Find research datasets worth reusing

opencc-by-4.0May 2020View details →

Molecular dynamics simulation data of regulatory ACT domain dimer of human phenylalanine hydroxylase (PAH) (dimer only)

Raw data of molecular dynamics simulations of regulatory ACT domain dimer. Simulation starts from the crystal pose (PDB: 5FII) and is motivated by this paper: Yunhui Ge, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. <a href="http://www.jbc.org/content/293/51/19532">Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</a> J. Biol. Chem., 2018, 293(51), pp 19532-19543

opencc-by-4.0May 2020View details →

Model data repository of "How sediment thickness influences subduction dynamics and seismicity"

This repository provides the code and data to run the Seismo-Thermo-Mechanical model with a sediment thickness Tsed of 4 km on a cluster using executables.

opencc-by-4.0Jun 2020View details →

Molecular recognition and dynamics of linear poly-ubiquitins: integrating coarse-grain simulations and experiments

Poly-ubiquitin chains are flexible multidomain proteins, whose conformational dynamics enable their molecular recognition by a large number of partners in multiple biological pathways. By using alternative linkage, it is possible to obtain poly-ubiquitin molecules with different dynamical properties. This flexibility is further increased by the possibility to tune the length of poly-ubiquitin chains. Characterizing the dynamics of poly-ubiquitins as a function of their length is thus relevant to understand their biology. Structural characterization of poly-ubiquitin conformational dynamics is challenging both experimentally and computationally due to increasing system size and conformational variability. Here, by developing highly efficient and accurate small-angle X-ray scattering driven Martini coarse-grain simulations, we characterize the dynamics of linear M1-linked di-, tri- and tetra-ubiquitin chains. Our data show that the behavior of the di-ubiquitin subunits is independent of the presence of additional ubiquitin modules. We propose that the conformational space sampled by linear poly-ubiquitins, in general, may follow a simple self-avoiding polymer model. These results, combined with experimental data from small angle X-ray scattering, biophysical techniques and additional simulations show that binding of NEMO, a central regulator in the NF-κB pathway, to linear poly-ubiquitin obeys a 2:1 (NEMO:poly-ubiquitin) stoichiometry in solution, even in the context of four ubiquitin units. Eventually, we show how the conformational properties of long poly-ubiquitins may modulate the binding with their partners in a length-dependent manner.

opencc-by-4.0Jun 2020View details →

Supplementary Information for Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS

Supplementary information for Páll, S., Zhmurov, A., Bauer, P., Abraham, M., Lundborg, M., Gray, A., Hess, B, & Lindahl, E.. (2020). Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS. The Journal of Chemical Physics, 2020 Contains benchmark methodology description as well as all inputs used in the application performance benchmarks included the paper.

opencc-zeroJun 2020View details →

Data from: Dynamic reorganization of neuronal activity patterns in parietal cortex dataset

Neuronal representations change as associations are learned between sensory stimuli and behavioral actions. However, it is poorly understood whether representations for learned associations stabilize in cortical association areas or continue to change following learning. We tracked the activity of posterior parietal cortex neurons for a month as mice stably performed a virtual-navigation task. The relationship between cells' activity and task features was mostly stable on single days but underwent major reorganization over weeks. The neurons informative about task features (trial type and maze locations) changed across days. Despite changes in individual cells, the population activity had statistically similar properties each day and stable information for over a week. As mice learned additional associations, new activity patterns emerged in the neurons used for existing representations without greatly affecting the rate of change of these representations. We propose that dynamic neuronal activity patterns could balance plasticity for learning and stability for memory.

opencc-by-4.0May 2020View details →

DynaRev - Dynamic Coastal Protection: Resilience of Dynamic Revetments Under Sea Level Rise

