Find research datasets worth reusing

Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processes (code)

GP-FBM and GP-Tool codes and algorithms as in publication day. For updated version: https://github.com/guilmont/GP-Tool

opencc-zeroSep 2021View details →

Capturing the dynamics of small populations: A retrospective assessment using long-term data for an island reintroduction

1. The art of population modelling is to incorporate factors essential for capturing a population's dynamics while otherwise keeping the model as simple as possible. However, it is unclear how optimal model complexity should be assessed, and whether this optimal complexity has been affected by recent advances in modelling methodology. This issue is particularly relevant to small populations because they are subject to complex dynamics but inferences about those dynamics are often constrained by small sample sizes. 2. We fitted Bayesian hierarchical models to long-term data on vital rates (survival and reproduction) for the toutouwai (Petroica longipes) population reintroduced to Tiritiri Matangi, a 220-ha New Zealand island, and quantified the performance of those models in terms of their likelihood of replicating the observed population dynamics. These dynamics consisted of overall growth from 33 (± 0.3) to 160 (± 6) birds from 1992–2018, including recoveries following five harvest events for further reintroductions to other sites. 3. We initially included all factors found to affect vital rates, which included inbreeding, post-release effects, density-dependence, sex, age and random annual variation, then progressively removed these factors. We also compared performance of models where data analysis and simulations were done simultaneously to those produced with the traditional two-step approach, where vital rates are estimated first then fed into a separate simulation model. Parametric uncertainty and demographic stochasticity were incorporated in all projections. 4. The essential factors for replicating the population's dynamics were density-dependence in juvenile survival and post-release effects, i.e. initial depression of survival and reproduction in translocated birds. Inclusion of other factors reduced the precision of projections, and therefore the likelihood of matching observed dynamics. However, this reduction was modest when the modelling was done in an integrated framework. In contrast, projections were much less precise when done with a two-step modelling approach, and the cost of additional parameters was much higher under the two-step approach. 5. These results suggest that minimization of complexity may be less important than accounting for covariances in parameter estimates, which is facilitated by integrating data analysis and population projections using Bayesian methods. 13-Aug-2021 --

Database for study: Database for study: The effects of leg preference and leg dominance on static and dynamic balance performance in highly-trained tennis players

This is the dataset underlying a study on the effects of leg preference and dominance on static and dynamic balance performance. The raw data outcomes for 90 (51 males, 39 females) tennis players are included. The data involve force plate metrics from  single-leg quiet stance and single-leg landing tasks.

opencc-zeroSep 2021View details →

Larval A. bishopi microsatellite data from: Metapopulation genetics of endangered reticulated flatwoods salamanders (Ambystoma bishopi) in a dynamic and fragmented landscape

The dataset consists of 9 microsatellite markers used to analyze reticulated flatwoods salamanders' (Ambystoma bishopi) population structure on Eglin AFB. Samples came from various breeding ponds and allele sizes were scored using GeneMapper (GeneMapper v4.0; Applied Biosystems). Data was collected via allele scoring in GeneMapper by two independent researchers. Allele sizes for each individual have been re-formatted for various programs using the microsatellite Add-in in Excel as well as by using the GenAlEx extension in Excel.

opennotspecifiedSep 2021View details →

Figure 3 in Quaternary range dynamics and taxonomy of the Mediterranean collared dwarf racer, Platyceps collaris (Squamata: Colubridae)

Figure 3. Species distribution models for Platyceps collaris in current conditions (A) and in conditions during the Last Glacial Maximum (B), the Last Interglacial (C), mid-Pleistocene (D) and mid-Pliocene (E). Black points in A indicate the records that were used for the species distribution modelling. The bottom right panel shows reconstructions of global temperature in the last 4 Myr relative to the peak Holocene temperature (Hansen & Sato, 2012), with grey arrows and dashed lines highlighting the temperature in the time periods used in the present study.

Additional data "Client binding shifts the populations of dynamic Hsp90 conformations through an allosteric network"

Additional data containing chemical shift perturbations and intensity changes of Hsp90 upon client binding, intermolecular PREs, and raw scattering data of Hsp90-client complexes.

