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4,753 results for “SHAPE”
Casting shape antiqua
Museum of arhcaeology of Lomonosov Moscow State University Source: Objaverse 1.0 / Sketchfab
Modelling Cell Shape in 3D Structured Environments: A Quantitative Comparison with Experiments
<p>This repository contains experimental data and computer scripts for the following publication: Link R, Jaggy M, Bastmeyer M, Schwarz US (2024) Modelling cell shape in 3D structured environments: A quantitative comparison with experiments. PLoS Comput Biol 20(4): e1011412. https://doi.org/10.1371/journal.pcbi.1011412</p> <p>There are two directories, “data” and “scripts”.</p> <p> <strong>1) </strong><strong>Directory data</strong></p> <p> WRL-files for experimental data generated with Imaris from Zeiss image files.</p> <p>The WRL-files can be converted to STL-files with MeshLab (<a href="https://www.meshlab.net/">https://www.meshlab.net</a>).</p> <p>The STL-files can be converted to FE-files for the SurfaceEvolver with our script CreateFeFile.py.</p> <p> The WRL-files are named according to the scaffolds:</p> <p>L*.wrl cells in L-shaped scaffolds (n=6).</p> <p>V*.wrl cells in V-shaped scaffolds (n=7).</p> <p>TRight*.wrl cells in right-triangle scaffolds (n=3).</p> <p>TEqui*.wrl cells in equilateral-triangle scaffolds (n=4).</p> <p><strong>2) </strong><strong>Directory scripts</strong></p> <p>ClusterSurfaceLinearPlugin: New CompuCell3D plugin needed to calculate linear surface energy functional for cells with nucleus (using the cluster concept).</p> <p>CompuCell3DScript: Hamiltonian_Comparison.cc3d is the main script for our simulations, uses the directory “Simulation”.</p> <p>CreateFeFile.py: generates surface evolver FE-file from STL-file. A STL-file can be generated from a WRL-file e.g. with MeshLab (<a href="https://www.meshlab.net/">https://www.meshlab.net</a>). </p> <p>SphericalHarmonicsAnalysis.ipynb: Python notebook that calculates the Fourier spectrum and Delta_30, needs WRL-file as input.</p> <p> </p>
Cell shape analysis
<p>Cell shape analysis<br> ---------------------------------------------<br> This package contains custom-written code associated with the paper "Direct observation of a crescent-shape chromosome in Bacillus subtilis" By Tišma et al. 2023</p> <p>See README's in subdirectories for specific content description </p> <p>Notes:<br> ----------------------------------------------<br> ## general<br> * code for extended cell analysis as used in the Cees Dekker Lab, 2017-onwards</p> <p>## associated publications<br> 1. [current submission] 'Direct observation of a crescent-shape chromosome in Bacillus subtilis'<br> Authors Miloš Tišma, Florian Patrick Bock, Jacob Kerssemakers, Aleksandre Japaridze, Stephan Gruber, Cees Dekker, submitted (2023).</p> <p>2. MukBEF-dependent chromosomal organization in widened Escherichia coli<br> Authors Aleksandre Japaridze, Raman van Wee, Christos Gogou, Jacob WJ Kerssemakers, Cees Dekker; (2022)<br> 3. Direct observation of independently moving replisomes in Escherichia coli<br> Authors Aleksandre Japaridze, Christos Gogou, Jacob WJ Kerssemakers, Huyen My Nguyen, Cees Dekker, Nat.Com (2020)<br> 4. Direct imaging of the circular chromosome in a live bacterium<br> Authors Fabai Wu, Aleksandre Japaridze, Xuan Zheng, Jakub Wiktor, Jacob WJ Kerssemakers, Cees Dekker, Nat.Com (2019)</p> <p>## package description<br> This package collects code to analyze multi-channel microscope images of cells. Patterns of interest may be extended, such as a fully labeled chromosome, or compact, as one or multiple labeled spots. The code is used to select and screen individual cells and to quantify locations of above labels. </p> <p>## package contents<br> * custom-written source code [Matlab] <br> * test data to demonstrate the software code</p> <p>## system requirements and used software<br> * Windows 10, 64bits <br> * Matlab Version 2021 [custom source code]<br> * Oufti Version .... <br> * Fiji(ImageJ) Version 1.52a<br> * Dip_image analysis software Version 2.9</p> <p>## installation guide<br> * please follow the installation instructions provided by above package distributors<br> * installation of all platforms should take less than a day on a standard PC</p> <p>## demo and instructions for use<br> * the code is divided in three main subsections (that are to be used in this order) and one extra:<br> * 'crop': works on microsocopic data, outputs data organized per cells<br> * 'donut': in-depth analysis on chromosome patterns and other labels ('spots')<br> * 'repli': follow-up analysis on spots<br> * 'topical subjects': shorter code platforms for various analyses<br> * see 'README.md' in each