Find research datasets worth reusing

opencc-by-4.0Dec 2021View details →

Dataset from "Monte Carlo-Discrete Dislocation Dynamics: A technique for studying the formation and evolution of dislocation structures"

Raw datasets used in the manuscript: N. Deka and R. B. Sills, Monte Carlo-Discrete Dislocation Dynamics: A technique for studying the formation and evolution of dislocation structures, Modelling and Simulation in Materials Science and Engineering, 2022 doi: 10.1088/1361-651X/ac41a2 See Readme.txt file for details.

opencc-zeroDec 2021View details →

Data from: The relationship between pathogen life history traits and metapopulation dynamics

Plant pathogen traits, such as transmission mode and overwintering strategy, may have important effects on dispersal and persistence, and drive disease dynamics. Still, we lack insights into how life-history traits influence spatiotemporal disease dynamics. We adopted a multifaceted approach, combining experimental assays, theory and field surveys, to investigate whether information about two pathogen life-history traits, infectivity and overwintering strategy, can predict pathogen metapopulation dynamics in natural systems. For this, we focused on four fungal pathogens (two rust fungi, one chytrid fungus and one smut fungus) on the forest herb Anemone nemorosa. Pathogens infecting new plants mostly via spores (the chytrid and smut fungi) had higher patch occupancies and colonization rates than pathogens mainly causing systemic infections and overwintering in the rhizomes (the two rust fungi). While the rust fungi more often occupied well-connected plant patches, the chytrid and smut fungi were equally or more common in isolated patches. Host patch size was positively related to patch occupancy and colonization rates for all pathogens. Predicting disease dynamics is crucial to understand the ecological and evolutionary dynamics of host-pathogen interactions, and to prevent disease outbreaks. Our study shows that combining experiments, theory and field observations is a useful way to predict disease dynamics.

Dynamic Tactility by Position-Encoded Spike Spectrum

Title: Dynamic Tactility by Position-Encoded Spike Spectrum Authors: Taeyeong Kim1, Jaehun Kim2, Insang You3, Joosung Oh1, Sung-Phil Kim2*, Unyong Jeong1* Affiliations: 1 Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea 2 Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea 3 Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea *Corresponding authors: spkim@unist.ac.kr, ujeong@postech.ac.kr

Data from: Dynamics in brain activation and behaviour in acute and repeated social defensive behaviour

In nature, confrontations between conspecifics are recurrent and related, in general, due to the lack of resources such as food and territory. Adequate defences against a conspecific aggressor are essential for the individual's survival and the group integrity. However, repeated social defeat is a significant stressor promoting several behavioural changes including social defence per se. What would be the neural basis of these behavioural changes? To build new hypotheses about this, we here investigate the effects of repeated social stress on the neural circuitry underlying motivated social defence behaviour in male mice. We observed that animals re-exposed to the aggressor three times spent more time in passive defence during the last exposure than in the first one. These animals also show less activation of the amygdalar and hypothalamic nuclei related to the processing of conspecific cues. In turn, we found no changes in the activation of the hypothalamic dorsal pre-mammillary nucleus (PMD) that is essential for passive defence. Therefore, our data suggest that the balance between the activity of circuits related to conspecific processing and the PMD determines the pattern of social defence behaviour. Changes in this balance may be the basis of the adaptations in social defence after repeated social defeat.

Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding

This dataset contains files of the molecular dynamics simulations performed in "Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding" study. Further information in presented in README.md file and the abstract of the study is presented below: "The nucleocapsid (N) protein of the SARS-CoV-2 virus, the causal agent of COVID-19, is a multifunction phosphoprotein that plays critical roles in the virus life cycle, including transcription and packaging of the viral RNA. To play such diverse roles, the N protein has two globular RNA-binding modules, the N- (NTD) and C-terminal (CTD) domains, which are connected by an intrinsically disordered region. Despite the wealth of structural data available for the isolated NTD and CTD, how these domains are arranged in the full-length protein and how the oligomerization of N influences its RNA-binding activity remains largely unclear. Herein, using experimental data from electron microscopy and biochemical/biophysical techniques combined with molecular modeling and molecular dynamics simulations, we showed that, in the absence of RNA, the N protein formed structurally dynamic dimers, with the NTD and CTD arranged in extended conformations. However, in the presence of RNA, the N protein assumed a more compact conformation where the NTD and CTD are packed together. We also provided an octameric model for the full-length N bound to RNA that was consistent with electron microscopy images of the N protein in the presence of RNA. Together, our results shed new light on the dynamics and higher-order oligomeric structure of this versatile protein."

Supplementary data for "Nanoscale damage production by dynamic tensile rupture in alpha-quartz"

In this dataset you can find sample data from simulations of crack propagation and python scripts that can be used to confirm the plots in the paper.  <ul> <li>"mainSimualtions" and "parameterVariations" contains the simulations where the crack propagates through alpha-quartz. <ul> <li>"mainSimulations" contain the data used for the plots in the manuscript. Each folder inside "mainSimulations" is one simulation.</li> <li>"parameterVariations" contain data for checking sensitivity to the simulation setup. The folder contains the subfolders: compressiveStress, loadingPlane0110, loadingRate and temperature. Each folder inside the subfolders is one simulation.</li> </ul> </li> <li>For each folder containing one simulations, we provide: <ul> <li>NAME.run: The input script</li> <li>NAME.data: The input data</li> <li>job.sh: Script to run the simulation</li> <li>log.lammps: Thermodynamic output from the simulation</li> <li>fracture_displacement.npy: Output providing the crack tip position with time</li> <li>Note that the pressures given in the folder names and in the simulations are in bars, not MPa.</li> </ul> </li> </ul>   <ul> <li>"verify_quartz_parameters" contains scripts and simulations performed to verify that the simulated material has properties similar those of alpha-quartz.</li> </ul>   <ul> <li> "mainSimualtions", "parameterVariations" and "verify_quartz_parameters" are in zip containers. In order to use them, please unzip them and leave the resulting folders in the same directory as this README file. </li> </ul>   <ul> <li>The python scripts "NAME.py" shows how to extract the relevant data from the lammps log files, which enables reproduction of the figures in the paper. See instructions below to use the scripts.</li> </ul> Installation instructions to make the python plot scripts working, assuming you already have numpy and matplotlib: > pip3 install git+https://github.com/henriasv/lammps-logfile.git   If this does not work, please contact Marthe Grønlie Guren, m.g.guren@geo.uio.no

Figure files for Charge-noise spectroscopy of Si/SiGe quantum dots via dynamically-decoupled exchange oscillations

This repository contains .fig (matlab) files corresponding to the figures in Charge-noise spectroscopy of Si/SiGe quantum dots via dynamically-decoupled exchange oscillations. The raw data are available from the corresponding author upon reasonable request.

Does salinization impact long-term Daphnia assemblage dynamics? Evidence from the sediment egg bank in a small hard-water lake

Salinization of freshwater ecosystems threatens global aquatic biodiversity. There is a need for studies that follow populations in situ during salinization to understand the effects on species and ecosystems. We follow 170 years of Daphnia dynamics in the sediment ephippia archive of a small urban lake near St. Paul, Minnesota, to characterize effects of severe recent salinization on lake Daphnia. We found modest changes in the flux of ephippia in this lake; all three key Daphnia functional groups remained in the assemblage throughout the period of salinization. Reconstruction of the size distribution of D. pulicaria demonstrated that predation pressure by fish may not have increased for the largest and most susceptible member of the assemblage despite cultural meromixis. Our findings highlight that in hardwater lakes, the effects of salinization are nuanced and require further investigation to better understand overall impacts of salinization on lake Daphnia assemblages.

