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1,274 results for “high-throughput”
Spectrophotometric and Fluorimetric High-Throughput Assays for Phenolic Acid Decarboxylase
<p>Biocatalytic decarboxylation of hydroxycinnamic acids yields phenolic styrenes, which are important precursors for antioxidants, epoxy coatings, adhesives and other polymeric materials. <em>Bacillus subtilis</em> decarboxylase (<em>Bs</em>PAD) is a cofactor-independent enzyme that catalyzes the cleavage of carbon dioxide from <em>p</em>-coumaric-, caffeic-, and ferulic acid with high catalytic efficiency. Real-time spectroscopic assays for decarboxylase reactions remove the necessity of extensive sample workup, which is required for HPLC, mass spectrometry, gas chromatography, or NMR methods. This work presents two robust and sensitive assays based on photometry and fluorimetry that allow decarboxylation reactions to be followed with high sensitivity while avoiding product extraction and long analysis times. Optimized assay procedures were used to measure <em>Bs</em>PAD activity in cell lysates and to determine the kinetic constants (<em>K</em><sub>M</sub> and <em>V</em><sub>max</sub>) of the purified enzyme for <em>p</em>-coumaric-, caffeic- and ferulic acid. Substrate inhibition was shown for caffeic acid.</p>
Dataset - Speeding up high-throughput characterization of materials libraries by active learning: autonomous electrical resistance measurements
<p>With the trend towards multinary materials and the associated increase in measurement time, there is a clear need for increasing the efficiency of measurement procedures. In systems requiring long materials characterization times, the implementation of active learning can help decreasing the measurement duration significantly. This dataset is part of the publication in Digital Discovery under the same title and holds the algorithm as well as the data used to test its performance. The algorithm leverages an active learning approach with a Gaussian process model capable of selecting the next measurement area of a library of materials based on the highest uncertainty. Ten materials libraries were manufactured by magnetron sputtering, the composition was measured with EDX and the electrical resistance was measured using the described test stand. The code can also be found on <a href="https://gitlab.ruhr-uni-bochum.de/fthelen/auto-resist-meas">Gitlab</a>.</p>
Data for: High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display
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MCount: An automated colony counting tool for high-throughput microbiology
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Data for: Tools and methods for high-throughput single-cell imaging with the mother machine
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Data from: Towards drift-free high-throughput nanoscopy through adaptive intersection maximization
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A high-throughput multispectral imaging system for museum specimens
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Data and scripts for: Genetic dissection of seasonal vegetation index dynamics in maize through aerial based high-throughput phenotyping
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Genotyping results of the FabaPanel for: Genetic erosion within the Fabada dry bean market class revealed by high-throughput genotyping
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Data from: Meroplankton diversity, seasonality and life-history traits across the Barents Sea Polar Front revealed by high-throughput DNA barcoding
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Simultaneous genotyping of snails and infecting trematode parasites using high-throughput amplicon sequencing.
