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3,576 results for “strain”
Nanomechanical probing and strain tuning of the Curie temperature in suspended Cr2Ge2Te6-based heterostructures
<p>Data files for Figs. 1-5 of the article "Nanomechanical probing and strain tuning of the Curie temperature in suspended Cr<sub>2</sub>Ge<sub>2</sub>Te<sub>6</sub>-based heterostructures" published in <em>npj 2D Materials and Applications</em>, DOI: , URL: </p>
Experimental Assessment of the Thermal Strain Distribution in Nb3Sn React & Wind Conductor Prototype for European DEMO
<p>The measured data, processed data and metadata related to the publication "Experimental Assessment of the Thermal Strain Distribution in Nb3Sn React & Wind Conductor Prototype for European DEMO" (doi: 10.1109/TASC.2022.3141699) are uploaded. The raw data correspond to susceptibility measurement as a function of temperature. Out of this measurement, strand distribution in the superconducting cable is determined by analysis.</p> <p>This work was supported by the Swiss National Science Foundation (SNF) under contract number 200021_179134.</p>
direct RNA seq data, triplicate of RSV - strain A2 in Calu-3 cells at 48 hours post infection
<p>Raw fastq data from Calue-3 cells infected with RSV strain A2</p>
Forearc faults in northern Cascadia do not accommodate elastic strain driven by the megathrust seismic cycle: Dataset
<p>Input files and codes for Harrichhausen, N., Morell, K.D., Regalla, C. Inner forearc faults in northern Cascadia do not accommodate elastic strain driven by the megathrust seismic cycle. Submitted to Seismica. 2024.</p> <p>See Readme.md for more information</p> <p>Version 1.1: Updated author list and funding information.</p> <p>Version 1.2: Updated matlab codes to work on Mac.</p>
Three-dimensional subnanoscale imaging of unit cell doubling due to octahedral tilting and cation modulation in strained perovskite thin films
<p>Transmission electron microscopy data used in the journal publication <a href="https://doi.org/10.1103/PhysRevMaterials.3.063605">"Three-dimensional subnanoscale imaging of unit cell doubling due to octahedraltilting and cation modulation in strained perovskite thin films"</a></p> <p><strong>Data files</strong></p> <p>There are two data types:</p> <ul> <li>Scanning TEM (STEM) diffraction patterns acquired with a Medipix3 detector (Merlin): m004_LSMO_LFO_STO_medipix.hdf5 <ul> <li>Acquired on a probe corrected Jeol ARM200CF</li> <li>Acceleration voltage: 200 kV</li> <li>Convergence semi-angle: 20.4 mrad (calibrated using the SrTiO<sub>3</sub> substrate HOLZ ring)</li> <li>Detector calibration: 1.357 mrad per pixel (calibrated using the SrTiO<sub>3</sub> substrate HOLZ ring)</li> </ul> </li> <li>Atomic resolution STEM data, both annular dark field (ADF) and annular bright field (ABF), which were acquired simultaneously: s007_ADF.hdf5, s007_ABF.hdf5</li> </ul> <p>The data can be loaded in python using h5py.</p> <p>For the Medipix3 data:</p> <pre><code class="language-python">import h5py f = h5py.File('m004_LSMO_LFO_STO_medipix.hdf5', mode='r') data = f['fpd_expt/fpd_data/data'] data_subset = data[0:16, 0:16, :, :]</code></pre> <p>For the STEM-ADF or STEM-ABF data:</p> <pre><code class="language-python">import h5py f = h5py.File('s007_ADF.hdf5', mode='r') data = f['Experiments/__unnamed__/data']</code></pre> <p>Exploring the Medipix3 dataset lazily, i.e. without loading the whole dataset into memory at the same time. Using pixStem:</p> <pre><code class="language-python">import pixstem.api as ps s = ps.load_ps_signal("003_stripe1.hdf5", lazy=True) s.plot()</code></pre> <p>Loading the STEM-ADF or STEM-ABF data using HyperSpy, which automatically loads the probe scaling:</p> <pre><code class="language-python">import hyperspy.api as hs s = hs.load("s007_ADF.hdf5") s.plot()</code></pre> <p><br> <strong>Processing files</strong></p> <p>All the TEM data has been processed using python scripts, which is named based on the type of processing:</p> <ul> <li>d00N_...: Medipix3 data processing</li> <li>a00N_...: Atomic resolution STEM-ADF and STEM-ABF processing using Atomap</li> </ul> <p>The scripts generate intermediate files, which are saved in folders with the same prefix as the scripts. So the d001_... script makes a folder named d001_... . These intermediate files are included here as zip-files, since Zenodo doesn't support folder structures.</p> <p>The python libraries required to run the scripts are listed in requirements.txt. Newer versions of the libraries will most likely also work.</p> <p>To setup the python environment with the required libraries, and run all the scripts:</p> <pre><code class="language-bash">pip3 install -r requirements.txt python3 run_all_scripts.py</code></pre> <p> </p>
