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57 results for “individual based models”
Hybridization selects for prime-numbered life cycles in Magicicada: an individual-based simulation model of a structured periodical cicada population
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Model for: Characterizing long‐term population conditions of the elusive red tree vole with dynamic individual‐based modeling
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SARS-CoV-2 transmission and control in a hospital setting: an individual-based modelling study
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Limiting scaring activities reduces economic costs associated with foraging barnacle geese: results from an individual-based model
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Shelled Pteropod individual-based model output for the publication: The impact of aragonite saturation variability on shelled pteropods: An attribution study in the California current system
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Data from: Linkage into care among newly diagnosed HIV-positive individuals tested through outreach and facility-based HIV testing models in Mbeya, Tanzania: a prospective mixed-method cohort study
Objective: Linkage to care is the bridge between HIV testing and HIV treatment, care and support. In Tanzania, mobile testing aims to address historically low testing rates. Linkage to care was reported at 14% in 2009 and 28% in 2014. The study compares linkage to care of HIV-positive individuals tested at mobile/outreach versus public health facility-based services within the first 6 months of HIV diagnosis. Setting: Rural communities in four districts of Mbeya Region, Tanzania. Participants: A total of 1012 newly diagnosed HIV-positive adults from 16 testing facilities were enrolled into a two-armed cohort and followed for 6 months between August 2014 and July 2015. 840 (83%) participants completed the study. Main outcome: measures We compared the ratios and time variance in linkage to care using the Kaplan-Meier estimator and Log rank tests. Cox proportional hazards regression models to evaluate factors associated with time variance in linkage. Results: At the end of 6 months, 78% of all respondents had linked into care, with differences across testing models. 84% (CI 81% to 87%, n=512) of individuals tested at facility-based site were linked to care compared to 69% (CI 65% to 74%, n=281) of individuals tested at mobile/outreach. The median time to linkage was 1 day (IQR: 1–7.5) for facility-based site and 6 days (IQR: 3–11) for mobile/outreach sites. Participants tested at facility-based site were 78% more likely to link than those tested at mobile/outreach when other variables were controlled (AHR=1.78; 95% CI 1.52 to 2.07). HIV status disclosure to family/relatives was significantly associated with linkage to care (AHR=2.64; 95% CI 2.05 to 3.39). Conclusions: Linkage to care after testing HIV positive in rural Tanzania has increased markedly since 2014, across testing models. Individuals tested at facility-based sites linked in significantly higher proportion and modestly sooner than mobile/outreach tested individuals. Mobile/outreach testing models bring HIV testing services closer to people. Strategies to improve linkage from mobile/outreach models are needed.
Individual-based eco-evolutionary models for understanding adaptation in changing seas
<p>As climate change threatens species' persistence, predicting the potential for species to adapt to rapidly changing environments is imperative for the development of effective conservation strategies. Eco-evolutionary individual-based models (IBMs) can be useful tools for achieving this objective. We performed a literature review to identify studies that apply these tools in marine systems. Our survey suggested that this is an emerging area of research fueled in part by developments in modeling frameworks that allow simulation of increasingly complex ecological, genetic, and demographic processes. The studies we identified illustrate the promise of this approach and advance our understanding of the capacity for adaptation to outpace climate change. These studies also identify limitations of current models and opportunities for further development. We discuss three main topics that emerged across studies: 1) effects of genetic architecture and non-genetic responses on adaptive potential; 2) capacity for gene flow to facilitate rapid adaptation; and 3) impacts of multiple stressors on persistence. Finally, we perform a set of simple simulations to demonstrate the approach and provide a framework for users to explore eco-evolutionary IBMs as tools for understanding adaptation in changing seas.</p>
Data and Scripts for "Timing matters in Macrophage / CD4+ T cell interactions: An agent-based model comparing Mycobacterium tuberculosis host-pathogen interactions between latently infected and naïve individuals"
<p>This contains the data and graphing scripts necessary to recreate all figures in the paper "Timing matters in Macrophage / CD4+ T cell interactions: An agent-based model comparing Mycobacterium tuberculosis host-pathogen interactions between latently infected and naïve individuals". Supplemental Material for the paper is also provided here. Please refer to the README.md for instructions on how to use. The model can be found at: https://github.itap.purdue.edu/ElsjePienaarGroup/LTBINaiveinvitroModel/ along with the uncalibrated parameter files and scripts to run on HPCs.</p>
Resource selection functions based on hierarchical generalized additive models provide new insights into individual animal variation and species distributions
<p>Habitat selection studies are designed to generate predictions of species distributions or inference regarding general habitat associations and individual variation in habitat use. Such studies frequently involve either individually indexed locations gathered across limited spatial extents and analyzed using resource selection functions (RSF), or spatially extensive locational data without individual resolution typically analyzed using species distribution models. Both analytical methodologies have certain desirable features, but analyses that combine individual- and population-level inference with flexible non-linear functions may provide improved predictions while accounting for individual variation. Here, we describe how RSFs can be fit using hierarchical generalized additive models (HGAMs) using widely available software, providing a means to explore individual variation in habitat associations and to generate species distribution maps. We used GPS tracking data from Golden Eagles (Aquila chrysaetos) from across eastern North America with four environmental predictors to generate monthly distribution models. We considered three model structures that assumed different amounts of individual variation in the functional relationship between predictors and habitat use and used k-fold cross-validation to compare model performance. Models accounting for individual variability in shape and smoothness of functional responses performed best. Eagles exhibited the least amount of individual variation in response to land cover variables during winter months, with most individuals more closely adhering to the population-level trend. During summer months, eagles exhibited more substantial individual variation in shape and smoothness of the functional relationships, suggesting some need to account for individual variation in eagle habitat use for both inferential and predictive purposes, during this time of year. Because they allow users to blend flexible functions with random effects structures and are well-supported by a variety of software platforms, we believe that HGAMs provide a useful addition to the suite of analyses used for modeling habitat associations or predicting species distributions.</p>
Efficacy of Manual Therapy Based on the Fascial Distortion Model in Individuals With Temporomandibular Disorder
ClinicalTrials.gov study NCT06134310. IPD Sharing: NO. Countries: 1. Publications: 0.
