Find research datasets worth reusing

Dataset for manuscript "Host-related and environmental factors influence long-term ectoparasite infestation dynamics of mouse lemurs in northwestern Madagascar" to be published in the American Journal of Primatology

This Excel-file contains three datasets, corresponding to the initial raw dataset resulting from all ectoparasite inspections (n = 2,241), the merged dataset used for host-related and temporal modeling (n = 1940), and the even more condensed dataset with one datapoint per individual used for climatic modeling (n = 583), respectively.

opencc-zeroMar 2023View details →

Does pre-spawning catch and release angling affect offspring telomere dynamics in Atlantic salmon

<div> The practice of 'catch and release' (C&R) angling confers a balance between animal welfare, conservation efforts and preserving the socio-economic interests of recreational angling. However, C&R angling can still cause exhaustion and physical injury, and often exposes the captured fish to the stress of air exposure. Therefore, the true conservation success of C&R angling depends on whether the angled individuals then survive to reproduction and whether there are any persisting effects on subsequent generations. Here we tested the hypothesis that the stress of C&R angling is then passed on to offspring. We experimentally manipulated the C&R experience of wild adult salmon prior to the spawning season. These parental fish either underwent a C&R simulation (which involved exercise with/without air exposure) or were left as control individuals. We then measured the telomere length of the arising offspring (at the larval stage of development) since previous studies have linked a shorter telomere length with reduced fitness/longevity and the rate of telomere loss is thought to be influenced by stress. Family-level telomere length was positively related to rate of growth. However, the telomere lengths of the salmon offspring were unrelated to the C&R experience of their parents. This may be due to there being no intergenerational effect of parental stress exposure on offspring telomeres, or to any potential effects being buffered by the significant telomere elongation mechanisms that are thought to occur during the embryonic and larval stages of development. While this may suggest that C&R angling has a minimal intergenerational effect on offspring fitness, there have been numerous other reports of negative C&R effects, therefore we should still be aiming to mitigate and refine such practices, in order to minimise their impacts on fish populations. </div>

Dynamic Vegetation Model Dynamic Organic Soil Terrestrial Ecosystem Model (DVM-DOS-TEM) simulations focused on Eight Mile Lake, Alaska and Imnavait Creek, Alaska [2000-2015]

This set of files store model simulations using the biosphere model Dynamic Vegetation Model Dynamic Organic Soil Terrestrial Ecosystem Model (DVM-DOS-TEM), developed to simulate biophysical and biogeochemical interactions between the soil, vegetation and atmosphere. To improve predictions of net carbon releases from thawing permafrost, we tested the sensitivity of a suite of model parameters. We analyzed the responses of ecosystem carbon balances to permafrost thaw by running site-level simulations at two long-term tundra ecological monitoring sites in Alaska: Eight Mile Lake (EML) and Imnavait Creek watershed (IMN). These sites are characterized by similar tussock tundra vegetation but differing soil drainage conditions and climate, IMN consists of well-drained soils, and EML has historically well-drained soils, however permafrost thaw has altered drainage conditions to wetter soils. Simulations were conducted at a 1km resolution, over a 1,000 km2 area (10x10 km square) centered on two long term ecological research sites in Alaska: Eight Mile Lake located in Interior Alaska (63.8900° N, 149.2535° W), and Imnavait creek watershed located on the northern foothills of the Brooks range (68°37′ N, 149°18′ W). Historical simulations are spanning the 2000 to 2015, and forced using climate simulations from the Climate Research Unit, time series 4.0. We ran 1,000 site level simulations for each model variable. The variables that are produced are gross primary productivity (GPP, in gC.m-2.m-1), net ecosystem exchange (NEE, gC.m-2.m-1), ecosystem respiration (RECO, gC/m2/m-1), active layer thickness (ALT, m), soil temperature (TLAYER,°C) at 5, 10, 40 cm depths, soil moisture (LWCLAYER, m-3/m-3) at 5, 10 cm depths, and snow depth (SNOWDEPTH, m), evapotransipiration(EET, mm/m2/time), potential evapotransipiration (PET, mm/m2/time), leaf area index (LAI, m2/m2), organic layer thickness (OLT, m). The data are stored as compiled csv files, with time as the index, and each model sample output stored in the columns. In addition, there is a postprocessing python script to demonstrate the step and workflow used to generate the individual csv files post processed from the raw model outputs stored as netcdfs.

