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8,565 results for “characterization”
Datasets for Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar
<p>These datasets accompany the analyses conducted under the study title "<span>Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar</span>"</p> <p>Accompanying R scripts with commentary to run these data can be found in the Github repository under release v1.0.0: https://github.com/bmtalbot/Humans_and_Lemurs_2017</p>
Data for: Characterization of large-scale preferential flow across continental United States
<p>Understanding preferential flow (PF) at large scales is critical for improving land management and groundwater (GW) quality. However, limited knowledge of this process, due to soil surface heterogeneity and observational constraints, hampers progress. In this study, we propose estimating effective PF at remote sensing footprint scale (4 – 9 km) by examining its impact on soil moisture (SM) distribution and shallow GW (SGW) table fluctuations (depth 5 m). Effective PF encompasses macropore, funnel, and finger flow pathways influencing SGW table fluctuations. We compiled daily SGW observations (2019-2021) from 19 continental US (CONUS) sites through USGS. Using inverse modeling in HYDRUS-1D, SGW data, and CHIRPS precipitation data, we inversely estimated soil hydraulic parameters of the dual porosity model (DPM) simulating vertical flow from soil surface to subsurface. Effective PF presence was inferred using three criteria: (1) daily precipitation >= the site-specific average across multiple (calibration) years, (2) daily observed SGW table increase, and (3) daily difference between observed and DPM simulated SGW tables 50% of the site-specific RMSE. Leveraging optimized DPM parameters and associated soil texture, classified PF events, and Soil Moisture Active Passive (SMAP L3E) satellite-based SM, a Random Forest algorithm with 10-fold cross validation predicted large-scale effective PF events. Results indicate seasonal dependence, with spring having the highest occurrence of PF events. The Random Forest model achieved 98% accuracy in predicting large-scale PF events, with SMAP SM and saturated hydraulic conductivity (Ks) among the 4 most impactful variables. Our approach provides a soil hydraulic property, site characteristic, soil texture and remote sensing based generalized tool to analyze large-scale effective PF.</p>
Data From: what mandrills leave behind: using fecal samples to characterize the major histocompatibility complex in a threatened primate
<p>The major histocompatibility complex (MHC) can be useful in guiding conservation planning because of its influence on immunity, fitness, and reproductive ecology in vertebrates. The mandrill (<em>Mandrillus sphinx</em>) is a threatened primate endemic to central Africa. Considerable research in this species has shown that the MHC is important for disease resistance, mate choice, and reproductive success. However, all previous MHC research in mandrills has focused on an inbred semi-captive population, so their genetic diversity may have been underestimated. Here we expand our current knowledge of mandrill MHC variation by performing next-generation sequencing of non-invasively collected fecal samples from a large wild horde in central Gabon. We observe MHC lineages and alleles shared with other primates, and we uncover 45 putative new class II MHC DRB alleles, including representatives of the DRB9 pseudogene, which has not previously been identified in mandrills. We also document methodological challenges associated with fecal samples in NGS-based MHC research. Even with high read depth, the replicability of alleles from fecal samples was lower than that of tissue samples, and allele assignments are inconsistent between sample types. Further, the common assumption that variants with very high read depth should represent true alleles does not appear to be reliable for fecal samples. Nevertheless, the use of degraded DNA in the present study still enabled significant progress in quantifying immunogenetic diversity and its evolution in wild primates.</p>
Figure 2 in Characterization of Eugenia uniflora accessions: a native species with great commercial potential in America
Figure 2. Collection sites of the 40 Surinam Cherry accessions in the state of Rio Grande do Sul with the cluster according to genetic similarity obtained with RAPD markers. Group I =; Group II =; Group III =).
Figure 1 in Characterization of Eugenia uniflora accessions: a native species with great commercial potential in America
Figure 1. Dendrogram of genetic similarity between the 40 Surinam Cherry, obtained from RAPD markers. The line indicates the 84% cut-off point based on the average similarity between populations.
Fig. 2 in Besnoitia tarandi in Canadian woodland caribou - Isolation, characterization and suitability for serological tests
Fig. 2. Growth of Besnoitia besnoiti Bb-EvoraCl2 (triangles) and Besnoitia tarandi Bt-CA-Quebec1 (crosses) as assessed by real-time PCR on in-vitro cultivated MARC-145 cells 24, 48 or 72 h p.i. Linear regression revealed that B. tarandi BtCA-Quebec1 grew faster than B. besnoiti BbEvoraCl2.