The Effect of Web-Based and Face-to-Face Education Based on the Health Promotion Model on Foot Care Behavior in Individuals With Type 2 Diabetes
ClinicalTrials.gov study NCT06780631. IPD Sharing: NO. Countries: 1. Publications: 5.
Evaluation of the Accuracy, Safety and Robustness of a Single-input-single-output (SISO) Model-based Predictive Closed-loop System to Guide Patient-individualized ICU Sedation
ClinicalTrials.gov study NCT00735631. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Clinical Study of Individualized Vancomycin Dosing Based on Population PK Model
ClinicalTrials.gov study NCT06161870. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Data from: Linkage into care among newly diagnosed HIV-positive individuals tested through outreach and facility-based HIV testing models in Mbeya, Tanzania: a prospective mixed-method cohort study
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Data from: Assessing the dynamics of natural populations by fitting individual based models with approximate Bayesian computation
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Resource selection functions based on hierarchical generalized additive models provide new insights into individual animal variation and species distributions
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Individual-based eco-evolutionary models for understanding adaptation in changing seas
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Data from: A comparison of regression methods for model selection in individual-based landscape genetic analysis
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Data from: The evolution of marine larval dispersal kernels in spatially structured habitats: analytical models, individual-based simulations, and comparisons with empirical estimates
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Code for Individual Based Model to assess impact of KHV release on carp population
<p><b>1: </b>Common carp (<i>Cyprinus carpio</i>) is one of the top global invasive vertebrates and can cause significant ecological damage. The Australian Government's National Carp Control Program (NCCP) proposes to release Koi Herpesvirus (KHV) to eradicate feral carp in one of the largest ecological interventions ever attempted. Ecological and human health risks have been highlighted regarding the release of a highly pathogenic viral biocontrol for an aquatic species. The efficacy of KHV has also been questioned, and it has not been demonstrated to produce lasting population reductions.</p> <p> </p> <p>2. We developed an individual-based model (IBM) to examine the ecological and evolutionary response of a carp population after KHV release. This simulated the interaction between fish life history, viral epidemiology, host genetic resistance and population demography to critically evaluate the impact of KHV release under optimal conditions and a "best case scenario" for disease transmission.</p> <p> </p> <p>3. KHV will rarely result in prolonged reductions or population extinctions. Crucially, realistic scenarios result in a rapidly rebounding population of resistant individuals. Additional measures aimed to reduce carp population recovery rate (e.g. with genetic engineering) require rapid efficacy to significantly reduce carp numbers alongside KHV.<br> </p> <p>4. Fish fecundity has an overwhelming influence on viral efficacy as a biocontrol agent when combined with genetic resistance within a population. A high probability of population extinction is only met when carp fecundity is reduced to 1% of biological observations.<br> </p> <p><span>5.<i> Synthesis and applications. </i></span>We use an individual-based model to evaluate the efficacy of Koi Herpesvirus biocontrol in Common <a>Ca</a>rp, and find that high host fecundity combined with genetic resistance results in rapid population rebound after initial large fish-kills. Biocontrol approaches relying on natural selection lose efficacy over successive generations as resistance genes increases in frequency. Given the intense logistical effort and risks to ecosystems and human health associated with large fish kills after viral release, we suggest that sustained manual removal, alongside ecological restoration to favour recovery of native species, provides a risk-free approach to reducing populations.<br> </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.