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3,576 results for “strain”
Borehole pressure and temperature data, barometric pressure and temperature data, solid Earth tidal strain, for OmanDP site BA1, 4/18 to 1/19
<p>Borehole (relative) pressure and temperature data for OmanDP site BA1: holes BA1B and BA1D from 4/18 to 1/19.</p> <p>Barometric pressure and temperature data for OmanDP site BA1 from 4/18 to 1/19.</p> <p>Earth tidal strain for the OmanDP site BA1: estimates from PyGTide software from 4/18 to 9/20.</p>
Mechanical behavior of C45 steel at high temperatures and high strain rates—experimental data set and numerical approach
<p>In this publication we provide experimental data of dynamic compression tests of four microstructural variants of the C45 steel alloy performed at high temperatures and high strain rates. The presented data evidences the presence of Dynamic Strain Aging (DSA) in the material. Moreover, we provided the MATLAB codes of a calibration approach to estimate the material parameters of a plasticity model that accounts for DSA.</p> <p>The file "Mechanical behavior of C45" contains:</p> <p>1) Folder EXP_DATA contains experimental data of dynamic compression tests of the C45 steel variants in .mat format. The data is organized in cell arrays, and every cell in the arrays contains the data of one experiment. The data of each experiment is arranged as four columns arrays, as: column 1: Plastic strain, column 2: Flow stress, column 3: absolute temperature, column 4: strain rate</p> <p>2) Matlab code named CALIBRATION.m which executes a calibration approach of a modified Johnson-Cook that accounts for DSA. The form of the model is the following:</p> <p><span class="math-tex">\(\sigma(\varepsilon ,T,\dot{\varepsilon}) = (A+B\varepsilon^n)\left(1+Cln\left(\frac{\dot{\varepsilon}}{\dot{\varepsilon}^{ref}}\right)\right)\left( 1-\left(\frac{T-T^{ref}}{T^{melt}-T^{ref}}\right)^m\right) +\sigma^{dsa}(\varepsilon ,T,\dot{\varepsilon}) \)</span></p> <p>with,</p> <p><span class="math-tex">\(σ^{dsa} (ε,T,\dotε )=\frac{B_1}{ν} \left(\frac{ε^β}{ ε ̇T} exp(-\frac{Q_m}{KT}) \right)^{\frac{2}{3}}\)</span>, <span class="math-tex">\(\frac{B_1}{\nu} = \frac{\psi \dot{\varepsilon}}{exp(\eta \frac{T}{\dot{\varepsilon}^\alpha})} \)</span></p> <p> </p> <p>The code CALIBRATION contains a data presentation section that can be used to generate plots to compare calibrated models with the experimental data. Further instructions are commented in the code CALIBRATION.m.</p>
Strain‐dependent differences in coordination of yeast signalling networks
<p>The yeast mitogen activated protein kinase pathways serve as a model system for understanding how network interactions affect the way in which cells coordinate the response to multiple signals. We have quantitatively compared two yeast strain backgrounds YPH499 and Σ1278b (both of which have previously been used to study these pathways) and found several important differences in how they coordinate the interaction between the high osmolarity glycerol (HOG) and mating pathways. In the Σ1278b background, in response to simultaneous stimulus, mating pathway activation is dampened and delayed in a dose dependent manner. In the YPH499 background, only dampening is dose dependent. Further, leakage from the HOG pathway into the mating pathway (crosstalk) occurs during osmostress alone in the Σ1278b background only. The mitogen activated protein kinase Hog1p suppresses crosstalk late in an induction time course in both strains but does not affect the early crosstalk seen in the Σ1278b background. Finally, the kinase Rck2p plays a greater role suppressing late crosstalk in the Σ1278b background than in the YPH499 background. Our results demonstrate that comparisons between laboratory yeast strains provide an important resource for understanding how signaling network interactions are tuned by genetic variation without significant alteration to network structure.</p>
Dataset for article titled "Assessing continuum plasticity postulates with grain stress and local strain measurements in triaxially compressed sand"
<p>Dataset containing raw and processed data from experiments presented in the article titled "Assessing continuum plasticity postulates with grain-scale stress and strain measurements in triaxially-compressed sand". An enclosed PDF file describes the data.</p>
Raw strain and temperature data for a dump truck, IFV, and semi-truck
<p>Horizontal strain measurements for a dump truck (D), an IFV (K), and a semi-truck (L). The measurements were taken from DTU smart road, which consists of four sections, each with six horizontal strain gauges placed at the bottom of the AC (150 mm depth). There is a reinforcement grid in section 1, 2, and 3. The data was taken as a part of the Master thesis: Investigation of asphalt pavements loaded by heavy off-road vehicles. The thesis contains further details.</p>
