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115 results for “biological processes”
MCR LTER: Coral Reef: Dead coral skeletons impair key recovery processes following coral bleaching; data for Kopecky et al., 2024 Global Change Biology
The data included in this data package were collected on the North shore of Moorea, French Polynesia, from 2015-2023 to explore how dead coral skeletons (e.g,, left after coral bleaching events) influence critical processes tied to coral reef resilience. Together, these various datasets were used for analyses in the manuscript entitled "Changing disturbance regimes, material legacies, and stabilizing feedbacks: dead coral skeletons impair key recovery processes following coral bleaching", published in Global Change Biology. These data are in support of a publication Kopecky et al. (2024) Global Change Biology, and were a part of the thesis of K. Kopecky. The manuscript title and author list are as follows: Changing disturbance regimes, material legacies, and stabilizing feedbacks: dead coral skeletons impair key recovery processes following coral bleaching. Kai Kopecky, Russell J. Schmitt, Sally J. Holbrook. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 22-24354 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2024). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.
Processed data to regenerate figures in Noecker et al, "Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta"
<p>This archive contains the processed source data for the publication by Noecker et al, "Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe <em>Eggerthella lenta</em>" (2023, in review). Data tables underlying each figure panel are included, except for the following panels:</p> <ul> <li>Figure S1A: Source data is in Table S1 of the publication</li> <li>Figure 6D: Source data can be found at NCBI GEO accession GSE212420 (supplementary counts data matrix)</li> </ul> <p>Raw metabolomics data can also be found at Metabolomics Workbench accession PR001620.</p> <p>Methods used to summarize these data and generate the figures are described in the manuscript Materials and Methods and figure captions. Code to generate all figures is also available at www.github.com/turnbaughlab/2022_Noecker_ElentaMetabolism and 10.5281/zenodo.7779454.</p>
Identification of factors determining the process of aggregation/agglomeration of metal oxide nanoparticles in a biological medium
<p>The model allows to identify factors determining the process of aggregation/agglomeration of metal oxide nanoparticles in a biological medium and to verify the importance of ion adsorption and protein adsorption in this process. </p> <p>Model confirms the significant effect of protein adsorption on the hydrodynamic diameter of metal oxide particles in the biological medium, and does not confirm the significant effect of ion adsorption in this process. It’s an example of modeling the properties of nanoparticles, where apart from the descriptors describing the structure of nanoparticles, there are also parameters characterizing the medium.</p>
Fig. 13 in Biological response to geochemical and hydrological processes in a shallow submarine cave
Fig. 13: The effect of hydrodynamics inside the Y-Cave, the location behind section B-B' (Fig. 2) at 5.5 m of depth, where the unusually coloured sediment sample was collected for analysis.
Fig. 12 in Biological response to geochemical and hydrological processes in a shallow submarine cave
Fig. 12: Limestone tablets from the three representative sites after the 1-year exposure period: A) with bioaccumulation at site 1; B) corroded at site 3; C) abraded at site 6 (Fig. 3, Tab. 1).
Fig. 11 in Biological response to geochemical and hydrological processes in a shallow submarine cave
Fig. 11: Cave features: A) stalactites in the chamber with the air pocket (section C-C'); B) submerged stalagmites and flowstones with a lack of marine cave biota (section C-C'); C) submerged scallops (asymmetrical, cuspate, oyster-shell-shaped dissolution depressions in the cave walls used as an indicator of flow direction; Murphy, 2012), (section D-D'); D) corroded cave walls (section F-F').
Fig. 5 in Biological response to geochemical and hydrological processes in a shallow submarine cave
Fig. 5: The annual variation of temperature along the Y-Cave (from August 23–27, 2003 to July 4/October 8, 2004). Measurement positions are given in Fig. 3 and depths in Table 1.
Fig. 10 in Biological response to geochemical and hydrological processes in a shallow submarine cave
Fig. 10: The mass (m.f.) and volume fractions (v.f.) of four sediment categories in the sediment sample collected behind section B-B' (Fig. 2), at 5.5 m of depth inside the Y-Cave; A) detrital terrigenous sediment>4 mm, B) mixed biogenic and terrigenous detritus, C) shells of gastropod Homalopoma sanguineum, D) other biogenic material – shells, tests and skeletons of other marine organisms.
Fig. 4 in Biological response to geochemical and hydrological processes in a shallow submarine cave
Fig. 4: Living communities inside the Y-Cave: A) the entrance part of the cave, vertical wall, depth 9 m, biocenosis of semi-dark caves (GSO, see text for explanation of acronym) dominated by numerous sponge species; B) the entrance part of the cave, ceiling, depth 6 m, GSO dominated by scleractinian coral Leptopsammia pruvoti; C) the entrance part of the cave, overhang, depth 7 m, GSO dominated by scleractinian coral Madracis pharensis; D) the entrance part of the cave, vertical wall (near the bottom), depth 9 m, GSO, a large specimen of the orange sponge Agelas oroides dominates the photo; E) the middle part of the cave, in front of the section C-C', bottom, depth 10 m, a massive white specimen of the sponge Chondrosia reniformis; F) the middle part of the cave, between sections C-C' and D-D', vertical wall and overhang, depth 5 m, the transition from GSO to biocenosis of caves and ducts in total darkness (GO, see text for explanation of acronym), the community is dominated by serpulids; G) the middle part of the cave, between sections C-C' and D-D', vertical wall, depth 5 m, transition from GSO to GO, a dense population of brachiopod Novocrania anomala, encrusting sponge Placospongia decorticans and serpulids; H) the end part of the cave, near the section G-G', vertical wall with overhang and horizontal shelf, depth 6 m, GO with scarce calcareous sponges and serpulids (see Fig. 2 for position of the sections).
