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258 results for “caging”
Shear Fracture Caging Test Videos
<p>These videos show shear fracture caging experiments conducted at Los Alamos National Laboratory. More informatio can be found at the following links: </p> <ol> <li>Journal publication: <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.geothermics.2024.103206" target="_blank" rel="noopener">https://doi.org/10.1016/j.geothermics.2024.103206</a></li> <li>Raw data for 8 shear fracture caging tests used in journal publication: <a href="https://doi.org/10.5281/zenodo.10951458" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.10951458</a></li> <li>Raw data for 5 shear fracture caging tests: <a href="https://doi.org/10.5281/zenodo.10956588" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.10956588</a></li> <li>Raw data for 14 shear fracture caging tests: <a href="https://doi.org/10.5281/zenodo.10957018" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.10957018</a></li> </ol>
Towards Fracture Caging in Shear Experiments
<p>The dataset presents experiment data collected during the learning and development process in setting up shear fracture caging experiments. Data from consistent and subsequent experiments can be found at doi.org/10.5281/zenodo.10951458 and doi.org/10.5281/zenodo.10956588. </p> <p>The ReadMeFirst.txt file explains the details.</p>
Knowledge Discovery from Porous Organic Cages Literature Using a Large Language Model
<p>This article presents a GPT-4-based literature reading method that incorporates multi-label text classification and a follow-up information extraction, in which the potential of GPT-4 can be fully exploited to rapidly extract valid information from the literature. In the process of multi-label text classification, the prompt-engineered GPT-4 demonstrated the ability to label text with proper recall rates according to the type of information contained in text, including authors, affiliations, synthetic procedures, surface area, and the CCDC number of corresponding cages. Additionally, GPT-4 demonstrated proficiency in information extraction, effectively transforming labeled text into concise tabulated data. Furthermore, we built a chatbot based on this database, allowing for quick and comprehensive searching across the entire database and responding for cage-related questions.</p>
DFT investigation on the application of pure and doped X12N12 (X = B and Al) fullerene-like nano-cages towards the adsorption of temozolomide
<p>The sensitivity of pure and doped X<sub>12</sub> N<sup><sub>12</sub></sup> (X = B and Al) fullerene-like nano-cages (FLNs) toward the anticancer drug temozolomide (TMZ) is probed herein at DFT/M06-2X-D3/6-311G(d,p) theoretical level in both gas phase and water. A noticeable affinity of the FLNs toward TMZ was observed along with the negative gas-phase adsorption energies -1.37 and -2.09 eV for the most stable configurations of pure B12N12 and Al12N12 pristines, respectively. Considerable charge transfer from TMZ to the FLNs was also revealed via NBO analysis and the Hirshfeld atomic charges, making the dipole moment vector of the molecular complexes to be oriented from the nano-cages to the TMZ moiety. Furthermore, a percentage decrease in the HOMO-LUMO energy gap (ΔEg) of 38.09 and 17.72 % was obtained for the B12N12 and Al12N12 nano-cages, respectively. The percentage change in ΔEg was found to be reduced upon doping and solvation of the FLNs. Finally, a recovery time in vacuum ultraviolet light of 1.06 s is found for the complex with pure B12N12, which in addition to the above-mentioned parameters make this boron nitride cage the best sensor for TMZ, among the FLNs considered in the present work.</p>
CAGE and txrevise promoter usage QTL summary statistics
