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1,449 results for “stranded”
DS_35 STRAND_DISPL
<p>Strand displacement. Double stranded overhang in invading strand, length = 35 bp. First three days simulations.</p>
DS_35_1 STRAND_DISPL
<p>Strand displacement. Double stranded overhang in invading strand, length = 35 bp. Second three days simulations.</p>
Fig. 3 in Crassicaudiasis in three geographically and chronologically distant Cuvier's beaked whales (Ziphius cavirostris) stranded off Brazil
Fig. 3. Typical Crassicauda oval-shaped larvated (A, B) and embryonated (C) eggs in urine of CBW-2.
Strand and Sundberg, 2015
Strand, M. and Sundberg, P., 2015. Phylum Nemertea. In Thorp and Covich__s Freshwater Invertebrates (pp. 205-209). Academic Press. <p></p>https://doi.org/10.1016/B978-0-12-385026-3.00011-5<p></p>
The future of coal investment, trade and stranded assets
<p>Dataset to support the publication "The future of coal investment, trade and stranded assets"</p>
Figure 4 in Stranded humpback whale (Megaptera novaeangliae) (Cetacea: Balaenopteridae) in Paraná River Delta, Buenos Aires Province, Argentina. Comments on the occurrence of marine
Figure 4. Median-joining network based on the cytochrome c oxidase subunit I mtDNA haplotypes of Megaptera novaeangliae. Haplotypes are represented with discs and colors that indicate geographical locations. Mutational steps are indicated with stripes.
Figure 1 in Stranded humpback whale (Megaptera novaeangliae) (Cetacea: Balaenopteridae) in Paraná River Delta, Buenos Aires Province, Argentina. Comments on the occurrence of marine
Figure 1. Paraná River delta map were Megaptera novaeangliae (CFA-MA-13084) was found dead (exact location is indicated with a black dot).
Fig. 3 in Whale Strandings In Indonesia, Including The First Record Of A Humpback Whale (Megaptera Novaeangliae) In The Archipelago
Fig. 3. Locations of humpback whale strandings in Bali
Fig. 1 in Whale Strandings In Indonesia, Including The First Record Of A Humpback Whale (Megaptera Novaeangliae) In The Archipelago
Fig. 1. Map of cetacean stranding events in Indonesia 1997–2007.
Processed data from Repair-seq screens of double-strand breaks
<p>Processed data from Repair-seq screens of double-strand breaks induced by SpCas9 and AsCas12a in the presence or absence of oligonucleotide homology donors.</p>
Annotated DNA Double Strand Break Ionizing Radiation-Induced Foci (gH2AX 53BP1) Confocal Microscopy, pt. 2
<p><strong>Summary</strong></p> <p>Dataset of confocal microscopy data of cells exposed to gamma-irradiation and immunostained with gH2AX and 53BP1.</p> <ul> <li>Nuclei segmentation Head and neck primocultures immunostained with gH2AX/53BP1, Training/Testing/Validation dataset (nucleus_segmentation.zip) (available in part 1, <a href="https://dx.doi.org/10.5281/zenodo.4067741">https://dx.doi.org/10.5281/zenodo.4067741</a>) </li> <li>IRIF Foci: Head and neck primocultures immunostained with gH2AX/53BP1, Training/Testing/Validation dataset. (foci_detection.zip) (available in part 1, <a href="https://dx.doi.org/10.5281/zenodo.4067741">https://dx.doi.org/10.5281/zenodo.4067741</a>)</li> <li>Cell lines: U-87 and NHDF Cells exposed to 0.5-8 Gy 30 min and 8h post irradiation - confocal microscopy data of gH2AX/53BP1/DAPI annotated for gH2AX, 53BP1 and colocalized foci separately (cell_lines_U87.zip and cell_lines_NHDF.zip, this part of dataset) </li> <li><strong>Code</strong>: the code is available at <a href="https://github.com/tomasvicar/DeepFoci">https://github.com/tomasvicar/DeepFoci</a></li> <li><strong>Preprint: </strong>Vicar et al, DeepFoci: Deep Learning-Based Algorithm for Fast Automatic Analysis of DNA Double Strand Break Ionizing Radiation-Induced Foci, <a href="https://doi.org/10.1101/2020.10.07.321927">10.1101/2020.10.07.321927</a></li> <li><strong>Publication: </strong>Vicar et al, TBA</li> </ul> <p><strong>Materials and methods</strong></p> <p><em>Dataset</em></p> <p>Following cells were used:</p> <p>1) The training/validation/testing datasets was based on patient-derived primary cell cultures prepared from spinocellular tumors and morphologically normal tissues adjacent to the tumor taken from patients suffering from head and neck cancer. The dataset was divided into two subsets: one for training, validation and testing the nucleus segmentation (237/10/30 fields of view (FOVs), respectively) and one for training, validation and testing the focus segmentation (239/60/100 FOVs). The dataset consisted of several cell types: a) tumor cells, b) tumor-associated fibroblasts, and c) cells from morphologically normal tissues. All cell types were fixed at different periods of time (0 (non-irradiated control), 0.5, 8 or 24 h PI) after exposure to 2 Gy of gamma-rays. The representation of cells in two subsets with respect to the cell type and post-irradiation time (i.e., DSB repair duration) was random.