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11,198 results for “organ”
Dataset for Quantitative description of metal center organization in single-atom catalysts
<p>Dataset for <strong>Quantitative description of metal center organization in single-atom catalysts </strong>by by K. Rossi, A. Ruiz-Ferrando, D. Faust Akl, V. Gimenez Abalos, J. Heras-Domingo, R. Graux, X. Hai, J. Lu, D. Garcia-Gasulla, N. López, J. Pérez-Ramírez, and S. Mitchell.</p> <p>The data is structured as follows:</p> <ul> <li>01_Micrographs: all micrographs employed in .tif and .png format. An <a href="https://imagej.net/">imageJ </a>macro to overlay coordinate files with images is attached.</li> <li>02_Ground_truth: contains the manually-labeled and predicted xy-coordinates of atomic positions including probabilities.</li> <li>03_All_detection_data: contains all automated predictions of atomic positions in the images of this study (uhd), and of Mitchell et. al in <em>JACS</em>, <strong>144</strong>, 8018-8029 (2022) (jacs_train, jacs_test). This folder further contains model weights and area segmentations needed to estimate the surface atomic densities.</li> <li>04_Trimetallic_analysis: Figures complementing Supplementary Figure S21.</li> </ul> <p> </p>
Functional organization of the mouse lemur Primate Microcebus murinus : from multilevel validation to comparison with humans
<p>Brain network organization in the mouse lemur (Microcebus murinus) Primate.<br> (comparison with humans)<br> Archives contain:<br> <br> - Dictionary learning analysis in mouse lemurs and humans showing networks identified in these two species.<br> <br> - Cerebral templates from mouse lemurs and humans (MNI template). They can be used to localize networks.<br> <br> - A functional atlas of the mouse lemur brain issued from resting fMRI. Resting-state functional MR images were recorded from 14 mouse lemurs at 11.7 Tesla (2 time point per animal).<br> - An atlas from human brain (issued from <a href="http://www.gin.cnrs.fr/fr/outils/aal-aal2/">http://www.gin.cnrs.fr/fr/outils/aal-aal...</a>) that can be used to attribute human cerebral networks.<br> <br> - Templates, atlases and networks can be easily observed together using ITK-SNAP (<a href="http://www.itksnap.org/">http://www.itksnap.org/</a>).</p> <p>if used for publication please cite: </p> <p><strong>Resting state functional atlas and cerebral networks in mouse lemur primates at 11.7 Tesla</strong><br> <strong>Clément M Garin</strong>, Nachiket A Nadkarni, Brigitte Landeau, Gaël Chételat, Jean-Luc Picq, Salma Bougacha, Marc Dhenain<br> Feb 2021<br> <strong>NeuroImage</strong> 226, 117589<br> DOI: 10.1016/J.NEUROIMAGE.2020.117589<br> <a href="https://www.sciencedirect.com/science/article/pii/S1053811920310740">https://www.sciencedirect.com/science/article/pii/S1053811920310740</a></p>
Icons illustrating aspects of data organization from the Data Literacy Initiative (DaLI) at TH Köln
<p>Icons created as part of the research project Data Literacy Initiative (DaLI) at TH Köln - University of Applied Sciences in Cologne, Germany. They illustrate aspects of best practices for data organization as recommended in Karl W. Broman & Kara H. Woo (2018) Data Organization in Spreadsheets, The American Statistician, 72:1, 2-10, DOI: 10.1080/00031305.2017.1375989.<br> </p> <p>When using any of the images please include the following attribution together with the DOI: This image was created by Jule Marie Schacht and Juliane Piecha for the Data Literacy Initiative (DaLI) at TH Köln and is used under a CC-BY license.</p> <p>The Data Literacy Initiative (DaLI) at TH Köln develops an interdisciplinary, modular program offering data literacy training to students from all fields.</p> <p>More information on the Data Literacy Initiative (DaLI) (in German): https://www.th-koeln.de/dali</p> <p>Illustrations created by: Jule Marie Schacht</p>
Evaluation dataset for Relation Extraction of relationships between Organisms and Natural-Products
