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8,565 results for “characterization”
Characterizing the groundwater flow pathways and recharge sources of a desert inter-dune aquifer system by geophysical approaches and multiple isotopes (B, H and O)
<p>Major cations and anions, and H, O, and B isotope data of South Sumujaran Lake of Badain Jaran Desert, China</p>
Data set to ''Volcano growth versus deformation by strike-slip faults: morphometric characterization through analogue modelling'
<p>This data set is the supplementary material to Grosse et al. (2020) 'Volcano growth versus deformation by strike-slip faults: morphometric characterization through analogue modelling', published in Tectonophysics (https://doi.org/10.1016/j.tecto.2020.228411). The data set consists of (1) 249 digital elevation models (DEMs) of each step of the the analogue experiments carried out, in standard ENVI format, zipped; and (2) an Excel file containing the DEM-derived morphometric parameters for each of the analogue models.</p> <p>Experiments were carried out at the analogue modelling lab of the Department of Geography at the Vrije Universiteit Brussel (Belgium). A granular mixture of fine-grained quartz sand and kaolin clay was used as analogue material. Experiments were conducted on a fixed table, on which a basal layer of granular material was placed. A basal plate attached to a step-motor was used to simulate pure strike-slip displacements of the basal layer. Volcano growth was simulated by depositing loads of granular material on top of the basal layer from a point source. The analogue models were photographed at regular time intervals during the experiments using four digital cameras. The photographs were used to generate synthetic digital elevation models (DEMs) with 0.2 mm spatial resolution of each step of the analogue models by applying the MICMAC digital stereo-photogrammetry software. The ENVI software was used to re-sample the DEMs to a 0.5 mm spatial resolution and apply the noise-reduction Lee filter. Morphometric data were then extracted from the DEMs by applying two IDL-language algorithms: NETVOLC, used to automatically calculate the volcano edifice basal outline, and MORVOLC, used to extract a set of morphometric parameters.</p>
Online Aerosol Chemical Characterization by Extractive Electrospray Ionization − Ultrahigh-Resolution Mass Spectrometry (EESI-Orbitrap)
<p>These datasets are the raw data presented in the presented work of "Online Aerosol Chemical Characterization by Extractive Electrospray Ionization − Ultrahigh-Resolution Mass Spectrometry (EESI-Orbitrap)" in <em>Environmental Science & Technology Journal</em>, doi:10.1021/acs.est.9b07090.</p> <p>Abstract: Current mass spectrometry techniques for the online measurement of organic aerosol (OA) composition are subjected to either thermal/ionization-induced artifacts or limited mass resolving power, hindering accurate molecular characterization. Here, we combined the soft ionization capability of extractive electrospray ionization (EESI) and the ultrahigh mass resolution of Orbitrap for real-time, near-molecular characterization of OAs. Detection limits as low as tens of ng m<sup>−3</sup> with linearity up to hundreds of μg m<sup>−3</sup> at 0.2 Hz time resolution were observed for single- and mixed-component calibrations. The performance of the EESI-Orbitrap system was further evaluated with laboratory-generated secondary OAs (SOAs) and filter extracts of ambient particulate matter. The high mass accuracy and resolution (140 000 at <em>m/z</em> 200) of the EESI-Orbitrap system enable unambiguous identification of the aerosol components’ molecular composition and allow a clear separation between adjacent peaks, which would be significantly overlapping if a medium-resolution (20 000) mass analyzer was used. Furthermore, the tandem mass spectrometry (MS<sup>2</sup>) capability provides valuable insights into the compound structure. For instance, the MS<sup>2</sup> analysis of ambient OA samples and lab-generated biogenic SOAs points to specific SOA precursors in ambient air among a range of possible isomers based on fingerprint fragment ions. Overall, this newly developed and characterized EESI-Orbitrap system will advance our understanding of the formation and evolution of atmospheric aerosols.</p> <p>Structure of the datasets: The raw data are separated into individual file of excel format for the figures. Simulation data from Figure 4 can be generated using the matlab code named <em>Figure4PeakSimulation.m.</em> </p>
Extensive Unified Thermo-Electric Module Characterization