</p> <p>2) The evaluation dataset was used to assess the robustness of segmentation procedures. It was composed of multiple types of differently treated cells in order to represent a highly challenging dataset maximally reflecting high biological and technical variability between samples, as it may appear in research or clinical practice. The dataset contained a) mesenchymal NHDF fibroblasts coming from a standard permanent cell line, b) radioresistant U-87 glioblastoma cells coming from a standard permanent cell line, c) tumor cells (CD90-) and tumor-associated fibroblasts (CD90+) prepared as a primary culture from a spinocellular tumors of patients (different from dataset 1) suffering from a head and neck cancer, and d) cells prepared as primary cultures from morphologically normal tissue adjacent to tumors of involved head and neck cancer patients. NHDF and U-87 cells received 0.5, 0, 1, 2, 4 and 8 Gy of gamma-rays and were fixed at 30 min and 8 h post-irradiation, while the primary cultures were only exposed to the dose of 2 Gy (for a limited amount of the cell material) and fixed at 0 (non-irradiated control), 0.5, 8 or 24 h post-irradiation times.</p> <p><em>Gamma irradiation</em></p> <p>The cells were irradiated at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic in a following schemes: (a) patient-derived primoculture was irradiated with a single dose of 2 Gy (D = 1 Gy/min) of gamma-rays (60Co, Chisostat, Chirana, CR) , (b) U-87 and NHDF cells were irradiated with doses 0.5-8 Gy (D = 1 Gy/min). Cells were irradiated in RPMI 1640 medium (37 °C, normal atmosphere). Confocal microscopy of gammaH2AX and 53BP1 foci immunodetection was consequently performed.</p> <p><em>Fluorescent staining</em></p> <p>DNA double strand breaks (DSBs) were quantified in different periods of time post-irradiation (30 min, 8h and 24h post irradiation) by means of $\gamma$H2AX and 53BP1 foci immunodetection combined with confocal microscopy. For details see \cite{falk2007chromatin}.</p> <p><em>Confocal microscopy</em></p> <p>The microscopy of samples was performed at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic. Leica DM RXA microscope (equipped with DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit and 488, 562, and 714 nm laser diodes with AOTF) was used for acquiring detailed cell images (100× oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 μm.</p> <p><strong>File description</strong></p> <p>all files are compressed hyperstack tiffs (50 Z slices and 3 fluorescent channels, XYCZ order), 100x magnification</p> <ul> <li>foci_detection.zip: IRIF Foci (available in part 1, <a href="https://dx.doi.org/10.5281/zenodo.4067741">https://dx.doi.org/10.5281/zenodo.4067741</a>): Head and neck primocultures immunostained with gH2AX/53BP1, Training/Testing/Validation dataset: FOVs 240/100/120 files for training, testing, and validation, organisation: <ul> <li>data_001.tif – 3channel Z.stack tiff</li> <li>mask_001.tif – respective Z stack mask with single points per IRIF focus (manual annotation, training and testing subsets only)</li> <li>data_description.xlsx – description of sample type (2Gy post irradiation times and characteristics of primary culture of squamous cell cancer of patients)</li> <li>data_001_pos.csv – manual annotation of gH2AX/53BPI IRIF foci by two experts – cordinates file (in 2D, validation only)</li> </ul> </li> <li>nucleus_segmentation.zip (available in part 1, <a href="https://dx.doi.org/10.5281/zenodo.4067741">https://dx.doi.org/10.5281/zenodo.4067741</a>) Nuclei segmentation Head and neck primocultures immunostained with gH2AX/53BP1, FOVs 237 Training/ 30 Testing/ 10 Validation dataset <ul> <li>data_001.tif – 3channel Z.stack tiff</li> <li>mask_001.tif – respective Z stack mask with manually annotated nucleus mask (manual annotation, training and testing subsets only)</li> <li>data_description.xlsx – description of sample type (2Gy post irradiation times and characteristics of primary culture of squamous cell cancer of patients)</li> </ul> </li> <li>U87.zip and NHDF.zip: Annotated gH2AX/53BP1 foci in cell lines exposed to increasing dose, annotations performed for gH2AX, 53BP1 and colocalized focus separatelly. 