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305 results for “characterization model”
Data set to ''Volcano growth versus deformation by strike-slip faults: morphometric characterization through analogue modelling'
<p>This data set is the supplementary material to Grosse et al. (2020) 'Volcano growth versus deformation by strike-slip faults: morphometric characterization through analogue modelling', published in Tectonophysics (https://doi.org/10.1016/j.tecto.2020.228411). The data set consists of (1) 249 digital elevation models (DEMs) of each step of the the analogue experiments carried out, in standard ENVI format, zipped; and (2) an Excel file containing the DEM-derived morphometric parameters for each of the analogue models.</p> <p>Experiments were carried out at the analogue modelling lab of the Department of Geography at the Vrije Universiteit Brussel (Belgium). A granular mixture of fine-grained quartz sand and kaolin clay was used as analogue material. Experiments were conducted on a fixed table, on which a basal layer of granular material was placed. A basal plate attached to a step-motor was used to simulate pure strike-slip displacements of the basal layer. Volcano growth was simulated by depositing loads of granular material on top of the basal layer from a point source. The analogue models were photographed at regular time intervals during the experiments using four digital cameras. The photographs were used to generate synthetic digital elevation models (DEMs) with 0.2 mm spatial resolution of each step of the analogue models by applying the MICMAC digital stereo-photogrammetry software. The ENVI software was used to re-sample the DEMs to a 0.5 mm spatial resolution and apply the noise-reduction Lee filter. Morphometric data were then extracted from the DEMs by applying two IDL-language algorithms: NETVOLC, used to automatically calculate the volcano edifice basal outline, and MORVOLC, used to extract a set of morphometric parameters.</p>
Data from: Characterizing morphological (co)variation using structural equation models: body size, allometric relationships and evolvability in a house sparrow metapopulation
Body size plays a key role in the ecology and evolution of all organisms. Therefore, quantifying the sources of morphological (co)variation, dependent and independent of body size, is of key importance when trying to understand and predict responses to selection. We combine structural equation modeling with quantitative genetics analyses to study morphological (co)variation in a meta-population of house sparrows (Passer domesticus). As expected, we found evidence of a latent variable 'body size', causing genetic and environmental covariation between morphological traits. Estimates of conditional evolvability show that allometric relationships constrain the independent evolution of house sparrow morphology. We also found spatial differences in general body size and its allometric relationships. On islands where birds are more dispersive and mobile, individuals were smaller and had proportionally longer wings for their body size. While in islands where sparrows are more sedentary and nest in dense colonies, individuals were larger and had proportionally longer tarsi for their body size. We corroborated these results using simulations and show that our analyses produce unbiased allometric slope estimates. This study highlights that in the short term allometric relationships may constrain phenotypic evolution, but that in the long term selection pressures can also shape allometric relationships.
Compositional Characterization of Glassy Volcanic Material From VNIR and MIR Spectra Using Partial Least Squares Regression Models
<p>This is supporting data for the paper titled "Compositional Characterization of Glassy Volcanic Material From VNIR and MIR Spectra Using Partial Least Squares Regression Models" by Leight et al. (submitted to JGR-P 11/23). Table S1 lists each spectrum used to train PLS models, its source, and which training datasets the spectrum was included in. Zip files contain the MIR and VNIR PLS model files. Model files are .asc, and can be run using the code at Ytsma, (2022), https://doi.org/10.5281/zenodo.7347345. </p>
Final products from "3D MODELING AS A CONSERVATION TOOL TO CHARACTERIZE ENDANGERED SEASONALLY FLOODED ECOSYSTEMS IN THE VOLTA GRANDE DO XINGU, AMAZON FOREST, PARÁ, BRAZIL"
