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10,561 results for “mechanics”
Components of spore capture device in "A simple mechanism for uncrewed aircraft bioaerosol sampling in the lower atmosphere"
<p>These STL files enable the 3D printing of the referenced spore capture device. The complete device can be assembled following printing of the: (1) petri dish holder base; (2) lid; and (3) flange. The STL file extension stands for stereolithography, colloquially referred to as Standard Triangle Language or Standard Tessellation Language, and is a popular file format for 3D printing. The 3D models were created, and can be viewed, with CAD software.</p>
Data for "A simple mechanism for uncrewed aircraft bioaerosol sampling in the lower atmosphere"
<p>Colony count data collected from Petri dishes, as described in "A simple mechanism for uncrewed aircraft bioaerosol sampling in the lower atmosphere." See the associated article for more information.</p>
Stress regimes in the Himalaya-Karakoram-Tibet, the western part of India-Eurasia collision: stress field implications based on focal mechanism solution data
<p>This dataset contains valuable information on earthquake events, including their location, magnitude, depth, and focal mechanism solutions. This README file provides detailed explanations of each header in the dataset, as well as information about the files included in the repository.<br><br><em>"Stress regimes in the Himalaya-Karakoram-Tibet, the western part of India-Eurasia collision: stress field implications based on focal mechanism solution data"</em> <strong>(Under Review)</strong><br> </p>
Dynamic sparse X-ray nanotomography reveals ionomer hydration mechanism in polymer electrolyte fuel-cell catalyst: Raw data and reconstruction software
<pre>Dynamic sparse X-ray nanotomography reveals ionomer hydration mechanism in polymer electrolyte fuel-cell catalyst: Raw data and reconstruction software Dataset structure: <strong>- Dynamic_PEFC_data.h5</strong> # Raw projection data for dynamic tomography imaging of PEFC catalyst hydration. - /sinogram # Sinogram of all projections, 3-dimensional array with axes (Nangle,X axis,Y axis). - /tomo_angle # Tomography rotation angle for each projection, 1D array with axis (Nangle). - /humidity_readout # Relative humidity value at the time each projection is measured, 1D array with axis (Nangle). - /Deform_X # X/Y/Z components for the deformation vector field which characterize nonrigid deformation of the sample. - /Deform_Y - /Deform_Z <strong>- liquid_simulation.h5</strong> # Numerical simulation of dynamic liquid filling process. - /sinogram # Sinogram of all projections, 3-dimensional array with axes (Nangle,X axis,Y axis). - /tomo_angle # Tomography rotation angle for each projection, 1D array with axis (Nangle). - /groundtruth_tomograms # Ground truth of the simulated tomograms, 4-dimensional array with axes (Timeframe,Y axis, Z axis, X axis). <strong>- phasetran_simulation.h5</strong> # Numerical simulation of gradual linear density change process. - /sinogram # Sinogram of all projections, 3-dimensional array with axes (Nangle,X axis,Y axis). - /tomo_angle # Tomography rotation angle for each projection, 1D array with axis (Nangle). - /groundtruth_tomograms # Ground truth of the simulated tomograms, 4-dimensional array with axes (Timeframe,Y axis, Z axis, X axis). Reconstruction codes: <strong>- astra_nonrigid.zip</strong> # Compressed python package of modified version of astra-toolbox with nonrigid computed tomography implementation. - /astra # Python package folder, need to be added to Python import search path (sys.path). # If the pre-compiled version doesn't work, source code of the pacakge can be downloaded: # https://github.com/zr-gao/astra-toolbox-nonrigid # Follow the instructions and requirements on the website to compile and install the package. <strong>- reconstruction_PEFC.py</strong> # Python script for sparse dynamic tomography of the PEFC dataset. # Need to be in the same folder with Dynamic_PEFC_data.h5 to load data. # Follow the instructions in the code to set reconstruction parameters and export results. # Requirements: cupy, numpy, astra(with nonrigid)*, h5py # * <strong>!!!