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189 results for “Biophysics”
Shared biophysical mechanisms determine early biofilm architecture development across different bacterial species
<p>These data are the numerical values that underlie the Figures 1 - 4, and the Supplementary Figures 1 - 10 for the article "Shared biophysical mechanisms determine early biofilm architecture development across different bacterial species" by the same authors. The content of the data files is organized according to the figures and figure panels of this article. </p>
Distribution of Biophysical Feasibility of Mangrove Reforestation in China and Southeast Asia
<p><a target="_blank">The spatially-explicit opportunities map for mangrove reforestation in China and Southeast Asia, a global hotspot of mangrove loss, used long-term satellite observations and a habitat suitability assessment. Extensive mangrove losses occurred in the region (165,079 ha), primarily caused by aquaculture expansion. Our results identify approximately 60% of the lost mangrove areas as biophysical feasibility for reforestation, primarily along the eastern coastlines of Indonesia. Mangroves reforestation in these areas could provide a climate change mitigation benefit of 26-28 Mt C.</a></p>
CEOS LPV DIRECT V2.1: A database of upscaled LAI, FAPAR and Fcover values for satellite biophysical product validation
<p>Ground references of high quality are needed to validate satellite-based products. The DIRECT V2.1 database compiles Leaf Area Index (LAI), fraction of absorbed photosynthetically active radiation (FAPAR) and fraction of vegetation cover (FCover) averaged values over a 3 km x 3 km area. The ground data was upscaled using high spatial resolution imagery following CEOS WGCV LPV (so called CEOS LPV) LAI validation good practices (Fernandes et al., 2014) to properly account for the spatial heterogeneity of the site. Ground measurements performed during several international Cal/Val activities, including VALERI, BigFoot, SAFARI-2000, CCRS, Boston University, were compiled by S. Garrigues (Garrigues et al., 2008) in the DIRECT database, and later ingested in the CEOS LPV OLIVE tool (Weiss et al., 2014) for accuracy assessment.</p> <p>F. Camacho reviewed DIRECT to remove those sites without understory measurements (Camacho et al., 2013) and after that expanded the database adding the ImagineS network of sites (Camacho et al., 2021). DIRECT V2.1 is the last update including 44 new sites from China (Fang et al., 2019; Song et al., 2021) and 2 more sites from ESA FRM4Veg project (Brown et al., 2021).</p> <p>The CEOS LPV DIRECT V2.1 database constitutes a major effort of the international community to provide ground reference for the validation of satellite-based LAI and FAPAR ECVs, with a total of 176 sites around the world (7 main biome types) and 280 LAI values, 128 FAPAR and 122 FCOVER values covering the period from 2000 to 2021.</p> <p> </p> <p><strong><u>Data description</u></strong></p> <ul> <li>LAI, LAIeff, FAPAR and FCOVER upscaled values over 3 km x 3 km.</li> <li>LAI_NoUnderstory, refers to sites where only overstory was measured and thus are not recommended for accuracy assessment of satellite products.</li> </ul> <p><strong><u>File contents</u></strong></p> <p>A Header " Sites":</p> <p>General information for each site (coordinates, landcover, method, reference)</p> <p>For each variable:</p> <ul> <li># number of the site (site description in Sites)</li> <li>Lat_cen, latitude centre of 3km x 3km</li> <li>Lon_cen, longitude centre of 3km x 3km</li> <li>Site name, name of the site</li> <li>Date, MM/DD/YYYY</li> <li>Mean, average value over 3km x 3km</li> <li>Uncert, uncertainty over 3 km x 3km (STD)</li> </ul> <p> </p>
Fig.1 in Preliminary Biophysical Assessment Of Forest Ecosystem Services: Two Model Area Examples
Fig.1. Ecosystem service class: biomass energy products. Indicator: potential energy wood supply within felling limits.
Fig. 2 in Preliminary Biophysical Assessment Of Forest Ecosystem Services: Two Model Area Examples
Fig. 2. Ecosystem service class: global climate regulation by reduction of GHG concentration. Indicator: Estimated carbon stock in live above-ground tree biomass.
