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506 results for “assessment model”
Data from: A refined modelling approach to assess the influence of sampling on palaeobiodiversity curves: new support for declining Cretaceous dinosaur richness
Modelling has been underdeveloped with respect to constructing palaeobiodiversity curves, but it offers an additional tool for removing sampling from their estimation. Here an alternative to subsampling approaches, which often require large sample sizes, is explored by the extension and refinement of a pre-existing modelling technique that uses a geological proxy for sampling. Application of the model to the three main clades of dinosaurs suggests that much of their diversity fluctuations cannot be explained by sampling alone. Furthermore, there is new support for a long-term decline in their diversity leading up to the K/Pg extinction event. At present use of this method with data that includes either lagerstätten or 'Pull of the Recent' biases is inappropriate, although partial solutions are offered.
Data from: Assessing the expected response to genomic selection of individuals and families in Eucalyptus breeding with an additive-dominant model
We report a genomic selection (GS) study of growth and wood quality traits in an outbred F2 hybrid Eucalyptus population (n=768) using high-density single-nucleotide polymorphism (SNP) genotyping. Going beyond previous reports in forest trees, models were developed for different selection targets, namely, families, individuals within families and individuals across the entire population using a genomic model including dominance. To provide a more breeder-intelligible assessment of the performance of GS we calculated the expected response as the percentage gain over the population average expected genetic value (EGV) for different proportions of genomically selected individuals, using a rigorous cross-validation (CV) scheme that removed relatedness between training and validation sets. Predictive abilities (PAs) were 0.40–0.57 for individual selection and 0.56–0.75 for family selection. PAs under an additive+dominance model improved predictions by 5 to 14% for growth depending on the selection target, but no improvement was seen for wood traits. The good performance of GS with no relatedness in CV suggested that our average SNP density (~25 kb) captured some short-range linkage disequilibrium. Truncation GS successfully selected individuals with an average EGV significantly higher than the population average. Response to GS on a per year basis was ~100% more efficient than by phenotypic selection and more so with higher selection intensities. These results contribute further experimental data supporting the positive prospects of GS in forest trees. Because generation times are long, traits are complex and costs of DNA genotyping are plummeting, genomic prediction has good perspectives of adoption in tree breeding practice.
Data from: A dynamic state model of migratory behavior and physiology to assess the consequences of environmental variation and anthropogenic disturbance on marine vertebrates
Integrating behavior and physiology is critical to formulating new hypotheses on the evolution of animal life-history strategies. Migratory capital breeders acquire most of the energy they need to sustain migration, gestation and lactation before parturition. Therefore, when predicting the impact of environmental variation on such species, a mechanistic understanding of the physiology of their migratory behavior is required. Using baleen whales as a model system, we developed a dynamic state variable model that captures the interplay among behavioral decisions, energy, reproductive needs and the environment. We applied the framework to blue whales (Balaenoptera musculus) in the Eastern North Pacific Ocean, and explored the effects of environmental and anthropogenic perturbations on female reproductive success. We demonstrate the emergence of migration to track prey resources, enabling us to quantify the trade-offs among capital breeding, body condition, and metabolic expenses. We predict that periodic climatic oscillations affect reproductive success less than unprecedented environmental changes do. The effect of localized, acute anthropogenic impacts depended on whales' behavioral response to the disturbance; chronic, but weaker, disturbances had little effect on reproductive success. Because we link behavior and vital rates by modeling individuals' energetic budgets, we provide a general framework to investigate the ecology of migration and assess the population consequences of disturbance, while identifying critical knowledge gaps.
Data from: Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)
Systematics at the species level is still marked by theoretical and empirical tensions amongst the desires to identify geographical lineages, delimit species, and estimate their relationships. These goals are often confounded because each relies, at least to some extent, on the others being known. However, recently developed methods can simultaneously address all three. Furthermore, next-generation genomic sequencing allows us to generate large-scale molecular data sets to examine variation within species at a fine scale. Finally, a renaissance in morphological species validation allows us to integrate historical species definitions with coalescent models for species delimitation. Here, we investigate the applicability of these methods in an empirical case, in the Nearctic snake genus Storeria. Integrating trait data into species delimitation reduces the number of species delimited from molecular data alone. Whereas molecular data support eight distinct species-level lineages, including morphological data reduces this to four. The taxa Storeria dekayi, Storeria occipitomaculata, Storeria storerioides, and Storeria victa are considered distinct, monotypic species, with no subspecies recognized. We highlight the need for careful assessment of species delimitation, combining both computational genetic methods as well as traditional character-based descriptions. It is now possible to identify phylogeographical lineages, delimit species using molecular and morphological data, and estimate their relationships in a single coherent set of analyses. Moving forward, this will allow for more rapid and objective assessments of cryptic diversity at the species level.
