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6,452 results for “Application”
ListeriaPredict Webinar - Application of novel predictive microbiology techniques to shelf-life studies on Listeria monocytogenes
<p>An EFSA funded ListeriaPredict Webinar - Application of novel predictive microbiology techniques to shelf-life studies on Listeria monocytogenes</p>
Raw data for Broaden the application of Yarrowia Lipolytica synthetic biology tools to explore the potential of Yarrowia clade biodiversity
<p>Raw data for growth curves and fluorescence/OD ratio for article "Broaden the application of Yarrowia Lipolytica synthetic biology tools to explore the potential of Yarrowia clade biodiversity"</p>
A 1D Model for Nucleation of Ice from Aerosol Particles: An Application to a Mixed-Phase Arctic Stratus Cloud Layer
<p>A 1D Model for Nucleation of Ice from Aerosol Particles:</p> <p>An Application to a Mixed-Phase Arctic Stratus Cloud Layer</p> <p>Daniel A. Knopf<sup>1</sup>*, Israel Silber<sup>2</sup>, Nicole Riemer<sup>3</sup>, Ann M. Fridlind<sup>4</sup>, Andrew S. Ackerman<sup>4</sup></p> <p><sup>1</sup>School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA</p> <p><sup>2</sup>Department of Meteorology and Atmospheric Science, Pennsylvania State University, University Park, PA, USA</p> <p><sup>3</sup>Department of Atmospheric Sciences, University of Illinois at Urbana–Champaign, Urbana, IL, USA</p> <p><sup>4</sup>NASA Goddard Institute for Space Studies, New York, NY, USA</p> <p> </p> <p>Corresponding author: Daniel Knopf (daniel.knopf@stonybrook.edu)</p> <p> </p> <p><strong>This repository contains all model output data in netCDF format to reproduce simulation results and corresponding figures given in above listed publication.</strong></p> <p>File name description:</p> <p>Type of parameterization: <em>INN, INAS, ABIFM</em></p> <p>INP treatment, diagnostic or prognostic: <em>diag, prog</em></p> <p>Aerosol size distribution:</p> <p><em>05mu</em>: monodisperse 0.5 μm diameter</p> <p><em>15mu</em>: monodisperse 0.5 μm diameter</p> <p><em>polydisperse</em>: polydisperse particle size distribution</p> <p>Model initialization and thermodynamic data: <em>model_data</em></p> <p>Aerosol/INP data: <em>aerosol_data</em>, <em>polydisperse_data</em></p> <p>Change in ice nucleation efficiency: <em>10X, 100X</em></p>
Supplementary material for "A Rapid, Open-Source CCT Predictor for Low Alloy Steels, and its Application to Compositionally Heterogeneous Material"
<p>The complete collection of measured, modelled and analysed data associated with the work "A Rapid, Open-Source CCT Predictor for Low Alloy Steels, and its Application to Compositionally Heterogeneous Material" and includes:</p> <ol> <li>Measured and analysed dilatometry data.</li> <li>Optical micrographs of as-cooled microstructures.</li> <li>Microhardness measurements of the as-cooled samples.</li> <li>PAG size analysis.</li> <li>Modelled CCT data.</li> <li>SA-540 EPMA data.</li> <li>Modelled results from adapting the model to consider SA-540 chemical heterogeneity.</li> <li>Full chemical analysis for each alloy examined.</li> <li>Modelled Thermo-Calc CCT data.</li> <li>Modelled JMatPro CCT data.</li> </ol>
Application of AlphaFold on metamorphic proteins - dataset
<p>The dataset comprises a set of five structures of metamorphic proteins used for the study.</p>
R Notebook and Dataset for "Usage-based perspective on argument realisation: A corpus study of Indonesian BUY verbs in applicative construction with -kan" (1.0.0)
