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308 results for “Dynamical system”
Data from: Evaluation of different bias correction methods for dynamical downscaled future projections of the California Current Upwelling System
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Spring and latch dynamics can act as control pathways in ultrafast systems
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Data from: Age-structure and transient dynamics in epidemiological systems
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Data and code for: The role of indirect interspecific effects in the stochastic dynamics of a simple trophic system
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Simple muscle-lever systems are not so simple: The need for dynamic analyses to predict lever mechanics that maximize speed
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SIM4NEXUS System Dynamics Model of Azerbaijan
<p>The System Dynamics Model covers all five sectors of the Nexus of Azerbaijan. Namely the climate, water, land, food and energy sector and their interlinkages. The SDM has been developed in the H2020 project SIM4NEXUS and is the base for a Serious Game on the Azerbaijani Nexus.</p>
Data from: Male social plasticity influences transient dynamics of alternative mating systems in water striders
Animal mating systems are often studied with the goal of understanding why species, populations, or groups vary from one another in the system they display. Although these differences are often treated as basically stable, it is also known that these systems may shift over time (e.g. from one breeding season to the next). There has been some study of how ecological factors correlate with these changes; however, few, if any, studies have investigated how the phenotypic composition of a group governs the timing and probability of system transitions. Groups of stream water striders (Aquarius remegis) can demonstrate quick and flexible transitions in mating system dynamics, with many groups eventually transitioning to a system in which a single, large male monopolizes mating opportunities. We asked if variation in individual- and group-level traits associated with morphology and behavior (e.g. size of the largest individual, variance in activity behavioral types, and average social plasticity) could partially explain the variability in how rapidly groups make this transition, if they make it all. Our results show that the average social plasticity of males in a group has important effects on the emergence timing of mating systems dominated by a single male.
Data from: Stream community richness predicts apex predator occupancy dynamics in riparian systems
Streams and adjacent riparian habitats represent linked terrestrial and aquatic ecosystems that exchange materials and energy. Recognized relationships among apex predators and ecosystem biodiversity led us to hypothesize that these predators in riparian-stream systems were more likely to be found in sites with high stream quality, defined as increased ecosystem function and integrity. In our freshwater study system, river otter (Lontra canadensis) and mink (Neovison vison) play critical roles as apex predators. We used multi-season occupancy modelling across 3 sampling years (2012-2014) to compare aspects of the stream communities that explain occupancy dynamics of river otter and mink, including their interactions with other semi-aquatic mammals. We surveyed for semi-aquatic mammals at 77 sites in 12 major watersheds in southern Illinois, USA (44,526 km<sup>2</sup>). Naïve occupancy differed among years but generally increased for river otter, and remained high (≥93.5%) for mink. Increasing substrate availability increased detectability of river otter, whereas mink detection varied by survey period. Occupancy of river otter during the initial survey period was higher in sites closer to reintroduction points. Probability of colonization of river otter was positively associated with macroinvertebrate index of biotic integrity, fish species richness, and beaver presence. Sites with high species richness of fish families preferred by river otter also had increased river otter persistence. Mink occupied sites with increased fish richness, muskrat presence, and mussel community index. Taken together, our results show occupancy of both mink and river otter were predicted by aspects of prey diversity and presence, indicating the importance of community composition in occupancy dynamics of riparian predators. Ultimately, these relationships suggest that habitat heterogeneity and system stability are important to apex predator site use. However, the relative role of bottom-up and top-down forcing in stream systems remains to be resolved.
