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348 results for “Core data”
Data from: The core of the matter – Importance of identification method and biological replication for benthic marine monitoring
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Data from: Group living and male dispersal predict the core gut microbiome in wild baboons
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Data to support: Anthropogenic influence on tropospheric reactive bromine since the pre-industrial: Implications for ice-core bromine trends
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AQUACOSM VIMS-Ehux – Core data
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Data from: Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range
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Cucumber core collection fruit morphological traits raw data (2019-2022)
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Data from: Toxicity and magnetometry evaluation of the uptake of core-shell maghemite-silica nanoparticles by neuroblastoma cells
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Survey of Core Facilities Raw Data
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Baltimore Ecosystem Study polar organic contaminant integrative sampler data for pharmaceuticals and personal care products in core sites within Gwynns Falls watershed and reference sites.
An ongoing component of the Baltimore urban long-term ecological research (LTER) project (Baltimore Ecosystem Study, BES) is the use of the watershed approach and monitoring of stream water quality to evaluate the impacts of multiple chemical stressors on urban stream ecosystem functioning within Baltimore. The LTER research has focused on the Gwynns Falls watershed, which spans a gradient from highly urban, urban-residential, and suburban zones. In addition, a forested watershed serves as a reference. The long-term sampling network includes four longitudinal sampling sites along the Gwynns Falls mainstem, as well as several small (40-100 ha) watershed within or near the Gwynns Falls, providing data on water quality in different land use zones of the watersheds. Each study site is continuously monitored for discharge and is sampled weekly for water chemistry. Those data are available elsewhere on the BES website. We are interested in studying the presence and concentrations of pharmaceuticals and personal care products (PPCPs) within urban streams, and then linking these PPCPs with various stream ecosystem functions. To quantify the concentrations of PPCPs in streams, we deploy polar organic contaminant integrative samples (POCIS), which integrate all organic contaminants that pass by them in a stream over a set period of deployment. These POCIS allow us to integrate the total amount of PPCPs within a stream over a set period of time, and then to relate these concentrations with other ecosystem processes. We monitored PPCP concentration in four suburban to urban sites within the Gwynns Falls, as well as one exurban and one forested stream monitoring site. Each POCIS was deployed for two weeks at a stream monitoring site in March 2012. After completion of the sampling period, POCIS were removed from the streams and shipped on ice to the University of Nebraska for extraction and quantification of recovered compounds. This dataset includes all compounds extracted and q
Tree core and ring data for 150 mature black spruce sites in interior Alaska
This data set contains sample information for tree core and ring analysis at 150 extensive black spruce sites in interior Alaska collected in the summers of 2000, 2001, 2002 across the interior of Alaska along the Taylor highway, Alaska highway, Parks highway, Elliot highway, Steese highway, and Dalton highway.
Supporting codes, data, and outputs to identify a type of lithofacies from rock-core digital photographs and to classify the lithofacies from well-log data
<p>This repository contains the codes and the data used in the study “Interpreting the Subsurface Lithofacies at High Lithological Resolution by Integrating Information from Well-log Data and Rock-core Digital Photographs”. The codes are used to identify the lithofacies type from rock-core digital photographs (clustering) and to predict the lithofacies from geophysical well-log data (classification). The lithofacies identification process, including feature extraction and clustering, was encoded by MATLAB, and the classification model was encoded by TensorFlow to construct a neural network-based classification model. </p>
Data from: Monitoring and predictive mapping of floristic biodiversity along a climatic gradient in ENSO's terrestrial core region, NW Peru
