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163 results for “dynamical evolution”
Statistical and Dynamic Model of Surface Morphology Evolution during Polishing in Additive Manufacturing
<p>This repository maintains data and code associated with our accepted paper in IISE Transactions titled "Statistical and Dynamical model of Surface Morphology Evolution during Polishing in Additive Manufacturing". To briefly summarize,</p> <p><strong>1. Polishing_stagewise_data.zip</strong> - Contains height values measured at 32 different locations on the 3D printed sample using an optical profilometer prior to polishing (Stage 0) and post every stage of polishing (Stages 1 to 6). Please refer to the following paper for experimentation details and process parameters: "<em>Jin, S., A. Iquebal, S. Bukkapatnam, A. Gaynor, and Y. Ding (2019, 10). A gaussian process model-guided surface polishing process in additive manufacturing. Journal of Manufacturing Science and Engineering 142, 1–17.</em>"</p> <p><strong>2. Initial_surface_generation.m</strong> - Script containing the Initial surface generation algorithm using the random circle packing algorithm. This file generates the surface asperity distribution and their graph connectivity of a 3D printed sample prior to polishing (Figure 4(b) in paper). One such realization is stored and compared with experimental data (Refer #3).</p> <p><strong>3. Stage0_fitted_data.mat</strong> - .mat file containing data pertaining to height measures of the 3D printed sample prior to polishing and generated initial surface (simulation) which is statistically similar to the actual data.</p> <p><strong>4. Parameter_fitting_Polishing.m</strong> - Script containing the model capturing polishing dynamics with network formation, evaluated at each stage of polishing. This file generates the Bearing Area Curves of the initial surface simulated after each stage of polishing and compares with experimental data (Figures 3, 5, 6, 7 and 8 in paper). (The script makes use of other functions defined in #5).</p> <p><strong>5. surface_roughness.m, graph_evolution.m, solve_for_d.m, KLDiv.m</strong> and <strong>Gen_hurst.m</strong> - Matlab scripts containing functions that are called within the main script (Parameter_fitting_Polishing.m)</p> <p><strong>6. Simulated_Annealing.zip</strong> - Zip file containing files related to Simulated Annealing Algorithm. Please read the <strong>README_Simulated_Annealing.txt</strong> for instructions to reproduce the optimized parameter solutions.</p> <p><strong>7. pub_fig.m</strong> - Script containing the formatting options for plots and figures.</p>
Data from: The sequential direct and indirect effects of mountain uplift, climatic niche and floral trait evolution on diversification dynamics in an Andean plant clade
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The evolution, complexity and diversity of models of long-term forest dynamics
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The evolution of dynamic and flexible courtship displays that reveal individual quality
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Eco‐evolutionary dynamics driven by fishing: from single species models to dynamic evolution within complex food webs
<p>Evidence of contemporary evolution across ecological time scales stimulated research on the eco-evolutionary dynamics of natural populations. Aquatic systems provide a good setting to study eco-evolutionary dynamics owing to a wealth of long-term monitoring data and the detected trends in fish life-history traits across intensively harvested marine and freshwater systems. In the present study, we focus on modelling approaches to simulate eco-evolutionary dynamics of fishes and their ecosystems. Firstly, we review the development of modelling from single-species to multispecies approaches. Secondly, we advance the current state-of-the-art methodology by implementing evolution of life-history traits of a top predator into the context of complex food web dynamics as described by the allometric trophic network (ATN) framework. The functioning of our newly developed eco-evolutionary ATNE framework is illustrated using a well-studied lake food web. Our simulations show how both natural selection arising from feeding interactions and size-selective fishing cause evolutionary changes in the top predator and how those feed back to its prey species and further cascade down to lower trophic levels. Finally, we discuss future directions, particularly the need to integrate genomic discoveries into eco-evolutionary projections.</p>