<p>In these .zip folders, you will find the products generated from flight missions carried out between November 7th to 14th, 2021, in the Volta Grande do Xingu, Pará, Brazil. <br>These results are presented as an integral part of the article titled '3D MODELING AS A CONSERVATION TOOL TO CHARACTERIZE ENDANGERED SEASONALLY FLOODED ECOSYSTEMS IN THE VOLTA GRANDE DO XINGU, AMAZON FOREST, PARÁ, BRAZIL' published on the doctoral thesis "Characterization and monitoring of the flooding dynamics and seasonally flooded environments of the Volta Grande do Xingu through remote sensing", available at <a href="https://doi.org/10.11606/T.106.2023.tde-02022024-211517">https://doi.org/10.11606/T.106.2023.tde-02022024-211517</a>. To understand the data processing methodology that led to these results, please refer to the thesis.<br>Each folder represents a flight mission. They are named by date and flight number (DD_MM_YYYY_FLIGHT#).<br>Within each folder, there are six files resulting from the processed flights: The georeferenced orthophoto and Digital Surface Model, which are raster files (.TIFs), the dense point cloud (.las), and the files composing the 3D Model generated by Agisoft Metashape (extensions .OBJ, .MTL, and .JPEG).<br>The .OBJ file is the primary file for visualizing the model, including the three-dimensional mesh formed by the points of the point cloud and containing geometry, texture, and color information. <br>The .MTL file contains the material description associated with the OBJ file and includes information about the visual properties of the model, such as texture, reflections, and materials. <br>The .JPEG files are the texture images used on the Digital Surface Model to generate the 3D model. This information provides the model with its realistic properties.<br>The .OBJ, .MTL and .JPEG files need to be together in the same folder for a complete 3D Model visualization (i.e., shape, color, and texture).<br>When using this data, please cite Affonso, A. A. (2023). <em>Caracterização e monitoramento da dinâmica de alagamento e dos ambientes sazonalmente alagáveis da Volta Grande do Xingu através de sensoriamento remoto</em>. Tese de Doutorado, Instituto de Energia e Ambiente, Universidade de São Paulo, São Paulo. doi:10.11606/T.106.2023.tde-02022024-211517. Recuperado em 2024-04-14, de www.teses.usp.br</p>
Fine-tuning of predictive microbiology models through microlocal characterization of foods by Nuclear Magnetic Resonance (NMR)
<p>Fine-tuning of predictive microbiology models through microlocal characterization of foods by Nuclear Magnetic Resonance (NMR)</p>
Characterization of the peripheral FAAH inhibitor, URB937, in animal models of acute and chronic migraine
<p>This dataset comprises the findings obtained in the study aimed at investigating the effects of URB937, a peripherally restricted fatty-acid amide hydrolase (FAAH) inhibitor, in two rat models that capture aspects of acute and chronic migraine, and are based on single or repeated administration of the vasodilating drug, nitroglycerin (NTG). The orofacial nocifensive behavior and mRNA levels of neuropeptides and pro-inflammatory cytokines along with tissue levels of anandamide and palmitoylethanolamide (PEA) were measured in trigeminal ganglia and medulla.</p> <p>All evaluations were made in rats that received a single injection of URB937 (1 mg/kg i.p.) either before or after NTG administration (10 mg/kg, i.p.) within the acute model, or daily URB937 (1 mg/kg i.p.) injections within the NTG (5 mg/kg, i.p.) chronic model. In the acute migraine model, we also investigated the effect of subtype-selective antagonist for cannabinoid receptors 1 and 2 (AM251 and AM630, respectively). Specifically, we achieved the following evaluations:</p> <p>1. Measurement of AEA and PEA levels: medulla and trigeminal ganglia were homogenized in cold methanol (2 ml) containing AEA-d4 and PEA-d4 as internal standards. After extraction the lipids were measured using a Xevo TQ UPLC-MS/MS system equipped with a reversed-phase BEH C18 column (2.1 × 50 mm, 1.7 μm particle size) (Waters, Milford, USA).</p> <p>2. Pain-related behavior in the orofacial formalin test: the face rubbing was measured counting the seconds the animal spent grooming the injected area (upper lip, lateral to the nose) with the ipsilateral forepaw or hindpaw 0–6 min (Phase I) or 12–45 min (Phase II) after formalin injection (50 µl, s.c.). The observation time was divided into 15 blocks of 3 min each.</p> <p>3. mRNA expression levels: calcitonin gene-related peptide (CGRP), interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-alpha) mRNA were evaluated in in medulla and trigeminal ganglia. mRNA levels were measured by rt-PCR. All samples were assayed in triplicate and gene expression levels were calculated according to 2−∆∆Ct = 2− (∆Ct gene − ∆Ct housekeeping gene) formula by using Ct (cycle threshold) values.</p>
