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990 results for “quantification”
Towards accurate quantification of ice content in permafrost of the Central Andes, part I: geophysics-based estimates from three different regions
<p>This data set contains two zip-files for a) the electrical resistivity tomography (ERT) data, and b) the refraction seismic tomography (RST) data used in</p> <p>Hilbich, C., Hauck, C., Mollaret, C., Wainstein, P., and Arenson, L. U.: Towards accurate quantification of ice content in permafrost of the Central Andes, part I: geophysics-based estimates from three different regions. The Cryosphere, 16, 1–28, https://doi.org/10.5194/tc-16-1845-2022.</p> <p> </p> <p><strong>1) Files included in allERT_Zenodo.zip:</strong></p> <p>(i) all ERT raw data files used in the paper,</p> <p>(ii) Topo_allERT.xlsx --> with the topography data of all profiles</p> <p>(iii) readme_ERT_files.txt --> with further explanations</p> <p> </p> <p><strong>2) Files included in allRST_Zenodo.zip:</strong></p> <p>(i) all RST raw data files used in the paper,</p> <p>(ii) Topo_xxx.txt with the topography data of each profile</p> <p>(iii) readme_RST_files.txt --> with further explanations</p> <p> </p> <p>Please consult the readme files first.</p>
Quantification of transgene expression in GSH AAVS1 with a novel CRISPR/Cas9 based approach reveals high transcriptional variation
<p>Inderbitzin, Loosli and colleagues employ a novel method to construct and extensively characterize DNA barcode libraries and apply CRISPR/Cas9 technology for targeted insertion into the safe harbor gene AAVS1 in Jurkat cells. This technique revealed high fluctuations in gene expression in AAVS1, spanning over two logs.</p>
First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing
<p>Insect declines are a global issue with significant ecological and economic ramifications. Yet we have a poor understanding of the genomic impact these losses can have. Genome-wide data from historical specimens has the potential to provide baselines of population genetic measures to study population change, with natural history collections representing large repositories of such specimens. However, an initial challenge in conducting historical DNA data analyses, is to understand how molecular preservation varies between specimens. Here, we highlight how Next Generation Sequencing methods developed for studying archaeological samples can be applied to determine DNA preservation from only a single leg taken from entomological museum specimens, some of which are more than a century old. An analysis of genome-wide data from a set of 113 red-tailed bumblebee (Bombus lapidarius) specimens, from five British museum collections, was used to quantify DNA preservation over time. Additionally, to improve our analysis and further enable future research we generated a novel assembly of the red-tailed bumblebee genome. Our approach shows that museum entomological specimens are comprised of short DNA fragments with mean lengths below 100 base pairs (BP), suggesting a rapid and large-scale post-mortem reduction in DNA fragment size. After this initial decline, however, we find a relatively consistent rate of DNA decay in our dataset, and estimate a mean reduction in fragment length of 1.9bp per decade. The proportion of quality filtered reads mapping our assembled reference genome was around 50 %, and decreased by 1.1 % per decade. We demonstrate that historical insects have significant potential to act as sources of DNA to create valuable genetic baselines. The relatively consistent rate of DNA degradation, both across collections and through time, mean that population level analyses - for example for conservation or evolutionary studies - are entirely feasible, as long as the degraded nature of DNA is accounted for. </p>
Supporting data and software for the article "Comprehensive and scalable quantification of splicing differences with MntJULiP"
<p>Supporting data and software for the publication "Comprehensive and scalable quantification of splicing differences with MntJULiP".</p>
Quantification of SARS-CoV-2 RNA in Wastewater Treatment Plants Mirrors the Pandemic Trend in Hong Kong
<p>The dataset included the SARS-CoV-2 and PMMoV virus concentration of WWTPs from December 24, 2020 to June 30, 2021 in Hong Kong, China.</p>
