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3,682 results for “ROOTS”
Orthodontically Induced External Apical Root Resorption with genetic and non-genetic factors
<p>Orthodontically Induced External Apical Root Resorption (OIEARR) dataset with genetic and non-genetic factors from a sample of 195 patients previously submitted to orthodontic treatment. Methodology for patient selection is described in published related works as well as materials and methods. Percentage of OIEARR were assessed in maxillary teeth: the four incisors and the two canines. Ten clinical and treatment variables were recorded: gender, age, treatment duration, premolar extractions, skeletal pattern, Hyrax appliance, functional appliance, overjet, anterior open bite and tongue thrust. Single nucleotide polymorphisms (SNPs) of six genes : rs114363 from <em>IL1B</em>; rs3102735 from <em>TNFRSF11B</em>, encoding OPG; rs1059703 from <em>I</em><em>RAK1</em>; rs315952 from <em>IL1RN</em>; rs1805034 from <em>TNFRSF11A</em>, encoding RANK; rs1718119 from <em>P2RX7</em>.</p>
Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method
<p>This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled "Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method".</p> <p>It also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.</p> <p>The repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.</p> <p>For details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee).</p>
Code and Data from: Segmenting Root Systems in X-Ray Computed Tomography Images Using Level Sets
<p>This record contains code and data for segmentation using a three-dimensional level-set method, written by Amy Tabb in C++. The record also contains two datasets of root systems in media imaged with X-Ray CT, and the results of running the code on those datasets. The code will also perform a pre-processing task in three-dimensional image sets, and a dataset for that purpose is included as well. This work is a companion to the paper : "Segmenting root systems in X-ray computed tomography images using level sets" (WACV 2018) by the authors or this record, and and open-access version of the paper is here -- https://arxiv.org/abs/1809.06398 . The code is also available from Github: https://github.com/amy-tabb/tabb-level-set-segmentation , using a DOI and stable releases https://doi.org/10.5281/zenodo.3344906.</p> <p>Format of the data:</p> <p>Three input datasets are provided; two for the segmentation functionality of the code, and one to test the pre-processing functionality. The two segmentation sets are the same as were used in the paper, and are CassavaDataset, and SoybeanDataset. The pre-processing set is CassavaSlices. The output set for Soybean is SoybeanResultsJul11. The Cassava result set is large, so I broke it into three compressed folders, CassavaResultsJul12_A, _B, _C. _B is the largest, and only contains the results overwritten on the original X-Ray images. Unless your connection to Zenodo is extremely fast, it will be faster to compute the result than to download it.</p> <p> </p> <p> </p><p> </p><p> </p> <p></p> <p></p>
The LAVA mutants defective in auxin-regulated primary or lateral root development.
<p><span>Regulation of PIN activity, polarity as well as auxin gradient generation and its canalisation remain crucial topics in plant developmental biology especially in the context of organogenesis like the formation new lateral roots. Here, we are presenting the LAVA (LR Alterations Visualised after Auxin) collection of 278 mutants, defective in auxin-induced lateral root (LR) morphogenesis. Those mutants were obtained from a forward genetic screen in which synthetic auxin 1-Naphtyl Acetic Acid (1-NAA) was used to induce LR formation in the mutagenized PIN3::PIN3-GFP population. Our database contains mutant root phenotyping and for a subset of the collection, we recorded PIN polarity and subcellular trafficking, cotyledon vasculature development, primary and LR gravitropism as well as aerial phenotypes with some reminiscent to auxin-regulated organogenesis aberrations. We are convinced that our dataset can serve as a unique tool to identify novel components of auxin signalling, transport, and cell polarity but also be of interest to the broader plant research community interested in the roots system architecture that is vital for plant survival, growth and adaptation to environmental conditions.</span></p> <p><span>The phenotype analysis of the mutant collection is summarized and organised in an Excel spreadsheet (2024-08-07_mutant_database_Table S1). The photographic material is organised in folder form (see Supporting Data S1 in this repository), where each folder number corresponds to a particular mutant and entry in the excel table.</span></p> <p><span> Mutant seeds will be available in the European Arabidopsis Stock Centre (NASC). The seed sending to the repository is in progress. </span></p> <p><span>The manuscript describing this work is currently being submitted to the research journal. Its version will be available on the open access Masaryk University repository.</span></p>
