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388 results for “Data element”
Data from: Abiotic legacies mediate plant-soil feedback during early vegetation succession on rare earth element mine tailings
<p>An increasing number of studies have shown how feedback interactions between plants and soil can influence primary and secondary succession. However, very little is known about the patterns and mechanisms of such plant-soil feedbacks on stressed mine tailings ecosystem, which can be severely contaminated by a range of toxic elements. </p> <p>In a two-phase plant-soil feedback experiment based on the rare earth element (REE) mine tailing soil, we investigated biotic (changes in bacterial and fungal community) and abiotic legacies (changes in chemical properties) of three pioneer grass species, and examined feedback effects of three grasses, two legumes and two woody plants with different root traits.</p> <p>Positive plant-soil feedback was found in Miscanthus sinensis, Paspalum thunbergii and Tephrosia candida, and neutral feedback was observed in other four plants. These effects corresponded with an increase of nutrients and total organic carbon, as well as a decrease of acidity and extractable aluminum and REEs. There were less signs of biotic changes in the conditioned tailings. </p> <p>The correlation analysis suggested a relationship between responses to soil legacies and root traits, as well as root economics spectrum. On the mine tailings, acquisitive species with higher specific root length appeared to have greater potential for positive feedback. </p> <p>Synthesis and application: Our study shows that early succession on contaminated REE mine tailings may lead to more positive plant-soil feedback than predicted based on results of non-contaminated soils, mainly due to the alleviation of abiotic stress in tailings. Therefore, the improvement of specific abiotic soil stress and the trait-based selection of acquisitive plants should be preferentially considered to promote the primary restoration of degraded land.</p>
Data from: LHFPL5 is a key element to the gating spring of cochlear hair cells: comparison of mechanotransduction channel activation in presence or absence of LHFPL5
<p>During auditory transduction, sound-evoked vibrations of the hair cell stereociliary bundles open mechanotransducer (MET) ion channels via tip links extending from one stereocilium to its neighbor. How tension in the tip link is delivered to the channel is not fully understood. The MET channel comprises a pore-forming subunit, transmembrane channel-like protein (TMC1 or TMC2), aided by several accessory proteins, including LHFPL5 (lipoma HMGIC fusion partner-like 5). We investigated the role of LHFPL5 in transduction by comparing MET channel activation in outer hair cells of <em>Lhfpl5-/- </em>knockout mice with those in <em>Lhfpl5+/-</em> heterozygotes. The 10-90 percent working range of transduction in <em>Tmc1+/+; Lhfpl5+/-</em> was 52 nm, from which the single-channel gating force, Z was evaluated as 0.34 pN. However, in <em>Tmc1+/+; Lhfpl5‑/- </em>mice,<em> </em>the<em> </em>working range increased to 123 nm and Z more than halved to 0.13 pN, indicating reduced sensitivity. Tip link tension is thought to activate the channel via a gating spring, whose stiffness is inferred from the stiffness change on tip link destruction. The gating stiffness was ~40 percent of the total bundle stiffness in wild-type but was virtually abolished in <em>Lhfpl5-/-,</em> implicating LHFPL5 as a principal component of the gating spring. The mutation <em>Tmc1 </em>p.D569N reduced the LHFPL5 immunolabeling in the stereocilia and like <em>Lhfpl5-/-</em> doubled the MET working range but other deafness mutations had no effect on the dynamic range. We conclude that tip-link tension is transmitted to the channel primarily via LHFPL5; residual activation without LHFPL5 may occur by direct interaction between PCDH15 and TMC1.</p>
Supplemental data and figures behind: Atom scale element and isotopic investigation of 25Mg-rich stardust from a H-burning supernova
<p>We have discovered a presolar olivine from ALH 77307 with the highest <sup>25</sup>Mg isotopic composition measured in a silicate to date (δ<sup>25</sup>Mg = 3025.1‰ ± 38.3‰).<strong> </strong>Its isotopic compositions challenge current stellar models, with modelling of Mg, Si and O showing a closest match to formation in a supernova where hydrogen ingestion occurred in the pre-supernova phase. Presolar grains within primitive astromaterials retain records of processes and environmental changes throughout stellar evolution. However, accessing these records has proved challenging due to the average grain size (~150 nm) of presolar silicates, their sensitivity to extraction agents and instrumental restrictions, limiting the range of isotopic and chemical signatures which can be studied per grain volume. Here, we present the first known detailed, geochemical study of a presolar silicate from a H-burning supernova, studied in 3D without contributions to the analysis volume and at unprecedented spatial resolutions (< 1 nm), essential for constraining physical and chemical processes occurring within this recently proposed stellar environment. From our results, we infer either; [1] condensation within an environment depleted of heavy elements compatible with the olivine lattice under the pressure and temperature conditions during condensation. [2] during periods of limited mixing either near the end of the pre-supernova phase or from a collapse so rapid localised pockets of different gas compositions formed.</p>