Laser-Induced Electronic and Vibronic Dynamics in the Pyrene Molecule and its Cation

We provide the codes and data required to generate each of the figures in our paper "Laser-Induced Electronic and Vibronic Dynamics in the Pyrene Molecule and its Cation". As well, the input files and key output files of the calculations are included.

opencc-zeroSep 2021View details →

Divergent patterns and spatial heterogeneity of soil nutrients in a complex and dynamic savanna landscape

Many grassy ecosystems around the world are experiencing woody encroachment. These woody encroachers often cause nutrient enrichment in the plant-soil environment, potentially facilitating their growth and reproduction. However, studies of encroachment effects on nutrient distributions have been confined to a few major elements (e.g., N, and P) and limited in spatial extent. We analyzed 19 elements in dominant plants and in georeferenced soils across a subtropical savanna landscape experiencing woody encroachment to quantify their spatial patterns and elucidate drivers responsible for these patterns. We found divergent patterns of spatial heterogeneity of these elements in surface soils across this complex landscape. Nutrient accumulation underneath woody canopies and redistribution by woody plants occurred in a subset of elements (i.e., N, P, S, Ca, Cu, and Sr). Though some of these elements are not necessarily growth-limiting, they do occur in higher concentrations in woody compared to herbaceous plants. Distributions of the other elements were closely related to spatial variation in soil pH, clay content, and slope rather than to woody encroachment. Our nuanced spatial sampling approach and analysis reveal significant variation in nutrient distributions in response to woody encroachment, and illustrate the role of landscape patterns in mediating ecosystem processes. These changes in the concentrations and distributions of key essential nutrients broaden our understanding of the biogeochemical consequences of woody encroachment, and provide new insights regarding the significance of long-term vegetation dynamics in dryland ecosystems.

Attack time analysis in dynamic attack trees via integer linear programming

Code and data corresponding to the paper "Attack time analysis in dynamic attack trees via integer linear programming"

openmit-licenseJun 2021View details →

Data for: Evolution of static and dynamical density correlations of one-dimensional soft-core bosons from the Tonks-Girardeau limit to a clustering fluid.

Data and scripts to reproduce the figures of the paper "Evolution of static and dynamical density correlations of one-dimensional soft-core bosons from the Tonks-Girardeau limit to a clustering fluid."

opencc-by-nc-4.0Sep 2021View details →

On the effect of morphology and particle-wall interaction on colloidal near-wall dynamics

Related publication: J. A. Rivera-Morán, Y. Liu, S. Monter, C. Hsu, P. Ruckdeschel, M. Retsch, M. K. Lisicki and P. R. Lang. On the effect of morphology and particle-wall interaction on colloidal near-wall dynamics. Soft Matter 2021. DOI: <a href="https://doi.org/10.1039/D1SM01191J">https://doi.org/10.1039/D1SM01191J</a> EUSMI proposal code: E190800323 We investigated the near-wall Brownian dynamics of different types of colloidal particles with a typical size in the 100 nm range using evanescent wave dynamic light scattering (EWDLS). In detail we studied dilute suspensions of silica spheres and shells with a smooth surface and silica particles with controlled surface roughness. While the near wall dynamics of the particle with smooth surface differ only slightly from the theoretical prediction for hard spheres colloids, the rough particles diffuse significantly slower. We analysed the experimental data by comparison with model calculations and suggest that the deviating dynamics of the rough particles are not due to increased hydrodynamic interaction with the wall. Rather, the particle roughness significantly changes their DLVO interaction with the wall, which in turn effects their diffusion.

Data and code to replicate the analyses in "Interpopulation differences in male reproductive effort drive the population dynamics of a host exposed to an emerging fungal pathogen"

Data and code used to run the analyses presented in the article "Interpopulation differences in male reproductive effort drive the population dynamics of a host exposed to an emerging fungal pathogen" published in Journal of Animal Ecology. Please cite this article if you use the data or write to the authors for a potential collaboration. If you require further details about the data please write to: andresvalenzuela.zoo@gmail or avalenzuela@ranitadedarwin.org. This study is part of an ongoing long-term monitoring program focused on the threatened Southern Darwin's frog (Rhinoderma darwinii), led by the Chilean non-profit organization ONG Ranita de Darwin (www.ranitadedarwin.org/monitoreo). This project has been funded by Zoo Leipzig, The National Geographic Society, Rufford Foundation, Weeden Foundation, Mohamed Bin Zayed Species Conservation Fund, VONA, Fundación Huilo Huilo, and Fundación MERI. We want to thank to the many volunteers that have kindly participated during this project.