679 annotated FOVs for both cell lines. <ul> <li>control.png - RGB control figure showing merge and annotated overlay</li> <li>data_53BP1.tif - TIFF Z-stack, confocal microcopy, 53BP1 channel</li> <li>data_DAPI.tif - TIFF Z-stack, confocal microcopy, DAPI channel</li> <li>data_gH2AX.tif - TIFF Z-stack, confocal microcopy, gH2AX channel</li> <li>labels.json - foci labels for individual channel</li> <li>mask.tif - generated Z-stack of nucleus mask</li> </ul> </li> </ul>
X-ray scattering datasets and simulations associated with the publication "Bio-SAXS of Single-Stranded DNA-Binding Proteins: Radiation Protection by the Compatible Solute Ectoine"
<p>This dataset contains the processed and analysed small-angle X-ray scattering data associated with all samples from the publications "Bio-SAXS of Single-Stranded DNA-Binding Proteins: Radiation Protection by the Compatible Solute Ectoine" (<a href="https://doi.org/10.1039/D2CP05053F">https://doi.org/10.1039/D2CP05053F</a>)</p> <p>Files associated with McSAS3 analyses are included, alongside the relevant SAXS data, with datasets labelled in accordance to the protein (G5P), its concentration (1, 2 or 4 mg/mL), and if Ectoine is present (Ect) or absent (Pure). PEPSIsaxs simulations of the GVP monomer (PDB structure: 1GV5 ) and dimer are also included.[1]</p> <p>TOPAS-bioSAXS-dosimetry extension for TOPAS-nBio based particle scattering simulations can be obtained from <a href="https://github.com/MarcBHahn/TOPAS-bioSAXS-dosimetry">https://github.com/MarcBHahn/TOPAS-bioSAXS-dosimetry</a> which is further described in <a href="https://doi.org/10.26272/opus4-55751">https://doi.org/10.26272/opus4-55751</a>.</p> <p>This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under grant number 442240902 (HA 8528/2-1 and SE 2999/2-1). We acknowledge Diamond Light Source for time on Beamline B21 under Proposal SM29806. This work has been supported by iNEXT-Discovery, grant number 871037, funded by the Horizon 2020 program of the European Commission.</p> <p>[1] S. Su, Y.-G. Gao, H. Zhang, T. C. Terwilliger and A. H.-J. Wang, Protein Science, 1997, 6, 771–780.</p> <p> </p> <p><br> </p>
Potential new species of pseudaliid lung nematode (Metastrongyloidea) from two stranded neonatal orcas (Orcinus orca) characterised by ITS-2 and COI sequences
<p class="MsoNormal"><span>Knowledge about parasite species of orcas, their prevalence and impact on the health status is scarce. Only two records of lungworm infections in orca exist from male neonatal orcas stranded in Germany and Norway. The nematodes were identified as <em>Halocercus</em> sp. (Pseudaliidae), which have been described in the respiratory tract of multiple odontocete species, but morphological identification to species level remained impossible due to the fragile structure and ambiguous morphological features. Pseudaliid nematodes (Metastrongyloidea) are specific to the respiratory tract of toothed whales and are hypothesized to have become almost extinct in terrestrial mammals. Severe lungworm infections can cause secondary bacterial infections and bronchopneumonia and are a common cause of mortality in odontocetes. DNA isolations and subsequent sequencing of the rDNA ITS-2 and mtDNA COI revealed nucleotide differences between previously described <em>Halocercus</em> species from common dolphin (<em>H. delphini</em>) and harbour porpoises (<em>H. invaginatus</em>) that were comparatively analysed, pointing towards a potentially new species of pseudaliid lungworm in orcas. New COI sequences of six additional metastrongyloid lungworms of seals and porpoises were derived to elucidate phylogenetic relationships and differences between nine species of Metastrongyloidea.</span></p>
Fig. 146 in A revision of the tracheline sac spider genus Cetonana Strand, 1929 in the Afrotropical Region, with descriptions of two new genera (Araneae Corinnidae)
Fig. 146. Distribution of Patelloceto gen. n. species in the continental Afrotropical Region.
