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12,393 results for “Materiality”
Supplementary Material: HIV-1-Induced Small T Cell Syncytia Can Transfer Virus Particles to Target Cells through Transient Contacts
<p>Videos supplementary to <em>Viruses</em> <strong>2015</strong>, <em>7</em>(12), 6590-6603; doi:10.3390/v7122959</p> <p><strong>Captions:</strong></p> <p><strong>Movie S1.</strong> <strong>HIV-1-infected cells in the lymph node of humanized mice.</strong></p> <p>Humanized BLT mice were injected in the footpad with HIV-nGFP, where GFP is highly enriched in cellular nuclei, and the draining popliteal lymph node prepared for MP-IVM at day 2. Representative infected cells (GFP+; green) that display one, two or three discernible nuclei are shown (<strong>top</strong>). In the bottom panels, green fluorescence signals above 80% of the intensity maximum were used to define cell nuclei, which are shown in white. The syncytium with two discernible nuclei remains elongated throughout the recording, while the syncytium with three discernible nuclei switches between coordinated and uncoordinated motility. Each individual frame is a maximum intensity projection of 11 <em>z</em>-stacks spaced 4 μm apart (for a total volume of 40 μm). Time is shown in minutes and seconds. Scale bar = 20 μm. See also Figure 1A.</p> <p><strong>Movie S2.</strong> <strong>Syncytia in the lymph node contact uninfected T cells without undergoing cell-cell fusion</strong>.</p> <p><em>In vitro</em>-generated central memory CD4+ T cells, either infected with HIV-GFP (GFP+; green) or uninfected (labeled with CellTracker Orange; red), were adoptively transferred by footpad injection into BLT mice pretreated with antiretroviral drugs (100 mg/kg FTC, 150 mg/kg TDF). After 12 h, the draining popliteal lymph node was prepared for MP-IVM. Two representative movies of T cell migration prior to (yellow circle) and during<br /> (blue circle) transient interactions with syncytia are shown, demonstrating cellular interactions without fusion. Each individual frame is a maximum intensity projection of 11 <em>z</em>-stacks spaced 4 μm apart (for a total volume of 40 μm). Time is shown in minutes and seconds. Scale bar = 40 μm. See also Figure 1F,G.</p> <p><strong>Movie S3.</strong> <strong>CD4</strong><strong>+ T cells in 3D culture form small syncytia with elongated morphology</strong>.</p> <p>Primary human CD4+ T cells isolated from a healthy donor were infected with VSV-G-pseudotyped NL4-3<sup>Gag-iGFP</sup> virus. The next day, cells were embedded in a 3D collagen gel as described in the Experimental Section, and 12 h later imaged live at 37 °C using a 20× objective on a DeltaVision widefield microscope. Six 3 µm-spaced Z-slices were taken every 20 s, and were subsequently projected into one image. The syncytium seen here in green has two nuclei located at opposite ends, and a central bulged region with high amounts of viral Gag. The diffuse fluorescence is a result of this syncytium being located at a higher part of the gel, where the limitations of widefield imaging become more prominent. See also Figure 2A.</p> <p><strong>Movie S4.</strong> <strong>Small CEM-SS syncytia in 3D culture can dynamically change their morphology</strong>.</p> <p>CEM-SS cells were infected with VSV-G-pseudotyped NL4-3<sup>Gag-iGFP</sup> virus. The next day, cells were embedded in a 3D Matrigel gel as described in the Experimental Section, and 24 h later imaged live at 37 °C using a<br /> 40× objective on a DeltaVision widefield microscope. Seven 2 μm-spaced Z-slices were taken every 5 min, and were subsequently projected into one image. A syncytium with two nuclei (dark areas within the cell in the GFP channel) begins with two lobes, which merge into a coordinated round morphology as the cell begins to migrate through the gel and leaves the plane of focus. See also Figure 2B.</p> <p><strong>Movie S5.</strong> <strong>CD4</strong><strong>+ T cells in 3D culture exhibit </strong><strong><em>in vivo</em>-like migratory behavior</strong>.</p> <p>Primary human CD4<sup>+</sup> T cells were infected, embedded in collagen, and imaged as in Movie S3 (though with a<br /> 10 s time lapse). The uninucleated infected cell migrating across the field moves by 108 μm over 560 s, for a mean velocity of 11.58 μm/min. Such fast directed amoeboid motility is not typically observed in classical 2D culture and requires the presence of a 3D ECM. See also Figure 2C.</p> <p><strong>Movie S6.</strong> <strong>Uninucleated infected cells and syncytia can transfer virus to target cells without fusion.