Dataset - Radially resolved dynamic inflow pitch step experiment in wind tunnel

The relevant turbine data of MoWiTO 1.8 and the preprocessed data presented in the following accepted paper are uploaded: Berger, F., Onnen, D., Schepers, J. G., and Kühn, M.: Experimental analysis of radially resolved dynamic inflow effects due to pitch steps, Wind Energ. Sci. Discuss. [preprint], https://doi.org/10.5194/wes-2021-70, accepted, 2021.   The dataset describes a pitch step experiment with a model wind turbine in a wind tunnel between a high rotor load and a low rotor load. Measurements of turbine loads, near wake flow and radius resolved induction measurements are available.

opencc-by-4.0Feb 2021View details →

Selection in space and time: individual tree growth is adapted to tropical forest gap dynamics

In the present study, we assessed genotypic diversity within closely-related sympatric tree species belonging to the widespread tropical tree species complex Symphonia globulifera. We addressed the fine-scale spatial and temporal genetic adaptations of individuals through differential growth strategies in response to forest gap dynamics. We finally compared the breadth of successional niches encountered by Symphonia species to other locally abundant species. Combining tree diameter censuses, indirect measures of light environment of the recent past and present, and single nucleotide polymorphisms (SNPs), we used population genomics, environmental association analyses, genome wide association and growth modelling to address the following questions: <ul> <li>Are individual genotypes structured by the mosaic of light and competition environments resulting from forest gap dynamics?</li> <li>Is the growth of individuals determined by genotypes?</li> <li>Is there an association between genotypic adaptations to gap dynamics and to growth?</li> <li>How are genotypic adaptations to gap dynamics and to growth structured in time, i.e., across life stages?</li> <li>Are breadths of successional niches for Symphonia species wider than those of other locally abundant species?</li> </ul> Find the analyses here : https://sylvainschmitt.github.io/GOING/introduction.html

opencc-zeroOct 2021View details →

Data from: Temporal dynamics of free‐living nitrogen fixation in the switchgrass rhizosphere

Here we present data associated with the manuscript, Temporal dyanmics of free-living nitrogen fixation in the switchgrass rhizosphere. Free-living nitrogen fixation (FLNF) represents an important terrestrial N source and is gaining interest for its potential to contribute plant available N to bioenergy cropping systems. Switchgrass, a cellulosic bioenergy crop, may be reliant on FLNF when particularly when grown on low N marginal lands. These potential contributions of FLNF to switchgrass and the controls on this process are not well understood. We evaluated drivers of FLNF rates and N-fixing microbial community composition in field-grown switchgrass systems over two years with high temporal sampling. We found climate variables to be strong drivers of FLNF in switchgrass systems, compared to other environmental and biological factors including soil nutrients and N-fixing microbial community composition. Increased soil moisture availability tended to promote FLNF, but extreme rainfall events appeared to be detrimental. These climate-related responses suggest FLNF-derived N contributions may be reduced under projected climate shifts. We also found a significant, but weak correlation between N-fixing microbial community composition and FLNF rates including an observed shift in community composition between 2017 and 2018 and a similarly significant difference in FLNF rates between years. Lastly, we found that seasonal FLNF N contributions, based on measurement with high temporal resolution, may meet up to 80% of switchgrass N demands.

opencc-zeroOct 2021View details →

Data from: Living, dead, and absent trees - How do moth outbreaks shape small-scale patterns of soil organic matter stocks and dynamics at the Subarctic mountain birch treeline?

Mountain birch forests (B. pubescens Ehrh. ssp. czerepanovii) at the subarctic treeline not only benefit from global warming, but are also increasingly affected by caterpillar outbreaks from foliage-feeding geometrid moths. Both of these factors have unknown consequences on soil organic carbon (SOC) stocks and biogeochemical cycles. We measured SOC stocks down to the bedrock under living trees and under two stages of dead trees (12 and 55 years since moth outbreak) and treeless tundra in northern Finland. We also measured in-situ soil respiration, potential SOC decomposability, biological (enzyme activities, microbial biomass), and chemical (N, mineral N, pH) soil properties. SOC stocks were significantly higher under living trees (4.1±2.1 kg m²) than in the treeless tundra (2.4±0.6 kg m²), and remained at an elevated level even 12 (3.7±1.7 kg m²) and 55 years (4.9±3.0 kg m²) after tree death. Effects of tree status on SOC stocks decreased with increasing distance from the tree and with increasing depth, i.e. a significant effect of tree status was found in the organic layer, but not in mineral soil. Soil under living trees was characterized by higher mineral N contents, microbial biomass, microbial activity, and soil respiration compared with the treeless tundra; soils under dead trees were intermediate between these two. The results suggest accelerated organic matter turnover under living trees but a positive net effect on SOC stocks. Slowed organic matter turnover and continuous supply of deadwood may explain why SOC stocks remained elevated under dead trees, despite the heavy decrease in aboveground C stocks. We conclude that the increased occurrence of moth damage with climate change would have minor effects on SOC stocks, but ultimately decrease ecosystem C stocks (49% within 55 years in this area), if the mountain birch forests will not be able to recover from the outbreaks.