Aerogel Spring-Back Correlates with Strain Recovery: Effect of Silica Concentration and Aging - Dataset
<p>Dataset corresponding to the scientific publication:</p> <p>Sivaraman, Deeptanshu, Shanyu Zhao, Subramaniam Iswar, Marco Lattuada, and Wim J. Malfait. "Aerogel Spring‐Back Correlates with Strain Recovery: Effect of Silica Concentration and Aging." <em>Advanced Engineering Materials</em> 23, no. 10 (2021): 2100376. <a href="https://doi.org/10.1002/adem.202100376">https://doi.org/10.1002/adem.202100376</a></p> <p>This project was funded by the Swiss National Science Foundation through grant 200021_179000 (W.J.M). S.I. acknowledges the Flemish agency “Agentschap Innoveren en Ondernemen” (VLAIO) for providing financial support of this research through subvention IWT 130668.</p>
HairSplitter: separating strains in metagenome assemblies with long reads
<p>Datasets, command lines and assemblies analyzed in the manuscript "HairSplitter: separating strains in metagenome assemblies with long reads".</p>
Transgenerational phenotypic plasticity of diapause induction and related fitness cost in a commercial strain of the parasitoid Aphidius ervi Haliday
<p>Dataset.</p> <p>Diapause is an adaptation that insects have evolved to synchronize their life cycle with that of seasonal climatic changes and resources availability. However, cues for its induction are not always clear and, in some cases, a maternal effect may be involved. At the population level, just a part of the individuals may exhibit diapause with important consequences in terms of winter survival. Moreover, clear indicators of diapause state are difficult to identify. Diapause induction was thus investigated in the aphid parasitoid species Aphidius ervi Haliday (Hymenoptera: Braconidae) developing in the aphid Sitobion avenae (Hemiptera: Aphididae) at four crossed photothermal regimes (16 °C and 8 °C, 16:8 h L:D and 8:16 h L:D), and during 2 successive generations. We analyzed the reliability of changes in mummy color to assess for the diapausing state compared to dissections, and we measured parasitoid morphological and physiological traits. We observed that the proportion of dark brown mummies increased after one generation under low photothermal regime compared to other regimes. No diapause was recorded at 16 °C, 16:8 h L:D, while we observed 16.2% and 67.5% diapause incidence at 8 °C, 8:16 h L:D, at 1st and 2nd generation, respectively. Diapause induction is thus increased by short day-length conditions and low temperatures as well as by maternal effects. All parasitoid life-history traits (weight, size, fat content, water content, egg-load, and longevity) were affected by the photothermal regime and/or the generation. These results raise new questions on the environmental thresholds needed to induce diapause and on survival and adaptation potential of commercially available parasitoid strains in different environments.</p>
Draft Genome Sequences of Two Bacteriocin-Producing Enterococcus faecium Strains Isolated from Nonfermented Animal Foods in Spain
<p>Raw sequences of two bacteriocin-producing Enterococcus faecium.</p> <p> </p>
Key files for: Comparative genomic analysis of Microcystis strain diversity using conserved marker genes
<p>Key data outputs to accompany the manuscript "Comparative genomic analysis of Microcystis strain diversity using conserved marker genes"</p>
TRACE-Omicron: Epidemiological Counterfactuals; Tractable Strain
<p>This repository contains the simulation data corresponding to the Epidemiological Counterfactuals under the Tractable Strain baseline scenario in "TRACE-Omicron: Policy Counterfactuals to Inform Mitigation of COVID-19 Spread in the United States" published in Advanced Theory and Simulations (doi:10.1002/adts.202300147)</p>
Data in support of: `Two-Dimensional Strain Mapping with Scanning Precession Electron Diffraction: An Investigation into Data Analysis Routines'
<p>This upload contains data in support of a manuscript currently under review. More details to follow.</p>
Genome annotation file containing predicted genome features of Phytophthora agathidicida (Strain: 3770, Assembly:ASM2572299v1)
<p>This is the genome annotation file (gff3) containing predicted genome features of the <em>Phytophthora agathidicida </em>(Strain: 3770) genome published in Cox et al (2022). This annotation file is associated with the following entries at Genbank:</p> <p>Assembly: ASM2572299v1<br> Biosample: SAMN19597867<br> BioProject: PRJNA734652</p> <p>Included in the file are predicted functional annotations from Blastp search of all predicted proteins sequences against the Swiss-Prot sequence database (Release 23/02).</p>
Supplementary Material to the Publication: Clonal relation between Salmonella enterica subspecies enterica serovar Dublin strains of bovine and food origin in Germany