BacSPaD: A robust bacterial strains' pathogenicity resource based on integrated and curated genomic metadata
<p>The vast array of omics data in microbiology presents significant opportunities for studying bacterial pathogenesis and creating computational tools for predicting pathogenic potential. However, the field lacks a comprehensive, curated resource that catalogs bacterial strains and their ability to cause human infections. Current methods for identifying pathogenicity determinants often introduce biases and miss critical aspects of bacterial pathogenesis.<br>In response to this gap, we introduce BacSPaD (Bacterial Strains’ Pathogenicity Database), a thoroughly curated database focusing on pathogenicity annotations for a wide range of high-quality, complete bacterial genomes. Our rule-based annotation workflow combines metadata from trusted sources with automated keyword matching, extensive manual curation, and detailed literature review. Our analysis classified 5,502 genomes as pathogenic to humans (HP) and 490 as non-pathogenic to humans (NHP), encompassing 532 species, 193 genera, and 96 families. Statistical analysis demonstrated a significant but moderate correlation between virulence factors and HP classification, highlighting the complexity of bacterial pathogenicity and the need for ongoing research. This resource is poised to enhance our understanding of bacterial pathogenicity mechanisms and aid in the development of predictive models. To improve accessibility and provide key visualization statistics, we developed a user-friendly web interface, accessible at<a href="https://bacspad.altrabio.com/"> </a><a href="https://bacspad.altrabio.com/"><u>https://bacspad.altrabio.com</u></a>.</p>
Stress-Strain Analysis of Polycrystalline Copper with Goss Texture Using Crystal Plasticity FEM
<pre>Stress-strain analysis of single-phase polycrystalline copper with a Goss texture using a cubic representative volume element (RVE) and periodic boundary conditions, performed with Abaqus through the crystal plasticity finite element method.</pre>
Supplementary Files for "Geodetic constraints on cratonic microplates and broad strain during rifting of thick Southern African lithosphere"
<p>This repository contains the supplementary files and tables for the manuscript:</p> <p><strong>Geodetic constraints on cratonic microplates and broad strain during rifting of thick Southern African lithosphere</strong></p> <p><strong>L. N. J. Wedmore<sup>1</sup>, Biggs, J.<sup>1</sup>, Floyd, M.<sup>2</sup>, Fagereng, Å.<sup>3</sup>, Mdala, H.<sup>4</sup>, Chindandali, P.<sup>5</sup>, Williams, J.<sup>3</sup>, Mphepo, F.<sup>4</sup></strong></p> <p><sup>1</sup>School of Earth Sciences, University of Bristol, Bristol, UK</p> <p><sup>2</sup>Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA</p> <p><sup>3</sup>School of Earth and Environmental Sciences, Cardiff University, Cardiff, UK</p> <p><sup>4</sup>Geological Survey Department, Mzuzu Regional Office, Mzuzu, Malawi</p> <p><sup>5</sup>Geological Survey Department, Zomba, Malawi</p> <p>This manuscriptis published in Geophysical Research Letters: <a href="https://doi.org/10.1029/2021GL093785">https://doi.org/10.1029/2021GL093785</a></p> <p>Please contact the author (luke.wedmore@bristol.ac.uk) for more information.</p> <p> </p> <p>File Information</p> <p>File S1 – Table of GNSS station velocities for the combined southern Malawi/GeoPRISMS/Saria et al. (2014) solution in the ITRF14 reference frame.</p> <p>File S2 – Table of GNSS station and the references for the data used in this paper.</p> <p>File S3 – Details of the sites used for the two-plate test and the results of this inversion.</p> <p>File S4 – Details of the sites used for the three-plate test and the results of this inversion.</p> <p>File S5 – A sig_neu command file with details of the random noise added to outlier sites within GLOBK.</p>
RAW SEM images mosaics dataset for the HRDIC strain localization study in shot peened Ni superalloy