This dataset contains processed data from the DynaRev experiments carried out in the Large Wave Flume (Grosser Wellenkanal, GWK) from 14-08-2017 to 29-09-2017 as a Transnational Access project within the EU funded project HYDRALAB+ (654110). The dataset provided under this DOI includes the post-processed data detailed in the article submitted to Scientific Data titled "High-resolution, prototype-scale laboratory measurements of nearshore wave processes and morphological evolution of a sandy beach with and without a dynamic cobble berm revetment" The overall aim of this project was to construct a prototype-scale beach and investigate the response of the beach to a rising sea level and storms with and without a cobble berm dynamic revetment structure (a gravel or shingle ridge placed around the wave runup limit). The response of two beach configurations was investigated under erosive wave conditions (Hs=0.8m, Tp=6.0s) and a total sea-level rise, SLR = 0.4 m: i) an unmodified  sand beach with an initially plane slope of 1:15, and ii) a natural beach profile with a dynamic revetment installed at the location of the natural berm before imposing SLR. SLR was imposed in 4 steps of 0.1 m with an initial water depth of 4.5 m above the flume base.  Each phase ran for a total of 58 hours, after which resilience testing under storm waves and accretive conditions was undertaken for a further 12 hours in each case. The changing profile of the sand beach and revetment was monitored throughout the experiments using a traditional profiler and a LiDAR array. Additional hydrodynamic measurements were obtained at the location of the offshore sandbar to investigate the process of bar formation and migration with SLR. The model set-up, experimental program and data structure are explained in the submitted Scientific Data paper. The data files are organised as detailed in "DynaRev_Data_Structure.doc".

opencc-by-4.0Jun 2020View details →

Sub-picosecond thermalization dynamics in condensation of strongly coupled lattice plasmons

Raw data used in manuscript Figures 1-7 of the publication. The data are in the form of .csv as read from a spectrometer.

opencc-by-4.0Jul 2020View details →

Supplementary data for "Molecular dynamics study of confined water in the periclase-brucite system under conditions of reaction-induced fracturing"

In this dataset you can find sample data from periclase and brucite simulations and python scripts that can be used to confirm the plots in the paper. <ul> <li>"bruciteSimualtions" and "periclaseSimualtions" contains the simulations where the mineral in contact with water is either brucite or periclase. Within each of these two folders, there are two subfolders, "waterProperties" and "waterThickness".  <ul> <li>The data in "waterProperties" is used to calculate water properties. Each folder inside "simulations" represent one simulation.</li> <li>The data in "waterThickness" is used to calculate the change in water film thickness with time under different conditions. The simulations are run for either 3 ns or 10 ns. Each folder inside "simulations_Xns" represent 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>Note that the pressures given in the folder names and in the simulations are in atm, not MPa.</li> </ul> </li> </ul>   <ul> <li>"bruciteSimulations" and "periclaseSimualtions" 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 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/regex-file-collector.git > 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

Data from: Understanding the social dynamics of breeding phenology: indirect genetic effects and assortative mating in a long distance migrant

Phenological traits, such as the timing of reproduction, are often influenced by social interactions between paired individuals. Such partner effects may occur when pair members affect each other's pre-breeding environment. Partner effects can be environmentally and/or genetically determined, and quantifying direct and indirect genetic effects is important for understanding the evolutionary dynamics of phenological traits. Here, using 26 years of data from a pedigreed population of a migratory seabird, the common tern ( Sterna hirundo ), we investigate male and female effects on female laying date. We find that female laying date harbors both genetic and environmental variation, and is additionally influenced by the environmental, and, to a lower extent, genetic, component of her mate. We demonstrate this partner effect to be largely explained by male arrival date. Interestingly, analyses of mating patterns with respect to arrival date show mating to be strongly assortative and, using simulations, we show that this assortative mating for arrival date leads to overestimation of partner effects. Our study provides evidence for partner effects on breeding phenology in a long distance migrant, while uncovering the potential causal pathways underlying the observed effects and raising awareness for confounding effects due to assortative mating or other common environmental effects.

