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Accompanying data for the paper "Experimental characterization of material strain-rate dependence based on full-field Data-Driven Identification"
<p>Experimental Data accompanying the paper "Experimental characterization of material strain-rate dependence based on full-field Data-Driven Identification" <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.ijimpeng.2024.105083" target="_blank" rel="noreferrer noopener">https://doi.org/10.1016/j.ijimpeng.2024.105083</a></p> <p>One (holed and double notched) specimen is dynamically loaded via an hydraulic tensile test machine (MTS-819, 20 kN) at 5 m/s. The specimen were cut from a 0.8 mm-thick DC04 (XES French standards) sheet in the rolling direction provided by ONERA. Reference image is captured using a high definition camera (29 Mpix, Prosilica GT from Stemmer) combined with the same objective lens than the one used for experiments. Deformed sample images are captured using the rotating mirror Ultra-high speed (HR-UHS) Cordin camera Model 580 at 68 kfps with a resolution of 3296 x 2472 pixels. The field of view is 35.8mm x 47.9mm leading to a pixel size of 14.49um. Ufreckles <a href="https://doi.org/10.5281/zenodo.1433776">10.5281/zenodo.1433775</a> is used to perform FE-based DIC using T3P1 linear triangular elements and a Tikhonov regularisation (over 3 elements). Eventually, kinematic data and load measurement are used to identify stress fields via Data-Driven stress Identification (DDI) method.</p> <p>Are provided:</p> <ul> <li>raw images, camera distortion modes and parameters, load net force and timeline</li> <li>kinematic fields obtained from Digital Image Correlation</li> <li>Stress fields identified using Data-Driven stress Identification</li> </ul> <p>Matlab Codes to produce results (working with Ufreckles)</p> <ul> <li>MultiSensor_DIC_script.m: in /Codes/ is the main script to run DIC</li> <li>Shape functions: in /Codes/shape_functions/ containing Zernike polynomial shape functions and deconvolution algorithm to get effective displacement from total displacement knowing camera distortions</li> </ul> <p> </p>
Strain Measurements made in the blade with FBG and DFO sensors.
<p><span>Record of Strain measurements made in the blade with FBG and DFO sensors. The blade strain measurements are collected in order to carry out monitoring activities of the structural health of the blade developed as part of the MAREWIND project.</span></p>
Bending strain in 3D topological semi-metals
<p>We present an experimental set-up for the controlled application of strain gradients by mechanical piezoactuation on 3D crystalline microcantilevers that were fabricated by focused ion beam machining. A simple sample design tailored for transport characterization under strain at cryogenic temperatures is proposed. The topological semi-metal Cd<sub>3</sub>As<sub>2</sub> serves as a test bed for the method, and we report extreme strain gradients of up to 1.3%μm<sup>−1</sup> at a surface strain value of≈0.65% at 4K. Interestingly, the unchanged quantum transport of the cantilever suggests that the bending cycle does not induce defects via plastic deformation. This approach is a first step towards realizing transport phenomena based on structural gradients, such as artificial gauge fields in topological materials.</p>
Digesta and Plasma Metabolomics of Rainbow Trout Strains with Varied Tolerance of Plant-Based Diets Highlights Potential for Non-Lethal Assessments of Enteritis Development
<p>The replacement of fishmeal in aquafeeds is essential to the sustainability of aquaculture. Besides the procurement of alternative protein sources, fish can also be selected for better performance on plant-based alternative diets. Rainbow trout (<em>Oncorhynchus mykiss</em>) is one such species in which the strain ARS-<em>Sel</em>has been selected for higher growth and enhanced utilization when fed soy-based diets. The aim of this study was to compare fish growth, and plasma and digesta metabolomes between the ARS-<em>Sel</em>and two commercial strains (CS-1 and CS-2), when fed a plant-protein diet (PM) and a fishmeal-based diet (FM) and correlate them with the onset of enteritis. An NMR-metabolomics approach was taken to assess plasma and digesta metabolite profiles. Diet and strain showed significant effects on fish growth, with the ARS-<em>Sel</em>fish receiving the PM diet reaching the highest final weight at sampling. Multivariate analysis revealed differences between plasma metabolite profiles of ARS-<em>Sel</em>and CS (CS-1 considered together with CS-2) PM-fed groups in the early stages of the enteritis development, which was confirmed by a histological approach. In digesta, no differences were observed between groups. As reported in previous studies the ARS-<em>Sel</em>strain performed better than the commercial strains when fed the PM diet. </p>
Progressive failure analysis of slip zone soils with strain-softening behavior and implications for landslide triggering mechanisms
<p>All figure for paper entitled “Progressive failure analysis of slip zone soils with strain-softening behavior and implications for landslide triggering mechanisms”</p>
Phenotypic, genetic, and epigenetic data from 29 Serratia marcescens strains from an evolution experiment
<p>This dataset contains phenotypic, genetic, and epigenetic data from 29 <em>Serratia marcescens</em> strains from an evolution experiment. In a previous study (https://doi.org/10.1111/evo.12148), the bacterium <em>S. marcescens</em> was left to evolve from a common ancestor culture in replicated populations kept under different temperature regimes, and evolved clones were isolated and their phenotypes measured. Here, we randomly selected 28 evolved clones from this experiment, as well as the original reference strain, and used PacBio single molecule real-time (SMRT) sequencing to obtain genetic and epigenetic (N6-methyladenine modifications, m6A) data. The goal of our study was to obtain a detailed description of the methylation landscape of <em>S. marcescens</em> and to examine the potential contributions of genetic and epigenetic changes to phenotypic adaptation.</p>
Figure 6 in Morphological ontogeny and molecular analyses of geographic strains of two closely related Neoseiulus species (Acari: Phytoseiidae)
Figure 6 Neoseiulus womersleyi (Schicha). Deutonymph (female); A – dorsum; B – venter.