Data on respiration, substrate incorporation, and soil compound concentration in response to simulated root exudation
<p>In this study we used reverse microdialysis to release a mixture of <sup>13</sup>C-labeled substrates into intact meadow and forest soil cores (6-hour long) to simulate root exudation. We utilized three different artificial root exudates: sugars (glucose, fructose), organic acids (acetate, succinate), and a combination of sugars and organic acids (glucose, fructose, acetate, succinate); alongside a water-only control for comparison.</p> <p>We collected compounds from soil solutions and measured respiration. Due to <sup>13</sup>C-labeled substrate we could differentiate between substrate-derived respiration and SOM-derived respiration. Additionally, we extracted lipid fatty acids from soil and measured their <sup>13</sup>C incorporation.<br><br></p>
A Comprehensive Dataset of Kurdish Body Part Terminology with Proto-Indo-European Roots
<p><strong>Overview</strong></p> <p>This dataset delves into the rich linguistic heritage of Kurdish body part terminology, tracing its roots back to the Proto-Indo-European (PIE) language. It comprises a comprehensive collection of 50 Kurdish body part terms, each meticulously analyzed through 24 linguistic features, uncovering their historical development and connections to other Indo-European languages.</p> <p><br><strong>Key Features</strong></p> <p>- Comprehensive Analysis: The dataset provides a detailed analysis of 1200 fundamental linguistic features, with each feature branching out to explore other related features. Additionally, it delves into the internal structure and phonetic evolution of Kurdish terminology throughout history.<br>- Categorization: The dataset categorizes the Kurdish body part terms into four distinct groups: external anatomical parts, upper torso and limbs, lower torso and limbs, and internal anatomical parts. This comprehensive categorization facilitates a nuanced exploration of the linguistic evolution and interconnections within the domain of body part terminology.<br>- Etymological Information: For each Kurdish term, the dataset provides in-depth etymological information, including its PIE root, Indo-Iranian and Indo-European cognates, and references to relevant scholarly sources.<br>- Linguistic Features: The dataset includes 24 linguistic features for each term, allowing for a comprehensive comparative analysis. These features include gender, morphological features, possessive form, etymological summary, syllabification, stress pattern, semantic field, example sentence, cultural significance, case, evolution of meaning, semantic shift, sound changes, phonetic changes, and Kurdish idiomatic proverbs.</p> <p><strong>Contact</strong><br>For any questions, please contact Marwan Hamay at marwan.hamay@rwth-aachen.de.</p>
root tensile strength
<p>datasets containing information on the root tensile strength for the following plant species: </p> <p>- Ash</p> <p>- Goat willow</p> <p>- Basket willow</p> <p>- Sycamore/maple</p> <p>- Silene dioica</p> <p>- Erigeron acris</p> <p>Root tensile strength was measured with a universal testing machine. Root tensile strength is a useful variable for estimating the degree of soil reinforcement provided by plant roots </p>
Phenotypic diversity of root architecture and genotypic variation in durum wheat under salt stress
<p>Supplementary data consists of Principal Components values for traits detected under salt and control conditions (S1); Markers' locations onto the durum wheat reference genome associated with QTL (S2); Markers associated with genes from NCBI database (S4); PCR results and alleles distribrution</p>
Satellite-driven 10km global root-zone soil moisture analysis for drought monitoring
