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2,960 results for “elements”
Dealing with Sub-pixel Landscape Elements in Distributed Rainfall-Runoff Modelling in Agricultural Catchments
<p>The <strong>Input_Data.zip</strong> file contains the processed data used as input data for the research paper "<strong>Dealing with Sub-pixel Landscape Elements in Distributed Rainfall-Runoff Modelling in Agricultural Catchments</strong>".</p> <ul> <li>The <strong>Digital Elevation Models (DEMs)</strong> are adapted from the 5 m resolution "DEM DHMV II" (available from <a href="https://download.vlaanderen.be/Producten/Detail/938">https://download.vlaanderen.be/Producten/Detail/938</a>). The scaling factors used to calculate per-pixel values of upscaled hydro-physical parameters are derived from the digital elevation model.</li> <li>The raster files representing the <strong>Manning's roughness coefficient</strong> in the watershed for 2006, 2007, 2013, 2016 and 2019 are based on landcover datasets created by combining the Flemish agricultural parcel dataset for each year (available from https://www.vlaanderen.be/datavindplaats/catalogus/landbouwgebruikspercelen-lv-2021) with the road network dataset (available from <a href="https://www.vlaanderen.be/digitaal-vlaanderen/onze-oplossingen/basiskaart-vlaanderen-grb">https://www.vlaanderen.be/digitaal-vlaanderen/onze-oplossingen/basiskaart-vlaanderen-grb</a>) and digitised polygons of forested areas based on areal images (<a href="https://www.vlaanderen.be/datavindplaats/catalogus/orthofotomozaiek-grootschalig-winteropnamen-kleur-2013-2015-vlaanderen">https://www.vlaanderen.be/datavindplaats/catalogus/orthofotomozaiek-grootschalig-winteropnamen-kleur-2013-2015-vlaanderen</a>).</li> <li>The <strong>vegetated landscape element (vLE) configurations</strong> were created based on agricultural parcel boundaries (available from <a href="https://www.vlaanderen.be/datavindplaats/catalogus/landbouwgebruikspercelen-lv-2021">https://www.vlaanderen.be/datavindplaats/catalogus/landbouwgebruikspercelen-lv-2021</a>) and rasterising them.</li> <li><strong>Rainfall intensity measurements</strong> were extracted from <a href="http://waterinfo.be">waterinfo.be</a> for the station with name "Niel-bij-St.-Truiden_P", number "01P09_012", and coordinates (LAT/LON) "50.7378581908062/5.14225742349451".</li> <li><strong>Discharge measurements </strong>were extracted from <a href="http://waterinfo.be">waterinfo.be</a> for the discharge station with name "Gingelom/Heulegracht" and number "LS09_15F".</li> </ul> <p>The <strong>scripts.zip</strong> file contains the scripts used to process the data.</p> <p>The Output.zip file contains the output files created by the scripts while making use of the Python-based Landlab model environment (<a href="https://landlab.github.io/#/">https://landlab.github.io/#/</a>)</p> <p> </p> <p>This research was funded by Fonds Wetenschappelijk Onderzoek (FWO), grant number 1SB6821N.</p>
The validity of the bioaccumulation index versus the bioaccumulation factor for assessment of element accumulation in black soldier fly larvae
<p>Dataset for the input-output calculations to evaluate bioaccumulation factor (BAF) and bioaccumulation index (BAI) in comparison with true element retention rate in black soldier fly larvae (BSFL). The results suggest a higher agreement of true element retention rate with BAF than with BAI. https://doi.org/10.3920/JIFF2023.0021</p>
Ultraconserved elements support the elevation of a new avian family, Eurocephalidae, the white-crowned shrikes
<p>In this study, we infer genus-level relationships within shrikes (Laniidae), crows (Corvidae), and their allies using ultraconserved elements (UCEs). We confirm previous results of the Crested Shrikejay (<em>Platylophus</em> <em>galericulatus</em>) as comprising its own taxonomic family and find strong support for its sister relationship to laniid shrikes. We also find strong support that the African-endemic genus <em>Eurocephalus</em>, which comprises two allopatric species (<em>E. ruppelli </em>and<em> E. anguitimens</em>), are not shrikes. We propose elevating the white-crowned shrikes to their own family, Eurocephalidae. </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>
Figure S2. Spearman correlation matrix representing the relationships between the essential trace elements within each biological matrix
<p>Blue represents a positive correlation, while red represents a negative correlation. Color intensity is proportional to the correlation strength. Strikethrough values represent insignificant/negligible associations (p>0.05). Cr, chromium; Cu, copper; Fe, iron; Li, lithium; Mn, manganese; Mo, molybdenum; Se, selenium; Zn, zinc</p>
FIGURE 2 in New discovery of rhyncholites and conchorhynchs (cephalopod jaw elements) from the Upper Cretaceous Mount Laurel Formation of Delaware
FIGURE 2. Measured morphological characters in rhyncholites and conchorhynchs. Scale bars = 2 mm.
Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Mapping MGEs in oral plaque biofilms at high specificity
<p>We stained for the GFP gene in samples that contained mixtures of plaque and GFP-transformed E. coli. We mapped mefE, an AMR gene located on a plasmid and encoding an antibiotic efflux pump, in the plaque metagenomic data of volunteer A but not volunteer B. To test the efficacy of gel embedding and clearing, we used orthogonal FISH probes, designed to not target any sequence in the plaque. We identified a T7-like prophage via metagenomic analysis and developed probes targeting its capsB gene, which encodes the minor capsid protein. We identified a highly prevalent prophage of the class Caudoviricetes with a large terminase gene, termL, and were able to design a large set of FISH probes to stain in three different colors simultaneously. We identified three non-plasmid AMR genes within metagenome assembled genomes: patA, patB, and adeF.</p>
Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Optimization of single molecule MGE FISH
<p>We used <em>Escherichia coli </em>transformed with pJKR-H-tetR plasmids encoding an inducible <em>GFP</em> gene as a model system to assess and optimize MGE-FISH on a confocal microscope. We designed FISH probes for the non-coding strand of the <em>GFP</em> gene, used non-transformed <em>E. coli </em>as a negative control, and tested six different FISH protocols.<strong> </strong></p>
Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Combined taxonomic mapping and MGE mapping
<p>We used rRNA FISH to stain five common oral genera, <em>Veillonella, Streptococcus, Corynebacterium, Lautropia, </em>and <em>Neisseria</em>, each with a different fluorophore, and we used MGE-FISH to stain the <em>termL</em> gene of an active prophage with a sixth fluorophore. </p> <p>We chose a target panel of 18 genera that are highly abundant and prevalent in human plaque and designed a HiPR-FISH probe panel using a 5-fluorophore combinatorial barcoding scheme. Using MGE-FISH, we stained a plasmid carrying mefE, subunit of a major-facilitator-superfamily antibiotic efflux pump. </p>
Transposable elements potentiate radiotherapy-induced cellular immune reactions via RIG-I-mediated virus-sensing pathways
<p>Mass spectrometry-based proteomics source data.</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>
Temperature measurements of full-scale wall element using Type K thermocouples to observe internal convection in loose-fill wood fiber insulation
<p>Internal convection of insulation materials is a phenomenon that occurs when a construction element is subjected to a temperature difference on either side of the element, as the temperature difference inside the insulation will facilitate an onset of air movement due to thermal buoyancy. This dataset represents the results of 11 unique experiments conducted at Aalborg University at the Department of the Built Environment, where a full-scale wall element insulated with loose-fill wood fiber insulation is investigated for internal convection. A large guarded hotbox is used to control the boundary conditions of either side of the wall element, to imitate a construction element subjected to external and internal boundary conditions, similar to a wall in a house. This dataset can be used to benchmark other insulation materials investigated at similar boundary conditions.</p> <p>The dataset is structured into steady-state experiments and dynamic experiments, where a total of 7 unique cases are conducted in steady-state conditions, and 4 unique cases are conducted in dynamic conditions. The dataset for the steady-state experiments is structured by the temperature difference that the full-scale wall element is exposed to, from the cold and hot side, while the dynamic experiments are structured by the amplitude of the temperature variation, along with if an artificial sun is used or not.</p> <p>The results for the internal convection of the loose-fill wood fiber insulation show similar results as other studies that have conducted experiments on other insulation materials.</p> <p>For more information, see doi: 10.54337/aau488363266</p>
