Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
237
datasets available to search
ShareScore release 0.9.0
Dataset results
237 results for “animal models”
Counting animals in aerial images with a density map estimation model
Open the record for dataset details and reuse information.
Data from: A hierarchical model for jointly assessing ecological and anthropogenic impacts on animal demography
Open the record for dataset details and reuse information.
Monitoring animal populations with cameras using open, multistate, N-mixture models
Open the record for dataset details and reuse information.
Vocalization data and scripts to model reindeer rut activity using on-animal acoustic recorders and machine learning
Open the record for dataset details and reuse information.
How to build a dinosaur: musculoskeletal modelling and simulation of locomotor biomechanics in extinct animals
<p>The intersection of paleontology and biomechanics can be reciprocally illuminating, helping to improve paleobiological knowledge of extinct species and furthering our understanding of the generality of biomechanical principles derived from study of extant species. However, working with data gleaned primarily from the fossil record has its challenges. Building on decades of prior research, we outline and critically discuss a complete workflow for biomechanical analysis of extinct species, using locomotor biomechanics in the Triassic theropod dinosaur <em>Coelophysis </em>as a case study. We progress from the digital capture of fossil bone morphology to creating rigged skeletal models, to reconstructing musculature and soft tissue volumes, to the development of computational musculoskeletal models, and finally to the execution of biomechanical simulations. Using a three-dimensional musculoskeletal model comprising 33 muscles, a static inverse simulation of the mid-stance of running shows that <em>Coelophysis </em>probably used more upright (extended) hindlimb postures, and was likely capable of withstanding a vertical ground reaction force of magnitude more than 2.5 times body weight. We identify muscle force-generating capacity as a key source of uncertainty in the simulations, highlighting the need for more refined methods of estimating intrinsic muscle parameters such as fibre length. Our approach emphasizes the explicit application of quantitative techniques and physics-based principles, which helps maximize results robustness and reproducibility. Although we focus on one specific taxon and question, many of the techniques and philosophies explored here have much generality to them, so they can be applied in biomechanical investigation of other extinct organisms.</p>
VFTS meeting: animation of main-sequence model evolution
<p>This animation shows the evolution of our binary and single stellar models from 2Myr to 100Myr. We populate 3763 binaries, whose primary mass is in the range of 3Msun to 100Msun, following a Salpeter IMF with an exponent of -2.37. The mass ratio is uniformly distributed from 0.1 to 1. The orbital period logP is uniformly distributed from the minimum value at which the two stars would contact initially to 3.5. Both components rotate at half of their critical velocities initially. </p> <p>Considering a binary fraction of 70%, we populate 1612 single stars with vi=0.5. In addition, we also populate 537 slowly-rotating single stars with vi=0.2 to reproduce the observed blue MS in young star clusters. The number is chosen such that the ratio between the slow and fast rotators is 1/3, which is the same as the ratio of observed blue and red MS stars. </p> <p>Gravity darkening and observational errors are included. Filled circles correspond to single stellar models, while open symbols correspond to binaries with different companions. Single stellar tracks with vi=0.5 are plotted with solid grey lines. The black dotted line represents the ZAMS line of vi=0.2 single stellar models. In the legend, the number in each group outside the parenthesis corresponds to the number of stars whose color and magnitude are in the figure range. While the number in the parenthesis corresponds to the number of stars above the orange dashed line, which is 1.75 mag below the turn-off magnitude. </p>
Weight loss, insulin resistance, and study design confound results in a meta-analysis of animal models of fatty liver
The classical drug development pipeline necessitates studies using animal models of human disease to gauge future efficacy in humans, however there is a low conversion rate from success in animals to humans. Non-alcoholic fatty liver disease (NAFLD) is a complex chronic disease without any established therapies and a major field of animal research. We performed a meta-analysis with meta-regression of 603 interventional rodent studies (10,364 animals) in NAFLD to assess which variables influenced treatment response. Weight loss and alleviation of insulin resistance were consistently associated with improvement in NAFLD. Multiple drug classes that do not affect weight in humans caused weight loss in animals. Other study design variables, such as age of animals and dietary composition, influenced the magnitude of treatment effect. Publication bias may have increased effect estimates by 37-79%. These findings help to explain the challenge of reproducibility and translation within the field of metabolism.
