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3,576 results for “strain”
Supplementary dataset to publication: Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes.
<p>This is the modified supplemented material to the publication “Complete genome sequence of ovine Mycobacterium avium subsp. paratuberculosis strain JIII-386 (MAP-S/type III) and its comparison to MAP-S/type I, MAP-C, and M. avium complex genomes”.</p> <p>The complete circular genome of Mycobacterium avium subsp. paratuberculosis (MAP) strain JIII-386 from Germany, closed by Nanopore technology in this study, was presented and compared with the draft genome of JIII-386, previously published in [doi:10.1093/gbe/ew154], the closed genome of the MAP-S/type I strain Telford, the MAP-S/type III draft genome of strain S397, twelve closed MAP-C (type II) strains and eight closed Mycobacterium avium (M. a.) strains of subsp. hominissuis (MAH) and subsp. avium (MAA). Structural comparisons clearly revealed the mosaic nature of MAP genomes, the differences between MAP subtypes I, II and III, and the higher diversity of MAP-S compared to MAP-C genomes. </p> <p>The material provides a wealth of detailed results from these analyses and comparisons. These include a list of identified ncRNA and Riboswitches, as well as additional genes in finished JIII-386, the gene content of identified prophage regions, copy number of identified transposable elements and a list of selected virulence-associated genes in the different MAP-type (I - III) strains. The genomic islands identified and included genes along with their predicted functions were presented for six MAP genomes (belonging to MAP-S/type I and III, and MAP-C), one MAH genome and one MAA genome. One table shows the corresponding genomic islands in the genomes of JIII-386, Telford and three MAP-C genomes. Furthermore, homologous genes of known MAP-S specific Large Sequence Polymorphisms regions (LSP<sup>S</sup> = LSP-S) were recorded in different MAP-S type strains, one MAH and one MAA strain, as well as genes of deletions #1 (LSP<sup>A</sup>-20), #2, and s-delta-1, previously described as MAP-S-specific deletions, their presence or absence in 3 MAP-S, 12 MAP-C, 4 MAH, and 4 MAA strains were listed. Different presence or absence of genes, but also identified frameshifts or disruptions of various virulence-associated genes could lead to the different MAP-type specific phenotypic characteristics. Comprehensive core and pan genome analyses (results listed in six tables) revealed unique genes and genes likely to have been acquired by horizontal gene transfer in different MAP types and subtypes, but also emphasized the highly conserved and close relationship, and the complex evolution of M. a. strains.</p> <p> </p>
Dataset of "The Impact of Local Strain Fields in Noncollinear Antiferromagnetic Films"
<p>Antiferromagnets hosting structural or magnetic order that breaks time reversal symmetry are of increasing interest for “beyond von Neumann” computing applications because the topology of their band structure allows for intrinsic physical properties, exploitable in integrated memory and logic function. One such group are the noncollinear antiferromagnets. Essential for domain manipulation is the existence of small net moments found routinely when the material is synthesized in thin film form and attributed to symmetry breaking caused by spin canting, either from the Dzyaloshinskii–Moriya interaction or from strain. Although the spin arrangement of these materials makes them highly sensitive to strain, there is little understanding about the influence of local strain fields caused by lattice defects on global properties, such as magnetization and anomalous Hall effect. This premise is investigated by examining noncollinear antiferromagnetic films that are either highly lattice mismatched or closely matched to their substrate. In either case, edge dislocation networks are generated and for the former case, these extend throughout the entire film thickness, creating large local strain fields. These strain fields allow for finite intrinsic magnetization in seemingly structurally relaxed films and influence the antiferromagnetic domain state and the intrinsic anomalous Hall effect. The dataset consists of total energies calculated by density functional theory (VASP). The experimental data presented in the paper were obtained by international partners not supported by OP-JAK project.</p>
