Find research datasets worth reusing

The model data of Potential Impact of Spring Thermal Forcing over the Tibetan Plateau on the Following Winter El Niño–Southern Oscillation

This is the model data of "Potential Impact of Spring Thermal Forcing over the Tibetan Plateau on the Following Winter El Niño–Southern Oscillation". The data includes the last 20 years data of control run (CTRL), the 20 years data of TP–T experiment, and the wave activity flux difference between ensemble means of TP–T and CTRL. 2D is two dimensions. 3D is three dimensions.

Amyloid-beta 16-22 peptide monomer simulation with the CHARMM-Drude force field and OpenMM (Run 1)

Amyloid-beta 16-22 peptide (monomer) simulations with the CHARMM-Drude force field and OpenMM. This is the first independent simulation runs out of 3. Part 1-2 are 200 ns long, 3-8 are 100 ns each. Total trajectory length is 1 microseconds. Frame saving frequency is 10 ps. The system contains ~ 150 mM NaCl.

Data for "Spurious forces can dominate the vorticity budget of ocean gyres on the C-grid"

This contains data for the submitted paper "Spurious forces can dominate the vorticity budget of ocean gyres on the C-grid" which has been submitted to JAMES.

opencc-by-4.0Jul 2021View details →

Data for Jucker and Goyal, Ozone-forced Southern Annular Mode during Antarctic Stratospheric Warming Events, Geophysical Research Letters 2022

Data from climate model simulations and reanalysis which were analysed in associated paper. Read README.md file for detailed information on each file.

opencc-by-4.0Jun 2021View details →

Forcing Space Data

Data associated with “Forcing Space: an alternative to regime diagrams for predicting characteristics of turbulence in the ocean surface mixing layer.” Ann E. Gargett The data provided here is from a bottom-mounted RD Instruments (RDI) VADCP, deployed during 2003 at 39.4569 N, 74.2458 W, the primary node of a cabled observatory (LEO-15) then located ~ 7km offshore of the Tuckerton Field Station of Rutgers University. The VADCP was deployed on April 1, 2003, with initial instrument adjustment completed on April 25, 2003.  Data recording ended on October 30, 2003.

opencc-by-4.0Mar 2022View details →

Glacier model simulations of moraine building forced by interannual variability in climate

A set of 2,000-year simulations of moraine building by a glacier flowing through a synthetic alpine landscape forced by interannual variability in weather imposed on an otherwise stable climate. Moraine relief is shown for a standard deviation in mean annual air temperature (dT) of 0.5°C, 1.5°C, and 3.0°C around a long-term mean of 7.0°C. Simulations were made using the ice-flow model iSOSIA (Egholm et al., 2011, Geomorphology).

opencc-by-4.0Apr 2022View details →

A low-cost wireless bite force measurement device - Calibration data

Raw data for a low-cost wireless bite force measurement device calibration. The folder contains the data recorded during 3 different sessions for both the 1D load cell "1D-TAS606" sensor and two accurate 6 axis force transducer "3D-FT Sensors"

opencc-by-4.0Apr 2022View details →

Reconstructed, Long-Term Meteorological Forcing and Mass Balance over Glaciers in High Mountain Asia

%%%%  Reconstructed_WRF_Forcing_HMA.mat %%%%%%%% A reconstructed, long-term data series of meteorological data for three glaciers in distinct regions of High Mountain Asia. The meteorological forcing consists of hourly Weather Research and Forecasting (WRF) data bias-corrected by high elevation, off-glacier automatic weather station (AWS) data.  The variables of the forcing data consist of 2m air temperature ('T' °C), relative humidity ('RH' %), air pressure ('PRESS' hPa), incoming shortwave ('SWIN' Wm-2) and longwave ('LWIN' Wm-2) radiation, precipitation ('PP', mm hr) and wind speed ('FF' m s-1).  The period of the timeseries ranges from January 1981 to December 2019.  Data are available for the following glaciers (bias-corrected to the given coordinates / elevation of the off-glacier AWS) Yala Glacier, Nepal (28.237°N 85.619°E, 5090 m a.s.l.) - 'AWS Yala Basecamp' (AWS Data available on the ICIMOD RDS) Parlung Glacier Number 4 (29.245°N 96.928°E, 4600 m a.s.l.) - 'AWS4600' (Contact author Wei Yang for AWS data requests) Mugagangqiong Glacier (32.234°N, 87.485°E, 5850 m a.s.l.) - 'AWS5850' (Contact author Wei Yang for AWS data requests)   Data are stored as matlab tables in .mat files. Data were created using Matlab version 2020b.    %%%%  Reconstructed_Mass_Balance_HMA.mat %%%%%%%% Reconstructed cumulative mass balances for the aforementioned glaciers (values in m w.e.)