Evaluation of the silkworm lemon mutant as an invertebrate animal model for human sepiapterin reductase deficiency
Human sepiapterin reductase deficiency is an inherited disease caused by SPR gene mutations and is a monoamine neurotransmitter disorder. Here, we investigated whether the silkworm lemon mutant could serve as a model of sepiapterin reductase deficiency. A point mutation in the BmSPR gene led to a five amino acid deletion at the carboxyl terminus in the lemon mutant. In addition, classical phenotypes seen in sepiapterin reductase deficient patients were observed in the lemon mutant, including a normal phenylalanine level, a decreased dopamine and serotonin content, and an increased neopterin level. A recovery test showed that replenishment of L-dopa significantly increased the dopamine level in the lemon mutant. The silkworm lemon mutant also showed negative behavioral abilities. These results suggest that the silkworm lemon mutant has an appropriate genetic basis and meets the biochemical requirements to be a model of sepiapterin reductase deficiency. Thus, the silkworm lemon mutant can serve as a candidate animal model of sepiapterin reductase deficiency, which may be helpful in facilitating accurate diagnosis and effective treatment options of sepiapterin reductase deficiency.
Data from: Estimating abundance of an open population with an N-mixture model using auxiliary data on animal movements
Accurate assessment of abundance forms a central challenge in population ecology and wildlife management. Many statistical techniques have been developed to estimate population sizes because populations change over time and space, and to correct for the bias resulting from animals that are present in a study area but not observed. The mobility of individuals makes it difficult to design sampling procedures that account for movement into and out of areas with fixed jurisdictional boundaries. Aerial surveys are the gold standard used to obtain data of large mobile species in geographic regions with harsh terrain, but these surveys can be prohibitively expensive and dangerous. Estimating abundance with ground based census methods have practical advantages, but it can be difficult to simultaneously account for temporary emigration and observer error to avoid biased results. Contemporary research in population ecology increasingly relies on telemetry observations of the states and locations of individuals to gain insight on vital rates, animal movements, and population abundance. Analytical models that use observations of movements to improve estimates of abundance have not been developed. Here we build upon existing multi-state mark recapture methods using a hierarchical N-mixture model with multiple sources of data, including telemetry data on locations of individuals, to improve estimates of population sizes. We used a state-space approach to model animal movements to approximate the number of marked animals present within the study area at any observation period, thereby accounting for a frequently changing number of marked individuals. We illustrate the approach using data on a population of elk (Cervus elaphus nelsoni) in Northern Colorado, USA. We demonstrate substantial improvement compared to existing abundance estimation methods and corroborate our results from the ground based surveys with estimates from aerial surveys during the same seasons. We develop a hierarchical Bayesian N-mixture model using multiple sources of data on abundance, movement and survival to estimate the population size of a mobile species that uses remote conservation areas. The model improves accuracy of inference relative to previous methods for estimating abundance of open populations.
