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266 results for “experimental models”
Data from: Fertility and mortality impacts of experimental heatwave conditions on different life stages and their reproductive recovery in a model insect
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Overriding hindcast experimental results in MIROC6 climate model
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Data from: Using dynamic N-mixture models to test cavity limitation on northern flying squirrel demographic parameters using experimental nest box supplementation.
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Experimental evidence of warming-induced disease emergence and its prediction by a trait-based mechanistic model
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Experimental data and linear model for "Asymmetric internal tide generation in the presence of a steady flow"
<p>This dataset contain the experimental data, analyses, and linear model that are described in the manuscript</p> <p>"Asymmetric internal tide generation in the presence of a steady flow". submitted to Journal of Geophysical Research - Oceans.</p> <p>The folder data_density_fields_fluxes contains the experimental density fields (itXX/results/densityfields) and energy fluxes (itXX/results/fluxes) for the five experiments described in the manuscript: exp I (it17), exp II (it16), exp III (it15), exp IV (it13) and exp (V) (it 18).</p> <p>The Dossmannetal_wavesolution.m file is the linear model described in the manuscript for internal wave generation over a ridge.</p>
Experimental and Simulation Results of "Hemodynamic study in 3D printed stenotic coronary artery models: experimental validation and transient simulation"
<p>This repository contains the experimental and simulation results of the submitted article "Hemodynamic study in 3D printed stenotic coronary artery models: experimental validation and transient simulation" by Carvalho, V., Rodrigues, N., Ribeiro, R., Costa, P., Lima, R., Teixeira, S. </p>
Hydraulic hysteresis of unsaturated pyroclastic soils: experimental investigation and model calibration
<p>In many geotechnical applications, especially in the study of weather-induced landslides, a reliable soil hydraulic characterization under unsaturated conditions is required. Currently, the experimental techniques neglecting hydraulic hysteresis represent the greatest limitation to landslide forecasting. Here, experimental data from a new procedure to obtain an unsaturated soil hydraulic characterization are reported. These allows us to evaluate the soil hydraulic properties not only along the main drying path but also along wetting/drying cycles. Pyroclastic soil samples collected at a test site located at Mount Faito in the Campania region (southern Italy) were tested. The experimental investigation consisted of a forced evaporation test followed by a number of wetting-drying cycles. </p>
WASHTREET - Hydraulic, wash-off and sediment transport experimental data obtained in an urban drainage physical model
<p><strong>WASHTREET</strong><strong> -</strong> <strong>Hydraulic, wash-off and sediment transport experimental data obtained in an urban drainage physical model.</strong></p> <p>This dataset contains the results from the tests carried out at a laboratory physical model in the Hydraulic Laboratory of the Centre for Technological Innovation in Construction and Civil Engineering (CITEEC) at the University of A Coruña (Spain) as part of the <a href="https://zenodo.org/communities/washtreet">WASHTREET project</a>. The objective of the project is to perform a series of high-resolution experiments where urban surface wash-off and sediment transport through gully pots and pipes were accurately measured in laboratory-controlled conditions in a separate drainage system.</p> <p>The experimental facility is a 36 m2 full-scale street section and consists of a rainfall simulator placed over a concrete street surface with two gully pots that drain runoff into an underground pipe system. Further details of the physical model are provided in ‘1_Physical_model_description.pdf’. Two zip files with rain intensity distributions (‘2_Rain_intensity_maps.zip’) and model topographies (‘3_Elevation_data.zip’) complete physical model information as accurately measured inputs for hydraulic, wash-off and sediment transport experiments. ‘4_Hydraulic_tests_description.pdf’ describes experimental procedure, equipment, measuring points, results and data set files of the hydraulic characterization of the experiments. Data regarding these hydraulic tests is included in ‘5_Hydraulic_tests.zip’. In these tests, flow in both gully pots and in the pipe system outlet, and a total of 6 surface and 6 pipe depths were measured by ultrasound distance sensors for the different simulated rains.</p> <p>‘6_Washoff_tests_description.pdf’ includes information of the experimental initial conditions, the different sediment granulometries used, measuring points, experimental procedure and result files regarding wash-off and sediment transport experiments. Data files of a total of 23 tests are included in ‘7_Wash-off_tests.zip’. In these experiments, an initial mass of sediment is distributed over the model surface, and the wash-off and sediment transport processes are measured during a steady and uniform rainfall by total suspended solids (TSS) and particle size distribution (PSD) samples at the entrance of gully pots and at the pipe system outlet. Online turbidity measurements at pipe system outlet, pipe depths and flow at pipe system outlet are also measured during the experiments. Results regarding mass balances, which are performed at the end of the experiment to assess the final distribution of sediments, are also included. At last, some relevant photos and videos taken during the experiments are provided in ‘8_Multimedia.zip’. </p> <p>Flow measurements have been used in Naves et al. (2019) (DOI: <a href="https://doi.org/10.1016/j.jhydrol.2019.05.003">10.1016/j.jhydrol.2019.05.003</a>), together with the related datasets <a href="http://www.doi.org/10.5281/zenodo.3239401">WASHTREET - PIV data</a> and <a href="http://www.doi.org/10.5281/zenodo.3241337">WASHTREET - Structure from Motion data</a>, to calibrate a 2D shallow water model.