<p>Experimental results for the extensive characterization of the low-cost module TES1-12730 by Thermonamic Electronics Corporation, obtained using the Unified Method for Thermo-Electric Module characterization (see references). Data are processed and visualized using MATLAB version 9.7.0.1319299 (R2019b) Update 5.</p> <p>Tests are obtained for 14 operating temperature values with step 3 °C between 10 °C and 49 °C.</p> <p>Datasets include:</p> <ul> <li>Thermocouple-based characterization ( 14 temperature difference values: with step 3 °C between 6 °C and 45 °C )</li> <li>Thermistor-based characterization ( 24 temperature difference values: ten with step 0.3 °C between 0.3 °C and 3 °C and fourteen with step 3 °C between 6 °C and 45 °C )</li> </ul> <p>Softwares include:</p> <ul> <li>importData: function for importing data from files in column vectors</li> <li>analyzeData: script for data processing (suffix _TC and _NTC for thermocouples and thermistor respectively)</li> <li>plotResults: script for extensive plot of parameters mean, relative std and std</li> <li>plotMean: script for quick plot of the parameters mean</li> </ul>
Nanoparticle Tracking Analysis: A powerful tool for characterizing magnetosome preparations - Supplementary
<p>Nanoparticle Tracking Analysis: A powerful tool for characterizing magnetosome preparations - Supplementary materials</p>
Characterizing and classifying neuroendocrine neoplasms through microRNA sequencing and data mining
<p>Neuroendocrine neoplasms (NENs) are clinically diverse and incompletely characterized cancers that are challenging to classify. MicroRNAs (miRNAs) are small regulatory RNAs that can be used to classify cancers. Recently, a morphology-based classification framework for evaluating NENs from different anatomic sites was proposed by experts, with the requirement of improved molecular data integration. Here, we compiled 378 miRNA expression profiles to examine NEN classification through comprehensive miRNA profiling and data mining. Following data preprocessing, our final study cohort included 221 NEN and 114 non-NEN samples, representing 15 NEN pathological types and five site-matched non-NEN control groups. Unsupervised hierarchical clustering of miRNA expression profiles clearly separated NENs from non-NENs. Comparative analyses showed that miR-375 and miR-7 expression is substantially higher in NEN cases than non-NEN controls. Correlation analyses showed that NENs from diverse anatomic sites have convergent miRNA expression programs, likely reflecting morphologic and functional similarities. Using machine learning approaches, we identified 17 miRNAs to discriminate 15 NEN pathological types and subsequently constructed a multi-layer classifier, correctly identifying 217 (98%) of 221 samples and overturning one histologic diagnosis. Through our research, we have identified common and type-specific miRNA tissue markers and constructed an accurate miRNA-based classifier, advancing our understanding of NEN diversity.</p>
Dataset in "Marine Sediment Characterized by Ocean-Bottom Fiber-Optic Seismology" by Spica et al., 2020 in Geophysical Research Letters
<p>3000fullhisy: raw data to reproduce Fig. 2<br> ppsdspec.npz: all spectrogram as shown in Fig. 3a<br> AllVelMods: All velocity model shown in Fig. 3b<br> ac.out.final.npz: auto-correlation image in Fig. 3c<br> DAS11_lpf5.stack51.grd: Earthquake wavefield as shown in Fig. 3d</p>
Data from: The preparation and characterization of uniform nanoporous structure on glass
<p>A novel fabrication method of uniform porous structures on the glass surface is proposed. The hydrofluoric acid fog formed by air-jet atomization etches the glass surface to fabricate nanoporous structure (NPS) on glass surface. This NPS shows the enhanced average light transmittance of ~92.9% and the superhydrophilic property with a contact angle less than 1° which presents an excellent anti-fog property. Passivated by fluorosilane, the NPS shows nearly the superhydrophobic property with a contact angle of 141.2°. This fabrication method has shown promising application prospects due to its simplicity, low cost and efficiency, which can be easily applied to large-scale industrial production.</p>
Identification and characterization of novel splice variants of human farnesoid X receptor
<p>Dataset related to publication:</p> <blockquote> <p>Mustonen E-K, Lee SML, Nieß H, Schwab M, Pantsar T, Burk O: "Identification and characterization of novel splice variants of human farnesoid X receptor". <em>Archives of Biochemistry and Biophysics</em> <a href="https://doi.org/10.1016/j.abb.2021.108893">https://doi.org/10.1016/j.abb.2021.108893</a></p> </blockquote> <p> </p> <p>Including:</p> <p>I. Full-length raw-trajectories of the 1 microsecond Desmond simulations (-out.cms, trj)</p>
Museum epigenomics: characterizing cytosine methylation in historic museum specimens