Understanding the impact of host networking elements on traffic bursts: Raw measurement data
<p>This record contains the raw trace files gathered by the Valinor network traffic burst measurement framework in Redis dump (rdb) format. Please refer to the artifact repository for instructions on how to parse and use the datasets:</p> <p><a href="https://github.com/hopnets/valinor-rawdata">hopnets/valinor-rawdata: Raw Redis datasets containing the measurement results of Valinor NSDI '23 paper (github.com)</a></p>
Simplified Preservation of Equal Pathways Solid Element
<p>The files contain the raw data of the experiments shown in the article: "Simple Preservation of Equal Pathways Solid Element". </p>
Radionuclide, particle size and elemental geochemistry analysis results of the Poechos sediment core, northern Peru
<p>This database presents the particle size, elemental geochemistry and radionuclide analyses carried out on the 19CO3 core (IGSN number: 10.58052/IEFOU0009) collected in June 2019 in the Poechos reservoir (Peru). These results are part of the publication <em>" El Niño-Southern Oscillation (ENSO)-driven hypersedimentation in the Poechos Reservoir, northern Peru "</em> available via the following link: http://dx.doi.org/10.5194/egusphere-2022-1233</p> <p>Corresponding authors: anthony.foucher@lsce.ipsl.fr</p> <p>Particle size analysis was performed using a laser grain sizer Malvern Mastersizer 3000 allowing to measure the grain size distribution between 10 nm and 3.5 mm. Particle size was measured on the sandy layers identified along the core (n=19) Grain size parameters such as d10, d50, d90 and raw are present on the file: <em>Particle_size_POECHOS-reservoir_Foucher-et-al</em></p> <p>Sediment core sections were analyzed with an Avaatech X-Ray Fluorescence core scanner (XRF) available at the Laboratoire des Sciences du Climat et de l’Environnement (Gif-sur-Yvette, France) with a 0.5 cm resolution. These data are available on the file: <em>XRF_core_scanner_POECHOS-reservoir_Foucher-et-al</em></p> <p>Gamma spectrometry measurements were obtained using HPGe detectors (Canberra/Ortec) available at the Laboratoire des Sciences du Climat et de l’Environnement. Short-lived radionuclides (e.g., caesium-137 (137Cs) and excess of lead-210 (210Pbex)) were measured in 12 samples of dry sediment (≈10g) collected along the sedimentary sequence (approximatively every 40 cm). The data are available on the file: <em>Radionuclides_POECHOS-reservoir_Foucher-et-al</em></p>
Raw target enrichment of conserved element sequence data for 24 black coral species
<p><span>Deep-sea lineages are generally thought to arise from shallow-water ancestors, but this hypothesis is based on a relatively small number of taxonomic groups. Anthozoans, which include corals and sea anemones, are significant contributors to the faunal diversity of the deep sea, but the timing and mechanisms of their invasion into this biome remain elusive. Here, we reconstruct a fully resolved, time-calibrated phylogeny of 83 species in the order Antipatharia (black coral) to investigate their bathymetric evolutionary history. Our reconstruction indicates that extant black coral lineages first diversified in continental slope depths (~250–3,000 m) during the early Silurian (~437 Ma) and subsequently radiated into, and diversified within, both continental shelf (<250 m) and abyssal (>3,000 m) habitats. Ancestral state reconstruction analysis suggests that the appearance of morphological features that enhanced the ability of black corals to acquire nutrients coincided with their invasion of novel depths. Our findings have important conservation implications for anthozoan lineages, as the loss of "source" slope lineages could threaten millions of years of evolutionary history and confound future invasion events, thereby warranting protection. </span></p>
CTCF BINDING PATTERNS DEFINE TADS AND BOUNDARY ELEMENTS IN HUMAN AND MOUSE GENOMES
