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491 results for “Population of models”
Fig. 3 in Using a spatial mark-resight model to estimate the parameters of a wild pig (Sus scrofa) population in Singapore
Fig. 3. Map of the Central Catchment Nature Reserve showing the day and night fixes of the collared pig. The home ranges are calculated from the monthly 95% Kernel Density Estimate (KDE), while the aggregate home range was calculated from the 99% KDE from all six months. The Seletar Expressway (SLE) is pointed out on the map and the satellite overlay was adapted from Google Earth.
Fig. 2 in Using a spatial mark-resight model to estimate the parameters of a wild pig (Sus scrofa) population in Singapore
Fig. 2. The density map showing the number of activity centres per kilometer square, the locations of the camera points (circles), 143 out of 856 GPS locations from the collared pig (black dots) and the boundary of the Central Catchment Nature Reserve. Only a fraction of the GPS locations was plotted to prevent the colored pixels from being obscured. Each pixel is 1 km2. X and Y coordinates are in kilometers.
Data from: Dinosaurian survivorship schedules revisited: new insights from an age-structured population model
<p>Little is known on dinosaur population biology due to insufficient information on age-dependent fecundities and mortalities. So far, survivorship curves (hereafter SC) of only six dinosaurs (four tyrannosaurs, one ceratopsian, one hadrosaur) were erected from bone assemblages of aged specimens. They indicate high survival throughout most of their life with presumable higher mortalities after hatching and increasing mortalities towards its end. However, all studies ignored that assemblages must preserve stationary age distributions (i.e., the population's age distribution is stable and its size is constant over time as overall population fecundities match mortalities, hereafter SAD population) to infer a reliable SC for a taxon.</p> <p>To assess SCs of these dinosaurs, I built a simple population model with age-dependent fecundities and survival rates. Its few input parameters are maximum longevity, age at sexual maturation and maximum annual offspring number, on which information exists in these dinosaurs. As bone histological studies and scaling relationships provide estimates on its three parameters, my model is also applicable to other extinct taxa.</p> <p> Modelling suggests that bone assemblages did not preserve SAD populations. SCs determined for SAD populations of <i>Albertosaurus sarcophagus</i>,<i> Gorgosaurus libratus</i>, <i>Dasplatosaurus torosus</i> and <i>Tyrannosaurus rex</i> indicated that low mortalities follow high mortalities early in their life or that mortalities were rather constant throughout their life. In <i>Psittacosaurus lujiatuensis</i> modelling suggests low mortalities throughout most of its life that increase towards its end. The SC of <i>Maiasaura peeblesorum</i> was not questioned by my model as it is unable to capture sigmoidal or other composite SCs.</p>
Populations of local direction-selective cells encode global motion patterns generated by self-motion. Data, Code and Model.
<p>Directional tuning of the population of local motion detectors T4/T5 in the visual system of the fruit fly <em>Drosophila melanogaster</em>. Direction tuning and receptive field location was measured by recording responses to visual stimuli containing dark or bright edges/stripes moving into 8 directions. All provided MATLAB scripts were used to analyze and illustrate data show in the manuscript 'Populations of local direction-selective cells encode global motion patterns generated by self-motion.'</p> <p>All data were obtained using <em>in vivo </em>two photon microscopy. Image time series were preprocessed using SIMA python software for motion alignment and further processed using custom written matlab or python code.</p> <p>Please find all relevant information to use the code in the README file.</p>
single-cell RNAseq data (data set 1) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data
<p>The present dataset (dataset1) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from CRC samples downloaded from the GEO website (<strong>GSE81861). </strong></p> <p>see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data</p> <p>and github: https://github.com/sysbiolux/scFASTCORMICS</p> <p>For more information, version updates of the scFASTCORMICS. </p>
Evaluating the role of the nuclear microenvironment in gene function by population-based modeling
<p>This repository accompanies the manuscript "<strong>Evaluating the role of the nuclear microenvironment in gene function by population-based modeling</strong>", available in <em>Nature Structural & Molecular Biology</em>.</p> <p>It contains the files for the population of 3D structures for GM12878 in 200-kb resolution generated using IGM (https://github.com/alberlab/igm) and the derived structural features. Please see README.txt for more information.</p> <p>For any inquiries please reach out to Dr. Frank Alber (falber@g.ucla.edu).</p>
Whole genome demographic models indicate divergent effective population size histories shape contemporary genetic diversity gradients in a montane bumble bee