Trophic cascades alter eco-evolutionary dynamics and body size evolution
<p><span class="MsoIntenseEmphasis"><span>Trait evolution in predator-prey systems can feed back to the dynamics of interacting species as well as cascade to impact the dynamics of indirectly linked species (eco-evolutionary trophic cascades; EETC). A key mediator of trophic cascades is body mass, as it both strongly influences and evolves in response to predator-prey interactions. Here we use Gillespie Eco-Evolutionary Models to explore EETCs resulting from top predator loss and mediated by body mass evolution. Our four trophic level food chain model uses allometric scaling to link body mass to different functions (ecological pleiotropy) and is realistically parameterized from the FORAGE database to mimic the parameter space of a typical freshwater system. To track real-time changes in selective pressures, we also calculated fitness gradients for each trophic level. As predicted, top predator loss generated alternating shifts in abundance across trophic levels, and depending on the nature and strength in changes to fitness gradients, also altered trajectories of body mass evolution. Although more distantly linked, changes in the abundance of top predators still affected the eco-evolutionary dynamics of the basal producers, in part because of their relatively short generation times. Overall, our results suggest that impacts on top predators can set off transient eco-evolutionary trophic cascades with the potential for widespread indirect impacts on food webs.</span></span></p>
An ulvophycean marine green alga produces large parthenogenetic isogametes as predicted by the gamete dynamics model for the evolution of anisogamy
<p>In eukaryotes, the gamete size difference between the two sexes (anisogamy) evolved from gametes of equal size in both mating types (isogamy) and is plausibly claimed to generate sexual selection in morphology and behaviour. The gamete dynamics (GD) model for anisogamy evolution combines gamete limitation and competition and predicts that, if gametes of both mating types can develop parthenogenetically (i.e. without fusing with the opposite mating type), large isogamy can evolve under gamete-limited conditions. Ulvophycean marine green algae that exhibit various gametic systems from isogamy to anisogamy are important models for testing such theories. However, in most previous papers, whether a species is isogamous or anisogamous has not been examined statistically, which leaves the above theoretical prediction untested. We reveal (i) that the gametic system of <em>Struvea okamurae</em> is large isogamy using a generalized linear mixed model (GLMM), which accounted for the variation of gamete size among individual gametophytes, and (ii) that gametes of this alga can actually develop parthenogenetically, contrary to a previous report. Habitat environments and gametic behaviour suggest that this alga might experience gamete-limited conditions. <em>S. okamurae</em> seems to produce large parthenogenetic isogametes following GD model predictions, as an adaptation to deep waters.</p>
Dynamical ising dataset for the paper Machine learning stochastic differential equations for the evolution of order parameters of classical many-body systems in and out of equilibrium
<p>This dataset provide the evolution in time for the magnetizaion in the 2D Ising model evolved with Gluber dynamics for a lattice of size 64 x 64.</p>
Data from "Bending the course of evolution: how mutualistic interactions affect macroevolutionary dynamics of diversification in mimetic Ithomiini butterflies"
<p>Data and codes for the analyses from Chazot et al. "Bending the course of evolution: how mutualistic interactions affect macroevolutionary dynamics of diversification in mimetic Ithomiini butterflies". Check README for more information about the files. </p>
Data from "Allostery and evolution: a molecular journey throught the structural and dynamical landscape of an enzyme super family."
<p>This data accompanies the paper entitled Allostery and evolution: a molecular journey throught the structural and dynamical landscape of an enzyme super family.</p> <p>The zip archive contains: </p> <p>1- Starting configurations of the proteins after equilibration in PDB format and trajectories of unrestrained molecular dynamics simulations with the positions of the proteins every 100 ps in XTC gromacs format are provided for all systems. </p> <p>2- The free energy profiles and histograms are provided for all umbrella sampling simulations and the scripts used to run it with gromacs.</p>