<p><em><strong>Msci thesis from Industrial Placement at Politecnico di Milano</strong></em></p> <p> </p> <p><strong>Abstract</strong></p> <p>In eukaryotes, the genome is highly packaged inside the nucleus. This hierarchical structure requires complex compartmentation and organization. Topologically associating domains (TADs) serve as architectural units in the 3D genome, functioning to regulate and constrain gene interaction. TAD boundaries are enriched in the CCCTC-binding factor (CTCF). Due to the asymmetric nature of the CTCF motif, it exhibits differing orientations based on the strand it is localized. Motif orientation is crucial for loop formation, which is facilitated in a convergent orientation. While the relationship between TADs and CTCF motif patterns has been described in humans, the model remained to be corroborated in other mammals. </p> <p>We conducted a comparative analysis by applying the research conducted in humans to the mouse genome. By integrating ChIP-seq data, we examined the CTCF sites based on ChIP-seq peak consolidation, signal value, and motif p-value. This analysis aimed to comprehend the binding profile of CTCF and elucidate its complexity in terms of binding strength and cross-tissue conservation. Mouse genome CTCF motifs were categorized into cluster patterns based on their relative orientation. Following this classification, the distribution of each pattern was studied using ChIP-seq-related descriptors. We then built a TAD boundary collection based on the insulation score. Boundary consolidation and length, insulation score, and CTCF number were used to reconcile CTCF to TAD boundary function. The cluster patterns were then mapped to TAD and TAD boundaries to elucidate their structure based on the spatial arrangement of CTCF.</p> <p>The distribution of ChIP-seq-validated CTCF sites within TAD boundaries revealed a well-defined structure, characterized by an abundance of the divergent pattern. Boundaries with the highest insulation scores exhibited both a high consolidation and CTCF enrichment. This set of boundaries was used to study TAD structure. An increment of the convergent pattern was observed inside TADs. The individual CTCF sites on the interior of the TAD were further organized into left and right sections, corresponding to an opposing directional arrangement to TAD boundaries. Significantly, the ChIP-seq data contained many unannotated peaks and non-signal motifs. These were associated with a high motif p-value, low ChIP-seq signal, low consolidation, and a less structured arrangement of CTCF clustering. Moreover, non-signal motifs were underrepresented within TAD boundaries and displayed a disorderly distribution.</p> <p>The human model of CTCF-dependent TAD structure was confirmed in mice. The model suggested the inherent alternation between convergent and divergent patterns, with these CTCF sites conferring characteristic properties upon TADs and their boundaries. These traits encompass the change of preferential genomic interaction and boundary insulation capability. Thus, the orientation-based clustering of CTCF sites was further validated as a good method to define TADs in a precise organized manner.</p>
Shape functions and Integration quadrature of nine 3D transition elements
<p>This file houses the text files and Matlab function files that contain the shape functions and integration quadrature of nine 3D transition elements. The Matlab function file also computes the Shape function gradient matrix that can be readily used for FE applications.</p>
Copy number variation introduced by a massive mobile element underpins global thermal adaptation in a fungal wheat pathogen - Supplementary Tables..
<p>Supplementary Tables S1 - S11 of the manuscript <strong>Copy number variation introduced by a massive mobile element underpins global thermal adaptation in a fungal wheat pathogen. </strong></p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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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.
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