Data from: Climate warming drives Himalayan alpine plant growth and recruitment dynamics

<ul> <li>Understanding how climate influences plant reproduction and growth at contrasting range limits is crucial for predicting how species' ranges may shift in response to ongoing climate change. Trees and shrubs have shown warming-induced increases in performance at upper elevation limits but reduced performance at lower distributional limits due to warming-driven drought limitation. Whether these differential responses are also valid for alpine forbs exposed to accelerated warming remains largely unknown. </li> <li>We examined climate signal recorded in annual growth and recruitment over the past sixty years in the alpine forb Potentilla pamirica in Western Himalayas, and tested whether the responses to recent climate warming differ between dry steppe, wet alpine and cold subnival zone within the species 5250-5900 m elevation range. We reconstructed recruitment and growth chronologies from 1019 individuals spanning 1-73 years, and more than 21,500 annual growth rings.</li> <li>We identified contrasting climatic controls of recruitment and growth at opposite elevation range margins, as well as contrasting demographic trends identified from age distributions. In lower-elevation steppes, recruitment increased with high late-winter snowfall and decreased with high summer temperatures, while growth increased with high summer precipitation. Conversely, warm winters and summers in higher-elevation alpine and subnival zones support growth and recruitment, while snowy winters reduce them, especially at their upper elevation limit. The age distribution revealed greater numbers of younger individuals, indicating healthy growing populations, in the alpine habitat, while evidence of ageing plant populations was observed in steppe and subnival zones.</li> <li>Accelerated warming since the 1990s reduced growth and recruitment in dry steppes while supporting plant performance in the alpine habitat. The recruitment in the subnival zone did not peak during the past warmest decade due to concomitant extreme snowfall events. </li> <li>Synthesis: Our results bring novel information on population-specific climate dependency of plant recruitment, growth, and population dynamics, suggesting a high vulnerability of high elevation Himalayan ecosystems to climate change. This is partly balanced by high species longevity and slow radial growth securing a long-term population persistence. Continuing trends of extreme snowfall events at higher elevations and droughts at lower elevations may lead to species range contraction.</li> </ul>

Data from: Detecting the population dynamics of an autosomal sex-ratio distorter transgene in malaria vector mosquitoes

1. The development of genetically modified mosquitoes and their subsequent field release offers innovative and cost-effective approaches to reduce mosquito-borne diseases, such as malaria. A sex-distorting autosomal transgene has been developed recently in G3 mosquitoes, a lab strain of the malaria vector Anopheles gambiae s.l. The transgene expresses an endonuclease called I-PpoI during spermatogenesis, which selectively cleaves the X chromosome to result in ~95% male progeny. Following the World Health Organization Guidance Framework for the testing of genetically modified mosquitoes, we assessed the dynamics of this transgene in large cages using a joint experimental-modelling approach. 2. We performed a four-month experiment in indoor large cages to study the population genetics of the transgene. The cages were set up to mimic a simple tropical environment with a diurnal light-cycle, constant temperature, and constant humidity. We allowed the generations to overlap to engender a stable age structure in the populations. We constructed a model to mimic the experiments, and used the experimental data to infer the key model parameters. 3. We identified two fitness costs associated to the transgene. First, transgenic adult males have reduced fertility and, second, their female progeny have reduced pupal survival rates. Our results demonstrate that the transgene is likely to disappear in less than three years under our confined conditions. Model predictions suggest this will be true over a wide range of background population sizes and transgene introduction rates. 4. Synthesis and applications: Our semi-field indoor cage experiments are in line with WHO guidance recommendations in regards to the development and testing of self-limiting technologies. Since the transgenic strain (Ag(PMB)1) has been considered for genetic vector control of malaria, our results are fundamentally important for determining expectations on the persistence of the transgene post-release. Our results provide a demonstration of the self-limiting nature of the transgene, and indicate that longevity will be further reduced by fitness costs that were not previously identified. Finally, our study has showcased an alternative and effective method for characterising the phenotypic expression of a transgene in an insect pest population.

