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11,506 results for “Dynamics”
EOL Dynamic Hierarchy version 3.1 with higher classification
<p>The Encyclopedia of Life (EOL, eol.org) aggregates biodiversity information from more than 400 sources and provides access to the data through taxon pages, visual query and application programming interfaces. Scientific names are essential elements of the data integration infrastructure, but their shortcomings as key identifiers are well documented. Complex automated workflows and continuous manual curation are required to address idiosyncrasies of source taxonomies, variation in data quality, and conflicting taxonomic opinions. To achieve a harmonized taxonomic view of EOL content, names from data sources are mapped to a dynamic reference hierarchy (<a title="EOL Dynamic Hierarchy all versions" href="https://doi.org/10.5281/zenodo.13239662">see current version here</a>) using an algorithm that leverages canonical name strings, hierarchical information (ancestry, descendants), taxonomic ranks, synonym data, and author strings. Names that cannot be associated with a reference taxon are still accessible, but their unmapped status excludes them and any associated content from certain core EOL functions. For more information about the EOL taxonomy, see <a href="https://eol.org/docs/eol-dynamic-hierarchy">EOL Dynamic Hierarchy</a>.</p>
Wood Brook catchment: A coupled phenology – surface energy balance model to understand stream – subsurface temperature dynamics
<p>This folder contains data, model input files, model executable and source code required to reproduce results in the paper:"Evaluating a coupled phenology – surface energy balance model to understand stream – subsurface temperature dynamics in a mixed-use farmland catchment" by Han Qiu, Phillip Blaen, Sophie Comer-Warner, David M. Hannah, Stefan Krause and Mantha S. Phanikumar (Water Resources Research).</p> <p>The catchment (referred to herein as Wood Brook, Mill Brook, Mill Haft, BIFOR) is a mixed-use farmland catchment in central England. The "Data" folder contains information needed to create model input files. The "Figures" folder contains MS excel files with observed data (streamflows, groundwater heads, stream, streambed and groundwater temperatures etc) and simulation results to recreate the figures in the WRR paper. The other three folders contain model inputs, outputs and source code.</p>
Jensen_etal_2022_molecular_dynamics_simulation_data
<p>Full molecular dynamics simulation data set accompanying Jensen et al, 2022, containing (i) representative coordinates and measurements described therein, (ii) simulation trajectories, and (iii) GROMACS input files.</p>
Social-ecological cascade effects of land-use on vertebrate pest dynamics in arid agricultural communities
<p>Extensive land conversion to agriculture in drylands and associated resource use have wide-ranging impacts on desert ecosystems globally. Incorporating the impacts of human-social aspects is thus imperative in examining ecological interactions. The provision of agricultural inputs in these resource-scarce regions supports invasive and pest species, negatively impacting both agricultural productivity and native desert ecosystems. Understanding the spatial dynamics of invasive and pest species requires analyzing both bottom-up resource availability factors underlying animal distributions and top-down biological controls. Here, we evaluate the social-ecological cascading effects of dryland agriculture on vertebrate pest communities in dryland agricultural communities of Israel. Our study region is characterized by 18 agricultural cooperatives with distinct crop regimes due to contrasting social decision-making and resource allocation schemes (i.e., communal Kibbutzim vs. privatized Moshavim). Crop choices further affect land management (e.g., enclosed vs. open farm systems) and resource intensity. This system is ideal to study trophic mechanisms underlying animal assemblages between agricultural regimes. We examine the role of agricultural land-use practices on pest spatial distributions based on multi-year vertebrate pest observations with agricultural datasets. We use structural equation modelling (SEM) to quantify the relative importance of added agricultural resources underlying bottom-up and top-down trophic processes regulating vertebrate pest assemblages. Results reveal that crop choices determine pest distributions through bottom-up processes directly, while simultaneously driving pest competitive interactions through indirect top-down cascades impacting pest communities. For example, due to the indirect negative effect of wolves on meso-predators (foxes and jackals) mediated by livestock, the total positive effect of livestock on the abundance of meso-predators is reduced. Our study illustrates the social-ecological cascading effects of agricultural regimes on pest community assemblages mediated by contrasting agricultural land-use practices. Considering the expansion of dryland agro-ecological systems globally, understanding the intricate cascading pathways of predator- and prey-pest communities has important implications for agricultural management, biological invasions in drylands and fragile desert environments.</p>