<p>Root-zone soil moisture condition is an important component of water cycle at all spatial scales, as it controls various hydrological, biological and meteorological processes such as plant transpiration and hydraulic redistribution. Passive microwave remote sensing offers the possibility to access to near-surface (0 - 5cm) soil moisture measurements over large areas, providing valuable information for agricultural and water resource management. However, the spatial resolution of satellite soil moisture estimates from passive microwave sensor is relatively coarse (25 to 50km) and infrequent in time. Data assimilation algorithms are widely used to obtain spatially complete and daily continuous soil moisture estimates from intermittent remotely sensed soil moisture data and numerical models. </p> <p>The dataset contains the most recent global surface and root-zone soil moisture conditions at 10km generated from the Satellite-Guided Root-zone moisture Analysis and Forecasting System (S-GRAFS) from 2015 to 2022. S-GRAFS is a near-real time data assimilation system that combines complementary information from model simulations and satellite observations to provide soil moisture estimates at near surface and root-zone. In S-GRAFS, satellite soil moisture observations from Soil Moisture Active Passive (SMAP) are assimilated into a simple first-order autoregressive model that captures the soil moisture conditions in response to precipitation. Satellite precipitation from Global Precipitation Measurement (GPM) is used to drive the model to simulate near surface soil moisture at 5cm. The assimilation of SMAP data relies on the four-dimensional variational (4DVAR) method to adjust the modelled surface soil moisture towards observations within a 4-day assimilation window. Soil Water Index (SWI) is then derived from the analysed surface soil moisture using an exponential filter and represents the root-zone soil wetness at approximate 1m depth. The surface and root-zone wetness from S-GRAFS can be converted into absolute soil moisture content using soil physical properties to provide essential support for a wide variety of hydrological and agricultural applications.</p>
Reproducibility package for Using root economics traits to predict biotic plant soil-feedbacks
<p>Using root economics space to predict biotic plant soil-feedbacks presents a novel framework linking below ground ecological theory to plant soil feedback effects. We show how to calculate root functional distance and location of two plant species in root economics space and how these measures can help to predict the strength and direction of the plant soil feedback between them. </p> <p>Contains data and scripts to reproduce analysis and figures for the manuscript (https://github.com/ggpmrutten/linkingRES-PSF)</p>
Data for: The function of stilt roots in the growth strategy of Socratea exorrhiza (Arecaceae) at two neotropical sites
<p>We provide the raw and processed data used in the following study: Goldsmith, G. R., & Zahawi, R. A. (2007). The function of stilt roots in the growth strategy of Socratea exorrhiza (Arecaceae) at two neotropical sites. <em>Revista de Biología Tropical</em>, <em>55</em>(3-4), 787-793.</p> <p><strong>Methods</strong> can be found in the file entitled "README-GoldsmithZahawi-SocrateaData-5Mar23F.txt," while metadata for data columns can be found in the file entitled: "GoldsmithZahawi-SocrateaMetaData-5March2023.csv."</p> <p><strong>Original Published Abstract</strong>: Arboreal palms have developed a variety of structural root modifications and systems to adapt to the<br> harsh abiotic conditions of tropical rain forests. Stilt roots have been proposed to serve a number of functions<br> including the facilitation of rapid vertical growth to the canopy and enhanced mechanical stability. To examine<br> whether stilt roots provide these functions, we compared stilt root characteristics of the neotropical palm tree<br> Socratea exorrhiza on sloped (>20º) and flat locations at two lowland neotropical sites. S. exorrhiza (n=80 trees)<br> did not demonstrate differences in number of roots, vertical stilt root height, root cone circumference, root cone<br> volume, or location of roots as related to slope. However, we found positive relationships between allocation<br> to vertical growth and stilt root architecture including root cone circumference, number of roots, and root cone<br> volume. Accordingly, stilt roots may allow S. exorrhiza to increase height and maintain mechanical stability<br> without having to concurrently invest in increased stem diameter and underground root structure. This strategy<br> likely increases the species ability to rapidly exploit light gaps as compared to non-stilt root palms and may also<br> enhance survival as mature trees approach the theoretical limits of their mechanical stability.</p>
Data_Schönauer et al. (2023)_Root and branch hydraulic functioning and trait coordination across organs in drought-deciduous and evergreen tree species of a subtropical highland forest
