Find research datasets worth reusing

opencc-by-4.0May 2024View details →

Dataset: Blue carbon dynamics across a salt marsh-seagrass ecotone in a cool-temperate South African estuary

This is a dataset of organic carbon, nitrogen, and phosphorus content from the Olifants estuary. The study was designed to investigate drivers of variability at different spatial scales and across the salt marsh-seagrass ecotone. Samples were collected in March 2023 from three selected sites (upper, middle, and lower) in the estuary. Each site featured three transects, extending from the salt marsh vegetation of mixed species through the Zostera capensis seagrass meadows towards the water. Sediment cores were taken to a depth of 50 cm, but only the top 0-5 cm section was analyzed. Carbon and nitrogen content were measured using an Elementar Vario EL Cube Elemental CHNS Analyzer, while phosphorus was determined by ICP at Central Analytical Facilities  (Stellenbosch University).   <table> <tbody> <tr> <td> Sampling site </td> <td> GPS coordinates </td> </tr> <tr> <td> Upper </td> <td> 31°39'45.27"S, 18°11'42.40"E </td> </tr> <tr> <td> Middle </td> <td> 31°40'56.46"S, 18°12'3.72"E </td> </tr> <tr> <td> Lower </td> <td> 31°41'39.85"S, 18°11'15.95"E </td> </tr> </tbody> </table>   File description CHNS_Dataset_SM&INT.xlsx: Data for intermediate sample measurements including percent organic carbon content and and percent nitrogen content for all sites ICP_Data_INT.xlsx: Data for Phosphorus content and other related measurements for the upper site.

dryad40/100

Regional and local factors interact to shape colonization and extinction dynamics of invasive Hydrilla verticillata in a patchy landscape

Understanding the response of species to global change requires disentangling the drivers of their distributions across landscapes. Colonization and extinction processes, shaped by the interplay of landscape-level and local patch-level factors, are key determinants of these distributions. However, disentangling the influence of these factors, when larger-scale processes manifest at local scales, remains a challenge. We addressed this challenge by investigating the colonization and extinction dynamics of the aquatic plant, Hydrilla verticillata, in a complex riverine rock pool system. This system, with hundreds of rock pools experiencing varying flooding frequencies, provided a natural laboratory to examine how a single landscape-level disturbance can differentially impact colonization and extinction depending on local patch characteristics to shape species distributions. Using five years of data across over 500 sites and more than 5,000 surveys, we employed dynamic occupancy models to model colonization, extinction, and changes in Hydrilla patch occupancy while accounting for imperfect detection. Our results revealed that larger, infrequently flooded pools closer to the river were more likely to be colonized. In contrast, local extinction of Hydrilla was more likely in smaller pools closer to the river that flooded frequently. These findings underscore the importance of considering context-dependence in species distribution models. The same landscape-level disturbance (flooding) had opposing effects on colonization and extinction, with the direction and magnitude of these effects varying with local patch characteristics. Our study highlights the need for integrating local and landscape-level factors, and considering how larger-scale processes play out at the patch level, to understand the complex dynamics that shape species distributions.

opencc-zeroMay 2024View details →

opencc-by-4.0May 2024View details →

Microscopic understanding of NMR signals by dynamic mean-field theory for spins

Data collection for several plots of the article <a href="https://doi.org/10.1016/j.ssnmr.2024.101936">Microscopic understanding of NMR signals by dynamic mean-field theory for spins</a>. Each hdf5-file contains one or several datasets of a specific figure. The datasets are described by the attribute "description".

Many-body quantum dynamics of spin-orbit coupled Andreev states in a Zeeman field

We provide the raw data used to produce Figs.3-6-7-8-9-10-11 of our paper "Many-body quantum dynamics of spin-orbit coupled Andreev states in a Zeeman field"

opencc-zeroJun 2024View details →

dryad40/100

Data from: Individual energetics scale up to community coexistence: Movement, metabolism and biodiversity dynamics in fragmented landscapes

Unraveling the intricate mechanisms that govern community coexistence remains a daunting challenge, particularly amidst ongoing environmental change. To understand the response of individual animals to environmental change, physiology and individual metabolism are often studied. However, this perspective is currently largely lacking in community ecology. We argue that the integration of individual metabolism into community theory can offer new insights into coexistence. We present the first individual-based metabolic community model for a terrestrial mammal community to simulate energy dynamics and home range behavior in different environments. Using this model, we investigate how ecologically similar species coexist and maintain their energy balance under food competition. Only if individuals of different species are able to balance their incoming and outgoing energy over the long-term will they be able to coexist. After thoroughly testing and validating the model against real-world patterns such as of home range dynamics and field metabolic rates, we applied it as a case study to scenarios of habitat fragmentation - a widely discussed topic in biodiversity research. First, comparing single-species simulations with community simulations, we find that the effect of habitat fragmentation on populations is strongly context-dependent. While populations of species living alone in the landscape were mostly positively affected by fragmentation, the diversity of a community of species was highest under medium fragmentation scenarios. Under medium fragmentation, energy balance and reproductive investment were also most similar among species. We therefore suggest that similarity in energy balance among species promotes coexistence. We argue that energetics should be part of community ecology theory, as the relative energetic status and reproductive investment can reveal why and under what environmental conditions coexistence is likely to occur. As a result, landscapes can potentially be protected and designed to maximize coexistence. The metabolic community model presented here can be a promising tool to investigate other scenarios of environmental change or other species communities to further disentangle global change effects and preserve biodiversity.