<p>Understanding historical range shifts and population size variation provides important context for interpreting contemporary genetic diversity. Methods to predict changes in species distributions and model changes in effective population size (N<sub>e</sub>) using whole genomes make it feasible to examine how temporal dynamics influence diversity across populations. We investigate N<sub>e</sub> variation and climate-associated range shifts to examine the origins of a previously observed latitudinal heterozygosity gradient in the bumble bee <em>Bombus</em> <em>vancouverensis</em> Cresson (Hymenoptera: Apidae: <em>Bombus</em> Latreille) in western North America. We analyze whole genomes from a latitude-elevation cline using sequentially Markovian coalescent models of N<sub>e</sub> through time to test whether relatively low diversity in southern high-elevation populations is a result of long-term differences in N<sub>e</sub>. We use Maxent models of the species range over the last 130,000 years to evaluate range shifts and stability. N<sub>e</sub> fluctuates with climate across populations, but more genetically diverse northern populations have maintained greater Ne over the late Pleistocene and experienced larger expansions with climatically favorable time periods. Northern populations also experienced larger bottlenecks during the last glacial period which matched the loss of range area near these sites, however, bottlenecks were not sufficient to erode diversity maintained during periods of large N<sub>e</sub>. A genome sampled from an island population indicated a severe postglacial bottleneck, indicating that large recent post-glacial declines are detectable if they have occurred. Genetic diversity was not related to niche stability or glacial-period bottleneck size. Instead, spatial expansions and increased connectivity during favorable climates likely maintain diversity in the north while restriction to high elevations maintains relatively low diversity despite greater stability in southern regions. Results suggest genetic diversity gradients reflect long-term differences in N<sub>e</sub> dynamics and also emphasize the unique effects of isolation on insular habitats for bumble bees. Patterns are discussed in the context of conservation under climate change.</p>
Celluloepidemiology: a novel paradigm for quantifying infectious disease dynamics through T-cell modelling on a population level
<p>T-cell receptor sequencing (TCR-seq) was performed on enriched CD8+ T-cells. TCR clonotype annotation was performed using MiXCR v.3.0.13 with the default input parameters.</p> <p>Full origin and method description available in:<br>Celluloepidemiology: a novel paradigm for quantifying infectious disease dynamics through T-cell modelling on a population level</p>
Data from: Evaluating the importance of individual heterogeneity in reproduction to Weddell seal population dynamics using integral projection models
<ol> <li>Identifying and accounting for unobserved individual heterogeneity in vital rates in demographic models is important for estimating population-level vital rates and identifying diverse life-history strategies, but much less is known about how this individual heterogeneity influences population dynamics.</li> <li>We aimed to understand how the distribution of individual heterogeneity in reproductive and survival rates influenced population dynamics using vital rates from a Weddell seal population by altering the distribution of individual heterogeneity in reproduction, which also altered the distribution of individual survival rates through the incorporation of our estimate of the correlation between the two rates and assessing resulting changes in population growth.</li> <li>We constructed an integral projection model (IPM) structured by age and reproductive state using estimates of vital rates for a long-lived mammal that has recently been shown to exhibit large individual heterogeneity in reproduction. Using output from the IPM, we evaluated how population dynamics changed with different underlying distributions of unobserved individual heterogeneity in reproduction.</li> <li>Results indicate that the changes to the underlying distribution of individual heterogeneity in reproduction cause very small changes in the population growth rate and other population metrics. The largest difference in the estimated population growth rate resulting from changes to the underlying distribution of individual heterogeneity was less than 1%.</li> <li>Our work highlights the differing importance of individual heterogeneity at the population level compared to the individual level. Although individual heterogeneity in reproduction may result in large differences in the lifetime fitness of individuals, changing the proportion of above- or below-average breeders in the population results in much smaller differences in annual population growth rate. For a long-lived mammal with stable and high adult-survival that gives birth to a single offspring, individual heterogeneity in reproduction has a limited effect on population dynamics. We posit that the limited effect of individual heterogeneity on population dynamics may be due to canalization of life-history traits.</li> </ol>
National forest inventory data for a size-structured forest population model
<p>In forest communities, light competition is a key process for community assembly. Species' differences in seedling and sapling tolerance to shade cast by overstory trees is thought to determine species composition at late-successional stages. Most forests are distant from these late-successional equilibria, impeding a formal evaluation of their potential species composition. To extrapolate competitive equilibria from short-term data, we therefore introduce the JAB model, a parsimonious dynamic model with interacting size-structured populations, which focuses on sapling demography including the tolerance to overstory competition. We apply the JAB model to a two-"species" system from temperate European forests, i.e. the shade-tolerant species Fagus sylvatica L. and the group of all other competing species. Using Bayesian calibration with prior information from external Slovakian national forest inventory (NFI) data, we fit the JAB model to short timeseries from the German NFI. We use the posterior estimates of demographic rates to extrapolate that F. sylvatica will be the predominant species in 94% of the competitive equilibria, despite only predominating in 24% of the initial states. We further simulate counterfactual equilibria with parameters switched between species to assess the role of different demographic processes for competitive equilibria. These simulations confirm the hypothesis that the higher shade-tolerance of F. sylvatica saplings is key for its long-term predominance. Our results highlight the importance of demographic differences in early life stages for tree species assembly in forest communities.</p>
