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45 results for “in situ experiment”
Underwater Photosynthetically Active Radiation (PAR) from in-situ Lake Primary Production Experiments in the McMurdo Dry Valleys of Antarctica (1995-2024, ongoing)
As part of the Long Term Ecological Research (LTER) project in the McMurdo Dry Valleys of Antarctica, PAR is measured at one depth during primary production experiments in Dry Valley Lakes. This data set quantifies instantaneous underwater PAR at 10-meter depths in Lakes Bonney and Hoare, and at 7-meter depth in Lake Fryxell (depths vary after 2008, check data file for actual depth). Ambient PAR was also measured at the air-ice interface from each of these lakes.
Immunoglobulin G: SEC-SAXS experiment using in house SAXS instrument with in situ UV-Vis
<p>SEC-SAXS experiment using in house SAXS instrument</p> <p>Sample: Immunoglobuline G<br>Buffer: 50mM Tris, 50 mM NaCl, pH 7.6</p> <table> <tbody> <tr> <td><strong>File Name</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>SAXS_raw.zip</td> <td>Raw, unreduced data (2D images) in HDF5 format</td> </tr> <tr> <td>SAXS_reduced.zip</td> <td>SAXS data, azimutaly reduced (1D curves). Q-vaules are in 1/nm</td> </tr> <tr> <td>SAXS_UV_raw.zip</td> <td>Raw UV-Vis absorption data collected using in-situ spectrometer</td> </tr> <tr> <td>SAXS_UV_processed.zip</td> <td>UV-Vis data collected using in-situ spectrometer. Absorbance at 280nm extracted as a time series</td> </tr> <tr> <td>HPLC_raw.zip</td> <td>Data from HPLC system natively exported from control software (Unicorn)</td> </tr> <tr> <td>HPLC_extracted.zip</td> <td>Data from HPLC system exported to CSV</td> </tr> <tr> <td>DS11_fractions.zip</td> <td>UV-Vis absorption data collected usig micro volume spectrometer (DeNovix DS-11) on fractions collected using fraction collector.</td> </tr> </tbody> </table> <p> </p>
A Dataset for In-situ synchrotron tomography experiments to investigate anisotropic damage of line pipe steel
<p>In this study, anisotropic ductility and associated damage mechanisms of a grade X100 line pipe steel were investigated using in-situ synchrotron-radiation computed tomography (SRCT) of notched round bars. Line pipe materials have anisotropic mechanical properties, such as tensile strength, ductility and toughness. Specimens were tested for loading along both rolling (L) and transverse (T) directions. The <em>in-situ</em> data collected allowed quantifying both specimen deformation (evolution of the cross section) and microscopic damage parameters such as porosity, void shape and void orientation. The data sets provide here are related to the paper <em>"On the origin of the anisotropic damage of X100 line pipe steel, Part I: in-situ synchrotron tomography experiments"</em> being published in <a href="https://www.springer.com/journal/40192">Integrating Materials and Manufacturing Innovation</a>. For each testing direction, dataset are provided using hdf5 and xdmf standarded exchange format. A compressed file is also provided in connection with the analyses explained in the article.</p>
Data-Mining of In-Situ TEM Experiments: Towards Understanding Nanoscale Fracture
<p>Datasets for the publication in the "Computational Materials Science". This is essentially a snapshot of the gitlab repository https://gitlab.com/computational-materials-science/public/publication-data-and-code/2022-data-mining-of-in-situ-tem-experiments that might contain additional updates and scripts. A version of the manuscript can also be found at https://arxiv.org/abs/2206.11355</p>
Data from: Multimodal in situ datalogging quantifies inter-individual variation in thermal experience and persistent origin effects on gaping behavior among intertidal mussels (Mytilus californianus)
In complex habitats, environmental variation over small spatial scales can equal or exceed larger-scale gradients. This small-scale variation may allow motile organisms to mitigate stressful conditions by choosing benign microhabitats, whereas sessile organisms may rely on other behaviors to cope with environmental stresses in these variable environments. We developed a monitoring system to track body temperature, valve gaping behavior, and posture of individual mussels (Mytilus californianus) in field conditions in the rocky intertidal zone. Neighboring mussels' body temperatures varied by up to 14°C during low tides. Valve gaping during low tide and postural adjustments, which could theoretically lower body temperature, were not commonly observed. Rather, gaping behavior followed a tidal rhythm at a warm, high intertidal site; this rhythm shifted to a circadian period at a low intertidal site and for mussels continuously submerged in a tidepool. However, individuals within a site varied considerably in time spent gaping when submerged. This behavioral variation could be attributed in part to persistent effects of mussels' developmental environment. Mussels originating from a wave-protected, warm site gaped more widely, and they remained open for longer periods during high tide than mussels from a wave-exposed, cool site. Variation in behavior was modulated further by recent wave heights and body temperatures during the preceding low tide. These large ranges in body temperatures and durations of valve closure events - which coincide with anaerobic metabolism - support the conclusion that individuals experience "homogeneous" aggregations such as mussel beds in dramatically different fashion, ultimately contributing to physiological variation among neighbors.