<p>Museum genomics has transformed the field of collections-based research, opening up a range of new research directions for paleontological specimens as well as natural history specimens collected over the past few centuries. Recent work demonstrates that it is possible to characterize epigenetic markers such as DNA methylation in well preserved ancient tissues. This approach has not yet been tested in traditionally prepared natural history specimens such as dried bones and skins, the most common specimen types in vertebrate collections. In this study, we developed and tested methods to characterize cytosine methylation in dried skulls up to 76 years old. Using a combination of ddRAD and bisulphite treatment, we characterized patterns of cytosine methylation in two species of deer mouse (Peromyscus spp.) collected in the same region in Michigan in 1940, 2003, and 2013–2016. We successfully estimated methylation in specimens of all age groups, although older specimens yielded less data and showed greater interindividual variation in data yield than newer specimens. Global methylation estimates were reduced in the oldest specimens (76 years old) relative to the newest specimens (1–3 years old), which may reflect post-mortem hydrolytic deamination. Methylation was reduced in promoter regions relative to gene bodies and showed greater bimodality in autosomes relative to female X chromosomes, consistent with expectations for methylation in mammalian somatic cells. Our work demonstrates the utility of historic specimens for methylation analyses, as with genomic analyses; however, studies will need to accommodate the large variance in the quantity of data produced by older specimens.</p>
Characterizing the nectar microbiome of the non-native tropical milkweed, Asclepias curassavica, in an urban environment
<p>In increasingly urban landscapes, the loss of native pollen and nectar floral resources is impacting ecologically important pollinators. Increased urbanization has also brought about the rise of urban gardens which introduce new floral resources that may help replace those the pollinators have lost. Recently, studies have shown that the microbial communities of nectar may play an important role in plant-pollinator interactions, but these microbial communities and the floral visitors in urban environments are poorly studied. In this study we characterized the floral visitors and nectar microbial communities of <i>Ascelpias curassavica</i>, a non-native tropical milkweed commonly, in an urban environment. We found that the majority of the floral visitors to <i>A. curassavica</i> were honey bees followed closely by monarch butterflies. We also found that there were several unique visitors to each site, such as ants, wasps, solitary bees, several species of butterflies and moths, Anna's hummingbird, and the tarantula hawk wasp. Significant differences in the nectar bacterial alpha and beta diversity were found across the urban sites, although we found no significant differences among the fungal communities. We found that the differences in the bacterial communities were more likely due to the environment and floral visitors rather than physiological differences in the plants growing at the gardens. Greater understanding of the impact of urbanization on the nectar microbiome of urban floral resources and consequently their effect on plant-pollinator relationships will help to predict how these relationships will change with urbanization, and how negative impacts can be mitigated through better management of the floral composition in urban gardens.<br> </p>
Global Characterization of Megakaryocytes in Bone Marrow, Peripheral Blood, and Cord Blood by Single-cell RNA Sequencing
<p><span><span>Megakaryocytes (MK) are mainly derived from bone marrow (BM) and are mainly involved in platelet production. Recent studies have shown that MK derived from BM may have immune function, and that MK from peripheral blood (PB) are associated with prostate cancer. We analyzed more than 1.2 million single-cell transcriptome data from 132 samples of PB, BM, and cord blood (CB) from healthy individuals and patients, and obtained 4474 MK single cell and 14 MK subtypes. We found that MK were widely distributed and the amount of MK in PB was more than that in BM and there were specificity MK subtypes in PB. We found classical MK1 with typical MK characteristics and non-classical MK2 closely related to immunity which was the most common subtype in BM and CB. Classical MK1 was closely related to Non-Small Cell Lung Cancer (NSCLC) and has diagnostic ability. MK2 may have potential adaptive immune function and play a role in tumor NSCLC and autoimmune diseases Systemic Lupus Erythematosus. This study deepened our understanding of MK and suggested that MK had potential immune functions and was involved in various diseases.</span></span></p>
Data from: Characterization of rhizome transcriptome and identification of a rhizomatous ER body in the clonal plant Cardamine leucantha