opencc-zeroMar 2023View details →

Identifying temporal dynamics in post-release survival of a restored large ungulate

Wildlife translocation is an important conservation tool for restoring species and reducing global biodiversity decline; however, this practice is challenging for wildlife, and translocated individuals must adjust to their release landscapes for restoration success. The period following release is a vulnerable time for wildlife and determining when animals acclimate following translocation improves long-term estimates of population dynamics and allows researchers to efficiently tailor translocation design and post-release management to each population's needs. We evaluated demographic acclimation and investigated changes in post-release survival of a population of 106 elk (Cervus canadensis) translocated to Missouri, U.S.A., from 2011 to 2013 using generalized survival modeling. We defined the acclimation period as the duration of time prior to stabilization in mortality risk relative to time from release, and we evaluated acclimation duration from flexible plots of estimated mortality hazards across time. We simultaneously investigated factors contributing to post-release survival and compared survival rates and mortality sources observed during acclimation and post-acclimation periods. Elevated mortality risk for translocated elk spanned a 5-month acclimation period following release, with an additional one-year period reflecting reduced, but still elevated, mortality hazards. Baseline hazards during the initial 5-month acclimation period were approximately four times higher than the subsequent 4.4 years following release. Release cohort, but not age class or sex, was associated with post-release mortality risk, and mortality sources within the acclimation period tended to be undetermined with greater frequency relative to mortalities occurring after the acclimation period. Synthesis and applications. Our results highlight the utility of flexible modeling approaches to evaluate dynamic post-release responses of translocated populations. Translocated elk demonstrated a pronounced demographic acclimation period that spanned five months following release. Changes in mortality sources and the timing of stabilization in mortality hazards suggest that demographic acclimation in translocated elk was associated with adjustments in physiological stress and movement rates that stabilize over a similar post-release duration. Improving post-release monitoring and assessment of restored populations by evaluating temporal dynamics of manifold biological and ecological responses of translocated animals.

Plasticity of neuronal dynamics in the lateral habenula for cue-punishment associative learning.

The brain’s ability to associate threats with external stimuli is vital to execute essential behaviours including avoidance. Disruption of this process contributes instead to the emergence of pathological traits which are common in addiction and depression. However, the mechanisms and neural dynamics at the single-cell resolution underlying the encoding of associative learning remain elusive. Here, employing a Pavlovian discrimination task in mice we investigate how neuronal populations in the lateral habenula (LHb), a subcortical nucleus whose excitation underlies negative affect, encode the association between conditioned stimuli and a punishment (unconditioned stimulus).

opencc-zeroMar 2023View details →

Wildfire impacts on seedbank and vegetation dynamics in Calluna heath

Moorlands dominated by Calluna vulgaris (hereafter Calluna) are globally rare and under increasing threat of wildfires due to climate change. The soil seedbank is important for community resilience, but research on its contribution to regenerating vegetation after moorland fires has, to date, focused on prescribed fire or on the short-term (≤ 2 year) impacts of wildfire. To address the role of the seedbank in long-term vegetation regeneration, we studied a chronosequence of six wildfire sites within a Scottish moorland catchment, ranging from 2 to 64 years since burning. We recorded vegetation composition and sampled the seedbank. Calluna and Erica spp. comprised 66 % and 27 % of germinated seeds, respectively, and the majority of vegetation species were not represented in the seedbank. Canonical Correspondence Analysis (CCA) revealed that time since fire was a strong predictor of vegetation species composition, but it had no effect on seedbank composition, suggesting that the same species dominate the seedbank regardless of burning. Whilst total seed density was not affected by time since wildfire, the effect on the non-Calluna seedbank was more notable. The proportion of non-Calluna species decreased with time in both vegetation and seedbank as Calluna cover was re-established and the seedbank of other species became gradually depleted. Whilst relative non-Calluna cover in the vegetation was at a maximum in recently burnt areas and then declined with time since fire, the species richness and proportion of non-Calluna in the seedbank followed a unimodal pattern after fire and reached a peak after approximately 35 years. Our results contribute to the knowledge of how moorland ecosystems regenerate after severe disturbances, which are likely to become more common as the climate changes.