</strong> Nonrigid computed tomography is used for the reconstruction, therefore the astra package with nonrigid implementation (in astra_nonrigid.zip) is required. <strong>- reconstruction_simulation.py</strong> # Python script for sparse dynamic tomography of numerical simulations. # Need to be in the same folder with liquid_simulation.h5 or phasetran_simulation.h5, loaded filename is selected in the code. # Follow the instructions in the code to set reconstruction parameters and export results. # Requirements: cupy, numpy, astra**, h5py # ** Reconstruction of numerical simulations does not use nonrigid computed tomography, therefore both the astra_nonrigid.zip and the official astra-toolbox package will work. # To download and install the official astra-toolbox refer to the repository: # https://github.com/astra-toolbox/astra-toolbox</pre>
Changes in gene expression during germination reveal pea genotypes with either 'quiescence' or 'escape' mechanisms of waterlogging tolerance
<p>Waterlogging causes germination failure in pea (<em>Pisum sativum</em> L.). Three genotypes (BM-3, NL-2 and Kaspa) contrasting in ability to germinate in waterlogged soil were exposed to different durations of waterlogging. Whole genome RNAseq was employed to capture differentially expressing genes. The ability to germinate in waterlogged soil was associated with testa colour and testa membrane integrity as confirmed by electrical conductivity measurements. Among the most differentially regulated genes, upregulated gene tyrosine protein kinase responsible for metabolic regulation and downregulated LOX5 involved in fat metabolism indicated energy preservation in tolerant Kaspa, while in the other tolerant NL-2 subtilase family protein and PNC2 involved in protein and fat metabolism respectively showed upregulated expression suggesting energy utilization during waterlogging. By contrast, in sensitive genotype BM-3 high upregulation was recorded for the kunitz-type trypsin/protease inhibitor whose role is blocking the activity of protein metabolism leading to excessive lipid metabolism causing membrane leakage and subsequent seed damage. Pathway analyses based on gene ontologies showed seed storage protein metabolism as upregulated in tolerant genotypes and downregulated in the sensitive genotype. Understanding the tolerance mechanism provides a platform to breed for adaptation to waterlogging stress at germination in pea. </p>
Changes in gene expression during germination reveal pea genotypes with either 'quiescence' or 'escape' mechanisms of waterlogging tolerance
<p>Waterlogging causes germination failure in pea (<em>Pisum sativum</em> L.). Three genotypes (BM-3, NL-2 and Kaspa) contrasting in ability to germinate in waterlogged soil were exposed to different durations of waterlogging. Whole genome RNAseq was employed to capture differentially expressing genes. The ability to germinate in waterlogged soil was associated with testa colour and testa membrane integrity as confirmed by electrical conductivity measurements. Among the most differentially regulated genes, upregulated gene tyrosine protein kinase responsible for metabolic regulation and downregulated LOX5 involved in fat metabolism indicated energy preservation in tolerant Kaspa, while in the other tolerant NL-2 subtilase family protein and PNC2 involved in protein and fat metabolism respectively showed upregulated expression suggesting energy utilization during waterlogging. By contrast, in sensitive genotype BM-3 high upregulation was recorded for the kunitz-type trypsin/protease inhibitor whose role is blocking the activity of protein metabolism leading to excessive lipid metabolism causing membrane leakage and subsequent seed damage. Pathway analyses based on gene ontologies showed seed storage protein metabolism as upregulated in tolerant genotypes and downregulated in the sensitive genotype. Understanding the tolerance mechanism provides a platform to breed for adaptation to waterlogging stress at germination in pea. </p>