Figure 7 in Within-tree distribution and seasonal dynamics of Eutetranychus banksi and Euseius stipulatus (Acari: Tetranychidae, Phytoseiidae) on citrus: Implications for the biological control of the pest

Figure 7 Mean proportion of phytoseiids per leaf outside or inside the canopy (a), on the adaxial or abaxial side of the leaves (b), white or red coloured (c), and collected on fruits (d), whenE. banksi occurred or was absent. Capped bars represent ± standard error (SE). Significant differences are denoted with asterisks. Chi square contingency test:P <0.001.

Figure 1 in Within-tree distribution and seasonal dynamics of Eutetranychus banksi and Euseius stipulatus (Acari: Tetranychidae, Phytoseiidae) on citrus: Implications for the biological control of the pest

Figure 1 Mean number ofE. banksi(a–d) and phytoseiid mites (e–h) per leaf or per cm2 of leaves and fruits. Capped bars represent ± standard error (SE). Bars with different letters are significantly different (Wilcoxon rank-sum test).

Figure 5 in Within-tree distribution and seasonal dynamics of Eutetranychus banksi and Euseius stipulatus (Acari: Tetranychidae, Phytoseiidae) on citrus: Implications for the biological control of the pest

Figure 5 (a–d) Representation of the binomial (logit-link) generalized linear models (GLMs) showing the relationship between the proportion

Figure 3 in Within-tree distribution and seasonal dynamics of Eutetranychus banksi and Euseius stipulatus (Acari: Tetranychidae, Phytoseiidae) on citrus: Implications for the biological control of the pest

Figure 3 Seasonal relative abundance of motile forms of phytoseiid species in four (2018) and six (2019) citrus orchards. Percentage of each species per sampling is represented. The summer decline

Figure 4 in Within-tree distribution and seasonal dynamics of Eutetranychus banksi and Euseius stipulatus (Acari: Tetranychidae, Phytoseiidae) on citrus: Implications for the biological control of the pest

Figure 4 Variation in the spatial distribution and body coloration of phytoseiid in relation to the abundanceE. of banksi in four (2018) and six (2019) citrus orchards. Grey bars indicate the percentage of phytoseiids collected outside the canopy, on the leaf adaxial sides, fruits occupied by phytoseiids, and red phytoseiids (primary y-axis), in relation with the mean numberE of. banksi per leaf or fruit represented as a solid line (secondary, y-axis). Capped bars represent ± standard error (SE).

Figure 2 in Within-tree distribution and seasonal dynamics of Eutetranychus banksi and Euseius stipulatus (Acari: Tetranychidae, Phytoseiidae) on citrus: Implications for the biological control of the pest

Figure 2 Seasonal trends ofE. banksi and phytoseiid mites on leaves (solid line, first y-axis) and fruits (broken line, second y-axis) in four and six citrus orchards in 2018 and 2019 respectively. Mean number of mites collected per sampling unit (all the stages were pooled together). Note that first and second y-axis scales are different. Mean (solid line), maximum and minimum daily temperatures in °C (broken lines) and mean daily relative humidity (RH) were represented.

Molecular dynamics simulation of SpoIVFB:Pro-SigmaK complex (in POPE/POPG mixture)

Simulation in 2:1 POPE:POPG mixture. Found here are all files needed to reproduce or visualize the results of molecular dynamics simulation of the SpoIVFB intramembrane protease bound to the transcription factor Pro-sigmaK. The protein complex was embedded in a POPE:POPG bilayer using CHARMM-GUI and simulated using OpenMM. The README file is a C-shell script that will run equilibration and 250ns of unrestrained simulation.  Individual output (.out) and trajectory (.dcd) files are provided for each checkpoint of the simulation. A combined trajectory containing 250 ns of unrestrained simulation is also provided (combined_250ns_traj.dcd). Together with the step5_input.psf file, this combined dcd file can be used with common software such as VMD to visualize the molecular dynamics trajectory.

