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51 results for “root model”
Data from: A rapid and scalable method for multilocus species delimitation using Bayesian model comparison and rooted triplets
Multilocus sequence data provide far greater power to resolve species limits than the single locus data typically used for broad surveys of clades. However, current statistical methods based on a multispecies coalescent framework are computationally demanding, because of the number of possible delimitations that must be compared and time-consuming likelihood calculations. New methods are therefore needed to open up the power of multilocus approaches to larger systematic surveys. Here, we present a rapid and scalable method that introduces 2 new innovations. First, the method reduces the complexity of likelihood calculations by decomposing the tree into rooted triplets. The distribution of topologies for a triplet across multiple loci has a uniform trinomial distribution when the 3 individuals belong to the same species, but a skewed distribution if they belong to separate species with a form that is specified by the multispecies coalescent. A Bayesian model comparison framework was developed and the best delimitation found by comparing the product of posterior probabilities of all triplets. The second innovation is a new dynamic programming algorithm for finding the optimum delimitation from all those compatible with a guide tree by successively analyzing subtrees defined by each node. This algorithm removes the need for heuristic searches used by current methods, and guarantees that the best solution is found and potentially could be used in other systematic applications. We assessed the performance of the method with simulated, published, and newly generated data. Analyses of simulated data demonstrate that the combined method has favorable statistical properties and scalability with increasing sample sizes. Analyses of empirical data from both eukaryotes and prokaryotes demonstrate its potential for delimiting species in real cases.
Dataset: Bridging Time-series Image Phenotyping and Functional-Structural Plant Modeling to Predict Adventitious Root System Architecture
<p>Dataset for Bridging Time-series Image Phenotyping and Functional-Structural Plant Modeling to Predict Adventitious Root System Architecture manuscript submitted to Plant Phenomics. The dataset contains raw and processed root architecture images, RhizoVision trait outputs, and the associated R scripts for statistical analysis and model parameterization.</p>
Data from: A rapid and scalable method for multilocus species delimitation using Bayesian model comparison and rooted triplets
Open the record for dataset details and reuse information.
Root biomass distribution simulated by the DyRoot model
<p>A database of root biomass distribution simulated by the DyRoot model.</p>
Machine learning based root stress calculation model for gears with progressive curved path of contact
<p><em>A machine learning based model for calculation of root stress in gears with a progressive curved path of contact is proposed. The prediction model is used as a surrogate model to the finite element analysis simulations, from which the data was collected. The results of the validation of all the methods are presented. Further validation was done with new simulations.</em></p>
Modeling plant roots spectral induced polarization signature - data
<p>Data used for Figures</p>
Data from: Heterogeneous models place the root of the placental mammal phylogeny
Heterogeneity among life traits in mammals has resulted in considerable phylogenetic conflict, particularly concerning the position of the placental root. Layered upon this are gene- and lineage-specific variation in amino acid substitution rates and compositional biases. Life trait variations that may impact upon mutational rates are longevity, metabolic rate, body size and germ line generation time. Over the past 12 years, three main conflicting hypotheses have emerged for the placement of the placental root. These hypotheses place: the Atlantogenata (common ancestor of Xenarthra plus Afrotheria), the Afrotheria, or the Xenarthra as the sister group to all other placental mammals. Model adequacy is critical for accurate tree reconstruction and by failing to account for these compositional and character exchange heterogeneities across the tree and dataset, previous studies have not provided a strongly supported hypothesis for the placental root. For the first time, models that accommodate both tree and dataset heterogeneity have been applied to mammal data. Here we show the impact of accurate model assignment and the importance of datasets in accommodating model parameters while maintaining the power to reject competing hypotheses. Through these sophisticated methods, we demonstrate the importance of model adequacy, dataset power and provide strong support for the Atlantogenata over other competing hypotheses for the position of the placental root.