Cell-ACDC: segmentation, tracking, annotation and quantification of microscopy imaging data (dataset)
<p>This repository includes all the data generated or analysed during the preparation of Cell-ACDC publication, including test datasets for testing the software.</p> <p>Cell-ACDC is open-source software available on GitHub <a href="https://github.com/SchmollerLab/Cell_ACDC">here</a>.</p>
Visualization and quantification of carbon 'rusty sink' by rice root iron plaque: mechanisms, functions, and global implications
<p><span>Paddies contain 78% higher organic carbon (C) stocks than adjacent upland soils, and iron (Fe) plaque formation on rice roots is one of the mechanisms that traps C. The process sequence, extent and global relevance of this C stabilization mechanism under oxic/anoxic conditions remains unclear. We quantified and localized the contribution of Fe plaque to C stabilization in a microoxic area (</span><span>rice </span><span>rhizosphere) and</span> <span>evaluated the role of this C trap toward global C sequestration in paddy soils. Visualization and localization of pH by imaging with planar optodes, enzyme activities by zymography,</span> <span>and root exudation by 14C imaging, as well as upscale modeling enabled linkage of three groups of rhizosphere processes that are responsible for C stabilization from the micro- (root) to the macro- (ecosystem) level. The 14C activity in soil (reflecting stabilization of rhizodeposits) with Fe2+ addition was 1.4−1.5 times higher than that in the control and phosphate addition soils. Perfect co-localization of the hotspots of β-glucosidase activity (by zymography) with exudation showed that labile C and high enzyme activities were localized within Fe plaques. </span><span>Fe</span><span>2+</span> <span>addition </span><span>to </span><span>soil and its</span><span> microbial oxidation to Fe3+ by radial oxygen release from rice roots increased </span><span>Fe</span><span> plaque (Fe3+) formation by 1.7−2.5 times. The C trapped</span><span> by </span><span>Fe plaque was 1.1 times higher after Fe2+ addition. Therefore, Fe plaque formed from amorphous and complex Fe on root surface act as a "rusty sink" for C. Upscaling by model revealed the global significance of C preservation within Fe3+ complexes in paddy soils. Considering the area of coverage of paddy soils globally, radial oxygen loss from roots and bacterial Fe oxidation may trap up to 130 Mg C in Fe plaques per rice season. This represents an important annual surplus of new and stable C to the existing C pool</span> <span>under long-term rice cropping.</span></p>
ObjectJ files for Quantification of ejaculate transfer and removal
<p>Dataset accompanying manuscript "Evolution and co-evolution of the suck behaviour, a postcopulatory female resistance trait that manipulates received ejaculate" . These are the ObjectJ files that were used for quantification of ejaculate transfer and removal in <em>Macrostomum hamatum</em>, described in the manuscript.</p>
Multi-Level Monte Carlo Models for Flood Inundation Uncertainty Quantification - Dataset
<p>Dataset used for the analysis of Multi-level Monte Carlo methods for flood inundation uncertainty quantification. This includes:</p> <ol> <li>Flood model simulations for Dyce, Glasgow and Inverurie across three resolutions (5m/10m/20m).</li> <li>Data for violin plot figures with code.</li> </ol>
Bulk NGS/allele quantification - Highly efficient generation of isogenic pluripotent stem cell models using prime editing
<p>This file contains sequencing results for bulk NGS and amplicons covering specific regions of interest related to prime editing of hPSCs. </p>
Microscopic Quantification of Oxygen Consumption across Cortical Layers
