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51 results for “root model”
Modelled root zone storage capacities Hubbard Brook WS5
Modelled root zone storage capacities for the Hubbard Brook Experimental Forest - Watershed 5. Root zone storage capacities were derived based on a simple water balance based model (Nijzink et al. 2016). Long term equilibrium root zone storage capacities yearly root zone storage capacities were determined.
Modelled root zone storage capacities HJ Andrews
Modelled root zone storage capacities for the HJ Andrews Experimental Forest - Watershed 1. Root zone storage capacities were derived based on a simple water balance based model (Nijzink et al. 2016). Long term equilibrium root zone storage capacities yearly root zone storage capacities were determined.
Modelled root zone storage capacities Hubbard Brook
Modelled root zone storage capacities for the Hubbard Brook Forest - Watershed 2. Root zone storage capacities were derived based on a simple water balance based model (Nijzink et al. 2016). Long term equilibrium root zone storage capacities yearly root zone storage capacities were determined.
Generalized linear model with elastic net regularization and convolutional neural network for evaluating Aphanomyces root rot severity in lentil
<p>Red-Green-Blue (RGB) imaging was used to evaluate Aphanomyces root rot in 547 lentil accessions and lines. The root images were pre-processed by removing image background. This dataset (6,460 root images) was used to build two machine learning models — generalized linear model with elastic net regularization and convolutional neural network— to classify root images into three classes. Details about the methodology and results are described in Marzougui et al. (2020, Plant Phenomics).</p> <p>The excel file includes Aphanomyces root rot disease visual scores (<em>Root_Rating</em>), unique identifier for each lentil accession/line (<em>Lentil_ID</em>), unique identifier for each experiment (<em>Experiment</em>), and unique identifier for each image (<em>Lab_ID</em>).</p>
Accounting for environmental variation in co‐occurrence modelling reveals the importance of positive interactions in root‐associated fungal communities
<p>Understanding the role of interspecific interactions in shaping ecological communities is one of the central goals in community ecology. In fungal communities, measuring interspecific interactions directly is challenging because these communities are composed of large numbers of species, many of which are unculturable. An indirect way of assessing the role of interspecific interactions in determining community structure is to identify the species co-occurrences that are not constrained by the environmental conditions. In this study, we investigated co-occurrences among root-associated fungi, asking whether fungi co-occur more or less strongly than expected based on the environmental conditions and the host plant species examined. For this purpose, we generated molecular data on root-associated fungi of five plant species evenly sampled along an elevational gradient at a high Arctic site. We analysed the data using a joint species distribution modelling approach that allowed us to identify those co-occurrences that could be explained by the environmental conditions and the host plant species, as well as those co-occurrences that remained unexplained and thus more likely reflect interactive associations. Our results indicate that positive interactions play an important role in shaping microbial communities in arctic plant roots. In particular, we found that mycorrhizal fungi are especially prone to positively co-occur with other fungal species. Our results bring new understanding to the structure of arctic interaction networks by suggesting that interactions among root-associated fungi are predominantly positive.</p>
Conflict over the eukaryote root resides in strong outliers, mosaics and missing data sensitivity of site-specific (CAT) mixture models
Abstract Phylogenetic reconstruction using concatenated loci ("phylogenomics" or "supermatrix phylogeny") is a powerful tool for solving evolutionary splits that are poorly resolved in single gene/protein trees (SGTs). However, recent phylogenomic attempts to resolve the eukaryote root have yielded conflicting results, along with claims of various artefacts hidden in the data. We have investigated these conflicts using two new methods for assessing phylogenetic conflict. ConJak uses whole marker (gene or protein) jackknifing to assess deviation from a central mean for each individual sequence, while ConWin uses a sliding window to screen for incongruent protein fragments (mosaics). Both methods allow selective masking of individual sequences or sequence fragments in order to minimize missing data, an important consideration for resolving deep splits with limited data. Analyses focused on a set of 76 eukaryotic proteins of bacterial-ancestry previously used in various combinations to assess the branching order among the three major divisions of eukaryotes: Amorphea (mainly animals, fungi and Amoebozoa), Diaphoretickes (most other well-known eukaryotes and nearly all algae) and Excavata, represented here by Discoba (Jakobida, Heterolobosea, and Euglenozoa). ConJak analyses found strong outliers to be concentrated in under-sampled lineages, while ConWin analyses of Discoba, the most under-sampled of the major lineages, detected potentially incongruent fragments scattered throughout. Phylogenetic analyses of the full data using an LG-gamma model support a Discoba sister scenario (neozoan-excavate root), which rises to 99-100% bootstrap support with data masked according to either protocol. However, analyses with two site-specific (CAT) mixture models yielded widely inconsistent results and a striking sensitivity to missing data. The neozoan-excavate root places Amorphea and Diaphoretickes as more closely related to each other than either is to Discoba, a fundamental relationship that should remain unaffected by additional taxa.