Fig. 5 in Detection and characterization of diverse coccidian protozoa shed by California sea lions
Fig. 5. Indirect fluorescence antibody test of California sea lion sporulated oocyst cultures. Zoites derived from cultivated oocysts from animal CSL10089 (A), CSL10092 (B), and CSL10100 (C) were tested using serum from a Sarcocystis neurona-infected horse. Image D shows reactivity of serum from the S. neurona-infected horse to S. neurona culture isolate snUCD-1. Image E shows a lack of seroreactivity of negative control serum from a S. neurona-negative horse to zoite culture from CSL10089. Scale bars are 15 Mm.
Fig. 3 in Detection and characterization of diverse coccidian protozoa shed by California sea lions
Fig. 3. Three California sea lion haul-out sites (red circles) on the central California coast where fecal samples were collected from free-ranging animals. Field sample identifiers for test-positive samples are given (Ãno-, PL- and WR-) at each location. Coccidian parasite genotypes and species amplified in sample DNA are indicated in parentheses: A, Coccidia A; B, Coccidia B; Sn, Sarcocystis neurona-like; unchar, uncharacterized species. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.).
Data and code for figures: Design, fabrication and characterization of kinetic-inductive force sensors for scanning probe applications
<p>This directory contains the datasets, code (if applicable) for measurement libraries, data processing and figure generation for the research article "Design, fabrication and characterization of kinetic-inductive force sensors for scanning probe applications", Beilstein J. Nanotechnol. 2024, 15, 242-255.</p>
An Approach Based on an Increased Bandpass for Enabling the Use of Internal Standards in Single Particle ICP-MS: Application to AuNPs Characterization
<p>This dataset contains the raw data corresponding to the figures of the publication https://doi.org/10.3390/nano13121838</p>
Associated code and data for "A disease network-based deep learning approach for characterizing melanoma (doi:10.1002/IJC.33860)"
<p>This deposit contains the data, code, and analysis to recreate the results in the manuscript - Lai X, Zhou JF, Wissely A, Heppt M, Maier A, Berking C, Vera J, Zhang L. A disease network-based deep learning approach for characterizing melanoma. International Journal of Cancer. 2022; 150(6): 1029- 1044. <a href="http://www.researchgate.net/publication/355774213_A_disease_network-based_deep_learning_approach_for_characterizing_melanoma">doi:10.1002/IJC.33860</a>.</p> <p>If you have used the code for your research, please cite the original publication. Thank you very much.</p> <p> </p> <p> </p>
Watching the watchers: Camera identification and characterization using retro-reflections - Dataset
<p>A focused imaging system such as a camera will reflect light directly back at a light source in a retro-reflection (RR) or cat-eye reflection. RRs provide a signal that is largely independent of distance providing a way to probe cameras at very long ranges. We find that RRs provide a rich source of information on a target camera that can be used for a variety of remote sensing tasks to characterize a target camera including predictions of rotation and camera focusing depth as well as cell phone model classification. We capture three RR datasets to explore these problems with both large commercial lenses and a variety of cell phones. This repository contains time-synced videos from the perspective of both a retro-reflective probe and a target camera that can be used to train algorithms for different remote sensing tasks. We include a dataset for cellphone classification, target camera rotation prediction, and target camera focusing depth prediction.</p>
Quantitative results of the analysis of human native and bioengineered tissues corresponding to the work "Histological, histochemical and immunohistochemical characterization of NANOULCOR nanostructured fibrin-agarose human cornea substitutes generated by tissue engineering"
<p>Dataset containing the quantitative results of the histochemical and immunohistochemical analysis of the following human tissues:</p> <ul> <li>Control native cornea (CTR-C)</li> <li>Control native limbus (CTR-L)</li> <li>Artificial cornea generated by tissue engineering (HAC)</li> </ul> <p>Each tissue type was subjected to histochemical and immunohistochemical analyses and results were quantified using ImageJ software to determine average intensities and area fractions corresponding to positive staining signal for each marker.</p>