Shifting Dynamics in International Trade Networks: A Longitudinal Analysis of Major Exporting Economies (1992-2020): A case of the US, China, India, Japan and South Korea

This article aims to analyze the changes in trading networks by bringing out aspects of centrality and reciprocity among participating countries. The research considers the trade relations of five export countries, namely, The U.S., China, India, Japan, and South Korea from 1992 to 2020. We examine whether trade networks are truly becoming more bidirectional over the long term and how the political and economic crises that have occurred in the past 30 years affect the structure of trade networks. The article presents key findings on the changes in the network structure of international trade over the past 30 years. The network structure has become more reciprocal for most product categories, and the center of the trade network has shifted from the United States to China. The analysis also demonstrated that the center of the network has shifted from U to C for all product categories, except for raw materials. The study also highlights the significant impact of global events and crises on the international trade network structure, emphasizing the importance of considering geopolitical events and economic shocks in understanding trade dynamics.

Molecular dynamics-generated ensemble dataset of ubiquitin; for "PROTHON: A Local Order Parameter-Based Method for Efficient Comparison of Protein Ensembles"

The molecular dynamics-generated ensemble dataset (229Mb zip file) for ubiquitin, used in the manuscript "PROTHON: A Local Order Parameter-Based Method for Efficient Comparison of Protein Ensembles", submitted to the Journal of Chemical Information and Modeling (JCIM). The dataset consists of 6 .dcd files, and one .pdb file.

A unified meta-ecosystem dynamics model: Integrating herbivore-plant subwebs with the intermittent upwelling hypothesis

Determining the relative influence of biotic and abiotic processes in structuring communities at local to large spatial scales is best understood using a biogeographic comparative-experimental approach. Using this approach, previous work suggests that intertidal community dynamics (top-down and bottom-up effects) vary unimodally along an upwelling-based productivity gradient, termed the Intermittent Upwelling Hypothesis (IUH). Evidence consistent with the IUH comes from the sessile invertebrate/predator (SIP) subweb in certain rocky intertidal communities, but whether this pattern extends to macrophyte/herbivore (MH) subwebs is unknown. Here we ask: Are MH subwebs also structured as predicted by the IUH? What is the relative importance of herbivory and predation in structuring these communities? Under what conditions do ecological subsidies like nutrients or propagule production drive community dynamics? And are omnivorous interactions important? We hypothesize that MH subwebs are driven by a new construct, the Grazing-Weakening Hypothesis (GWH), which states that MH interactions weaken monotonically with increasing nutrients, with strong (weak) herbivory and low (high) macrophyte productivity at low (high) nutrients. We explored local-to-large spatial scale dynamics of both subwebs using a biogeographic comparative-experimental factorial field experiment testing joint and separate effects of herbivores and predators between two continents. Experiments at ten sites ranging across from persistent upwelling to persistent downwelling regimes ran for 26-29 months in Oregon and California, and New Zealand South Island. For the MH subweb, results were consistent with the GWH: herbivory declined and macrophytes increased with increasing nutrients. As expected, results for the SIP subweb were consistent with the IUH: predator effect size was unimodally related to upwelling. Overall, herbivory explained more variation in community structure than did predation, especially in New Zealand. Omnivory was weak, sessile invertebrates outcompeted macrophytes, and ocean-driven subsidies provided the basic template driving ecosystem dynamics. We propose a unified Meta-Ecosystem Dynamics Model (MEcoDynaMo) combining MH and SIP results: with increased upwelling, sessile invertebrates and underlying dynamics vary unimodally (as in the IUH), while herbivory decreases and macrophytes generally increase. While this model was based on research in temperate ecosystems varying in upwelling regime, its wider applicability remains to be tested.