In vivo characterization of antibodies directed against TREAT-AD target proteins in mouse model of AD pathology
<p><em>In vivo </em>characterization of antibodies directed against TREAT-AD target proteins (Moesin, CD44, Midkine, and SFRP1) in the 5xFAD mouse model</p>
CharM: a model for characterizing serviced-based architectures
<p>This dataset provides materials used and produced in the context of the research study leading to the paper <em>CharM: a model for characterizing serviced-based architectures</em>.</p> <p><strong>Research Objective</strong></p> <p>The main goal of this paper was <em>to develop and evaluate a model for characterizing the architecture of service-based systems, adopting microservices guidelines</em>. The model developed is named CharM and is organized into four dimensions that characterize service-based systems' architecture based on static metrics related to the structural attributes of size and coupling. The CharM was evaluated empirically through two case studies and one survey. This paper presents the result of the evaluation through the survey with 58 participants.</p> <p><strong>Research Questions</strong></p> <ul> <li><strong>RQ:</strong> How to characterize the architecture of SBS to guide architectural decision making? <ul> <li><strong>RQ1:</strong> To which extent does the CharM support understanding a service-based architecture?</li> <li><strong>RQ2:</strong> To which extent does the CharM support a service-based architecture maintenance?</li> <li><strong>RQ3:</strong> To which extent does the CharM support communicating a service-based architecture to stakeholders?</li> <li><strong>RQ4:</strong> How easy is it to understand the CharM?</li> <li><strong>RQ5:</strong> Does the participants' experience influences the perceived usefulness and ease of understanding of the CharM?</li> </ul> </li> </ul> <p>Material available</p> <ul> <li><strong>charm_evaluation_questionnaire.pdf</strong> - this questionnaire was designed to evaluate the use and ease of understanding of the CharM;</li> <li><strong>CharM presentation YouTube video</strong> - an overview presentation of the CharM and its dimensions and metrics, available at: <a href="http://available at: https://youtu.be/VQRqG9hLBSQ">https://youtu.be/VQRqG9hLBSQ</a>;</li> <li><strong>CharM demonstration YouTube video</strong> - a demonstration of a simple application of the CharM on the fictional Pingr System, available at: <a href="https://youtu.be/bK9Yg9jmQXY">https://youtu.be/bK9Yg9jmQXY</a>;</li> <li><strong>charm_related_research_summary.pdf</strong> - containing the summary of the related studies' analysis;</li> <li><strong>charm_acm_checklist.pdf</strong> - checklist of the ACM Empirical Standards "Engineering Research" and "Questionnaire Surveys";</li> <li><strong>charm_evaluation_quantitative_analysis.zip</strong> <ul> <li><strong>charm_evaluation_valid_answers.csv</strong> - spreadsheet containing the valid answers of the survey participants;</li> <li><strong>charm_evaluation_quantitative_analysis.ipynb</strong> - Python code with the quantitative analysis of CharM's evaluation;</li> <li><strong>requirements.txt</strong> - text file containing the specification of the necessary requirements to execute the Python code.</li> </ul> </li> </ul>
A novel technique to simulate and characterize a yarn's mechanical behavior based on a geometrical fiber model extracted from micro-CT imaging: geometry and simulation data
<p>This dataset contains the original µCT scan data, the scripts and intermediate results for the generation of the geometrical fiber model, as well as the structural simulation files and their experimental validation data described in the paper <a href="https://journals.sagepub.com/doi/10.1177/00405175221137009">"A novel technique to simulate and characterize a yarn's mechanical behavior based on a geometrical fiber model extracted from micro-CT imaging"</a>, published in Textile Research Journal.</p>
Shear strength characterization and statistical modelling of 12 hardwood timber species from the Congo Basin
Open the record for dataset details and reuse information.