Correlation-based Analysis of the Influence of Bound Constraint Handling Methods on Population Dynamics in Differential Evolution
<p>The dataset is based on the average values collected over 5 independent runs, considering the largest common number of<br>iterations for LSHADE algorithm coupled with ’sat’, ’midT’, ’midB’, ’unif’, ’beta’, ’mir’, ’tor’, ’expC_R’, ’expC_T’, ’expC_B’, ’vectR’, ’vectT’, ’vectB’, ’mahalanobis’ correction methods, on BBOB function f3, 4, 5, 16, 23, instance 1</p> <p>Plots for the averaged values are included for measures 'pop_size', 'best', 'error', 'prob_infeas', 'genMutatedComponent', 'genSuccessMutants','meanImprovements', 'varPop', 'avgF', 'avgCR', 'extension', 'shape', 'eccentricity', 'kl_unif'</p>
Data and Code for "Comparing the Effects of Euclidean Distance Matching and Dynamic Time Warping in the Clustering of COVID-19 Evolution"
<p>This repository contains the datasets and data sources, analysis code, and workflow associated with the manuscript "<em>Comparing the Effects of Euclidean Distance Matching and Dynamic Time Warping in the Clustering of COVID-19 Evolution</em>". The following resources are provided:</p> <ul> <li> <p><strong>Data Files</strong>:</p> <ul> <li><code>time_series_data.csv</code>: A curated time series dataset with dates as rows and NUTS 2 regions as columns. Each column is labeled using a 4-letter abbreviation format "CC.RR", where "CC" represents the country code and "RR" represents the region code. This same abbreviation is also included in the accompanying GeoJSON file.</li> <li><code>geometry_data.geojson</code>: A GeoJSON file representing the spatial boundaries of the NUTS 2 regions, with the same 4-letter abbreviations used in the CSV file. EPSG:4326.</li> <li><code>COVID19_data_sources.xlsx</code>: This Excel file contains important metadata regarding the sources of COVID-19 data used in this study. It includes: <ul> <li>Source of the data for each country</li> <li>Official website(s)</li> <li>The agency responsible for the data</li> <li>Description of the processing steps used to curate the data into the final time series.</li> </ul> </li> </ul> </li> <li> <p><strong>Code</strong>:</p> <ul> <li><code>analysis.py</code>: A Python script used to process and analyze the data. This code can be run using Python 3.x. The libraries required to run this script are listed in the first lines of the code. The code is organized in different numbered sections (1), (2), ... and sub-sections (1a), (1b) ... Make sure to run the script one (sub-)section at a time, so that everything stays overviewable and you don't get all the output at once.</li> </ul> </li> <li> <p><strong>Workflow</strong>:</p> <ul> <li><code>workflow.png</code> : A detailed workflow according to the Knowledge Discovery in Databases (KDD) process, outlining the steps involved in processing and analyzing the data, including the methods used. This workflow provides a comprehensive guide to reproducing the analysis presented in the paper.</li> </ul> </li> </ul>
Data from: Complex dynamics underlie the evolution of imperfect wing pattern convergence in butterflies
Adaptive radiation is characterized by rapid diversification that is strongly associated with ecological specialization. However, understanding the evolutionary mechanisms fueling adaptive diversification requires a detailed knowledge of how natural selection acts at multiple life-history stages. Butterflies within the genus Adelpha represent one of the largest and most diverse butterfly lineages in the Neotropics. Although Adelpha species feed on an extraordinary diversity of larval hosts, convergent evolution is widespread in this group suggesting that selection for mimicry may contribute to adaptive divergence among species. To investigate this hypothesis, we conducted predation studies in Costa Rica using artificial butterfly facsimiles. Specifically, we predicted that non-toxic, palatable Adelpha species that do not feed on host plants in the family Rubiaceae would benefit from sharing a locally convergent wing pattern with the presumably toxic Rubiaceae-feeding species via reduced predation. Contrary to expectations, we found that the presumed mimic was attacked significantly more than its locally convergent model, at a frequency paralleling attack rates on both novel and palatable prey. Although these data reveal the first evidence for protection from avian predators by the supposed toxic, Rubiaceae-feeding Adelpha species, we conclude that imprecise mimetic patterns have high costs for Batesian mimics in the tropics.