Molecular dynamics simulation of SpoIVFB:Pro-SigmaK complex ("pore water" added over membrane re-entrant loop)

Simulation originally starting with "pore water" above the membrane re-entrant loop. Found here are all files needed to reproduce or visualize the results of molecular dynamics simulation of the SpoIVFB intramembrane protease bound to the transcription factor Pro-sigmaK. The protein complex was embedded in a POPE_POPG_DAG_CL bilayer using CHARMM-GUI, and the "generate pore water" feature was used to initially fill the area above the membrane re-entrant loop with water (as opposed to lipids initially being placed in this vicinity). The system was equilibrated and and simulated using OpenMM. The README file is a C-shell script that will run equilibration and 250ns of unrestrained simulation.  Individual output (.out) and trajectory (.dcd) files are provided for each checkpoint of the simulation. A combined trajectory containing 250 ns of unrestrained simulation is also provided (combined_250ns_traj.dcd). Together with the step5_input.psf file, this combined dcd file can be used with common software such as VMD to visualize the molecular dynamics trajectory.

Molecular dynamics simulation of SpoIVFB:Pro-SigmaK complex (replicate 4)

Replicate simulation 4/4 Found here are all files needed to reproduce or visualize the results of molecular dynamics simulation of the SpoIVFB intramembrane protease bound to the transcription factor Pro-sigmaK. The protein complex was embedded in a POPE_POPG_DAG_CL bilayer using CHARMM-GUI and simulated using OpenMM. The README file is a C-shell script that will run equilibration and 250ns of unrestrained simulation.  Individual output (.out) and trajectory (.dcd) files are provided for each checkpoint of the simulation. A combined trajectory containing 250 ns of unrestrained simulation is also provided (combined_250ns_traj.dcd). Together with the step5_input.psf file, this combined dcd file can be used with common software such as VMD to visualize the molecular dynamics trajectory.

Molecular dynamics simulation of SpoIVFB:Pro-SigmaK complex (replicate 3)

Replicate simulation 3/4 Found here are all files needed to reproduce or visualize the results of molecular dynamics simulation of the SpoIVFB intramembrane protease bound to the transcription factor Pro-sigmaK. The protein complex was embedded in a POPE_POPG_DAG_CL bilayer using CHARMM-GUI and simulated using OpenMM. The README file is a C-shell script that will run equilibration and 250ns of unrestrained simulation.  Individual output (.out) and trajectory (.dcd) files are provided for each checkpoint of the simulation. A combined trajectory containing 250 ns of unrestrained simulation is also provided (combined_250ns_traj.dcd). Together with the step5_input.psf file, this combined dcd file can be used with common software such as VMD to visualize the molecular dynamics trajectory.

Molecular dynamics simulation of SpoIVFB:Pro-SigmaK complex (replicate 2)

Replicate simulation 2/4 Found here are all files needed to reproduce or visualize the results of molecular dynamics simulation of the SpoIVFB intramembrane protease bound to the transcription factor Pro-sigmaK. The protein complex was embedded in a POPE_POPG_DAG_CL bilayer using CHARMM-GUI and simulated using OpenMM. The README file is a C-shell script that will run equilibration and 250ns of unrestrained simulation.  Individual output (.out) and trajectory (.dcd) files are provided for each checkpoint of the simulation. A combined trajectory containing 250 ns of unrestrained simulation is also provided (combined_250ns_traj.dcd). Together with the step5_input.psf file, this combined dcd file can be used with common software such as VMD to visualize the molecular dynamics trajectory.

Dataset for "Self-heating effects and switching dynamics in graphene multiterminal Josephson junctions"

Dataset containing raw measurement data and simulation results for the manuscript "Self-heating effects and switching dynamics in graphene multiterminal Josephson junctions".

Figure 1 in Composition and spatio-temporal dynamics of aquatic bird community in humid areas of Alto Parana Atlantic Forest

Figure 1. Map of the RPPN Foz do Rio Aguapeí and location of the six studied areas in the RPPN Foz do Rio Aguapeí. Legend: (1) Lagoa São Gabriel; (2) Lagoa das Piranhas; (3) Lagoa dos Porcos; (4) Constructed wetland; (5) Aguapei river –; and (6) Lagoa da sede. Sources: CESP (2013) and Google Earth (2021).

Figure 2 in Composition and spatio-temporal dynamics of aquatic bird community in humid areas of Alto Parana Atlantic Forest

Figure 2. Cumulative curve of the 52 waterfowl bird species in the RPPN Foz do Rio Aguapeí showing stability from sample 27 to 31.

Figure 3 in Composition and spatio-temporal dynamics of aquatic bird community in humid areas of Alto Parana Atlantic Forest

Figure 3. NMDS (stress of 0.097) of the spatial distribution of the aquatic bird community recorded by the transect method in the lagoons of the RPPN Foz do Aguapeí, during the dry (rounded symbols) and rainy seasons (square symbols). Legend: LS = Lagoa da Sede; LSG = Lagoa São Gabriel; LP = Lagoa da Piranha and LPO = Lagoa dos Porcos.