<p>We used a FEI Magellan HR 400L FE-SEM with a theoretical resolution of ≤ 0.9 nm at <1kV and ≤ 0.8 nm at ≥ 5kV to take backscattered electron images of the fine, homogeneous distributed gold speckle pattern obtained by remodelling of a thin gold layer previously deposited on the polished sample surface. The images were obtained at a working distance of 3.5 mm, 5 kV and 0.8 nA beam current. Mosaics of 30x15 images were used to cover 950x420 µm<sup>2</sup>. Each image contains 2048 x 1768 pixels and has a horizontal field of view of 43 µm. The images were overlapped by 20% to enable easy stitching prior to the digital image correlation. We obtained 7 mosaics, one before tensile testing and 6 after each deformation step.</p> <p>This set of images at different strain steps is coupled with the EBSD data set in https://doi.org/10.5281/zenodo.4730184, the HRDIC strain maps in http://doi.org/10.5281/zenodo.4728016 and data visualisation scripts in http://doi.org/10.5281/zenodo.4727939</p> <p>0_def corresponds to the undeformed sample, while 1_def to 6_def were obtained after each deformation step.</p>
Molecular characterization and genetic diversity of four undescribed novel oleaginous Mortierella alpina strains from Libya
<p>A large number of undiscovered fungal species still exist on earth, which can be useful for bioprospecting, particularly for single cell oil (SCO) production. <em>Mortierella</em> is one of the significant genera in this field and contains about hundred species. Moreover, <em>M. alpina </em>is the main single cell oil producer / arachidonic acid producer at commercial scale under this genus.</p>
Mycobacteroides abscessus subp. bolletii strain associated with a persistent infection (genome assembly and annotation dataset)
<p>This dataset includes the assembled contigs (.fasta and .gbk files), the nucleotide sequences of the prediction transcripts (.ffn files) and the respective amino acid sequences of the translated CDS sequences (.faa files) of a <strong><em>Mycobacteroides abscessus subp. bolletti </em></strong>strain associated with a persistente infection. (genome anotation was performed using Bakta v1.2.2 https://github.com/oschwengers/bakta)</p> <p>The raw sequence reads were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB57933; Run Accession: ERR10554471).</p>
Dyadic encounter unfamiliar female pairs over 2 days – 16p11.2 Del mouse strain – WT-WT - 5220_5175
<p>We evaluated the social interactions and communication between unfamiliar individuals in pairs. For these recordings of social behaviour and ultrasonic communication, we focused on pairs of individuals since we currently cannot identify the emitter of USVs when animals were interacting closely. Therefore, we recorded undisturbed dyadic interactions between two unfamiliar individuals (from two different housing cages) of the same age (14-20 weeks of age) and genotype for 47h (two days and nights). For that purpose, we coupled the Live Mouse Tracker system (plugin 931) with one CM16/CMPA microphone (Avisoft Bioacoustics, Glienecke, Germany) connected to the Avisoft Ultrasound Gate 416 (300 kHz sampling rate, 16-bit format; trigger: level of this channel; pre-trigger: 1 s; hold time: 1 s; duration > 0.005 s; trigger event: 2 % energy in 25-125 kHz with entropy < 50%; Avisoft Bioacoustics, Glienecke, Germany). LMT and Avisoft systems were synchronised based on the protocol described in (de Chaumont et al., 2021). Each upload includes the sqlite database from LMT (processed, with USV synchronised) and a zip file with all USVs sequences automatically recorded by Avisoft.</p>
Dyadic encounter unfamiliar female pairs over 2 days – 16p11.2 Del mouse strain – Del:+-Del/+ - 5194_5231
<p>We evaluated the social interactions and communication between unfamiliar individuals in pairs. For these recordings of social behaviour and ultrasonic communication, we focused on pairs of individuals since we currently cannot identify the emitter of USVs when animals were interacting closely. Therefore, we recorded undisturbed dyadic interactions between two unfamiliar individuals (from two different housing cages) of the same age (14-20 weeks of age) and genotype for 47h (two days and nights). For that purpose, we coupled the Live Mouse Tracker system (plugin 931) with one CM16/CMPA microphone (Avisoft Bioacoustics, Glienecke, Germany) connected to the Avisoft Ultrasound Gate 416 (300 kHz sampling rate, 16-bit format; trigger: level of this channel; pre-trigger: 1 s; hold time: 1 s; duration > 0.005 s; trigger event: 2 % energy in 25-125 kHz with entropy < 50%; Avisoft Bioacoustics, Glienecke, Germany). LMT and Avisoft systems were synchronised based on the protocol described in (de Chaumont et al., 2021). Each upload includes the sqlite database from LMT (processed, with USV synchronised) and a zip file with all USVs sequences automatically recorded by Avisoft.</p>
