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3,682 results for “ROOTS”
Dataset for "Root Length Estimation: Automated Minirhizotron Image Analysis with Convolutional Networks without Segmentation"
<p>This data contains 4015 root images, splitted into 4 datasets, acquired using two minirhizotron (MR) system types - manual (Dataset 1 & Dataset 4) and automated (Dataset 2 & Dataset 3). It includes four crop species (corn, pepper, melon, and tomato) grown under various abiotic stresses. The data was acquired by researchers from Ben-Gurion University of the Negev, Beer Sheva, Israel, and used for research of automated TRL estimation with Convolutional Neural Networks.</p> <p>The annotations were conducted manually using the Rootfly software (Wells and Birchfield, Clemson University, South Carolina, USA), and data were transformed as CSV formats. In this software, the annotator must draw a root by marking points along the selected root. These points usually correspond to the coordinates at the start and the end of the root, and curving points along the root. These points are then connected in a line, the length of which reflects the real length of the selected root. The annotations has been done for all roots within an image, and for all images in the provided dataset.</p> <p>The provided annotations include the total root length (TRL) per image (mm) and the coordinates of annotated points.</p> <p>The annotations are given in two types of files:</p> <p>"TRL.csv" files: contain the image names and corresponding TRL values (mm).</p> <p>"pointsOutput.csv" files: contain the annotated image names and the coordinates of the points of the roots in the image (if the image contains roots) in the form of x1, y1, x2, y2, x3, y3, etc. It the image doesn't have roots, the file contains only its name.</p>
Fungal community composition and genetic potential regulate fine root decay in northern temperate forests
<p>Understanding how genetic differences among soil microorganisms regulate spatial patterns in litter decay remains a persistent challenge in ecology. Despite fine root litter accounting for ~50% of total litter production in forest ecosystems, far less is known about the microbial decay of fine roots relative to aboveground litter. Here, we evaluated whether fine root decay occurred more rapidly where fungal communities have a greater genetic potential for litter decay. Additionally, we tested if linkages between decay and fungal genes can be adequately captured by delineating saprotrophic and ectomycorrhizal fungal functional groups based on whether they have genes encoding certain ligninolytic class II peroxidase enzymes, which oxidize lignin and polyphenolic compounds. To address these ideas, we used a litterbag study paired with fungal DNA barcoding to characterize fine root decay rates and fungal community composition at the landscape scale in northern temperate forests, and we estimated the genetic potential of fungal communities for litter decay using publicly available genomes. Fine root decay occurred more rapidly where fungal communities had a greater genetic potential for decay, especially of cellulose and hemicellulose. Fine root decay was positively correlated with ligninolytic saprotrophic fungi and negatively correlated with ECM fungi with ligninolytic peroxidases, likely because these saprotrophic and ectomycorrhizal functional groups had the highest and lowest genetic potentials for plant cell wall degradation, respectively. These fungal variables overwhelmed direct environmental controls, suggesting fungal community composition and genetic variation are primary controls over fine root decay in temperate forests at regional scales.</p>
Dataset for: The barrier to radial oxygen loss protects roots against hydrogen sulphide intrusion and its toxic effect
<ul> <li> <span>The root barrier to radial O<sub>2</sub> loss (ROL) is a key root trait preventing </span><span>O<sub>2</sub></span><span> loss from roots to anoxic soils thereby enabling root growth into anoxic, flooded soils. </span> </li> <li> <span>We hypothesized that the ROL barrier can also prevent intrusion of hydrogen sulphide (H<sub>2</sub>S), a potent phytotoxin in flooded soils. Using H2S and </span><span>O<sub>2</sub></span><span>-sensitive microsensors, we measured the apparent permeance to </span><span>H<sub>2</sub>S</span><span> of rice roots and tested whether restricted </span><span>H<sub>2</sub>S</span><span> intrusion reduced its adverse effects on root respiration and if </span><span>H<sub>2</sub>S</span><span> could induce the formation of a ROL barrier.</span> </li> <li> <span>The ROL barrier reduced apparent permeance to </span><span>H<sub>2</sub>S</span><span> by almost 99%, greatly restricting </span><span>H<sub>2</sub>S</span><span> intrusion. The ROL barrier acted as a shield towards </span><span>H<sub>2</sub>S</span><span>; </span><span>O<sub>2</sub></span><span> consumption in roots with a ROL barrier remained unaffected at high </span><span>H<sub>2</sub>S</span><span> concentration (500 µM), compared to a 67% decline in roots without a barrier. Importantly, low </span><span>H<sub>2</sub>S</span><span> concentrations induced the formation of a ROL barrier.</span> </li> <li> <span>In conclusion, the ROL barrier plays a key role in protecting against </span><span>H<sub>2</sub>S</span><span> intrusion, and </span><span>H<sub>2</sub>S</span><span> can act as an environmental signalling molecule for the induction of the barrier. The study demonstrates the multiple functions of the suberized/lignified outer part of the rice root beyond that of restricting ROL.</span> </li> </ul>