Evaluation of the silkworm lemon mutant as an invertebrate animal model for human sepiapterin reductase deficiency
<p><span>Human sepiapterin reductase deficiency is an inherited disease caused by <i>SPR</i> gene mutations and is a monoamine neurotransmitter disorder. Here, we investigated whether the silkworm <i>lemon<sup> </sup></i>mutant could serve as a model of sepiapterin reductase deficiency. A point mutation in the<i> BmSPR</i> gene led to a five amino acid deletion at the carboxyl terminus in the <i>lemon</i> mutant. In addition, classical phenotypes seen in sepiapterin reductase deficient patients were observed in the <i>lemon</i> mutant, including a normal phenylalanine level, a decreased dopamine and serotonin content, and an increased neopterin level. A recovery test showed that replenishment of L-dopa significantly increased the dopamine level in the <i>lemon<sup> </sup></i>mutant. The silkworm <i>lemon</i> mutant also showed negative behavioral abilities. These results suggest that the silkworm <i>lemon</i> mutant has an appropriate genetic basis and meets the biochemical requirements to be a model of sepiapterin reductase deficiency. Thus, the silkworm <i>lemon</i> mutant can serve as a candidate animal model of sepiapterin reductase deficiency, which may be helpful in facilitating accurate diagnosis and effective treatment options of sepiapterin reductase deficiency.</span></p>
Enhanced mTORC1 signaling and protein synthesis in pathologic alpha-synuclein cellular and animal models of Parkinson's disease
<p>Pathologic alpha-synuclein plays an important role in the pathogenesis of alpha-synucleinopathies such as Parkinson's disease (PD). Disruption of proteostasis is thought to be central to pathologic alpha-synuclein (alpha-syn) toxicity; however, the molecular mechanism of this deregulation is poorly understood. Here we report that pathologic alpha-syn activates the mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) leading to enhanced mRNA translation via binding tuberous sclerosis protein (TSC) 2 and destabilizing the TSC1-TSC2 complex. Genetic and pharmacologic inhibition of mTOR and protein synthesis rescue the dopamine neuron loss, behavioral deficits, and aberrant biochemical signaling in the alpha-syn preformed fibril (PFF) and Drosophila alpha-syn transgenic models of pathologic alpha-syn induced degeneration. Our findings establish a potential molecular mechanism by which pathologic alpha-syn activates mTORC1 leading to enhanced protein synthesis and concomitant neurodegeneration in PD.</p>
Model of the Watt Steam Engine with animation
Eugène Bourdon (1808–1884) – artist / maker ca. 1835, Paris A nineteenth-century model of the Watt steam engine. It allowed to demonstrate the principle of the steam engine's operation by mechanically turning a flywheel and connecting the machinery to an external source of steam or compressed gas. For more images and further information, visit: https://muzea.malopolska.pl/en/objects-list/2763 Inventory number: 4988; 993/V Localisation of the physical object: Jagiellonian University Museum, Collegium Maius, Kraków, Poland Digitalisation: Regional Digitalisation Lab, Małopolska Institute of Culture in Kraków, Poland; "Virtual Museums of Małopolska" Project 3D model & animation by Stanisław Ogarek as a diploma work at Tischner European University. Source: Objaverse 1.0 / Sketchfab
Data to support publication figures and animation scripts at GitHub: Modeling weather-driven long-distance dispersal of spruce budworm moths (Choristoneura fumiferana)