Dyadic encounter unfamiliar female pairs over 2 days – 16p11.2 Del mouse strain – Del:+-Del/+ - 5186_5172
<p>We evaluated the social interactions and communication between unfamiliar individuals in pairs. For these recordings of social behaviour and ultrasonic communication, we focused on pairs of individuals since we currently cannot identify the emitter of USVs when animals were interacting closely. Therefore, we recorded undisturbed dyadic interactions between two unfamiliar individuals (from two different housing cages) of the same age (14-20 weeks of age) and genotype for 47h (two days and nights). For that purpose, we coupled the Live Mouse Tracker system (plugin 931) with one CM16/CMPA microphone (Avisoft Bioacoustics, Glienecke, Germany) connected to the Avisoft Ultrasound Gate 416 (300 kHz sampling rate, 16-bit format; trigger: level of this channel; pre-trigger: 1 s; hold time: 1 s; duration > 0.005 s; trigger event: 2 % energy in 25-125 kHz with entropy < 50%; Avisoft Bioacoustics, Glienecke, Germany). LMT and Avisoft systems were synchronised based on the protocol described in (de Chaumont et al., 2021). Each upload includes the sqlite database from LMT (processed, with USV synchronised) and a zip file with all USVs sequences automatically recorded by Avisoft.</p>
Dyadic encounter unfamiliar female pairs over 2 days – 16p11.2 Del mouse strain – Del/+-Del/+ - 5170_5256
<p>We evaluated the social interactions and communication between unfamiliar individuals in pairs. For these recordings of social behaviour and ultrasonic communication, we focused on pairs of individuals since we currently cannot identify the emitter of USVs when animals were interacting closely. Therefore, we recorded undisturbed dyadic interactions between two unfamiliar individuals (from two different housing cages) of the same age (14-20 weeks of age) and genotype for 47h (two days and nights). For that purpose, we coupled the Live Mouse Tracker system (plugin 931) with one CM16/CMPA microphone (Avisoft Bioacoustics, Glienecke, Germany) connected to the Avisoft Ultrasound Gate 416 (300 kHz sampling rate, 16-bit format; trigger: level of this channel; pre-trigger: 1 s; hold time: 1 s; duration > 0.005 s; trigger event: 2 % energy in 25-125 kHz with entropy < 50%; Avisoft Bioacoustics, Glienecke, Germany). LMT and Avisoft systems were synchronised based on the protocol described in (de Chaumont et al., 2021). Each upload includes the sqlite database from LMT (processed, with USV synchronised) and a zip file with all USVs sequences automatically recorded by Avisoft.</p>
Dyadic encounter unfamiliar female pairs over 2 days – 16p11.2 Del mouse strain – WT-WT - 5160_5182
<p>We evaluated the social interactions and communication between unfamiliar individuals in pairs. For these recordings of social behaviour and ultrasonic communication, we focused on pairs of individuals since we currently cannot identify the emitter of USVs when animals were interacting closely. Therefore, we recorded undisturbed dyadic interactions between two unfamiliar individuals (from two different housing cages) of the same age (14-20 weeks of age) and genotype for 47h (two days and nights). For that purpose, we coupled the Live Mouse Tracker system (plugin 931) with one CM16/CMPA microphone (Avisoft Bioacoustics, Glienecke, Germany) connected to the Avisoft Ultrasound Gate 416 (300 kHz sampling rate, 16-bit format; trigger: level of this channel; pre-trigger: 1 s; hold time: 1 s; duration > 0.005 s; trigger event: 2 % energy in 25-125 kHz with entropy < 50%; Avisoft Bioacoustics, Glienecke, Germany). LMT and Avisoft systems were synchronised based on the protocol described in (de Chaumont et al., 2021). Each upload includes the sqlite database from LMT (processed, with USV synchronised) and a zip file with all USVs sequences automatically recorded by Avisoft.</p>
Dyadic encounter unfamiliar female pairs over 2 days – 16p11.2 Del mouse strain – Del/+-Del/+ - 5224_5173