Screening the maize rhizobiome for consortia that improve Azospirillum brasilense root colonization and plant growth outcomes
<p>Data corresponds to results from: <em>Barua N, Clouse KM, Ruiz Diaz DA, Wagner MR, Platt TG and Hansen RR (2023) Screening the</em> <em>maize rhizobiome for consortia that improve Azospirillum brasilense root colonization and plant growth outcomes. Front. Sustain. Food Syst. 7:1106528. doi: 10.3389/fsufs.2023.1106528</em></p>
Data of "Pen mates' interactions, potential precursors of damaging behaviours, object manipulation, straw rooting, and primary activity: A detailed data set in undocked pigs under dietary protein restriction"
<p>Damaging behaviours, such as tail biting, are common problems in pig production, compromising animal welfare and causing economic losses. Detailed studies are impeded by the difficulty of directly observing these behaviours. Tail biting is a broader phenomenon that begins long before lesions manifest, and behavioural problems caused by various stressors present themselves weeks before they escalate to damaging behaviour, resulting in serious injuries. Therefore, detailed data on behaviours, which can be considered precursors of tail biting, such as oral and nasal manipulation of conspecifics, should be collected. The present data were collected in the course of a large study on the genetic potential of protein efficiency, in which the crude protein content in the diet was reduced to 80% of the recommendations. Dietary protein reduction is a promising way to reduce nitrogen emissions in pig manure, but its implications for animal welfare are not yet clear. Pigs differ phenotypically and genetically in their ability to utilise dietary proteins; therefore, there might be individual differences in how they cope with the protein reduction. Here, we present detailed data of focal observations of 95 pigs at an experimental farm with undocked tails that were fed a protein-reduced diet. Pigs were observed directly in their home pens for 5 min each on four different days. All actions directed towards objects in the pen, interactions with and confrontations among pen mates, and straw rooting behaviour and general activity were recorded. After the behavioural observations, wounds on different parts of the body and the cleanliness of the pigs were noted. The protein efficiency of 94 pigs was obtained. The data set comprises six tables. The first table contains information on the animals, including the identities of their parents, farrowing group, sex, and protein efficiency. The other data tables contain four 5-min observations of each pig on 10 object-manipulation behaviours; 150 interaction behaviours, including reactions; 14 confrontation behaviours and their outcomes and reactions; 10 mounting behaviours, including reactions; two rooting behaviours; seven basic behaviours; and an index of general activity. The observations took place under comparatively good housing conditions. Pigs were not tail-docked and were given fresh straw daily, <em>ad libitum</em> access to feed, floor space above the legal requirements (only a partially slatted floor), and daily cleaning of pens, and they were closely monitored for signs of damaging behaviour; all of these are favourable conditions as they limit stress and the risk of damaging behaviour. These data can be used to further explore the relationships of specific behaviours and phenomena and their association with protein efficiency. The ethogram can be used as a template for further observations. Practitioners could use the data to support pigs’ need for occupation, such as by providing sufficient straw.</p>
Acer and Quercus root traits plasticity