Dataset of "Strain-Engineered Ir Shell Enhances Activity and Stability of Ir-Ru Catalysts for Water Electrolysis: An Operando Wide-Angle X-Ray Scattering Study"
<p>Ir-Ru alloys with high Ru content serve as stable and highly active catalysts for the oxygen evolution reaction (OER) in Proton Exchange Membrane Water Electrolyzers (PEM-WEs), enabling efficient operation with remarkably low Ir loadings (150 µg cm-²). Despite this, the mechanisms behind their enhanced stability remain unclear. In this study, we employ operando Wide-Angle X-ray Scattering (WAXS) and complementary ex-situ techniques to investigate the structural evolution of these magnetron-sputtered alloys within a PEM-WE cell. Our results reveal that, upon potential application, Ru is leached from the surface, leading to the formation of a bimetallic Ir-Ru@IrOx core-shell structure. The Ir shell, significantly strained by the underlying Ir-Ru core, exhibits substantially higher catalytic activity than pure Ir. Notably, the Ir-Ru 25:75 catalyst shows superior stability over Ir-Ru 50:50, despite its higher Ru content, due to a more robust Ir shell that protects subsurface Ir and Ru from oxidation and dissolution. This study not only clarifies the performance-enhancing mechanisms of Ir-Ru catalysts but also suggests that other, more economical materials such as Co, Os, or Ti could serve as effective cores in Ir-M systems, offering a pathway to more cost-effective catalysts for PEM-WE applications.</p>
Comparative proteomics analysis of whole-cell catalyst of K. rhizophila strain SA117 catabolism of SMX
<p><span>Sulfamethoxazole (SMX), an oral sulfonamide antibiotic, presents significant environmental challenges due to its persistence and potential role in promoting antibiotic resistance. The bacterial strain <em><span>Kocuria rhizophila</span></em> SA117, isolated from polluted soils, has demonstrated a remarkable capability to metabolize SMX. Proteomic analysis revealed the presence of various enzymes and metabolic pathways that may contribute to SMX degradation, including those involved in para-aminobenzoate condensation and protocatechuate metabolism. Notably, the genome of SA117 harbors eight monooxygenase genes, including those related to antibiotic biosynthesis and flavin family monooxygenases. Additionally, several cytochrome c-encoding genes, known for their role in respiratory versatility and potential application in bioremediation, were identified. Genes associated with sulfur metabolism, including an iron-sulfur cluster gene cluster (SufB, C, D, R, E) linked to oxidative stress response, were also found. A comparative proteomic study under SMX exposure highlighted significant upregulation of stress-related proteins. These findings underscore the metabolic adaptability of <em><span>Kocuria rhizophila</span></em> SA117 and its potential application in the bioremediation of SMX-contaminated environments.</span></p>
Ring-shear experiments with strain markers
<p><strong>Experiment overview</strong></p> <table> <caption> </caption> <thead> <tr> <th scope="col">ID</th> <th scope="col">Shearing velocity [mm/min]</th> <th scope="col">Effective normal stress [kPa]</th> </tr> </thead> <tbody> <tr> <td>mdt4</td> <td>7.00</td> <td>6</td> </tr> <tr> <td>mdt5</td> <td>0.70</td> <td>6</td> </tr> <tr> <td>mdt6</td> <td>0.07</td> <td>6</td> </tr> <tr> <td>mdt7</td> <td>7.00</td> <td>50</td> </tr> <tr> <td>mdt8</td> <td>0.70</td> <td>50</td> </tr> <tr> <td>mdt9</td> <td>0.07</td> <td>50</td> </tr> </tbody> </table> <p><br> <strong>Apparatus and material</strong></p> <p>These experiments were conducted in a ring-shear apparatus at the Department of Geoscience, Aarhus University, with a sample chamber volume of 14,48 l. The till was Mid-Danish Till deposited at the Last Glacial Maximum, and sampled at Knud Strand, Denmark. All shearing commenced under water-saturated conditions, and I used BB-gun pellets as strain markers.</p> <p>Please see the following publication for more technical details on the ring-shear apparaturs:</p> <blockquote> <p>Damsgaard, A., D. L. Egholm, J. A. Piotrowski, S. Tulaczyk, N. K. Larsen, and K. Tylmann (2013), Discrete element modeling of subglacial sediment deformation, J. Geophys. Res. Earth Surf., 118, 2230–2242, doi:10.1002/2013JF002830.