Supporting datasets for "Dynamical Equilibrium between Brønsted and Lewis Sites in Zeolites: Framework-Associated Octahedral Aluminum"

Tar of directory tree containing input files for VASP and CASTEP calculations of local geometries and NMR parameters (both static and dynamic) for systems described in the manuscript, including CHA and MOR in H form, various Si/Al ratios and water loadings.

Molecular dynamics (MD) simulations methods and results on cyclooctene oxides in ACN/water hybrid electrolytes

Molecular dynamics (MD) simulations methods and extended results used for the Perspective article entitled “Fine tuning of electrosynthesis pathways by modulation of electrolyte solvation structure”

Workflow for Remote Sensing for Forest Dynamics and Its Implications for Tree Outside Forest over Maryland, U.S.A.

The workflow shows the process of using the data to plot the figures in the paper "Remote Sensing for Forest Dynamics and Its Implications for Tree Outside Forest over Maryland, U.S.A."

Molecular Simulation Data Associated with the Manuscript "Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor"

Molecular Simulation Data Associated with the Manuscript "Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor" by Jie Heng, Yunfei Hu, Guillermo Pérez-Hernández, Asuka Inoue, Jiawei Zhao, Xiuyan Ma, Xiaoou Sun, Kouki Kawakami, Tatsuya Ikuta, Jienv Ding, Yujie Yang, Lujia Zhang, Sijia Peng, Xiaogang Niu, Hongwei Li, Ramon Guixà-González, Changwen Jin, Peter W. Hildebrand, Chunlai Chen & Brian K. Kobilka Nature Communications 2023, <a href="https://doi.org/10.1038/s41467-023-37233-1">https://doi.org/10.1038/s41467-023-37233-1</a> The representative molecular dynamics (MD) trajectories shown in the Supplementary Fig. 8, Variable contacts of the β2AR CT can be 3D visualized in the browser in the following link: <ul> <li><a href="https://proteinformatics.uni-leipzig.de/mdsrv.html?load=file://base/B2CT/variants.ngl"> https://proteinformatics.uni-leipzig.de/mdsrv.html?load=file://base/B2CT/variants.ngl</a></li> </ul>

Data and code for analyzing the spatiotemporal dynamics of laurel wilt in the southeastern US

Data and code required to reproduce findings and figures from analyses of the spatiotemporal dynamics of laurel wilt in the southeastern United States.

Data from: A meta-analysis of plant tissue O2 dynamics

This dataset includes 1,567 recorded tissue O2 levels from 112 plant species extracted from published literature. The data forms the basis of the publication "A meta-analysis of plant tissue O2 dynamics" with the following abstract: Adequate tissue O2 supply is crucial for plant functioning. We therefore aimed at identifying environmental conditions and plant characteristics affecting plant tissue O2 status. We extracted data and performed meta-analysis on > 1,500 published tissue O2 measurements from 112 species. Tissue O2 status ranged from anoxic conditions in especially roots, to > 53 kPa in submerged, photosynthesizing shoots. Using information-theoretic model selection, we identified 'submergence', 'light', 'tissue type' as well as 'light × submergence' interaction as significant drivers of tissue O2 status. Median O2 status was especially low (< 50% of atmospheric equilibrium) in belowground rhizomes, potato tubers and root nodules. Mean shoot and root O2 was ~25% higher in light than in dark when shoots had atmospheric contact. However, light showed a significant interaction with submergence on plant O2, with a submergence-induced 44% increase in light, compared with a 42% decline in dark, relative to plants with atmospheric contact. During submergence, ambient water column O2 and shoot tissue O2 correlated stronger in darkness than in light conditions. Although miniaturised Clark-type O2 electrodes in particular have resulted in enhanced understanding of plant O2 dynamics, the use of non-invasive methods is still lacking behind its widespread use in mammalian tissues.

