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1,084 results for “substrate”
Substrate recognition and cryo-EM structure of the ribosome-bound TAC toxin of Mycobacterium tuberculosis
<p>Datasets for the Figures 2 and S2 of the manuscript "Substrate recognition and cryo-EM structure of the ribosome-bound TAC toxin of Mycobacterium tuberculosis".</p> <p> </p> <p>The HTML files describe the analysis and the raw counts after nEMOTE-conv treatment.</p> <p>There are 5 files for each MMEMOTExx dataset:</p> <p>EmoteBarcodesReport.csv = summary<br> UnambNegTable.csv = counts of unique cuts on the reverse strand<br> UnambPosTable.csv = counts of unique cuts on the forward strand<br> AmbPosTable.csv = counts of all cuts on the forward strand<br> AmbNegTable.csv = counts of all cuts on the reverse strand</p> <p> </p>
Benchmark: Axisymmetric liquid droplets on viscoelastic substrates
<p>We report on the data from a numerical benchmark of a stationary axisymmetric droplet on viscoelastic Neo-Hookean substrates obtained using FEniCS. Numerical results using our Lagrangian phase-field approach are compared with results by Van Brummelen et al. and by Aland & Mokbel.</p>
Elevational patterns in tropical bryophyte diversity differ among substrates: a case study on Baru volcano, Panama
<p><strong>Questions. </strong>Bryophytes attain their highest diversity in tropical mountain forests. Although distribution patterns have been described, little emphasis has been placed on comparing patterns among substrates (e.g., terrestrial, epiphytic). Understanding these patterns is important, because they determine not only the pool of genetic resources, but also the functioning of these forest ecosystems. Therefore, we studied how bryophyte species diversity changes with elevation, how elevational patterns differ between substrate types, and how elevational trends relate to environmental drivers.</p> <p><strong>Location. </strong>Baru Volcano, Panama.</p> <p><strong>Methods. </strong>At each of eight elevations, between 1900 and 3300 m, bryophytes were collected in 600-cm<sup>2</sup> plots from six substrate types with four replicates. Species cover was registered as a measure of relative abundance. Species richness and community structure were determined and related to elevation, substrate types, and environmental drivers at three scales (plots, sets of four replicate plots per substrate per elevation, and all plots at each elevation).</p> <p><strong>Results. </strong>Bryophyte species richness decreased towards higher elevations, at all three scales and on all substrates except bryophytes on soil, for which, at the plot scale, richness peaked at higher elevations than on the other substrates. Relative humidity explained richness slightly better than elevation. Communities at the lowest elevations had the most uneven compositions, due to the presence of many small species with low abundance.</p> <p><strong>Conclusions. </strong>In studies on the spatial distribution of bryophyte diversity, it is essential to consider different substrates and spatial scales separately. If substrates differ in their elevational species-richness patterns, climate and land-use change may affect bryophyte diversity patterns not only directly, but also indirectly via changes in substrate availability. Therefore, a better understanding of the spatial variation in bryophyte diversity in mountains is essential to elucidate the effects of environmental change on this important group of plants and their implications for ecosystem functioning.</p> <p>FILE: Main data base_JVC.xlsx</p> <p>Sheet=TaxonomicInformation</p> <p>Our database contains taxonomic information on bryophyte species collected along an elevation gradient on the Baru volcano, Panama.</p> <p>Sheet=data</p> <p>The relative abundance of each species or morpho-species is included per 600-cm2 plot in each of the six considered substrates (soil = terricolous, rock = saxicolous, decomposing downed log (i.e. lying on the ground) = lignicolous, tree base = epiphytic on tree base, tree trunk = epiphytic on tree trunk, and understorey branch = epiphytic on branch).</p> <p>Sheet: climatic info<br> In addition, we present the information on the climate recorded between April and December 2017.<br> Acronyms: elev: elevation, tempmean: mean temperature over the measurement period (°C), tempmin: minimum temperature over the measurement period (°C), tempmax: maximum temperature over the measurement period (°C), rhmean: mean relative humidity over the measurement period (%), rhmin: minimum relative humidity over the measurement period (%), rhmax: maximum relative humidity over the measurement period (%), cancov: canopy-cover (%), heican: height of the canopy ( m).</p>
Effect of different feeding substrates on the production of in-sect-derived frass fertilizers for effective alleviation of ammonium (NH4+) toxicity - Raw Data and Supplementary Materials
<p>Raw data and Supplementary Materials for the submitted Article Titled: "Effect of different feeding substrates on the production of in-sect-derived frass fertilizers for effective alleviation of ammonium (NH4+) toxicity". Submitted to Agronomy-Basel MDPI. </p>
La2NiO4+δ-Based Memristive Devices Integrated on Si-Based Substrates
<p>Data for publication: La<sub>2</sub>NiO<sub>4+δ</sub>-Based Memristive Devices Integrated on Si-Based Substrates</p>
Electronic Supplementary Information: Impact of a suspension drop onto a hot substrate: diminution of splash and prevention of film boiling
<p>This database includes Electronic Supplementary Information for <em>Soft Matter </em>manuscript: Impact of a suspension drop onto a hot substrate: diminution of splash and prevention of film boiling. </p> <p>The supplementary videos to Fig. 4: </p> <ul> <li>supplementary_video_fig_4_a-d.mp4</li> <li>supplementary_video_fig_4_e-h.mp4</li> <li>supplementary_video_fig_4_i-l.mp4</li> </ul> <p> </p> <p>and the supplementary videos to Fig. 12 (please do not regard to the file name)</p> <ul> <li>supplementary_video_fig_11_a-d.mp4</li> <li>supplementary_video_fig_11_e-h.mp4</li> <li>supplementary_video_fig_11_i-l.mp4</li> </ul>
Methane production data for fed-batch assays amended with graphene oxide and two standard substrates
<p>The spreadsheet contains all the data generated using the Automatic Methane Potential Tests System (AMPTS) for fed-batch experiments containing graphene oxide (GO) at 0, 5, 10, and 20 mg of GO per g of volatile solids (VS).</p> <p>Also, the dataset is divided accordingly to the two substrates used, i.e., glucose (G) and microcrystalline cellulose (C).</p>
Substrates and a novel component in hSnd2-dependent ER protein targeting