Data for: Coupling dynamic energy budget and population dynamic models to inform stock enhancement in fisheries management
<p><span>Extensive applications of fishery stock enhancement worldwide bring up broad concerns about its negative effects, creating a pivotal need for science-based assessment and planning of enhancement strategies. However, the lack of mechanistic understanding of enhanced population dynamics, particularly the density-dependent processes, leads to compromise in model development and limits the capacity in predicting enhancement effects. Here, we developed an individual-based model based on dynamic energy budget theory and full life history processes, to understand the mechanism of density dependence in population dynamics that emerge from individual-level processes. We demonstrated the utility of the model framework by applying it </span><span>to an extensively enhanced species, Chinese prawn (<em>Fenneropenaeus chinensis</em></span><span>, Penaeidae</span><span>). The model could yield projections reflecting the observed trajectory of population biomass and yields. The model also delineated the key effects of density dependence on the vital rates of growth, fecundity, and starvation mortality. Regarding the manifold effects of stock enhancement, we demonstrated a dampened shape in population biomass and yields with increasing magnitude of enhancement, and trade-offs between the ecological and economic objectives, i.e., pursuing high benefit might compromise the wild population without proper management. Furthermore, we illustrated the possibility of combining stock enhancement and harvest regulation in promoting population recovery while maintaining fisheries yields. We highlight the potential of the proposed model for understanding density dependence in enhancement program, and for designing integrated management strategies. The approach developed herein may serve as a general approach to assess the population dynamics in stock enhancement and inform enhancement management.</span><span> </span></p>
Data for 'Population density affects sexual selection in an insect model'
<p>Data set (.csv file), analysis code (.R file) and readme (.txt file giving details for dataset and code) accompanying the publication 'Population density affects sexual selection in an insect model' (Winkler L, Eilhardt R, Janicke T, 2023).</p>
Data from: Partitioning variance in population growth for models with environmental and demographic stochasticity
<ol> <li>How demographic factors lead to variation or change in growth rates can be investigated using life table response experiments (LTRE) based on structured population models. Traditionally, LTREs focused on decomposing the asymptotic growth rate, but more recently decompositions of annual 'realized' growth rates have gained in popularity.</li> <li>Realized LTREs have been used particularly to understand how variation in vital rates translates into variation in growth for populations under long-term study. For these, complete population models may be constructed by combining data in an integrated population model (IPM). IPMs are also used to investigate how temporal variation in environmental drivers affect vital rates. Such investigations have usually come down to estimating covariate coefficients for the effects of environmental variables on vital rates, but formal ways of assessing how they lead to variation in growth rates have been lacking. </li> <li>We extend realized LTREs in two ways. First, we further partition the contributions from vital rates into contributions from temporally varying factors that affect them. The decomposition allows us to compare the resultant effect on the growth rate of different environmental factors that may each act via multiple vital rates. Second, we show how realized growth rates can be decomposed into separate components from environmental and demographic stochasticity. The latter is typically omitted in LTRE analyses.</li> <li>We illustrate how to use the approach in an IPM for data from a 26-year study on northern wheatears (Oenanthe oenanthe), a migratory passerine bird breeding in an agricultural landscape. For this population, consisting of around 50–120 breeding pairs per year, we partition variation in realized growth rates into environmental contributions from temperature, rainfall, population density, and unexplained random variation via multiple vital rates, and from demographic stochasticity.</li> <li>The case study suggests that variation in first-year survival via the random component, and adult survival via temperature are two main factors behind environmental variation in growth rates. More than half of the variation in growth rates is suggested to come from demographic stochasticity, demonstrating the importance of this factor for populations of moderate size.</li> </ol>
EuroSAT Model Zoo: A Dataset of Diverse Populations of Neural Network Models - EuroSAT