opencc-zeroApr 2022View details →

Residual force enhancement is reduced in permeabilized fiber bundles from mdm muscles

Residual force enhancement (RFE) is the increase in steady-state force after active stretch relative to the force after isometric contraction at the same final length. The mdm mutation in mice, characterized by a small deletion in N2A titin, has been proposed to prevent N2A titin-actin interactions so that active mdm muscles are more compliant than WT. This decrease in active muscle stiffness should be associated with reduced RFE. We investigated RFE in permeabilized soleus (SOL) and extensor digitorum longus (EDL) fiber bundles from wild type and mdm mice. On each fiber bundle, we performed active and passive stretch from an average sarcomere length of 2.6 - 3.0 &[mu]m at a slow rate of 0.04 &[mu]m/s, as well as isometric contractions at the initial and final lengths. One-way ANOVA showed that SOL and EDL fiber bundles from mdm mice exhibited significantly lower RFE than WT (P < 0.0001). This result is consistent with previous observations in single myofibrils and intact muscles. However, it contradicts the results from a previous study which appeared to show that compensatory mechanisms could restore titin force enhancement in single fibers from mdm psoas. We suggest that force enhancement measured previously in mdm single fibers was an artifact of the high variability in passive tension found in degenerating fibers, which begins after ~24 days of age. The results are consistent with the hypothesis that RFE is reduced in mdm skeletal muscles due to impaired Ca2+ dependent titin-actin interactions resulting from the small deletion in N2A titin.

opencc-zeroApr 2022View details →

Data from: Decipher soil organic carbon dynamics and driving forces across China using machine learning

The dynamics of soil organic carbon (SOC) play a critical role in modulating global warming. However, the long-term spatiotemporal changes of SOC at large scale and the impacts of driving forces remain unclear. In this study, we investigated the dynamics of SOC in different soil layers across China through the 1980s to 2010s using a machine learning approach and quantified the impacts of the key factors based on factorial simulation experiments. Our results showed that the latest (2000-2014) SOC stock in the first meter soil (SOC100) was 80.68 ± 3.49 Pg C, of which 42.6% was stored in the top 20 cm, sequestrating carbon with a rate of 30.80 ± 12.37 g C m-2 yr-1 since the 1980s. Our experiments focusing on the recent two periods (2000s and 2010s) revealed that climate change exerted the largest relative contributions to SOC dynamics in both layers and warming or drying can result in SOC loss. However, the influence of climate change weakened with soil depth, while the opposite for vegetation growth. Relationships between SOC and forest canopy height further confirmed this strengthened impact of vegetation with soil depth, and highlighted the carbon sink function of deep soil in mature forest. Moreover, our estimates suggested that SOC dynamics in 71% of topsoil were controlled by climate change and its coupled influence with environmental variation (CE). Meanwhile CE and the combined influence of climate change and vegetation growth dominated the SOC dynamics in 82.05% of the first meter soil. Additionally, the national cropland topsoil organic carbon increased with a rate of 23.6 ± 7.6 g C m-2 yr-1 since the 1980s, and the widely applied nitrogenous fertilizer was a key stimulus. Overall, our study extended the knowledge about the dynamics of SOC and deepened our understanding about the impacts of the primary factors.

Driving Forces of Extreme Updrafts Associated with Convective Bursts in the Eyewall of a Simulated Tropical Cyclone

The model-simulated data used in this study are uploaded here. Due to the large number, the original simulation data are available on request (qnn_nancy@yahoo.com).