Fig. 105 in A revision of the tracheline sac spider genus Cetonana Strand, 1929 in the Afrotropical Region, with descriptions of two new genera (Araneae Corinnidae)
Fig. 105. Distribution of Afroceto plana sp. n. and A. porrecta sp. n. in southern Africa.
Fig. 117 in A revision of the tracheline sac spider genus Cetonana Strand, 1929 in the Afrotropical Region, with descriptions of two new genera (Araneae Corinnidae)
Fig. 117. Distribution of Afroceto rontunda sp. n. and A. spicula sp. n. in South Africa.
Fig. 55 in A revision of the tracheline sac spider genus Cetonana Strand, 1929 in the Afrotropical Region, with descriptions of two new genera (Araneae Corinnidae)
Fig. 55. The distribution of Afroceto bulla sp. n. and A. bisulca sp. n. in South Africa.
Fig. 42 in A revision of the tracheline sac spider genus Cetonana Strand, 1929 in the Afrotropical Region, with descriptions of two new genera (Araneae Corinnidae)
Fig. 42. The distribution of Afroceto martini (Simon, 1897) comb. n. in southern and East Africa.
Fig. 50 in A revision of the tracheline sac spider genus Cetonana Strand, 1929 in the Afrotropical Region, with descriptions of two new genera (Araneae Corinnidae)
Fig. 50. The distribution of Afroceto arca sp. n. in southern Africa.
Project files provided as supporting information to the manuscript "Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations"
<p><strong>README file to the project files provided as supporting information to the manuscript “Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations"</strong></p> <p>Authors: Manuel Micheloni, Lorenzo Petrolli, Gianluca Lattanzi and Raffaello Potestio<br> ==================================</p> <p>The .zip file is structured as follows:</p> <p>##############<br> 0_DNA_Sequence<br> ##############</p> <p>The folder contains:<br> • DNAsequence.txt: the DNA molecule employed in the study. <br> • ecseq.txt: the structure of the DNA. Each nucleotide (LAMMPS residue ID) is associated with the chemical type of the nucleic base.</p> <p>###################<br> 1_DSB_MDSimulations<br> ###################</p> <p>• MDSimulations: <br> The LAMMPS MD simulation scripts.<br> The subfolders are structured and named after different DSB motifs (folders 0,1, …,3) providing different external forces (folders 1000, 1100, 1200 refers to the respective average end-to-end distance). The latter subfolders provides:</p> <p>I. LMP_script provides the LAMMPS input file.</p> <p>II. the local internal energy contributions from the nucleotides involved with the residual contact interface between broken DNA moieties (data/1.E); </p> <p>III. coordinates of the nucleotides involved with the residual contact interface between the DNA moieties (data/2.POS);</p> <p>IV. the binary LAMMPS data file, employed as starting coordinates for the DSB MD simulation (/input_structure).</p> <p><br> • ScriptsAndAnalysis:<br> The scripts employed to analyze the DSB process. </p> <p>I. /00_GeneralScripts all the MATLAB functions employed for the analysis.</p> <p>II. /1_SigmoidalFitting provides the scripts from a sigmoidal fitting procedure [1] on the internal energy profile of the nucleotides between the strand breaks (Section 2 of the Supplementary Material). <br> [1] R P (2022). sigm_fit (https://www.mathworks.com/matlabcentral/fileexchange/42641-sigm_fit), MATLAB Central File Exchange. Retrieved July 2, 2022.</p> <p><br> ##################<br> 2_DNAFreeDiffusion<br> ##################</p> <p>• SIM:<br> It contains the MD simulations of the freely-diffusing DNA. Namely, the MSD of the DNA molecule, the input structure, and the LAMMPS simulation scripts are reported in /data, /input_structure, and /LMP_scripts respectively.</p> <p><br> • ANALYSIS:<br> It provides the script employed to estimate the diffusion coefficient of the DNA molecule and the time-scaling factor \Gamma(\zeta).</p> <p>#######################<br> 3_ForceAnalysis<br> #######################</p> <p>• data<br> It contains the forces computed from the MD simulations of the intact DNA molecules subject to the external force of 0.42, 0.88 and 3.06 pN. All data are stored in pickle format.<br> The README file contains additional information.</p> <p><br> NOTE1: Most data/scripts are saved according to the format .mat, employed by MATLAB Ⓡ, a numerical computing environment and proprietary programming language developed by MathWorks.</p> <p>NOTE2: For the force data manipulation, we acknowledge the use of LammpsFileManipulation package (https://pypi.org/project/LammpsFileManipulation/)</p>
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.