contrast, increased linear plasticity in the inflection point (shift) hindered adaptive evolution. Additionally, populations in moderate warming scenarios showed greater adaptive evolution of the inflection point compared with extreme warming scenarios, suggesting that the proximity of existing phenotypes to new optimal phenotypes influences evolutionary outcomes. Unexpectedly, we found greater population persistence under high climate variability, due to the increased production of rare-sex individuals in unusually cold years. Our results demonstrate that different forms of phenotypic plasticity have crucially different effects on adaptive evolution. Plasticity that prevented sex ratio bias hindered the evolution of the inflection point, while plasticity that exacerbated sex ratio bias promoted adaptation to environmental change.

opencc-zeroAug 2023View details →

opencc-by-4.0Aug 2023View details →

In Crystallo Lattice Adaptivity Triggered by Solid-Gas Reactions of Cationic Group 7 Pincer Complexes

3DED/microED datasets of [Mn(iPr-PONOP)(CO)3][BArF4] collected using a Thermo Fisher Scientific Glacios microscope equipped with a Ceta-D Camera associated with the publication "In Crystallo Lattice Adaptivity Triggered by Solid-Gas Reactions of Cationic Group 7 Pincer Complexes" published in Chem. Commun. Data collection details: 200kV, nanoprobe, gun lens 8, spot size 11, 30 µm C2 aperture. Illuminated area was ~1 µm. Under these conditions flux is 0.06 – 0.07 e-/Å^2/s. Camera length calibrated from Al powder was 958.5 mm. Data acquired using EPU-D with following settings: 2x binning, 2°/s, 0.5s exposure, rolling shutter, noise reduction mode enabled.  MRC format images can be processed with DIALS using the FormatMRC dxtbx format (distributed with DIALS from version 3.5 onwards), use goniometer.axes=1,0,0.

Fig. 4 in Density functional theory study on the coupling and reactions of diferuloylputrescine as a lignin monomer

Fig. 4. Gibbs free energies of reaction for radical coupling to form quinone methides and rearomatization for cross-coupled diferuloylputrescine-coniferyl alcohol dimers.

Fig. 3 in Density functional theory study on the coupling and reactions of diferuloylputrescine as a lignin monomer

Fig. 3. Gibbs free energies of reaction for radical coupling to form quinone methides and rearomatization for homo-coupled diferuloylputrescine dimers.

Fig. 2 in Density functional theory study on the coupling and reactions of diferuloylputrescine as a lignin monomer

Fig. 2. Optimized geometries for diferuloylputrescine, the diferuloylputrescine radical (with spin densities) and homo-coupled diferuloylputrescine dimers.

Fig. 7 in Density functional theory study on the coupling and reactions of diferuloylputrescine as a lignin monomer

Fig. 7. Gibbs free energy of reaction for dehydrogenation and bond dissociation of cross-coupled diferuloylputrescine-coniferyl alcohol dimers.

Fig. 6 in Density functional theory study on the coupling and reactions of diferuloylputrescine as a lignin monomer

Fig. 6. Gibbs free energy of reaction for dehydrogenation and bond dissociation of homo-coupled diferuloylputrescine dimers.

Fig. 59 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana

Fig. 59. Putative reaction catalyzed by HTH (HOTHEAD). Shown are the successive oxidations of the ω-hydroxyl group to the aldehyde and eventually, to the carboxy-group, leading to an α,ω-dicarboxylic acid. Members of the GMC oxidoreductases typically react readily with dioxygen to produce hydrogen peroxide.

Fig. 57 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana

Fig. 57. Reaction catalyzed by DNA-photolyases. The excited state reduced FAD is generated via activation by an additional antenna chromophore (top). In the case of CRY3 N5,N10-methenyltetrahydrofolate was shown to act as the antenna chromophore (G¨obel et al., 2017). During the repair reaction the reduced FAD returns to the ground state and requires re-activation by the antenna chromophore for the next reaction cycle. While the redox state of the flavin cofactor does not change in the overall reaction, intermediate transfer or electrons is critical for the reaction mechanism (see text).

Fig. 56 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana

Fig. 56. The oxidation of glycolate catalyzed by glycolate oxidase. Glycolate, the shortest substrate of the family of 2-hydroxy acid oxidases, is oxidized to glyoxylate in the peroxisomes. The members of the family feature different chain-length specificities (see text for further details). The reduced FMN is reoxidized by dioxygen yielding hydrogen peroxide.

Fig. 58 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana

Fig. 58. Flavoenzymes involved in the generation of ROS in A. thaliana. A total of 68 flavin-dependent enzymes were found to be involved in the formation of ROS in A. thaliana, either as hydrogen peroxide or superoxide radical (dark blue, taken from Table 1). Out of these 68, 48 enzymes were predicted to be present in a single cellular compartment, 19 were in at least two and one enzyme was predicted in at least three cellular compartments. The enzymes are ubiquitously distributed across the different cellular compartments (AP, apoplast = 19; PX, peroxisome = 15; PM, plasma membrane = 12; M, mitochondria = 11; Cyto, cytosol = 12; CP, chloroplast = 10; N, nucleus = 4; G, Golgi and EX, extracellular region = 2 and ER, endoplasmic reticulum = 1 enzyme). The predicted ROS producing flavoproteins from Table 5 are shown in light blue. Out of 18, 13 enzymes were predicted to be present in a single cellular compartment and 5 were predicted to be present at least in two. (PM = 2; M = 1; Cyto = 2; CP = 10; N = 3; EX = 2, EMS, endomembrane system = 1 and ER = 2). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 53 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana

Fig. 53. Mechanism of action of quiescin sulfhydryl oxidase. The enzyme possesses two pairs of cysteines (see text) of which only the proximal pair is shown in the figure. In the resting state, the two proximal cysteines form an intramolecular disulfide that is reduced via interaction with the reduced dithiol of the thioredoxin domain. The reduced proximal dithiol then reduces the FAD, which is reoxidized by dioxygen.