</p> </blockquote> <p><br> <strong>Data files and format</strong></p> <p><em>Sensor data during shear</em></p> <p>These data files are named in the style "<ID>-stress-shear.tsv", where<br> ID refers to the experiment ID seen in the table above.</p> <p>The values are tab-separated, with the following columns and units:</p> <ol> <li>Shearing distance [mm]</li> <li>Normal stress [kPa]</li> <li>Shear stress [kPa]</li> <li>Dilation [mm]</li> </ol> <p>Important!: The shear stress readings are unreliable due to sensor failure.</p> <p><em>Strain marker data</em></p> <p>These data files are named in the style "<ID>-shear-disp.tsv". The values are tab-separated, with the following columns and units:</p> <ol> <li>Marker position along shear direction [mm]</li> <li>Marker depth [mm]</li> </ol> <p><br> <strong>Author and funding</strong></p> <p>Anders Damsgaard <anders@adamsgaard.dk>, Department of Geoscience, Aarhus University</p> <p>This dataset is part of a project that has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 897967.</p>
Refinements for Bragg coherent X-ray diffraction imaging: Electron backscatter diffraction alignment and strain field computation
<p>Here we present the final crystal reconstructions and analysis scripts for the paper titled "Refinement for Bragg coherent X-ray diffraction imaging: Electron backscatter diffraction alignment and strain field computation" published in Journal of Applied Crystallography, 55, 2022. Please see the README file for more information.</p>
Manipulating a host-native microbial strain compensates for low microbial diversity by increasing weight gain in a wild bird population
<h1>Manipulating a host-native microbial strain compensates for low microbial diversity by increasing weight gain in a wild bird population</h1> <h1> </h1> <p>These files contain data on bacteria present in the guts of wild great tit (Parus major) obtained from faecal samples and sequenced using Illumina MiSeq. These data resulted from an experiment which provided supplementary mealworms at the nest during the breeding season at number of woodland sites in Cork, Ireland. Approximately half of these nests were given mealworms covered in a freeze dried bacterial powder containing the bacteria Lactobacillus kimchicus, which had been isolated from great tit faeces from the previous season. This treatment aimed to disrupt the gut microbiota of the treatment birds in order to provide evidence for the gut microbiotas role in birds health and fitness. Included here are the 3 elements necessary to create a 'phyloseq object' containing the sample metadata, ASV (Amplicon Sequence Variant) count table and a taxonomy table. The metadata file includes the alpha diversity scores for each individual. The data include all negative control samples taken during sample collection and library preparation, which were removed before the main analyses. All analyses, except for the beta-diversity analyses, were conducted in R. All R code is available on GitHub (https://github.com/shan-e-s\). Raw Sequence data are available in the European Nucleotide Archive under access number PRJEB74941, and ERS18960426-ERS18960697.</p> <h2> </h2> <h2>## Description of the data and file structure </h2> <p>Taxonomy, ASV and metadata files required to create a phyloseq object in R. metadata.csv file contains data on individual birds (i.e. individual samples). The metadata includes descriptions of the bird itself and it's environment, namely:</p> <ul> <li>Rownames: unique sample ID for each sample, corresponds with asvTable.csv. </li> <li>Nest: unique identifier for the nest box associated with the bird being sampled. </li> <li>Sample.ID: unique identifier for the faecal sample or control sample.</li> <li>Bird.ID: Identity of the bird the sample came from, note some individuals sampled twice so some bird.ID's may reoccur in metadata with different Sample.ID.</li> <li>Date: Date the sample was taken dd/mm/yyyy.</li> <li>Day: Date the sample was taken, in days since 1st March.</li> <li>Ring.Mark: British Trust for Ornithology (BTO) metal ring ID where applicable. Birds only ringed at D15 so some young birds do not have IDRings.