GAIA model simulate data of doubled CO2 (Forces, advections, and winds)

This dataset contains forces, advections, and winds output from the GAIA model, that are related to the Figures in the paper. The forces and advections are divided by the Coriolis parameter or a zonal mean absolute vorticity.

Data: Thorax Vibration and Force Generation During Non-Flight Behaviors in Carpenter Bees (Xylocopa: Apidae): Implications for Floral Buzzing

Interval data from the manuscript "Thorax Vibration and Force Generation During Non-Flight Behaviors in Carpenter Bees (Xylocopa: Apidae): Implications for Floral Buzzing "

A Semi-Empirical Framework for Ice Sheet Response Analysis under Oceanic Forcing in Antarctica and Greenland

Supplementary material for Luo, X. & Lin, T. (2022). “A Semi-Empirical Framework for Ice Sheet Response Analysis under Oceanic Forcing in Antarctica and Greenland.” Climate Dynamics, in press. <a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1007%2Fs00382-022-06317-x&data=05%7C01%7CXiao.Luo%40ttu.edu%7C2a6949c147dd4aa9880f08da345e55ae%7C178a51bf8b2049ffb65556245d5c173c%7C0%7C0%7C637879877007681605%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=2G3mD6n0ZOogcEFQcuCCElFmgKE0%2B%2F5KPTtzBeq8kM4%3D&reserved=0">https://doi.org/10.1007/s00382-022-06317-x</a> This repository contains data and scripts that are used to facilitate the analysis of Greenland and Antarctica ice sheet melting induced by ocean warming. The GCM directory contains ocean potential temperature time series for both Antarctica ice shelves near open sea retrieved from FGOALS-s2 under RCP 6.0 and Greenland store glacier retrieved from MIROC5 under RPC8.5 and HadGEM3-GC31-MM projections under update of RCP8.5 based on SSP5. The raw data are accessed from CMIP5 (https://esgf-node.llnl.gov/search/cmip5/) and CMIP6 (https://esgf-node.llnl.gov/search/cmip6/) projects respectively and the processed data deposited here are stored in Excel format. The WOD directory contains the NetCDF files of Present-Day ocean conditions including temperature, salinity, depth, and other variables retrieved from World Ocean Database (WOD).  The data are deposited as NetCDF format. The Analysis directory contains 3 subdirectories that illustrates the analysis workflow for both Greenland and Antarctica.          The Antarctica subdirectory contains the analysis codes to reproduce Antarctica ice shelf melting response and future projection. Antarctica_analysis.m is the main routine for computation and plotting, and the other files are input files including PISM/PICO simulations outputs and ocean temperature time series retrieved from CMIP5 project that can be found on the previous GCM directory.          The Greenland subdirectory contains the main routine store_analysis.m for Greenland Store glacier computation and plotting, the response time series (store.mat), perturbed response time series (store_pert.mat), ocean temperature projection (store_temp.mat) generated by MIROC5, and subglacial runoff time series (store_runoff.mat) estimated from annual basin surface runoff using MAR data forced by MIROC5 under RCP8.5.          The Historical subdirectory contains the data and scripts used for the historical analyses in the main text. AIS_melt_historical.m is the main script of the analysis, along with two other plotting functional scripts including plot_melt_rate.m and plot_ocean_temp.m. The input files include the PISM/PICO simulations outputs, which are the same files in Antarctica subdirectory, and other 2 input files that contain the temperature time series from 6 CMIP5 GCMs.

opencc-zeroMay 2022View details →

A B cell actomyosin arc network couples integrin co-stimulation to mechanical force-dependent immune synapse formation

B-cell activation and immune synapse (IS) formation with membrane-bound antigens are actin-dependent processes that scale positively with the strength of antigen-induced signals. Importantly, ligating the B-cell integrin, LFA-1, with ICAM-1 promotes IS formation when antigen is limiting. Whether the actin cytoskeleton plays a specific role in integrin-dependent IS formation is unknown. Here we show using super-resolution imaging of mouse primary B cells that LFA-1: ICAM-1 interactions promote the formation of an actomyosin network that dominates the B-cell IS. This network is created by the formin mDia1, organized into concentric, contractile arcs by myosin 2A, and flows inward at the same rate as B-cell receptor (BCR): antigen clusters. Consistently, individual BCR microclusters are swept inward by individual actomyosin arcs. Under conditions where integrin is required for synapse formation, inhibiting myosin impairs synapse formation, as evidenced by reduced antigen centralization, diminished BCR signaling, and defective signaling protein distribution at the synapse. Together, these results argue that a contractile actomyosin arc network plays a key role in the mechanism by which LFA-1 co-stimulation promotes B-cell activation and IS formation.