<p>This is the data from the publication "Monitoring and predictive mapping of floristic biodiversity along a climatic gradient in ENSO's terrestrial core region, NW Peru" (<a href="http://onlinelibrary.wiley.com/doi/10.1111/ecog.05091/abstract">http://onlinelibrary.wiley.com/doi/10.1111/ecog.05091/abstract</a>).</p> <p>The code (including figures, appendices and the manuscript) can be found directly in the <a href="https://github.com/jannes-m/2020-enso-tdf">GitHub repository</a>.</p> <p><strong>Data sources and description</strong></p> <p>Column descriptions for all tables can be found in <em>variable_description.ods. </em>Following tables are stored in <em>tables.gpkg</em>:</p> <ol> <li>plot_species_matrix_2011: Plot species matrix recorded in 2011</li> <li>plot_species_matrix_2012: Plot species matrix recorded in 2012.</li> <li>plot_species_matrix_2016: Plot species matrix recorded in 2016.</li> <li>plot_species_matrix_2017: Plot species matrix recorded in 2017.</li> <li>lifeform: Lifeforms of the recorded species</li> <li>plot_variables: Variables specific to the plots such as height of the first tree layer, cover of dead wood, etc.</li> <li>soil: Edaphic variables.</li> <li>topography: Topographic variables.</li> <li>streets: Streets and dirt tracks in the study area.</li> <li>towns: Polygons displaying the outline of the cities Paita, Piura and Chulucanas.</li> <li>rivers: Lines displaying the major rivers in the study area.</li> <li>study_area: Outline of the study area.</li> <li>peru: Outline of Peru.</li> <li>neighbors: Outline of Peru's neighbors (Bolivia, Brazil, Chile, Colombia, Ecuador).</li> <li>coast: Coastal strip of and close to the study area.</li> <li>precipitation: Precipitation measured at the three climatic stations (Paita, Piura, Chulucanas).</li> <li>experiment_count: species counted per visit (irrigation-fertilization experiment).</li> <li>experiment_irrigation: Rain input by time during the irrigation-fertilization experiment.</li> <li>experiment_cover: Cover of each plant species per visit and per experimental plot (irrigation-fertilization experiment).</li> </ol>
Supporting data used in the paper: Xi Chen, 2020, The LMARS based shallow-water dynamical core on generic gnomonic cubed-sphere geometry
<p># Simulation results of the unstaggered shallow water model</p> <p>This repository contains the supporting data used in the paper: Xi Chen, 2020, The LMARS based shallow‐water dynamical core on generic gnomonic cubed‐sphere geometry, DOI: 10.1029/2020MS002280</p> <p><br> Organization of the repository:</p> <p>The tar archive with this data submission has a:</p> <p>doc directory contains a README.md with information regarding naming conventions to label the model configurations for a shallow water test simulation. Additional information can also be found in README.md. Table 4 in the paper provides additional details.</p> <p>The data directory contains the supporting data files (NetCDF format). </p> <p> </p>
LA-ICP-MS data of the Chongce ice core
<p>LA-ICP-MS data of the Chongce ice core</p>
Supplementary data for "History and future of the Martian dynamo and implications of a hypothetical solid inner core"
<p>This dataset contains the results of the calculations we carried out for the submitted manuscript titled "History and future of the Martian dynamo and implications of a hypothetical solid inner core". The data are organized into the following three groups: 1) radial_profiles; 2) histories; and 3) parameter_space_exploration. The first group, "radial_profiles", describes the radial density structure, and corresponding profiles of pressure, gravity, enclosed mass, and thermal expansivity for our simplified models of Earth and Mars. The second group, "histories", contains the results of our thermal evolution calculations for our reference Earth case and our five reference cases for Mars. For each case, there is a header file describing the input parameters, the derived parameters, and the contents of the accompanying tables of values. The third group, "parameter_space_exploration", contains the data that is partially illustrated in Figures 11-16, in which we show various outcomes across a wide range of multidimensional parameter space. All files are in ASCII format. Header files explain their contents in plain language and/or with reference to variables described in the paper. Data tables are tab-delimited.</p>
Data from: A 454 survey reveals the community composition and core microbiome of the common bed bug (Cimex lectularius) across an urban landscape
Elucidating the spatial dynamic and core constituents of the microbial communities found in association with arthropod hosts is of crucial importance for insects that may vector human or agricultural pathogens. The hematophagous Cimex lectularius (Hemiptera: Cimicidae), known as the human bed bug, has made a recent resurgence in North America, as well as worldwide, potentially owing to increased travel, climate change and resistance to insecticides. A comprehensive survey of the bed bug microbiome has not been performed to date, nor has an assessment of the spatial dynamics of its microbiome. Here we present a survey of internal and external bed bug microbial communities by amplifying the V4–V6 hypervariable region of the 16S rDNA gene region followed by 454 Titanium sequencing using 31 individuals from eight distinct collection locations obtained from residences in Cincinnati, OH. Across all samples, 97% of the microbial community is made up of two dominant OTUs, previously identified as the α-proteobacterium Wolbachia and an unnamed γ-proteobacterium from the Enterobacteriaceae. Microbial communities varied among host locations for measures of community diversity and exhibited structure according to collection location. This broad survey represents the most in-depth assessment, to date, of the microbes that associate with bed bugs.