<p>This repository contains the dataset and R codes for our paper that has been published in <a href="http://www.aa.tufs.ac.jp/en/publications/nusa">NUSA</a> (<i>Linguistic studies of languages in and around Indonesia</i>) special volume (74) on "Applicatives in Austronesian Languages".</p><h4>How to cite the paper</h4><p>Rajeg, Gede Primahadi Wijaya & I Wayan Arka. 2023. Usage-based perspective on argument realisation: A corpus study of Indonesian BUY verbs in applicative construction with -<i>kan</i>. In Jocelyn Aznar, Christian Döhler & Jozina Vander Klok (eds.), <i>NUSA (special issue on "Applicatives in Austronesian Languages")</i>, vol. 74, 83–114. <a href="https://tufs.repo.nii.ac.jp/records/2000019">https://tufs.repo.nii.ac.jp/records/2000019</a>.</p><h4>Description of the repository</h4><p>The .qmd file contains the R codes used to produce the quantitative analyses in the paper, including the statistical figures. This .qmd file also interweaves some text narratives with the codes. The file is published as a webpage at: <a href="https://gederajeg.github.io/applicative-buy/">https://gederajeg.github.io/applicative-buy/</a></p><p>The raw, annotated concordance data is located in the <a href="https://github.com/gederajeg/applicative-buy/tree/main/data">data</a> directory.</p><p>The statistical figures can also be accessed individually <a href="https://github.com/gederajeg/applicative-buy/tree/main/nusa-applicative-code_files/figure-html">here</a>.</p>
Towards a practical framework to "ethics by design" data sharing and machine learning applications
<p>Responsible AI and data-driven applications can only be developed when teams integrate the ethical principles directly into the development process. An important prerequisite is the involvement of a diverse group of stakeholders who build and are affected by AI and data systems. We present a practical framework that helps teams build trustworthy AI systems and data strategies by combining expertise and training from philosophy, law, machine learning and design.</p>
NOTES OF USE OF WEB APPLICATION TO VISUALIZE ALTERNATIVE SPLICING FOR BIOMEDICINE
<p>This is examples files of output generated by GeneAPPExplorer. GeneAPP(registered software) is a web-based application for integrating, exploring, and visualizing alternative splicing data. It consists of a client-server pipeline suite that provides users with the resources to integrate raw outputs from differential alternative splicing (DAS) analyses from different tools with multiple biological databases to provide graphical representations and robust results that guide the selection of candidate targets for experimental validation.</p>
The essential-use concept: a valuable tool to guide decision-making on applications for authorisation under REACH?
<p>Supporting Information from The essential-use concept: a valuable tool to guide decision-making on applications for authorisation under REACH?</p>
Unit-cell-thick zeolitic imidazolate framework films for membrane application
<p>raw data for the manuscript with title of Unit-cell-thick zeolitic imidazolate framework films for membrane application</p>
Noncentrosymmetric Lanthanide-Based MOF Materials Exhibiting Strong SHG Activity and NIR Luminescence of Er3+: Application in Nonlinear Optical Thermometry
<p>Optically active luminescent materials based on lanthanide ions attract significant attention due to their unique spectroscopic properties, nonlinear optical activity, and the possibility of application as contactless sensors. Lanthanide metal-organic frameworks (Ln-MOFs) that exhibit strong second-harmonic generation (SHG) and are optically active in the NIR region are unexpectedly underrepresented. Moreover, such Ln-MOFs require ligands that are chiral and/or need multistep synthetic procedures. Here, we show that the NIR pulsed laser irradiation of the noncentrosymmetric, isostructural Ln-MOF materials (MOF-Er<sup>3+</sup> (1) and codoped MOF-Yb<sup>3+</sup>/Er<sup>3+</sup> (2)) that are constructed from simple, achiral organic substrates in a one-step procedure results in strong and tunable SHG activity. The SHG signals could be