<p>A curated evaluation dataset for end-to-end Relation Extraction of relationships between organisms and natural-products.</p> <p>Details about the manual annotation:</p> <ul> <li>For Chemicals: <ul> <li>The chemical labels are annotated as they appear in the abstract.</li> <li>In abstracts, singular chemicals and classes of chemicals produced by a specific organism were distinguished.</li> <li>The "type" attribute {“chemical”, “class”} is used to indicate the nature of the mentioned name.</li> <li>A "class" attribute for chemical entities has also been included if class information is present in the abstract.</li> <li>A Wikidata and PubChem identifiers were assigned to chemicals and classes when available.</li> </ul> </li> <li>For Organisms: <ul> <li>The organism labels are annotated as they appear in the abstract.</li> <li>If in an abstract, the genus name was mention first, e.g. "Plakinastrella sp." and then the specie name e.g "Plakinastrella clathrata" is precise, then only the specie name is used.</li> <li>A Wikidata identifier was assigned to all organisms.</li> <li>In some abstracts, only the genus name is mentioned.</li> </ul> </li> <li>For Relations: <ul> <li>Only the relations explicitly mentioned in the abstract are reported in the output labels.</li> <li>Relations are reported in their order of appearance in the abstract.</li> </ul> </li> </ul>
DMS measurements dataset for manuscript "Classification of Volatile Organic Compounds by Differential Mobility Spectrometry Based on Continuity of Alpha Curves"
<p>Differential mobility spectrometry dispersion plots collected for the manuscrit "Classification of Volatile Organic Compounds by Differential Mobility Spectrometry Based on Continuity of Alpha Curves". The measurement files are located in the folders that represent certain week and day of measurement. The folders containing measurements are named with the following pattern: [chemical abbreviation]_[dilution rate]. For example "2PEtOH_1o10k" means that the folder contains measurement of 2-phenylethanol diluted with propylene glycol in volumetric proportion 1/10 000. Another example is "nBuOH_1o100" - n-Butanol diluted with propylene glycol in volumetric proportion 1/100. Please find the abbreviations in the article referred.</p> <p>For the first five weeks only 1/100 dilutions were measured. The last two weeks (weeks 6 and 7) 1/10 000 dilutions were measured. However, Carvone 1/100 was measured again on week 6 due to suspicion of faulty measurements during the previous weeks. The faulty measurements were not confirmed, and thus there 25 more samples of Carvone with dilution rate 1/100.</p>
Nevada Desert FACE Facility Soil Organic Carbon Data
This data set is the result of soils analysis from the Nevada Desert Free-Air CO2 Enrichment Facility (NDFF) experiment in the Mojave Desert and reports soil organic carbon (%C) and delta 13C stable isotope values. These soils were collected at the end of the NDFF experiment in 2007 and stored at Cornell University until analysis in 2018. Soils were harvested from 6 cover types (5 perennial vegetation covers and unvegetated interspace soils) from 0-100 cm in the soil profile in 20 cm increments. Soils were pretreated for inorganic carbon removal using an acid fumigation technique with HCl. Bulk density from NDFF plots is provided (kg soil* ha ^ -1) so that SOC stocks may be calculated. These data provide the basis for a publication challenging the prevailing idea that arid ecosystems will increase soil organic carbon stocks under long term elevated CO2.
Experimental microcosm incubations assessing the effect of hypoxia on aqueous iron and organic carbon, pH, sediment organic carbon, and sediment iron-bound organic carbon
To assess the effect of changing oxygen concentrations on coupled carbon and iron cycling in freshwater ecosystems, we performed 6-week microcosm incubations. Incubations were inoculated with sediment and water from Falling Creek Reservoir, Vinton, VA, USA. We started the experiment with 102 microcosms split evenly into oxic and hypoxic treatments. After two weeks, we switched the treatment of approximately half of the remaining microcosms, generating a total of four oxygen regimes: hypoxic, oxic, hypoxic to oxic, and oxic to hypoxic. We sampled the microcosms destructively approximately twice per week, collecting aqueous samples for total and dissolved carbon and iron, as well as sediment samples for organic carbon and iron-bound organic carbon analysis. Iron-bound organic carbon was determined using citrate-bicarbonate-dithionite extractions.