<p>The cerebral cortex is organized in cortical layers that differ in their cellular density, composition, and wiring. Cortical laminar architecture is also readily revealed by staining for cytochrome oxidase – the last enzyme in the respiratory electron transport chain located in the inner mitochondrial membrane. It has been hypothesized that a high-density band of cytochrome oxidase in cortical layer IV reflects higher oxygen consumption under baseline (unstimulated) conditions. Here, we tested the above hypothesis using direct measurements of the partial pressure of O<sub>2</sub> (pO<sub>2</sub>) in cortical tissue by means of 2-photon phosphorescence lifetime microscopy (2PLM). We revisited our previously developed method for extraction of the cerebral metabolic rate of O<sub>2</sub> (CMRO<sub>2</sub>) based on 2-photon pO<sub>2</sub> measurements around diving arterioles and applied this method to estimate baseline CMRO<sub>2</sub> in awake mice across cortical layers. To our surprise, our results revealed<em> a decrease in baseline CMRO<sub>2</sub> from layer I to layer IV</em>. This decrease of CMRO<sub>2</sub> with cortical depth was paralleled by <em>an increase in tissue oxygenation. </em>Higher baseline oxygenation and cytochrome density in layer IV may serve as an O<sub>2</sub> reserve during surges of neuronal activity or certain metabolically active brain states rather than baseline energy needs. Our study provides the first quantification of microscopically resolved CMRO<sub>2</sub> across cortical layers as a step towards better understanding of the brain energy metabolism.</p>
Mitochondria morphology quantification datasheet of different MIGA2 expressing cells
<p>Mitochondria morphology quantification datasheet of different MIGA2 constructs expressing Hela cells: WT, MIGA2 KO, MIGA2 KO cells transfected with WT MIGA2, MIGA2 KO cells transfected with MIGA2 mutants (M1, M2, M3).</p>
Lipid droplet quantification datasheet of different MIGA2 constructs expressing cells
<p>Lipid droplet quantification datasheet of different MIGA2 constructs expressing Hela cells: WT, MIGA2 KO, MIGA2 KO cells transfected with WT MIGA2, MIGA2 KO cells transfected with MIGA2 mutants.</p>
Data supplementing the article "Avoiding quantification bias in metabarcoding: application of a cell biovolume correction factor in diatom molecular biomonitoring" V. Vasselon, A. Bouchez, F. Rimet, S. Jacquet, R. Trobajo, M. Corniquel, K. Tapolczai, I. Domaizon submitted to Methods in Ecology and Evolution journal
<p>These data supplement the article "Avoiding quantification bias in metabarcoding: application of a cell biovolume correction factor in diatom molecular biomonitoring" V. Vasselon, A. Bouchez, F. Rimet, S. Jacquet, R. Trobajo, M. Corniquel, K. Tapolczai, I. Domaizon submitted to Methods in Ecology and Evolution journal</p> <p>The directory contains the following files:</p> <p>1<strong>5 fastq files raw reads (5 mock communities, 3 replicates)</strong><strong>.rar </strong>- contains the 15 fastq files provided by the sequencing platform with demultiplexed DNA reads (raw data prior any bioinformatics treatments).</p> <p><strong>15 fastq files information.xlsx</strong> :</p> <p>- contains the information relative to the 15 fastq files corresponding to the PGM raw data of the 5 mock communities (sequenced with 3 replicates), including: the ID of the fastq files, the mock community name, the replicate number, the final sample Id and the number of raw reads per fastq file.</p> <p>- contains the information of the proportion of the 8 diatoms species (%) used to create the 5 mock communities (estimated from microscopy).</p>
Fine-scale Quantification of Absorbed Photosynthetically Active Radiation (APAR) in Plantation Forests with 3D Radiative Transfer Modeling and LiDAR Data
<p>In recent years, LiDAR technology has gained widespread attention for its ability to provide precise 3D vertical structural data for various objects, particularly forests. In our dataset, we utilized LiDAR data to reconstruct intricately detailed three-dimensional representations of specific larch forest landscapes. These detailed forest structural models enable us to drive three-dimensional radiative transfer models, analyze the radiation budget of the forest canopy, and gain valuable insights into fine-scale forest management strategies.</p> <p>This is the research work we conducted by combining the aforementioned 3D forest scenes with the 3D RTM LESS. If you use our data, please cite our article. You can access our publication via DOI: 10.34133/plantphenomics.0166.</p> <p>We welcome researchers interested in a wide range of fields, such as vegetation ecological applications, to communicate with us by combining 3D vegetation modeling.</p> <p><br><br></p>
Quantification of losses in agriculture production in eastern Ukraine due to the Russia-Ukraine war