</li> <li>Site: ID of woodland site that bird was sampled at.</li> <li>Chick.LetterID: ID letter differentiates between different birds from the same nest. Either 'A'-'F' for nestlings, 'Fe' for females or 'M' for males.</li> <li>Age.code: BTO age code.</li> <li>Age.category: Age category that bird is in. D8 = 8 days post hatching, D15 = 15 days post hatching, adult = 1+ years post hatching.</li> <li>Sex: Bird's sex, only determined for adult birds. Fe = Female, M = Male.</li> <li>Wing_mm: Wing length in mm.</li> <li>Tarsus_mm: minimum tarsus length of bird in mm.</li> <li>Weight_g: bird's weight in grams.</li> <li>Faecal.Sample: bird's age at sampling.</li> <li>newRing: whether bird was fitted with a new BTO ring. Only relevant to adults.</li> <li>Treatment: the experimental treatment group that the bird was in. Either 'Treatment' when nest given L. kimchicus treated mealworms or 'Control' when nest given plain mealworms.</li> <li>Notes: field notes.</li> <li>Main.sample: indicates whether this sample was the main sample to be used for analysis, an alternative sample taken as a backup.</li> <li>Plate: the ID of the PCR plate which the sample was amplified on.</li> <li>Azenta_noPeriod: sample ID given to sequencing facility without special characters. Corresponds to fastq files and ASV table counts.</li> <li>Qubit_prePool: samples qubit score before pooling.</li> <li>Date_extracted: date the sample was extracted on dd/mm/yyyy.</li> <li>SampleType: whehther the sample was a 'main' sample intended for downstream analysis, a 'control' sample for detecting contamination during library preparation, a 'duplicate' for detecting PCR issues, a 'label_error' where sample was suspected of being mislabelled at some point, a 'repeat' sample intended to detect errors or issues, a 'contam' sample which was suspected of being contaminated, a 'common' sample used across different PCR plates to detect issues. Extraction_notes: notes regarding the DNA extraction of the sample. </li> <li>LibPrep_notes: notes regarding the library preparation of the sample.</li> <li>Ring.Mark.lab: the ring or sample ID written on the sample tube, recorded to help detect mislabelling.</li> <li>Post_lab_notes: notes regarding issues found post sequencing.</li> <li>NumberOfReads: number of sequence reads associated with the sample. </li> <li>DistanceToEdge: distance between nest and woodland edge in metres. </li> <li>BroodSize.D8: number of nestlings in the nest at day-8 post hatching. </li> <li>BroodSize.D15: number of nestlings in the nest at day-15 post hatching.</li> <li>firstEggLayDate: Date the first egg in the clutch was laid, in days since 1st March.</li> <li>lastEggLayDate: Date the last egg in the clutch was laid, in days since 1st March.</li> <li>Observed: number of unique ASV's (or taxa) detected in the sample.</li> <li>Chao1: Chao1 diversity of the sample.</li> <li>Shannon: Shannon diversity of the sample.</li> </ul> <p>The file 'taxonomy.csv' contains the taxonomic breakdown of each bacterial Amplicon Sequence Variant (ASV) found in the dataset from Phylum to Species. Obtained by using the Naive Bayes Classifier against the Silva (v138) taxonomic database.</p> <p>The file 'asvTable.csv' contains counts of each amplicon sequence variant's occurrence for each individual sample. Samples are rows and taxa are columns.</p> <p> </p> <h2>Sharing/Access information </h2> <p>All R code is available on GitHub (https://github.com/shan-e-s\). Raw Sequence data are available in the European Nucleotide Archive under access number PRJEB74941, and ERS18960426-ERS18960697.</p>
Genome drafts of Lotmaria passim strains C2 and C3 isolated from honeybees in Spain
<p>Lotmaria passim is a highly prevalent parasite of honeybees. Herein is reported the draft genome sequences of L. passim C2 and C3 strains of 27.15 Mbp and 26.94 Mbp, respectively. The genomes were sequenced using Illumina MiSeq platform and will allow for further comparative and functional genomics studies.</p>
Data and code related to the paper: "Integrated stretchable pneumatic strain gauges for electronics-free soft robots"