Data for: Effects of habitat management on rodent diversity, abundance, and virus infection dynamics

As anthropogenic factors continue to degrade natural areas, habitat management is needed to restore and maintain biodiversity. However, the impacts of different habitat management regimes on ecosystems have largely focused on vegetation analyses, with limited evaluation of downstream effects on wildlife. We compared the effects of grassland management regimes (prescribed burning, cutting/haying, or no active management) on rodent communities and the viruses they hosted. Rodents were trapped in 13 existing grassland sites in Northwest Arkansas, USA during 2020 and 2021. Rodent blood samples were screened for antibodies against three common rodent-borne virus groups: orthohantaviruses, arenaviruses, and orthopoxviruses. We captured 616 rodents across 5953 trap nights. Burned and unmanaged sites had similarly high abundance and diversity, but burned sites had a higher proportion of grassland species than unmanaged sites; cut sites had the highest proportion of grassland species but the lowest rodent abundance and diversity. A total of 38 rodents were seropositive for one of the three virus groups (34 orthohantavirus, three arenavirus, and one orthopoxvirus). Thirty-six seropositive individuals were found in burned sites, and two orthohantavirus-seropositive individuals were found in cut sites. Cotton rats and prairie voles, two grassland species, accounted for 97% of the rodents seropositive for orthohantavirus. Our study indicates that prescribed burns lead to a diverse and abundant community of grassland rodent species when compared to other management regimes; as keystone taxa, these results also have important implications for many other species in food webs. Higher prevalence of antibodies against rodent-borne viruses in burned prairies shows an unexpected consequence likely resulting from robust host population densities supported by the increased habitat quality of these sites. Ultimately, these results provide empirical evidence that can inform grassland restoration and ongoing management strategies.

Cell tracking data from: Automated timelapse data segmentation reveals in vivo cell state dynamics

Embryonic development proceeds as a series of orderly cell state transitions built upon noisy molecular processes. Here, we defined gene expression and cell motion states using single cell RNA sequencing data and in vivo timelapse cell tracking data of the zebrafish tailbud. We performed a parallel identification of these states using dimensional reduction methods and a change point detection algorithm. Both types of cell states were quantitatively mapped onto embryos, and we utilized the cell motion states to study the dynamics of biological state transitions over time. The time average pattern of cell motion states is reproducible among embryos. However, individual embryos exhibit transient deviations from the time average forming left-right asymmetries in collective cell motion. Thus, the reproducible pattern of cell states and bilateral symmetry arises from temporal averaging. In addition, collective cell behavior can be a source of asymmetry rather than a buffer against noisy individual cell behavior.

Optimal prey for red fox cubs – an example of dual optimizing foraging strategy in foxes from a dynamic wetland habitat

The red fox (Vulpes vulpes) is the most abundant mesopredator in the Central-European region. Detailed knowledge about their feeding behavior is important both from ecological and wildlife management reasons. Food choices of foxes are poorly predictable in high-biodiversity marshlands. The main aim of our study was to sample parallel the main food-type abundances in the study area and analyze the diet of fox cubs and cohabiting adults across three years during the period of maternal dependence of the cubs. According to the optimal foraging theory, we predicted that the cubs' diet would show higher energy content, would be more varied, and the individual prey species fed to the young would be larger. We analyzed the composition of adult fox and cub fecal samples collected separately around dens in a marshland of western Hungary, May 2014, 2017 and 2020, when the abundance values of main food sources differed. Rodents and waterfowl dominated the diet, but their relative occurrence in the samples showed yearly variations. We found that vixens follow a dual optimizing foraging strategy regarding their provisioning of the cubs and their own diet. Adult foxes optimized their diet according to the actual yearly abundances of their main food sources. Additionally, they preferred prey items that can be consumed at the site of capture (large carrion and small individual prey items). Cubs on the other hand were provisioned with optimal high-energy food, even if those in question became less abundant in that year. Vixens mostly fed to their young either larger rodents and waterfowl, or multiple small rodents at a time – these types of prey are both optimal for transportation as a single load. Providing optimal prey at an early age in a changing environment may contribute to the ecological success of the red fox.

EMD data for the paper "Impact of ad-hoc post-processing parameters on the lubricant viscosity calculated with equilibrium molecular dynamics simulations"

This archive contains the post-processing data obtained from EMD simulations of 2,2,4-Trimethylhexane lubricant molecule under various operating conditions. The EMD simulations were performed using LAMMPS with COMPASS force field. (See manuscript and README for details.)