Find research datasets worth reusing

Live-cell imaging of LLC-PK1 cells microtubule dynamics

Stable LLC-PK1 cell line (ATCC:CL-101) was generated and provided by Michael W. Davidson [1,2]. Using a Zeiss Celldiscoverer 7 microscope with a 100X/1.47 NA oil-immersion objective (Plan-Apochromat, Zeiss) and a sCMOS sensor (Hamamatsu, ORCA-Fusion, C15440-20UP), cultured LLC-PK1 cells expressing mEmerald-EB3 were imaged with a 43 nm pixel size. Exposure time was 100 ms, with each frame being captured every two seconds. During acquisition, temperature and CO2 control was set to 37°C and 5%, respectively. mEmerald-EB3 was excited using a 488 nm laser at 1% power, with a FITC filter for fluorescence collection. Acquisition software ZEN 3.2 (blue edition) was used for the imaging protocol. 1. Rizzo, M. A., Davidson, M. W., & Piston, D. W. (2009). Fluorescent protein tracking and detection: fluorescent protein structure and color variants. Cold Spring Harbor Protocols, 2009(12), pdb-top63. 2. Huang, F., Hartwich, T., Rivera-Molina, F. et al. Video-rate nanoscopy using sCMOS camera–specific single-molecule localization algorithms. Nat Methods 10, 653–658 (2013).

opencc-zeroJul 2022View details →

Coupled dynamics of the North Equatorial Countercurrent and Intertropical Convergence Zone with relevance to the double-ITCZ problem

The North Equatorial Counter Current (NECC) is an important component of the tropical Pacific upper-ocean circulation. This current flows against easterly trade winds and transports warm water from the Western Pacific warm pool eastward. Its core follows the latitudinal position of the Intertropical Convergence Zone (ITCZ) – a salient feature of tropical atmospheric circulation characterized by convective clouds and intense rainfall. The trade winds converge towards the ITCZ, creating a local minimum in zonal winds and generating a positive wind stress curl that maintains an eastward current despite the westward winds. That the wind curl associated with the ITCZ is a critical driver of the NECC is well established. However, here we show that the relationship between the ITCZ and the NECC is more complex and involves positive feedback: a stronger NECC transports warmer water from the western Pacific to the east thus increasing SST along its path, intensifying convection within the ITCZ and hence strengthening wind stress curl, further strengthening the NECC. We refer to this large-scale feedback as the Wind curl - Advection - SST - Precipitation (WASP) feedback. To confirm the NECC-ITCZ coupling we conduct numerical simulations using a coupled model (CESM) in which we progressively strengthen the surface Ekman component of the NECC and observe the intensification of the ITCZ and the entire NECC. Consequently, a weak NECC leads to a weak ITCZ, which can contribute to the double ITCZ problem in climate models, since weak wind convergence north of the equator enables stronger convergence to the south.

opencc-zeroJul 2022View details →

Antheridiogen controls spatial dynamics of sex‐expression in naturally occurring gametophytes of the tree fern Cyathea multiflora

Background and aims: Antheridiogen systems are an important and widespread mechanism by which sex expression is controlled and genetic diversity maintained in fern gametophyte populations. However, antheridiogens have rarely been studied outside of the laboratory and little is known about their function in natural populations. Combining predictions based on field and laboratory study, we document the sexual structure of tree fern gametophyte populations and test the effects of antheridiogen in situ. Key results: In all populations, sex ratios indirectly indicate antheridiogen activity. No hermaphroditic gametophytes were identified in any population. Female gametophytes are randomly distributed in each population while male gametophytes tend to cluster. In two of the populations, male sex expression is spatially dependent on females, providing direct evidence of antheridiogen function in situ. Conclusions: This study provides the first documentation of spatial sex expression in natural gametophyte populations of an antheridiogen-producing tree fern species. The profound impact of antheridiogen on gametophyte sex expression in field settings suggests this system is intimately tied to mating systems, fitness, and genetic diversity in Cyathea multiflora.

Sintering of alumina nanoparticles: comparison of interatomic potentials, molecular dynamics simulations, and data analysis

This is the dataset for the publication in MSMSE 2022 containing all plot scripts and data for reproducing all figures. The dataset is a snapshot of the repository https://gitlab.com/computational-materials-science/public/publication-data-and-code/2022_MSMSE_Roy_et_al_MD-sintering (SHA 7ad2f421deb055f3384c00ba29f2fb1acd0e78ea) that might contain additional/newer data and scripts.