<p>This folder contains the raw data and Matlab scripts to reproduce the plots and supplementary movies for the paper:</p> <p>Anastasia Koivikko, Vilma Lampinen, Mika Pihlajamäki, Kyriacos Yiannacou, Vipul Sharma & Veikko Sariola, "Integrated Stretchable Pneumatic Strain Gauges for Electronics-Free Soft Robots", Communications Engineering, 1, 14 (2022).</p> <p><a href="https://doi.org/10.1038/s44172-022-00015-6">Link to the paper</a>.</p> <p>The scripts were tested on Matlab R2021a on Windows.</p> <p>Generally speaking, there is a folder containing the plotting scripts for each figure. In most cases, the folder contains scripts named <strong>plot<...>.m</strong> that recreate the actual plots. Some folders also have a scripts <strong>analyze<...>.m</strong> to analyze the data; these need to be run before the actual plotting.</p> <p>For more details, please see the paper.</p>
Data publication supplementing "Novel nanoindentation strain rate sweep method for continuously investigating the strain rate sensitivity of materials at the nanoscale"
<p>This data publication contains the results of nanoindentation tests on Fused silica, nanocrystalline nickel, a nanocrystalline FeCr alloy, a bulk metallic glass, the superplastic alloy Zn-22%Al and single crystalline aluminum as well as the method files developed for the G200 nanoindenter. It supplements the publication "Novel nanoindentation strain rate sweep method for continuously investigating the strain rate sensitivity of materials at the nanoscale". The materials are described in more detail in the respective publication. The data publication takes over the sample naming convention from the related publication. </p><p>Nanoindentation measurement were performed by H. Holz at the Max-Planck Institut für Eisenforschung GmbH, Max-Planck-Straße 1, 40237 Düsseldorf, Germany using a G200 nanoindenter (KLA, Milpitas, CA, USA), equipped with a modified Berkovich diamond indenter tip of the type 171-561-500 with a serial number of C-0040446 from Synton MDP (Nidau, Switzerland). Constant strain rate tests, strain rate jump tests, strain rate sweep tests and strain rate sweep reversal tests were performed on each material in Continuous Stiffness Measurement (CSM) mode. The maximum indentation depth was 2200 nm, the CSM amplitude 2 nm and the CSM frequency 45 Hz. Strain rates were varied within the range 0.001 – 0.1 s-1. Further information on the test protocol can be found in the corresponding publication.</p><p>The subfolder "Nanoindentation data" contains the raw data for all valid indents as output by the NanoSuite © software v 7.1.7 and converted to the semicolon-separated format. The naming convention for the folder in which the CSV files are located in gives first the used material, then the method used with additional information to the parameters inputted for the method such as strain rate and indentation depth all separated by an underscore. An example can be "FS_CSR_01s-1" for a constant strain rate tests performed on fused silica with a strain rate target of 0.1 s-1 or "Nc-Ni_SweepReversal_005s-1_0005s-1" for a sweep reversal test performed on the nanocrystalline nickel sample with a targeted initial and ending strain rate of 0.05 s-1 and a strain rate target at which the strain rate direction gets reversed of 0.005 s-1. The CSV files are named either "Results" giving the average results of each test, "Required Inputs" giving information about the parameters used for the experiments, "Inputs Editable Post Test" giving information about the analysis parameters to obtain the results from, and "Test XXX" which include the Raw data of the corresponding test number. In each file the first row gives the data description e.g., "Time", the second row the physical unit e.g., "s" for seconds and from the third row the measured values.</p><p>The Nano Suite method files to perform the experiments on KLA G200 instruments is provided in the folder "G200 methods". The method for the strain rate sweep experiments is called "Strain Rate Sweep.msm" and the method for the strain rate sweep reversal experiments "Strain Rate Sweep Reversal.msm". This method is provided as is and shall be used at your own risk. The authors explicitly decline responsibility for any physical or immaterial damage resulting from the use of this method. Should minor issues occur, some feedback to the authors would be greatly appreciated.</p>
ds-uct-002: Root Canal Strain: X-Ray micro-CT of four teeth before and after root canal procedure.