<p><u><span>Introduction</span></u><span>: Plant nutrient acquisition strategies range along a spectrum from autonomous foraging to investment in cooperative foraging through mycorrhizal associations. However, in temperate ecosystems, </span><span>many plant species encounter contrasted levels of symbiont availability in open fields versus closed forests<span>. Little is known about how fungal partner availability may be associated with intraspecific variation in other root foraging traits in natural settings.</span></span></p> <p><u><span>Methods</span></u><span>: Here, we addressed this issue by sampling saplings from two tree species: the arbuscular mycorrhizal (AM) <em>Acer rubrum</em> and the ectomycorrhizal (ECM) <em>Quercus rubra</em> from open fields (AM-dominated) and adjacent forest plots (ECM-dominated). For each species and environment, we measured morphological, architectural, and symbiotic root traits.</span></p> <p><u><span>Results</span></u><span>: For the open field, <em>Quercus</em> had greater specific root length (SRL) while <em>Acer</em> had higher AM colonization and root diameter. In the closed forest, the opposite pattern was observed, namely <em>Quercus</em> had higher ECM colonization and <em>Acer</em> greater SRL. </span></p> <p><u><span>Discussion</span></u><span>: Both species showed evidence of a shift toward autonomous root foraging in the habitat with low expected symbiont abundance (open field for <em>Quercus</em> and forest for <em>Acer</em>). </span><span>Although the confounding effects of site abiotic properties could not be strictly controlled in this study, these results suggest that plants might adjust root foraging traits according to local habitat conditions.</span></p> <p><u><span>Synthesis</span></u><span>: Our results shed new light on the intraspecific variation in plant position along the so-called "collaboration gradient", and suggest that mycorrhizal symbiont availability, along with other factors such as competition and site properties, may contribute to this variation.</span></p>
Data and statistical analysis scripts for manuscript on pennycress roots & response to nitrate using 3D gel system
<p>Data and statistical analysis scripts for manuscript on pennycress roots & response to nitrate using 3Dgel system</p> <blockquote> <p><strong>A temporal analysis and response to nitrate availability of 3D root system architecture in diverse pennycress (<em>Thlaspi arvense</em> L.) accessions</strong> - [<a href="https://doi.org/10.3389/fpls.2023.1145389">https://doi.org/10.3389/fpls.2023.1145389</a>]</p> </blockquote> <p>The following files contains:</p> <ul> <li><code>gel_data_preprocessing_20221024.R</code> - R statistics script for pre-processing data files from 3Dgel system GIARoots & DynamicRoots raw output</li> <li><code>gel_dataprocessing_20221229.R</code> - R statistics script for data processing of pre-processed 3D gel data</li> <li><code>TaGNS_N_Spring32.zip</code> - CSV data files and R statistics script for Spring32 grown under high, low, trace and zero N treatments.</li> <li><code>TaGNE_N_Accessions.zip</code> - CSV data files and R statistics script for 3 accessions under high and trace N treatments.</li> <li><code>TaGAA_N_Accessions.zip</code> - CSV data files and R statistics script for 24 diverse pennycress lines grown under high N conditions.</li> </ul>
Antigravitropic PIN polarization maintains non-vertical growth in lateral roots
<p>Datasets and gel images associated with the manuscript: <strong>Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. </strong></p>
Root mutualistic fungi tailor the induction of direct and indirect antiherbivore defense strategies to enhance plant resistance
<p>GCMS raw data in netCDF format for the manuscript "Root mutualistic fungi tailor the induction of direct and indirect antiherbivore defense strategies to enhance plant resistance" </p> <p>Mutualistic microbes can trigger plant defenses against herbivores. Little is known about how microbes orchestrate multiple induced defense strategies that may trade-off against each other. We investigated how two root mutualistic fungi trigger simultaneously direct and indirect antiherbivore-defenses, and the regulatory mechanisms involved</p>
Cotton root cross-sections under water deficit
<p>This experiment is describing the analysis of the root cross-sections. The roots were collected in the lab of Prof. Avat Shekoofa (Uni. of Tennessee), and the root samples were sent to Julkowska lab (BTI). Magda did hand cross-sections and stained them with toluidine blue to visualize the xylem vessels. The individual images were stitched into an ortho-mosaic using Photoshop.</p>
Fine-root production in boreal peatland forests: effects of stand and environmental factors
<p>Fine-root production (FRP) data along with climatic variables (annual precipitation, temperature sum, and latitude) and stand variables (tree stand stem volume; tree stand basal area; stand basal area of tree species including Scots pine, Norway spruce and deciduous trees; site type; peat type; peat depth; C:N ratio of topmost 20 cm peat layer; grouping of sites to nutrient rich and nutrient poo; average soil water-table level) from 28 forestry-drained peatland forest sites in Finland,</p> <p>FRP and its depth distribution were estimated using ingrowth cores. The ingrowth cores were installed between October 15th and November 27th, 2013, and recovered after two years in late November 2015.</p>
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>
Data from: Frog limbs in deep time: is jumping locomotion at the roots of the anuran Bauplan?