Dataset for "Low-cloud feedback in CAM5-CLUBB: physical mechanisms and parameter sensitivity analysis"
<p>This repository contains the data of 512 perturbed-parameter ensemble experiments and CAM5-CLUBB default experiments for the paper "Low-cloud feedback in CAM5-CLUBB: physical mechanisms and parameter sensitivity analysis".</p> <p>In this paper, the quasi-Monte Carlo (QMC) sampling approach is applied to explore the high-dimensional space. 512 samples are generated with the 18 perturbed parameters. For each parameter sample, a pair of experiments is performed: the control one is based on the climatological sea surface temperature (SST), and the 4K experiment applies a uniform +4K SST perturbation to the control experiment. The total of 1024 simulations are then performed. In addition, CAM5-CLUBB default experiments that adopt the default values of the 18 selected parameters as in Bogenschutz et al. (2013) are performed to provide detailed model diagnostics for analyzing physical mechanisms of the cloud feedback, and they include both control and +4K simulations. Each simulation is run for 5 years and 4 months, forced by climatological SSTs. Monthly mean results from the last 5 years are analysed in this study.</p> <p>Note: data uploaded here is annual-mean and the dimension name 'time' in the files (CAM5-CLUBB_PPE_512*.nc) is the number of 512 PPE member.</p>
Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition
<p>This repository contains code to accompany the manuscript titled</p> <p><strong>Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition</strong></p> <p>by <strong>Carly D. Kenkel and Line K. Bay</strong><br> </p> <p>In this study, we used a phylogenetically controlled design to investigate the role of vertical symbiont transmission, an evolutionary mechanism predicted to enhance cooperation and holobiont fitness of reef-building corals. Six species of coral, three vertical transmitters and their closest horizontally transmitting relatives, were fragmented and subjected to a two-week thermal stress experiment. Symbiont cell density, photosynthetic function and translocation of photosynthetically fixed carbon between symbionts and hosts were quantified to assess changes in physiological metrics of fitness and cooperation. Amplicon sequencing of the <em>Symbiodinium</em> ITS-2 locus was used to investigate differences in symbiont community composition among focal species. We did not observe universally higher levels of cooperation in vertically transmitting species. However, the reduction in cooperation at the onset of bleaching was marginally associated with symbiont community diversity. Analysis of ITS2 amplicon sequence data suggest that it may not be vertical transmission <em>per se</em> that influences host-symbiont cooperation, but genetic uniformity of the symbiont community.</p> <p>Repository contents:</p> <ul> <li> <p><strong>TraitDataAnalysis.R:</strong> Annotated R script for generating figures and re-creating statistical analyses</p> <ul> <li> <p><strong>RsquaredGLMM.R:</strong> Accessory R script for running RsquaredGLMM analyses, called by <strong>TraitDataAnalysis.R</strong></p> </li> <li> <p><strong>NSF_RunningPam.csv</strong>: Input file for statistical analysis. Contains photophysiological data. Column headers are as follows:</p> <ul> <li> <p>Tank: Number of experimental tank in which experimental coral fragment was held</p> </li> <li> <p>Treatment: short-hand notation for sample treatments (e.g. ctrl1-5 = control temperature, genotypes 1-5)</p> </li> <li> <p>Water: source sump for temperature controlled water jackets for each set of treatment tanks</p> </li> <li> <p>Position: numerical rack position of coral fragment within experimental treatment tank</p> </li> <li> <p>Species: Coral species (Amil=<em>A. millepora</em>, Maqe=<em>M. aequituberculata</em>, Gast=<em>G. astreata</em>, Gach=<em>G. acrhelia</em>, Plob=<em>P. lobata</em>, Gcol=<em>G. columna</em>)</p> </li> <li> <p>Genotype: source colony origin of individual coral fragments within species</p> </li> <li> <p>Temp: experimental