Data from: Heterogeneous models place the root of the placental mammal phylogeny
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AirMOSS: L4 Modeled Volumetric Root Zone Soil Moisture, 2012-2015
This data set provides hourly gridded soil moisture estimates derived from hydrologic modeling at nine AirMOSS sites across North America. The AirMOSS L4 RZSM product represents a temporal interpolation of intermittent AirMOSS L2/3 RZSM retrievals into a temporally-continuous, multi-layer, hourly soil moisture product. The L4 RZSM data have the same spatial resolution (3-arcsecs or ~100 m), and the same temporal coverage (generally Fall 2012 through Fall 2015), as the underlying L2/3 RZSM data. The L4 RZSM data were produced by the integration of the Level 2/3 product and other ancillary information into the Penn State Integrated Hydrologic Model (PIHM). Many key applications for AirMOSS data products, including the calculation of net ecosystem exchange (NEE), require temporally continuous RZSM estimates such as those provided here.
Signatures of altered gene expression in dorsal root ganglia of a Fabry disease mouse model
GEO Series GSE104625. Mus musculus. 8 samples. Type: Expression profiling by array.
Lineage-specific iPSC-Derived SMC Modeling Predicts Integrin Alpha-V Antagonism Reduces Aortic Root Aneurysm Formation in Marfan Syndrome Mice
GEO Series GSE223807. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Postoperative pain and dorsal root ganglia transcriptomic signatures in a novel rat model of total knee arthroplasty
GEO Series GSE195833. Rattus norvegicus. 18 samples. Type: Expression profiling by high throughput sequencing.
Single-nuclei RNA Sequencing Reveals Distinct Transcriptomic Signatures of Rat Dorsal Root Ganglia in a Disc-associated Chronic Low Back Pain Model
GEO Series GSE289659. Rattus norvegicus. 16 samples. Type: Expression profiling by high throughput sequencing.
Desipramine Induces Anti-inflammatory Dorsal Root Ganglion Transcriptional Signatures in the Murine Spared Nerve Injury Model
GEO Series GSE261676. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing.
Circular RNA, long non-coding RNA and mRNA transcriptomic profiles in a rat lumbosacral spinal roots avulsion model
GEO Series GSE203053. Rattus. 6 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Neuronal cell lines as model dorsal root ganglion neurons: a transcriptomic comparison
GEO Series GSE75811. Mus musculus; Homo sapiens; Rattus rattus. 4 samples. Type: Expression profiling by high throughput sequencing.
Intrinsic Gata4 expression sensitizes the aortic root to dilation in a Loeys-Dietz syndrome mouse model
GEO Series GSE267204. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Expression profiling of contralateral dorsal root ganglia of a rat model of complex regional pain syndrome type-I uncovers potential mechanisms involved in mirror-image pain
GEO Series GSE174299. Rattus norvegicus. 8 samples. Type: Expression profiling by high throughput sequencing.
Chickpea Roots Undergoing Colonisation by Phytophthora medicaginis do not Display Hormone Accumulation nor Signalling Typically Associated with Model Leaf Hemibiotrophic Diseases
GEO Series GSE182741. Cicer arietinum; Phytophthora medicaginis. 16 samples. Type: Expression profiling by high throughput sequencing.
Maize Root Domain Shift Image Datasets, Segmentation Models, and RhizoVision Explorer Settings
<p>This .zip file contains the following: 1) a .csv file used for RhizoVision Explorer settings, 2) root segmentation .pkl models developed using RootPainter, and 3) folders of maize root images collected in the field and greenhouse experiment that were used to train models and that were manually annotated to generate ground-truth datasets.</p> <p>For clarification, the segmentation model file named "000053_1679678936_V7_2021_tiled.pkl" is the growth stage-specific V7 field model. The segmentation model file named "000040_1679498247_R2_2021_tiled.pkl" is the growth stage-specific R2 field model. The segmentation model file named "000022_1679880442_V7plusR2_2021_tiled.pkl" is the fine-tuned V7+R2 field model. The segmentation model file named "000059_1687007135_V7R2_Tiled_Combined_2021.pkl" is the combined V7+R2 field model. The segmentation model file named "000068_1687361521_V7extendedR2_tiled_2021.pkl" is the extended V7+R2 field model. The segmentation model file named "000027_1681159536_GH_R2_tiled.pkl" the R2 greenhouse model. The segmentation model file named "000059_1680366870_GH_V9_tiled.pkl" is the V9 greenhouse model.</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.