Molecular dynamics dataset of Synaptotagmin-1

This dataset contains all-atom molecular dynamics trajectories of synaptotagmin-1 C2A (calcium free). Each trajectory is 2 µs long and the total cumulated simulation time is 184 µs. Details, including the molecular dynamics setup, are given in Hempel, T.; Plattner, N.; Noé, F. Coupling of Conformational Switches in Calcium Sensor Unraveled with Local Markov Models and Transfer Entropy. J. Chem. Theory Comput. 2020, 16 (4), 2584–2593. <a href="https://doi.org/10.1021/acs.jctc.0c00043">https://doi.org/10.1021/acs.jctc.0c00043</a>.

Copper binding leads to increased dynamics in the regulatory N-terminal domain of full-length human copper transporter ATP7B

Dataset from article "Copper binding leads to increased dynamics in the regulatory N-terminal domain of full-length human copper transporter ATP7B" Contains simulation input files and reduced trajectories.  The files are sorted into four folders: reA_apo, reA_holo, reB_apo, reB_holo. Each folder contains the following (types of) files: Topology file:                                           topol.top Index file:                                                 index.ndx Production mdp files for each replica:     production_rep{i}.mdp Starting structures as .gro files:              ATP7B_E2_re{A/B}_{apo/holo}_rep{i}_start.gro 10 ns step trajectories in .xtc format:      ATP7B_E2_re{A/B}_{apo/holo}_rep{i}_trajectory.xtc Folder with equilibration restraints:         restraints Folder with topology and forcefield:        toppar

Content Analysis on System Dynamics Modelling Application in Agriculture

The data is a compilation of journal articles retrieved from three databases - Scopus, Web of Science, and Science Direct, using this Boolean search string: ("system dynamics" OR "systems thinking" OR "causal loop diagram") AND ("Agri*" OR "Food" OR "Crop" OR "Meat" OR "Animal" OR "Livestock")).

Data from: Learning to predict spatio-temporal movement dynamics from weather radar networks

This dataset contains the following: <ul> <li>data: <ul> <li>preprocessed: hourly European weather radar data (here: radar) and aggregated simulation outputs (here: abm), combined with ERA5 reanalysis data and Voronoi tessellation details</li> <li>shapes: geographical shapes used for plotting</li> </ul> </li> <li>results: trained models and corresponding results for both simulated data (here: abm) and weather radar data (here: radar).</li> <li>figures: final figures presented in our paper "Learning to predict spatio-temporal movement dynamics from weather radar networks" to summarize the results</li> </ul> The corresponding code used to train and evaluate models is archived here: <a href="https://doi.org/10.5281/zenodo.6921595">10.5281/zenodo.6921595</a>.

Data supplement for "Wetting dynamics under periodic switching on different scales: Characterization and mechanisms"

Data set and python code to recreate the figures of "Wetting dynamics under periodic switching on different scales: Characterization and mechanisms". Additionally, it includes the oomph-lib Code to reproduce the data for the simulations in the mesoscopic thin-film model.

opencc-by-4.0Jun 2022View details →

DATASET_Effect Of Electronic Doping And Traps On Carrier Dynamics In Tin Halide Perovskites_BOLLA_v1

This document contains the data supporting the peer-reviewed publication : Effect of electronic doping and traps on carrier dynamics in tin halide perovskites by Treglia et al.  (Materials Horizons, 2022, 9, 1763 - 1773) .

Optical motion capturing of change of direction motions reconstructed with inverse kinematics and dynamics and optimal control simulation

This is the data belonging to the publication "Change the direction: 3D optimal control simulation by directly tracking marker and ground reaction force data". This study investigated the feasibility and accuracy of reconstructing, especially change of direction motions with a 3D full-body musculoskeletal model by tracking marker and ground reaction force (GRF) data in optimal control simulations. We recorded in total 30 trials with optical motion capture. Using this data, we compared inverse methods (inverse kinematics and dynamics) to coordinate tracking simulations and marker tracking simulations. Please see the README and the publication for further details.

Ab initio molecular dynamics trajectories of liquid water at the interface with hBN sheets

Ab initio molecular dynamics trajectories of water confined between hBN sheets for different confinement widths and system sizes. This repository contains data supporting the findings of the paper:  G. Tocci, M. Bilichenko, L. Joly, M. Iannuzzi, Ab initio nanofluidics: disentangling the role of the energy landscape and of density correlations on liquid/solid friction, Nanoscale, 12, 10994-11000 (2020). DOI: 10.1039/D0NR02511A.