easily collected, exciting the materials in a broad NIR spectral range, from ≈800 to 1500 nm, resulting in the intense color of emission, observed in the entire visible spectral region. Moreover, upon excitation in the range of ≈900 to 1025 nm, the materials also exhibit the NIR luminescence of Er<sup>3+</sup> ions, centered at ≈1550 nm. The use of a 975 nm pulse excitation allows simultaneous observations of the conventional NIR emission of Er<sup>3+</sup> and the SHG signal, altogether tuned by the composition of the Ln-MOF materials. Taking the benefits of different thermal responses of the mentioned effects, we have developed a nonlinear optical thermometer based on lanthanide-MOF materials. In this system, the SHG signal decreases with temperature, whereas the NIR emission band of Er<sup>3+</sup> slightly broadens, allowing ratiometric (Er<sup>3+</sup> NIR 1550 nm/SHG 488 nm) temperature monitoring. Our study provides a groundwork for the rational design of readily available and self-monitoring NLO-active Ln-MOFs with the desired optical and electronic properties.</p>
Development and application of a qPCR-based genotyping assay for Ophidiomyces ophidiicola to investigate the epidemiology of ophidiomycosis
Ophidiomycosis (snake fungal disease) is an infectious disease caused by the fungus Ophidiomyces ophidiicola to which all snake species appear to be susceptible. Significant variation has been observed in clinical presentation, progression of disease, and response to treatment, which may be due to genetic variation in the causative agent. Recent phylogenetic analysis based on whole-genome sequencing identified that O. ophidiicola strains from the United States formed a clade distinct from European strains, and that multiple clonal lineages of the clade are present in the United States. The purpose of this study was to design a qPCR-based genotyping assay for O. ophidiicola, then apply that assay to swab-extracted DNA samples to investigate whether the multiple O. ophidiicola clades and clonal lineages in the United States have specific geographic, taxonomic, or temporal predilections. To this end, six full genome sequences of O. ophidiicola representing different clades and clonal lineages were aligned to identify genomic areas shared between subsets of the isolates. Eleven hydrolysis-based Taqman primer-probe sets were designed to amplify selected gene segments and produce unique amplification patterns for each isolate, each with a limit of detection of 10 or fewer copies of the target sequence and an amplification efficiency of 90–110%. The qPCR-based approach was validated using samples from strains known to belong to specific clades and applied to swab-extracted O. ophidiicola DNA samples from multiple snake species, states, and years. When compared to full-genome sequencing, the qPCR-based genotyping assay assigned 75% of samples to the same major clade (Cohen's kappa = 0.360, 95% Confidence Interval = 0.154–0.567) with 67–77% sensitivity and 88–100% specificity, depending on clade/clonal lineage. Swab-extracted O. ophidiicola DNA samples from across the United States were assigned to six different clonal lineages, including four of the six established lineages and two newly defined groups, which likely represent recombinant strains of O. ophidiicola. Using multinomial logistic regression modeling to predict clade based on snake taxonomic group, state of origin, and year of collection, state was the most significant predictor of clonal lineage. Furthermore, clonal lineage was not associated with disease severity in the most intensely sampled species, the Lake Erie watersnake (Nerodia sipedon insularum). Overall, this assay represents a rapid, cost-effective genotyping method for O. ophidiicola that can be used to better understand the epidemiology of ophidiomycosis.