Dataset from "Employing hidden Markov models to assess the genetic content of genome assemblies"
<p>Dataset used to reach the conclusions in "Employing hidden Markov models to assess the genetic content of genome assemblies".</p>
Sampling data accompanying "An aerosol activation metamodel of v1.2.0 of the pyrcel cloud parcel model: Development and offline assessment for use in an aerosol-climate model"
<p>Datasets recording sampling results, accompanying the manuscript <em>An aerosol activation metamodel of v1.2.0 of the pyrcel cloud parcel model: Development and offline assessment for use in an aerosol-climate model, </em>Rothenberg, D. and Wang, C., submitted, GMD. Please see the included README for more details.</p>
Effects of individualized Electrical Impedance Tomography and image reconstruction settings upon the assessment of regional ventilation distribution: Comparison to 4-dimensional Computed Tomography in a porcine model
<p>Reconstruction Models used for identification of optimal settings for comparison to CT images. Forward models are available in the supplement of the article but were removed form the inverse models due to redundance storage within each model.</p> <p>Prior reconstruction in EIDORS, forward models have to be added again to<em> imdl.fwd_model</em> and <em>imdl.jacobian_background.fwd_model</em>.</p>
Figure 2 in Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)
Figure 2. Map of Storeria ranges and sampling locations, showing geographical extent of populations, and range of former species with respect to re-delimited taxa. A, previous geographical extent of Storeria occipitomaculata is shown in red; circles indicate sampling localities. The asterisk indicates the sample of Storeria 'hidalgoensis' examined for morphology, with the range of this subpopulation, now considered part of S. occipitomaculata, indicated in pink. The range of Storeria storerioides is indicated in blue, with the sampling locality indicated by a square. B, previous geographical extent of Storeria dekayi is shown in yellow, with pentagons indicating sampling localities of S. dekayi, triangles indicating Storeria victa, and a line drawn to approximate the range boundary. The asterisk in the Central American population indicates the collection location of the specimen of Storeria 'tropica' examined for morphology, which is now considered part of S. dekayi.
Data Set of Paper on An Architecture Model-Based Framework for Continuous Data Protection Legal Assessments
<p>Data Set of Paper "An Architecture Model-Based Framework for Continuous Data Protection Legal Assessments".<br>The data set contains illustrations of the example used for evaluating accuracy, including all variations, and model instances of the case studies used for evaluating applicability.</p>
OpenET model data for assessing the accuracy of OpenET satellite-based evapotranspiration data to support water resource and land management applications
<h2>Overview</h2> <p>This dataset includes daily and monthly evapotranspiration (ET) data from the remote sensing models that comprise the [OpenET](https://openetdata.org/) ensemble as described in Melton et al., 2022 (https://doi.org/10.1111/1752-1688.12956); these data were extracted at specific locations within the contiguous United States that coincide with *in situ* measurement stations, including eddy covaraiance, Bowen-ratio, and lysimeter stations. Model ET data where extracted at each site in this dataset using flux footprints as described in Volk et al., (2023) (https://doi.org/10.1016/j.agrformet.2023.109307). These model data alongside the corresponding *in situ* ET data (https://doi.org/10.1016/j.dib.2023.109274) were subsequently used in the manuscript for the OpenET Phase II Intercomparison and Accuracy Assessment (https://doi.org/10.1038/s44221-023-00181-7). </p> <h3><br>Description of the data and file structure</h3> <p>The dataset is in a compressed (zipped) archive titled "OpenET_PhaseII_model_ET_dataset", so first it needs to be downloaded and extracted. The dataset is comprised of just three files. The first file is a Microsoft Excel file "Station_metadata.xlsx" that contains information about the *in situ* ET measurement stations where the OpenET model data was extracted. This file contains information such as site ID's, coordinates, land cover information, and site principal investigator (PI) contact information. Again, the corresponding *in situ* ET data are not included in this dataset. The other two files are tab-delimited text files containing timeseries the OpenET model data themselves, namely the daily ET [mm/day] and monthly ET [mm/month] as extracted for each model and the ensemble value as used in the OpenET Phase II Intercomparison and Accuracy Assessment. </p> <h3><br>Access information and code/software</h3> <p>OpenET data that was used here was produced using operational methods that are implemented on the Google Earth Engine platform. Monthly OpenET model data can be retrieved through Google Earth Data Catalog (e.g., https://developers.google.com/earth-engine/datasets/catalog/OpenET_ENSEMBLE_CONUS_GRIDMET_MONTHLY_v2_0) or through the [online data explorer](https://openetdata.org/) or using the [OpenET API](https://openetdata.org/api-info/).</p>