<p>OHEJP Project: BeOne</p> <p><em>Salmonella enterica </em>serovar Dublin (<em>S</em>. Dublin) is a host-adapted serovar that causes enteritis and/or systemic diseases in cattle. Because the serovar is not host-specific, it can infect other species, including human beings, causing severe disease and a higher mortality rate than other non-typhoidal serovars. Given that human illnesses are primarily caused by contaminated milk, milk products, and beef, data on the genetic connection between <em>S</em>. Dublin strains from livestock and food should be analyzed. </p> <p>Whole genome sequencing (WGS) was performed on 144 <em>S</em>. Dublin strains from cattle and 30 strains from food. Multilocus sequence typing (MLST) found that the majority of livestock and food isolates were of the sequence type ST-10. As discovered by core-genome Single-Nucleotide Polymorphisms Typing and core-genome MLST, 14 of 30 strains from food origin were clonally related to at least one strain from cattle. Without outliers, the remaining 16 food-borne strains fit into the genomic structure of <em>S</em>. Dublin in Germany. WGS demonstrated to be an effective method not only for learning about the epidemiology of Salmonella strains, but also for detecting clonal relationships between organisms isolated at different stages of production. This study discovered a strong genetic link between <em>S</em>. Dublin strains from cattle and food, and thus the potential to cause human infections. <em>S</em>. Dublin strains from both origins have a nearly comparable collection of virulence factors, emphasizing their ability to produce severe clinical symptoms in animals as well as humans, emphasizing the importance of effective <em>S</em>. Dublin management in a farm to fork strategy.</p>
Research data for: Replicative Acinetobacter baumannii strains interfere with phagosomal maturation by modulating the vacuolar pH
<p>Bacterial pneumonia is a common infection of the lower respiratory tract that can afflict patients of all ages. Multidrug-resistant strains of <em>Acinetobacter</em> <em>baumannii</em> are increasingly responsible for causing nosocomial pneumonias, thus posing an urgent threat. Alveolar macrophages play a critical role in overcoming respiratory infections caused by this pathogen. Recently, we and others have shown that new clinical isolates of <em>A. baumannii</em>, but not the common lab strain ATCC 19606 (19606), can persist and replicate in macrophages within spacious vacuoles that we called Acinetobacter Containing Vacuoles (ACV). In this work, we demonstrate that the modern <em>A. baumannii</em> clinical isolate 398, but not the lab strain 19606, can infect alveolar macrophages and produce ACVs in vivo in a murine pneumonia model. Both strains initially interact with the alveolar macrophage endocytic pathway, as indicated by EEA1 and LAMP1 markers; however, the fate of these strains diverges at a later stage. While 19606 is eliminated in an autophagy pathway, 398 replicates in ACVs and are not degraded. We show that 398 reverts the natural acidification of the phagosome by secreting large amounts of ammonia, a by-product of amino acid catabolism. We propose that this ability to survive within macrophages may be critical for the persistence of clinical <em>A. baumannii </em>isolates in the lung during a respiratory infection.</p>
Data for: Genome editing of an African elite rice variety confers resistance against endemic and emerging Xanthomonas oryzae pv. oryzae strains
<p class="MsoNormal"><span>Bacterial leaf blight (BB) of rice, caused by <em>Xanthomonas oryzae </em>pv<em>. oryzae</em> (<em>Xoo</em>), threatens global food security and the livelihood of small-scale rice producers.<em> </em>Analyses of <em>Xoo</em> collections from Asia, Africa and the Americas demonstrated complete continental segregation, despite robust global rice trade. Here, we report unprecedented BB outbreaks in Tanzania. The causative strains, unlike endemic African <em>Xoo</em>, carry Asian-type TAL effectors targeting the sucrose transporter <em>SWEET11a</em> and iTALes suppressing <em>Xa1</em>. Phylogenomics clustered these strains with <em>Xoo</em> from Southern-China. African rice varieties do not carry effective resistance. To protect African rice production against this emerging threat, we developed a hybrid CRISPR-Cas9/Cpf1 system to edit all known TALe-binding elements in three <em>SWEET</em> promoters of the East African elite variety Komboka. The edited lines show broad-spectrum resistance against Asian and African strains of <em>Xoo</em>, including strains recently discovered in Tanzania. The strategy could help to protect global rice crops from BB pandemics.</span></p>
Johnson 2023 Strain Rate and Velocity Realizations for Western US