Material suplementar para o artigo: Usability Evaluation of mobile banking applications in the context of the elderly in a city of Ceará
<p>Material suplementar:</p> <ol> <li>Questionário diagnóstico</li> <li>Questionário pós-teste</li> <li>Questionário diagnóstico questões abertas</li> <li>Questionário pós-teste questões abertas</li> <li>TCLE</li> </ol>
CARDIOMYOCYTE RYANODINE RECEPTOR CLUSTERS EXPAND AND COALESCE AFTER APPLICATION OF ISOPROTERENOL
<p>This is data that was used to generate the figures and tables for the Journal of General Physiology paper<br> CARDIOMYOCYTE RYANODINE RECEPTOR CLUSTERS EXPAND AND COALESCE AFTER APPLICATION OF ISOPROTERENOL</p> <p>The data is in two parts: i) Blink data that records the positions of blinks collected from fluorescently labelled ryanodine receptors on the surface of rat ventricular myocytes. ii) Cluster data that records parameters from each of the clusters created by the blink data. </p> <p>The blink data was used to generate Figs. 1 to 4, S3 to S5, while cluster data was used to generate the tables<br> and Figs. 5 to 9. More detailed explanations of the data are in the files blinkinfo.html and clustinfo.html in their respective<br> directories.</p>
The application of unmanned aerial vehicle (UAV) surveys and GIS to the analysis and monitoring of recreational trail conditions - dataset
<p>This dataset contains data used to test the protocol for high-resolution mapping and monitoring of recreational impacts in protected natural areas (PNAs) using unmanned aerial vehicle (UAV) surveys, Structure-from-Motion (SfM) data processing and geographic information systems (GIS) analysis to derive spatially coherent information about trail conditions (Tomczyk et al., 2023). Dataset includes the following folders:</p> <ol> <li>Cocora_raster_data (~3GB) and Vinicunca_raster_data (~32GB) - a very high-resolution (cm-scale) dataset derived from UAV-generated images. Data covers selected recreational trails in Colombia (Valle de Cocora) and Peru (Vinicunca). UAV-captured images were processed using the structure-from-motion approach in Agisoft Metashape software. Data are available as GeoTIFF files in the UTM projected coordinate system (UTM 18N for Colombia, UTM 19S for Peru). Individual files are named as follows [location]_[year]_[product]_[raster cell size].tif, where: <ul> <li>[location] is the place of data collection (e.g., Cocora, Vinicucna)</li> <li>[year] is the year of data collection (e.g., 2023)</li> <li>[product] is the tape of files: DEM = digital elevation model; ortho = orthomosaic; hs = hillshade</li> <li>[raster cell size] is the dimension of individual raster cell in mm (e.g., 15mm)</li> </ul> </li> <li> <p>Cocora_vector_data. and Vinicunca_vector_data – mapping of trail tread and conditions in GIS environment (ArcPro). Data are available as shp files. Data are in the UTM projected coordinate system (UTM 18N for Colombia, UTM 19S for Peru).</p> </li> </ol> <p>Structure-from-motio<span> </span>n processing was performed in Agisoft Metashape (<a href="https://www.agisoft.com/">https://www.agisoft.com/</a>, Agisoft, 2023). Mapping was performed in ArcGIS Pro (<a href="https://www.esri.com/en-us/arcgis/about-arcgis/overview">https://www.esri.com/en-us/arcgis/about-arcgis/overview</a>, Esri, 2022). Data can be used in any GIS software, including commercial (e.g. ArcGIS) or open source (e.g. QGIS).</p> <p>Tomczyk, A. M., Ewertowski, M. W., Creany, N., Monz, C. A., & Ancin-Murguzur, F. J. (2023). The application of unmanned aerial vehicle (UAV) surveys and GIS to the analysis and monitoring of recreational trail conditions. <em>International Journal of Applied Earth Observations and Geoinformation</em>, 103474. doi:<a href="https://doi.org/10.1016/j.jag.2023.103474"> https://doi.org/10.1016/j.jag.2023.103474</a></p>
MCProj interactive applications
<p>MCView applications from the paper:</p> <p>MCProj: metacell projection for interpretable and quantitative use of transcriptional atlases.</p> <p> </p> <p> </p>
Datasets used in "Evidential Deep Learning: Enhancing Predictive Uncertainty Estimation for Earth System Science Applications"