Occupancy in dynamic systems: accounting for multiple scales and false positives using environmental DNA to inform monitoring
<div class="page"> <div class="section"> <p>Occupancy is an important metric to understand current and future trends in populations that have declined globally. In addition, occupancy can be an efficient tool for conducting landscape-scale and long-term monitoring. A challenge for occupancy monitoring programs is to determine the appropriate spatial scale of analysis and to obtain precise occupancy estimates for elusive species. We used a multi-scale occupancy model to assess occupancy of Columbia spotted frogs in the Great Basin, USA, based on environmental DNA (eDNA) detections. We collected three replicate eDNA samples at 220 sites across the Great Basin. We estimated and modeled ecological factors that described watershed and site occupancy at multiple spatial scales simultaneously while accounting for imperfect detection. Additionally, we conducted visual and dipnet surveys at all sites and used our paired detections to estimate the probability of a false positive detection for our eDNA sampling. We applied the estimated false positive rate to our multi-scale occupancy dataset and assessed changes in model selection. We had higher naïve occupancy estimates for eDNA (0.37) than for traditional survey methods (0.20). We estimated our false positive detection rate per qPCR replicate at 0.023 (95% CI: 0.016-0.033). When the false positive rate was applied to the multi-scale dataset, we did not observe substantial changes in model selection or parameter estimates. Conservation and resource managers have an increasing need to understand species occupancy in highly variable landscapes where the spatial distribution of habitat changes significantly over time due to climate change and human impact. A multi-scale occupancy approach can be used to obtain regional occupancy estimates that can account for spatially dynamic differences in availability over time, especially when assessing potential declines. Additionally, this study demonstrates how eDNA can be used as an effective tool for improved occupancy estimates across broad geographic scales for long-term monitoring.</p> </div> </div>
Data from: Microbe biogeography tracks water masses in a dynamic oceanic frontal system
PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN ANOTHER PUBLICATION. PLEASE SEE http://dx.doi.org/10.1098/rsos.160829. Dispersal limitation, not just environmental selection, plays an important role in microbial biogeography. The distance–decay relationship is thought to be weak in habitats where dispersal is high, such as in the pelagic environment, where ocean currents facilitate microbial dispersal. Most studies of microbial community composition to date have observed little geographical heterogeneity on a regional scale (100 km). We present a study of microbial communities across a dynamic frontal zone in the southwest Indian Ocean and investigate the spatial structure of the microbes with respect to the different water masses separated by these fronts. We collected 153 samples of free-living microorganisms from five seamounts located along a gradient from subtropical to subantarctic waters and across three depth layers: (i) the sub-surface chlorophyll maximum (approx. 40 m), (ii) the bottom of the euphotic zone (approx. 200 m), and (iii) the benthic boundary layer (300–2000 m). Diversity and abundance of microbial operational taxonomic units (OTUs) were assessed by amplification and sequencing of the 16S rRNA gene on an Illumina MiSeq platform. Multivariate analyses showed that microbial communities were structured more strongly by depth than by latitude, with similar phyla occurring within each depth stratum across seamounts. The deep layer was homogeneous across the entire survey area, corresponding to the spread of Antarctic intermediate water. However, within both the sub-surface layer and the intermediate depth stratum there was evidence for OTU turnover across fronts. The microbiome of these layers appears to be divided into three distinct biological regimes corresponding to the subantarctic surface water, the convergence zone and subtropical. We show that microbial biogeography across depth and latitudinal gradients is linked to the water masses the microbes persist in, resulting in regional patterns of microbial biogeography that correspond to the regional scale physical oceanography.
Data from: Population dynamics of an Arctiid caterpillar-tachinid parasitoid system using state-space models
1. Population dynamics of insect host–parasitoid systems are important in many natural and managed ecosystems and have inspired much ecological theory. However, ecologists have a limited knowledge about the relative strengths of species interactions, abiotic effects and density dependence in natural host–parasitoid dynamics. Statistical time-series analyses would be more informative by incorporating multiple factors, measurement error and noisy dynamics. 2. We use a novel maximum likelihood and model-selection analysis of a state-space model for host–parasitoid dynamics to examine 21 years of annual census data for woolly bear caterpillars (Platyprepia virginalis) and their locally host-specific tachinid parasitoids (Thelaira americana). 3. Caterpillar densities varied by three orders of magnitude and were driven by density dependence and precipitation from the previous March but not detectably by parasitoids, despite variable and sometimes high (>50%) parasitism. 4. Fly fluctuations, as estimated from per cent parasitism, were affected by density dependence and precipitation from the previous July. There was marginal evidence that host abundance drives fly fluctuations as a generic linear effect but no evidence for classical Nicholson–Bailey coupling. 5. The state-space model analysis includes new methods for likelihood calculation and allows a balanced consideration of effect magnitude and statistical significance in a nonlinear model with multiple alternative explanatory variables.
DynaBench: A benchmark dataset for learning dynamical systems from low-resolution data (minimal)
