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544 results for “integrated models”
A new method for integrating ecological niche modeling with phylogenetics to estimate ancestral distributions
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Data from: Integrated species distribution models fitted in INLA are sensitive to mesh parameterisation
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Datasets used for Multi-omics integration using Deep Learning and other state-of-the-art regression models
<p>This repository link contains the LIHC files that were downloaded using TCGA Assembler 2 and used in the publication for benchmarking DL and other state-of-the-art regression models.</p> <p>The contents are as follows.</p> <p>Gene level CNA , filename= "<a href="https://zenodo.org/api/files/15943ba8-5f3d-4397-8eb2-98ed85693b79/LIHC__genome_wide_snp_6__GeneLevelCNA.txt">LIHC__genome_wide_snp_6__GeneLevelCNA.txt</a>"</p> <p>DNA Methylation data around 1500 bp around TSS (450K) , filename= "<a href="https://zenodo.org/api/files/15943ba8-5f3d-4397-8eb2-98ed85693b79/LIHC_Methylation450__SingleValue__TSS1500__Both.txt">LIHC_Methylation450__SingleValue__TSS1500__Both.tx</a>t"</p> <p>RNASeq data, filename= "<a href="https://zenodo.org/api/files/15943ba8-5f3d-4397-8eb2-98ed85693b79/LIHC_RNASeq__illuminahiseq_rnaseqv2__GeneExp.txt">LIHC_RNASeq__illuminahiseq_rnaseqv2__GeneExp.txt</a>"</p>
Supplemental data for "Initial land use/cover distribution substantially affects global carbon and local temperature projections in the integrated Earth System Model." Article published as Global Biogeochemical Cycles publication 2019B006383
<p>These are supporting data for Global Biogeochemical Cycles publication 2019B006383: "Initial land use/cover distribution substantially affects global carbon and local temperature projections in the integrated Earth System Model." They include data for all of the regular and supplemental figures.</p>
Figure 4 from: Prieß-Buchheit J, Aro AR, Demirova I, Lanzerath D, Stoev P, Wilder N (2020) Rotatory role-playing and role-models to enhance the research integrity culture. Research Ideas and Outcomes 6: e53921. https://doi.org/10.3897/rio.6.e53921
Figure 4 Quotes from Pierre Curie (2012) Marie Curie: With Autobiographical Notes by Marie Curie, Dover Publication: Mineola New York, p.70 and Russell, Bertrand (2004) History of Western Philosophy, London, p.864. Figures designed by Freepik from www.flaticon.com.
Integrated Performance Evaluation of Extended Queueing Network Models with Line
<p>Numerical examples in the paper "Integrated Performance Evaluation of Extended Queueing Network Models with Line" by G. Casale accepted for publication in the Winter Simulation Conference (WSC) 2020.</p>
Data from: Why we should care about movements: Using spatially explicit integrated population models to assess habitat source-sink dynamics
<p>1. Assessing the source-sink status of populations and habitats is of major importance for understanding population dynamics and for the management of natural populations. Sources produce a net surplus of individuals (per capita contribution to the metapopulation >1) and will be the main contributors for self-sustaining populations, whereas sinks produce a deficit (contribution < 1). However, making these types of assessments is generally hindered by the problem of separating mortality from permanent emigration, especially when survival probabilities as well as moved distances are habitat-specific.<br> 2. To address this long-standing issue, we propose a spatial multi-event Integrated Population Model (IPM) that incorporates habitat-specific dispersal distances of individuals. Using information about local movements, this IPM adjusts survival estimates for emigration outside the study area.<br> 3. Analyzing 24 years of data on a farmland passerine (the northern wheatear Oenanthe oenanthe) we assessed habitat-specific contributions, and hence the source-sink status and temporal variation of two key breeding habitats, while accounting for habitat- and sex-specific local dispersal distances of juveniles and adults. We then examined the sensitivity of the source-sink analysis by comparing results with and without accounting for these local movements.<br> 4. Estimates of first-year survival, and consequently habitat-specific contributions, were higher when local movement data were included. The consequences from including movement data were sex specific, with contribution shifting from sink to likely source in one habitat for males, and previously noted habitat differences for females disappearing.<br> 5. Assessing the source-sink status of habitats is extremely challenging. We show that our spatial IPM accounting for local movements can reduce biases in estimates of the contribution by different habitats, and thus reduce the overestimation of the occurrence of sink habitats. This approach allows combining all available data on demographic rates and movements, which will allow better assessment of source-sink dynamics and better informed conservation interventions.</p>
Data from: Integrated population modelling reveals a perceived source to be a cryptic sink
Demographic links among fragmented populations are commonly studied as source-sink dynamics, whereby source populations exhibit net recruitment and net emigration, while sinks suffer net mortality but enjoy net immigration. It is commonly assumed that large, persistent aggregations of individuals must be sources, but this ignores the possibility that they are sinks instead, buoyed demographically by immigration. We tested this assumption using Bayesian integrated population modelling of Greenland white-fronted geese (Anser albifrons flavirostris) at their largest wintering site (Wexford, Ireland), combining capture–mark–recapture, census and recruitment data collected from 1982 to 2010. Management for this subspecies occurs largely on wintering areas; thus, study of source-sink dynamics of discrete regular wintering units provides unprecedented insights into population regulation and enables identification of likely processes