<p>This dataset contains promoter usage QTL summary statistics obtained using <a href="https://github.com/eQTL-Catalogue/qtlmap">QTLmap</a>. QTLmap_summary_CAGE.txt contains summary statistics for CAGE, QTLmap_summary_txrevise-25.txt for regular <a href="https://github.com/kauralasoo/txrevise">txrevise</a> and QTLmap_summary_txrevise-supplemented-20.txt for txrevise with the new generated annotations.</p> <p>This dataset contains the promoter annotations obtained with CAGE as part of the FANTOM5 project, cleaned and reformatted using <a href="https://github.com/andreasvija/cage/blob/master/qtlmap_prep/clean_promoters.R">this code</a> for the purpose of QTL mapping, that were used to obtain the aforementioned summary statistics. They can be found in Cleaned_FANTOM5_promoter_annotations.tsv.</p> <p> </p> <p>QTL summary statistics column descriptions:</p> <p>molecular_trait_object_id - gene</p> <p>molecular_trait_id - top promoter for the gene</p> <p>n_traits - how many promoters were tested for the gene</p> <p>n_variants - how many genetic variants were tested for the promoter</p> <p>variant - top genetic variant for the promoter</p> <p>chromosome - chromosome</p> <p>position - promoter's top genetic variant start position</p> <p>pvalue - nominal p-value of the association between the promoter and genetic variant</p> <p>beta - the fitted linear model's regression coefficent</p> <p>p_perm - empirical p-value calculated using permutations</p> <p>p_beta - estimated empirical p-value based on the beta distribution, this is the recommended p-value column</p>
Data for "Competitive aminal formation during the synthesis of a highly soluble, isopropyl-decorated imine porous organic cage"
<div>In the following subdirectories are the input and output of DFT and conformer calculations for this publication:</div> <div> </div> <div>DOI: 10.1039/D3CC00072A</div> <div> </div> <div>Previously uploaded in <span>10.5281/zenodo.8432296 and </span><a href="https://github.com/andrewtarzia/citable_data" rel="noopener noreferrer"><span>https://github.com/andrewtarzia/citable_data</span></a></div> <div> </div> <div>sub-directories:</div> <div> <ul> <li>intermediate_calculations/<br> <ul> <li>Input intermediate structures, incl. amine, aldehyde and water precursors, as `.mol` files.</li> <li>Output structures from GFN2-xTB optimisation as `_opt.mol` and `_opt.xyz` files.</li> <li>GFN2-xTB energies for different solvents as `_SOLV.ey` files.</li> <li>`.csv` files containing:<br> <ul> <li>all_total_energies.csv : Total energy of all intermediates from all methods. [column `xtbgas` is the one used in the manuscript]</li> <li>all_formation_energies.csv : Formation energy of all intermediates from all methods. [column `xtbgas` is the one used in the manuscript]</li> <li>all_formation_energies_per_imine.csv : Formation energy per imine bond formed of all intermediates from all methods. [column `xtbgas` is the one used in the manuscript]</li> </ul> </li> </ul> </li> <li>intermediate_calculations/gaussian_calculations/ [note that these are not used in the manuscript] <ul> <li>Gaussian16 input and output for DFT calculations on the intermediates.</li> <li>Structures are the GFN2-xTB optimised structures.</li> <li>File names match the directory above as such `NAME_opt_SOLV_METHOD.gau/log`<br> <ul> <li>SOLV include `gas`, `dcm` (dichloromethane) and `cfm` (chloroform).</li> <li>METHOD inclde `pbe` (PBE1PBE/Def2TZVP) and `mp2` (MP2/aug-cc-pVDZ).</li> </ul> </li> </ul> </li> <li>intermediate_calculations/orca_calculations/ [note that these are not used in the manuscript]<br> <ul> <li>Orca input and output for DFT calculations on the intermediates.</li> <li>Structures for B97-3c optimisation are the GFN2-xTB optimised structures.<br> <ul> <li>Result for each intermediate are saved as `_o_NAME_opt_B97-3c.xyz`.