<p><strong>Summary</strong>:<br> .X-Ray micro-computed tomography (micro-CT) of four teeth before (TomoB) and after (TomoA) simulation of root canal treatment and retreatment procedures instrumented with strain-gauge, including reconstructions, for two different resolutions (TomoB and TomoA with voxel sizes of 20.0 μm and 10.5 μm, respectively).<br> .The 3D image was generated with an X-Ray micro-CT Scanner version Xradia Versa 510 from Zeiss performed by A Pereira at the UFF micro-CT Facility.<br> .For use of these data, please remember to cite the DOI of the Zenodo repository and relevant papers.</p> <p><strong>Details</strong>:<br> .Tomo1B/Tomo2B/Tomo3B/Tomo4B (1024) - Voxel size: 20.0 μm; Sample-source: 45.0 mm; Sample-detector: 110 mm; Optical magnification: 0.4X; Filter: LE#1; Beam energy: 60 kV; Power: 5 W; Exposure time: 2.0 sec; Projections: 1600.<br> .Tomo1A/Tomo2A/Tomo3A/Tomo4A (2048) - Voxel size: 10.5 μm; Sample-source: 48.2 mm; Sample-detector: 110 mm; Optical magnification: 0.4X; Filter: LE#2; Beam energy: 60 kV; Power: 5 W; Exposure time: 7.0 sec; Projections: 1600.</p> <p><strong>Contents</strong>:<br> ._info_ds-uct-002.txt<br> .ds-uct-002_root_canal_strain_tomo1b_20um_8bits.zip<br> .ds-uct-002_root_canal_strain_tomo2b_20um_8bits.zip<br> .ds-uct-002_root_canal_strain_tomo3b_20um_8bits.zip<br> .ds-uct-002_root_canal_strain_tomo4b_20um_8bits.zip<br> .ds-uct-002_root_canal_strain_tomo1a_10um_8bits.zip<br> .ds-uct-002_root_canal_strain_tomo2a_10um_8bits.zip<br> .ds-uct-002_root_canal_strain_tomo3a_10um_8bits.zip<br> .ds-uct-002_root_canal_strain_tomo4a_10um_8bits.zip<br> .PB_PARECER_CONSUBSTANCIADO_CEP_2650528.pdf</p>
Tuning the Thermal Stability and Photoisomerization of Azoheteroarenes through Macrocycle Strain
<p>Azobenzene and its derivatives are one of the most-widespread molecular scaffolds in a range of modern applications, as well as in fundamental research. After photoexcitation, azo-based photoswitches revert back to the most stable isomer in a timescale ( ) that determines the range of potential applications. Attempts to bring to extreme values prompted to the development of azobenzene and azoheteroarene derivatives that either rebalance the E- and Z- isomer stabilities, or exploit unconventional thermal isomerization mechanisms. In the former case, one successful strategy has been the creation of macrocycle strain, which tends to impact the E/Z stability asymmetrically, and thus significantly modify . On the bright side, bridged derivatives have shown an improved optical switching owing to the higher quantum yields and absence of degradation. However, in most (if not all) cases, bridged derivatives display a <em>reversed</em> thermal stability (more stable Z-isomer), and smaller than the acyclic counterparts, which restricts their potential interest to applications requiring a fast forward and backwards switch. In this paper, we investigate the impact of alkyl bridges to the thermal stability of phenyl-azoheteroarenes using computational methods, and we reveal that is indeed possible to combine such improved photo-switching characteristics while preserving the <em>regular</em> thermal stability (more stable E-isomer), and increased values under the appropriate connectivity and bridge length.</p>
Time-lapse 3D confocal microscopy videos of mitochondrial dynamics in human alveolar epithelial cells (A549-DsRed) infected with Mycobacterium marinum (Mmar) strains