Fig. 8 in In situ experiments on the effect of low pH on the ultrastructure of the seagrasses Cymodocea nodosa and Posidonia oceanica Abstract
Fig. 8: A-H. TEM micrographs of young epidermal cells of C. nodosa after three weeks transfer at S2 area. A. Surface view of epidermal cells. They are disorganized and most of the organelles are not easily seen. B. Epidermal cell with wavy cell walls and a central nucleus with loose and partially disrupted nuclear membrane. C. A group of peripherally distributed mitochondria containing a rather amorphous mass of destroyed cristae. D. Dictyosome with rounded and loose cisternae. E. Disorganized chloroplasts with remnants of thylakoids and starch grains. F. Cortical cytoplasmic area with disorganized mitochondria and inflated ER fragments. G. Higher magnification of inflated fragments of RER with attached electron-dense material. H. ER membrane-like network with projecting edges filled with electron-dense material. Scale bars = 2 μm (A), 1μm (B) 0.5μm (C), 0.2 (D, E, F) and 0.1 (G, H).
Fig. 6 in In situ experiments on the effect of low pH on the ultrastructure of the seagrasses Cymodocea nodosa and Posidonia oceanica Abstract
Fig. 6: A-E. TEM micrographs of young epidermal cells of C. nodosa after three weeks transfer at S1 area. A. Group of epidermal cells that appear empty, with most of the cell elements disorganized and distorted. B. Higher magnification of a nucleus with condensed masses of chromatin which covered most of the nucleoplasm. The nuclear membrane appears loose and discontinuous. C. Cytoplasmic area showing dictyosomes with few cisternae and numerous swollen fragments of rough ER (RER) D. Fragmented ER membranes traversing the cortical cytoplasm. E. Disorganized chloroplasts with large starch grains surrounded by a system of electron-dense elongated or round plastoglobuli. Mitochondria with a few broken and sometimes dilated cristae are also observed. Scale bars = 1 μm (A), 0.5μm (B, C, E) and 0.2μm (D).
Fig. 5 in In situ experiments on the effect of low pH on the ultrastructure of the seagrasses Cymodocea nodosa and Posidonia oceanica Abstract
Fig. 5: A-C. TEM micrographs of young epidermal cells of P. oceanica after one week transfer at S2 area. A. Epidermal cell with increased number of chloroplasts and mitochondria. B. Chloroplast with oval-shaped and rod-like plastoglobuli around starch grains. Mitochondria with very few fragmented cristae are also visible. C. Dictyosomes and fragmented ER network extended along the cell periphery. Scale bars = 1 μm (A), and 0.5μm (B, C).
Fig. 9 in In situ experiments on the effect of low pH on the ultrastructure of the seagrasses Cymodocea nodosa and Posidonia oceanica Abstract
Fig. 9: A-F. TEM micrographs of young epidermal cells of P. oceanica after three weeks transfer at S2 area. A. Group of epidermal cells that appear distorted, with wavy cell walls. B. Part of an epidermal cell with a central nucleus with disorganized nuclear membrane. The nucleus is surrounded by remnants of cell organelles and an electron-dense ER network. C. Chloroplasts with remnants of thylakoids and plastoglobuli, and disorganized mitochondria. Both appear empty and destroyed. D. Starch grains from disorganized chloroplasts appear dispersed in the cytoplasm. E. Cytoplasmic area with structures of ER network connected and/or filled with electron-dense material. F. Higher magnification of inflated, swollen RER cisternae, filled with electron-dense material. Scale bars = 2 μm (A), 1μm (B) 0.2 (C, D, E,) and 0.1 (F).
Fig. 1 in In situ experiments on the effect of low pH on the ultrastructure of the seagrasses Cymodocea nodosa and Posidonia oceanica Abstract
Fig. 1: A-E. TEM micrographs of young epidermal cells of C. nodosa control material. A. Paradermal section of an epidermal cell. Note its orthogonal shape, the dense cytoplasm, and the large nucleus occupying most of the cell space. B. Higher magnification of the peripheral part of the cell of Fig. A, showing the cell wall and cortical endoplasmic reticulum (ER). C. Cytoplasmic area taken from a plant transferred for one week to S1 area. Note the increased number of mitochondria, dictyosomes and ER, compared to the control. D. Epidermal cell after transfer for one week from S1. It shows a prominent central nucleus, undifferentiated chloroplasts with few grana and an increased number of mitochondria and ER membranes. E. Higher magnification of a cortical cytoplasmic area of a cell like D showing an extended ER network distributed in the cell periphery. Scale bars = 2 μm (A), 1μm (D) and 0.2μm (B, C, E).