temperature treatment (ctrl: 27°C ; heat: 31°C)</p> </li> <li> <p>Treat: whether experimental corals received C14-labeled bicarbonate (bicarb), artemia or were sampled separately for Gene Expression Analysis (not presented in this manuscript)</p> </li> <li> <p>EQY: Effective quantum yield of <em>Symbiodinium</em> photosystem II as measured using PAM fluorometry</p> </li> <li> <p>Date: Actual calendar date of measure</p> </li> <li> <p>Transmission: coral symbiont transmission mode</p> </li> <li> <p>Reef: reef site of original coral collection</p> </li> <li> <p>Date: experimental date of measure</p> </li> </ul> </li> <li> <p><strong>TraitData.csv:</strong> Input file for statistical analysis. Contains all physiological trait data.</p> <ul> <li> <p>Includes columns as described above for the Running_Pam file in addition to columns containing raw trait data as described in the manuscript.</p> </li> </ul> </li> <li> <p><strong>TraitData_DaysAsCols.csv:</strong> Reformatted input file with trait data split by sampling day across columns</p> </li> </ul> </li> <li> <p><strong>DADA2Analysis.R:</strong> Annotated R script for generating figures and running ITS2 amplicon analyses</p> <ul> <li> <p>GeoSymbio_ITS2_LocalDatabase_verForPhyloseq.fasta: FASTA file of the GeoSymbio ITS2 reference database <a href="https://sites.google.com/site/geosymbio/">https://sites.google.com/site/geosymbio/</a>, formatted for use with the R prograom Phyloseq</p> </li> <li> <p>SeqVars_6Feb.fasta: FASTA file of identified sequence variants resulting from DADA2 analysis</p> </li> <li> <p>OutputDADA_6Feb.csv: Counts of sequence variants by sample</p> </li> <li> <p>Raw FASTQ paired end read files can be downloaded from NCBI's SRA: PRJNA338365</p> </li> </ul> </li> </ul>
NMR data - Mechanism and regioselectivity of the anionic oxidative rearrangement of 1,3-diketones towards all-carbon quaternary carboxylates
<p>NMR characterisation raw data for the publication:</p> <p>Mechanism and regioselectivity of the anionic oxidative rearrangement of 1,3-diketones towards all-carbon quaternary carboxylates</p>
Data supporting publication: Nanoscale Mechanical Manipulation of Ultrathin SiN Membranes Enabling Infrared Near-Field Microscopy of Liquid-Immersed samples
<p>This repository includes the data corresponding to the figures shown in the journal article entitled Nanoscale Mechanical Manipulation of Ultrathin SiN Membranes Enabling Infrared Near-Field Microscopy of Liquid-Immersed samples, published in small. </p>
Data for "A promiscuous mechanism to phase separate eukaryotic carbon fixation in the green lineage"
<p>This repository contains all raw data associated with the manuscript:</p> <p>"<em><strong>A promiscuous mechanism to phase separate eukaryotic carbon fixation in the green lineage</strong></em>"</p> <p> </p> <p>The files are organised according to their appearance as figures in the manuscript.</p> <p>Within each of the zipped figure folders is a <strong>_readme.txt</strong> file that contains information about the raw data provided for each figure.</p>
1D cell trajectories as studied in "Cell-mechanical parameter estimation from 1D cell trajectories using simulation-based inference"
<p>Trajectories of motile cells represent a rich source of data that provide insights into the mechanisms of cell migration via mathematical modeling and statistical analysis. Here, we present trajectories of MDA-MB-231 breast cancer cells and MCF-10A breast epithelial cells. Cells were confined to 1D using fibronectin lanes and exposed to three different treatments, namely the actin polymerisation inhibitor Latrunculin A (LatA), the ROCK inhibitor Y-27632 (Y27) and a control. Each csv file contains a number of 24h long trajectories of cells corresponding to the name of the file. The column names are:</p> <p>`traject_id`: The trajectories are numbered, starting from 0 in each file.</p> <p>`time (h)`: Time in h, starting at 0h for each trajctory and ending at 24h with a temporal resolution of 2min.</p> <p>`x_front`: Position of the cell's front.</p> <p>`x_nucleus`: Position of the cell's nucleus, where x_nucleus=0 for the first time point of the trajectory</p> <p>`x_rear`: Position of the cell's rear.</p> <p>The data was analysed in our study "Cell-mechanical parameter estimation from 1D cell trajectories using simulation-based inference". Further information can be found there. </p>
