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293 results for “Clamping”
Supplementary Data for the manuscript 'The Rad9-Rad1-Hus1 DNA repair clamp is found in Microsporidia'
<p>This dataset contains the supplementary data files for the manuscript titled 'The Rad9-Rad1-Hus1 DNA repair clamp is found in Microsporidia'.</p>
Capacitance clamp demonstration in rat dentate gyrus granule cells
<p>Dataset for a demonstration of the capacitance clamp, a variant of the dynamic clamp technique, which allows to virtually modify the capacitance of a biological neuron (or any electrically excitable cell).</p> <p>Code for analysis and further explanations will be made available. </p>
National Severe Storms Laboratory Mobile Soundings during Lapse-Rate (CLAMPS trailer)
<p>This dataset includes files from the National Severe Storms Laboraory mobile sounding units operated during the LAPSE-RATE field campaign. The files contained here are for each individual sounding launched from the CLAMPS trailer owned and operated by the University of Oklahoma, along with a readme file explaining the data format and processing.</p>
OU/NSSL CLAMPS Doppler Lidar Data from LAPSE-RATE
<p>Doppler lidars transmit pulses of 1.5 um wavelength laser energy into the atmosphere, which scatters off aerosol particles and hydrometeors. The lidar measures the intensity of this return, as well as its radial velocity. The lidar has a scanner which allows the system to scan anywhere in the hemisphere, and typically a fixed scan strategy is used. The Doppler lidar data are provided in three different netCDF files: one containing the stare data (DLFP), one containing the PPI data (DLPPI), and the last containing the processed VAD data (DLVAD). These files are provided in netCDF format.</p> <p>For LAPSE-RATE, the OU DL scan strategy consisted of a 24-point plan position indicator (PPI) scan at 70 degree elevation angle, a 6-point PPI at 45 degrees, and a vertical stare. The sequence ran every 5 minutes with the stare filling in the remaining time after the two PPI scans.</p>
OU/NSSL CLAMPS Microwave Radiometer and Surface Meteorological Data from LAPSE-RATE
<p>The microwave radiometer measures downwelling microwave radiance in 14 channels from 22.2 to 60.0 GHz at 1 s temporal resolution. It is one of the core instruments in the Collaborative Lower Atmospheric Mobile Profiling System (CLAMPS-1) facility.</p> <p>A simple statistical retrieval is performed to retrieve precipitable water vapor (PWV) and liquid water path (LWP) from the observations at 23.8 and 31.4 GHz (Turner et al. 2007).</p> <p>This microwave radiometer has a Vaisala all-weather met station included. This station is positioned about two feet above the back of the CLAMPS trailer. It is possible that the trailer is affecting these met station observations in some conditions. Note that the wind data in these files are likely not representative of true environmental wind. Due to power requirements, CLAMPS was positioned close to a building, which likely influenced the wind speed and direction. Any wind data should be used with caution.</p> <p> </p> <p>References:</p> <p>Turner, D. D., S. A. Clough, J. C. Liljegren, E. E. Clothiaux, K. E. Cady-Pereira, and K. L. Gaustad, 2007: Retrieving Liquid Wat0er Path and Precipitable Water Vapor From the Atmospheric Radiation Measurement (ARM) Microwave Radiometers. <em>IEEE Transactions on Geoscience and Remote Sensing</em>, <strong>45</strong>, 3680–3690, <a href="https://doi.org/10.1109/TGRS.2007.903703">https://doi.org/10.1109/TGRS.2007.903703</a>.</p>
OU/NSSL CLAMPS AERIoe Temperature and Water Vapor Profile Data from LAPSE-RATE