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Data from: Accelerated high-throughput imaging and phenotyping system for small organisms
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Development of a high-throughput small molecule screening assay for phenotypical characterization of lysosomal storage disorder-affected cells, with infantile cystinosis as a proof of principle
<p>Together with the Pivot Park Screening Centre we performed a drug screen on CTNS-/- proximal tubule cells. For this we developed an assay to evaluate LC3-II positive puncta, and which may be applied for any disease in which autophagy plays an important role. The screen was optimized by the hotel for a 384 well format, making it useful for high throughput screening. The screen was performed with 1280 compounds from the Prestwick library.</p>
Cognitive map-based navigation in wild bats revealed by a new high-throughput tracking system
<p>Seven decades of research on the "cognitive map", the allocentric representation of space, have yielded key neurobiological insights, yet we still lack field evidence from free-ranging wild animals. Using a system capable of tracking dozens of animals simultaneously at high accuracy and resolution, we assembled a large dataset of 172 foraging Egyptian fruit bats comprising >18M localizations collected over 3,449 bat-nights across 4 years. Detailed track analysis, combined with translocation experiments, revealed that wild bats seldom exhibit random search but instead repeatedly forage in goal-directed, long and straight flights that include frequent shortcuts. Alternative non-map-based strategies were ruled out by simulations, time-lag embedding and other trajectory analyses. Our results are consistent with expectations from cognitive map-like navigation and support previous neurobiological evidence from captive bats. </p>
Data from: Unraveling hierarchical genetic structure in a marine metapopulation: a comparison of three high-throughput genotyping approaches
<p>Marine metapopulations often exhibit subtle population structure that can be difficult to detect. Given recent advances in high-throughput sequencing, an emerging question is whether various genetic approaches, in concert with improved sampling designs, will substantially improve our understanding of genetic structure in the sea. To address this question, we explored hierarchical patterns of structure in the coral reef fish <i>Elacatinus lori</i> using a high-resolution approach with respect to both genetic and geographic sampling. Previously, we identified three putative <i>E. lori</i> populations within Belize using traditional genetic markers and sparse geographic sampling: barrier reef and Turneffe Atoll; Glover's Atoll; and Lighthouse Atoll. Here, we systematically sampled individuals at ~10 km intervals throughout these reefs (1,129 individuals from 35 sites) and sequenced all individuals at three sets of markers: 2,418 SNPs; 89 microsatellites; and 57 non-repetitive nuclear loci. At broad spatial scales, the markers were consistent with each other and with previous findings. At finer spatial scales, there was new evidence of genetic substructure, but our three marker sets differed slightly in their ability to detect these patterns. Specifically, we found subtle structure between the barrier reef and Turneffe Atoll, with SNPs resolving this pattern most effectively. We also documented isolation by distance within the barrier reef. Sensitivity analyses revealed that the number of loci (and alleles) had a strong effect on the detection of structure for all three marker sets, particularly at small spatial scales. Taken together, these results illustrate empirically that high-throughput genotyping data can elucidate subtle genetic structure at previously-undetected scales in a dispersive marine fish.</p>
Applying RGB- and Thermal-Based Vegetation Indices from UAVs for High-Throughput Field Phenotyping of Drought Tolerance in Forage Grasses
<p>Basic data from publication <a href="https://doi.org/10.3390/rs13010147">https://doi.org/10.3390/rs13010147</a></p> <p><strong>All_TDRdata.csv</strong> contains the data from 48 TDR sensors (30 cm) installed in the three rainout shelters.</p> <ul> <li>Sensors 1 - 18 were installed vertically to obtain soil moisture content averaged over the 10 - 40 cm profile, on 6 locations per shelter</li> <li>Sensors 19-21 were installed diagonally to obtain soil moisture content averaged over the 20 - 40 cm profile on one location per shelter</li> <li>Sensors 22-24 were installed diagonally to obtain soil moisture content averaged over the 40 - 60 cm profile on one location per shelter</li> <li>Sensors 25-27 were installed horizontally to obtain soil moisture content at 10 cm depth on one location per shelter</li> <li>Sensors 28-30 were installed horizontally to obtain soil moisture content at 20 cm depth on one location per shelter</li> <li>Sensors 31-33 were installed horizontally to obtain soil moisture content at 30 cm depth on one location per shelter</li> <li>Sensors 34-36 