subdirectory for a detailed step-by-step descriptions, in order of appearance or importance in the analysis pipeline<br> * see 'README_code_annotations.md' in each subdirectory for a full collection of all custom function descriptions<br> * demo data for two cells is provided to illustrate workings and settings. Running this demo data typically only takes a few minutes<br> * for new data, follow the setup as described via the demo data <br> <br> ## contributions<br> ---------------------------------------------- <br> * F. Wu and X. Zheng originally wrote and assembled the original code package<br> * J.Kerssemakers organized, re-edited and expanded the 'crop' code package<br> * J.Kerssemakers wrote the 'donut' and 'repli' code packages<br> * A. Japaridze, Raman van Wee, Christos Gogou and M.Tisma contributed to analysis design<br> * J.Kerssemakers and M.Tisma contributed to 'topical subjects'</p> <p>## disclaimer<br> ---------------------------------------------<br> This code was custom written and shared to illustrate used algorithms, analysis pathways etc. in relation to published results. The code was regularly used and tested. However, small bugs, not relevant for the data analysis as present in publications may still be around. Interested users are expected to have a sufficient knowledge of Matlab code to understand and adapt the code to their own wishes.</p>
Figure 2 in Using geometric morphometrics for integrative taxonomy: an examination of head shapes of milksnakes (genus Lampropeltis)
Figure 2. The eleven landmarks used for geometric morphometric analyses (A) and the Procrustes superimpostition consensus of the landmarks averaged across all specimens (B).
Figure 4 in Using geometric morphometrics for integrative taxonomy: an examination of head shapes of milksnakes (genus Lampropeltis)
Figure 4. Thin-plate splines of each species warped from the Procrustes consensus alignment of all species.
Figure 1 in Using geometric morphometrics for integrative taxonomy: an examination of head shapes of milksnakes (genus Lampropeltis)
Figure 1. Representatives of the six milksnake species used in the present study; A, Lampropeltis triangulum. B, Lampropeltis gentilis. C, Lampropeltis elapsoides. D, Lampropeltis polyzona. E, Lampropeltis abnorma. F, Lampropeltis micropholis.
Photophysical results of V-shaped ambipolar, nitrogen-doped π-Conjugated polycyclic aromatic hydrocarbon TADF emitters obtained in the project 2022/45/B/ST5/03712
<p>The files presents photophysical results of the set of emitters analysed for OLED applications in the project NCN OPUS 2022/45/B/ST5/03712.</p> <p>Chem. Commun., 2023,59, 2815-2818</p>
Fam134c and Fam134b shape axonal endoplasmic reticulum architecture in vivo
<p>Endoplasmic reticulum (ER) remodeling is vital for cellular organization. ER-phagy, a selective autophagy targeting ER, plays an important role in maintaining ER morphology and function. The FAM134 protein family, including FAM134A, FAM134B, and FAM134C, mediates ER-phagy. While FAM134B mutations are linked to hereditary sensory and autonomic neuropathy in humans, the physiological role of the other FAM134 proteins remains unknown. To address this, we investigated the roles of FAM134 proteins using single and combined knockouts (KOs) in mice. Single KO in young mice showed no major phenotypes, but combined <em>Fam134b</em> and <em>Fam134c</em> deletion (<em>Fam134b/c<sup>dKO</sup>)</em> led to rapid neuromuscular and somatosensory degeneration, resulting in premature death. <em>Fam134b/c<sup>dKO</sup></em> mice show rapid loss of motor and sensory axons in the peripheral nervous system. Long axons from <em>Fam134b/c<sup>dKO</sup></em> mice exhibited expanded tubular ER with a transverse ladder-like appearance, whereas no obvious abnormalities were observed in cortical ER. Our study unveils critical roles of FAM134C and FAM134B in the formation of tubular ER network in axons of both motor and sensory neurons.</p>
Data for: Interplay of abiotic conditions, density, and body size in shaping demography in a high-elevation toad population