</p> <p>The WASHTREET project is being developed in the scope of the PhD thesis of the first author, which is in receipt of a Spanish Ministry of Science, Innovation and Universities predoctoral grant [FPU14/01778]. The project also receive funding from the Spanish Ministry of Science, Innovation and Universities under POREDRAIN project RTI2018-094217-B-C33 (MINECO/FEDER-EU)</p> <p> </p> <p>Derived publications:</p> <ul> <li>Naves, J., Anta, J., Suárez, J., & Puertas, J. (2020). Hydraulic, wash-off and sediment transport experiments in a full-scale urban drainage physical model. <em>Scientific Data</em>, <em>7</em>(1), 1-13. <a href="https://doi.org/10.1038/s41597-020-0384-z">https://doi.org/10.1038/s41597-020-0384-z</a></li> <li>Naves, J., Rieckermann, J., Cea, L., Puertas, J., & Anta, J. (2020). Global and local sensitivity analysis to improve the understanding of physically-based urban wash-off models from high-resolution laboratory experiments. <em>Science of The Total Environment</em>, <em>709</em>, 136152. <a href="https://doi.org/10.1016/j.scitotenv.2019.136152">https://doi.org/10.1016/j.scitotenv.2019.136152</a></li> <li>Naves, J., Anta, J., Puertas, J., Regueiro-Picallo, M., & Suárez, J. (2019). Using a 2D shallow water model to assess Large-Scale Particle Image Velocimetry (LSPIV) and Structure from Motion (SfM) techniques in a street-scale urban drainage physical model. <em>Journal of Hydrology</em>, <em>575</em>, 54-65. <a href="https://doi.org/10.1016/j.jhydrol.2019.05.003">https://doi.org/10.1016/j.jhydrol.2019.05.003</a></li> <li>Naves, J., Anta, J., Suárez, J., & Puertas, J. (2020). Development and Calibration of a New Dripper-Based Rainfall Simulator for Large-Scale Sediment Wash-Off Studies. <em>Water</em>, <em>12</em>(1), 152. <a href="https://doi.org/10.3390/w12010152">https://doi.org/10.3390/w12010152</a></li> </ul>
Application of Different Building Representation Techniques in HEC-RAS 2-D for Urban Flood Modeling Using the Toce River Experimental Case
<p>The output of numerical simulation in HEC-RAS 2-D</p>
Data: Experimental evidence of warming-induced disease emergence and its prediction by a trait-based mechanistic model
<p>Predicting the effects of seasonality and climate change on the emergence and spread of infectious disease remains difficult, in part because of poorly understood connections between warming and the mechanisms driving disease. Trait-based mechanistic models combined with thermal performance curves arising from the Metabolic Theory of Ecology (MTE) have been highlighted as a promising approach going forward; however, this framework has not been tested under controlled experimental conditions that isolate the role of gradual temporal warming on disease dynamics and emergence. Here, we provide experimental evidence that a slowly warming host – parasite system can be pushed through a critical transition into an epidemic state. We then show that a trait-based mechanistic model with MTE functional forms can predict the critical temperature for disease emergence, subsequent disease dynamics through time, and final infection prevalence in an experimentally warmed system of <i>Daphnia </i>and a microsporidian parasite. Our results serve as a proof of principle that trait-based mechanistic models using MTE sub-functions can predict warming-induced disease emergence in data-rich systems – a critical step towards generalizing the approach to other systems.</p>
Data from: Effect of detection heterogeneity in occupancy-detection models: an experimental test of time-to-first-detection methods
Imperfect detection can bias estimates of site occupancy in ecological surveys but can be corrected by estimating detection probability. Time-to-first-detection (TTD) occupancy models have been proposed as a cost-effective survey method that allows detection probability to be estimated from single site visits. Nevertheless, few studies have validated the performance of occupancy-detection models by creating a situation where occupancy is known, and model outputs can be compared with the truth. We tested the performance of TTD occupancy models in the face of detection heterogeneity using an experiment based on standard survey methods to monitor koala (Phascolarctos cinereus) populations in Australia. Known numbers of koala faecal pellets were placed under trees, and observers, uninformed as to which trees had pellets under them, carried out a TTD survey. We fitted five TTD occupancy models to the survey data, each making different assumptions about detectability, to evaluate how well each estimated the true occupancy status. Relative to the truth, all five models produced strongly biased estimates, overestimating detection probability and underestimating the number of occupied trees. Despite this, goodness-of-fit tests indicated that some models fitted the data well, with no evidence of model misfit. Hence, TTD occupancy models that appear to perform well with respect to the available data may be performing poorly. The reason for poor model performance was unaccounted for heterogeneity in detection probability, which is known to bias occupancy-detection models. This poses a problem because unaccounted for heterogeneity could not be detected using goodness-of-fit tests and was only revealed because we knew the experimentally determined outcome. A challenge for occupancy-detection models is to find ways to identify and mitigate the impacts of unobserved heterogeneity, which could unknowingly bias many models.