influencing population dynamics at Wexford and among 70 other Greenland white-fronted goose wintering subpopulations. Using results from integrated population modelling, we parameterized an age-structured population projection matrix to determine the contribution of movement rates (emigration and immigration), recruitment and mortality to the dynamics of the Wexford subpopulation. Survival estimates for juvenile and adult birds at Wexford and adult birds elsewhere fluctuated over the 29-year study period, but were not identifiably different. However, per capita recruitment rates at Wexford in later years (post-1995) were identifiably lower than in earlier years (pre-1995). The observed persistence of the Wexford subpopulation was only possible with high rates of immigration, which exceeded emigration in each year. Thus, despite its apparent stability, Wexford has functioned as a sink over the entire study period. These results demonstrate that even large subpopulations can potentially be sinks, and that movement dynamics (e.g. immigration) among winters can dramatically obscure key processes driving subpopulation size. Further, novel population models which integrate capture–mark–recapture, census and recruitment data are essential to correctly ascribing source-sink status and accurately informing development of site-safeguard networks.
Data from: Integrated population models poorly estimate the demographic contribution of immigration
<p class="BodyA">Estimating the contribution of demographic parameters to changes in population growth is essential for understanding why populations fluctuate. Integrated Population Models (IPMs) offer a possibility to estimate contributions of additional demographic parameters, for which no data have been explicitly collected: typically immigration. Such parametersare often subsequently highlighted as important drivers of population growth. Yet, accuracy in estimating their temporal variation, and consequently their contribution to changes in population growth rate, has not been investigated.</p> <p class="BodyA">To quantify the magnitude and cause of potential biases when estimating the contribution of immigration using IPMs, we simulated data (using Northern Wheatear <i>Oenanthe oenanthe </i>population estimates) from controlled scenarios to examine potential biases and how they depend on IPM parameterization, formulation of priors, the level of temporal variation in immigration, and sample size. We also used empirical data on populations with known rates of immigration: Soay Sheep <i>Ovis aries</i> and Mauritius kestrel <i>Falco punctatus</i> with zero immigration and<i> </i>grey wolf <i>Canis lupus</i> in Scandinavia with<i> </i>near-zero immigration.</p> <p class="Default">IPMs strongly overestimated the contribution of immigration to changes in population growth in scenarios when immigration was simulated with zero temporal variation (proportion of variance attributed to immigration = 63% for the more constrained formulation and real sample size) and in the wild populations, where the true number of immigrants was zero or near-zero (Kestrel 19.1-98.2%, Sheep 4.2-36.1%, Wolf 84.0-99.2%). Although the estimation of immigration in the simulation study became more accurate with increasing temporal variation and sample size, it was often not possible to distinguish between an accurate estimation from data with high temporal variation versus an overestimation from data with low temporal variation. Unrealistically large sample sizes may be required to estimate the contribution of immigration well.</p> <p class="Body">To minimise the risk of overestimating the contribution of immigration (or any additional parameter) in IPMs, we recommend to: (i) look for evidence of variation in immigration before investigating its contribution to population growth, (ii) simulate and model data for comparison to the real data, and (iii) use explicit data on immigration when possible.</p>
Data from: The 'golden kelp' Laminaria ochroleuca under global change: integrating multiple eco-physiological responses with species distribution models
1. The loss of marine foundation species, in particular kelps at temperate latitudes, has been linked to climatic drivers and co-occurring human perturbations. Ocean temperature and nutrients typically co-vary over local and regional scales and play a crucial role on kelp dynamics. Examining their independent and interactive effects on kelp physiological performance is essential to understand and predict patterns of kelp distribution, particularly under scenarios of global change. 2. Crossed combinations of ocean temperatures and availability of nutrients were experimentally tested on juveniles of the 'golden kelp', Laminaria ochroleuca, from the northwestern Iberian Peninsula. Eco-physiological responses included: survival, growth and total N content. Results were embedded into a Species Distribution Model (SDM), which relates presence records and climatic and non-climatic data to forecast distribution patterns of L. ochroleuca under different climate change scenarios. 3. Temperatures above 24.6 ºC were lethal irrespective of nutrients. Optimal growth of juvenile sporophytes occurred between 12 °C and 18 ºC and no nutrient limitation. The SDM, where ocean temperature was the main predictor of kelp distribution in line with temperature thresholds given by eco-physiological responses, suggests a future expansion towards northern latitudes and a retreat from the southern limit/boundary of the current distribution. 4. Synthesis. Range-shifting of the golden kelp can have severe ecological impacts at regional and local scales. The expansion or retraction of the species along the European coast seems to be modulated mainly by temperature, but nutrient availability would be key to maintain optimal physiological performance. Our work highlights that the combination of empirical and modelling approaches is accessible to researchers and crucial to build more robust predictions of ecological and biogeographic responses of habitat-forming species to forecasted environmental change.