<p>The precipitation type (p-type) dataset (ptype.parquet) comprises observational weather reports sourced from the Meteorological Phenomena Identification Near the Ground (mPING) project, combined with corresponding numerical weather prediction data from the NOAA Rapid Refresh (RAP) model. These crowd-sourced mPING reports offer precipitation type labels (rain, snow, sleet, and freezing rain) across North America, while the RAP model provides atmospheric data, including temperature, humidity, and wind profiles, on pressure levels.</p> <p> </p> <p>The RAP data covers the contiguous United States (CONUS) from 2015 to 2022 on an hourly 13km grid. The mPING observations are matched to the nearest RAP grid cell and hour, allowing the two data sources to be merged into a labeled dataset suitable for classification tasks. </p> <p> </p> <p>The surface layer flux dataset (surface_layer.csv) contains high-frequency meteorological observations spanning from 2013 to 2015, collected at the Cabauw Experimental Site in the Netherlands. It includes measurements of various variables such as temperature, humidity, wind, radiation, and soil moisture, recorded every 10 minutes. The target output encompasses friction velocity, sensible heat, and latent heat.</p> <p><br> The code used for processing the datasets and training neural network models is available in the Miles-Guess repository (<a href="https://github.com/ai2es/miles-guess">https://github.com/ai2es/miles-guess</a>).</p>
Data for "Absolute binding free energy calculation based on the fragment molecular orbital method and its application in designing novel SHP-2 allosteric inhibitors"
<p>Data for publication "Absolute binding free energy calculation based on the fragment molecular orbital method and its application in designing novel SHP-2 allosteric inhibitors".All structures of complex and input files for FMO , FMO/SMD , FMO/PCM , and COSMO calculation are provided .</p>
DLC networks from: Application of a novel deep learning based 3D videography workflow to bat flight data
<p>Studying the detailed biomechanics of flying animals relies on producing accurate three-dimensional coordinates for key anatomical landmarks. Traditionally, this is achieved through manual digitization of animal videos, a labor-intensive task that grows more so with increasing frame rates and numbers of cameras. In this study, we present a workflow that combines deep learning-powered automatic digitization with intelligent filtering and correction of mislabeled points using 3D information. We tested our workflow using a particularly challenging scenario – bat flight. First, we documented bats flying steadily in a wind tunnel. We compared the results from manually digitizing bats with markers applied to anatomical landmarks against using our automatic workflow on the same bats without markers. In our second test case, we compared manual digitization against our automated workflow for bats exhibiting complex maneuvers in a large flight arena. We found that the variation between the 3D coordinates from our workflow and those from manual digitization was less than a millimeter larger than the variation between 3D coordinates resulting from two different human digitizers. The reduced reliance on manual digitization stemming from this work has the potential to significantly increase the scalability of studies into the detailed biomechanics of animal flight.</p>
Evaluating the use of non‐invasive hair sampling and ddRAD to characterize populations of endangered species: Application to a peripheral population of the European mink
<p>The application of next‐generation sequencing (NGS) to non‐invasive samples is one of the most promising methods in conservation genomics, but these types of samples present significant challenges for NGS. The European mink (<em>Mustela lutreola</em>) is critically endangered throughout its range. However, important aspects such as census size and inbreeding remain still unknown in many populations, so it is crucial to develop new methods to monitor this species. In this work, we placed hair tubes along riverbanks in a border area of the Iberian population, which allowed the genetic identification of 76 European mink hair samples. We then applied a reduced representation genomic sequencing (ddRAD) technique to a subset of these samples to test whether we could extract sufficient genomic information from them. We show that several problems with the DNA, including contamination, fragmentation, oxidation, and possibly sample mixing, affected the samples. Using various bioinformatic techniques to reduce these problems, we were able to unambiguously genotype 19 hair samples belonging to six individuals. This small number of individuals showed that the demographic status of the species in this peripheral population is worse than expected. The data obtained also allowed us to perform preliminary analyses of relatedness and inbreeding. Although further improvements in sampling and analysis are needed, the application of the ddRAD technique to non‐invasively obtained hairs represents a significant advance in the genomic study of endangered species.</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.