Amyloid-beta 16-22 peptide monomer simulation (150 mM NaCl) with the CHARMM36m force field and Gromacs (Run 3)

MD simulations of the Amyloid-beta 16-22 monomer at 150 mM NaCl concentration with CHARMM36m force field and Gromacs. This repository contains the third out of three independent runs.  Files belong to the publication "<a href="https://doi.org/10.1021/acs.jcim.0c01063">https://doi.org/10.1021/acs.jcim.0c01063</a>" All the simulation parameters and force field files are uploaded into this repository. Simulations are done with Gromacs 2018.3 Total simulation time is 500 ns. Frames are saved with 100 ps frequency.

opencc-zeroJun 2022View details →

Different functional networks underlying human walking with pulling force fields acting in forward or backward directions

Walking with pulling force fields acting at the body center of mass (in the forward or backward directions) is compatible with inclined walking and is used in clinical practice for gait training. From the perspective of known differences in the motor strategies that underlie walking with the respective force fields, the present study elucidated whether the adaptation acquired by walking on a split-belt treadmill with either one of the force fields affects subsequent walking in other directions. Walking with the force field induced an adaptive and de-adaptive behavior of the subjects, with the aspect evident in the anterior breaking and posterior propulsive impulses of the ground reaction force as parameters. In the parameters, the adaptation acquired during walking with a force field acting in one direction was transferred to that in the opposite direction only partially. Furthermore, the adaptation that occurred while walking in a force field in one direction was rarely washed out by subsequent walking in a force field in the opposite direction and thus was maintained independently of the other. These results demonstrated possible independence in the neural functional networks capable of controlling walking in each movement task with an opposing force field.

opencc-zeroJun 2022View details →

The force response of muscles to activation and length perturbations depends on length history

Recent studies have demonstrated that muscle force is not determined solely by activation under dynamic conditions, and that length history has an important role in determining dynamic muscle force. Yet, the mechanisms for how muscle force is produced under dynamic conditions remain unclear. To explore how muscle force production is determined under dynamic conditions, we investigated the effects of muscle stiffness, activation, and length perturbations on muscle force. First, submaximal isometric contraction was established for whole soleus muscles. Next, the muscles were actively shortened at three velocities. During active shortening, we measured muscle stiffness at L0 and the force response to time-varying activation and length perturbations. We found that muscle stiffness increased with activation but decreased as shortening velocity increased. The slope of the relationship between maximum force and activation amplitude differed significantly among shortening velocities. Also, the intercept and slope of the relationship between length perturbation amplitude and maximum force decreased with shortening velocities. As shortening velocities were related with muscle stiffness, the results suggest that length history determines muscle stiffness and the history-dependent muscle stiffness influences the contribution of activation to muscle force and the contribution of length perturbations to muscle force. A three-parameter viscoelastic model that included a linear spring and linear damper in parallel with tunable history-dependent spring stiffness proportional to measured muscle stiffness predicted history-dependent muscle force with high accuracy. The results and simulations support the hypothesis that muscle force under dynamic conditions can be accurately predicted as the force response of a history-dependent viscoelastic material to length perturbations.

opencc-zeroJun 2022View details →

Joining forces in Ochnaceae phylogenomics: A tale of two targeted sequencing probe kits

Premise: Both universal and family-specific targeted sequencing probe kits are becoming widely used for the reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships. Methods: We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit, and a family-specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies-coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support. Results: For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae-specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae-specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. The merging of data obtained with the two kits resulted in a well-supported phylogenetic tree. Conclusions: The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family-specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.