<p>Data used in</p> <p>Schönauer, M., Hietz, P., Schuldt, B., and Rewald, B. (2023). Root and branch hydraulic functioning and trait coordination across organs in drought-deciduous and evergreen tree species of a subtropical highland forest. Frontiers in plant science 14, 1127292. doi: 10.3389/fpls.2023.1127292</p>
Data from: Kir2.1 modulation in macrophages sensitises dorsal root ganglion neurons through TNF secretion after nerve injury
<p>This data pertain to the manuscript titled "Kir2.1 modulation in macrophages sensitises dorsal root ganglion neurons through TNF secretion after nerve injury", currently in preprint on BioRxiv (https://doi.org/10.1101/2023.06.21.545843). 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>Example images of section of mouse dorsal root ganglion (DRG) after spared nerve injury (SNI), labelled for CX3CR1+ cells, Ki67 and MHC class II by immunohistochemistry.</li> <li>LC-MS-MS proteomic data set of CX3CR1+ cells from DRG of mice after SNI.</li> <li>Voltage clamp data of CX3CR1+ cells from DRG of mice after SNI</li> <li>Electrophysiological data sets (multi-electrode array, current clamp and voltage clamp) of dissociated DRG neurons treated with medium conditioned by CX3CR1+ or GFAP+ cells sorted from ipsilateral or contralateral DRG from mice after SNI. In addition, pharmacological treatments were added to the conditioned medium (CM).</li> </ul>
Unraveling the secrets of plant roots: Simplified method for large scale root exudate sampling and analysis in Arabidopsis thaliana
<p>Plants exude a plethora of compounds, both above- and below ground, to communicate with their environment. Although much is known about this communication above ground, we are only beginning to fathom the identity, level of variation, and role of below-ground chemical signals in a plant’s life. There have been many challenges associated with establishing a standardized methodology for studying root-exuded compounds, thus their role in plant-environment communication is still not well described.</p> <p>Here, we develop an interdisciplinary workflow to explore the natural variation in root exudate chemical composition of the model plant <em>Arabidopsis thaliana</em>. We highlight key challenges associated with sampling strategies and develop a framework for analyzing narrow and broad-scale patterns in root exudate composition of a large sample set of natural <em>A. thaliana</em> accessions.</p> <p>Our method consists of <em>in vitro</em> cultivation of individual seedlings inside a plastic mesh followed by a short hydroponic sampling period in micro quantities of ultrapure water. The mesh eases handling individual plants of varying sizes, thus making this setup advantageous for large-scale characterization of root exudates of individual plants in axenic conditions, and can be easily extended for prolonged temporal exudate collection experiments. Furthermore, a short sampling duration minimizes the experiment duration from days to mere hours, and is validated by yielding sufficient signal even with the small volume of sampling solution. An untargeted metabolic profiling analytical approach using ultra-high performance liquid chromatography coupled with mass spectrometry (UHPLC-QTOF-MS), followed by compound identification using open access software MZMine3 and SIRIUS 5, was used to capture a broad picture of the root exudate composition of <em>A. thaliana</em> accessions. This methodology can be broadly applied for investigating the role of root exudates as signals involved in plant belowground interactions. We report the first findings from the analysis here with results from Columbia genotype.</p> <p>We include here</p> <p> </p> <p>In <strong>Raw datafiles</strong>: The raw datasets obtained from MZmine 3 analysis, which contains aligned features of Columbia genotypes (Sheet1) as well as control samples (Sheet2). The dataset consists of <em>feature (row)ID, average (mass-to-charge ratios) m/z</em> and <em>retention times (RT)</em> across samples for individual features. It also includes sample-specific information including <em>feature status, name, m/z, RT, feature peak height,</em> and <em>area</em>. We also include a filtered datasheet excluding the features obtained in control as well as samples (Sheet3). Sheet 4 contains the phenotypic data on the number of leaves and rosette size of the 28 replicates at the time of sampling, along with the total peak area for each sample from MZmine data.