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244 results for “Model Organisms”
Code and data for results and figures of the manuscript "Multi-million year cycles in modelled δ13C as a response to astronomical forcing of organic matter fluxes." submitted to Earth System Dynamics
<p>This dataset contains the code of the model used in the manuscript submitted to Earth System Dynamics "Multi-million year cycles in modelled δ13C as a response to astronomical forcing of organic matter fluxes.". It also contains some model outputs and code to draw the figures.</p>
Supplementary material 2 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
P-distance matrix : Explanation note: P-distance matrix over all specimens as EXCEL-file. Export from MEGA7.
Supplementary material 1 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
Complete sequences dataset : Explanation note: Complete sequences dataset of all specimens of this study in format FASTA.
Supplementary material 3 from: Reip HS, Wesener T (2018) Intraspecific variation and phylogeography of the millipede model organism, the Black Pill Millipede Glomeris marginata (Villers, 1789) (Diplopoda, Glomerida, Glomeridae). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 93-131. https://doi.org/10.3897/zookeys.741.21917
P-distance – geographical distance : Explanation note: P-distance – geographical distance table of all G. marginata specimens as EXCEL-file.
Secondary organic aerosol formation from smoldering and flaming combustion of biomass: a box model parametrization based on volatility basis set
<p>Here, we studied the aging of emissions from flaming and smoldering-dominated wood fires in three different residential stoves, across a wide range of aging temperatures (-10°C, 2°C and 15°C) and emission loads. Organic gases (OGs) acting as SOA precursors were monitored by a proton transfer reaction time-of-flight mass spectrometer (PTR-TOF-MS), while the evolution 10 of the aerosol properties during aging in the smog chamber was monitored by a high resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS). We developed a novel box model based on the volatility basis set (VBS) to determine the volatility distributions of the oxidation products from different precursor classes found in the emissions, grouped according to their emission pathways and SOA production rates.</p>
Environmentally induced lipidome adaptation in the bacterial model organism M. extorquens
<p>Cells, from microbes to man, adapt their membranes in response to the environment to maintain functionality. How cells sense environmental change/stimuli and adapt their membrane accordingly is unclear. In particular, how lipid composition changes and what lipid structural features are necessary for homeostatic adaptation remains relatively undefined. Here, we examine the simple yet adaptive lipidome of the plant-associated Gram-negative bacterium <em>Methylobacterium extorquens </em>over<em> </em>a range of chemical and physical conditions. Using shotgun lipidomics, we explored adaptivity over varying temperature, hyperosmotic and detergent stress, carbon sources, and cell density. Globally, we observed that as few as 10 lipids, representing ca. 30% of the lipidome, characterized by 9 structural features account for 90% of the total changes. We revealed that variations in lipid structural features are not monotonic over a given range of conditions (e.g. temperature) and are not evenly distributed across lipid classes. Thus, despite the compositional simplicity of this lipidome, the patterns in lipidomic remodeling suggest a highly adaptive mechanism with many degrees of freedom. Our observations reveal constraints on the minimal lipidomic requirements for an adaptive membrane and provide a resource for unraveling the design principles of living membranes.</p>
Dataset for "Sources of organic aerosols in Europe: A modelling study using CAMx with modified volatility basis set scheme"
<p>Model data for figures in the publication "Sources of organic aerosols in Europe: A modelling study using CAMx with modified volatility basis set scheme"</p> <p>Jiang, J., Aksoyoglu, S., El-Haddad, I., Ciarelli, G., Denier van der Gon, H. A. C., Canonaco, F., Gilardoni, S., Paglione, M., Minguillón, M. C., Favez, O., Zhang, Y., Marchand, N., Hao, L., Virtanen, A., Florou, K., O’Dowd, C., Ovadnevaite, J., Baltensperger, U., and Prévôt, A. S. H.: Sources of organic aerosols in Europe: A modelling study using CAMx with modified volatility basis set scheme, Atmos. Chem. Phys., 2019.</p> <p> All the data are stored in .mat file, and the variable names are self-explanatory.</p> <p> </p> <p> </p> <p> </p>
Self-organized transport model of spark discharge development and its application to the process of lightning initiation in a thundercloud
<p>This video visualizes results obtained by a small-scale transport model of electrical discharge formation in a thundercloud. The model discharge tree is a dynamic graph, nodes and edges of which are capacitive and conductive elements, respectively, electrical parameters of which vary with time. In the framework of the used approach, a heated well-conducting lightning leader channel is formed by combining the currents of tens of thousands of streamers, each of which initially has a negligible conductivity and a temperature, which does not differ from the ambient value. The model leader has electrical characteristics, which are intermediate between the laboratory long spark and the developed lightning channel, which is expected for an “immature” lightning leader.</p>
Predicting the pro-longevity or anti-longevity effect of model organism genes with enhanced Gaussian noise augmentation-based contrastive learning on protein-protein interaction networks