Transcriptomic characterization of 2D and 3D human induced pluripotent stem cell-based in vitro models as New Approach Methodologies for developmental neurotoxicity testing
<p><strong>Abstract:</strong> The safety and developmental neurotoxicity (DNT) potential of chemicals remain critically understudied due to limitations of current in vivo testing guidelines, which are low throughput, resource-intensive, and hindered by species differences that limit their relevance to human health. To address these issues, robust new approach methodologies (NAMs) using deeply characterized cell models are essential. This study presents the comprehensive transcriptomic characterization of two advanced human-induced pluripotent stem cell (hiPSC)-derived models: a 2D adherent and a 3D neurosphere model of human neural progenitor cells (hiNPCs) differentiated up to 21 days. Using high-throughput RNA sequencing, we compared gene expression profiles of 2D and 3D models at three developmental stages (3, 14, and 21 days of differentiation). Both models exhibit maturation towards post-mitotic neurons, with the 3D model maturing faster and showing a higher prevalence of GABAergic neurons, while the 2D model is enriched with glutamatergic neurons. Both models demonstrate broad applicability domains, including excitatory and inhibitory neurons, astrocytes, and key endocrine and especially the understudied cholinergic receptors. Comparison with human fetal brain samples confirms their physiological relevance. This study provides novel in-depth applicability insights into the temporal and dimensional aspects of hiPSC-derived neural models for DNT testing. The complementary use of these two models is highlighted: the 2D model excels in synaptogenesis assessment, while the 3D model is particularly suited for neural network formation as observed as well in previous functional studies with these models. This research marks a significant advancement in developing human-relevant, high-throughput DNT assays for regulatory purposes.</p> <p><strong>This data sets contains:</strong></p> <p><strong>Tab. S1</strong> - Significant genes results</p> <p><strong>Tab. S2</strong> - Enriched pathways_GO_Biological Processes</p> <p><strong>Tab. S3</strong> - Enriched pathways_GO_Cellular Components</p> <p><strong>Tab. S4</strong> - Enriched pathways_GO_Molecular Function</p> <p><strong>Tab. S5</strong> - Enriched pathways_KEGG</p> <p><strong>Tab. S6</strong> - EnrichEnriched pathways_Panther</p> <p><strong>Tab. S7</strong> - Enriched pathways_Reactome</p> <p><strong>Tab. S8</strong> - Gene counts</p> <p><strong>Tab. S9</strong> - Gene selection for targeted analysis</p>
Thermodynamic characterization of the (H2 + C3H8) system significant for the hydrogen economy: Experimental (p, rho, T) determination and equation of-state modelling
<p>File: 2023_IJHE_Manuscript_repository.docx</p> <p>This is an author-created, un-copyedited version of an article accepted for publication in the International Journal of Hydrogen Energy (2023, 48 (23), 8645-8667). The editor of the Journal is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher-authenticated, Open-Access version is available online at: https://doi.org/10.1016/j.ijhydene.2022.11.170<br><br>File: 2023_IJHE_Results_Repository.xlsx</p> <p>This is the MS Excel data file of the paper. </p> <p> </p> <p> </p>
Characterization of NAD(P)H and FAD autofluorescence signatures in an isolated-perfused rat heart model
<p>Raw data concerning publication titled "Characterization of NAD(P)H and FAD autofluorescence signatures in an isolated-perfused rat heart model"</p> <p>Abstract</p> <p>Autofluorescence spectroscopy is a promising label-free approach to characterize biological samples with demonstrated potential to report structural and biochemical alterations in tissues in a number of clinical applications. We report a characterization of the ex vivo autofluorescence fingerprint of cardiac tissue, exploiting a Langendorff-perfused isolated rat heart model to induce physiological insults to the heart, with a view to understanding how metabolic alterations affect the autofluorescence signals. Changes in the autofluorescence intensity and lifetime signatures associated with reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and flavin adenine dinucleotide (FAD) were characterized during oxygen- or glucose-depletion protocols. Results suggest that both NAD(P)H and FAD autofluorescence intensity and lifetime parameters are sensitive to changes in the metabolic state of the heart owing to oxygen deprivation. We also observed changes in NAD(P)H fluorescence intensity and FAD lifetime parameter on reperfusion of oxygen, which might provide information on reperfusion injury, and permanent tissue damage or changes to the tissue during recovery from oxygen deprivation. We found that changes in the autofluorescence signature following glucose-depletion are, in general, less pronounced, and most clearly visible in NAD(P)H related parameters. Overall, the results reported in this investigation can serve as baseline for future investigations of cardiac tissue involving autofluorescence measurements.</p>