Fig. 3 in In situ experiments on the effect of low pH on the ultrastructure of the seagrasses Cymodocea nodosa and Posidonia oceanica Abstract
Fig. 3: A-E. Interphase epidermal cells of young leaves under different pH levels. In all figures, green represents tubulin immunofluorescence and blue represents Hoechst staining of DNA. A. Transfer of CN to pH 7.8 for 1 week: thick MT bundles showing a slightly aberrant orientation. B. Transfer of PO to pH 7.8 for 1 week: MT bundles oriented perpendicularly to the long leaf axis. C. Transfer of CN to pH 6.8 for 1 week: fragmented MT bundles with slightly aberrant orientations. D. Transfer of CN to pH 7.8 for 3 weeks: short, fragmented, and curved MT bundles with aberrant orientations. E. Transfer of PO at pH 7.8 for 3 weeks: depolymerization and disassembly of interphase MTs with loss of proper orientation. Scale bar = 10 μm.
Fig. 4 in In situ experiments on the effect of low pH on the ultrastructure of the seagrasses Cymodocea nodosa and Posidonia oceanica Abstract
Fig. 4: A-C. TEM micrographs of young epidermal cells of C. nodosa after one week transfer at S2 area. A. Epidermal cell with undifferentiated chloroplasts and increased number of mitochondria. B. Higher magnification of a chloroplast with a few developing grana. C. Higher magnification of a mitochondrion with very few cristae. Scale bars = 0.5 μm (A, B, C).
Fig. 7 in In situ experiments on the effect of low pH on the ultrastructure of the seagrasses Cymodocea nodosa and Posidonia oceanica Abstract
Fig. 7: A-D. TEM micrographs of young epidermal cells of P. oceanica after three weeks transfer at S1 area. A. Part of an epidermal cell of P. oceanica with warped cell walls, distorted cytoplasm, and a large nucleus with condensed chromatin masses. B. Chloroplast with remnants of disorganized cisternae and round plastoglobuli. C. Chloroplasts with large starch grains surrounded by a system of electron-dense elongated and/or round plastoglobuli. Mitochondria with a few broken dilated cristae are visible. D. Fragmented ER membranes arranged along the cell periphery. Scale bars = 1 μm (A), 0.5μm (B, C) and 0.2μm (D).
Litterfall production and litter decomposition experiments: in-situ datasets of nutrient fluxes in two Bornean lowland rain forests associated with Acacia invasion
<p>This dataset contains the original data from which the figures and tables for the article "Differential impacts of <em>Acacia</em> invasion on nutrient fluxes in two distinct Bornean lowland tropical rain forests" were prepared. It documents parameters relevant to nutrient fluxes via litterfall production and leaf litter decomposition rates from 2016 to 2017 in two selected lowland rainforests in Brunei Darussalam that are associated with <em>Acacia</em> invasion. Both litterfall sample collection and litter decomposition bag experiments followed standard protocols. Leaf litterfall fractions from the litterfall production experiment were analysed for nutrient contents of nitrogen (N), phosphorus (P), potassium (K), magnesium (Mg), and calcium (Ca). Nutrient addition and nutrient use efficiency values were calculated based on nutrient concentration and monthly leaf litterfall production in the different habitat types studied. The mean percentage of litter mass remaining, K day<sup>-1</sup>, K year<sup>-1</sup>, half-life t<sub>0.5</sub>, pH values, and nutrient concentrations (N, P, K, Mg, Ca) were calculated for leaf litter samples collected after 336 days in the different habitats.</p>
Data from: Multimodal in situ datalogging quantifies inter-individual variation in thermal experience and persistent origin effects on gaping behavior among intertidal mussels (Mytilus californianus)
Open the record for dataset details and reuse information.