</strong></p> <p>CEM-SS cells were infected, embedded in Matrigel, and imaged as in Movie S4. Virus transfer from a uninucleated infected cell (top) and a syncytium (bottom left) to a number of target cells (denoted by T) can be seen here.<br /> The uninucleated infected cell transfers virus to target cells T1–T5, and the syncytium transfers virus to target cells T6–T7. Images shown represent brightfield in gray (bottom right), or Gag-iGFP in green, shown either with normal scaling (bottom left, and merged with brightfield at top right), or with a 0.6 gamma correction applied and enhanced scaling to better show appearance of Gag-iGFP puncta on target cells (top left). Scale bar = 30 μm. A yellow arrow indicates the moment where the uninucleated infected cell begins transferring virus to target cells T1–T3, and all of the other transfer events in this field are happening at roughly the same time. At this time, Gag-iGFP puncta appear to distribute between cells T1–T3 in a progressive fashion, beginning from the point of contact with the infected cell (see also Figure 3A, middle panel). Cells T4 and T5 also receive virus particles from this infected cell, and T4 can be seen migrating away at the end. Also note a trail of released virus left behind by the uninucleated infected cell as it migrates from left to right from 08:00:00 to 09:10:00 (see also Movies S7 and S9, Figure 4 for similar events in syncytia). The syncytium’s targets, T6 and T7, are already in intimate contact with it at the start of the movie, and are obscured by lobes of the syncytium. At the 10:45:00 mark, cell T6 breaks free from the syncytium, now harboring a large amount of virus particles on its surface, as the syncytium slowly migrates away, and cell T7 also appears to harbor virus particles on its surface by the final time point.</p> <p><strong>Movie S7.</strong> <strong>A virus transfer event between a syncytium and two uninfected target cells.</strong></p> <p>CEM-SS cells were infected, embedded in Matrigel, and imaged as in Movies S4 and S6. The syncytium shown here initially has two nuclei, but soon fuses with an uninfected cell and now has three clearly visible nuclei. It remains stationary for several hours, before beginning to migrate towards a pair of uninfected target cells (top). Very soon after contact, virus particles can be seen covering the surface of both cells, one of which eventually migrates away. See also Figure 3A (left panel). Note also another instance of a dense accumulation of cell-free virus particles in what appears to be a pocket within the hydrogel that the syncytium moves one of its lobes out of, revealing the deposited free virus, before it moves back into the pocket. See also Figure 4A.</p> <p><strong>Movie S8.</strong> <strong>Cell-to-cell transfer of virus can take place while cells are migrating.</strong></p> <p>CEM-SS cells were infected, later mixed with CMAC-labeled uninfected CEM-SS cells (shown in blue), embedded in collagen, and imaged as above. A syncytium with two nuclei (one of which bears CMAC signal, indicating that it formed recently and not before the infected culture was mixed with the labeled uninfected cells) migrates across the field. Its trailing edge contacts an uninfected CMAC-labeled cell, which is then dragged along with it, and finally dropped in the corner of the field. The target cell now bears virus particles on its surface, and is no longer in contact with the syncytium, which has moved into a different focal plane and stopped migrating (not shown). The image was refocused at the 10:30:00 mark to better show the target cell and the virus particles on its surface. Note that this movie also shows an instance of newly synthesized Gag-iGFP appearing in a previously uninfected cell (not the target cell contacted by the syncytium). This non-CMAC labeled uninfected cell appears in the bottom left of the field at 07:20:00 and exhibits steadily increasing diffuse intracellular signal, as documented in Figure 3A (right) and Figure 3B,C (green traces).</p> <p><strong>Movie S9.</strong> <strong>Migrating infected cells can deposit a trail of released virus particles</strong>.</p> <p>CEM-SS cells were infected, embedded in Matrigel, and imaged as in Movies S4, S6, and S7. A syncytium with 3 nuclei switches into a coordinated morphology and begins migrating across the field. Released virus particles can be seen in its wake (also shown enlarged and with increased brightness as an inset). Shortly after the end of the movie, the cell-free virus accumulation appeared to dissipate (not shown), but it could not be determined whether this was because of photobleaching or if they had in fact diffused away. See also Figure 4B.</p>