Supplemental to: Physical and mechanical depth relationships of rocks from the Rotokawa Geothermal Reservoir, Taupō Volcanic Zone, New Zealand
<p>This contains supplementary informations for the Manuscript </p> <p>Physical and mechanical depth relationships of rocks from the Rotokawa Geothermal Reservoir, TaupōVolcanic Zone, New Zealand</p> <p>submitted for review at the New Zealand Journal of Geology and Geophysics</p>
Integration of High-Tc Superconductors with High-Q-Factor Oxide Mechanical Resonators (Dataset)
<p>Micro-mechanical resonators are building blocks of a variety of applications in basic science and consumer electronics. This device technology is mainly based on well-established and reproducible silicon-based fabrication processes with outstanding performances in term of mechanical <em>Q</em>-factor and sensitivity to external perturbations. Broadening the functionalities of micro-electro-mechanical systems (MEMS) by the integration of functional materials is a key step for both applied and fundamental science. However, combining functional materials with silicon-based devices is challenging. An alternative approach is directly fabricating MEMS based on compounds inherently showing non-trivial functional properties, such as transition metal oxides. Here, a full-oxide approach is reported, where a high-Tc superconductor YBa<sub>2</sub>Cu<sub>3</sub>O<sub>7</sub> (YBCO) is integrated with high <em>Q</em>-factor micro-bridge resonators made of single-crystal LaAlO<sub>3</sub> (LAO) thin films. LAO resonators are tensile strained, with a stress of about 350 MPa, show a <em>Q</em>-factor above 200k, and have low roughness. YBCO overlayers are grown ex situ by pulsed laser deposition and YBCO/LAO bridges show zero resistance below 78 K and mechanical properties similar to those of bare LAO resonators. These results open new possibilities toward the development of advanced transducers, such as bolometers or magnetic field detectors, as well as experiments in solid state physics, material science, and quantum opto-mechanics.</p>
ADDRESSING TAX COMPLIANCE ISSUES FOR LOAN-BASED PAYMENT TYPES: DEVELOPMENT OF THE TAX BUFFER MECHANISM AND ITS USE IN THE FINTECH INDUSTRY
<p>In the modern world of the fintech industry, tax changes are one of the key problems, especially with fixed loans. This study examines the Tax Buffer mechanism, designed to effectively manage tax obligations that vary depending on the jurisdiction and stages of delivery of goods. The main task of the mechanism is to automatically recalculate taxes to minimize the risk of errors and reduce the burden on the accounting and legal departments of the company. The implementation of this solution allows you to reduce the number of manual operations, reduce transaction costs and improve the customer experience by eliminating the need to notify users of every change in the amount of taxes. The results of the implementation of the mechanism have shown its high efficiency: a significant reduction in the number of errors and financial disputes, as well as an increase in operational efficiency. The Tax Buffer mechanism is an important innovation that helps to increase the resilience of fintech companies to changes in tax legislation.</p>
Influence of the cochlear partition's flexibility on the macro mechanisms in the inner ear