</li> </ul> </li> <li>Structures for the MP2 single-point are the B97-3c output. [note that these are not used in the manuscript]</li> <li>File names match the directory above as such `o_NAME_opt_METHOD.in/out`<br> <ul> <li>All calculations performed in gas phase.</li> <li>METHOD inclde `B97-3c` (composite method) and `MP2` (RI-MP2 cc-pVTZ). [note that these are not used in the manuscript]</li> </ul> </li> </ul> </li> <li>conformer_calculations/<br> <ul> <li>Eight zipped directories for four diamines and four imines used in conformer analysis including all optimised conformer structures and their energies.</li> <li>Four zipped directories (`opls_structures`) containing Macromodel/OPLS3e conformers.</li> </ul> </li> </ul> </div> <p> </p>
Data for "High-Throughput Computational Evaluation of Low Symmetry Pd2L4 Cages to Aid in System Design"
<p>In the following subdirectories are the input and output of Gaussian calculations + structures from screening for this publication:</p> <p>chemrxiv: <a href="https://chemrxiv.org/engage/chemrxiv/article-details/60c758e0ee301c7eadc7b7df">10.26434/chemrxiv.14604294</a></p> <p>Published: <a href="https://onlinelibrary.wiley.com/doi/10.1002/anie.202106721">10.1002/anie.202106721</a></p> <p>Previously uploaded in 10.5281/zenodo.8432296 and <a href="https://github.com/andrewtarzia/citable_data" rel="noopener noreferrer">https://github.com/andrewtarzia/citable_data</a></p> <p>Software repository: <a href="https://github.com/andrewtarzia/unsymm_match">github.com/andrewtarzia/unsymm_match</a></p> <p>screening_structures directory:</p> <ul> <li>contains the structures from xTB optimisation that were used in ranking in structures.tar.gz as `.mol` files</li> <li>all_cage_results.txt contains their properties for ranking</li> </ul> <p>single_point_dft directory:</p> <ul> <li>contains the structures and output of single point DFT calculations</li> <li>during the revision process, we confirmed (based on reviewer suggestions) our DFT validation results using ORCA 4.2.1 with PBE0 and B97-3c in the gas phase. These results were consistent with our previous ones, so were not added to the manuscript. But are useful for future work! <ul> <li>These results are in the s_orca directory.</li> </ul> </li> </ul> <p>free_energy_calculations directory:</p> <ul> <li>during the revision process, it was suggested to calculate the free energies using the xTB method (low-cost) and compare that to the total energies we use.</li> <li>the script `run_gfn2_free_energy.py` in the unsymm_match code repository does this for top candidate ligands using the stko.XTB class. <ul> <li>for each structure, the free energy is output to a .fey file.</li> </ul> </li> </ul>
Data for "Orientational self-sorting in cuboctahedral Pd cages"
<p>In the following subdirectories are the input and output of GFN2-xTB and Gaussian calculations for this publication:</p> <p>Published: 10.1039/d2sc03856k</p> <p>Previously uploaded in 10.5281/zenodo.8432296 and <a href="https://github.com/andrewtarzia/citable_data" rel="noopener noreferrer">https://github.com/andrewtarzia/citable_data</a></p> <p>xtb_m12_structures directory:</p> <ul> <li>contains the structures from xTB optimisation as "_opt.mol"</li> </ul> <p> <br>dft_m12_IO_structures directory:</p> <ul> <li>contains the structures input and output files of Gaussian calculations and optimisations performed by Victor Posligua</li> <li>HSE and PBE0 optimised structures are separated into directories.</li> </ul> <p><br>xtb_m24_structures directory:</p> <ul> <li>contains the input and output structures of XTB optimisations of Pd24L48 cages.</li> <li>cleaned.xyz : initial structures, cleaned from provided .pdb files</li> <li>opt.xyz : optimised structures</li> </ul> <p> </p>
Evaluating the fillet quality and sensory characteristics of Atlantic salmon (Salmo salar) fed black soldier fly larvae meal for whole production cycle in sea cages
Open the record for dataset details and reuse information.