Background material for systematic review of literature on ICT acceptance among community dwelling elderly
<p>This is a zip file containing RIS files and PDF files that provide detailed background information about the study.</p>
Supplementary material: Hysteresis of nanocyclinders with Dzyaloshinskii-Moriya interaction
<p>This repository provides the supplementary material to the paper <em>"Hysteresis of nanocyclinders with Dzyaloshinskii-Moriya interaction"</em>.</p> <p>Included in the repository are the raw data files used to produce the figures found in the paper as well as Jupyter notebooks to reproduce them.</p> <p>The PDFs generated from these notebooks are also included in this repository.</p>
Self-Organized Construction with Continuous Building Material: Higher Flexibility based on Braided Structures
<p>Paper material.</p>
Supplementary material: Modeling and Compensating Temperature-dependent Non-uniformity Noise in IR Microbolometer Cameras
<p><strong>Abstract</strong>: Images rendered by uncooled microbolometer-based infrared (IR) cameras are severely degraded by the spatial non-uniformity (NU) noise. The NU noise imposes a fixed-pattern over the true images, and the intensity of the pattern changes with time due to the temperature instability of such cameras. In this paper, we present a novel model and a compensation algorithm for the spatial NU noise and its temperature-dependent variations. The model separates the NU noise into two components: a constant term, which corresponds to a set of NU parameters determining the spatial structure of the noise, and a dynamic term, which scales linearly with the fluctuations of the temperature surrounding the array of microbolometers. We use a black-body radiator and samples of the temperature surrounding the IR array to offline characterize both the constant and the temperature-dependent NU noise parameters. Next, the temperature-dependent variations are estimated online using both a spatially uniform Hammerstein-Wiener estimator and a pixelwise least mean squares (LMS) estimator. We compensate for the NU noise in IR images from two long-wave IR cameras. Results show an excellent non-uniformity correction performance and a root mean square error of less than 0.25◦C, when array’s temperature varies approximately 15◦C.</p>
Data for article Pesticide seed dressings can affect the activity of various soil organisms and reduce decomposition rate of plant material, BMC Ecology
<p>Raw data for article "Pesticide seed dressings can affect the activity of various soil organisms and reduce decomposition rate of plant material" published in BMC Ecology</p>
Data and Scripts for "Bridging the gap to mesoscale radiation materials science with transient grating spectroscopy"
<p>This release contains all the files required to reproduce the data, figures, and tables in this paper's initial submission as a manuscript. All input files, output files, LAMMPS scripts and atomic configurations, MATLAB data processing scripts, raw plot databases, and plotting scripts can be found here.</p>
Training material for RNA sequencing
<p><strong>RNA-seq</strong> (<strong>RNA sequencing</strong>) uses high-throughput (HTS) data to reveal the presence and quantity of RNA in a biological sample at a given moment in time.</p> <p>RNA-Seq is used to analyze the continually changing cellular transcriptome. Specifically, RNA-Seq facilitates the ability to look at alternative gene spliced transcripts, post-transcriptional modifications, gene fusion, mutations/SNPs and changes in gene expression.<sup>[4]</sup> In addition to mRNA transcripts, RNA-Seq can look at different populations of RNA to include total RNA, small RNA, such as miRNA, tRNA, and ribosomal profiling.</p>
Training material for RNA sequencing
<p><strong>RNA-seq</strong> (<strong>RNA sequencing</strong>) uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment in time.</p> <p>RNA-Seq is used to analyze the continually changing cellular transcriptome. Specifically, RNA-Seq facilitates the ability to look at alternative gene spliced transcripts, post-transcriptional modifications, gene fusion, mutations/SNPs and changes in gene expression.<sup>[4]</sup> In addition to mRNA transcripts, RNA-Seq can look at different populations of RNA to include total RNA, small RNA, such as miRNA, tRNA, and ribosomal profiling.</p>
Training material for exome sequencing