Data from: Experimental heatwaves compromise sperm function and cause transgenerational damage in a model insect
Climate change is affecting biodiversity, but proximate drivers remain poorly understood. Here, we examine how experimental heatwaves impact on reproduction in an insect system. Male sensitivity to heat is recognised in endotherms, but ectotherms have received limited attention, despite comprising most of biodiversity and being more influenced by temperature variation. Using a flour beetle model system, we find that heatwave conditions (5 to 7 °C above optimum for 5 days) damaged male, but not female, reproduction. Heatwaves reduce male fertility and sperm competitiveness, and successive heatwaves almost sterilise males. Heatwaves reduce sperm production, viability, and migration through the female. Inseminated sperm in female storage are also damaged by heatwaves. Finally, we discover transgenerational impacts, with reduced reproductive potential and lifespan of offspring when fathered by males, or sperm, that had experienced heatwaves. This male reproductive damage under heatwave conditions provides one potential driver behind biodiversity declines and contractions through global warming.
Data from: Differential temperature sensitivity of synaptic and firing processes in a neural mass model of epileptic discharges explains heterogeneous response of experimental epilepsy to focal brain cooling
Experiments with drug-induced epilepsy in rat brains and epileptic human brain region reveal that focal cooling can suppress epileptic discharges without affecting the brain's normal neurological function. Findings suggest a viable treatment for intractable epilepsy cases via an implantable cooling device. However, precise mechanisms by which cooling suppresses epileptic discharges are still not clearly understood. Cooling experiments in vitro presented evidence of reduction in neurotransmitter release from presynaptic terminals and loss of dendritic spines at post-synaptic terminals offering a possible synaptic mechanism. We show that termination of epileptic discharges is possible by introducing a homogeneous temperature factor in a neural mass model which attenuates the post-synaptic impulse responses of the neuronal populations. This result however may be expected since such attenuation leads to reduced post-synaptic potential and when the effect on inhibitory interneurons is less than on excitatory interneurons, frequency of firing of pyramidal cells is consequently reduced. While this is observed in cooling experiments in vitro, experiments in vivo exhibit persistent discharges during cooling but suppressed in magnitude. This leads us to conjecture that reduction in the frequency of discharges may be compensated through intrinsic excitability mechanisms. Such compensatory mechanism is modelled using a reciprocal temperature factor in the firing response function in the neural mass model. We demonstrate that the complete model can reproduce attenuation of both magnitude and frequency of epileptic discharges during cooling. The compensatory mechanism suggests that cooling lowers the average and the variance of the distribution of threshold potential of firing across the population. Bifurcation study with respect to the temperature parameters of the model reveals how heterogeneous response of epileptic discharges to cooling (termination or suppression only) is exhibited. Possibility of differential temperature effects on post-synaptic potential generation of different populations is also explored.
Data from: Avian malaria: a new lease of life for an old experimental model to study the evolutionary ecology of Plasmodium
Avian malaria has historically played an important role as a model in the study of human malaria, being a stimulus for the development of medical parasitology. Avian malaria has recently come back to the research scene as a unique animal model to understand the ecology and evolution of the disease, both in the field and in the laboratory. Avian malaria is highly prevalent in birds and mosquitoes around the world and is amenable to laboratory experimentation at each stage of the parasite's life cycle. Here, we take stock of 5 years of experimental laboratory research carried out using Plasmodium relictum SGS1, the most prevalent avian malaria lineage in Europe, and its natural vector, the mosquito Culex pipiens. For this purpose, we compile and analyse data obtained in our laboratory in 14 different experiments. We provide statistical relationships between different infection-related parameters, including parasitaemia, gametocytaemia, host morbidity (anaemia) and transmission rates to mosquitoes. This analysis provides a wide-ranging picture of the within-host and between-host parameters that may bear on malaria transmission and epidemiology.