<p>This dataset is used to estimate vital rates of a common toad (<em>Bufo bufo</em>) alpine population, and how they are associated with either abiotic (environmental conditions), biotic (in our case population size), and individual factors (body size). We have individual capture histories for the period 1993-2020 for 1615 males and 933 females, as well as body size measurements taken during capture events. For more info about the study system see: https://peercommunityjournal.org/articles/10.24072/pcjournal.240/</p> <p>We run a capture-mark-recapture model coupled with a growth model, the latter to obtain information on body size for the years when the individuals were not captured. Aside from sex-specific survival, we estimate female breeding probability, since they show intermittent breeding. We include as covariates for these vital rates the length of the active season, the temperature at emergence from hibernation, population size, and body size. </p> <p>We obtained climatic data for the period 1980–2020 from the DaymetCH dataset (data obtained from Bioclimatic maps of Switzerland © WSL, based on station data from the Federal Office of Meteorology and Climatology MeteoSwiss, and elaborated by the Land Change Science group, WSL).</p> <p>The README file further describes each uploaded file</p>
Supplementary material 1 from: Heller K-G, Hemp C (2024) Egg shape and size in Phaneropterinae and other Tettigonioidea (Orthoptera, Ensifera): A global review with new data. Journal of Orthoptera Research 33(1): 103-112. https://doi.org/10.3897/jor.33.116173
Supplementary material 1 from: Heller K-G, Hemp C (2024) Egg shape and size in Phaneropterinae and other Tettigonioidea (Orthoptera, Ensifera): A global review with new data. Journal of Orthoptera Research 33(1): 103-112. https://doi.org/10.3897/jor.33.116173
Supplementary material 2 from: Heller K-G, Hemp C (2024) Egg shape and size in Phaneropterinae and other Tettigonioidea (Orthoptera, Ensifera): A global review with new data. Journal of Orthoptera Research 33(1): 103-112. https://doi.org/10.3897/jor.33.116173
Supplementary material 2 from: Heller K-G, Hemp C (2024) Egg shape and size in Phaneropterinae and other Tettigonioidea (Orthoptera, Ensifera): A global review with new data. Journal of Orthoptera Research 33(1): 103-112. https://doi.org/10.3897/jor.33.116173
Host-level biodiversity shapes the dynamics and networks within the coral reef microbiome
<p>This is the repository associated with the manuscript <strong>Host-level biodiversity shapes the dynamics and networks within the coral reef microbiome</strong>. It contains all data files used for figures presented in the manuscript. The code to reproduce the files can be found on <a href="https://github.com/SushiLab/coralmicrobiome-hostbiodiversity)">GitHub</a>.</p> <p> </p> <h2>Files</h2> <p><br><code>raw_host-associated_1.asvs.tsv --> ASV table, host-associated samples</code><br><code>raw_host-associated_2.asvs.tsv --> ASV table, host-associated samples</code><br><code>raw_free-living_1.asvs.tsv --> ASV table, Sterivex samples</code><br><code>raw_free-living_2.asvs.tsv --> ASV table, Sterivex samples</code><br><code>metadata_host-associated.csv --> metadata, host-associated samples</code><br><code>metadata_free-living.csv --> ASV table, Sterivex samples</code><br><code>asv_dat_taxinfo.tsv --> taxonomy annotated using SILVA v138.1</code><br><code>asv_bctab.tsv --> square-root transformed Bray-Curtis dissimilarities </code><br><code>asv_richtab.tsv --> Hill number diversity indices</code><br><code>asv_shared.tsv --> number of shared ASVs</code><br><code>pathway_list_cat.csv --> KEGG pathway list with hand-annotated categories</code><br><code>KEGG_path_to_ko.tsv --> KEGG file mapping pathways to KOs</code></p> <p> </p>
CellMet: Extracting 3D shape metrics from cells and tissues
<p>This dataset supports the manuscript title "CellMet: Extracting 3D shape metrics from cells and tissues". It contains segmented images (mask.tif) of severals tissues. </p>
Contextual factors shaping progress towards global migration goals
<p>Two datasets for the analysis of the information extracted from qualitative migration scenarios published between 2008 and 2023 with the goal of studying which socioeconomic, environmental, political, and technological changes can promote progress towards the 23 objectives contained in the Global Compact for safe, orderly, and regular migration.</p> <p>Data in the file fullmetadata.xlsx contain meta information on the scenarios and the publications in which they appeared, including the names of the authors, the scenario names, and their time and geographic coverage. </p> <p>Data in the file fulldataextraction contain information about the objectives in the Global Compact for Migration towards which authors noted potential progress in each scenario. It also contains information about the drivers that characterize each scenario.</p>
Nitrogen and phosphorus concentrations shape tetracycline effects on Microcystis aeruginosa and Microcystis flos-aquae
<p>Continuous contamination of aquatic resources with broad-spectrum antibiotics, such as tetracycline, nitrogen and phosphorus disrupts the population dynamics of non-target organisms, including cyanobacteria, in freshwater ecosystems.</p>