<h3>This repository contains the necessary data and code used to support major results and findings of the research on "Quantification of losses in agriculture production in eastern Ukraine due to the Russia-Ukraine war". It encompasses:</h3> <h3>1. The generated 10-m crop type map of Ukraine in 2020<br>2. Validation sample sets for crop type and planting condition<br>3. Python and JavaScript code for reproducing main figures and tables in the manuscript, including sample-based area estimation, economic loss calculation, NDVI difference computation, and regression analysis</h3> <h3>For more information, please refer to our accompanying paper:</h3> <p>Bin Chen, Ying Tu, Jiafu An, Shengbiao Wu, Chen Lin, and Peng Gong. "Quantification of losses in agriculture production in eastern Ukraine due to the Russia-Ukraine war". Communications Earth & Environment (2024).</p>
Code and Data for "Probabilistic Eddy Identification with Uncertainty Quantification"
<p>The code and data used in the paper "Probabilistic Eddy Identification with Uncertainty Quantification".</p>
Quantification of volatile organic compound emissions from unconventional oil and gas development
<p>Oil and gas (O&G) development in the U.S. has accelerated in the past two decades, aided by unconventional extraction techniques including hydraulic fracturing and horizontal drilling. Potential environmental and health impacts of volatile organic compounds (VOCs) originating from O&G activities in populated regions have raised concerns. In Broomfield, Colorado, six new O&G well pads were approved for development in 2017 and an air monitoring program was established in October 2018 to collect weekly and plume-triggered air samples. This study addresses the limited existing knowledge of activity-specific VOC emission rates from unconventional O&G development (UOGD), utilizing these observations and dispersion model simulations through emission inversion methods. Emissions are characterized from well drilling, hydraulic fracturing, coiled tubing/millout, flowback, and production operations.</p> <p>Substantial variations in average VOC emission rates, determined using weekly canister observations, are observed across different UOGD phases. Drilling and coiled tubing/millout operations exhibit the highest VOC emission rates, attributed to hydrocarbon release from shale formations and drilling mud. In contrast, hydraulic fracturing gives lower emission rates, consistent with injection of fluids into the well, minimizing the probability of subsurface hydrocarbon emissions. Diesel-powered engines are identified as the primary ethyne sources during hydraulic fracturing. Production was characterized by lower VOC emission rates than pre-production phases but remains an important emission category due to its long duration (decades). Internal variations of emission rates within each phase highlight the complexity of factors and activities influencing emission rates, including, for example, vertical vs. horizontal drilling and periodic maintenance activities. VOC emission rates associated with drilling mud volatilization and hydraulic fracturing suggest that previously published emission estimates (EPA (2022), and Hecobian et al. (2019)) underestimate VOC emission rates during these activities. Significantly lower emission rates during flowback compared to previous work (Hecobian et al., 2019) reveal how improved management practices, including tankless, closed-loop fluid handling systems have effectively reduced what used to be a dominant source of pre-production VOC emissions. Plume-triggered samples, capturing transient high-concentration plumes, reveal short-term VOC emission rates approximately ten times higher for drilling and flowback than determined from weekly samples. In the case of flowback, short-term emission pulses have been linked to periodic emptying of sand canisters used to trap fracking sand emerging from previously fracked wells.</p>
Waste Characterization, Quantification, and Composting in Cape Maclear, Malawi
<p>This dataset contains information on waste characterization and quantification, current soil conditions, and agricultural practices of farmers from Cape Maclear, Malawi. </p>
Inferring Surface NO2 over Western Europe: A Machine Learning Approach with Uncertainty Quantification
<p>The data that serves to substantiate the analysis presented in the article.</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.