Porewater sulfide, sediment sulfur, and organic matter data in West Falmouth Harbor, 2017-2019
West Falmouth Harbor (West Falmouth, MA, USA) has been experiencing a dramatic increase in nitrogen loading from an upgradient municipal wastewater treatment facility since the early 2000’s. As part of a long-term study into the effects of this nitrogen enrichment, each summer in 2017-2019 we sampled sediment and porewater to assess the relationship between belowground sulfur and carbon pools and seagrass health. This dataset contains information on porewater sulfide, porewater sulfate to chloride molar ratios, sediment organic matter, and sediment total sulfur from sites across three basins of West Falmouth Harbor that receive varying inputs of nitrogen. The data supports findings reported in Haviland et al., 2022 (https://doi.org/10.1002/lno.12025).
Sediment organic matter at two stations in West Falmouth Harbor between 2007 and 2016
West Falmouth Harbor (West Falmouth, MA, USA) has been experiencing a dramatic increase in nitrogen loading from an upgradient municipal wastewater treatment facility since the early 2000’s. As part of a long-term study into the effects of this nitrogen enrichment, we have measured multiple biogeochemical processes at two locations within the harbor at either end of the eutrophication gradient - one in the well-flushed outer harbor (OH) and one in the inner basin closer to the dominant groundwater N source (Snug Harbor, SH). Samples of the top 4cm of the sediment profile were taken each year and analyzed for organic matter content via loss on ignition in the top 1cm and the sediment from 3-4cm deep. In a subset of years, intermediate depths were quantified, as well as samples below 4cm. Note, calculations for loss on ignition do not account for the weight of salt from porewater dried with the samples. A separate analysis found that salt accounts for between 3 and 19% of the dry weight of the sediment, depending on porosity. A calibration was done with percent carbon in 2009, showing a tight linear correlation between carbon content and organic matter across the entire site (%LOI = 2.71*%C + 0.2471).
Organic and inorganic carbon concentration and stable isotope composition in poorly drained agricultural soils in Iowa, USA
We measured soil organic carbon (SOC) and inorganic carbon (carbonate) in samples collected along topographic gradients in agricultural fields in Iowa, USA, in 2018. We also measured stable isotopes of SOC, soil nitrogen, and carbon in respired CO2 to provide additional context for organic matter dynamics. Additional physical, chemical, and hydrologic variables were measured on these samples and in the field sites to understand mechanisms underlying patterns in soil organic and inorganic carbon.
Total organic carbon, total nitrogen, and iron-bound organic carbon in surficial sediment and settling particulate material from Falling Creek and Beaverdam Reservoirs in 2019 and 2021
This dataset includes measurements of sediment properties (total organic carbon, total nitrogen, and iron-bound organic carbon) in surficial sediment and sedimenting material from two reservoirs: Falling Creek and Beaverdam Reservoirs, both located in Vinton, VA, USA. To measure surficial sediment properties, sediment cores were collected at the deepest site in each reservoir using a gravity corer, and the top 1 cm was frozen then lyophilized. Sediment cores were collected approximately once per month in both reservoirs throughout the stratified period (May–November) in 2019 and 2021, though sampling frequency and duration varied by reservoir and year. Sedimenting material was sampled using sediment traps suspended approximately 1 m above the sediment in both reservoirs. Iron-bound organic carbon was measured using the citrate-bicarbonate-dithionite method, and we used a CN analyzer (Elementar VarioMax, Ronkonkoma, NY, USA) to determine the amount of OC per unit mass of sediment.