Replication data for "Raided by the storm: How three decades of thunderstorms shaped U.S. incomes and wages"
<p>Replication data for "Raided by the storm: How three decades of thunderstorms shaped U.S. incomes and wages" (Coronese et al., JEEM 2024) - <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.jeem.2024.103074" target="_blank" rel="noreferrer noopener"><span><span>https://doi.org/10.1016/j.jeem.2024.103074</span></span></a></p> <p>This repository contains raw data supporting the replication of figures and tables presented in both the main paper and the Supplementary Information. Replication codes are available at: <a href="https://github.com/CoMoS-SA/thunderstorms" target="_new" rel="noopener">https://github.com/CoMoS-SA/thunderstorms</a></p>
Nanoengineered Shape-memory Hemostat - Dataset
<p>This data set contains all raw data and data analysis files associated with the following manuscript: </p> <div>Nanoengineered Shape‐Memory Hemostat</div> <div>Article DOI: 10.1002/smsc.202400321</div> <div>Published in Small Science by Wiley-VCH GmbH.</div> <div> </div> <div>Authors: Sarah E. Hargett# (1), Giriraj K. Lokhande# (1), Joseph Duran (1), Zanir Hirani (1), Lindy K. Jang (1,2), Samantha Foster (3), Kaivalya A. Deo (1), Sasha George (4), Mahjabeen Javed (1), Taylor H. Ware (1,4), Duncan J. Maitland* (1), Akhilesh K. Gaharwar* (1,3,4,5)</div> <div>#Equally contributed</div> <div>*Corresponding authors</div> <div> </div> <div>1. Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, TX, 77843, USA</div> <div>2. Materials Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA</div> <div>3. Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX, 77843, USA</div> <div>4. Department of Materials Science and Engineering, College of Engineering, Texas A&M University, College Station, TX, 77843, USA</div> <div>5. Center for Remote Health Technologies and Systems, Texas A&M University, College Station, TX, 77843, USA</div> <div> </div> <div>Funding information: </div> <div>Department of Defense: W81XWH2210932</div> <div>American Heart Association: 24PRE1200460</div> <div>Division of Materials Research: 2041671</div> <div>National Institute of Biomedical Imaging and Bioengineering: EB026265</div> <div>Texas A&M University</div>
DATASET - Climate heterogeneity shapes the diversity of specialist beetle species across mountains in Malaysia
Open the record for dataset details and reuse information.
Research data for: Direct DLP-based 3D-printing of metallopolymers featuring shape-memory abilities
<p><span>This study presents for the first time the direct digital light processing (DLP) based three-dimensional (3D) printing of metallopolymers featuring different kinds of metal complexes. 2-Phenoxyethyl acrylate and ligand-containing monomers based on terpyridine, and triphenylmethyl(trt)‑histidine are utilized. After successful complexation of zinc(II) and nickel(II) salts, respectively, within the monomer mixture the polymerization <em>via</em> photo-induced printing is performed. The hereby obtained smart materials can be printed in any form ranging from simple rectangular rods to complex hollow structures. Inductively coupled plasma optical emission spectroscopy (ICP-OES) and Fourier-transform (FT) Raman spectroscopy reveal the successful imbedding and implementation into the polymeric structure. Additionally, an imaging across the 3D-printed structure could be performed indicating the equal distribution of the complexes in the structure. Furthermore, the 3D-printed specimens feature excellent shape-memory behavior. Thermo-mechanical analysis (TMA) reveals fixity rates after mechanical deformation up to 100% and recovery rates up to 99%.</span></p> <p><span> </span></p>
Sampled Structures from Diffusion Models for Protein SHAPES
<p>Data associated with SHAPES (Structural and Hierarchical Assessment of Proteins with Embedding Similarity)</p> <ul> <li><code>rmsd.tar.gz</code> : RMSD and TM scores of ESMFold predicted structures with original designed backbones.</li> <li><code>mpnn.tar.gz</code> : ProteinMPNN designed sequences.</li> <li><code>raster.tar.gz</code> : CATH and sampled structures annotated with the grid square label after rasterization. Also includes the specific structures which are displayed in the raster plots.</li> <li><code>dssp.tar.gz</code> : Secondary structure frequences computed by DSSP.</li> <li><code>samples.tar.gz</code> : All sampled structures.</li> </ul> <p>Due to size, the ESMFold predicted structures for eight ProteinMPNN-designed sequences per sampled backbone are not included.</p> <p> </p> <p>Code: <code>proteinshapes-main.zip</code></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.