<div>The dataset consists of time-lapse, 3D confocal images of mitochondrial dynamics in human alveolar epithelial cells (A549-DsRed) infected with Mycobacterium marinum (Mmar) strains. Images were captured at 60X magnification in an environmental chamber at 35°C for live-cell imaging. Host cell mitochondria were labeled with red fluorescent protein (RFP) and infected with both wildtype (wt) and ESAT-6 operon knockout mutant labeled with green fluorescent protein (GFP) at MOI of 100 for 24 hours at 35°C. Infected cells were identified and analyzed to explore the effect of pathogenic mycobacteria on mitochondrial morphology over time.</div> <div> </div> <div>More details available in this preprint: <a href="https://doi.org/10.48550/arXiv.2411.06035">https://doi.org/10.48550/arXiv.2411.06035</a></div>
Gene tagging and gene deletion resources for Leishmania mexicana MNYC/BZ/62/M379 Cas9/T7 strain
<p><em>primers_barcodes.csv</em>: List of primer sequences necessary for N and C terminus gene tagging, as well as gene deletion in the Leishmania mexicana MNYC/BZ/62/M379 Cas9/T7 strain. Each row contains the gene name and the DF (downstream forward), DR (downstream reverse), DSG (downstream guide sRNA), UF (upstream forward), UFB (upstream forward including a gene-unique 17nt barcode sequence), UR (upstream reverse), USG (upstream guide sRNA), VF (verification forward) and VR (verification reverse) primer sequences. Empty cells indicate that it was not possible to design this primer for this gene. Guide sRNA perfect match and off-target counts are included as well. The primer sequences were designed using LeishGEdit (http://www.leishgedit.net). Barcode sequences and assigned IDs for the unique identification of knock-out or tagged strains are included as separate columns. For recommended methods for endogenous tagging or gene deletion see Beneke <em>et al., </em>R. Soc. Open Sci.4170095 (2017), for generating barcoded deletion mutants see Beneke and Gluenz, Mol. Biochem. Parasitol. 239 (2020).</p> <p><em>genome.gff</em>: Annotated genome of the <em>L. mexicana</em> MNYC/BZ/62/M379 strain, genetically modified to express T7 RNA polymerase and Cas9. The annotation is provided in a combined GFF3 / FASTA format that also includes the sequences of the chromosomes and small contigs. The annotation also specifies polyadenylation sites (PAS features) and splice leader acceptor sites (SLAS features) which were used to refine the boundaries of protein-coding sequences as well as 3' and 5' untranslated regions over the reference genome of <em>L. mexicana</em> MNYC/BZ/62/M379<em>.</em></p> <p><em>c9t7_sequences.fasta</em>: Raw chromosome and contig sequences in FASTA format.</p> <p><em>c9t7_transcripts.fasta</em>: mRNA transcript sequences in FASTA format (includes 5' and 3' UTRs).</p> <p><em>c9t7_transcript_CDSs.fasta</em>: Coding sequences in FASTA format.</p> <p><em>c9t7_predicted_protein_sequences.fasta</em>: Predicted protein amino acid sequences in FASTA format.</p> <p>Note: This version provides an update for <em>c9t7_transcript_CDSs.fasta, c9t7_predicted_protein_sequences.fasta</em> and <em>genome.gff</em>, correcting an off-by-one sequence coordinate in 48 of the the protein-coding genes.</p>
Strain path change characterization of dual-phase steel (DP780) using non-linear strain path experiments: true strain-stress and equivalent strain-stress data
<p>Strain path change characterization of dual-phase steel (DP780) using non-linear strain path experiments: true strain-stress and equivalent strain-stress data.</p>
Annotation of the the assembled genome of Fusarium oxysporum f. sp. albedinis strain 133, the causal agent of date palm dieback.