In situ soil N mineralization in gopher mounds and soil under gopher mounds:Experiment 014 - Successional Dynamics on a Resampled Chronosequence
The purpose of this observational study is to describe the dynamics of ecosystem succession. The change in the number, type, and amount of plant and grazing animal species is monitored in more than 20 fields. These fields were previously cultivated, but then abandoned from agriculture at various times in the past. The fields were left undisturbed for plants to develop from seeds within the soil or brought into the fields by wind or animals. Permanent transects have been established in these abandoned fields for purposes of sampling in a consistent location from year to year. Permanent plots along these transects have been used to sample soil nutrients, (in particular, nitrogen) abundance of vegetation, species composition and herbivore populations. The sampling occurs approximately every 6 years. In the initial survey, 100 quadrats of size 1 by 0.5 m were sampled per field in 23 different fields. Abandoned fields included in E014 are 4, 5, 10, 21, 24, 26, 27, 28, 32, 35, 39, 40, 41, 44, 45, 47, 53, 70, 72, 76, 77. Fields 22(B), 29(A), and 69(C) were originally included in E014 but used for other purposes shortly after the start of the study. This experiment was established in 1983 and 1989 by principal investigators Johannes Knops and David Tilman. Past work at CDR and elsewhere has demonstrated an overriding influence of fire frequency in maintaining prairie openings and oak savanna at the prairie-forest border. Fire regimes harm some types of species while favoring others and drive light and nutrient dynamics, which in turn drive community functional attributes and diversity levels. Ultimately, fire frequency interacts with climate, N deposition, land use, and biotic invasion to determine the outcomes of tree-grass interactions and the dynamics of vegetation at ecotones such as the prairie-forest border in Minnesota. In 2006 each field was divided in half, and one half randomly chosen for periodic prescribed burning (a fire every other year). We anticipate that th
Data reduction for in situ synchrotron tomography experiments
<p>This dataset corresponds to a series of phase-enhanced tomographic images recorded during a monotonic mechanical tensile test with a polymer material.<br> <br> Tomographic measurements were performed at the PSICHE beamline, SOLEIL synchrotron. The reconstructed voxel size is 1.3 µm. The reconstruction was performed with pyHST (filtered back-projection) using the paganin filter with a propagation distance of 15 pixels. Each tomography measurement consists of 1000 radiographs of 1024×2048 pixels acquired over 180°. The binary reconstructed volumes are therefore 1024×2048×2048 voxels encoded with a dynamic range of 32 bits (floating-point).<br> <br> The 44 measurements taken during the mechanical test represent a volume of 700 GB. The reduction strategy used is based on a thresholding of the specimen in each volume and a zeroing of the voxels outside the sample. In the preserved voxels, the binary representation of each value is truncated to have a precision of the order of the experimental uncertainties: the insignificant least significant bits are replaced by 0s which, combined with a transposition of the order of the bits just before compression (bit shuffling), makes it possible to drastically increase the compressibility of the data. The data is arranged in an HDF5 container using block access with on-the-fly compression/decompression. The total size of the dataset is thus reduced with a reduction ratio of 16:1 using Zstandard level 1. The mask used as well as even smaller volumes (pixel binning 2×2 and 4×4, dynamic range reduction on 4 or 8 bits) are added to allow fast access to very small data if needed, in the same fashion as the thumbnail used in some 2D image formats.<br> <br> The footprint of the reduced version as described is 47 GB. The format is self-described and contains additional metadata.</p>
Data for the publication "Hydrogen penetration into the NiTi superelastic alloy investigated in-situ by synchrotron diffraction experiments"
<p>This dataset contains the data to the research paper "Hydrogen penetration into the NiTi superelastic alloy investigated in-situ by synchrotron diffraction experiments". The paper describes a<span> microstructural evolution caused by a hydrogen permeation into the NiTi superelastic alloy, which was investigated in-situ using the X-ray synchrotron diffraction. The diffraction data, electrochemical data, TEM pictures, lattice parameters for ab-initio DFT calculations and input parametrs for FEM calculations are included.</span></p>
Videos: The crystallization mechanism of gel-derived SiO2-TiO2 amorphous nanobeads elucidated by high-temperature in-situ experiments
<p>Supplementary materials detailing high-temperature in-situ TEM experiments.</p> <p>Main article available at: <a href="https://doi.org/10.1021/acs.cgd.3c00300">https://doi.org/10.1021/acs.cgd.3c00300</a></p> <p> </p>
Data from: Macrofouling communities and the degradation of plastic bags in the sea: an in situ experiment
The increasing amount of plastic littered into the sea may provide a new substratum for benthic organisms. These marine fouling communities on plastic have not received much scientific attention. We present, to our knowledge, the first comprehensive analysis of their macroscopic community composition, their primary production and the polymer degradation comparing conventional polyethylene (PE) and a biodegradable starch-based plastic blend in coastal benthic and pelagic habitats in the Mediterranean Sea. The biomass of the fouling layer increased significantly over time and all samples became heavy enough to sink to the seafloor. The fouling communities, consisting of 21 families, were distinct between habitats, but not between polymer types. Positive primary production was measured in the pelagic, but not in the benthic habitat, suggesting that large accumulations of floating plastic could pose a source of oxygen for local ecosystems, as well as a carbon sink. Contrary to PE, the biodegradable plastic showed a significant loss of tensile strength and disintegrated over time in both habitats. These results indicate that in the marine environment, biodegradable polymers may disintegrate at higher rates than conventional polymers. This should be considered for the development of new materials, environmental risk assessment and waste management strategies.
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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.