Supporting material for "Pharmacological validation of individual animal locomotion, temperature and behavioural analysis in group-housed rats using a novel automated home cage analysis system: a comparison with the modified Irwin test"
<p>The data were uploaded to support the manuscript "Pharmacological validation of individual animal locomotion, temperature and behavioural analysis in group-housed rats using a novel automated home cage analysis system: a comparison with the modified Irwin test" for the submission to Journal of Pharmacological and Toxicological Methods.</p>
Fracture Caging in a Porous Lab Fault: Experiment Dataset (sensor coordinates added)
<p>Update: Sensor coordinates and make that were missing from the previous version were added. </p> <p>We conducted shear fracture caging experiments at the Fractured Earth Laboratory to investigate the potential of fracture caging in limiting induced seismicity in the fault. The experiments involved an injection of fluid into a repeatably constructed assembly of two aluminum wedges bonded by plaster, which is critically loaded for shear-slip. Meanwhile, fluid production is enabled using a five-spot pattern of pre-drilled boundary wells (i.e., a fracture cage). Injected fluid was a gear oil with 8.81 cP viscosity at room temperature . Syringe pumps were used to control and measure the injection rate, volume, and pressure. Microseismic activity was recorded using 16 acoustic emission (AE) sensors that were equally split into high-magnitude and high-sensitivity acquisition systems. Over the course of experiments, raw data collected includes AE waveforms from high-magnitude and high-sensitivity systems, post-mortem shear fracture photos, and synchronized timeseries data for 8 tests, which are presented here. </p>
Porous shape-persistent rylene imine cages with tunable optoelectronic properties and delayed fluorescence
<p>A simultaneous combination of porosity and tunable optoelectronic properties, common in covalent organic frameworks, is rare in shape-persistent organic cages. Yet, organic cages offer important molecular advantages such as solubility and modularity. Herein, we report the synthesis of a series of chiral imine organic cages with three built-in rylene units by means of dynamic imine chemistry and we investigate their textural and optoelectronic properties. Thereby we demonstrate that the synthesized rylene cages can be reversibly reduced at accessible potentials, absorb from UV up to green light, are porous, and preferentially adsorb CO<sub>2</sub> over N<sub>2</sub> and CH<sub>4</sub> with a good selectivity. In addition, we discovered that the cage incorporating three perylene-3,4:9,10-bis(dicarboximide) units displays an efficient delayed fluorescence. Time-correlated single photon counting and transient absorption spectroscopy measurements suggest that the delayed fluorescence is likely a consequence of a reversible intracage charge-separation event. Rylene cages thus offer a promising platform that allows combining the porosity of processable materials and photochemical phenomena useful in diverse applications such as photocatalysis or energy storage.</p>
Control mice (non-infected with S. mansoni parasites) - cage 1 - Liver histopathology data.
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas in liver of control mice (non-infected with S. mansoni parasite). These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 10/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area (_TRICH.czi) and (_HE.czi) files.</p>
NMR Relaxometry data for publication "Engineered Nonviral Protein Cages Modified for MR Imaging"
<p>NMRD profiles collected with field-cycling NMR relaxometry of a water solution of Gd-C4-IA, and of AaLS-13 and OP protein cages labeled with the gadolinium(III) complex.</p> <p>Published in: https://doi.org/10.1021/acsabm.2c00892</p> <p>NMRD data acquisition and analysis was performed with the support of the PRIN 2017A2KEPL project “Rationally designed nanogels embedding paramagnetic ions as MRI. probes”, and the European Commision through H2020 FET-Open project HIRES-MULTIDYN<br> award no. 899683 and H2020 INFRAIA iNEXT-Discovery (Structural Biology Research Infrastructures for Translational Research and Discovery) award no. 871037.</p>
Data on female oviposition behaviour of the Pararge aegeria butterfly in outdoor cages (2019–2020)