Figure 2 in Morphological ontogeny and molecular analyses of geographic strains of two closely related Neoseiulus species (Acari: Phytoseiidae)
Figure 2 Neoseiulus longispinosus (Evans). Deutonymph (female); A – dorsum; B – venter.
Figure 4 in Morphological ontogeny and molecular analyses of geographic strains of two closely related Neoseiulus species (Acari: Phytoseiidae)
Figure 4 Neoseiulus longispinosus (Evans). Larva; A – dorsum; B – venter.
Figure 8 in Morphological ontogeny and molecular analyses of geographic strains of two closely related Neoseiulus species (Acari: Phytoseiidae)
Figure 8 Neoseiulus womersleyi (Schicha). Larva; A – dorsum; B – venter.
Figure 3 in Morphological ontogeny and molecular analyses of geographic strains of two closely related Neoseiulus species (Acari: Phytoseiidae)
Figure 3 Neoseiulus longispinosus (Evans). Protonymph; A – dorsum; B – venter.
Figure 7 in Morphological ontogeny and molecular analyses of geographic strains of two closely related Neoseiulus species (Acari: Phytoseiidae)
Figure 7 Neoseiulus womersleyi (Schicha). Protonymph; A – dorsum; B – venter.
Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation
<p>Faecal microbiota transplantation (FMT) is an efficacious therapeutic intervention, but its clinical mode of action and underlying microbiome dynamics remain poorly understood. Here, we analysed the metagenomes associated with 142 FMTs, in a time series-based meta-study across five disease indications. We quantified strain-level dynamics of 1,089 microbial species based on their pangenome, complemented with 47,548 newly constructed metagenome-assembled genomes. Using subsets of procedural-, host- and microbiome-based variables, LASSO-regularised regression models accurately predicted the colonisation and resilience of donor and recipient microbes, as well as turnover of individual species. Linking this to putative ecological mechanisms, we found these sets of variables to be informative of the underlying processes that shape the post-FMT gut microbiome. Recipient factors and complementarity of donor and recipient microbiomes, encompassing entire communities to individual strains, were the main determinants of individual strain population dynamics, and mostly independent of clinical outcomes. Recipient community state and the degree of residual strain depletion provided a neutral baseline for donor strain colonisation success, in addition to inhibitive priority effects between species and conspecific strains, as well as putatively adaptive processes. Our results suggest promising tunable parameters to enhance donor flora colonisation or recipient flora displacement in clinical practice, towards the development of more targeted and personalised therapies.</p>
Supplementary data for "Timely vaccine strain selection and genomic surveillance improves evolutionary forecast accuracy of seasonal influenza A/H3N2"
<p>Supplementary materials associated with the manuscript by Huddleston and Bedford titled "Timely vaccine strain selection and genomic surveillance improves evolutionary forecast accuracy of seasonal influenza A/H3N2".</p>
VC40429 Million Mutation Project strain | 2016-02-18T15:35:45+00:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=R9NQgQB60H4</li> <li><b>strain</b> : VC40429</li> <li><b>timestamp</b> : 2016-02-18T15:35:45+00:00</li> <li><b>gene</b> : -N/A-</li> <li><b>chromosome</b> : -N/A-</li> <li><b>allele</b> : -N/A-</li> <li><b>strain_description</b> : Million Mutation Project strain</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : clockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : VC40429 on food L_2016_02_18__15_35_45___5___4</li> <li><b>total time (s)</b> : 898.967</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 6.08706</li> <li><b>number of segmented skeletons</b> : 26118</li> </ul>
VC40429 Million Mutation Project strain | 2016-02-23T11:40:46+00:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=Y8OI94QgXRc</li> <li><b>strain</b> : VC40429</li> <li><b>timestamp</b> : 2016-02-23T11:40:46+00:00</li> <li><b>gene</b> : -N/A-</li> <li><b>chromosome</b> : -N/A-</li> <li><b>allele</b> : -N/A-</li> <li><b>strain_description</b> : Million Mutation Project strain</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : clockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : VC40429 on food L_2016_02_23__11_40_46___5___2</li> <li><b>total time (s)</b> : 899.0</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 6.08706</li> <li><b>number of segmented skeletons</b> : 25666</li> </ul>