An enhanced single Gaussian point continuum finite element formulation using automatic differentiation: Source code and data
<p>This dataset contains the source code and the data with an example of uniaxial strain of an enhanced single Gaussian point continuum finite elemnet formulation using automatic differentiation.</p> <p> </p> <p>This contribution presents a low-order 3D finite element formulation with hourglass stabilization using automatic differentiation. Here, the former Q1STc element formulation is enhanced by an approximation-free computation of the inverse of the Jacobian. The improved version is termed "Q1STc+."</p> <p> </p> <p>The corresponding publication is:</p> <p><br>Pacolli, N., Awad, A., Kehls, J., Sauren, B., Klinkel, S., Reese, S., Holthusen, H.<br><em>An enhanced single Gaussian point continuum finite elemnet formulation using automatic differentiation.</em></p> <p>Standalone_Elementroutine: <em>Q1STc+_Codes</em> contains:</p> <ul> <li><strong>main.f90</strong>: Standalone routine for local uniaxial strain test</li> <li><strong>Makefile</strong>: Makefile to create executable "Q1STc+"</li> <li><strong>elem40.f90</strong>: Element routine "Q1STc+" with elem_sub.f90 as the subroutine written in AceGen</li> <li><strong>mat52.f90</strong>: Elasto-plastic material routine with all subroutines written in AceGen</li> <li><strong>elem_mat_select.f90</strong>: The selected material routine (Here: mat52)</li> <li><strong>elem_subs.f90</strong>: Subroutines for elem40.f90</li> <li><strong>mat_subs.f90</strong>: Subroutines for mat52.f90</li> </ul>
OPT data from: A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint
<p><span>The acquisition of movable jaws was a major event during vertebrate evolution. The role of NK3 homeobox 2 (Nkx3.2) transcription factor in patterning the primary jaw joint of gnathostomes (jawed vertebrates) is well known, however, knowledge about its regulatory mechanism is lacking. In this study, we report a proximal enhancer element of <em>Nkx3.2</em> that is deeply conserved in most gnathostomes but undetectable in the jawless hagfish and lamprey. This enhancer is active in the developing jaw joint region of the zebrafish <em>Danio rerio</em>, and was thus designated as <em>jaw joint regulatory sequence 1</em> (JRS1). We further show that JRS1 enhancer sequences from a range of gnathostome species, including a chondrichthyan and mammals, have the same activity in the jaw joint as the native zebrafish enhancer, indicating a high degree of functional conservation despite the divergence of cartilaginous and bony fish lineages or the transition of the primary jaw joint into the middle ear of mammals. Finally, we show that deletion of JRS1 from the zebrafish genome using CRISPR/Cas9 results in a significant reduction of early gene expression of <em>Nkx3.2</em> and leads to transient jaw joint deformation and partial fusion. The emergence of this <em>Nkx3.2 </em>enhancer in early gnathostomes may have contributed to the origin and shaping of the articulating surfaces of vertebrate jaws.</span></p>
Data Availability - DRAFT - 'Process-based similarity' revealed by discharge-dependent relative submergence dynamics of thousands of large bed elements
<p>Datasets and R code related to confidential manuscript submission entitled "‘Process-based similarity’ revealed by discharge-dependent relative submergence dynamics of thousands of large bed elements". Restrictions apply to the availability of the 2014 DTM and 2D model results, which were used under contractual agreement from the project sponsor. These are available from the senior author with the permission of Yuba Water Agency. Restrictions apply to the availability of the 2014 DTM and 2D model results, which were used under contractual agreement from the project sponsor. These are available from the senior author with the permission of Yuba Water Agency.</p>
Ultraconserved element data for phylogenomic placement of the jumping spider genus Iranattus Prószyński, 1992 (Salticidae, Plexippini, Plexippina)
<p>The jumping spider genus <em>Iranattus</em> Prószyński, 1992 has been placed in the Harmochirina based on morphology. We use phylogenomic evidence based on ultraconserved element (UCE) data to show that it belongs instead in the subtribe Plexippina.</p>
Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen - Supplementary Data files
<p>Supplementary Data file 3-4 included in the manuscript Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen. </p>
Input data of the mixed meshes used in: J. Grošelj, M. Kapl, M. Knez, T. Takacs, V. Vitrih, C1-smooth isogeometric spline functions of general degree over planar mixed meshes: The case of two quadratic mesh elements, Applied Mathematics and Computation 460 (2024) 128278; DOI: 10.1016/j.amc.2023.128278
Open the record for dataset details and reuse information.