<p><span>We studied oviposition behavior in a butterfly (</span><em><span>Pararge aegeria</span></em><span>)</span><span> that used to be confined to forest, but recently colonized anthropogenic areas too. This provides an ideal study system when trying to understand the underlying processes of niche expansion and colonisation success. The dataset produced allows us to test to what extent ecotype origin (agricultural vs. forest landscape types) and larval developmental conditions (open field vs. canopy-covered forest floors) affect multiple features of oviposition behahaviour. We also performed multiple behavioural trials per individual and considered changes in oviposition site preference within and over trials. </span></p> <p>The two provided files contain all behavioral or independent variables that were obtained during behavioural tracking of the oviposition behaviour of the Speckled Wood butterfly (<em>Pararge aegeria</em>) in an outdoor cage in 2019 and 2020.</p> <p>In the<strong> 'femdata' </strong>file, each line contains all dependent (e.g., proportion of time spent active) and independent variables (e.g. ecotype) that apply for a single observation trial of 30 minutes of a single individual.In total, 211 observation trials were performed, by 110 different female individuals. </p> <p>In the <strong>'ovimdata' </strong>file, each line contains all variables for a single oviposition bout (i.e., if a butterfly curls its abdomen on a surface and lays eggs). Examples include number of eggs per bout, the height above ground where an egg was laid and temperature at the egg laying site. These data were for example used to track changes over consecutive bouts within a single trial. In total 275 oviposition bouts were observe, laid by 85 different female individuals.</p> <p>Data of the ovimdata file were also implemented in the femdata file. For example, in the femdata file information can be obtained about the properties of the first oviposition bout an individual made during that trial (starting with 'b1').</p>
Data for: Food Anticipatory Behaviour on European Seabass in Sea Cages: Activity-, Positioning- and Density-based approaches
<p>Telemetry and sensory data data for:</p> <p>Food Anticipatory Behaviour on European Seabass in Sea Cages: Activity-, Positioning- and Density-based approaches</p> <p>Please read the README.txt file before working with the data.</p>
Squirrel-Cage Induction Motor Fault Diagnosis Dataset
<p>The <strong>Squirrel Cage Induction Motor Fault Diagnosis Dataset</strong> is a multi-sensor data collection gathered to expand research on anomaly detection, fault diagnosis, and predictive maintenance, mainly using non-invasive methods such as thermal observation or vibration measurement. The measurements were gathered using an advanced <em>Wrocław University of Science and Technology</em> laboratory designed to simulate and study motor defects. The collected dataset is licensed under a <em>Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International</em> License.</p> <p>Available data:</p> <ul> <li>thermal images</li> </ul> <p>The example dataset utilization is presented in the GitHub repository: <a href="https://github.com/MatPiech/motor-fault-diagnosis/tree/main">motor-fault-diagnosis</a></p> <p>Related publications:</p> <ul> <li><a href="https://ein.org.pl/Unraveling-Induction-Motor-State-through-Thermal-Imaging-and-Edge-Processing-A-Step,170114,0,2.html">Unraveling Induction Motor State through Thermal Imaging and Edge Processing: A Step towards Explainable Fault Diagnosis</a></li> </ul>
Validation of Fracture Caging to Contain Hydraulic Fractures: Timeseries, Videos, and Model Script
<p>The data file include an Excel spreadsheet and two videos for each experimental test.</p> <p>You can start with reading the ReadMeFirst.txt file to understand the whole structure of the dataset.</p> <p>The caging_model.txt file includes python codes to calculate critical flow rates and uncaged fracture radius according to the theory that the authors developed and will be published soon.</p>
Anterior Bridging Cage With Bone Substitute Versus Localized Autobone in Transforaminal Lumbar Interbody Arthrodesis
ClinicalTrials.gov study NCT02485574. IPD Sharing: NO. Countries: 1. Publications: 30.
Lumbar Fusion With Nexxt Spine 3D-Printed Titanium Interbody Cages
ClinicalTrials.gov study NCT03647501. IPD Sharing: NO. Countries: 1. Publications: 18.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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DANDI Archive for NWB datasets
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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.