were installed horizontally to obtain soil moisture content at 40 cm depth on one location per shelter</li> <li>Sensors 37-39 were installed horizontally to obtain soil moisture content at 50 cm depth on one location per shelter</li> <li>Sensors 40-42 were installed horizontally to obtain soil moisture content at 60 cm depth on one location per shelter</li> <li>Sensors 43-45 were installed horizontally to obtain soil moisture content at 70 cm depth on one location per shelter</li> <li>Sensors 46-48 were installed horizontally to obtain soil moisture content at 80 cm depth on one location per shelter</li> </ul> <p>Climate.txt contains the daily averaged microclimatic data</p> <p>PhenotypingData.csv contains the phenotypic data from the UAV flights and the breeder scores</p> <p> </p>
Elemental vacancy diffusion database from high-throughput first-principles calculations for fcc and hcp structures
<p><br /> This work demonstrates how databases of diffusion-related properties can be developed from high-throughput ab initio calculations. The formation and migration energies for vacancies of all adequately stable pure elements in both the face-centered cubic (fcc) and hexagonal close packing (hcp) crystal structures were determined using ab initio calculations. For hcp migration, both the basal plane and z-direction nearest-neighbor vacancy hops were considered. Energy barriers were successfully calculated for 49 elements in the fcc structure and 44 elements in the hcp structure. These data were plotted against various elemental properties in order to discover significant correlations. The calculated data show smooth and continuous trends when plotted against Mendeleev numbers. The vacancy formation energies were plotted against cohesive energies to produce linear trends with regressed slopes of 0.317 and 0.323 for the fcc and hcp structures respectively. This result shows the expected increase in vacancy formation energy with stronger bonding. The slope of approximately 0.3, being well below that predicted by a simple fixed bond strength model, is consistent with a reduction in the vacancy formation energy due to many-body effects and relaxation. Vacancy migration barriers are found to increase nearly linearly with increasing stiffness, consistent with the local expansion required to migrate an atom. A simple semi-empirical expression is created to predict the vacancy migration energy from the lattice constant and bulk modulus for fcc systems, yielding estimates with errors of approximately 30%.</p> <p>Files:</p> <p>figure_excel_files.zip:</p> <p>Excel files for figures in the publication, and excel files of main data tables for FCC and HCP vacancy formation energies and vacancy migration energies.</p> <p>fcc_hvf_hvm.tar.gz and hcp_hvf_hvm.tar.gz:</p> <p>Raw VASP files corresponding to FCC and HCP vacancy formation energies and vacancy migration energies.<br /> <br /> bulk_modulus.tar.gz:</p> <p>Raw VASP files corresponding to FCC bulk modulus calculations.<br /> </p>
Antarctic eukaryotic soil diversity of the Prince Charles Mountains revealed by high-throughput sequencing
<p>Analysis scripts and raw data for manuscript titled: "<em>Antarctic eukaryotic soil diversity of the Prince Charles Mountains revealed by high-throughput sequencing</em>" </p>
Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?
<p>The 8 benthic samples from Mainland France (stream Edian, stream Aire, lake Geneva), Sweden (stream Dåmman, Agricultural stream, lake Båtkåjaure) and Mayotte (stream Dapani, stream Majimbini) were collected by scraping material from the surface of stones, following the French standard (AFNOR 2007) used in routine biomonitoring programs.DNA was extracted from each sample (2 replicates) using five DNA extraction methods, followed by the amplification of a short rbcL DNA barcode (312bp) specific to diatoms. PCR products were then sequenced in one random direction using the Ion Torrent™ Personal Genome Machine® (PGM) System according to the manufacturer’s instructions. The data file contains one fastq file per library sequenced with the raw DNA reads, as provided by the sequencing platform (demultiplexing performed by the sequencing platform). An excel file is also provided to make the link between the fastq file number and the sample information (sample origin, DNA extraction method used, number of raw reads).</p>
Shark-dust: Application of high-throughput DNA sequencing of processing residues for trade monitoring of threatened sharks and rays
<p>Data repository accompanying manuscript titled of "Shark-dust: Application of high-throughput DNA sequencing of processing residues for trade monitoring of threatened sharks and rays."</p> <p>Prasetyo, A. P., Murray, J. M., Kurniawan, M. F. A. K., Sales, N. G., McDevitt, A. D., & Mariani, S. (2023). Shark-dust: Application of high-throughput DNA sequencing of processing residues for trade monitoring of threatened sharks and rays. Conservation Letters, 16, e12971. https://doi.org/10.1111/conl.12971</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.