<p>The AERIoe algorithm (Turner and Loehnert 2014, Turner and Blumberg 2018) retrieves profiles of temperature and water vapor mixing ratio, together with cloud properties for a single-layer cloud (i.e., LWP, effective radius), from AERI-observed infrared radiance spectrum. The data can be used to characterize the evolution of the planetary boundary layer and boundary layer clouds.</p> <p>This dataset was collected at the Moffat Consolidated School in Moffat, CO during the LAPSE-RATE field campaign. The AERIoe retrieval was run at 15-minute resolution to match the cadence of the UAS that was colocated with the CLAMPS facility. This is a physical-iterative retrieval method. The retrieval of thermodynamic profiles from spectral infrared radiance observations is an ill-posed problem, and thus constraints need to be included in the retrieval algorithm to provide physically plausible results. Here, we use a climatology of 2022 radiosonde profiles collected from Denver during July as our prior information in an optimal estimation framework.</p> <p>As the method uses an optimal estimation framework, a full error covariance matrix of each solution is included in the output file. The 1-sigma uncertainty of each retrieved variable, which is derived from the error covariance matrix, is included for each scientific field and is named "sigma_X", where "X" is the name of the scientific field (e.g., 'temperature'). The information content in the AERI observations, which is in the "dfs" field, on the thermodynamic profiles is primarily concentrated in the lowest 3 km or up to cloud base; the retrieved data should not be used above that level (or used with caution).</p> <p> </p> <p>References:</p> <p>Turner, D. D., and U. Löhnert, 2014: Information Content and Uncertainties in Thermodynamic Profiles and Liquid Cloud Properties Retrieved from the Ground-Based Atmospheric Emitted Radiance Interferometer (AERI). <em>J. Appl. Meteor. Climatol.</em>, <strong>53</strong>, 752–771, <a href="https://doi.org/10.1175/JAMC-D-13-0126.1">https://doi.org/10.1175/JAMC-D-13-0126.1</a>.</p> <p>Turner, D. D., and W. G. Blumberg, 2019: Improvements to the AERIoe Thermodynamic Profile Retrieval Algorithm. <em>IEEE J. Sel. Top. Appl. Earth Observations Remote Sensing</em>, <strong>12</strong>, 1339–1354, <a href="https://doi.org/10.1109/JSTARS.2018.2874968">https://doi.org/10.1109/JSTARS.2018.2874968</a>.</p>
ASDF Evaluation Dataset + Corner Clamp Base
<p>Evaluation data for ASDF and Corner Clamp Base Training Data</p> <p> </p> <blockquote> <p>@article{schieber2024asdf,<br> title={ASDF: Assembly State Detection Utilizing Late Fusion by Integrating 6D Pose Estimation},<br> author={Schieber, Hannah and Li, Shiyu and Corell, Niklas and Beckerle, Philipp and Kreimeier, Julian and Roth, Daniel},<br> journal={arXiv preprint arXiv:2403.16400},<br> year={2024}<br>}</p> </blockquote>
In situ clamped beam bending of accumulative roll bonded Cu/Nb with 63 nm individual layer thickness
<p>In situ scanning electron microscope (SEM) videos of clamped beam bending of Cu/Nb ARB nanolaminates with 63 nm layer thickness. Each video contains the video captured with SEM and the corresponding measured load vs. displacement curve.</p> <p>The beams were fabricated using focused ion beam (FIB) milling from bulk Cu/Nb sample produced in Los Alamos National Lab, USA. The sample was made using accumulative roll bonding (ARB) process, described in ref. [1]. </p> <p>All the beam lengths are aligned either with rolling direction (RD) of the sample of transfer direction of the sample (TD). RD and TD are used to denote the beam length direction in the videos and the table below. Each beam has a rectangular notch located in the center of the beam length. Each notch spans through the beam width. Owing to limited accuracy of FIB, the notch depth was not always same at the front and rear sides of the beam (typically, smaller at the rear sides)</p> <p>Beam geometries:</p> <p>Id | Length, µm | Width, µm | Thickness, µm | Notch depth (front), nm | Notch width (front), nm</p> <p>RD1 | 42 | 5.4 | 4.4 | 1100 | 100</p> <p>RD2 | 20 | 2.8 | 3.1 | 1200 | 300</p> <p>RD3 | 21 | 3 | 2.2 | 700 | 100</p> <p>TD1 | 40 | 4.8 | 5 | 1000 | 250</p> <p>TD2 | 20 | 3 | 2.5 | 700 | 230 </p> <p>TD3 | 19 | 3.3 | 3 | 900 | 300</p> <p>TD4 | 19 | 3.5 | 2.6 | 750 | 360</p> <p>All the beams were loaded using Hysitron PI85 picoindenter with truncated cone shape (5 µm diameter). The indenter tip was aligned with the notch location and the middle of beam width. RD3 beam had some misalignment along the width.</p> <p>All the beams, except RD3 beam, were loaded under displacement control with displacement rates between 5nm/s to 10nm/s until failure. RD3 beam was loaded under load control with loading rate ~33µN/s. </p> <p>The SEM videos were captured using JEOL JSM-7600F SEM. </p> <p>[1] Irene J Beyerlein et al. “Interface-driven microstructure development and ultra high strength of bulk nanostructured Cu-Nb multilayers fabricated by severe plastic deformation”. In: Journal of materials research 28.13 (2013), pp. 1799–1812</p>