Data from: Future projections of biodiversity and ecosystem services in Europe with two integrated assessment models
<p>Projections of future changes in biodiversity and ecosystem services (BES) are of increasing importance to inform policy and decision-making on options for conservation and sustainable use of BES. Scenario-based modelling is a powerful tool to assess these future changes. This study assesses the consequences for BES in Europe under four socio-environmental scenarios designed from a BES perspective. We evaluated these scenarios using two integrated assessment models (IMAGE-GLOBIO and CLIMSAVE IAP, respectively). </p> <p><strong>Veerkamp, C. J</strong>., Dunford. R. W., Harrison, P. A., Mandryk, M., Priess, J. A., Schipper, A. M., Stehfest, E., & Alkemade, R. (2020). Future projections of biodiversity and ecosystem services in Europe with two integrated assessment models. <em>Regional Environmental Change,</em> 20, 103. <a href="https://doi.org/10.1007/s10113-020-01685-8">https://doi.org/10.1007/s10113-020-01685-8</a> </p>
Integrated Modeling of Flow, Soil Erosion, and Nutrient Dynamics in a Regional Watershed: Assessing Natural and Human-Induced Impacts
<p>Attached file is the verification data for the submitted manuscript "Integrated Modeling of Flow, Soil Erosion, and Nutrient Dynamics in a Regional Watershed: Assessing Natural and Human-Induced Impacts" .</p>
Assessing the fate and behaviour of plant nutrients in aquaponic systems by chemical equilibrium modelling: A meta-analytical approach
<p>Cleaned dataset and Visual MINTEQ input files (without and without assumed presence of dissolved organic matter) for each record in the dataset.</p>
Enhancing Credit Risk Assessment in Digital Finance through a Hybrid Deep Learning Model Integrated with Blockchain on the Edge of Things F
<p><span>This work proposes a credit risk assessment model using deep learning models such as self-attention generative adversarial networks (SA-GAN) and deep multi-layer perceptron (DMLP). Blockchain is used to improve the security aspects of the model by employing Brakerski-Gentry-Vaikuntanathan (BKV) encryption technique. Further, the proposed system is implemented in Edge-of-things network and communications are enabled via LoRaWAN server.</span></p>
Software file and numerical results of Modelling heat transfer for assessing the convection length in ventilated caves
<p>The Comsol file corresponding to the reference case as shown in Figures 4-6 as well as all the numerical results for the rest of the figures are available here.</p>
Dataset associated with the manuscript " Locally developed models improve the accuracy of remotely assessed metrics as a rapid tool to classify sandy beach morphodynamics"
<p>Raw dataset associated with the manuscript " Locally developed models improve the accuracy of remotely assessed metrics as a rapid tool to classify sandy beach morphodynamics"</p>
Dataset for Assessing the mycotoxin-related health impact of shifting from meat-based diets to soy-based meat analogues in a model scenario based on Italian consumption data
<p>Dataset used for <strong>Assessing the mycotoxin-related health impact of shifting from meat-based diets to soy-based meat analogues in a model scenario based on Italian consumption data.</strong></p>
Fig. 3. A 50 in Phylogenomic Variation at the Population-Species Interface and Assessment of Gigantism in a Model Wolf Spider Genus (Lycosidae, Schizocosa)
Fig. 3. A 50% majority rule consensus tree from MSC-bootstrap analysis of the "All individuals" dataset. Color labels as in figures 1 and 2.
Fig. 2 in Phylogenomic Variation at the Population-Species Interface and Assessment of Gigantism in a Model Wolf Spider Genus (Lycosidae, Schizocosa)
Fig. 2. Maximum likelihood tree of the "All individuals" concatenated dataset generated with IQ-TREE.Topology with branch lengths in substitutions/site shown in bottom left. Black dots indicate deeper nodes with bootstrap and SH-like aLRT both under 90, otherwise deeper nodes are above 90. Support values for shallow nodes not shown.
Fig. 1 in Phylogenomic Variation at the Population-Species Interface and Assessment of Gigantism in a Model Wolf Spider Genus (Lycosidae, Schizocosa)
Fig. 1. Collection locations in western North America. Colors for S. MCCooki are based on phylogenetic group assignment (see Fig. 2). Female (left) and male (right) S. MaxiMa from Davis, CA shown in inset.
ScienceDex guides
Understand access before you commit
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.