Ab initio molecular dynamics trajectories of liquid water at the interface with graphene sheets

Ab initio molecular dynamics trajectories of water in contact with graphene sheets for different confinement widths and system sizes This repository contains data supporting the findings of the paper:  G. Tocci, M. Bilichenko, L. Joly, M. Iannuzzi, Ab initio nanofluidics: disentangling the role of the energy landscape and of density correlations on liquid/solid friction, Nanoscale, 12, 10994-11000 (2020). DOI: 10.1039/D0NR02511A.

Supporting experimental data for "Z-average and Polydispersity Index of Dynamic Light Scattering" by Bazzoni et al.

Data (auto-correlation functions used for preparing Figure 5-8) accompanying manuscript "Z-average and Polydispersity Index of Dynamic Light Scattering" by Bazzoni et al.   1.       “Figure 5_ACFs.zip” Large sets of autocorrelation functions (ASCII format) recorded to demonstrate heteroscedastic and angle-dependent uncertainties. Each file may list the basic parameters, instrument’s estimation of Z-average (not evaluated and not used by us), the auto-correlation function, and a low temporal-resolution trace of the scattering intensity. Figure 5 is based on the analyses of subsets of this data set. 2.       “Figure 6 & 7_ACFs.zip” Large sets of autocorrelation functions (ASCII format) recorded to demonstrate the impact of uncertainty on precision, and the impact of duration and photon counting rate on the signal-to noise ratio. Each file may list the basic parameters, instrument’s estimation of Z-average (not evaluated and not used by us), the auto-correlation function, and a low temporal-resolution trace of the scattering intensity. Figure 6 and 7 are based on the analyses of subsets of this data set. 3.       “Figure 8_ACFs.zip” Large sets of autocorrelation functions (ASCII format) recorded to demonstrate the positive impact of data averaging on precisions. Each file may list the basic parameters, instrument’s estimation of Z-average (not evaluated and not used by us), the auto-correlation function, and a low temporal-resolution trace of the scattering intensity. Figure 8 is based on the analyses of subsets of this data set.

opencc-zeroAug 2022View details →

Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time

Aim: We tested if historical demographic changes of populations occurring on the floodplains of a major Amazon Basin tributary could be associated with range expansions from upper and middle sections of the river, following the establishment of widespread river-created environments during the Late Pleistocene and Holocene. Location: Solimões River, Western Amazon, South America. Taxon: Myrmoborus lugubris, Thamnophilus cryptoleucus and Myrmotherula assimilis. Methods: We explored spatial patterns of genetic diversity and connectivity among sampled localities using thousands of Ultra-Conserved Elements. Range expansions were tested with alternative methods. We quantified habitat preference for the analyzed species to test whether the occupation of dynamic habitats could predict spatial patterns of genetic diversity. Results: Our study did not support shared population range expansions related to historical regionalized changes in habitat availability. We found considerable variation in the spatial distribution of the genetic diversity between studied taxa, and that species with higher levels of specialization to dynamic environments have a more heterogeneous distribution of genetic diversity and reduced levels of gene flow across space. Main conclusions: Our results suggest that demographic expansions along the Solimões River might be linked to spatially homogeneous oscillation in the distribution of floodplain environments, promoting effective population size changes but not range expansion. We found that habitat specificity might be a good predictor of population connectivity along the Amazonian floodplains.

Ab initio molecular dynamics trajectories of liquid water at the interface with MoS2 sheets

Ab initio molecular dynamics trajectories of water confined between MoS2 sheets for different confinement widths and system sizes. This repository contains data supporting the findings of the paper:  G. Tocci, M. Bilichenko, L. Joly, M. Iannuzzi, Ab initio nanofluidics: disentangling the role of the energy landscape and of density correlations on liquid/solid friction, Nanoscale, 12, 10994-11000 (2020). DOI: 10.1039/D0NR02511A.

Dataset - Experimental analysis of the dynamic inflow effect due to coherent gusts

Here the processed experimental data of the accepted paper given below is documented and made available: Berger, F., Neuhaus, L., Onnen, D., Hölling, M., Schepers, G., and Kühn, M.: Experimental analysis of the dynamic inflow effect due to coherent gusts, Wind Energ. Sci. Discuss. [preprint], https://doi.org/10.5194/wes-2022-2, accepted, 2022.

opencc-by-4.0Jul 2021View details →

Ecological determinants of rabies virus dynamics in vampire bats and spillover to livestock

Data and scripts for the publication

Dataset for Conformational dynamics of loop L3 in OmpF: Implications towards antibiotic translocation and voltage gating

Dataset supporting the work in the publication titled, "Conformational dynamics of loop L3 in OmpF: Implications  towards antibiotic translocation and voltage gating".