<p>Exome sequencing means that all protein-coding genes in a genome are sequenced.</p> <p>In Humans, there are ~180,000 exons that makes up 1% of the human genome which contain ~30 million base pairs. Mutations in the exome have usually a higher impact and more severe consequences, than in the remaining 99% of the genome.</p> <p>With exome sequencing, one can identify genetic variation that is responsible for both Mendelian and common diseases without the high costs associated with whole-genome sequencing. Indeed, exome sequencing is the most efficient way to identify the genetic variants in all of an individual's genes. Exome sequencing is cheaper also than whole-genome sequencing. </p> <p> </p> <p>For training on exome sequencing data analysis, the Galaxy community proposes two tutorials (https://github.com/bgruening/training-material/tree/master/Exome-Seq). Here, you can find the needed datasets for these tutorials.</p>
Supplementary material for paper: Unified Functional Safety Assessment of Industrial Automation Systems
<p>This collection contains supplementary material for the paper titled <strong>Unified Functional Safety Assessment of Industrial Automation Systems</strong> accepted in IEEE TII. This archive provides all information needed to recreate the results presented in the paper including the following:</p> <ol> <li>A technical report presenting proofs of trace equivalence between Function Block Networks and the generated PRISM Models.</li> <li>A set of examples and benchmarks used for experimentation in the said research paper.</li> <li>The results of the analysis presented in the paper are also contained here in the form of spreadsheets contained in file <em>PRISMResults.xlsx</em>.</li> <li>Each of the included sub-folders contains a README.md file describing the system and provides instructions to recreate these results.</li> </ol>
Supporting Material to "Statistical Fault Attacks on Nonce-Based Authenticated Encryption Schemes"
<p>supporting_material_code/setX/ct_fault.txt: each line corresponds to one ciphertext received from the device under test while encrypting a plaintext. The bytes are separated by a comma. For every encryption a fault has been injected:</p> <p>set1: Laser fault injections targeting an AES co-processor on a smartcard microcontroller.</p> <p>set2: Clock tampering targeting an AES co-processor implemented on a general-purpose microcontroller.</p> <p>set3 & 4: Clock tampering targeting an AES software implementation (AVR crypto lib ASM) implemented on a general-purpose microcontroller (ATXmega256A3).</p> <p>supporting_material_code/main.cpp: program for key recovery which takes as input the faulty ciphertexts (ct_fault.txt)</p> <p> </p>
The Influence of Optical Material Properties on the Perception of Liquids
<p>Dataset relative to the following publication:</p> <p>Jan Jaap R. van Assen, Roland W. Fleming (2016). Influence of optical material properties on the perception of liquids. Journal of Vision, 16(15):12, 1–20. doi: 10.1167/16.15.12.</p> <p>One zip file contains the datasets of the various experiments.</p> <p>The second zip file contains the liquid stimuli used during the experiments.</p>
Supplementary Material Douglas-fir data
<p>Supplementary information of the three Douglas-fir trials, family numbers, and pedigree data including identity information of trees, fathers, and mothers of the paper entitled: <strong>Identification and joint modeling of competition effects and environmental heterogeneity in three Douglas-fir (<em>Pseudotsuga menziesii</em> var. <em>menziesii</em>) trials.</strong></p>
Supporting material: Improving the Identification of Phenotypic Abnormalities and Sexual Dimorphism in Mice
<p>Supporting material for the manuscript titled "<strong>Improving the Identification of Phenotypic Abnormalities and Sexual Dimorphism in Mice", </strong>accepted for publication in Genetics.</p> <p>This material enables a complete reproducible analysis of the results presented.</p>
Additional materials used in the paper "Towards Continuous Scientific Data Analysis and Hypothesis Evolution" on the Proceedings of the Thirty-First AAAI Conference on Artificial Intelligence (AAAI-17)
<p>This bundle contains a web page describing the materials used in the evaluation of the paper, along with references to the software and datasets, provenance metadata and workflows used. All the scripts and descriptions are included as well.</p>
Supplementary material for "Patient portal adoption rates: a systematic literature review and meta-analysis"