Model configuration files and forcing data for Implementing deep soil and dynamic root uptake in Noah-MP (v4.5): impact on Amazon dry-season transpiration
<p>This repository includes the model configuration files, input data, and forcing data used for simulations in Bieri et al. (2025) - <em>Implementing deep soil and dynamic root uptake in Noah-MP (v4.5): impact on Amazon dry-season transpiration.</em></p> <ul> <li>forcing.tar.gz - Compressed folder containing HRLDAS Noah-MP model forcing NetCDF files <ul> <li>These forcing files were derived from the NASA Global Land Data Assimilation System (GLDAS; Beaudoing et al. 2020)</li> <li>The compressed file contains 3-hourly forcing files for the entire simulation period (01 Jun 2000 to 31 Dec 2019)</li> </ul> </li> <li>wrfinput_d01 - NetCDF file used as HRLDAS input file in HRLDAS Noah-MP simulations <ul> <li>Generated from WRF WPS (https://github.com/wrf-model/WPS)</li> </ul> </li> <li>Namelist files <ul> <li>namelist.hrldas.ROOT - Model namelist settings used for ROOT experiment</li> <li>namelist.hrldas.SOIL - Model namelist settings used for SOIL experiment</li> <li>namelist.hrldas.GW - Model namelist settings used for GW experiment</li> <li>namelist.hrldas.CONTROL - Model namelist settings used for FD (CONTROL) experiment</li> </ul> </li> </ul>
Text-fig. 1. Spermophilinus bredai (VON MEYER, 1848): 3D models of a right upper jaw with (abnormal) P3, P4 and all molars (mirrored; NMA-2019-1/2352). a – the specimen in occlusal view showing the relative position of the three roots in place of P3 (yellow) compared to P4 (green); b – same view, with focus on P3–P4; c – lingual view; d – mesial view. Scale bars 2 mm. in Dental Anomaly In A Middle Miocene Fossil Of The Genus Spermophilinus (Rodentia, Sciuridae) From Southern Germany
Text-fig. 1. Spermophilinus bredai (VON MEYER, 1848): 3D models of a right upper jaw with (abnormal) P3, P4 and all molars (mirrored; NMA-2019-1/2352). a – the specimen in occlusal view showing the relative position of the three roots in place of P3 (yellow) compared to P4 (green); b – same view, with focus on P3–P4; c – lingual view; d – mesial view. Scale bars 2 mm.
Data and code for: A quantitative model for spatio-temporal dynamics of root gravitropism
<p>This repository contains the experimental data presented in "A quantitative model for spatio-temporal dynamics of root gravitropism" and Python scripts for the presented root model.</p>
Accounting for environmental variation in co‐occurrence modelling reveals the importance of positive interactions in root‐associated fungal communities
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Conflict over the eukaryote root resides in strong outliers, mosaics and missing data sensitivity of site-specific (CAT) mixture models
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Assessing confidence in root placement on phylogenies: an empirical study using non-reversible models for Mammals
<p>Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny. In order to compensate for the inability of these models to root the tree, many researchers use external information such as using outgroup taxa or additional assumptions such as molecular-clocks. In this study, we investigate the utility of non-reversible models to root empirical phylogenies and introduce a new bootstrap measure, the <i>rootstrap</i>, which provides information on the statistical support for any given root position.</p> <p>Availability and implementation: rootstrap support is implemented in IQ-TREE 2 and a tutorial is available at the iqtree webpage <a href="http://www.iqtree.org/doc/Rootstrap">http://www.iqtree.org/doc/Rootstrap</a>. In addition, a python script is available at <a href="https://github.com/suhanaser/Rootstrap">https://github.com/suhanaser/Rootstrap</a></p>
Training dataset and final models used in "Digging roots is easier with AI"
<p>See the paper ''Digging roots is easier with AI' for an explanation of how the models and datasets were created.</p> <p>The images are extracted from the larger datasets available from 10.5281/zenodo.4300067 using the RootPainter software.</p>
Data from: A shared pattern of midfacial bone modelling in hominids suggests deep evolutionary roots for human facial morphogenesis