opencc-zeroJun 2020View details →

Data from: Estimating transmission dynamics and serial interval of the first wave of COVID-19 infections under different control measures: A statistical analysis in Tunisia from February 29 to May 5, 2020

Background: Describing transmission dynamics of the outbreak and impact of intervention measures are critical to planning responses to future outbreaks and providing timely information to guide policy makers decision. We estimate serial interval (SI) and temporal reproduction number (Rt) of SARS-CoV-2 in Tunisia. Methods: We collected data of investigations and contact tracing between March 1, 2020 and May 5, 2020 as well as illness onset data during the period February 29-May 5, 2020 from National Observatory of New and Emerging Diseases of Tunisia. Maximum likelihood (ML) approach is used to estimate dynamics of Rt. Results: 491 of infector-infectee pairs were involved, with 14.46% reported pre-symptomatic transmission. SI follows Gamma distribution with mean 5.30 days [95% CI 4.66-5.95] and standard deviation 0.26 [95% CI 0.23-0.30]. Also, we estimated large changes in Rt in response to the combined lockdown interventions. The Rt moves from 3.18 [95% CI 2.73-3.69] to 1.77 [95% CI 1.49-2.08] with curfew prevention measure, and under the epidemic threshold (0.89 [95% CI 0.84-0.94]) by national lockdown measure. Conclusions: Overall, our findings highlight contribution of interventions to interrupt transmission of SARS-CoV-2 in Tunisia.

opencc-zeroJun 2020View details →

Community-level reorganizations following migratory pollinator dynamics along a latitudinal gradient

Predicting how communities re-arrange in response to changes in species composition remains a key challenge in ecology. Migratory species, which enter and leave communities across latitudinal gradients, offer us a unique opportunity to evaluate community and species-level responses to a shift in community composition. We focused on a migratory hummingbird and the communities that host it along a latitudinal and species diversity gradient. Our results show higher niche overlap in more diverse communities, allowing resident species to compensate for the loss of the migrant in providing pollination services. Contrastingly, in less diverse communities, the migrant behaves as a specialist, monopolizing abundant resources. In its absence, its role is not fully covered by resident species, resulting in a decrease in the fruit set of the migrant´s preferred plant species. These results help us understand the potential impacts of biodiversity loss and have important implications for community persistence given expected changes in the migratory behaviors of some species.

Data from: High rates of carbon and dinitrogen fixation suggest a critical role of benthic pioneer communities in the energy and nutrient dynamics of coral reefs

1. Following coral mortality in tropical reefs, pioneer communities dominated by filamentous and crustose algae efficiently colonize substrates previously occupied by coral tissue. This phenomenon is particularly common after mass coral mortality following prolonged bleaching events associated with marine heatwaves. 2. Pioneer communities play an important role for the biological succession and reorganization of reefs after disturbance. However, their significance for critical ecosystem functions previously mediated by corals, such as the efficient cycling of carbon (C) and nitrogen (N) within the reef, remains uncertain. 3. We used 96 carbonate tiles to simulate the occurrence of bare substrates after disturbance in a coral reef of the central Red Sea. We measured rates of C and dinitrogen (N2) fixation of pioneer communities on these tiles monthly over an entire year. Coupled with elemental and stable isotope analyses, these measurements provide insights into macronutrient acquisition, export, and the influence of seasonality. 4. Pioneer communities exhibited high rates of C and N2 fixation within 4 – 8 weeks after the introduction of experimental bare substrates. Ranging from 13 to 25 μmol C cm−2 d−1 and 8 to 54 nmol N cm−2 d−1, respectively, C and N2 fixation rates were comparable to reported values for established Red Sea coral reefs. This similarity indicates that pioneer communities may quickly compensate for the loss of benthic productivity by corals. Notably, between 40 and 85% of fixed organic C was exported into the environment, constituting a vital source of energy for the coral reef food web. 5. Our findings suggest that benthic pioneer communities may play a crucial, yet overlooked role in the C and N dynamics of oligotrophic coral reefs by contributing to the input of new C and N after coral mortality. While not substituting other critical ecosystem functions provided by corals (e.g. structural habitat complexity and coastal protection), pioneer communities likely contribute to maintaining coral reef nutrient cycling through the accumulation of biomass and import of macronutrients following coral loss.