Elucidating the Polymorphism of Xanthone: A Crystallization and Characterization Study
<p>Dataset related to the publication: "Elucidating the Polymorphism of Xanthone: A Crystallization and Characterization Study". Accepted in Crystal Growth and Design on February 9th, 2024.</p> <p>Abstract: The aim of this work is to shed light on the polymorphism of xanthones, a class of oxygenated molecules well known for their bioactivity, including antioxidant, anticancer, and anti-inflammatory effects. Understanding the polymorphism of xanthones can enable the design of novel solid products for pharmaceutical, nutraceutical, and agrochemical applications. Prior to this work, two entries accounting for different space groups were deposited for 9-xanthone in the Cambridge Structure Database (CSD): an orthorhombic P212121 and a monoclinic P21 structure solved at room and low temperatures, respectively. However, the very high similarity between these two structures and the lack of clear differences in the physical properties (e.g., thermal behavior) suggested the possibility of the existence of only one crystal structure. In fact, the differences shown in the literature data might be related to the chosen operating parameters, as well as the instrumental resolution of the single-crystal X-ray diffraction experiments. In the work presented here, the ambiguity in the polymorphism of xanthone is investigated using thermal analysis, powder and synchrotron single-crystal XRD, and optical microscopy. Additionally, a workflow for the correct identification of twinned crystal structures, which can be applied to other polymorphic systems, is presented. Such workflow combines the collection of a large data set of high-resolution diffraction patterns using synchrotron radiation with the use of principal component analysis, a dimensionality reduction technique, for a quick and effective identification of phase transitions happening during the data collection. Crystallization experiments were designed to promote the formation of different crystal structures of xanthone that were recrystallized based on past literature and beyond.</p>
Characterization and morphometry of prone and affected watersheds by hydro-geomorphological processes in the Serra do Mar Mountain Range, southeastern Brazil: foundation for planning and mitigation actions.
<p>Data: shapefile, tables, and kmz files. </p> <ol> <li>SHAPEFILES</li> </ol> <p>- Dataset with watersheds mapped in the Serra do Mar Paulista Region in the follow cities:</p> <ul> <li>Ubatuba (Abbvr. WU)</li> <li>Caraguatatuba (Abbvr. WC)</li> <li>São Sebastião (Abbvr. WSS)</li> <li>Bertioga (Abbvr. WB)</li> <li>Santos (Abbvr. WS)</li> <li>Praia Grande (Abbvr. WPG)</li> <li>Cubatão (Abbvr. WCUB)</li> <li>São Vicente (Abbvr. WSV)</li> <li>Itanhaém (Abbvr. WITA)</li> <li>Peruíbe (Abbvr. WPERU)</li> <li>Iguape (Abbvr. WIGUA)</li> <li>Itariri (Abbvr. WITR)</li> <li>Pedro de Toledo (Abbvr. WPDT)</li> <li>Iporanga (Abbvr. WIPORA)</li> <li>Apiaí (Abbvr. WAPI)</li> <li>Itaoca Abbvr. WITAO)</li> </ul> <p>- Each shapefile contain information about altitude (min., max, and mean), area (km²), and length (km). </p> <p>- Debris-flow Inventory shapefile.</p> <p> 2. TABLES</p> <ul> <li>Tables for the watersheds mapped in each cities also contain information about the morphometric parameters (melton ratio, basin relief, and relief ratio).</li> <li>Debris-flow inventory information. </li> </ul> <p> </p>
Fig. 1 in Evidence for intercontinental parasite exchange through molecular detection and characterization of haematozoa in northern pintails (Anas acuta) sampled throughout the North Pacific Basin
Fig. 1. Approximate locations in North America and East Asia at which northern pintail tissue samples were collected during 2011–2012 to test for haemosporidian infection. Regions (i.e. Alaska, California, and Japan) and sub-regions (Koyukuk-Nowitna NWR, Yukon-Kuskokwim Delta NWR, Izembek NWR, Sacramento Valley, San Joaquin Valley) for sampling locations are indicated (NWR = National Wildlife Refuge). The number of tissue samples per location is indicated in parentheses. Sample tissue was whole blood unless indicated by an asterisk (signifying wing muscle tissue).