<p>The attached file contains the searches used to review the literature and identify papers evaluating usage, usability and influence on decision making of patient portals (Supplementary Table 1).</p> <p>Supplementary Table 2 and Supplementary Table 3 contains references and individual studies characteristics of included studies.</p>
Temporal and spatial evaluation of satellite-based rainfall estimates across the complex topographical and climatic gradients of Chile (supplementary material)
<p>This file contains the <strong>Supplement</strong> (both raw observed precipitation data and figures obtained as output of the analysis) accompanying the manuscript '<strong>hess-2016-453'</strong> submitted to the HESS journal (http://www.hydrology-and-earth-system-sciences.net/).</p> <p><strong>Title</strong>: "Temporal and spatial evaluation of satellite-based rainfall estimates across the complex topographical and climatic gradients of Chile"</p> <p> </p> <p><strong>Abstract</strong></p> <p>Accurate representation of the real spatio-temporal variability of catchment rainfall inputs is currently severely limited. Moreover, spatially interpolated catchment precipitation is subject to large uncertainties, particularly in developing countries and regions which are difficult to access. Recently, satellite-based rainfall estimates (SRE) provide an unprecedented opportunity for a wide range of hydrological applications, from water resources modelling to monitoring of extreme events such as droughts and floods.</p> <p>This study attempts to exhaustively evaluate -for the first time- the suitability of seven state-of-the-art SRE products (TMPA 3B42v7, CHIRPSv2, CMORPH, PERSIANN-CDR, PERSIAN-CCS-adj, MSWEPv1.1 and PGFv3) over the complex topography and diverse climatic gradients of Chile. Different temporal scales (daily, monthly, seasonal, annual) are used in a point-to-pixel comparison between precipitation time series measured at 366 stations (from sea level to 4600 m a.s.l. in the Andean Plateau) and the corresponding grid cell of each SRE (rescaled to a 0.25° grid if necessary). The modified Kling-Gupta efficiency was used to identify possible sources of systematic errors in each SRE. In addition, five categorical indices (PC, POD, FAR, ETS, fBIAS) were used to assess the ability of each SRE to correctly identify different precipitation intensities.</p> <p>Results revealed that most SRE products performed better for the humid South (36.4-43.7°S) and Central Chile (32.18-36.4°S), in particular at low- and mid-elevation zones (0-1000 m a.s.l.) compared to the arid northern regions and the Far South. Seasonally, all products performed best during the wet seasons autumn and winter (MAM-JJA) compared to summer (DJF) and spring (SON). In addition, all SREs were able to correctly identify the occurrence of no rain events, but they presented a low skill in classifying precipitation intensities during rainy days. Overall, PGFv3 exhibited the best performance everywhere and for all time scales, which can be clearly attributed to its bias-correction procedure using 217 stations from Chile. Good results were also obtained by the research products CHIRPSv2, TMPA 3B42v7 and MSWEPv1.1,while CMORPH, PERSIANN-CDR and the real-time PERSIANN-CCS-adj were less skillful in representing observed rainfall. While PGFv3 (currently available up to 2010) might be used in Chile for historical analyses and calibration of hydrological models, the high spatial resolution, low latency and long data records of CHIRPS and TMPA 3B42v7 (in transition to IMERG) show promising potential to be used in meteorological studies and water resources assessments. We finally conclude that despite improvements of most SRE products, a site-specific assessment is still needed before any use in catchment-scale hydrological studies.</p>
Figure 1. - Diagram showing abbreviations of geometric terms used to describe truncate flabellids. Left: lateral view of an anthocyathus; center: basal scar of an anthocyathus; right: edge view of an anthocyathus. Abbreviations defined in Materials section.
Figure 1. - Diagram showing abbreviations of geometric terms used to describe truncate flabellids. Left: lateral view of an anthocyathus; center: basal scar of an anthocyathus; right: edge view of an anthocyathus. Abbreviations defined in Materials section.
Supplementary material 1: Number of Pteridaceae species by gender in Togo from: The Pteridaceae family diversity in Togo - Biodiversity Data Journal 3: e5078 (15 July 2015) https://doi.org/10.3897/BDJ.3.e5078
Number of Pteridaceae species by gender in Togo
ScienceDex guides
Understand access before you commit
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.