Jumping the green wall: the use of PNA-DNA clamps to enhance microbiome sampling depth in wildlife microbiome research
As microbiome research moves away from model organisms to wildlife, new challenges for microbiome high throughput sequencing arise caused by the variety of wildlife diets. High levels of contamination are commonly observed emanating from the host (mitochondria) or diet (chloroplast). Such high contamination levels affect the overall sequencing depth of wildlife samples thus decreasing statistical power and leading to poor performance in downstream analysis. We developed an amplification protocol utilizing PNA-DNA clamps to maximize the use of resources and to increase the sampling depth of true microbiome sequences in samples with high levels of plastid contamination. We chose two study organisms, a bat (Leptonyteris yerbabuenae) and a bird (Mimus parvulus), both relying on heavy plant-based diets that sometimes lead to traces of plant-based faecal material producing high contamination signals from chloroplasts and mitochondria. On average, our protocol yielded a 13-fold increase in bacterial sequence amplification compared with the standard protocol (Earth Microbiome Protocol) used in wildlife research. For both focal species, we were able significantly to increase the percentage of sequences available for downstream analyses after the filtering of plastids and mitochondria. Our study presents the first results obtained by using PNA-DNA clamps to block the PCR amplification of chloroplast and mitochondrial DNA from the diet in the gut microbiome of wildlife. The method involves a cost-effective molecular technique instead of the filtering out of unwanted sequencing reads. As 33% and 26% of birds and bats, respectively, have a plant-based diet, the tool that we present here will optimize the sequencing and analysis of wild microbiomes.
Patch-clamp recordings from dorsal raphe neurons
<p>This dataset contains whole-cell electrophysiological recordings (patch-clamp recordings) from three cell types in mice:</p> <ul> <li>serotonin (5-HT) neurons,</li> <li>somatostatin (SOM)-expressing GABA interneurons, and</li> <li>layer 5 pyramidal neurons.</li> </ul> <p>5-HT and GABA neurons were recorded in the dorsal raphe nucleus (DRN), which is the main source of serotonergic input to the forebrain. Together, they make up the majority of the neurons found in the DRN.</p> <p>This dataset can be used to investigate the intrinsic electrophysiological properties of these two types of DRN neurons and contrast them with another abundant and well-studied cell type, the L5 pyramidal neuron.</p> <p>This data was used in <a href="https://doi.org/10.7554/eLife.72951" rel="noopener" title="Temporal derivative computation in the dorsal raphe network revealed by an experimentally-driven augmented integrate-and-fire modeling framework | eLife">our paper</a> describing a spiking neural network model of the dorsal raphe nucleus:</p> <p>Emerson F. Harkin, Michael B. Lynn, Alexandre Payeur, Jean-François Boucher, Léa Caya-Bissonnette, Dominic Cyr, Chloe Stewart, André Longtin, Richard Naud, and Jean-Claude Béïque. Temporal derivative computation in the dorsal raphe network revealed by an experimentally-driven augmented integrate-and-fire modeling framework. eLife, 2023. doi: 10.7554/eLife.72951</p>
Jumping the green wall: the use of PNA-DNA clamps to enhance microbiome sampling depth in wildlife microbiome research
Open the record for dataset details and reuse information.
Patch-clamp recordings from dorsal raphe neurons
Open the record for dataset details and reuse information.