Supporting biophysical data for "The ecosystem wilting point defines drought response and recovery of a Quercus-Carya forest"
<p>The data in this product support analyses in the paper titled "The ecosystem wilting point defines drought response and recovery of a Quercus-Carya forest".</p> <p>The data in this submission include leaf area index (LAI_MOFLUX_2008_2009_2012.csv) and soil water retention curves (MOFLUX_SWRC_data.csv).</p> <p><strong>Leaf area index</strong></p> <p>Each data record in LAI_MOFLUX_2008_2009_2012.csv consists of transect level mean single-sided leaf area index (LAI) values for 5 transects measured during the growing seasons of years 2008, 2009, and 2012. Records are uniquely identified by Year and DOY (day of year). Data were collected using a plant canopy analyzer (model LAI-2000). Data columns are defined by headers. Missing data are represented by values of -9999.</p> <p>Table 1. Header definitions of LAI_MOFLUX_2008_2009_2012.csv data file.</p> <table> <tbody> <tr> <td>Column</td> <td>Header name</td> <td>Definition</td> </tr> <tr> <td>1</td> <td>Year</td> <td>Year of observation</td> </tr> <tr> <td>2</td> <td>DOY</td> <td>Day of year of observation</td> </tr> <tr> <td>3</td> <td>LAI_SE</td> <td>Mean LAI of southeast transect</td> </tr> <tr> <td>4</td> <td>LAI_S</td> <td>Mean LAI of south transect</td> </tr> <tr> <td>5</td> <td>LAI_SW</td> <td>Mean LAI of southwest transect</td> </tr> <tr> <td>6</td> <td>LAI_W</td> <td>Mean LAI of west transect</td> </tr> <tr> <td>7</td> <td>LAI_NW</td> <td>Mean LAI of northwest transect</td> </tr> </tbody> </table> <p><strong>Soil water retention curves</strong></p> <p>Soil water retention curves for two soil depth ranges (0-30 cm and >30 cm) are reported in MOFLUX_SWRC_data.csv. Soil samples were collected near the MOFLUX tower. Samples were evaluated periodically for soil water potential using a dewpoint potentiometer (Decagon Devices, Model WP4C) and a pressure plate as they dried over time.</p> <p>There are 4 columns of data in MOFLUX_SWRC_data.csv. The first two columns contain data for the 0-30 cm depth range, and the second columns contain data for the >30 cm depth range. Each curve is defined by volumetric water content (VWC, %) and soil water potential (SWP, MPa). Missing data are represented by values of -9999.</p> <p> </p>
Example meshes for 'Human brain solute transport quantified by glymphatic MRI-informed biophysics during sleep and sleep deprivation'
<p>Example meshes for 'Human brain solute transport quantified by glymphatic MRI-informed biophysics during sleep and sleep deprivation'</p> <p>The meshes contain DTI. To read the mesh to FEniCS, see e.g., <a href="https://github.com/bzapf/braintransport/blob/24ba4e37a3d6fadb37c249ca7f717a7355f48f30/optimal_velocity/postprocess_phi.py#L12">here </a>.</p> <p>Find the simulation codes for the manuscript here:</p> <p><a href="https://github.com/bzapf/braintransport">https://github.com/bzapf/braintransport</a></p>
Combining Solid-State NMR with Structural and Biophysical Techniques to Design Challenging Protein-Drug Conjugates
<p>Solid-state NMR spectra (DARR and NCA) of rehydrated freeze-dried free TTR and TTR in the presence of Tafamidis and Taf-PTX</p> <p>Reference citation: Combining Solid-State NMR with Structural and Biophysical Techniques to Design Challenging Protein-Drug Conjugates. Angew Chem Int Ed Engl. 2023 Jun 5:e202303202. doi: 10.1002/anie.202303202. PMID: 37276329.</p>
Uncovering circuit mechanisms of current sinks and sources with biophysical simulations of primary visual cortex
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Quantitative modulation of a spatial enhancer through the biophysical properties of a transcription factor binding site
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Microscopy and biophysical data for: Synthetic control of actin polymerization and symmetry breaking in active protocells
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Data from: Parameters used in the endotherm biophysical model for each species
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Data for: Economic and biophysical limits to seaweed farming for climate change mitigation
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Biophysical Controls on Sediment Suspension in South Bay, VA 2013-2014
Research was conducted in South Bay, Virginia, a shallow (1-2 m mean depth) subtidal coastal bay on the Delmarva Peninsula. Hydrodynamic measurements including current velocity, wave characteristics, shear stress, as well as biological samples, light and SSC data were recorded for 1-3 weeks over 2 consecutive years during the spring, summer, fall and winter seasons. See: Ross Timmerman 2014. Biophysical Controls on Sediment Suspension in a Shallow Coastal Bay. M.S. Thesis, University of Virginia. Data tables are included for sediment characteristics, wave height, wave vector measurements and light.