<p>The rhizome is a plant organ that develops from a shoot apical meristem but penetrates into belowground environments. To characterize the gene expression profile of rhizomes, we compared the rhizome transcriptome with those of the leaves, shoots and roots of a rhizomatous Brassicaceae plant, <i>Cardamine leucantha.</i> Overall, rhizome transcriptomes were characterized by the absence of genes that show rhizome-specific expression and expression profiles intermediate between those of shoots and roots. Our results suggest that both endogenous developmental factors and external environmental factors are important for controlling the rhizome transcriptome. Genes that showed relatively high expression in the rhizome compared to shoots and roots included those related to belowground defense, control of reactive oxygen species, and cell elongation under dark conditions. A comparison of transcriptomes further allowed us to identify the presence of an ER body, a defense-related belowground organelle, in epidermal cells of the <i>C. leucantha </i>rhizome, which is the first report of ER bodies in rhizome tissue.</p>
Characterization of descriptors in machine learning for data-based sputtering yield prediction
<p>figures and a table</p>
Characterization of photorecruitable Guanine Exchange Factors for the study of Rho GTPases in endothelial cells
<p>Time lapses of respective figures belonging to the report titled "<strong>Characterization of photorecruitable Guanine Exchange Factors for the study of Rho GTPases in endothelial cells"</strong>. This report was written as part of the Msc programe in Biomedical Science of the University of Amsterdam. </p>
Rapid synthesis and characterization of silver-loaded graphene oxide nanomaterials and their antibacterial applications
<p>All original data used in figures and tables of the manuscript are available in the dataset, which includes the X-ray diffraction, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, transmission electron microscopy, scanning electron microscopy with energy dispersion spectroscopy, zeta potential analysis and antibacterial properties measurement. Ultrasound was practically used in large-scale production of water-soluble silver/graphene oxide (Ag/GO) by reducing the silver ions (Ag+) attached to graphene oxide into silver nanoparticles. The infrared and X-ray photoelectron spectra indicated that there is a strong interaction between Ag and GO. The morphology analysis showed that AgNPs having a monodisperse size was well dispersed on the surface of the GO nanosheet. The zeta potential analysis showed that the Ag/GO nanomaterials suspension has high stability. In addition, the Ag/GO nanomaterials exhibited an effective antibacterial activity against Escherichia coli and Staphylococcus aureus.</p>
Snapshots, frequency contact maps analysis, Poisson Boltzmann calculations, and data scripts for characterization of structural and energetic differences between conformations of the SARS-CoV-2 spike protein
<p><strong>Molecular dynamics simulation</strong> trajectories, which have been performed using the Amber ff14SB force field running with the Amber18 package at the NSF-funded (OAC-1826915, OAC-1828163) ELSA high performance computing cluster at The College of New Jersey. Simulation methodology and further details are described in [1] and [2]. For further details on the trajectories, please contact Joseph Baker (bakerj@tcnj.edu).</p> <p>The <strong>Poisson Boltzmann </strong>energy calculations have been achieved by using the input_files.tar.xz found here and solving the Poisson Boltzmann equation with pygbe. A more detailed example and tutorial can be found at [4]. For further details contact Horacio V Guzman.</p> <p><strong>The dataset contains </strong></p> <ul> <li><strong>A total of 30 snapshots of the three trajectories (10 snapshots each system = two per replica x 5 replicas/system):</strong></li> </ul> <ol> <li>SARS-CoV-2002 spike protein with three RBD in the down positions: "COV2-DDD/PDB/" .</li> <li>SARS-CoV-2002 spike protein with one RBD in the up and two RBD in the down positions: "COV2-UDD/PDB/".</li> <li>SARS-CoV-2002 spike protein with two RBD in the up and one RBD in the down positions: "COV2-DUU/PDB/".</li> </ol> <ul> <li><strong>Input files for Poisson-Boltzmann analysis</strong>:</li> </ul> <ol> <li>PoissonBoltzmann/input_files.tar.xz</li> </ol> <ul> <li><strong>Data for the frequency contact map and processing scripts</strong>:</li> </ul> <ol> <li>cov2-ddd.pdb, cov2-udd.pdb, cov2-duu.pdb reference PDB files.</li> <li>Contact maps [3] at "COV2-DDD/CONTACT_MAP/", "COV2-UDD/CONTACT_MAP/", "COV2-DUU/CONTACT_MAP/".</li> <li>frequency.lua: get frequency of contacts from a set of contacts map files.</li> <li>diff_frequency.lua: get differential frequency of contacts from a set of frequency files.</li> <li>Frequency of contacts listed in frequency.data files at "COV2-DDD/", "COV2-UDD/" and "COV2-DUU/" directories.</li> </ol> <p>Read the "INFO" files for further informations.</p> <p>This dataset and the code is part of a collaboration between:</p> <ul> <li>The Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland (supported by the National Science Centre, Poland, under grant No. 2017/26/D/NZ1/0046)</li> <li>Department of Chemistry, The College of New Jersey, New Jersey, United States (supported by National Science Foundation under grant numbers OAC-1826915 and OAC-1828163).</li> <li>Jozef Stefan Institute, Ljubljana, Slovenia (supported by the Slovenian Research Agency (Funding No. P1-0055)).