Data for 'Mapping and characterization of avalanches on mountain glaciers with Sentinel-1 satellite imagery'
<div>This dataset contains avalanche deposit outlines (as shapefiles) derived for the study 'Mapping and characterization of avalanches on mountain glaciers with Sentinel-1 satellite imagery'</div> <div> </div> <div>They were outlined at three different sites (Mt Blanc, Everest and Hispar regions) for the periods 11/2016-10/2021 (Mt Blanc) and 11/2017-10/2022 (Everest and Hispar). The time period is indicated in the file name.</div> <div> </div> <div>For each dataset we give the raw outlines (Automated_outlines_dates), the manually updated (Automated_outlines_dates_ManualUpd) and the manually updated after accounting for surface elevation change (Automated_outlines_dates_ManualUpd_shifted). </div> <div> </div> <div>In order to know which scenes were used for the mapping (if no avalanche was detected, we did not provide a shapefile, but this doesn't been that there is a gap in the Sentinel-1 time series), we provide a Sentinel1_date file that shows all the Sentinel-1 RGB pairs that we used to detect the avalanches.</div> <div> </div> <div>We also provide as geotiffs the temporally aggregated outlines (Automated_outlines_dates_ManualUpd_shifted_aggregated; over one specific year yn - from 01/11/yn-1 to 01/11/yn - or the full study period):</div> <div>- as heatmaps (where the value of each pixel corresponds to the number of avalanches that occured) </div> <div>- as binary maps of deposits (where 1 is when an avalanche occured over the time period and 0 is where none were detected).</div> <div> </div> <div> </div> <div>Finally we provide a csv file for each region with metrics per glacier:</div> <div> </div> <div>RGI ID</div> <div>Glacier size (in m^2)</div> <div>Catchment size (in m^2)</div> <div>Area of slopes steeper than 30° (in m^2)</div> <div>The area of total deposits detected (by summing all the pixels of the deposit binary maps) in the ascending obits (in m^2)</div> <div>The area of total deposits detected (by summing all the pixels of the deposit binary maps) in the descending obits (in m^2)</div> <div>The avalanche activity detected (by summing all pixels of the heat maps) in the ascending orbits (in m^2)</div> <div>The avalanche activity detected (by summing all pixels of the heat maps) in the descending orbits (in m^2)</div> <div>The area of the glacier visible in the ascending orbits (in m^2)</div> <div>The area of the glacier visible in the descending orbits (in m^2)</div> <div> </div> <div> </div> <div>The main Google Earth Engine and Matlab scripts used to pre-process the Sentinel-1 GRD images and to map the avalanches are available on GitHub: https://github.com/MarinKneib/S1_avalanches</div> <div> </div>
Figure 2 in Setogenesis and characterization of the new moult substages in the freshwater shrimp Palaemon argentinus (Nobili, 1901) (Caridea: Palaemonidae)
Figure 2. Uropod microphotography of Palaemon argentinus, pre-moult substages. a, D 0: formation of the epidermal line with the distance of the epidermis toward the setal matrix indicates apolysis. b, D ': new setae crossing the gap and reaching the setal base 1 of the old setae. c, D '': epidermis invagination around the setal axis. d, D ''': new setae inserted in the setal cone of old setae; setal 1 1 axes more visible. e, D 2: last pre-moult stage; setal axis pigmented. f, Ecdysis, shedding of the new setae from the setae of the old exoskeleton. Abbreviations: e.l, epidermal line; s.m, setal matrix; ↔ apolysis; n.s, new setae; s.b, setal base; e, epidermis; s.a, setal axis.
Figure 1 in Setogenesis and characterization of the new moult substages in the freshwater shrimp Palaemon argentinus (Nobili, 1901) (Caridea: Palaemonidae)
Figure 1. Posterior region of Palaemon argentinus. a, Circle indicates the observed region of the uropods (U) and setae (S) for determining the moult stages. b, Microphotography in intermoult. Abbreviations: s.m, setal matrix; s.n, setal node; s.b, setal base.
Figure 4 in Setogenesis and characterization of the new moult substages in the freshwater shrimp Palaemon argentinus (Nobili, 1901) (Caridea: Palaemonidae)
Figure 4. Uropod microphotography of Palaemon argentinus. a, Early post-moult (A): vesicular inclusions fill the setae, setal nodes that are a bit dense. b, substage B 1: of vesicular inclusions to levels where setal cone will be formed. c, Substage B 2: beginning of the formation of septum, setal base formed, and the presence of vesicular inclusions in setal cone. d, Intermoult: absence of vesicular inclusions in setal cone. Abbreviations: v.i, vesicular inclusions; s.n, setal nodes; s.b, setal base.
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.