Climate change reshapes the eco-evolutionary dynamics of a Neotropical seed dispersal system

Aim: Global changes will redistribute biodiversity, reshaping ecological interactions and ecosystem processes. The distribution decoupling of plants and their mutualistic seed dispersers, for instance, may have overlooked eco-evolutionary effects. How animal-dispersed plants will respond to changes in the distribution of their seed dispersers is, however, an open question. Here, we forecast the consequences of climate change and frugivory interactions for the spatial distribution and seed size evolution of a Neotropical palm. Location: Atlantic forests of South America Time period: Present day, end of 21st Century Major taxa studied: Thirty-two species of frugivorous birds, and a palm (Euterpe edulis). Methods: Future patterns of animal-plant co-occurrence were derived from ecological niche models, climate forecasts, projections of future forest loss, and seed dispersal simulations. We further explored the evolutionary effect of the spatial reorganization of interactions by modelling palm seed sizes as function of changes in the distribution of frugivore traits. Results: Our models indicate that future climate change and deforestation may reduce the palm's suitable distribution by 20-50%. However, our simulations suggest that 66% of all remaining future suitable distribution (76.200 km²) would still be inaccessible to the palm without the active dispersal of seeds by frugivores. In addition, novel frugivore communities are projected to have smaller body mass and gape size (-23% and -10%, respectively), due to the loss of large frugivores, which may translate into a 6–17% reduction of seed sizes across the palm's remaining distribution. Main conclusion: Our projections indicate that frugivore seed dispersal may be critical to allow occupancy of future habitat by the studied plant. However, loss of large frugivores may affect trait selection regimes, creating hotspots of plant evolution towards smaller seeds. We argue that such complex dynamics from species-specific responses to global change may drive the distribution and evolution of several interacting partners worldwide.

Data from: A multi-tissue view on telomere dynamics and postnatal growth

Trade-offs between growth and self-maintenance are common in nature, such that early-life effects on growth can generate lasting consequences on survival and longevity. Telomeres – putative biomarkers of self-maintenance – may link early growth with these later phenotypic effects, but evidence for growth-telomere trade-offs is mixed. Null or even positive relationships between growth and telomeres may be driven by heterogeneity in resource availability or invariable allocation towards telomere maintenance within a population. We used nestling tree swallows (Tachycineta bicolor) to assess the directionality and timing of relationships between growth and telomere length in several tissues. We focused on two important phases of growth: first, the peak of postnatal growth occurring around 6-days old when nestlings grow by ~33% in a single day, and subsequently, the later phase of growth occurring as body mass plateaus near adult size at 12-days old. We quantified telomere attrition in blood during postnatal growth, as well as telomere length in the blood, brain, adrenals, and liver at 12-days old. Growth was unrelated to telomere length in the liver and telomere dynamics in blood. However, brain telomere length was positively correlated with peak growth, and adrenal telomere length was positively related to later growth, particularly for chicks that had experienced a temporary stressor. These observations suggest that variation in resource availability may mask trade-offs, generating positive correlations between growth and telomere length at the population level. They also provide insights into complex relationships between growth and self-maintenance that can be revealed by looking in multiple tissues.

Raw data movie-file for the analysis of dynamics in the location of the large sphere under crowding condition with hard and soft boundaries.

The raw data movie-file indicate that time-dependent change in the location of large sphere under differrent degrees of crowding of numbers small spheres with hard and soft boundaries.