</li> <li>School of engineering in bioinformatics, University of Talca, Talca, Chile.</li> </ul> <p>[1] Rodrigo A. Moreira, Mateusz Chwastyk, Joseph L. Baker, Horacio V Guzman, & Adolfo B. Poma. (2020). All-atom simulations snapshots and contact maps analysis scripts for SARS-CoV-2002 and SARS-CoV-2 spike proteins with and without ACE2 enzyme (Version 0.1) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3817447</p> <p>[2] Chad W. Hopkins, Scott Le Grand, Ross C. Walker, and Adrian E. Roitberg. Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning. Journal of Chemical Theory and Computation 2015 11 (4), 1864-1874. http://doi.org/10.1021/ct5010406</p> <p>[3] Rodrigo A. Moreira, Mateusz Chwastyk, Joseph L. Baker, Horacio V Guzman, & Adolfo B. Poma. Quantitative determination of mechanical stability in the novel coronavirus spike protein. Nanoscale, 2020,12, 16409-16413. <a href="https://doi.org/10.1039/D0NR03969A">https://doi.org/10.1039/D0NR03969A</a></p> <p>[4] https://github.com/pyF4all</p>
Surface appearance assessment as a tool for characterizing silver tarnishing
<p>A video presentation of the poster with same title.</p> <p>Abstract of poster: The aim of this study is to create a methodological approach based on imaging techniques and computer vision that can be used as a tool for the characterization of silver tarnish and the presence of fingerprints on silver museum objects. To this extend, material properties of artificially tarnished silver coupons were examined, with the aim to classify the degree of tarnish and to detect fingerprints. Surface alterations were assessed using visual inspection, colorimetry, gloss measurements and monochromatic Reflectance Transformation Imaging (RTI). For the chemical characterization Scanning Electron Microscopy equipped with Energy Dispersive X-rays Spectroscopy (SEM-EDS) and Linear Scanning Voltammetry (LSV) was implemented.</p>
Wetland delineation and characterization layers 2014-2017, Rwanda
<p>Wetlands are highly productive ecosystems and provide a range of goods and services on local to global scales and have become key sites of agricultural development in sub-Saharan Africa. This is the case for East African countries such as Rwanda, where agricultural expansion into wetlands and agricultural intensification are crucial elements of the government's strategy to increase food production and decrease dependence from global food markets. However, spatially explicit information of the location and status of wetlands for informed decision making is lacking or not up to date. In the related research article, we therefore develop a framework comprising the following spatial layers: Delineation, Surface Water Occurrence (SWO), Land Use/Land Cover (LULC) classification and Wetland Use Intensity (WUI). These layers are based on satellite imagery from the European Copernicus Programme and cover the whole of Rwanda. The Delineation is derived from a static Potential Wetlands layer and Sentinel-2 imagery using object-based image analysis (OBIA). The SWO is a per-pixel count of the times a location was detected as flooded using Sentinel-1 imagery. For the LULC classification, an object-based decision tree classifier is applied to Sentinel-2 imagery in Combination with the Delineation layer and the SWO. The WUI layer is based on the Absolute Mean Spectral Dynamics indicator depicting pixel-wise changes in reflectance values in Sentinel-2 bands relevant for wetland vegetation and hydrological dynamics. All layers refer to the year 2017, except for the SWO layer, which covers surface water dynamics from 2014 to 2017. The layers can be used individually or in combination and thus adapted to the different information needs for sustainable wetland management.<br> This dataset contains the Potential Wetlands map based on topographic indices, the Wetland Delineation derived from it, the Surface Water Occurrence layer, the Land Use/Land Cover map, and the Wetland Use Intensity layer. For appropriate map display we provide QGIS layerstyle files associated with these layers.</p>
Data archive for the peer-reviewed journal article "Detailed characterization of the CAPS single scattering albedo monitor (CAPS PMssa) as a field-deployable instrument for measuring aerosol light absorption with the extinction-minus-scattering method"
<p>Data archive accompanying the peer-reviewed journal article "Detailed characterization of the CAPS single scattering albedo monitor (CAPS PMssa) as a field-deployable instrument for measuring aerosol light absorption with the extinction-minus-scattering method". In 2020 this article was accepted for publication in the journal <em>Atmospheric Measurement Techniques</em>. Data are uploaded in the form of ascii text files, Igor Pro experiment files (.pxp), and Jupyter notebook files. In addition, a Jupyter notebook file is included containing an implementation of the error model used in the paper.</p>
ScienceDex guides
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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.