Small, coastal temperate rainforest watersheds dominate organic carbon transport to the northeast Pacific Ocean
The northeast Pacific Coastal Temperate Rainforest (NPCTR) extending from southeast Alaska to northern California is characterized by high precipitation and large stores of recently fixed biological carbon. We show that 3.4 Tg-C yr-1 as DOC is exported from the NPCTR drainage basin to the coastal ocean. More than 56% of this riverine DOC flux originates from thousands of small (mean = 118 km2), coastal watersheds that comprise 22% of the NPCTR drainage basin. The average DOC yield from NPCTR coastal watersheds (6.20 g-C m-2 yr-1) exceeds that from Earth’s tropical regions by roughly a factor of three. The highest yields occur in small, coastal watersheds in the central NPCTR due to the balance of moderate temperature, high precipitation, and high soil organic carbon stocks. These findings indicate that DOC export from NPCTR watersheds may play an important role in regional-scale heterotrophy within near-shore marine ecosystems in the northeast Pacific. These are the datasets used in this analysis
Effects of drying temperature on potential carbon mineralization and water-extractable organic carbon in Iowa cropland and riparian buffer soils
Measuring carbon dioxide (CO2) produced after re-wetting a previously dried soil is an increasingly popular soil health assay, but there is disagreement on the optimal soil drying temperature. We tested whether soil drying temperature impacts water-extractable organic carbon (WEOC) and soil CO2 emissions (potential carbon mineralization) following rewetting of dried soil. Samples were collected at four sites in north-central Iowa, US, and each site had soils planted to corn/soybean or perennial vegetation. The dataset includes measurements of WEOC prior to the incubation experiment, and measurements of CO2 flux and its stable carbon isotope ratio over the course of a 28-day incubation. The manuscript describing these data is under review in Geoderma.
2018 Priming experiment to investigate dissolved organic matter turnover
This dataset is associated with an experiment that was conducted on the University of Florida's campus to evaluate the role of priming in dissolved organic matter turnover. Incubations were established with dissolved organic matter substrates derived from a 13C-labeled algal substrate, mangrove peat derived dissolved organic matter leachate, and a primed condition with both algal and peat substrates. A seawater control was also included. This dataset includes measurements of water chemistry, carbon dioxide, stable isotopes, and gene counts for clusters of orthologous genes (COG). For more information, please refer to Morrison et al., Mangrove peat and algae leachates elicit rapid and contrasting molecular and microbial responses in coastal waters.
Fungal traits associated with soil organic matter formation, Harvard Forest, Petersham MA, 2020-2023
Soil microbes are a major source of organic residues that accumulate as soil organic matter (SOM), the largest terrestrial reservoir of carbon on Earth. As such, there is growing interest in determining the microbial traits that drive SOM formation and stabilization; however, whether certain microbial traits consistently predict SOM accumulation across different functional pools (e.g., total vs. stable SOM) is unresolved. To address these uncertainties, we incubated individual species of fungi in SOM-free model soils, allowing us to directly relate the physiological, morphological, and biochemical traits of fungi to their SOM formation potentials. We find that the formation of different SOM functional pools is associated with distinct fungal traits, and that ‘multifunctional’ species with intermediate investment across this key grouping of traits (namely, carbon use efficiency, growth rate, turnover rate, and biomass protein and phenol contents) promote SOM formation, functional complexity, and stability. Our results highlight the limitations of categorical trait-based frameworks that describe binary (high/low) trade-offs between microbial traits, instead emphasizing the importance of synergies among microbial traits for the formation of functionally complex SOM.