VC40429 Million Mutation Project strain | 2016-02-24T16:38:27+00:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=pMOKi15Bf84</li> <li><b>strain</b> : VC40429</li> <li><b>timestamp</b> : 2016-02-24T16:38:27+00:00</li> <li><b>gene</b> : -N/A-</li> <li><b>chromosome</b> : -N/A-</li> <li><b>allele</b> : -N/A-</li> <li><b>strain_description</b> : Million Mutation Project strain</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : anticlockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : VC40429 on food R_2016_02_24__16_38_27___5___4</li> <li><b>total time (s)</b> : 898.967</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 6.08706</li> <li><b>number of segmented skeletons</b> : 26048</li> </ul>
VC40429 Million Mutation Project strain | 2016-02-09T14:55:57+00:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=fJyNAZ_ShcM</li> <li><b>strain</b> : VC40429</li> <li><b>timestamp</b> : 2016-02-09T14:55:57+00:00</li> <li><b>gene</b> : -N/A-</li> <li><b>chromosome</b> : -N/A-</li> <li><b>allele</b> : -N/A-</li> <li><b>strain_description</b> : Million Mutation Project strain</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : clockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : VC40429 on food L_2016_02_09__14_55_57___5___2</li> <li><b>total time (s)</b> : 898.967</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 6.08706</li> <li><b>number of segmented skeletons</b> : 26241</li> </ul>
VC40429 Million Mutation Project strain | 2016-02-10T14:17:03+00:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=4i4Y-or1TiI</li> <li><b>strain</b> : VC40429</li> <li><b>timestamp</b> : 2016-02-10T14:17:03+00:00</li> <li><b>gene</b> : -N/A-</li> <li><b>chromosome</b> : -N/A-</li> <li><b>allele</b> : -N/A-</li> <li><b>strain_description</b> : Million Mutation Project strain</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : anticlockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : VC40429 on food R_2016_02_10__14_17_03___5___1</li> <li><b>total time (s)</b> : 899.0</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 6.08706</li> <li><b>number of segmented skeletons</b> : 26579</li> </ul>
VC40429 Million Mutation Project strain | 2016-02-05T11:40:42+00:00
<blockquote> <p>This experiment is part of the <em>C.elegans behavioural database</em>. For more information and the complete collection of experiments visit http://movement.openworm.org</p> </blockquote> <ul> <li><b>preview link</b> : https://www.youtube.com/watch?v=BCrua7ce3Y8</li> <li><b>strain</b> : VC40429</li> <li><b>timestamp</b> : 2016-02-05T11:40:42+00:00</li> <li><b>gene</b> : -N/A-</li> <li><b>chromosome</b> : -N/A-</li> <li><b>allele</b> : -N/A-</li> <li><b>strain_description</b> : Million Mutation Project strain</li> <li><b>sex</b> : hermaphrodite</li> <li><b>stage</b> : adult</li> <li><b>ventral_side</b> : clockwise</li> <li><b>media</b> : NGM agar low peptone</li> <li><b>arena</b> : <ul> <li><b>style</b> : petri</li> <li><b>size</b> : 35</li> <li><b>orientation</b> : away</li> </ul> </li> <li><b>food</b> : OP50</li> <li><b>habituation</b> : 30m wait</li> <li><b>who</b> : Laura Grundy</li> <li><b>protocol</b> : Method in E. Yemini et al. doi:10.1038/nmeth.2560. Worm transferred to arena 30 minutes before recording starts.</li> <li><b>lab</b> : <ul> <li><b>name</b> : William R Schafer</li> <li><b>location</b> : MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK</li> </ul> </li> <li><b>software</b> : <ul> <li><b>name</b> : tierpsy (https://github.com/ver228/tierpsy-tracker)</li> <li><b>version</b> : cbfc23eb4f1ac2f29be75ade7a937eed58a5b219</li> <li><b>featureID</b> : @OMG</li> </ul> </li> <li><b>base_name</b> : VC40429 on food L_2016_02_05__11_40_42___5___1</li> <li><b>total time (s)</b> : 898.967</li> <li><b>frames per second</b> : 30.03</li> <li><b>video micrometers per pixel</b> : 6.08706</li> <li><b>number of segmented skeletons</b> : 25984</li> </ul>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.