Dynamic morphological plasticity in response to emergence timing in Abutilon theophrasti (Malvaceae)
<p>Selections on emergence time might be conflicting, suggesting the existence of the optimal emergence time for plants. However, we know little about this and how morphological plasticity contributes to the strategies of plants in response to emergence timing. To better understand this issue in a dynamic perspective, we conducted a field experiment by subjecting plants of <em>Abutilon theophrasti</em> to four emergence treatments (ET1~ET4) and measuring a number of mass and morphological traits on them at different growth stages (I~IV). At day 50, 70 and/or final harvest, among all ET treatments, plants germinated in late spring (ET2) performed the best in total mass, spring germinants (ET1) and ET2 performed better in stem allocation, stem and root diameters than later germinants (ET3 and ET4); summer germinants (ET3) had the highest reproductive mass and allocation, while late-summer germinants (ET4) had the greatest leaf mass allocation, with greater or canalized leaf number and root length traits than others. Plants that emerged in late spring can maximize their growth potential, while those with either advanced or delayed emergence are still capable of adaptation via allocation and morphological plasticity. Early germinants (ET1 and ET2) preferred stem growth to leaf and reproductive growth, due to sufficient time for reproduction in growth season. With limited time for growth, plants emerged late may prefer to quicken leaf growth (indicated by increased leaf mass allocation and leaf number) at the cost of stem or root growth for complete life cycle, reflecting both positive and negative effects of delayed emergence.</p>
Examining the use of Dynamic Data when undertaking Monolith to Microservice Architecture Migration
<p>A spreadsheet that shows the process of the Rapid Review protocol conducted in this MSc thesis.</p> <p> </p> <p>The IEEE search engine was used to retrieve quality, peer-reviewed papers. The search for primary studies in IEEE was restricted between 2015 and 2021 inclusive. The time frame commenced in 2015 as it was the year that microservice architecture started to gain traction in the industry and academia. Topics were identified such as; Monolith, Microservices, Migration and Dynamic Data. </p> <p>The selection procedure was based on the following criteria:</p> <ul> <li>The study must be in English.</li> <li>The study must be a primary study.</li> <li>The study must be in the context of migrating a monolith architecture to a microservice architecture using a dynamic data collection tool to gather dynamic data.</li> <li>The migration context of the study must be in Java as it is widely used when building enterprise software.</li> </ul> <p>The procedure was defined in 3 stages in which the set of criteria was applied. The first stage involved reading the title and keywords of the articles; the second stage involved reviewing the abstract of each article, and finally, the third stage involved a complete reading of each article.</p> <p> </p> <p> </p>
Code from: A theoretical framework for trait-based eco-evolutionary dynamics: population structure, intraspecific variation, and community assembly
<p>How is trait diversity in a community apportioned between and within co-evolving species? Disruptive selection may result in either a few species with large intraspecific trait variation (ITV) or many species with different mean traits but little ITV. Similar questions arise in spatially structured communities: heterogeneous environments could result in either a few species that exhibit local adaptation or many species with different mean traits but little local adaptation. To date, theory has been well-equipped to either include ITV or to dynamically determine the number of coexisting species, but not both. Here, we devise a theoretical framework that combines these facets, and apply it to the above questions of how trait variation is apportioned within and between species in unstructured and structured populations, using two simple models of Lotka-Volterra competition. For unstructured communities, we find that as the breadth of the resource spectrum increases, ITV goes from being unimportant to crucial for characterizing the community. For spatially structured communities on two patches, we find no local adaptation, symmetric local adaptation, or asymmetric local adaptation depending on how much the patches differ. Our framework provides a general approach to incorporate ITV in models of eco-evolutionary community assembly.</p>