Dissolved organic matter characterization for seasonal synoptic sampling of 100 urban streams in Boston, Massachusetts (USA) from 2021-2022
This dataset contains dissolved organic matter (DOM) characteristics from surface water samples collected at 100 urban stream locations in the greater Boston, Massachusetts metropolitan area. Samples were collected four times (September 2021, November 2021, April 2022, and July 2022) to capture spatial and seasonal variation in DOM characteristics. Fluorescent optical properties were measured on filtered water samples to understand the chemical composition of DOM. Excitation-Emission Matrices (EEMs) were measured using a Horiba Aqualog spectrometer. DOM characteristics were quantified using both standard fluorescence and absorbance metrics as well as through parallel factor (PARAFAC) analysis. These data were collected as part of the Carbon in Urban Rivers Biogeochemistry (CURB) Project. Detailed field data and site data are published separately and can be linked using the “curbid” and “synoptic_event” columns in each dataset.
Dissolved organic carbon concentrations for seasonal synoptic sampling of 100 urban streams in Boston, Massachusetts (USA) from 2021-2022
This dataset contains dissolved organic carbon (DOC) concentrations from surface water samples collected at 100 urban stream locations in the greater Boston, Massachusetts metropolitan area. Samples were collected four times (September 2021, November 2021, April 2022, and July 2022) to capture spatial and seasonal variation in DOC concentrations. Filtered stream samples were analyzed for dissolved organic carbon concentration. These data were collected as part of the Carbon in Urban Rivers Biogeochemistry (CURB) Project. Detailed field data and site data are published separately and can be linked using the “curbid” and “synoptic_event” columns in each dataset.
Higgins et al. 2024 study on dissolved organic matter controls and effects at the IISD Experimental Lakes Area, Northwestern Ontario, Canada, 1970-2019
This dataset represents long-term ecological reserch data collected at the IISD Experimental Lakes Area, Northwestern Ontario, Canada (1970 - 2019) used to support a research study reported in (Higgins et al. 2024). The study examines the relationships between long-term changes in precipitation, dissolved organic matter (DOM) loading and lake concentrations, and various physical, chemical and biological indicators.
Dissolved organic carbon concentrations for seasonal synoptic sampling of 100 urban streams in Miami, Florida (USA) from 2021-2022
This dataset contains dissolved organic carbon concentrations from surface water samples collected at 100 urban stream and canal locations in the greater Miami, Florida metropolitan area. Samples were collected five times across different seasons to capture spatial and seasonal variation in DOC concentration. These events include the wet seasons of 2021 and 2022, as well as the dry season of 2022, specifically: Summer 2021 (Wet; July 8 to July 27), Fall 2021 (Wet; September 27 to October 7), Winter 2022 (Dry; January 3 to January 13), Spring 2022 (Dry; April 7 to April 23), and Summer 2022 (Wet; June 1 to June 13). These data were collected as part of the Carbon in Urban Rivers Biogeochemistry (CURB) Project. Detailed field data and site data are published separately and can be linked using the “curbid” and “synoptic_event” columns in each dataset.
Dissolved organic matter characterization for seasonal synoptic sampling of 100 urban streams in Miami, Florida (USA) from 2021-2022
This dataset contains dissolved organic matter (DOM) characteristics from surface water samples collected at 100 urban stream and canal locations in the greater Miami, Florida metropolitan area. Samples were collected five times across different seasons to capture spatial and seasonal variation in DOC concentration. These events include the wet seasons of 2021 and 2022, as well as the dry season of 2022, specifically: Summer 2021 (Wet; July 8 to July 27), Fall 2021 (Wet; September 27 to October 7), Winter 2022 (Dry; January 3 to January 13), Spring 2022 (Dry; April 7 to April 23), and Summer 2022 (Wet; June 1 to June 13). Fluorescent optical properties were measured on filtered water samples to understand the chemical composition of DOM. Excitation-Emission Matrices (EEMs) were measured using a Horiba Aqualog spectrometer. DOM characteristics were quantified using both standard fluorescence and absorbance metrics as well as through parallel factor (PARAFAC) analysis. These data were collected as part of the Carbon in Urban Rivers Biogeochemistry (CURB) Project. Detailed field data and site data are published separately and can be linked using the “curbid” and “synoptic_event” columns in each dataset.
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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.