<p>We evaluated the social interactions and communication between unfamiliar individuals in pairs. For these recordings of social behaviour and ultrasonic communication, we focused on pairs of individuals since we currently cannot identify the emitter of USVs when animals were interacting closely. Therefore, we recorded undisturbed dyadic interactions between two unfamiliar individuals (from two different housing cages) of the same age (14-20 weeks of age) and genotype for 47h (two days and nights). For that purpose, we coupled the Live Mouse Tracker system (plugin 931) with one CM16/CMPA microphone (Avisoft Bioacoustics, Glienecke, Germany) connected to the Avisoft Ultrasound Gate 416 (300 kHz sampling rate, 16-bit format; trigger: level of this channel; pre-trigger: 1 s; hold time: 1 s; duration > 0.005 s; trigger event: 2 % energy in 25-125 kHz with entropy < 50%; Avisoft Bioacoustics, Glienecke, Germany). LMT and Avisoft systems were synchronised based on the protocol described in (de Chaumont et al., 2021). Each upload includes the sqlite database from LMT (processed, with USV synchronised) and a zip file with all USVs sequences automatically recorded by Avisoft.</p>
Dyadic encounter unfamiliar female pairs over 2 days – 16p11.2 Del mouse strain – Del/+-Del/+ - 5171_5164
<p>We evaluated the social interactions and communication between unfamiliar individuals in pairs. For these recordings of social behaviour and ultrasonic communication, we focused on pairs of individuals since we currently cannot identify the emitter of USVs when animals were interacting closely. Therefore, we recorded undisturbed dyadic interactions between two unfamiliar individuals (from two different housing cages) of the same age (14-20 weeks of age) and genotype for 47h (two days and nights). For that purpose, we coupled the Live Mouse Tracker system (plugin 931) with one CM16/CMPA microphone (Avisoft Bioacoustics, Glienecke, Germany) connected to the Avisoft Ultrasound Gate 416 (300 kHz sampling rate, 16-bit format; trigger: level of this channel; pre-trigger: 1 s; hold time: 1 s; duration > 0.005 s; trigger event: 2 % energy in 25-125 kHz with entropy < 50%; Avisoft Bioacoustics, Glienecke, Germany). LMT and Avisoft systems were synchronised based on the protocol described in (de Chaumont et al., 2021). Each upload includes the sqlite database from LMT (processed, with USV synchronised) and a zip file with all USVs sequences automatically recorded by Avisoft.</p>
Dyadic encounter unfamiliar female pairs over 2 days – 16p11.2 Del mouse strain – Del/+-Del/+ - 5185_5165
<p>We evaluated the social interactions and communication between unfamiliar individuals in pairs. For these recordings of social behaviour and ultrasonic communication, we focused on pairs of individuals since we currently cannot identify the emitter of USVs when animals were interacting closely. Therefore, we recorded undisturbed dyadic interactions between two unfamiliar individuals (from two different housing cages) of the same age (14-20 weeks of age) and genotype for 47h (two days and nights). For that purpose, we coupled the Live Mouse Tracker system (plugin 931) with one CM16/CMPA microphone (Avisoft Bioacoustics, Glienecke, Germany) connected to the Avisoft Ultrasound Gate 416 (300 kHz sampling rate, 16-bit format; trigger: level of this channel; pre-trigger: 1 s; hold time: 1 s; duration > 0.005 s; trigger event: 2 % energy in 25-125 kHz with entropy < 50%; Avisoft Bioacoustics, Glienecke, Germany). LMT and Avisoft systems were synchronised based on the protocol described in (de Chaumont et al., 2021). Each upload includes the sqlite database from LMT (processed, with USV synchronised) and a zip file with all USVs sequences automatically recorded by Avisoft.</p>
Dyadic encounter unfamiliar female pairs over 2 days – 16p11.2 Del mouse strain – WT-WT - 5163_5199
<p>We evaluated the social interactions and communication between unfamiliar individuals in pairs. For these recordings of social behaviour and ultrasonic communication, we focused on pairs of individuals since we currently cannot identify the emitter of USVs when animals were interacting closely. Therefore, we recorded undisturbed dyadic interactions between two unfamiliar individuals (from two different housing cages) of the same age (14-20 weeks of age) and genotype for 47h (two days and nights). For that purpose, we coupled the Live Mouse Tracker system (plugin 931) with one CM16/CMPA microphone (Avisoft Bioacoustics, Glienecke, Germany) connected to the Avisoft Ultrasound Gate 416 (300 kHz sampling rate, 16-bit format; trigger: level of this channel; pre-trigger: 1 s; hold time: 1 s; duration > 0.005 s; trigger event: 2 % energy in 25-125 kHz with entropy < 50%; Avisoft Bioacoustics, Glienecke, Germany). LMT and Avisoft systems were synchronised based on the protocol described in (de Chaumont et al., 2021). Each upload includes the sqlite database from LMT (processed, with USV synchronised) and a zip file with all USVs sequences automatically recorded by Avisoft.</p>
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.