Examining the use of Dynamic Data when undertaking Monolith to Microservice Architecture Migration
<p>A spreadsheet that shows the selected studies from conducting the Rapid Review protocol in this MSc thesis. The steps can be seen in this <a href="https://zenodo.org/record/7174010#.Y2ZXkuzP0UF">link</a>.</p>
Molecular dynamics simulations of the tripartite interface (Syt1_C2B—SNARE—Cpx Complex)
<p>Synaptic transmission is mediated by an orchestra of presynaptic proteins that precisely control and trigger fusion between synaptic vesicles and the neuron terminal at the active zone upon an action potential. Critical to this process are the neuronal SNAREs (Soluble N-ethylmaleimide sensitive factor Attachment protein REceptor), the Ca2+-sensor synaptotagmin, the activator/regulator complexin, and other factors. Here we present the data for molecular dynamics simulations of the tripartite interface bewteen these proteins. </p>
PROGRESS IN COUPLING COMPUTATIONAL THERMODYNAMICS AND COMPUTATIONAL FLUID DYNAMICS TO SUPPORT MOLTEN SALT REACTOR APPLICATIONS (Revised)
<p>This research was undertaken, in part, thanks to funding from the Canada Research Chairs program and the Discovery Grant Program of the Natural Sciences and Engineering Research Council of Canada. This study is in direct support of the SAMOSAFER project.</p> <p> </p>
Molecular Dynamics simulation
<p>Molecular Dynamics of a protein + POPC membrane system (Beta2-adrenergic receptor, PDB ID:5D5A).</p> <p>Equilibration time: 20 ns.</p> <p>Simulation time: 100 ns.</p> <p>Software: OpenMM: 7.7.0</p> <p>Forcefield:amber14, tip3p</p>
In situ tuning of dynamical Coulomb blockade in hybrid nanowire devices
<p>This repository contains the raw data and processing Python scripts corresponding to the paper "In situ tuning of dynamical Coulomb blockade in hybrid nanowire devices"</p>
Code and dataset for neural dynamics of causal inference in the macaque frontoparietal circuit
<p>Natural perception relies inherently on inferring causal structure in the environment. However, the neural mechanisms and functional circuits essential for representing and updating the hidden causal structure and corresponding sensory representations during multisensory processing are unknown. To address this, monkeys were trained to infer the probability of a potential common source from visual and proprioceptive signals based on their spatial disparity in a virtual reality system. The proprioceptive drift reported by monkeys demonstrated that they combined previous experience and current multisensory signals to estimate the hidden common source and subsequently updated the causal structure and sensory representation. Single-unit recordings in premotor and parietal cortices revealed that neural activity in the premotor cortex represents the core computation of causal inference, characterizing the estimation and update of the likelihood of integrating multiple sensory inputs at a trial-by-trial level. In response to signals from the premotor cortex, neural activity in the parietal cortex also represents the causal structure and further dynamically updates the sensory representation to maintain consistency with the causal inference structure. Thus, our results indicate how the premotor cortex integrates previous experience and sensory inputs to infer hidden variables and selectively updates sensory representations in the parietal cortex to support behavior. This dynamic loop of frontal-parietal interactions in the causal inference framework may provide the neural mechanism to answer long-standing questions regarding how neural circuits represent hidden structures for body awareness and agency.</p>
Population dynamics of little brown bats (Myotis lucifugus) at summer roosts: apparent survival, fidelity, abundance, and the influence of winter conditions