Videos of dynamic rupture in models of the 2004 Sumatra-Andaman earthquake published in Madden et al. (2022) "The state of pore fluid pressure and 3D megathrust earthquake dynamics" JGR-Solid Earth

Videos of dynamic rupture from models based on the 2004 Sumatra-Andaman earthquake presented in Madden, E. H., T. Ulrich, A.-A. Gabriel (2022). The state of pore fluid pressure and 3D megathrust earthquake dynamics, Journal of Geophysical Research - Solid Earth, <a href="https://doi.org/10.1029/2021JB023382">https://doi.org/10.1029/2021JB023382</a>. (Previous preprint available at: <a href="https://doi.org/10.1002/essoar.10508297.1">https://doi.org/10.1002/essoar.10508297.2</a>.)

opencc-by-4.0Aug 2020View details →

VTSet: Benchmarking Label Dynamics of VirusTotal Engines

This is the dataset of paper "<a href="https://dl.acm.org/doi/abs/10.1145/3372297.3420013?casa_token=kjEVVowQXwwAAAAA:yso4l50ERdLPRQ01jr5k66lmYFDMclL2UELFqTjRRcZ2GuLvPjfX1oN0Jzj3m5kxw9DyJXZXtss">Benchmarking Label Dynamics of VirusTotal Engines</a>" in CCS 2020. Please refer to the paper for more information.

opencc-zeroDec 2021View details →

Collaboration for conservation: assessing country-wide carnivore occupancy dynamics from sparse data

Aim: Assessing the distribution and persistence of species across their range is a crucial component of wildlife conservation. It demands data at adequate spatial scales and over extended periods of time, which may only be obtained through collaborative efforts, and the development of methods that integrate heterogeneous datasets. We aimed to combine existing data on large carnivores to evaluate population dynamics and improve knowledge on their distribution nationwide. Location: Botswana Methods: Between 2010 – 2016, we collated data on African wild dog, cheetah, leopard, brown and spotted hyaena, and lion gathered with different survey methods by independent researchers across Botswana. We used a multi-species, multi-method dynamic occupancy model to analyse factors influencing occupancy, persistence, and colonisation, while accounting for imperfect detection. Lastly, we used the gained knowledge to predict the probability of occurrence of each species countrywide. Results: Wildlife areas and communal rangelands had similar occupancy probabilities for most species. Large carnivore occupancy was low in commercial farming areas and where livestock density was high, except for brown hyaena. Lion occupancy was negatively associated with human density; lion and spotted hyena occupancy was high where rainfall was high, while the opposite applied to brown hyaena. Lion and leopard occupancy remained constant countrywide over the study period. African wild dog and cheetah occupancy declined over time in the south and north, respectively, whereas both hyaena species expanded their ranges. Countrywide predictions identified the highest occupancy for leopards and lowest for the two hyaena species. Main Conclusions: We highlight the necessity of data sharing and propose a generalisable analytical method that addresses the challenges of heterogeneous data common in ecology. Our approach, which enables a comprehensive multi-species assessment at large spatial and temporal scales, supports the development of data-driven conservation guidelines and the implementation of evidence-based management strategies nationally and internationally.

Simulating a Chemically-Fueled Molecular Motor with Nonequilibrium Molecular Dynamics

This .zip file contains the code, simulation scripts and settings, and figure generation scripts for our manuscript "Simulating a Chemically-Fueled Molecular Motor with Nonequilibrium Molecular Dynamics."  More detailed descriptions are found in the 0README.txt files within the .zip folder.   Manuscript link: https://arxiv.org/abs/2102.06298   Manuscript abstract: Most computer simulations of molecular dynamics take place under equilibrium conditions—in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are introduced to those simulations to probe one type of nonequilibrium response to external forces. Catalysts and molecular motors, however, function based on the nonequilibrium dynamics induced by a chemical reaction's thermodynamic driving force. In this scenario, simulations require chemostats capable of preserving the chemical concentrations of the nonequilibrium steady state. We develop such a dynamic scheme and use it to observe cycles of a new particle-based classical model of a catenane-like molecular motor. Molecular motors are frequently modeled with detailed-balance-breaking Markov models, and we explicitly construct such a picture by coarse graining the microscopic dynamics of our simulations in order to extract rates. This work identifies inter-particle interactions that tune those rates to create a functional motor, thereby yielding a computational playground to investigate the interplay between directional bias, current generation, and coupling strength in molecular information ratchets.