<p>The datasets used to evaluate Enhanced Gaussian noise augmentation-based contrastive learning (EGsCL) against predicting the pro-longevity or anti-longevity effect of model organism gene. This repo also includes the pretrained encoders that obtained the best predictive performance for each organism (see Table 2).</p>
Data from: Spatiotemporal diversification of the true frogs (Genus Rana): a historical framework for a widely studied group of model organisms
True frogs of the genus Rana are widely used as model organisms in studies of development, genetics, physiology, ecology, behavior, and evolution. Comparative studies among the more than 100 species of Rana rely on an understanding of the evolutionary history and patterns of diversification of the group. We estimate a well-resolved, time-calibrated phylogeny from sequences of six nuclear and three mitochondrial loci sampled from most species of Rana, and use that phylogeny to clarify the group's diversification and global biogeography. Our analyses consistently support an "Out of Asia" pattern with two independent dispersals of Rana from East Asia to North America via Beringian land bridges. The more species-rich lineage of New World Rana appears to have experienced a rapid radiation following its colonization of the New World, especially with its expansion into montane and tropical areas of Mexico, Central America, and South America. In contrast, Old World Rana exhibit different trajectories of diversification; diversification in the Old World began very slowly and later underwent a distinct increase in speciation rate around 29–18 Ma. Net diversification is associated with environmental changes and especially intensive tectonic movements along the Asian margin from the Oligocene to early Miocene. Our phylogeny further suggests that previous classifications were misled by morphological homoplasy and plesiomorphic color patterns, as well as a reliance primarily on mitochondrial genes. We provide a phylogenetic taxonomy based on analyses of multiple nuclear and mitochondrial gene loci.
Natural history of model organisms: the secret (group) life of Drosophila melanogaster larvae and why it matters to developmental ecology
<ol> <li>Model organisms such as <i>Drosophila melanogaster</i> have been key tools for advancing our fundamental and applied knowledge in biological and biomedical sciences. However, model organisms have become intertwined with the idea of controlled and stable laboratory environments, and their natural history has been overlooked.</li> <li>In holometabolous insects, lack of natural history information on larval ecology has precluded major advances in the field of developmental ecology, especially in terms of manipulations of population density early in life (i.e., larval density). This is because of relativistic and to some extent, arbitrary methodologies employed to manipulate larval densities in laboratory studies. As a result, these methodologies render comparisons between species impossible, precluding our understanding of macroevolutionary responses to population densities during development that can be derived from comparative studies.</li> <li>We recently proposed a new conceptual framework to address this issue and here, we provide the first natural history investigation of <i>Drosophila melanogaster </i>larval density under such framework. First, we characterised the distribution of larval densities in wild population of <i>D. melanogaster </i>using rotting apples as breeding substrate in a suburban area in Sweden.</li> <li>Next, we compiled the commonly used methodologies for manipulating larval densities in laboratory studies from the literature and found that the majority of laboratory studies did not manipulate larval densities below or above the densities observed in nature, suggesting that we have yet to study true life-history and physiological responses to low and high population densities during <i>D. melanogaster</i> development.</li> <li>This is, to our knowledge, the first direct natural history account of larval density in nature for this model organism. Our study paves the way for a more integrated view of organismal biology which re-incorporates natural history of model organisms into hypothesis-driven research in developmental ecology.</li> </ol>
Dataset: A model of tension-induced fiber growth predicts white matter organization during brain folding
<p>This dataset contains models, MRI data, and code associated with "A model of tension-induced fiber growth predicts white matter organization during brain folding" in <em>Nature Communications </em>(accepted 27 Oct 2021).</p> <p>Included files:</p> <ol> <li>NatCommMRIdata.zip - MRI data and associated MATLAB code for analysis of each subject</li> <li>folding_with_fibers.mph - model file used to generate results in Main Text. Modifiable parameters include stress-dependent fiber elongation rate, initial fiber volume fractions, initial geometry, and cortical growth rate. Compatible with COMSOL Multiphysics (version 5.3).</li> <li>folding_with_fibersECM.mph - model file corresponding to Supplementary Fig. 2. Compatible with COMSOL Multiphysics (version 5.3).</li> <li>folding_with_fibers_linear.mph - model file corresponding to Supplementary Fig. 3. Compatible with COMSOL Multiphysics (version 5.3).</li> </ol> <ol> </ol>
Supplementary material 1 from: van Gestel CAM, Loureiro S, Zidar P (2018) Terrestrial isopods as model organisms in soil ecotoxicology: a review. In: Hornung E, Taiti S, Szlavecz K (Eds) Isopods in a Changing World. ZooKeys 801: 127-162. https://doi.org/10.3897/zookeys.801.21970
Supporing information : Explanation note: Table S1: Overview of literature data on the toxicity of selected chemicals to isopods exposed through food or soil.