<p>This repository contains the research data for the article Kersten, S., Taschke, H., & Vorländer, M. (2024). Influence of the cochlear partition’s flexibility on the macro mechanisms in the inner ear. Hearing Research, 109127. <a href="https://doi.org/10.1016/j.heares.2024.109127">https://doi.org/10.1016/j.heares.2024.109127</a>.</p> <p>It includes a finite element model of the inner ear, simulation results, and a Python script with code used for the analysis.</p> <div> <h2>Abstract</h2> <div> <div>Recent studies have highlighted the anatomy of the cochlear partition (CP), revealing insights into the flexible nature of the osseous spiral lamina (OSL) and the existence of a flexible cochlear partition bridge (CPB) between the OSL and the basilar membrane (BM). However, most existing inner ear models treat the OSL as a rigid structure and ignore the CPB, neglecting their potential impact on intracochlear sound pressure and motion of the BM. In this paper, we investigate the effect of the CP’s flexibility by including the OSL and CPB as either rigid or flexible structures in a numerical anatomical model of the human inner ear. Our findings demonstrate that the flexibility of the OSL and the presence of the CPB significantly affect cochlear macro mechanisms, including differential intracochlear sound pressure, resistive behavior in cochlear impedances, CP stiffness, and BM velocity. These results emphasize the importance of considering the flexibility of the entire CP to enhance our understanding of cochlear function and to accurately interpret experimental data on inner ear mechanics.</div> </div> </div>
Stacks of microCT Scans, Cell size, weight, volume and thallus size data supporting the paper 'Mechanical regulation of tissue flatness in Marchantia'
<div> <div> <div> <p>These data are the supporting elements to the following paper: 'Mechanical regulation of tissue flatness in Marchantia'</p> </div> </div> </div> <p> .tif files contain MicroCT (MCT) scans of 16-day-old <em>Marchantia polymorpha</em> thalli. Three genotypes were analysed here: <strong><em>fer-2</em></strong> mutant (from Mecchia et al., 2022), <strong>FER-OE #9</strong> (proMpEF1::MpFERONIA-mCitrine trangenic line 9)<strong> </strong>from Mecchia et al., 2022), and Tak-1 (WT line). These plants were grown in 3 different media: Gamborgh B5 + vitamins and 0.6, 1.2 and 2.5% agar, and one stress condition consisting of the adjunction of a thin PDMS film at 4, to mimich external mechanical stimulus (only performed on thalli grown on 1.2% agar).</p> <p>MicroCT scans were performed at the faculity of odontology of Université Paris-Cité (Plateform imagerie du vivant) with the technical support of Lotfi Slimani and Baptiste Casel. https://piv.u-paris.fr/micro-ct-haute-resolution/ </p> <p>All files already have embeded scales.</p> <p>Each file name consists of a unique ID number in the following form:</p> <p>P+<LETTER>+<NUMBER>-<CONDITION></p> <p>-LETTER: One letter = one imaging session</p> <p>-NUMBER: Individual and Genotype: 33-40 -> Tak1; 200-207-><em>fer-2</em>; 41-49 -> FER-OE</p> <p>-CONDITION : AGAR0.6/AGAR2.5/PDMS. Absence of condition indicates growth on standard medium (1.2% agar). PDMS indicated growth on standard medium and supplementation of a topping PDMS film at day 4)</p> <p> </p> <p>-Volume data were calculated from MicroCT scans</p> <p>-thallus projected surfaces were calculated from MicroCT scans</p> <p><a href="https://zenodo.org/api/records/13981438/draft/files/Lambda%20curvature%20calculation.ipynb/content" target="_blank" rel="noopener noreferrer">-Lambda curvature calculation.ipynb</a> is suited for MorphographX mesh exported .txt files.</p> <p> </p> <p> </p> <p> </p>
Mechanical Stretch Inhibition Sensitizes Proprioceptors to Compressive Stresses
<p>A repetitive gait cycle is an archetypical component within the behavioural repertoire of many if not all<br> animals including humans. It originates from mechanical feedback within proprioceptors to adjust the<br> motorprogram during locomotion and thus leads to a periodic orbit in a low dimensional space. Here,<br> we investigate the mechanics, molecules and neurons responsible for proprioception in Caenorhabditis<br> (C.) elegans to gain insight into how mechanosensation shapes the orbital trajectory to a well-defined<br> limit cycle. We used genome editing, force spectroscopy and multiscale modeling and found that<br> alternating tension and compression with the spectrin network of a single proprioceptor encodes<br> body posture and informs TRP-4/NOMPC and TWK-16/TREK2 homologs of mechanosensitive<br> ion channels during locomotion. In contrast to a widely accepted model of proprioceptive ‘stretch’<br> reception, we found that proprioceptors activated locally under compressive stresses in vivo and in<br> vitro, and propose that this property leads to compartmentalized activity within long axons delimited<br> by curvature-dependent mechanical stresses.</p>