<p>This data set contains inversion results presented in Johnson (2023, submitted to JGR, Disagreements in geodetically inferred strain rates in the Western US with stress orientations and geologic moment rates). The data files contain 1500 realizations of 3 surface strain rate components and two velocity components. </p>
Variation among strains of Borrelia burgdorferi in host tissue abundance and lifetime transmission determine the population strain structure in nature
<p class="MsoNormal">Pathogen life history theory assumes a positive relationship between pathogen load in host tissues and pathogen transmission. Empirical evidence for this relationship is surprisingly rare due to the difficulty of measuring transmission for many pathogens. The comparative method, where a common host is experimentally infected with a set of pathogen strains, is a powerful approach for investigating the relationships between pathogen load and transmission. The validity of such experimental estimates of strain-specific transmission is greatly enhanced if they can predict the pathogen population strain structure in nature.</p> <p class="MsoNormal"><em>Borrelia burgdorferi</em> is a multi-strain, tick-borne spirochete that causes Lyme disease in North America. This study used 11 field-collected strains of <em>B. burgdorferi</em>, a rodent host (<em>Mus musculus, </em>C3H/HeJ) and its tick vector (<em>Ixodes scapularis</em>) to determine the relationship between pathogen load in host tissues and lifetime host-to-tick transmission (HTT). Mice were experimentally infected via tick bite with 1 of 11 strains. Lifetime HTT was measured by infesting mice with <em>I. scapularis </em>larval ticks on 3 separate occasions. The prevalence and abundance of the strains in the mouse tissues and the ticks were determined by qPCR. We used published databases to obtain estimates of the frequencies of these strains in wild <em>I. scapularis</em> populations.</p> <p>Spirochete loads in ticks and lifetime HTT varied significantly among the 11 strains of <em>B. burgdorferi</em>. Strains with higher spirochete loads in the host tissues were more likely to infect feeding larvae, which molted into nymphs with a higher probability of <em>B. burgdorferi</em> infection (<em>i.e.</em>, higher HTT). Our laboratory-based estimates of lifetime HTT were predictive of the frequencies of these strains in wild <em>I. scapularis</em> populations. For <em>B. burgdorferi</em>, the strains that establish high abundance in host tissues and that have high lifetime transmission are the strains that are most common in nature.</p>
Micrographs of strains with MultiduBE before and after induction
<p>For the verification of MultiduBE-promoted fluorescent and morphology diversification, the crRNA array YKTmf5C-Sp4 was assembled into the mixture of pWLT-duBE-1a and pWLT-duBE-2b and then transformed into strain BSZRG-CmYKT. The results colonies were scraped from the plate and inoculated in a 50-mL sterile tube containing 10 mL LB media with kanamycin for pre-culture for about 10 h. Subsequently, the pre-culture was inoculated in a 14-mL sterile tube containing 2 mL LB-kanamycin media without aTC and a 14-mL sterile tube containing 2 mL LB-kanamycin media with 0.5 μM aTC, respectively. The two group cultures (without induction and with induction) were analyzed by Laser Scanning Confocal Microscopy (LSCM) and flow cytometry.</p>
gapseq reconstruction for 36 human gut bacterial strains with known amino acid auxotrophy status
<p>The data set contains genome-scale metabolic network reconstructions for 36 bacterial genomes, for which the auxotrophy/prototrophy status for amino acids has been reported in scientific literature based on laboratory experiments. Auxotrophy/Prototrophy information and the respective PubMed-IDs (PMID) are summarized in "Validation_models_Metadata.csv". Network reconstructions were made using gapseq (development version: 1.2 commit 2dfa8c80 ; Sequence DB md5sum: bf8ba98 (2023-02-15, Bacteria).</p> <p>The models were reconstructed using the following workflow.</p> <pre><code># Reaction & Pathway prediction ./gapseq find -b 200 -v 1 -p all -k -t Bacteria <genomeID>.fna.gz # Transporter prediction ./gapseq find-transport -b 200 -k <genomeID>.fna.gz # Draft network reconstruction ./gapseq draft -r <genomeID>-all-Reactions.tbl -t <genomeID>-Transporter.tbl -b Bacteria -c <genomeID>.fna.gz -p <genomeID>-all-Pathways.tbl -u 200 -l 100 # gapfill/growth medium prediction ./gapseq medium -m <genomeID>-draft.RDS -p <genomeID>-all-Pathways.tbl -c "cpd00007:0" # Gap-filling # (If H2 is part of the medium) ./gapseq fill -m <genomeID>-draft.RDS -n <genomeID>-medium.csv -c <genomeID>-rxnWeights.RDS -g <genomeID>-rxnXgenes.RDS -b 100 -e highH2 # (If H2 is not part of the medium) ./gapseq fill -m <genomeID>-draft.RDS -n <genomeID>-medium.csv -c <genomeID>-rxnWeights.RDS -g <genomeID>-rxnXgenes.RDS -b 100</code></pre> <p> </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
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.