<p>Protein import into the endoplasmic reticulum (ER) is essential for about 30% of the human proteome. It involves targeting of precursor proteins to the ER and insertion into or translocation across the ER membrane. Furthermore, it relies on signals in the precursor polypeptides and components, which read the signals and facilitate their targeting to a protein-conducting channel in the ER membrane, the Sec61 complex. Compared to the SRP- and TRC-dependent pathways, little is known about the SRP-independent/SND pathway. Our aim was to identify additional components and characterize the client spectrum of the human SND pathway. The established strategy of combining depletion of the central hSnd2-component from HeLa cells with proteomic- and differential protein abundance-analysis was used. The SRP and TRC targeting pathways were analyzed in comparison. TMEM109 was characterized as hSnd3. Unlike SRP but similar to TRC, the SND clients are predominantly membrane proteins with N-terminal, central, or C-terminal targeting signals.</p>
No Escape: The Influence of Substrate Sodium on Plant Growth and Tissue Sodium Responses
<p>This dataset contains data from a systematic review carried out to understand substrate sodium's influence on plant growth and sodium accumulation strategies. Accordingly, we carried out a systematic review of plants' responses to variation in substrate sodium concentrations. We compared biomass and tissue-sodium accumulation among 107 cultivars or populations (67 species in 20 plant families), broadly expanding beyond the agricultural and model taxa for which several generalizations previously had been made. We hypothesized a priori response models for each population's growth and sodium accumulation as a function of increasing substrate NaCl and used Bayesian Information Criterion to choose the best model. Additionally, using a phylogenetic signal analysis, we tested for phylogenetic patterning of responses across taxa. The influence of substrate sodium on growth differed across taxa, with most populations experiencing detrimental effects at high concentrations. Irrespective of growth responses, tissue sodium concentrations for most taxa increased as sodium concentration in the substrate increased. We found no strong associations between type of growth response and type of sodium accumulation response across taxa. Although experiments often fail to test plants across a sufficiently broad range of substrate salinities, non-crop species tended toward higher sodium tolerance than domesticated species. Moreover, some phylogenetic conservatism was apparent, in that evolutionary history helped predict the distribution of total-plant growth responses across the phylogeny, but not sodium accumulation responses. Our study reveals that saltier plants in saltier soils prove to be a broadly general pattern for sodium across plant taxa. Regardless of growth responses, sodium accumulation mostly followed an increasing trend as substrate sodium levels increased.</p>
Accommodating a Hexagonal Zeta-phase Mn2N Film on a Cubic MgO (001) Substrate
<p>The figures associated with this paper can be derived from the following raw data set:</p> <p> </p> <p><strong>Figure 2.opju:</strong> This file contains the numerical data that can be used to generate line profiles shown in the Figure 2. It consist of two set of data for Figure 2(a) and Figure2(b). The data set are clearly labelled. This fie can be opened using Origin software.</p> <p> </p> <p><strong>Figure 3.opju: </strong>This file contains three set of raw data for Fig.3(a), Fig.3(b), and Fig.3(c) used in the mauscript. Those data set can be opened using Origin software.</p> <p> </p> <p><strong>Figure 5.opju: </strong>The raw data for XRD and AES are given in this file. This file contains two sheets and are labellled properly. This also can be opend using Origin software.</p> <p> </p> <p><strong>Figure 6(a).SM4/ Figure 6(c).SM4/Figure 6(d).SM4/: </strong>The raw data for STM images shown in Fig. 6 are given in the .SM4 format. It can be opened in WSxM software or other SPM mage processing software. These files are not drift and scale corrected. To do the drift correction in the image we used corel draw sotware and scanner calibration factors were applied for scale correction.</p> <p> </p> <p><strong>Figure 7.xlsx: </strong>The numerical data for surface formation enery plot given in Fig. 7 is given in this file. It can be opened in Excel/Origin software.</p> <p> </p> <p><strong>Figure 8(b).cube/ Figure 8(d).cube: </strong>The raw file for the simulated STm images are given in these files. These files can be opened in Vesta software.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 10
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 10 comprises an image series of 255 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the T1 detector of the SEM at high vacuum. Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 05
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 05 comprises an image series of 500 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 6 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 03
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 03 comprises an image 3D model of a <em>Giardia lamblia</em> cell adhered to the plastic substrate of a culture dish. The model was generated by segmentation of the entire cell, the cell nuclei (red) and the ventral disc cytoskeleton (yellow) in an image series of 276 images which was recorded by SBF SEM (see dataset 01). Section interval was 50 nm and pixel size 10 nm. The data folder contains the model-file (Imaris-format) and a 360° rotation of the model as video file (mp4-format).</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 02
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 02 comprises an image series of 1462 images recorded of a <em>Giardia lamblia</em> cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.5 mbar). Original pixel size was 5 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 09
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 09 comprises an image series of 400 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 08
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 08 comprises an image series of 299 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 3 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 04
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 04 comprises an image series of 120 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the T1 detector of the SEM at high vacuum. Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 07
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 07 comprises an image series of 318 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 8 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 06
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 06 comprises an image series of 215 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 01
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 01 comprises an image series of 276 images recorded of a <em>Giardia lamblia</em> cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the DBS detector of the SEM at low vacuum (0.5 mbar). Original pixel size was 4 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.