Fig. 1 in Biological response to geochemical and hydrological processes in a shallow submarine cave
Fig. 1: The non-linear relationship between CO and Ca2+ con2 centrations in H 2O-CO2-CaCO3 solution. Each mixture (e.g. C) of the saturated solutions A and B lies on the straight line between them in the zone of undersaturation with respect to calcite, producing an aggressive solution that dissolves the surrounding carbonate (after Gabrovšek & Dreybrodt (2010)).
Fig. 8 in Biological response to geochemical and hydrological processes in a shallow submarine cave
Fig. 8: Temperature, salinity and depth profiles recorded with the CTD probe during a dive inside the Y-Cave (August 27, 2003), 1 – vertical profile at the cave opening; 2 – vertical profile inside the cave entrance part; 3 – vertical profile at the turning point, section C-C'; 4 to 6 – vertical profiles in the inner part of the cave: 4 at approximately section E-E', 5 at approximately section G-G' and 6 at approximately section H-H'.
Fig. 3 in Biological response to geochemical and hydrological processes in a shallow submarine cave
Fig. 3: The positions of temperature and light intensity data loggers inside the Y-Cave (dark circles - temperature data loggers; white circles - light intensity data loggers). Four loggers with their photosensitive cell facing upwards are marked with a black dot; the remaining cells were positioned to face the entrance of the cave.
Fig. 9 in Biological response to geochemical and hydrological processes in a shallow submarine cave
Fig. 9: Variation of light intensity over a period of 11 days (June 19–30, 2006) at representative sites within the Y-Cave (Fig. 3): logger 1 – the entrance of the cave; logger 4 – the central part of the cave; logger 10 – the innermost part of the cave.
Fig. 6 in Biological response to geochemical and hydrological processes in a shallow submarine cave
Fig. 6: The comparison of the tidal (solid line) and temperature (dashed line) fluctuation from February 2–8, 2004. Temperature records are from logger 4 (Fig. 3), and tides from the nearest tide gauge in Zadar port.
Fig. 7 in Biological response to geochemical and hydrological processes in a shallow submarine cave
Fig. 7: Vertical temperature profiles inside and outside the YCave taken with the CTD probe (August 27, 2003); the profile labelled with a dotted line was taken at approximately section H-H', the profile labelled with a solid line at approximately section G-G'.
Fig. 2 in Biological response to geochemical and hydrological processes in a shallow submarine cave
Fig. 2: The location, cross-section and layout of the Y-Cave on Dugi Otok Island, Croatia, with characteristic profiles.
Happy Mother - Healthy Baby: Supplement Study on Biological Processes Underlying Anxiety During Pregnancy
ClinicalTrials.gov study NCT04566861. IPD Sharing: YES. Countries: 1. Publications: 4.
Custom made python script using network assignment and scoring to estimate the impact of biological processes.
Open the record for dataset details and reuse information.
Local plant diversity and soybean biological control 2011 Harvest Measures:Biodiversity II: Effects of Plant Biodiversity on Population and Ecosystem Processes
Biodiversity II (E120) is designed to determine how the number of plant species affects the dynamics of ecological processes at the population, community, and ecosystem levels. By experimentally manipulating the number of species and the kinds of species, the amount of plant growth and the change from year to year, that result can be examined. Plots are large (9m x 9m actively maintained) and well-replicated, allowing responses of plant pathogens, insect herbivores, seed predators, soil parameters, invasive plant species and other variables to also be studied. Plots were seeded in May 1994 to have 1, 2, 4, 8, or 16 species, with roughly 30 replicates of each diversity level. The species composition of each plot was chosen by random draw from a pool of 18 grassland perennials that included four warm-season (C4) grasses, four cool-season (C3) grasses, four legumes, four non-legume forbs, and two woody species. All species occur in monoculture allowing comparison of responses of each species in monoculture to combinations of these same species. The experiment was established in 1994 by the lead investigators David Tilman, Peter Reich, Johannes Knops, and David Wedin. Experiment 120 is similar to Experiment 123, but it uses larger plots to provide a large capacity for long-term subexperiments.
Local plant diversity and soybean biological control 2012 Aphid Surveys:Biodiversity II: Effects of Plant Biodiversity on Population and Ecosystem Processes
Biodiversity II (E120) is designed to determine how the number of plant species affects the dynamics of ecological processes at the population, community, and ecosystem levels. By experimentally manipulating the number of species and the kinds of species, the amount of plant growth and the change from year to year, that result can be examined. Plots are large (9m x 9m actively maintained) and well-replicated, allowing responses of plant pathogens, insect herbivores, seed predators, soil parameters, invasive plant species and other variables to also be studied. Plots were seeded in May 1994 to have 1, 2, 4, 8, or 16 species, with roughly 30 replicates of each diversity level. The species composition of each plot was chosen by random draw from a pool of 18 grassland perennials that included four warm-season (C4) grasses, four cool-season (C3) grasses, four legumes, four non-legume forbs, and two woody species. All species occur in monoculture allowing comparison of responses of each species in monoculture to combinations of these same species. The experiment was established in 1994 by the lead investigators David Tilman, Peter Reich, Johannes Knops, and David Wedin. Experiment 120 is similar to Experiment 123, but it uses larger plots to provide a large capacity for long-term subexperiments.
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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.