</p> <p>In <strong>Supplementary tables</strong>: The 354 metabolites obtained after filtering out control features are listed with their <em>mass-to-charge ratios</em>, <em>retention times, and the mean, variance and coefficient of variation of the peak areas </em>(Supplementary Table 1). Supplementary Table 2 details the features identified by SIRIUS 5 with their <em>mass-to-charge ratios, retention times, chemical formula, chemical annotations,</em> and corresponding <em>probabilities scored by SIRIUS</em></p> <p>In <strong>Extended data analysis:</strong> Contains supporting data analysis for reproducibility and validity of our method for root exudate collection and analysis in <em>Arabidopsis thaliana.</em> These extended data analyses enhance the understanding of the relationship between plant phenotypic traits, peak area, and variation in compound abundance</p>
Phloem anatomy constraints root system architecture development: theoretical clues from in silico experiments [software and dataset]
<p>Simulation software and results for "<strong>Phloem anatomy constraints root system architecture development: theoretical clues from in silico experiments</strong>"</p>
Data for Linkage mapping of root shape traits associated with market class in two biparental carrot populations
<p> </p> <p>This repository contains essential data to support the findings presented in the forthcoming publication titled "Linkage Mapping of Root Shape Traits Associated with Market Class in Two Biparental Carrot Populations." It includes VCF files for two distinct carrot biparental populations, as well as R code for filtering, constructing linkage maps, and conducting QTL analysis. Furthermore, the repository hosts phenotypic data gathered from these two biparental populations during the years 2020 and 2021.</p> <p>Two carrot genetic maps, one for each population, have been made available alongside their respective phenotypic data.</p> <p>The provided R code contains absolute working directory paths that may not function as intended on your system. The primary purpose of sharing this code is to offer readers insight into the techniques employed in this study. You may need to adapt the directory paths to suit your specific setup. </p> <p>To assist readers in understanding the logical sequence of steps involved in our linkage mapping project, the R code scripts have been sequentially numbered from 0 to 10.</p> <p>For more info contact: vegaalfaro@wisc.edu.</p>
Soil physical, chemical, and root data from forest stands at Thompson Farm in Durham, NH
In July 2019, quantitative soil pits were excavated alongside replicate power cores from three mature oak-pine forest stands at Thompson Farm (Durham, NH) to characterize soil physical and chemistry properties as well as root depth profiles in control and treatment plots associated with the Thompson Farm DroughtNet project, as well as in the footprint of the Ameriflux tower. Mean total sampling depth across all pits and cores was 84cm, though half of samples reached 100 cm or deeper. Chemical and isotopic analyses for each sample layer include pH, total N, total C, and stable isotope ratios of N and C. Physical data include soil mass, rock volume, bulk density, and soil texture. Oven-dried root mass in each sample layer was recorded in multiple size categories (from pits) or sorted to species (from power cores).
Decomposition of Fine Woody Roots: a Time Series Approach, 1995 to 2006
We examined the effects of species, initial substrate quality, and site differences on woody root decomposition and its nitrogen dynamics in Sitka spruce (Picea sitchensis), Douglas-fir (Pseudotsuga menziesii), and ponderosa pine (Pinus ponderosa) dominated forests in Oregon, U.S.A. using a time series approach. Roots of fourteen species and five size classes were placed in the field to incubate and then collected at pre-planned intervals to determine mass loss and nitrogen content.
Below ground root biomass, carbon and nitrogen concentrations by depth increments from the Anaktuvuk River Fire site in 2011
Below ground root biomass was measured by depth increments at three sites at and around the Anaktuvuk River Burn: severely burned, moderately burned and unburned. Roots were also analyzed for carbon and nitrogen concentrations.
Summary of below ground root biomass, carbon and nitrogen concentrations from the Anaktuvuk River Fire site in 2011
A summary of below ground root biomass, carbon and nitrogen concentrations, measured at three sites at and around the Anaktuvuk River Burn: severely burned, moderately burned and unburned.
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DANDI Archive for NWB datasets
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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.