Data from: A multiscale biophysical model for the recruitment of actin nucleating proteins at the membrane interface
<p>The dynamics and organization of the actin cytoskeleton are crucial to many cellular events such as motility, polarization, cell shaping, and cell division. The intracellular and extracellular signaling associated with this cytoskeletal network is communicated through cell membranes. Hence the organization of membrane macromolecules and actin filament assembly are highly interdependent. Although the actin-membrane linkage is known to happen through many routes, the major class of interactions is through the direct interaction of actin-binding proteins with the lipid class containing poly-phosphatidylinositols (PPIs). Among the PPIs, phosphatidylinositol bisphosphate (PI(4,5)P<sub>2</sub>) acts as a significant factor controlling actin polymerization in the proximity of the membrane by binding to actin-associated proteins. The molecular interactions between these actin-binding proteins and the membrane lipids remain elusive. Here, using molecular modeling, analytical theory, and experimental methods, we investigate the binding of three different actin-binding proteins, mDia2, NWASP, and gelsolin, to membranes containing PI(4,5)P<sub>2</sub> lipids. We perform molecular dynamics simulations on the protein-bilayer system and analyze the membrane binding in the form of hydrogen bonds and salt bridges at various PI(4,5)P<sub>2</sub> and cholesterol concentrations. Our experimental study with PI(4,5)P<sub>2</sub>-containing large unilamellar vesicles mimics the computational experiments. Using the multivalencies of the proteins obtained in molecular simulations and the cooperative binding mechanisms of the proteins, we also propose a multivalent binding model that predicts the actin filament distributions at various PI(4,5)P<sub>2 </sub>and protein concentrations.</p>
Data for "Bayesian inference for biophysical neuron models enables stimulus optimization for retinal neuroprosthetics"
<p>Experimental and precomputed data for the paper "Bayesian inference for biophysical neuron models enables stimulus optimization for retinal neuroprosthetics" by Oesterle et al. 2020 (DOI: <a href="https://doi.org/10.7554/eLife.54997">10.7554/eLife.54997</a>).</p> <p>The cone bipolar cell data has been described and published in the paper "Inhibition decorrelates visual feature representations in the inner retina" by Franke et al. 2017 (DOI: <a href="https://doi.org/10.1038/nature21394">10.1038/nature21394</a>). </p> <p>This data is both a supplement to the Oesterle et al. paper and the code for this paper.</p> <p>The code is available in this <a href="http://github.com/berenslab/CBC_inference">GitHub repository</a>.</p> <p>We recommend downloading the GitHub repository and to follow the instructions there.</p>
Data from: Non-invasive biophysical measurement of travelling waves in the insect inner ear
Frequency analysis in the mammalian cochlea depends on the propagation of frequency information in the form of a travelling wave (TW) across tonotopically arranged auditory sensilla. TWs have been directly observed in the basilar papilla of birds and the ears of bush-crickets (Insecta: Orthoptera) and have also been indirectly inferred in the hearing organs of some reptiles and frogs. Existing experimental approaches to measure TW function in tetrapods and bush-crickets are inherently invasive, compromising the fine-scale mechanics of each system. Located in the forelegs, the bush-cricket ear exhibits outer, middle and inner components; the inner ear containing tonotopically arranged auditory sensilla within a fluid-filled cavity, and externally protected by the leg cuticle. Here, we report bush-crickets with transparent ear cuticles as potential model species for direct, non-invasive measuring of TWs and tonotopy. Using laser Doppler vibrometry and spectroscopy, we show that increased transmittance of light through the ear cuticle allows for effective non-invasive measurements of TWs and frequency mapping. More transparent cuticles allow several properties of TWs to be precisely recovered and measured in vivo from intact specimens. Our approach provides an innovative, non-invasive alternative to measure the natural motion of the sensilla-bearing surface embedded in the intact inner ear fluid.
Supplemental Movie for "The basis of sharp spike onset in standard biophysical models"
<p>Simulation of extracellular field during action potential.</p>
Simulations For: Biophysical basis of filamentous phage tactoid-mediated antibiotic tolerance in P. aeruginosa
<p>Coordinate, simulation input and simulation output files for atomistic molecular dynamics simulations in Biophysical basis of filamentous phage tactoid-mediated antibiotic tolerance in P. aeruginosa. </p><p> </p>
Data for: Predation and biophysical context control long-term carcass nutrient inputs in an Andean ecosystem
<p>Animal carcass decomposition is an often-overlooked component of nutrient cycles. The importance of carcass decomposition for increasing nutrient availability has been demonstrated in several ecosystems, but impacts in arid lands are poorly understood. In a protected high desert landscape in Argentina, puma predation of vicuñas is a main driver of carcass distribution. Here, we sampled puma kill sites across three habitats (plains, canyons, and meadows) to evaluate the impacts of vicuña carcass and stomach decomposition on soil and plant nutrients up to 5 years after carcass deposition. Soil beneath both carcasses and stomachs had significantly higher soil nutrient content than adjacent reference sites in arid, nutrient-poor plains and canyons, but not in moist, nutrient-rich meadows. Stomachs had greater effects on soil nutrients than carcasses. However, we did detect higher plant N concentrations at kill sites. The biogeochemical effects of puma kills persisted for several years and increased over time, indicating that kills do not create ephemeral nutrient pulses, but can have lasting effects on the distribution of soil nutrients. Comparison to broader spatial patterns of predation risk reveals that puma predation of vicuñas is more likely in nutrient-rich sites, but carcasses have the greatest effects on soil nutrients in nutrient-poor environments, such that carcasses increase localized heterogeneity by generating nutrient hotspots in less productive environments. Predation and carcass decomposition may thus be important overlooked factors influencing ecosystem functioning in arid environments.</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.