Data from: The EGA+GNM framework: an integrative approach to modelling behavioural syndromes
1. Behavioural syndromes refer to correlated suites of behavioural traits exhibiting consistent among-individual variation, i.e. personality. Factor analysis (FA) is currently the dominant method for modelling behavioural syndromes in humans and animals. Although FA is useful for inferring the latent causes underlying trait correlations, it does not account for pairwise behavioural interactions that also contribute to syndrome structure. Given that latent factors and pairwise interactions are likely ubiquitous causes of trait covariation, both should be modelled simultaneously. Currently, however, behavioural ecologists lack an integrative framework for describing and inferring such behavioural syndromes. 2. Generalized network modelling (GNM), representing an integration of FA and Gaussian graphical modelling (GGM), meets this challenge. We provide a theoretical introduction to GNM as well as a method for detecting latent factors in GGMs called exploratory graph analysis (EGA). We then propose the novel EGA+GNM framework for modelling multiple sources of trait correlations and ensuring more robust causal inferences. To empirically demonstrate the utility of this framework, we compare models derived from EGA+GNM and FA using observational measures of social and arousal behaviour in common marmosets (Callithrix jacchus). 3. Using information-theoretic model comparison, we find support for the EGA+GNM models compared to models generated by FA. Two EGA+GNM models suggest that while latent factors contribute to the emergence of clustered sociability and arousal behaviours, correlations among these traits may also be partially explained by pairwise interactions. Additionally, these behavioural clusters are hypothesized to be causally linked by a positive pairwise interaction between allogrooming and activity level. 4. These results support our claim that EGA+GNM provides a superior and integrative framework for describing behavioural syndromes. Consequently, by simultaneously modelling both latent factors and pairwise interactions, behavioural ecologists can better understand the evolutionary causes and consequences of animal personality. A formal overview of the EGA+GNM framework and a R tutorial demonstrating its application are provided in the electronic supplementary material.
Data from: Sex-related online behaviors, perceived peer norms and adolescents' experience with sexual behavior: testing an integrative model
Research on the role of sex-related Internet use in adolescents' sexual development has often isolated the Internet and online behaviors from other, offline influencing factors in adolescents' lives, such as processes in the peer domain. The aim of this study was to test an integrative model explaining how receptive (i.e., use of sexually explicit Internet material [SEIM]) and interactive (i.e., use of social networking sites [SNS]) sex-related online behaviors interrelate with perceived peer norms in predicting adolescents' experience with sexual behavior. Structural equation modeling on longitudinal data from 1,132 Dutch adolescents (Mage T1 = 13.95; range 11-17; 52.7% boys) demonstrated concurrent, direct, and indirect effects between sex-related online behaviors, perceived peer norms, and experience with sexual behavior. SEIM use (among boys) and SNS use (among boys and girls) predicted increases in adolescents' perceptions of peer approval of sexual behavior and/or in their estimates of the numbers of sexually active peers. These perceptions, in turn, predicted increases in adolescents' level of experience with sexual behavior at the end of the study. Boys' SNS use also directly predicted increased levels of experience with sexual behavior. These findings highlight the need for multisystemic research and intervention development to promote adolescents' sexual health.
Post-resolution macrophages shape long-term tissue immunity and integrity in a mouse model of Streptococcus pneumonia.