Data from: Canopy facilitation outweighs elemental allelopathy in a metalliferous system during an exceptionally dry year
<p>The Elemental Allelopathy hypothesis states that the metal-rich litter of hyper-accumulating species may have a detrimental impact on neighbouring plants giving a competitive advantage to hyper-accumulators. Here, we aim to specify the conditions of application of this hypothesis in realistic field conditions, and its relative importance compared to other positive effects found in metalliferous systems. We disentangled the litter-induced elemental allelopathy and canopy effects of two metallophyte species (<em>Arenaria multicaulis</em> and <em>Hutchinsia alpina</em>) with different levels of leaf Zn and Cd accumulation on two ecotypes of <em>Agrostis capillaris</em> with different levels of metal tolerance. The experiment was conducted in two habitats with contrasting pollution levels in a former mining valley in the Pyrenees (France). The metallophyte species that accumulates more metals (<em>Hutchinsia alpina</em>) showed a strong elemental allelopathy effect on the target with lower metal tolerance in the habitat with lower pollution level, while the metallophyte species that accumulates less metals (<em>Arenaria multicaulis</em>) had no litter effect. Both metallophyte species had positive canopy effects likely due to the improvement of micro-climatic conditions. The drought that occurred during the experiment may have influenced these canopy effects, increasing their importance during the course of the study. For <em>Hutchinsia alpina </em>the positive canopy effects were stronger than the negative litter effects, resulting in overall positive effects on both target ecotypes.</p> <p><em>Synthesis.</em> Our results brought a better understanding of the occurrence of elemental allelopathy in metallophyte communities and its relative importance as compared to micro-climatic facilitation in a global warming context.</p>
Data and code for "Trace elements increase reproducibility of microbial growth"
<p>Data and code for the paper <em><a href="https://doi.org/10.1101/2024.07.15.603609">Trace elements increase reproducibility of microbial growth</a>.</em></p>
The coincidence degree between the geochemical behavior of elements and the periodic variation of elements based on geochemical data of C2 coal seam in the Fengfeng mining area of the Handan Coalfield in Hebei, China
<p>In this data-set, based on the geochemical data of C2 coal seam in the Fengfeng mining area of the Handan Coalfield in Hebei (China), where provided ideal coal samples changing continuously from low-rank metamorphic coal to high-rank metamorphic coal, the coincidence degree (or similarity degree) between the geochemical behavior of 57 elements and the periodic variation of elements during the thermal metamorphism process is calculated.</p>
Simulated data set of chimeric transposable elements.