Fitness of mCherry Reporter Tick-Borne Encephalitis Virus in Tick Experimental Models
<p>Figures and open datasets from the publication about the reporter TBEV in tick experimental models by Kevély et al., 2022 (<a href="https://doi.org/10.3390/v14122673">https://doi.org/10.3390/v14122673</a>)</p>
Network topology and patch connectivity affect dynamics in experimental and model metapopulations
<p>Biological populations are rarely isolated in space and instead interact with others via dispersal in metapopulations. Theory predicts that network connectivity patterns can have critical effects on network robustness, as certain topologies, such as scale-free networks, are more tolerant to disturbances than other patterns. However, at present, experimental evidence of how these topologies affect population dynamics in a metapopulation framework is lacking. We used experimental metapopulations of the aquatic protist <i>Paramecium tetraurelia</i> to determine how network topology influences occupation patterns. We created metapopulations engineered to be comparable in linkage density, but differing in their degree distribution. We compared random networks to scale-free networks by evaluating local population occupancy and abundance throughout 18-30 protist generations. In parallel, we used simulations to explore differences in patch occupation patterns among topologies. Under one scenario, random metapopulations of P. tetraurelia reached higher abundance and higher occupancy (proportion of occupied patches) compared to scale-free systems in both experimental and simulated systems, while in the other both types of metapopulations performed similarly. Increasing patch degree (i.e., number of connections per patch) reduced the probability of extinction of local populations in both types of networks. We suggest the interaction between colonization/extinction rates and network topology alters the likelihood of rescue effects which results in differential patterns of occupancy and abundance in metapopulations.</p>
Experimental and model-based investigation of the effect of the free- surface flow regime on the detection threshold of warm water inflow
<p>Experimental and numerical injections of warm water into a free surface flow. Different flow regimes were tested and detection thresholds were determined.</p> <p>Experiments were done in an outdoor flume, in June 2016. They were monitored by Fiber-Optic Distributed Temperature Sensing with a double-ended configuration and 20s time resolution. Two flume flow rates Q were tested. For each, a few injection flow rates were done, leading to a total of 10 experiments characterized by an injection ratio R. Only calibrated data are uploaded.</p> <p>Simulations were carried out on HEC-RAS 5.0, a 1D software developed by the US Army Corps of Engineers, and based on the experimental flume geometry. A total of 90 simulations were tested with different flow rates, injection percentage and thermal contrast ∆T between flowing water and injected water.</p> <p>Supplementary data can be found to understand the flume geometry, hydraulic characteristics (Reynolds, Peclet and Froude numbers) and exchanges with the atmosphere for both simulations and experiments.</p>
Experimental moisture content and water saturation and modeled output NAPL-phase saturation
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Data from: Computational and experimental characterization of dVHL establish a Drosophila model of VHL syndrome
The von Hippel-Lindau (VHL) cancer syndrome is associated with mutations in the VHL gene. The pVHL protein is involved in response to changes in oxygen availability as part of an E3-ligase that targets the Hypoxia-Inducible Factor for degradation. pVHL has a molten globule configuration with marginal thermodynamic stability. The cancer-associated mutations further destabilize it. The Drosophila homolog, dVHL, has relatively low sequence similarity to pVHL, and is also involved in regulating HIF1-α. Using in silico, in vitro and in vivo approaches we demonstrate high similarity between the structure and function of dVHL and pVHL. These proteins have a similar fold, secondary and tertiary structures, as well as thermodynamic stability. Key functional residues in dVHL are evolutionary conserved. This structural homology underlies functional similarity of both proteins, evident by their ability to bind their reciprocal partner proteins, and by the observation that transgenic pVHL can fully maintain normal dVHL-HIF1-α downstream pathways in flies. This novel transgenic Drosophila model is thus useful for studying the VHL syndrome, and for testing drug candidates to treat it.
Dual clumped isotope analyses and model calculations constrain equilibrium, experimentally-manipulated kinetic isotope effects, and mixing effects in calcite
<p>Replicate data for standards and samples; XRD data. </p>
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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.