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Data for "• Can we achieve atmospheric chemical environments in the laboratory? An integrated model-measurement approach to chamber SOA studies"
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Seamless integration of bioelectronic interface in an animal model via in vivo polymerization of conjugated oligomers
<p>Leveraging the biocatalytic machinery of living organisms for fabricating functional bioelectronic interfaces, in vivo, defines a new class of micro-biohybrids enabling the seamless integration of technology with living biological systems. Previously, we have demonstrated the in vivo polymerization of conjugated oligomers forming conductors within the structures of plants. Here, we expand this concept by reporting that Hydra, an invertebrate animal, polymerizes the conjugated oligomer ETE-S both within cells that expresses peroxidase activity and within the adhesive material that is secreted to promote underwater surface adhesion. The resulting conjugated polymer forms electronically conducting and electrochemically active μm-sized domains, which are inter-connected resulting in percolative conduction pathways extending beyond 100 μm, that are fully integrated within the Hydra tissue and the secreted mucus. Furthermore, the introduction and in vivo polymerization of ETE-S can be used as a biochemical marker to follow the dynamics of Hydra budding (reproduction) and regeneration. This work paves the way for well-defined self-organized electronics in animal tissue to modulate biological functions and in vivo biofabrication of hybrid functional materials and devices.</p>
Supplementary material 1 from: Dang NA, Jackson BM, Tomscha SA, Lilburne L, Burkhard K, Tran DD, Phi LH, Benavidez R (2022) Guidelines and a supporting toolbox for parameterising key soil hydraulic properties in hydrological studies and broader integrated modelling. One Ecosystem 7: e76410. https://doi.org/10.3897/oneeco.7.e76410
Supplementary Material S1
Supplementary material 2 from: Dang NA, Jackson BM, Tomscha SA, Lilburne L, Burkhard K, Tran DD, Phi LH, Benavidez R (2022) Guidelines and a supporting toolbox for parameterising key soil hydraulic properties in hydrological studies and broader integrated modelling. One Ecosystem 7: e76410. https://doi.org/10.3897/oneeco.7.e76410
Supplementary Material S2
Original data for "Multiple co-existing structures of an RNA four-way junction resolved by FRET, SAXS, and integrative modeling"
<p>Experimental single-molecule FRET data (Intensity ratio histograms) and starting structures used for rigid body docking for an RNA four-way junction related to the hairpin ribozyme.</p> <p> </p>
Integrating demography and distribution modelling for the iconic Leontopodium alpinum Colm. in the Romanian Carpathians
<p class="CxSpFirst"><span>Both climate change and human exploitation are major threats to plant life in mountain environments. One species that may be particularly sensitive to both of these stressors is the iconic alpine flower edelweiss (<i>Leontopodium alpinu</i>m Colm.). Its populations have declined across Europe due to over-collection for its highly prized flowers. Edelweiss is still subject to harvesting across the Romanian Carpathians but no study has measured to what extent populations are vulnerable to anthropogenic change. </span></p> <p class="CxSpMiddle"><span>Here we estimated the effects of climate and human disturbance on the fitness of edelweiss. We combined demographic measurements with predictions of future range distribution under climate change to assess the viability of populations across Romania. </span></p> <p class="CxSpMiddle"><span>We found that per-capita and per-area seed number and seed mass were similarly promoted by both favourable environmental conditions, represented by rugged landscapes with relatively cold winters and wet summers, and reduced exposure to harvesting, represented by the distance of plants from hiking trails. Modelling these responses under future climate scenarios suggested a slight increase in per-area fitness. However, we found plant ranges contracted by between 14 to 35% by 2050, with plants pushed into high elevation sites. </span></p> <p><i>Synthesis</i>. Both total seed number and seed mass are expected to decline across Romania despite individual edelweiss fitness benefiting from a warmer and wetter climate. More generally, our approach of coupling species distribution models with demographic measurements may better inform conservation strategies of ways to protect alpine life in a changing world.</p>
Data from: Computing the local field potential (LFP) from integrate-and-fire network models
Leaky integrate-and-fire (LIF) network models are commonly used to study how the spiking dynamics of neural networks changes with stimuli, tasks or dynamic network states. However, neurophysiological studies in vivo often rather measure the mass activity of neuronal microcircuits with the local field potential (LFP). Given that LFPs are generated by spatially separated currents across the neuronal membrane, they cannot be computed directly from quantities defined in models of point-like LIF neurons. Here, we explore the best approximation for predicting the LFP based on standard output from point-neuron LIF networks. To search for this best "LFP proxy", we compared LFP predictions from candidate proxies based on LIF network output (e.g, firing rates, membrane potentials, synaptic currents) with "ground-truth" LFP obtained when the LIF network synaptic input currents were injected into an analogous three-dimensional (3D) network model of multi-compartmental neurons with realistic morphology, spatial distributions of somata and synapses. We found that a specific fixed linear combination of the LIF synaptic currents provided an accurate LFP proxy, accounting for most of the variance of the LFP time course observed in the 3D network for all recording locations. This proxy performed well over a broad set of conditions, including substantial variations of the neuronal morphologies. Our results provide a simple formula for estimating the time course of the LFP from LIF network simulations in cases where a single pyramidal population dominates the LFP generation, and thereby facilitate quantitative comparison between computational models and experimental LFP recordings in vivo.
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.