Data from: Tracing the effects of eutrophication on molluscan communities in sediment cores: outbreaks of an opportunistic species coincide with reduced bioturbation and high frequency of hypoxia in the Adriatic Sea
Estimating the effects and timing of anthropogenic impacts on the composition of macrobenthic communities is challenging because early 20th century surveys are sparse and the corresponding intervals in sedimentary sequences are mixed by bioturbation. Here, to assess the effects of eutrophication on macrobenthic communities in the northern Adriatic Sea, we account for mixing with dating of the bivalve Corbula gibba at two stations with high sediment accumulation (Po prodelta) and one station with moderate accumulation (Isonzo prodelta). We find that, first, pervasively bioturbated muds typical of highstand conditions deposited in the early 20th century were replaced by muds with relicts of flood layers and high content of total organic carbon (TOC) deposited in the late 20th century at the Po prodelta. The 20th century shelly muds at the Isonzo prodelta are amalgamated but also show an upward increase in TOC. Second, dating of C. gibba shells shows that the shift from the early to the late 20th century is characterized by a decrease in stratigraphic disorder and by an increase in temporal resolution of death assemblages from ~25-50 years to ~10-20 years in both regions. This shift reflects a decline in the depth of the fully-mixed layer from more than 20 cm to few centimeters. Third, the increase in abundance of the opportunistic species C. gibba and the loss of formerly abundant, hypoxia-sensitive species coincided with the decline in bioturbation, higher preservation of organic matter, and higher frequency of seasonal hypoxia in both regions. This depositional and ecosystem regime shift occurred in ~1950 AD. Therefore, the effects of enhanced food supply on macrobenthic communities were overwhelmed by oxygen depletion even when hypoxic conditions are limited to few weeks per year in the northern Adriatic Sea. Preservation of trends in molluscan abundance and flood events in sedimentary sequences was enhanced by eutrophication that reduced bioturbational mixing.
Data from: Core genes evolve rapidly in the long-term evolution experiment with Escherichia coli
Bacteria can evolve rapidly under positive selection owing to their vast numbers, allowing their genes to diversify by adapting to different environments. We asked whether the same genes that evolve rapidly in the long-term evolution experiment with Escherichia coli (LTEE) have also diversified extensively in nature. To make this comparison, we identified ~2000 core genes shared among 60 E. coli strains. During the LTEE, core genes accumulated significantly more nonsynonymous mutations than flexible (i.e., noncore) genes. Furthermore, core genes under positive selection in the LTEE are more conserved in nature than the average core gene. In some cases, adaptive mutations appear to modify protein functions, rather than merely knocking them out. The LTEE conditions are novel for E. coli, at least in relation to its evolutionary history in nature. The constancy and simplicity of the environment likely favor the complete loss of some unused functions and the fine-tuning of others.
Data from: Diet breadth and exploitation of exotic plants shift the core microbiome of Cephaloleia, a group of tropical herbivorous beetles
The beetle genus Cephaloleia has evolved in association with tropical ginger plants and for many species their specific host plant associations are known. Here we show that the core microbiome of six closely related Costa Rican Cephaloleia species comprises only eight bacterial groups, including members of the Acinetobacter, Enterobacteriacea, Pseudomonas, Lactococcus, and Comamonas. The Acinetobacter and Enterobacteriacea together accounted for 35% of the total average 16S rRNA ribotypes recovered from all specimens. Further, microbiome diversity and community structure was significantly linked to beetle diet breadth, between those foraging on less than two plant types (specialists) versus over nine plant types (generalists). Moraxellaceae, Enterobacteriaceae, and Pseudomonadaceae were highly prevalent in specialist species, and also present in eggs, while Rickettsiaceae associated exclusively with generalist beetles. Bacteria isolated from Cephaloleia digestive systems had distinct capabilities and suggested a possible beneficial role in both digestion of plant-based compounds, including xylose, mannitol, and pectin, and possible detoxification, via lipases. Cephaloleia species are currently expanding their diets to include exotic invasive plants, yet it is unknown whether their microbial community plays a role in this transition. In this study, colonization of invasive plants was correlated with a dysbiosis of the microbiome, suggesting a possible relationship between gut bacteria and niche adaptation.
Data from: Chloroplast phylogenomic data support Paleocene - Eocene amphi-Pacific early radiation for the Asian Palmate core Araliaceae
Traditional phylogenies based on analysis of multiple genes have failed to obtain a well-resolved evolutionary history for the backbone of the Asian Palmate group of Araliaceae, the largest clade of the family. In this study we applied the genome skimming approach of next-generation sequencing to address whether the lack of resolution at the base of the Asian Palmate tree is due to molecular sampling error or the footprint of an ancient radiation. Twenty-nine complete plastid genomes of Araliaceae (17 newly sequenced) were analyzed (RAxML, Beast, Lagrange, BioGeoBears) to provide the first phylogenomic reconstruction of the group (95% of genera included). As a result, the early divergences of the Asian Palmate group have been clarified but the backbone of its core is not totally resolved, with short internal branches pointing to an ancient radiation scenario. East Asia is inferred as the most likely ancestral area for the Asian Palmate group (early Upper Cretaceous and the Paleocene) from which an early colonization of the Neotropics is inferred during the late Paleocene – early Eocene. The radiation of the core took place during the Paleocene – early Eocene, most likely in the context of the Boreotropical hypothesis. Recurrent episodes of southward migration (to the tropics) coupled with northern latitude local extinctions (promoting lineages geographic isolation) and northward expansion (promoting lineages contact that erased the trace of preceding geographic isolation) are hypothesized to have linked to the alternation of the cold and warm periods of the Eocene.
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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.