<ol> <li>White-nose syndrome (WNS) has caused the death of millions of bats, but the impacts have been more difficult to identify in western North America. Understanding how WNS, or other threats, impact western bats may require monitoring other roosts, such as maternity roosts and night roosts, where bats aggregate in large numbers.</li> <li>Little brown bats (<em>Myotis lucifugus</em>) are experiencing some of the greatest declines from WNS. Estimating survival and understanding population dynamics can provide valuable data for assessing population declines and informing conservation efforts.</li> <li>We conducted a 5-year mark-recapture study of two <em>M. lucifugus</em> roosts in Colorado. We used the robust design model to estimate apparent survival, fidelity, and abundance to understand population dynamics, and environmental covariates to understand how summer and winter weather conditions impact adult female survival. We compared the fidelity and capture probability of <em>M. lucifugus</em> between colonies to understand how bats use such roosts.</li> <li>Overwinter survival increased with the number of days with temperatures below freezing (β > 0.100, SE = 0.003), and decreased with the number of days with snow cover (β < -0.40, SE < 0.13). Adult female fidelity was higher at one maternity roost than the other. Overwinter and oversummer adult female survival were high (>0.90), and based on survival estimates and fungal-swabbing results we believe these populations have yet to experience WNS.</li> <li>Recapture of <em>M. lucifugus</em> using antennas that continuously read passive integrated transponder tags allows rigorous estimation of bat population parameters that can elucidate trends in abundance and changes in survival. Monitoring populations at summer roosts can provide unique population ecology data that monitoring hibernacula alone may not. Because few adult males are captured at maternity colonies, and juvenile males have low fidelity, additional effort should focus on understanding male <em>M. lucifugus </em>population dynamics.</li> </ol>
The supplementary (hourly output data & computational performance log) for OMARE of the Ocean Dynamics manuscript
<p>The supplementary (hourly output data & computational performance log) for OMARE of the Ocean Dynamics manuscript with the title: Computational performance and scalability Analysis for the flexible ocean Modeling framework of OMARE (Ocean Modeling with Adaptive REsolution).</p> <p>amr_wbc.tar.gz: The hourly output data of core prognostics (u, v, ssh, ts) of experiments X-AMR, X, S for OMARE in TianHe platform, including the picture results (png format).</p> <p>Computational_Performance.zip: The computational performance logs of the M, S, X, L-M-50, M-S-30, M-S-100, S-X-10, for OMARE in ThianHe and IntelCluster platform. The computational performance logs of X-AMR and I/O in TianHe platform.</p>
Diversification dynamics in the Neotropics through time, clades and biogeographic regions
<p><span>The origins and evolution of the outstanding Neotropical biodiversity are a matter of intense debate. A comprehensive understanding is hindered by the lack of deep-time comparative data across wide phylogenetic and ecological contexts. Here, we quantify the prevailing diversification trajectories and drivers of Neotropical diversification in a sample of 150 phylogenies (12,512 species) of seed plants and tetrapods and assess their variation across Neotropical regions and taxa. Analyses indicate that Neotropical diversity has mostly expanded through time (70% of the clades), while scenarios of saturated and declining diversity account for 21% and 9% of Neotropical diversity, respectively. </span><span>Five biogeographic areas are identified as distinctive units of long-term Neotropical evolution, including Pan-Amazonia, the </span><span>Dry Diagonal,</span><span> </span><span>and Bahama-Antilles. D</span><span>iversification dynamics do not differ across these areas, suggesting no geographic structure in long-term Neotropical diversification. In contrast, diversification dynamics differ across taxa: plant diversity mostly expanded through time (88%), while a substantial fraction (43%) of tetrapod diversity accumulated at a slower pace or declined toward the present. These opposite evolutionary patterns may reflect different capacities for plants and tetrapods to cope with past climate changes</span></p>
A framework for 210Pb model selection and its application to 37 cores from Eastern Canada to identify the dynamics and drivers of lake sedimentation rates
<ul> <li>Radioisotopic and ancillary data (i.e., estimated temperature, precipitation and population in lake watersheds)</li> <li>R-code script used in the establishment of 210Pb framework along with example spreadsheet</li> </ul> <p>Original publication: Baud, A., Aulard, C., Ghanbari, H., Fradette, M., Antoniades, D., Del Giorgio, P., Huot, Y., Francus, P., Smol, J. & Gregory‐Eaves, I. (2022). A framework for 210Pb model selection and its application to 37 cores from Eastern Canada to identify the dynamics and drivers of lake sedimentation rates. Earth Surface Processes and Landforms. https:</p>
Supplementary FIles for Cholesterol Biases the Conformational Landscape of the Chemokine Receptor CCR3: A MAS SSNMR-Filtered Molecular Dynamics Study