Theta: portfolio of CEGAR-based analyses with dynamic algorithm selection (Competition Contribution): Tool Archive

This archive contains the tool archive of Theta for SV-COMP 2022, which was also added as a release to the tool (<a href="https://github.com/ftsrg/theta/releases/tag/svcomp22-v1">here</a>).

Impact of runoff temporal distribution on ice dynamics.

These are the data related to the study about "Impact of runoff temporal distribution on ice dynamics."   by Basile de Fleurian, Richard Davy and Petra M. Langebroek                                                                                                                                                         The data are the results of ISSM simulations as described in the publication and saved on a netCDF4 format.                                   Each tar files contain 100 ".nc" files each exported from a single simulation.   <ul> <li>"TimeshiftXX" identifies each simulation and has its own starting time.</li> <li>"SL" represents season length available in short medium or long.</li> <li>"LR" represent the Lapse Rate value only the standard mid LR is available here as presented in the manuscript.</li> <li>"DT" represents the length of the initiation of the melt season available in short medium or long.</li> <li>"Temp" represents the intensity of the melt season length available in low medium or high.</li> </ul> The naming convention is such that : <ul> <li>"-SLlow-LRmid-DTmid" replaces "SLlow-TempHigh"</li> <li>"-SLmid-LRmid-DTmid" replaces "SLmid-Tempmid"</li> <li>"-SLhigh-LRmid-DTmid" replaces "SLhigh-Templow"    </li> </ul> The different variables and their units are described in the netCDF file. If you require further information or some variale that are not present in those files feel free to contact me at:                                                                                                basile.defleurian@uib.no

opennotspecifiedJan 2022View details →

Figure 1 in A theoretical composite model for population sex-specific shell size dynamics in Strombidae (Gastropoda, Neostromboidae)

Figure 1. Modelling male and females population distribution curves showing the mean size (μ) of each sex and the (1) Sex dependant factors: a) time to maturity; b) intra-male competition; c) femalespecific sexual selection; d) fecundity; (2) Inter-sex dependant factors: e) time to maturity; f) sex bias towards larger numbers of females; and (3) Population factors: g) environmental conditions; and h) universal size regulators that affect the size ratio between females and males.

opencc-zeroFeb 2022View details →

Data from: Dynamic body acceleration as a proxy to predict the cost of locomotion in bottlenose dolphins

Estimates of the energetic costs of locomotion (COL) at different activity levels are necessary to answer fundamental eco-physiological questions and to understand the impacts of anthropogenic disturbance to marine mammals. We combined estimates of energetic costs derived from breath-by-breath respirometry with measurements of overall dynamic body acceleration (ODBA) from biologging tags to validate ODBA as a proxy for COL in trained common bottlenose dolphins (Tursiops truncatus). We measured resting metabolic rate (RMR); mean individual RMR was 0.71–1.42 times that of a similarly sized terrestrial mammal and agreed with past measurements that used breath-by-breath and flow-through respirometry. We also measured energy expenditure during submerged swim trials, at primarily moderate exercise levels. We subtracted RMR to obtain COL, and normalized COL by body size to incorporate individual swimming efficiencies. We found both mass-specific energy expenditure and mass-specific COL were linearly related with ODBA. Measurements of activity level and cost of transport (the energy required to move a given distance) improve understanding of the COL in marine mammals. The strength of the correlation between ODBA and COL varied among individuals, but the overall relationship can be used at a broad scale to estimate the energetic costs of disturbance and daily locomotion costs to build energy budgets, and investigate the costs of diving in free-ranging animals where bio-logging data are available. We propose that a similar approach could be applied to other cetacean species.

Molecular dynamics simulations reveal the selectivity mechanism of structurally similar agonists to TLR7 and TLR8

Trajectory, topology and index files for TLR7 (apo), TLR7-R, TLR7-H, TLR7-G, TLR8 (apo), TLR8-R, TLR8-H, TLR8-G systems.