Supporting data for: Evolutionary drivers, morphological evolution and diversity dynamics of a surviving mammal clade: cainotherioids at the Eocene-Oligocene transition
<p><span><span><span><span><span><span><span><span><span><span><span>The Eocene-Oligocene transition (EOT) represents a period of global environmental changes particularly marked in Europe and coincides with a dramatic biotic turnover. Here, using an exceptional fossil preservation, we document and analyse the diversity dynamics of a mammal clade, Cainotherioidea (Artiodactyla), that survived the EOT and radiated rapidly immediately after. We infer their diversification history from Quercy Konzentrat-Lagerstätte (South-West France) at the species level using Bayesian birth-death models. We show that cainotherioid diversity fluctuated through time, with extinction events at the EOT and in the late Oligocene, and a major speciation burst in the early Oligocene. The latter is in line with our finding that cainotherioids had a high morphological adaptability following environmental changes throughout the EOT, which likely played a key role in the survival and evolutionary success of this clade in the aftermath. Speciation is positively associated with temperature and continental fragmentation in a time-continuous way, while extinction seems to synchronize with environmental change in a punctuated way. Within-clade interactions negatively affected the cainotherioid diversification, while inter-clade competition might explain their final decline during the late Oligocene. Our results provide a detailed dynamic picture of the evolutionary history of a mammal clade in a context of global change.</span></span></span></span></span></span></span></span></span></span></span></p>
Dynamic Evolution of Changbaishan Volcanism in Northeast China Illuminated by Machine Learning
<p><strong>This dataset is for our work entitled "<em>Dynamic Evolution of Changbaishan Volcanism in Northeast China Illuminated by Machine Learning</em>".</strong></p> <p><strong>This dataset includes: 1) The Cenozoic basalts in Changbaishan area used for predicting, 2) The IAB (Island Arc Basalts) and OIB (Ocean Island Basalts) samples used for training machine learning models.</strong></p>
Allele-specific collateral and fitness effects determine the dynamics of fluoroquinolone-resistance evolution
<p>Collateral sensitivity (CS), which arises when resistance to one antibiotic increases sensitivity towards other antibiotics, offers novel treatment opportunities to constrain or reverse the evolution of antibiotic resistance. The applicability of CS-informed treatments remains uncertain, in part because we lack an understanding of the generality of CS effects for different resistance mutations, singly or in combination. Here we address this issue in the Gram-positive pathogen <em>Streptococcus</em> <em>pneumoniae</em> by measuring collateral and fitness effects of clinically relevant <em>gyrA</em> and <em>parC</em> alleles, and their combinations, that confer resistance to fluoroquinolones. We integrated these results in a mathematical model which allowed us to evaluate how different <em>in</em> <em>silico</em> combination treatments impact the dynamics of resistance evolution. We identified common and conserved CS effects of different <em>gyrA</em> and <em>parC</em> alleles; however, the spectrum of collateral effects was unique for each allele or allelic pair. This indicated that allelic identity can impact the evolutionary dynamics of resistance evolution during monotreatment and combination treatment. Our model simulations, which included the experimentally derived antibiotic susceptibilities and fitness effects, and antibiotic-specific pharmacodynamics, revealed that both collateral and fitness effects impact the population dynamics of resistance evolution. Overall, we provide evidence that allelic identity and interactions can have a pronounced impact on collateral effects of different antibiotics and suggest that these need to be considered in models examining CS-based therapies.</p>
Dynamic evolution of locomotor performance independent of changes in extended phenotype use in spiders
<p>Many animals utilise self-built structures (extended phenotypes) to enhance body functions, such as thermoregulation, prey capture or defence. Yet, it is unclear whether the evolution of animal constructions supplements or substitutes body functions – with disparate feedbacks on trait evolution. Here, using brown spiders (Araneae: marronoid clade), we explored if the evolutionary loss and gain of silken webs as extended prey capture devices correlates with alterations in traits known to play an important role in predatory strikes – locomotor performance (sprint speed) and leg spination (expression of capture spines on front legs). We found that in this group high locomotor performance, with running speeds of over 100 body lengths per second, evolved repeatedly – both in web building and cursorial spiders. There was no correlation with running speed, and leg spination was only poorly correlated, relative to the use of extended phenotypes, indicating that web use does not reduce selective pressures on body functions involved in prey capture and defence per se. Consequently, extended prey capture devices serve as supplements rather than substitutions to body traits and may only be beneficial in conjunction with certain life history traits, explaining the rare evolution and repeated loss of trapping strategies in predatory animals.</p>
Dynamic Evolution of Pulmonary Nodules and Influence Factors of Its Clinical Decision-making
ClinicalTrials.gov study NCT04857333. IPD Sharing: NO. Countries: 1. Publications: 2.
Dynamic evolution of locomotor performance independent of changes in extended phenotype use in spiders
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Supporting data for: Evolutionary drivers, morphological evolution and diversity dynamics of a surviving mammal clade: cainotherioids at the Eocene-Oligocene transition
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Allen Brain Atlas
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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.