<p>Midfacial morphology varies between hominoids, in particular between great apes and humans for which the face is small and retracted. The underlying developmental processes for these morphological differences are still largely unknown. Here we investigate the cellular mechanism of maxillary development (bone modelling), and how potential changes in this process may have shaped facial evolution. We analysed cross-sectional developmental series of gibbons, orangutans, gorillas, chimpanzees and present-day humans (N=183). Individuals were organized into five age groups according to their dental development. To visualize each species' bone modelling pattern and corresponding morphology during ontogeny, maps based on microscopic data were mapped onto species-specific age group average shapes obtained using geometric morphometrics. The amount of bone resorption was quantified and compared between species. Great apes share a highly similar bone modelling pattern, whereas gibbons have a distinctive resorption pattern. This suggests a change in cellular activity on the hominid branch. Humans possess most of the great ape pattern, but bone resorption is high in the canine area from birth on, suggesting a key role of canine reduction in facial evolution. We also observed that humans have high levels of bone resorption during childhood, a feature not shared with other apes.</p>
Plant root growth against a mechanical obstacle: The early growth response of a maize root facing an axial resistance is consistent with the Lockhart model
<p>Plant root growth is dramatically reduced in compacted soils, affecting the growth of the whole plant. Through a model experiment coupling force and kinematics measurements, we probed the force-growth relationship of a primary root contacting a stiff resisting obstacle, that mimics the strongest soil impedance variation encountered by a growing root. The growth of maize roots just emerging from a corseting agarose gel and contacting a force sensor (acting as an obstacle) was monitored by time-lapse imaging simultaneously to the force.<br><br>The evolution of the velocity field along the root was obtained from kinematics analysis of the root texture with a PIV derived-technique. A triangular fit was introduced to retrieve the elemental elongation rate or strain rate. A parameter-free model based on the Lockhart law quantitatively predicts how the force at the obstacle modifies several features of the growth distribution (length of the growth zone, maximal elemental elongation rate, velocity) during the first 10 minutes. These results suggest a strong similarity of the early growth responses elicited either by a directional stress (contact) or by an isotropic perturbation (hyperosmotic bath).</p>
Embracing fine-root system complexity in terrestrial ecosystem modelling
<p>Model outputs for manuscript " <strong>Embracing fine-root system complexity in terrestrial ecosystem modelling</strong>".</p>
Data from: A shared pattern of midfacial bone modelling in hominids suggests deep evolutionary roots for human facial morphogenesis
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Plant root growth against a mechanical obstacle: The early growth response of a maize root facing an axial resistance is consistent with the Lockhart model
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Assessing confidence in root placement on phylogenies: an empirical study using non-reversible models for Mammals
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Kinetic Model Data: Effect of Calcium on the Bioavailability of Dissolved Uranium (VI) in Plant Roots under Circumneutral pH
We integrated field measurements, hydroponic experiments, microscopy, and spectroscopy to investigate the effect of Ca(II) on dissolved U(VI) uptake by plants in 1 mM HCO3 − solutions at circumneutral pH. The accumulation of U in plants (3.1−21.3 mg kg−1) from the stream bank of the Rio Paguate, Jackpile Mine, New Mexico served as a motivation for this study. Brassica juncea was the model plant used for the laboratory experiments conducted over a range of U (30−700 μg L−1) and Ca (0−240 mg L−1) concentrations. The initial U uptake followed pseudo-second-order kinetics. The initial U uptake rate (V0) ranged from 4.4 to 62 μg g−1 h−1 in experiments with no added Ca and from 0.73 to 2.07 μg g−1 h−1 in experiments with 12 mg L−1 Ca. No measurable U uptake over time was detected for experiments with 240 mg L−1 Ca. Ternary Ca−U−CO3 complexes may affect the decrease in U bioavailability observed in this study. Elemental X-ray mapping using scanning transmission electron microscopy−energy dispersive spectrometry detected U−P-bearing precipitates within root cell walls in water free of Ca. These results suggest that root interactions with Ca and carbonate in solution affect the bioavailability of U in plants. This study contributes relevant information to applications related to U transport and remediation of contaminated sites.
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International Brain Laboratory public data
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OpenNeuro
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