<p>Long-term studies of insect populations in the North American boreal forest have shown the vital importance of long-distance dispersal to the maintenance and expansion of insect outbreaks. In this work, we extend several concepts established previously in an empirically-based dispersal flight model with recent work on the physiology and behavior of the adult eastern spruce budworm (SBW) moth, Choristoneura fumiferana (Clem.). An outbreak of defoliating SBW in Quebec, ongoing since the mid-2000s, already covers millions of hectares of forests in eastern Canada and threatens to spread into neighboring areas through annual summertime episodes of long-distance dispersal. Such flight events in favorable conditions frequently include billions of SBW moths dispersing in the warm atmospheric boundary layer, typically starting around sunset and often lasting through several hours of wind-driven transport over hundreds of kilometers. Successful SBW dispersal to possibly distant host forest areas depends acutely on the weather. Here we describe the components and results of SBW–pyATM, an open-source individual-based modeling framework developed in Python for the simulation of these weather-driven SBW dispersal events. Using seasonal SBW phenology results from BioSIM at known outbreak locations and high-resolution Weather Research and Forecasting (WRF) model output, we focus on modeling dispersal flights over two successive nights in July 2013 in southern Quebec. Our flight model closely reproduces the SBW spatial patterns and motions observed by weather surveillance radar over the St. Lawrence estuary. With SBW–pyATM we can estimate landing locations for both male and female SBW and the resulting spatial patterns of egg distribution, allowing us eventually to forecast future larval defoliation activity in new locations where immigration could help overcome local limitations on SBW populations. This information could then support forest management decisions where SBW outbreaks threaten valuable resources.</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>
Raw Data for the article: Atrial Septostomy for Left Ventricular Unloading During Extracorporeal Membrane Oxygenation for Cardiogenic Shock: Animal Model
<p><strong>Objectives: </strong>The aim of this study was to quantify and understand the unloading effect of percutaneous balloon atrial septostomy (BAS) in acute cardiogenic shock (CS) treated with venoarterial (VA) extracorporeal membranous oxygenation (ECMO).</p> <p><strong>Background: </strong>In CS treated with VA ECMO, increased left ventricular (LV) afterload is observed that commonly interferes with myocardial recovery or even promotes further LV deterioration. Several techniques for LV unloading exist, but the optimal strategy and the actual extent of such procedures have not been fully disclosed.</p> <p><strong>Methods: </strong>In a porcine model (n = 11; weight 56 kg [53-58 kg]), CS was induced by coronary artery balloon occlusion (57 minutes [53-64 minutes]). Then, a step-up VA ECMO protocol (40-80 mL/kg/min) was run before and after percutaneous BAS was performed. LV pressure-volume loops and multiple hemoglobin saturation data were evaluated. The Wilcoxon rank sum test was used to assess individual variable differences.</p> <p><strong>Results: </strong>Immediately after BAS while on VA ECMO support, LV work decreased significantly: pressure-volume area, end-diastolic pressure, and stroke volume to ∼78% and end-systolic pressure to ∼86%, while superior vena cava and tissue oximetry did not change. During elevating VA ECMO support (40-80 mL/kg/min) with BAS vs without BAS, we observed 1) significantly less mechanical work increase (122% vs 172%); 2) no end-diastolic volume increase (100% vs 111%); and 3) a considerable increase in end-systolic pressure (134% vs 144%).</p> <p><strong>Conclusions: </strong>In acute CS supported by VA ECMO, atrial septostomy is an effective LV unloading tool. LV pressure is a key component of LV work load, so whenever LV work reduction is a priority, arterial pressure should carefully be titrated low while maintaining organ perfusion.</p>
Fig. 2 in A Review Of Major Impact Factors Of Hostilities Influencing Biodiversity In The Eastern Ukraine (Modeled On Selected Animal Species)
Fig. 2. Temporal distribution of numbers of ignitions in ATO zone in 2010–2014.