<p>This repository contains supplementary files for the initial submission of:</p> <p>Cholesterol Biases the Conformational Landscape of the Chemokine Receptor CCR3: A MAS SSNMR-Filtered Molecular Dynamics Study<br> Evan J. van Aalst, Corey J. McDonald, and Benjamin J. Wylie</p> <p>Files found in this repository include:<br> 1. Raw fids corresponding to the solid-state NMR spectra used in this work.<br> 2. The script, model structures, and predicted chemical shifts used in the COMPASS proof of concept.<br> 3. Input molecular dynamics files derived from CHARMM-GUI including all mdp files, initial model structure files, and the production script.<br> 4. Model structures per ns derived from MD trajectories with corresponding predicted chemical shift lists and associated experimental chemical shift lists.</p>
Effects of habitat types on the dynamic changes of allocation in carbon and nitrogen storage of vegetation-soil system in sandy grasslands
<p>The progressive restoration of degraded vegetation in semiarid and arid desertified areas undoubtedly formed different habitat types. The most plants regulate their growth by fixing carbon with their energy deriving from photosynthesis, carbon (C) and nitrogen (N) play the crucial role in regulating plant growth, community structure and function in the vegetation restoration progress. However, it is still unclear how habitat types affect the dynamic changes of allocation in C and N storage of vegetation-soil system in sandy grasslands. Here, we investigated plant community characteristics and soil properties across three successional stages of habitat types: semi-fixed dunes (SFD), fixed dunes (FD) and grasslands (G) in 2011, 2013 and 2015. We also examined the C and N concentrations of vegetation-soil system, and estimated their C and N storage. The C and N storage of vegetation system, soil and vegetation-soil system remarkably increased from SFD to G. The litter C and N storage in SFD, N storage of vegetation system in SFD and N storage of soil and vegetation-soil system in FD increased from 2011 to 2015, while aboveground plant C and N storage of FD were higher in 2011 than in 2013 and 2015. Most of C and N were sequestered in soil in the vegetation restoration progress. These results suggest that the dynamic changes of allocation in C and N storage in vegetation-soil systems varied with habitat types. Our study highlights that SFD has higher N sequestration rate in vegetation, while FD has the considerably N sequestration rate in the soil.</p>
The dynamics of social cohesion in response to simulated intergroup conflict in banded mongooses
<p>Intergroup conflict is widespread in nature and is proposed to have strong impacts on the evolution of social behaviour. The conflict-cohesion hypothesis predicts that exposure to intergroup conflict should lead to increased social cohesion to improve group success or resilience in future conflicts. There is evidence to support this prediction from studies of affiliative responses to outgroup threats in some animal societies. However, most of these studies have focused on behavioural changes over short time periods (minutes and hours after exposure to an outgroup), and hence very little is known about the dynamics and durability of responses to intergroup conflict over the longer term. We investigated this question by simulating intergroup encounters in wild banded mongooses (Mungos mungo) and measuring social behaviour before, during, and after these encounters over a five day period. We also ran control trials with non-threatening stimuli. Banded mongooses reacted immediately to intrusion stimuli by vocalising, grouping together and advancing on the stimulus. In the first five minutes after simulated intrusions, we saw an elevation in grooming levels, but in the hour after exposure grooming rates declined sharply, contrary to our expectation. In the two subsequent days grooming rates remained at this depressed rate. In control trials, the initial increase in grooming was not seen, but grooming declined compared in the longer term time periods. Grooming changed across time, but not in the same pattern as during intrusions, suggesting that intrusions had an impact above and beyond that of the experimental set-up. The dynamics of grooming responses were short-lived and more complex than we initially expected. We suggest this unexpected result may be linked to the frequency of aggressive intergroup encounters in this system. Our results indicate short-lived impacts of outgroup threat on measures of social cohesion in this species, but cannot confirm longer term changes.</p>
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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.