Dataset for Detailed Li-ion Battery Characterization Model for Economic Operation
<p>Dataset accompanying the research paper "Detailed Li-ion Battery Characterization Model for Economic Operation"</p>
Data and simulations files for the article "Accurate modeling and characterization of photothermal forces in optomechanics"
<p>Data and simulations files for the article "Accurate modeling and characterization of photothermal forces in optomechanics".</p>
A model-based approach to characterize enzyme-mediated response to antibiotic treatments: towards a model-guided classification
<p>This dataset, taken together with the scripts at <a href="https://gitlab.inria.fr/Public/InBio/esbl-escape">https://gitlab.inria.fr/Public/InBio/esbl-escape</a>, allows one to reproduce the analyses and figures of the article "A model-based approach to characterize enzyme-mediated response to antibiotic treatments: towards a model-guided classification".</p>
Dataset for "Characterization of rainwater infiltration within a controlled experiment by self-potential monitoring and modeling"
<p>This dataset provides the raw experimental data for the manuscript "Characterization of rainwater infiltration within a controlled experiment by self-potential monitoring and modeling". By imposing rainfall, we monitored the self-potential, volumetric water content, and temperature at different depths of a soil-column model within a water infiltration process. </p> <p> </p>
Model for: Characterizing long‐term population conditions of the elusive red tree vole with dynamic individual‐based modeling
<div class="abstract"> <p>Old growth forests are declining globally, threatening dependent wildlife. Many arboreal old‐growth obligates, such as the threatened red tree vole, are difficult to monitor for changes in habitat occupancy, and abundance. Yet, conservation planning relies on this information to prevent population declines. We integrated a range of species, habitat, and landscape change information to develop a dynamic habitat‐population model. The spatial individual‐based model simulated dynamic patterns of occupancy that responded to annual habitat maps, describing 36 years of observed change. We simulated population dynamics and local movement to characterize changes in occupancy and abundance, and the capacity of remaining habitat to support red tree voles. Red tree vole redistribution patterns strongly corresponded to wildfire footprints and timber extraction locations. Population strongholds are likely to exist in clumped pockets of old‐growth forest that were unaffected by wildfire and in protected old forest reserves. However, the exact number and locations of local clusters remain uncertain. Simulated population losses occurred at different paces in different places, underscoring the need for recurring evaluation of population changes with field occupancy surveys and modeled evaluations that can anticipate potential connectivity and extirpation thresholds. This modeling approach was effective at leveraging existing information for a data‐light species to assess how historical changes to the quantity, quality, and configuration of habitat likely influenced the potential landscape capacity, species abundance, and distribution. Dynamic individual‐based modeling can benefit conservation planning for red tree vole and other reclusive forest species by providing biologically nuanced assessments of abundance and distribution. Such models can also project the long‐term benefits and impacts of spatially explicit land management plans.</p> </div> <div class="abstract"></div>
Data for Cryogenic Characterization and Modeling of 14 nm Bulk FinFET Technology
<p>Data set for "Cryogenic Characterization and Modeling of 14 nm Bulk FinFET Technology"</p> <p>https://zenodo.org/record/6901637</p>
Improved dual-permeability model for characterizing the mass transfer process inside matrix blocks
<p>The dual-permeability model (DPM) is highly efficient for describing bimodal transport in heterogeneous porous media. However, it uses only one domain to describe the matrix blocks, and it therefore ignores the impact of the mass transfer process inside the matrix blocks at the microscale. Therefore, in this study, to investigate the effect of the mass transfer process in dual-permeability media and the computational accuracy when considering it, the dual-permeability model with a transition domain (DPMTD) is proposed based on the DPM. Comparison of the DPMTD with the DPM by applying them to a sand column experiment with the same concept as the model reveals that the DPMTD captures the bimodal transport (especially the first peak) more effectively because it calculates the rapid exchange of solute in the early stage more accurately. Subsequently, the same conclusion is reached when both models are applied to a reported solute displacement experiment for an Andisol. In short, we suggest that the mass transfer process inside matrix blocks needs to be characterized in the model to achieve higher accuracy and provides a new approach for modeling the solute transport of preferential flow.</p>
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.