<p><span>The unique body plan of frogs (Lissamphibia: Anura) has been largely conserved from at least 200 Myr and its evolution from a more generalized tetrapod condition is still poorly understood, in part due to the scarce early fossil record of Salientia, the anuran total-group. The origin of the anuran Bauplan has been classically explained as an adaptation to jumping, but recent studies incorporating new data in a phylogenetic context have challenged the popular jumping hypothesis. Here we revisit and test this hypothesis from a palaeobiological perspective by integrating limb data from a wide range of extant and fossil frogs. We first explored the evolution of limb proportions from the Jurassic to the Paleogene to understand when the present limb diversity originated and whether, and to what extent, limb proportions have been conserved over the last 200 Myr. We then inferred the locomotor capabilities of extinct species by phylogenetic flexible discriminant analysis and, from these inferences, we studied the locomotor diversity of frogs over geological time and reconstructed the ancestral state for frog-like salientians. The evolution of limb proportions is characterized by an early diversification that was underway in the Jurassic, followed by a repeated convergence over a limited area of the morphospace that was already explored by the Early Cretaceous. In agreement with this early limb diversity, the Jurassic stem species were also locomotory diverse and their inferred locomotor modes do not support the jumping hypothesis. We propose that the patterns found herein of repeated convergent evolution of both limb proportions and locomotor capabilities over geological time hamper any attempt to confidently infer the ancestral locomotion mode and, therefore, it might be time to start focusing on other hypotheses on the origin of the anuran Bauplan that are not related to locomotion.</span></p>
LHCHWG MSSM ROOT files
<p>This Zenodo record stores the ROOT files generated by the MSSM subgroup of the LHC Higgs Working Group (LHCHWG) to publicly distribute the physics information required to properly interpret LHC measurements and searches in the context of a variety of MSSM scenarios.</p> <p>The scenarios contained in this release are:</p> <ul> <li>the six scenarios presented in<strong> Eur.Phys.J.C 79 (2019) 7, 617</strong> (1808.07542 [hep-ph]);</li> <li> <p>the two heavy-SUSY/low-tb scenarios published in <strong>Eur.Phys.J.C 79 (2019) 3, 279</strong> (1901.05933 [hep-ph]);</p> </li> <li> <p>the three negative mu scenarios presented in <strong>Eur.Phys.J.C 80 </strong></p> </li> <li> <p><strong>(2020) 10, 916</strong> (2005.14536 [hep-ph];</p> </li> <li> <p>the hMSSM scenario introduced in <strong>JHEP 10 (2013) <a href="tel:028">028</a></strong> (1304.1787 [hep-ph]).</p> </li> </ul> <p>For each scenario, three ROOT files are provided, corresponding to cross-sections computed at 8, 13 and 14 TeV.</p> <p>For more information on the tools used to generate the predictions contained in the ROOT files, and on the structure of the ROOT files itself, we refer to the working group note <strong>LHCHWG-2021-001</strong> (https://cds.cern.ch/record/2791954/).</p> <p>For more information on the MSSM subgroup, please see the Twiki page at <a href="https://twiki.cern.ch/twiki/bin/view/LHCPhysics/LHCHWGMSSMNeutral">https://twiki.cern.ch/twiki/bin/view/LHCPhysics/LHCHWGMSSMNeutral</a>.</p> <p>Subscribe to <em>lhc-higgs-mssm-group@cern.ch </em>to receive the announce of the new releases, and for discussions.</p> <p>For any issue, information or request, please contact Emanuele Bagnaschi at the following address: <a href="mailto:emanuele.bagnaschi@cern.ch">emanuele.bagnaschi@cern.ch</a>.