<p>This is a minimal version of the DynaBench dataset, containing the first 5% of the data. The full dataset is available at <a href="https://professor-x.de/dynabench">https://professor-x.de/dynabench</a></p><p><strong>Abstract:</strong></p><p>Previous work on learning physical systems from data has focused on high-resolution grid-structured measurements. However, real-world knowledge of such systems (e.g. weather data) relies on sparsely scattered measuring stations. In this paper, we introduce a novel simulated benchmark dataset, DynaBench, for learning dynamical systems directly from sparsely scattered data without prior knowledge of the equations. The dataset focuses on predicting the evolution of a dynamical system from low-resolution, unstructured measurements. We simulate six different partial differential equations covering a variety of physical systems commonly used in the literature and evaluate several machine learning models, including traditional graph neural networks and point cloud processing models, with the task of predicting the evolution of the system. The proposed benchmark dataset is expected to advance the state of art as an out-of-the-box easy-to-use tool for evaluating models in a setting where only unstructured low-resolution observations are available. The benchmark is available at <a href="https://professor-x.de/dynabench">https://professor-x.de/dynabench</a>.</p><p><strong>Technical Info</strong></p><p>The dataset is split into 42 parts (6 equations x 7 combinations of resolution/structure). Each part can be downloaded separately and contains 7000 simulations of the given equation at the given resolution and structure. The simulations are grouped into chunks of 500 simulations saved in the hdf5 file format. Each chunk contains the variable "data", where the values of the simulated system are stored, as well as the variable "points", where the coordinates at which the system has been observed are stored. For more details visit the DynaBench website at <a href="https://professor-x.de/dynabench/">https://professor-x.de/dynabench/</a>. The dataset is best used as part of the dynabench python package available at <a href="https://pypi.org/project/dynabench/">https://pypi.org/project/dynabench/</a>.</p>
Dynamic shifts in the Southern Benguela Upwelling System since the latest Miocene
<p>The dataset consists of planktic foraminiferal abundance data and stable oxygen and carbon isotope records of shallow and deep-dwelling planktic foraminifera.</p>
Multiple Parameter Replica Exchange Gaussian Accelerated Molecular Dynamics for Enhanced Sampling and Free Energy Calculation of Biomolecular Systems
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Supplementary material for "Comprehensive framework for dynamic energy assessment of building systems using IFC graphs and Modelica"
<p>The provided files include the following:</p> <ul> <li>The IFC model of the demo building used in Section 2.</li> <li>The parsed space boundaries graph.</li> <li>The resulting fragmented space boundaries graph.</li> </ul>
Rapid microfluidic perfusion system enables controlling dynamics of intracellular pH regulated by Na+/H+ exchanger NHE1
<p>Dataset for manuscript titled "Rapid microfluidic perfusion system enables controlling dynamics of intracellular pH regulated by Na+/H+ exchanger NHE1."</p> <p>Version 2: additional data for Figure 2(e) and (f).</p>
Data and output files for the paper, "Dynamical systems inference at scale reveals intrinsic instability in the dysbiotic microbiome"
<p>The above files contain the output of the model, which we call MDSINE2, developed in the paper titled, "<em>Dynamical systems inference at scale reveals intrinsic instability in the dysbiotic microbiome</em>" (See https://github.com/gerberlab/MDSINE2_Paper for implementation details). More specifically, forward_sims.tgz contains the output of forward simulations in .npy format; mixed_prior_fixed.tgz contains the pickle files corresponding to the output of the MCMC simulations for fixed topology; mixed_prior_unfixed.tgz contains the pickle files corresponding to the output of the MCMC simulations for unfixed topology; other_files contains information on eigenvalues and cycles, results for Phylogenetic Neighborhood Analysis, Keystoneness Analysis and the output in .npy format for comparator methods; ASV_OTU_aggregate_and_plylogeneteic trees contains the plots of trajectories (relative abundance) of OTUS and their constituent ASVs, and of phylogenetic trees. </p>
Climate change reshapes the eco-evolutionary dynamics of a Neotropical seed dispersal system
<p><b>Aim</b>: 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.</p> <p><b>Location</b>: Atlantic forests of South America</p> <p><b>Time period</b>: Present day, end of 21st Century</p> <p><b>Major taxa studied: </b>Thirty-two species of frugivorous birds, and a palm (<i>Euterpe edulis</i>). </p> <p><b>Methods</b>: 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.</p> <p><b>Results</b>: 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.</p> <p><b>Main conclusion</b>: 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.</p>
Hemodynamic data from the Inspired Therapeutics NeoMate Mechanical Circulatory Support System for neonates and infants as tested in static mock circulatory loops, dynamic mock circulatory loops, and acute animal studies
<p>Inspired Therapeutics (Merritt Island, FL) is developing a mechanical circulatory support (MCS) system designed as a single driver with interchangeable, extracorporeal, magnetically levitated pumps. The NeoMate system design features an integrated centrifugal rotary pump, motor, and controller that will be housed in a single compact unit. Conceptually, the primary innovation of this technology will be the combination of disposable, low-cost pumps for use with a single, multi-functional, universal controller to support multiple pediatric cardiopulmonary indications. In response to the paucity of clinically available pediatric devices, Inspired Therapeutics is specifically targeting the underserved neonate and infant heart failure (HF) patient population first. In this article, we present the development of the prototype Inspired Therapeutics NeoMate System for pediatric left ventricular assist device (LVAD) support, and feasibility testing in static mock flow loops (H-Q curves), dynamic mock flow loops (hemodynamics), and in an acute healthy ovine model (hemodynamics and clinical applicability). The resultant hydrodynamic and hemodynamic data demonstrated the ability of this prototype pediatric LVAD and universal controller to function over a range of rotary pump speeds (500-6000 RPM), to provide pump flow rates of up to 2.6 L/min, and to volume unload the left ventricle in acute animals. Key engineering challenges observed and proposed solutions for the next design iteration are also presented.</p>
Code and data for results and figures of the manuscript "Multi-million year cycles in modelled δ13C as a response to astronomical forcing of organic matter fluxes." submitted to Earth System Dynamics
<p>This dataset contains the code of the model used in the manuscript submitted to Earth System Dynamics "Multi-million year cycles in modelled δ13C as a response to astronomical forcing of organic matter fluxes.". It also contains some model outputs and code to draw the figures.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.