Time Dependent Analysis of Rat Microglial Markers in Traumatic Brain Injury Reveals Dynamics of Distinct Cell Subpopulations

The repository contains seven zip files for flow cytometry data for rat microglia following Controlled cortical impact (CCI) collected at seven time points: 3 hours, 1 day, 2 days, 7 days 14 days, 21 days and 28 days. Each file contains 24 CSV files converted from the raw fcs file and text files that contain meta data about the file. Each file name depicts the information of whether it is Panel A (M1 in the file name) or Panel B (M2 in the file name) measurement and whether the measurement was conducted on the ipsilateral (ipsi) or contralateral (contra) side of the CCI, or sham conducted on the ipsilateral (ipsi) or contralateral (contra) sides. Below is the description of the columns of each file: <table> <tbody> <tr> <td> File column name </td> <td> Original name </td> <td> Panel A (M1) context </td> <td> PAnel B (M2) context </td> <td> Description </td> </tr> <tr> <td> F0 </td> <td> FSC-A </td> <td> FSC-A </td> <td> FSC-A </td> <td> Forward scattering Area </td> </tr> <tr> <td> F1 </td> <td> FSC-H </td> <td> FSC-H </td> <td> FSC-H </td> <td> Forward scattering Height </td> </tr> <tr> <td> F2 </td> <td> FSC-W </td> <td> FSC-W </td> <td> FSC-W </td> <td> Forward scattering Width </td> </tr> <tr> <td> F3 </td> <td> SSC-A </td> <td> SSC-A </td> <td> SSC-A </td> <td> Side scattering area </td> </tr> <tr> <td> F4 </td> <td> FITC-A </td> <td> FITC-A </td> <td> FITC-A </td> <td> Fluorescein isothiocyanate </td> </tr> <tr> <td> F5 </td> <td> PE-A </td> <td> CD32 </td> <td> CD200R </td> <td> Protein expression </td> </tr> <tr> <td> F6 </td> <td> PerCP-Cy5-5-A </td> <td> - </td> <td> CD163 </td> <td> Protein expression </td> </tr> <tr> <td> F7 </td> <td> PE-Cy7-A </td> <td> CD11 </td> <td> CD11 </td> <td> Protein expression </td> </tr> <tr> <td> F8 </td> <td> BV421-A </td> <td> P2Y12 </td> <td> P2Y12 </td> <td> Protein expression </td> </tr> <tr> <td> F9 </td> <td> BV510-A </td> <td> - </td> <td> - </td> <td> Dye  </td> </tr> <tr> <td> F10 </td> <td> Alexa Fluor 647-A </td> <td> CD86 </td> <td> RT1B </td> <td> Protein expression </td> </tr> <tr> <td> F11 </td> <td> APC-Cy7-A </td> <td> CD45 </td> <td> CD45 </td> <td> Protein expression </td> </tr> <tr> <td> F12 </td> <td> Event Time </td> <td> Event Time </td> <td> Event Time </td> <td>Event Time</td> </tr> </tbody> </table>

Collision-induced dissociation of protonated uracil water clusters probed by molecular dynamics simulations

This dataset contains the input and output files associated to the work of  "Collision-induced dissociation of protonated uracil water clusters probed by molecular dynamics simulations"

opencc-by-4.0Mar 2024View details →

EDOPT: Event-camera 6-DoF Dynamic Object Pose Tracking

The dataset can be used to test your event-based 6-DoF pose tracking algorithm. If you use any of this data, please cite the following publication: @inproceedings{glover2024,   title={EDOPT: Event-camera 6-DoF Dynamic Object Pose Tracking },   author={Glover, Arren and Gava, Luna and Li, Zhichao and Bartolozzi, Chiara},   booktitle={2024 IEEE International Conference on Robotics and Automation (ICRA)},   year={2024} } The dataset includes event-driven data and ground truth of 5 objects: dragon, jell-o, mustard, soup can, and spam. For each object, six different motions on independent axes are recorded.  To import .log files containing events, we suggest <a href="https://github.com/event-driven-robotics/bimvee">bimvee</a> Python library. Specifically, use the functions to import .log files: data = importIitYarp(filePathOrName=input_path) Ground-truth .csv files have 8 columns, each one corresponding to a different measure:  timestamp | x | y | z | qx | qy | qz | qw x, y, z refer to the object position in the camera reference frame, while qx, qy, qz and qw refer to the object orientation expressed in quaternions.