<p>This dataset is composed of 9,000 sequences of transposable elements (TEs) of 20,000 bp. Three cases of transposable elements with artifacts at the ends, with another chimeric TE or with simple repeats were considered for the generation of the sequences. The sequences of the first case consist of a DNA fragment + first TE + DNA fragment + second TE + DNA fragment. The sequences of the second case consist of a first TE + second TE + repeat of the first TE. The third case sequences consist of a microsatellite that is repeated in tandem by placing the extracted TE at position 10,000 (in the middle), occupying both sides to the ends. All TEs used in this dataset were taken from Dfam, for the species Drosophila melanogaster.</p> <p>The identifier of each sequence has the information about the case, TE Dfam identifier, TE initial position inside the sequence, and the TE length, all separated by "_". For example:</p> <p>Caso1_DF000001548.2_6926_5126</p> <p>File description:</p> <p>dataset.zip: The fasta file containing all the sequences</p> <p>features_data.npy.zip: A numpy file containing the numerical representation of the four TE+Aid plots generated for the sequences presented in the dataset.zip file. This data is actually a numpy array with dimensions 9000x256x256x3x4</p> <p>labels_data.numpy.zip: A numpy file containing the starting and ending position (normalized between 0 and 1) of each TE presented in the dataset.zip file.</p> <p>The last two files were generated to train a neural network for trimming out automatically artifacts in DNA sequences.</p>
Data for the article: Coupling of leaf elemental traits with root fungal community composition reveals a plant resource acquisition strategy in a desert ecosystem
<p><em>Purpose</em>: Plant-associated microbes enhance nutrient access and stress tolerance of the host species, and therefore, are crucial for plant traits and resource strategies. However, the links between aboveground plant traits and belowground microbes related to plant resource strategies under stressful conditions remain poorly understood.</p> <p><em>Methods</em>: We tested the relationships between leaf traits linked to water (carbon isotopic composition, δ<sup>13</sup>C) and nutrient use (elemental concentrations and stoichiometry) with microbial compositions in roots and rhizospheres of two dominant species (<em>Artemisia ordosica</em> and <em>Leymus secalinus</em>) in the Mu Us Desert, northern China.</p> <p><em>Results</em>: <em>L. secalinus</em> exhibited higher Mg and Mn concentrations, N:P ratios, stoichiometric flexibility, and root fungi:bacteria ratios, but lower foliar K and Ca concentrations and δ<sup>13</sup>C values than <em>A. ordosica</em>. The leaf N:P of <em>L. secalinus</em> increased with the root fungi:bacteria ratios, whereas the leaf N:P of <em>A. ordosica</em> decreased with the root fungi:bacteria ratios. The plant elemental levels (P, N, K, Ca, Mn, and δ<sup>13</sup>C) of <em>L. secalinus</em> but not <em>A. ordosica</em> were significantly related to their root fungal composition. Additionally, the random forest model identified four key fungal families in predicting leaf elemental traits for both plant species.</p> <p><em>Conclusion</em>: The results suggested tight coupling and coordination between leaf elemental traits and root microbial compositions (especially fungal communities) related to plant resource acquisition strategies. By regulating aboveground and belowground feedback loops through trait flexibility and root microbial compositions, the studied plant species can sustain their resource strategies under stressful environmental conditions.</p>
Data from: Whiskers provide time-series of toxic and essential trace elements, Se:Hg molar ratios, and stable isotope values of an apex Antarctic predator, the leopard seal
<p>In an era of rapid environmental change and increasing human presence, researchers need efficient tools for tracking contaminants to monitor the health of Antarctic flora and fauna. Here, we examined the utility of leopard seal whiskers as a biomonitoring tool that reconstructs time-series of significant ecological and physiological biomarkers. Leopard seals (<em>Hydrurga leptonyx</em>) are a sentinel species in the Western Antarctic Peninsula due to their apex predator status and top-down effects on several Antarctic species. However, there are few data on their contaminant loads. We analyzed leopard seal whiskers (n = 18 individuals, n = 981 segments) collected during 2018–2019 field seasons to acquire longitudinal profiles of non-essential (Hg, Pb, and Cd) and essential (Se, Cu, and Zn) trace elements, stable isotope (ẟ<sub>15</sub>N and ẟ<sub>13</sub>C) values and to assess Hg risk with Se:Hg molar ratios. Whiskers provided between 46 and 286 cumulative days of growth with a mean ~125 days per whisker (n = 18). Adult whiskers showed variability in non-essential trace elements over time that could partly be explained by changes in diet. Whisker Hg levels were insufficient (<20 ppm) to consider most seals being at "high" risk for Hg toxicity. Nevertheless, maximum Hg concentrations observed in this study were greater than that of leopard seal hair measured two decades ago. However, variation in the Se:Hg molar ratios over time suggest that Se may detoxify Hg burden in leopard seals. Overall, we provide evidence that the analysis of leopard seal whiskers allows for the reconstruction of time-series ecological and physiological data and can be valuable for opportunistically monitoring the health of the leopard seal population and their Antarctic ecosystem during climate change.</p>