<br> <br> <strong>Changelog</strong></p> <p>09/09/2023</p> <ul> <li>Added missing ggF cross sections at 14 TeV for the hMSSM</li> </ul> <p>04/07/2022</p> <ul> <li>Replaced all the ROOT files corresponding to the scenarios where HDECAY is used (mh125,mh125lc,mh125ls,mh125muneg_1,mh125muneg_2,mh125muneg_3,mh123align) with new versions generated with an update version of HDECAY-6.61 that resolve an issue with the genuine SUSY-QCD contributions to the <span class="math-tex">\(b\bar{b}\)</span> decay channels introduced in the original 6.61 release.</li> </ul> <p>07/03/2022</p> <ul> <li>Fixed various issues in the ROOT files of the MHH125 scenario</li> </ul> <p>02/12/2021</p> <ul> <li>First release on Zenodo;</li> <li>Updated the hMSSM ROOT file to the same setup used for the other scenarios (latest version of <a href="https://twiki.cern.ch/twiki/bin/edit/LHCPhysics/SusHi?topicparent=LHCPhysics.LHCHWGMSSMNeutral;nowysiwyg=1">SusHi</a>; <a href="https://twiki.cern.ch/twiki/bin/edit/LHCPhysics/PDF4LHC15?topicparent=LHCPhysics.LHCHWGMSSMNeutral;nowysiwyg=1">PDF4LHC15</a> recommendations; <span class="math-tex">\(b\bar{b}\)</span> cross-sections from the matched results provided by the bbH WG; inclusion of reference SM histograms);</li> <li>Added the cross sections for the VBF, Higgsstrahlung and ttH production processes for the three neutral Higgses and for the SM reference case;</li> <li>Added mixing information of the neutral Higgs sector;</li> <li>Added the trilinear self-coupling of the SM-like Higgs, and of a SM Higgs with the same (the latter at tree level and including the <span class="math-tex">\(m_t^4\)</span> term);</li> <li>Cleaned-up and reorganized the histograms with a more consistent naming;</li> <li>Removed the decay <span class="math-tex">\(H^{\pm} \to us\)</span> due to theoretical issues;</li> <li>Update to the HDECAY version 6.61 (<span class="math-tex">\(\Delta_b\)</span> with electroweak 2-loop corrections proportional to <span class="math-tex">\(\alpha_1\)</span>and <span class="math-tex">\(\alpha_2\)</span>; <span class="math-tex">\(m_t^4\)</span>term in the hMSSM trilinear self-coupling);</li> </ul>
Data from: Characterisation of GFAP-Expressing Glial Cells in the Dorsal Root Ganglion after Spared Nerve Injury
<p>This data pertain to the paper titled "Characterisation of GFAP-Expressing Glial Cells in the Dorsal Root Ganglion after Spared Nerve Injury " by Elena A. Konnova, Alexandru-Florian Deftu, Paul Chu Sin Chung, Marie Pertin, Guylène Kirschmann, Isabelle Decosterd and Marc R. Suter. The name of the data files correspond to the for each figure in the study. The data file in .csv format are organized so that they can easily be opened in R or other analysis language. To understand them and how they are labelled, it is advised to open the figure next to them and find the appropriate panel.</p><p>Here are included:</p><ul><li>the representative images of immunohistochemistry for GFAP, IBA1, Ki67, NeuN, ATF3, FABP7, GS, Cx43, Kir4.1, MBP, L1CAM in the dorsal root ganglia (DRG) of hGFAP-CFP mice after spared nerve injury (SNI).</li><li>the western blot images of DRG samples and FACS sorted CFP+ cells from the DRG of hGFAP-CFP mice after SNI</li><li>the voltage clamp data of GFAP+ cells from DRG of hGFAP-CFP mice after SNI</li></ul><p> </p>
Multi-scale effects on the hydraulic behaviour of a root-permeated and compacted soil
<p>Dataset obtained from multi-scale observations on the hydraulic behaviour of a root-permeated and compacted soil.</p>
Arbuscular mycorrhizal fungi in roots and soil respond differently to biotic and abiotic factors in the Serengeti
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Data from: Measuring leaf and root functional traits uncovers multidimensionality of plant responses to arbuscular mycorrhizal fungi
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Moisture-responsive root-branching pathways identified in diverse maize breeding germplasm
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Plastid and peroxisome movement tracks in the root cells of Arabidopsis thaliana
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