Integrated animal movement and spatial capture-recapture models: simulation, implementation, and inference
<p>Over the last decade, spatial capture-recapture (SCR) models have become widespread for estimating demographic parameters in ecological studies. However, the underlying assumptions about animal movement and space use are often not realistic. This is a missed opportunity because ecological questions related to animal space use, habitat selection, and behavior cannot be addressed with most SCR models, despite the fact that the data collected in SCR studies -- individual animals observed at specific locations and times -- can provide a rich source of information about how these processes relate to demographic rates. We developed SCR models that integrate complex movement processes that are typically inferred from telemetry data, including a simple random walk, correlated random walk (i.e., short-term directional persistence), and habitat-driven Langevin diffusion. We demonstrated how to formulate, simulate from, and fit these models with standard SCR data using Bayesian analysis methods. We evaluated their performance through a simulation study, where we varied the detection, movement, and resource selection parameters. We also examined different numbers of sampling occasions and assessed performance gains when including auxiliary location data collected from telemetered individuals. Across all scenarios, the integrated SCR movement models performed well in terms of abundance, detection, and movement parameter estimation. We found little difference in bias for the simple random walk model when reducing the number of sampling occasions from T=25 to T=15. We found some bias in movement parameter estimates under several of the correlated random walk scenarios, but incorporating auxiliary location data improved parameter estimates and significantly improved mixing during model fitting. The Langevin movement model was able to recover resource selection parameters from standard SCR data, which is appealing because it explicitly links the individual-level movement process with habitat selection and population density. We focused on closed population models, but movement models developed here could be extended to open SCR models. The movement process models could also be extended to accommodate additional "building blocks'' of random walks, such as central tendency (e.g., territoriality) or multiple movement behavior states, thereby providing a flexible and coherent framework for linking animal movement behavior to population dynamics, density, and distribution.</p>
Discrete element models for understanding the biomechanics of fossorial animals
<p><span>The morphological features of fossorial animals have continuously evolved in response to the demands of survival. However, </span><span>existing methods for animal burrowing mechanics are not capable of addressing the large deformation of substrate. T</span><span>he discrete element method (DEM) is able to overcome this limitation. In this study, we used DEM </span><span>to develop a general model to simulate the motion of an animal body part and its interaction with the substrate. The DEM also allowed us to easily change the forms of animal body parts to examine how those different forms affected the biomechanical functions. These capabilities of the DEM were presented through a case study of modelling the burrowing process of North American Badger. In the case study, the dynamics (forces, work, and soil displacements) of burrowing were predicted for different forms of badger claw and manus, using the model. Results showed that when extra digits are added to a manus, the work required for a badger to dig increases considerably, while the mass of soil dug only increases gradually. According to the proposed efficiency index (ratio of the amount of soil dug to the work required), the modern manus with 5 digits has indeed biomechanical advantage for their fossorial lifestyle, and the current claw curvature (25.3 mm in radius) is indeed optimal. The DEM is able to predict biomechanical relationships between functions and forms for any fossorial animals. Results can provide biomechanical evidences for explaining how the selective pressures for functions influence the morphological evolution in fossorial animals.</span></p>
Does mechanical loading restore ligament biomechanics after injury? A systematic review of studies using animal models
<p>This RevMan file accompanies our manuscript entitled "Does mechanical loading restore ligament biomechanics after injury? A systematic review of studies using animal models" published in <em>BMC Musculoskeletal Disorders</em>.</p> <p>The file hosts all outcomes (i.e., including tertiary outcomes) under "Data and analyses", as well as more detailed forest plots under "Figures". </p>
Modelling migraine-related features in the nitroglycerin animal model: trigeminal hyperalgesia is associated with affective status and motor behaviour
<p>This dataset comprises the findings obtained in the study aimed at exploring the correlation between trigeminal hyperalgesia and affective status or behavioral components in a migraine-specific animal model based on nitroglycerin administration (see article <em>Modelling migraine-related features in the nitroglycerin animal model: trigeminal hyperalgesia is associated with affective status and motor behaviour).</em></p> <p>In vivo assessments performed in male Sprague-Dawley rats four hours after treatment with nitroglycerin (10mg/kg, i.p.) or its vehicle:</p> <p>- in the open field test were evaluated: time spent (expressed in seconds) in the center of the apparatus as a measure of anxiety; distance (expressed in meters) travelled in the apparatus as a measure of motor behaviour; number of rearings as a measure of exploratory behaviour; time spent in grooming behavior (expressed in seconds) used as nociception index;</p> <p>- evaluation of trigeminal hyperalgesia 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 0–3 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><strong>RESULTS</strong></p> <p>The data analysis shows an inverse correlation between trigeminal hyperalgesia and motor or exploratory behavior, and a positive association with anxiety-like behavior of spontaneous grooming.</p> <p>These findings further expand on the translational value of the migraine-specific model based on nitroglycerin administration and prompt additional parameters that can be investigated to explore the complexity of the disease.</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.