<p>Annotation of the the assembled genome of <em>Fusarium oxysporum f. sp. albedinis</em> strain 133 (Khayi et al., 2020). Gene prediction and annotation were carried out using funnotate pipeline v1.8.1 (Stajich, 2020), which includes masking, ab initio gene-prediction training, using Augustus and Genmark, with the EST dataset reported to the Ganoderma mycocosm repository, gene prediction, and the assignment of functional annotation to protein-coding gene models.</p>
Fabrication of a Soft Robotic Gripper With Integrated Strain Sensing Elements Using Multi-Material Additive Manufacturing
<p>With the purpose of making soft robotic structures with embedded sensors, additive manufacturing techniques like fused deposition modeling (FDM) are popular. Thermoplastic polyurethane (TPU) filaments, with and without conductive fillers, are now commercially available. However, conventional FDM still has some limitations because of the marginal compatibility with soft materials. Material selection criteria for the available material options for FDM have not been established. In this study, an open-source soft robotic gripper design has been used to evaluate the FDM printing of TPU structures with integrated strain sensing elements in order to provide some guidelines for the material selection when an elastomer and a soft piezoresistive sensor are combined. Such soft grippers, with integrated strain sensing elements, were successfully printed using a multi-material FDM 3D printer. Characterization of the integrated piezoresistive sensor function, using dynamic tensile testing, revealed that the sensors exhibited good linearity up to 30% strain, which was sufficient for the deformation range of the selected gripper structure. Grippers produced using four different TPU materials were used to investigate the effect of the Shore hardness of the TPU on the piezoresistive sensor properties. The results indicated that the <em>in situ</em> printed strain sensing elements on the soft gripper were able to detect the deformation of the structure when the tentacles of the gripper were open or closed. The sensor signal could differentiate between the picking of small or big objects and when an obstacle prevented the tentacles from opening. Interestingly, the sensors embedded in the tentacles exhibited good reproducibility and linearity, and the sensitivity of the sensor response changed with the Shore hardness of the gripper. Correlation between TPU Shore hardness, used for the gripper body and sensitivity of the integrated <em>in situ</em> strain sensing elements, showed that material selection affects the sensor signal significantly.</p>
Dataset of MTBC strains for training/educational purposes
<p>20 WGS of representatives of the <em>Mycobacterium tuberculosis</em> complex. Names on the files are the same as the run accession number. Metadata associated can thus be obtained from NCBI or EBI using the respective accession number.</p>
Beyond Substrates: Strain Engineering of Ferroelectric Membranes
<p>Dataset for publication:</p> <p>Beyond Substrates: Strain Engineering of Ferroelectric Membranes</p> <p>D. Pesquera, E. Parsonnet, A. Qualls, R. Xu, A.J. Gubser, J. Kim, Y. Jiang, G. Velarde, Y. Huang, H.Y. Hwang, R. Ramesh, and L.W. Martin, Adv. Mater. <strong>32</strong>, 2003780 (2020).</p> <p> </p> <p>Matlab code for producing Fig.1d, Fig.2a and Fig.4b is given in .txt files</p>
Combining Horizontal Strain DAS and Local Seismic Stations in a Full Waveform Attribute Stacking Detector/Locator Algorithm: Verification Test for the Thorbjörn, Iceland, 2020 Unrest Episode
<p>We present a waveform stacking-based earthquake catalog of the seismicity unrest episode in the Svartsengi fissure swarm close to Mt. Thorbjörn, SW Iceland, which started in January 2020 and was still ongoing in January 2021. The magmatic unrest produced more than 5 earthquake swarms comprising thousands of individual events each. We were able to combine local and regional seismic networks with 6 months recording of a 17 km long distributed acoustic sensing (DAS) fibre optical cable with a channel resolution of 4 m. The kHz DAS data were downsampled to 200 Hz and stacked every 64 m. The catalog is based on a migration-based detector / locator technique as for instance implemented in Lassie (Pyrocko). In the accompanying we demonstrate the robustness in a wide variety of applications in seismology. For this dataset, we have extended Lassie to efficiently combine linear ultra-dense sensor arrays with sparse seismological networks.</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.