opencc-zeroAug 2020View details →

Data from: Juvenile social dynamics reflect adult reproductive strategies in bottlenose dolphins

The juvenile period is a challenging life history stage, especially in species with a high degree of fission-fusion dynamics, such as bottlenose dolphins, where maternal protection is virtually absent. Here, we examined how juvenile male and female bottlenose dolphins navigate this vulnerable period. Specifically, we examined their grouping patterns, activity budget, network dynamics, and social associations in the absence of adults. We found that juveniles live in highly dynamic groups, with group composition changing every 10 minutes on average. Groups were generally segregated by sex, and segregation was driven by same-sex preference rather than opposite-sex avoidance. Juveniles formed strong associations with select individuals, especially kin and same-sex partners, and both sexes formed cliques with their preferred partners. Sex-specific strategies in the juvenile period reflected adult reproductive strategies, in which the exploration of potential social partners may be more important for males (which form long-term alliances in adulthood) than females (which preferentially associate with kin in adulthood). Females spent more time alone and were more focused on foraging than males, but still formed close same-sex associations, especially with kin. Males cast a wider social net than females, with strong same-sex associations and many male associates. Males engaged in more affiliative behavior than females. These results are consistent with the social bonds and skills hypothesis and suggest that delayed sexual maturity in species with relational social complexity may allow individuals to assess potential associates and explore a complex social landscape without the risks associated with sexual maturity (e.g. adult reproductive competition; inbreeding).

Supplementary Materials for Time-Aligned Edge Plots for Dynamic Graph Visualization

Abstract: We present time-aligned edge plots: time- and edge-scalable representations of dynamic graphs. Vertices are mapped to two vertical parallel axes. The left axis depicts the source vertices, whereas the right one depicts the destination vertices. The time axis is horizontally embedded in-between the two axes, resulting in a two-dimensional graph layout. Edges are added by drawing straight lines connecting the corresponding source and destination vertices through time, while the pixels along the lines are used to encode the time-varying information. In this way, the depiction of edges at the individual timepoints is reduced to only a few pixels, resulting in a less cluttered representation of dynamic graphs, while the alignment of edges over time reveals the temporal patterns in the data and preserves the users' mental map. We evaluate our approach by comparing it theoretically and empirically against the state-of-the-art using dynamic graphs of varying complexities.

Flow Magnetic Tweezers: Gyrase dynamics under 3 different external torque conditions. Part 1/3

The video contains a whole field from a force spectroscopy experiment called Flow Magnetic Tweezers (FMT). It shows E. coli DNA Gyrase manipulating DNA topology by relaxing positive and introducing negative coils as well as response of gyrase to external torque of 2, 4 and 8 positive magnet turns. Part 1/3

Flow Magnetic Tweezers: Gyrase dynamics under 3 different external torque conditions. Part 3/3

Flow Magnetic Tweezers: Gyrase dynamics in presence of 20 uM drug Ciprofloxacin

The video contains a whole field from a force spectroscopy experiment called Flow Magnetic Tweezers (FMT). It shows E. coli DNA Gyrase manipulating DNA topology by relaxing positive and introducing negative coils in presence of 20 uM of Ciprofloxacin, reaction of Gyrase to external torque and eventual wash with SDS.

Flow Magnetic Tweezers: Gyrase dynamics under 3 different external torque conditions. Part 2/3