<p><strong>Abstract</strong></p> <p>In the last years, neural networks have evolved from laboratory environments to the state-of-the-art for many real-world problems. Our hypothesis is that neural network models (i.e., their weights and biases) evolve on unique, smooth trajectories in weight space during training. Following, a population of such neural network models (refereed to as “model zoo”) would form topological structures in weight space. We think that the geometry, curvature and smoothness of these structures contain information about the state of training and can be reveal latent properties of individual models. With such zoos, one could investigate novel approaches for (i) model analysis, (ii) discover unknown learning dynamics, (iii) learn rich representations of such populations, or (iv) exploit the model zoos for generative modelling of neural network weights and biases. Unfortunately, the lack of standardized model zoos and available benchmarks significantly increases the friction for further research about populations of neural networks. With this work, we publish a novel dataset of model zoos containing systematically generated and diverse populations of neural network models for further research. In total the proposed model zoo dataset is based on six image datasets, consist of 27 model zoos with varying hyperparameter combinations are generated and includes 50’360 unique neural network models resulting in over 2’585’360 collected model states. Additionally, to the model zoo data we provide an in-depth analysis of the zoos and provide benchmarks for multiple downstream tasks as mentioned before.</p> <p><strong>Dataset</strong></p> <p>This dataset is part of a larger collection of model zoos and contains the zoos trained on EuroSAT. All zoos with extensive information and code can be found at <a href="http://www.modelzoos.cc">www.modelzoos.cc</a>.</p> <p>This repository contains two types of model populations: the base model zoo ("eurosat_cnn_kaiming_uniform.zip"), as well as a collection of sparsified model zoos (filenames ending in "magn_XX.zip" or "ard.zip"). Zoos are trained with CNN models in configurations varying the seed only (seed), and sparsification is done through magnitude-based weight pruning ("magn_XX.zip") or varational dropout ("ard.zip").</p> <p>For more information on the zoos and code to access and use the zoos, please see <a href="http://www.modelzoos.cc">www.modelzoos.cc</a>.</p>
Data from: Personality determines population-level effects of microplastics consumption in a modelled population of stream-dwelling rainbow trout (Oncorhynchus mykiss)
<p>Microplastics in freshwater habitats are consumed by fish, including stream-dwelling salmonids, which can alter food consumption or negatively affect swimming and foraging behaviour. As population-level effects are largely unknown, a simulated population of stream-dwelling rainbow trout (<em>Oncorhynchus mykiss</em>) was created using the agent-based model 'inSTREAM 7' to model population-level effects (biomass) of behavioural changes caused by microplastics consumption. Individual fish were assigned all possible combinations of two personality traits (dominance, boldness/shyness), and consumed microplastics while foraging, while their abundance, body size, and microplastics consumption were tracked for three different life stages (fry, juvenile, adult) for a 10-year simulation period. Three additive scenarios were explored: a low-impact scenario with decreased food consumption, a medium-impact scenario with added lower swimming speed, and a high-impact scenario with added reductions in prey capture efficiency. Each was tested with microplastics concentrations of 0%, 1% (i.e., current levels), and 3% (i.e., future levels) of drift food. Overall, microplastics consumption did not strongly affect trout population abundance. Dominant adult trout consumed disproportionally more microplastics than all other fish, especially with higher microplastics concentrations. Different personality types were affected differently in the three scenarios: dominant and bold adults were smaller when food consumption was reduced, shy and subordinate adults were smaller when swimming speed was lowered, and all dominant adults, regardless of boldness, were smaller when foraging efficiency was impeded, with dominant and bold fry also less abundant in this scenario. However, effects on fish body size were only found with microplastic concentrations of 3%, indicating these outcomes can be prevented, as current levels of microplastics pollution are unlikely to affect salmonid body size. Nevertheless, microplastics ingestion represents an additional stressor that may potentially interact with a myriad of anthropogenic impacts that already affect wild salmonid populations.</p>
National forest inventory data for a size-structured forest population model
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Data: Applying stochastic and Bayesian integral projection modeling to amphibian population viability analysis
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Data from: Dinosaurian survivorship schedules revisited: new insights from an age-structured population model
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Population models used in: Method to assess potential magnitude of terrestrial European avian population reductions from ingestion of lead ammunition
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Data from: Partitioning variance in population growth for models with environmental and demographic stochasticity
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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.