Potential Cell Lysis Mechanisms for B. subtilis
<p><strong>Description:</strong></p> <p>A list of potential cell lysis mechanisms for Bacillus subtilis, cured and organized as part of the partnership between iGEM UANL and UNILA teams in the design of a Kill Switch for B. subtilis. For more information on both designs, check out the projects wikis:</p> <p>iGEM UNILA LatAm 2021: https://2021.igem.org/Team:UNILA_LatAm</p> <p>iGEM FCB-UANL 2021: https://2021.igem.org/Team:FCB-UANL</p> <p><strong>Columns:</strong></p> <ul> <li><strong>CRISPR:</strong> CRISPR systems developed for B. subtilis <ul> <li><strong>CRISPR Variant: </strong>Cas variant used in the system</li> <li><strong>Editing/Disruption Efficiency: </strong>System efficiency evaluated for multiple or single editions</li> <li><strong>Mechanisms: </strong>operating mechanism</li> <li><strong>Application: </strong>Main objective for the developed system</li> <li><strong>B. subtilis considerations: </strong>Particularities regarding the development of the system in B. subtilis</li> <li><strong>Year: </strong>year of publication</li> </ul> </li> <li><strong>TA Systems:</strong> Toxin-Antitoxin systems developed for B. subtilis <ul> <li><strong>Toxin-Antitoxin: </strong>Which antitoxins and toxins involved in the system </li> <li><strong>Type: </strong>TA System Type</li> <li><strong>Mechanism: </strong>operating mechanism</li> <li><strong>Application: </strong>Main objective for the developed system</li> </ul> </li> <li><strong>Sporulation: </strong>Control of sporulation events in B. subtilis <ul> <li><strong>Spores Control</strong></li> <li><strong>Type</strong></li> <li><strong>Mechanism: </strong>operating mechanism</li> <li><strong>Application: </strong>Main objective for the developed system</li> </ul> </li> <li> <strong>iGEM Applications:</strong> Kill Switch designs for B. subtilis since 2014. <ul> <li><strong>Kill Switch System: </strong>Design description of Kill switch systems</li> <li><strong>Type: </strong>System components</li> <li><strong>Mechanism: </strong>operating mechanism</li> <li><strong>Application: </strong>Main objective for the developed system</li> <li><strong>Test: </strong>Type of assessment performed by the team</li> <li><strong>Parts Registry: </strong>Parts submitted to the Registry of Standard Biological Parts.</li> </ul> </li> </ul> <p><strong>Remote Access:</strong> <a href="https://docs.google.com/spreadsheets/d/1PM7NS5JbfVLgjsa6s7L8yqBj_G1A5mSnKCPaeGmkIwg/edit#gid=0">Potential Cell Lysis Mechanisms for B. subtilis</a></p> <p> </p> <p> </p> <p> </p>
RMSD and Trp assays for "Structural analysis of a motor with increased mechanical output reveals new transitions in kinesin microtubule motility"
<p>This entry is for our manuscript, "Structural analysis of a motor with increased mechanical output reveals new transitions in kinesin microtubule motility" by Satoki Shibata*, Matthew Y. Wang*, Tsuyoshi Imasaki*, Hideki Shigematsu, Diego Ugarte La Torre, Yuanyuan Wei, Chacko Jobichen, Hajime Hagio, J. Sivaraman, Yuji Sugita, Sharyn A. Endow & Ryo Nitta.</p> <p>*Equal contribution</p> <p>Corresponding Authors: Tsuyoshi Imasaki*, Sharyn A. Endow, Ryo Nitta</p> <p>The deposited datasets are 1) beta-strand residue all-atom RMSD between kinesin-14 NcdY485K ADP and ADP + free Pi nucleotide states and 2) fluorimeter assays of NcdY485K intrinsic Trp fluorescence changes upon addition of free Pi . The data are presented in Fig. 6e, Fig. 7b,c and Supplementary Fig 10. Files are named for the figures in which the data are shown. A computer script for the RMSD analysis and methods for the fluorimeter assays and data analysis are included in the deposited files.</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.