Data from: Ultraconserved elements improve resolution of marmot phylogeny and offer insights into biogeographic history
<p class="MsoNormal"><span>Marmots (<em>Marmota</em> spp.) comprise a lineage of large-bodied ground squirrels that diversified rapidly in the Pleistocene, when the planet quickly transitioned to a drier, colder, and highly seasonal climate—particularly at high latitudes. Fossil evidence indicates the genus spread from North America, across Beringia, and into the European Alps over the course of only a few million years, beginning in the late Pliocene. Marmots are highly adapted to survive long and severely cold winters, and this likely favored their expansion and diversification over this time period. Previous phylogenetic studies have identified two major subgenera of marmots, but the timing of important speciation events and some species relationships have been difficult to resolve. Here we use ultraconserved elements and mitogenomes, with samples from all 15 extant species, to more precisely retrace how and when marmots came to inhabit a vast Holarctic range. Our results indicate marmots arose in North America in the mid Miocene (~16.3 Mya) and dispersed across the Bering Land Bridge in the late Pliocene (~3-4 Mya); in addition, our fossil-calibrated timeline is suggestive of the rise and spread of open grasslands as being particularly important to marmot diversification. The woodchuck (<em>M. monax</em>) and the Alaska marmot (<em>M. broweri</em>) are found to be more closely related to the Eurasian species than to the other North American species. Paraphyly is evident in the bobak marmot (<em>M. bobak</em>) and the hoary marmot (<em>M. caligata</em>), and in the case of the latter the data are highly suggestive of a second, cryptic species in the Cascade Mountains of Washington.</span></p>
cultural heritage elements in Andalusia and demographic data sorted by urban category
<p>Dataset concerning cultural heritage elements and demographic data in Andalusia at the municipality level, as they appear on SIMA (Sistema de Información Multiterritorial de Andalucía), March 2023. They have been sorted by urban category, depending on the number of inhabitants of each municipality: less than 1.000 inhabitants, 1.000 to 10.000 inhabitants, 10.000 to 100.000 inhabitants, and more than 100.000 inhabitants.</p>
Raw data for: Crosstalk between regulatory elements in the disordered TRPV4 N-terminus modulates lipid-dependent channel activity
<p>This repository contains raw data and code related to "Crosstalk between regulatory elements in the disordered TRPV4 N-terminus modulates lipid-dependent channel activity" by Goretzki et al.</p> <p>Included are molecular dynamics parameter files, initial structures after system equilibration, production trajectories, and final structures of simulations of:<br> 1. coarse-grained IDRs on membrane, and force and position data for restrained c-termini. Trajectories are subsampled with one frame every 50 ns.<br> 2. The tetrameric TRPV4 core in a POPC in atomistic resolution. Trajectories are sampled with one frame every 1 ns. <br> 3. The isolated ARD in solution in atomistic resolution. Trajectories are subsampled with one frame every 1 ns.</p> <p>Contact information:<br> Name: Stefan L. Schaefer<br> Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics<br> Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany<br> Email: stefan.schaefer@biophys.mpg.de</p> <p>Name: Ainara Claveras Cabezudo<br> Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics<br> Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany<br> Email: ainara.claveras@biophys.mpg.de</p>
Additional data and code for "You can move, but you can't hide: identification of mobile genetic elements with geNomad"
<ul> <li><strong>benchmark_data:</strong> Data used to train and evaluate the classification models.</li> <li><strong>giant_virus_data:</strong> Sequences and metadata of giant viruses identified in public metagenomes.</li> <li><strong>neural_network_training:</strong> Code used to train geNomad's neural network-based classification model.</li> <li><strong>provirus_data:</strong> Data used to train and evaluate the conditional random field model employed by geNomad to identify provirus regions.</li> <li><strong>reference_sequences:</strong> Sequences of chromosomes, plasmids, and viruses that were used to build geNomad's marker dataset and to generate the training data for the classification models.</li> </ul>
Data on elements in the litter produced by urban tree species (Jacaranda mimosifolia and Piscidia piscipula)
<p>These data were obtained in the metropolitan region of Xalapa, Veracruz, Mexico for a study related to the evaluation of chemical elements of the inflorescence litter produced by two species of trees that are established in urban sites. Specifically, the objective of this study was to evaluate the nutritional properties and chemical composition of inflorescence litter for two tree species commonly used in urban landscaping, Jacaranda (<em>Jacaranda mimosifolia)</em> and Jabin (<em>Piscidia piscipula</em>), and mixtures of inflorescence litter material with Andosol type soil in an experiment.</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.