Supplementary material 1 from: Lahey Z, Chen H, Dowton M, Austin AD, Johnson NF (2023) The genome of the egg parasitoid Trissolcus basalis (Wollaston) (Hymenoptera, Scelionidae), a model organism and biocontrol agent of stink bugs. Journal of Hymenoptera Research 95: 31-44. https://doi.org/10.3897/jhr.95.97654
Genome of the egg parasitoid Trissolcus basalis (Wollaston) (Hymenoptera, Scelionidae), a model organism and biocontrol agent of stink bugs
Data for "Models of orientational disorder in hybrid organic-inorganic piezoelectric materials"
<p>Data for "Models of orientational disorder in hybrid organic-inorganic piezoelectric materials"</p>
Organic aerosol sources in the Milan metropolitan area – Receptor modelling based on field observations and air quality modelling
<p>This is the data related to the paper "Organic aerosol sources in the Milan metropolitan area – Receptor modelling based on field observations and air quality modelling" in Atmospheric Environment</p> <p> </p>
Mammalian animal & human retinal organ culture as pre-clinical model to evaluate oxidative stress and antioxidant intraocular therapeutics
<p>Oxidative stress (OS) is involved in the pathogenesis of retinal neurodegenerative diseases like age-related macular degeneration (AMD) and diabetic retinopathy (DR) and an important target of therapeutic treatments. New therapeutics are tested in vivo despite limits in transferability and ethical concerns. Retina cultures using human tissue can deliver critical information and significantly reduce the number of animal experiments along with increased transferability. We cultured up to 32 retina samples derived from one eye, analyzed models’ quality, induced OS, and tested efficiency of antioxidative therapeutics. Bovine, porcine, rat, and human retinae were cultured in different experimental settings for 3-14 d. OS was induced by high-glucose or hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) and treated by Scutellarin, pigment epithelium-derived factor (PEDF), and/or granulocyte macrophage-colony stimulating factor (GM-CSF). Tissue morphology, cell viability, inflammation, and glutathione level were determined. Retina samples showed only moderate necrosis (23.83±5.05 increased to 27.00±1.66 AU PI-staining over 14 d) after 14 days in culture. OS was successfully induced (reduced ATP content of 288.3±59.9 vs. 435.7±166.8 nM ATP in controls); antioxidants reduced OS-induced apoptosis (from 124.20±51.09 to 60.80±319.66 cells/image after Scutellarin-treatment). Enhanced mammalian animal and human retina cultures allow reliable, highly transferable research on OS-triggered age-related diseases and pre-clinical testing during drug development.</p>
Data from "Connecting large-scale meteorological patterns to extratropical cyclones in CMIP6 climate models using self-organizing maps"
<p>The following files were used as data and analysis in the article "Connecting large-scale meteorological patterns to extratropical cyclones in CMIP6 climate models using self-organizing maps" (<a href="https://doi.org/10.1029/2022EF003211">https://doi.org/10.1029/2022EF003211</a>). In the study, we applied self-organizing maps (SOMs) as an automated machine-learning approach to characterize the large-scale meteorological patterns (LSMP) and associated frequency and intensity of discrete extratropical cyclone (ETC) events over the northeastern U.S. The dominant patterns of geopotential height variability are identified through SOM analysis of five reanalysis products during 1980 - 2019. ETC events are tracked using TempestExtremes and are integrated with SOMs to classify the accumulated cyclone activity associated with each pattern. We then evaluate the skill of CMIP6 historical experiments in simulating the LSMP and ETC events identified in the SOM. Please see the published paper for more details. Here we have archived: </p> <p>- data pre-processing scripts</p> <p>- code to run the self-organizing map analysis</p> <p>- code to calculate the SOM and ETC statistics</p> <p>- composites of 500-hPa geopotential height for each dataset as organized by the SOM</p> <p>- ETC tracking script and tracking output for each dataset</p> <p>- SOM output for each dataset </p>
Can the Enhanced Transtheoretical Model Intervention (ETMI) be Implemented in a Public Health Organization
ClinicalTrials.gov study NCT04819009. IPD Sharing: YES. Countries: 1. Publications: 3.
Effectiveness New Health Care Organization Model in Primary Care for Chronic Cardiovascular Disease Patients Based
ClinicalTrials.gov study NCT01826929. IPD Sharing: Not stated. Countries: 1. Publications: 21.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.