Novel developments in clamped geometries for fracture toughness testing
<p>Stable fracture toughness test geometries are useful in not only determining the monotonic fracture toughness, but also in capturing the R-curve behaviour and damage tolerance of materials under cyclic loading and extreme environments. The doubly clamped boundary condition offers such crack stability even in the most brittle materials. This talk will cover all aspects of clamped beams and wires in tension and bending as fracture toughness test geometries including their geometric factor solutions for linear elastic and elastic-plastic cases. Finite element simulations are used to explain the mechanics of crack stability for various beam and wire aspect ratios and crack configurations. Their varied applications in bulk materials, architectured systems, thin film multilayers and graded coatings will be shown.</p> <p><strong>Related publications</strong></p> <ol> <li>A. K. Mishra, A. Lambai and V. Jayaram, B. Nagamani Jaya, “The edge-notched clamped beam bend specimen as a fracture toughness test geometry”, Theoretical and Applied Fracture Mechanics, 105, 2020, 102409 (DOI: 10.1016/j.tafmec.2019.102409)</li> <li>B. Nagamani Jaya, Sanjit Bhowmick, S. A. Syed Asif, Oden L. Warren and Vikram Jayaram, “Optimization of clamped beam geometry for fracture toughness testing of micron-scale samples” Phil Mag Special Issue on Nanomech IV, Vol 95, 2015, 1945-1966 (DOI: 10.1080/14786435.2015.1010623)</li> <li>B. Nagamani Jaya and Vikram Jayaram, “Crack stability in edge notched clamped beam specimen under bending: modeling and experiments”, International Journal of Fracture, Vol 188, Issue 2, 2014, 213-228 (DOI: 10.1007/s10704-014-9956-2)</li> <li>B. Nagamani Jaya, Vikram Jayaram and Sanjay K. Biswas, “A new method for fracture toughness determination of graded (Pt,Ni)Al bond coats by microbeam bend tests”, Philosophical Magazine Special Issue on Nanomechanical Testing in Materials Research and Development III, Vol 92, Issue 25-27, 2012, 3326-3345. (DOI: 10.1080/14786435.2012.669068)</li> </ol>
Data sets comparing Ca(2+) dynamics in whole-cell and β-escin-based perforated patch clamp recordings in adult mouse brain slices.
<p># Hess-et-al-beta-escin-2020<br> Data of the "Data in Brief" article concerning the added buffer approach with beta-escin perforated patch.</p> <p>A joint work by: Simon Hess (`simon.hess@uni-koeln.de`), Christophe Pouzat (`christophe.pouzat@math.unistra.fr`), and Peter Kloppenburg (`peter.kloppenburg@uni-koeln.de`).</p> <p>## Content</p> <p>This repository contains:</p> <p>- Directory `data_whole_cell` contains the experimental data in [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) format. The data contains recordings of _Substantia nigra_ dopaminergic neurons recorded in the whole-cell configuration.<br> - Directory `data_beta_escin` contains the experimental data in [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) format. The data contains recordings of _Substantia nigra_ dopaminergic neurons recorded in the β-escin perforated patch clamp configuration.</p>
Replica Medieval Wood Clamp
This replica wood clamp is used to hold planks in place during boat building. The earliest known example dates from the late 12th Century with variants having been found in Britain, Scandinavia and Central Europe with usage still documented as late as the 17th century. Mostly constructed with an axe, craftsmen would utilize the natural curves in the grain of the wood as well as knots to increase durability, with beech, oak and dogwood comprising the species used in known examples. Now these clamps are being used by the boat building team at The Sutton Hoo Ships Company to reconstruct the 7th Century Anglo-Saxon Burial ship. The ship is being reconstructed in The Longshed, Woodbridge, Suffolk, UK and is viewable by the public when work is taking place. Please visit the website for further details and how you can get invovled https://saxonship.org/ Research by Alec Newland Photogrammetry generated in Agisoft Metashape by David Matzliach & Andy Spencer Source: Objaverse 1.0 / Sketchfab
Hose Clamp
This item was 3D scanned using a Creaform Go Scan 50. For more information about this object, feel free to visit: https://www.visitindy.com/indianapolis-firefighters-museum-historical-society For more information about the 3D Digitization Program at IUPUI visit: https://www.ulib.iupui.edu/digitalscholarship/3ddig Source: Objaverse 1.0 / Sketchfab
Patch clamp dataset for: A massively parallel assay accurately discriminates between functionally normal and abnormal variants in a hotspot domain of KCNH2
<p><span>Many genes, including <em>KCNH2</em>, contain </span><span>'hotspot' domains associated with a high density of variants associated with disease. This has led to the suggestion that variant location can be used as evidence supporting classification of clinical variants. However, it is not known what proportion of all potential variants in hotspot domains cause loss of function. Here, we have used a massively parallel trafficking assay to characterize all single-nucleotide variants in exon 2 of <em>KCNH2, </em>a known hotspot for variants that cause long QT syndrome type 2 and an increased risk of sudden cardiac death<em>. </em>Forty-two percent of <em>KCNH2</em> exon 2 variants caused at least 50 % reduction in protein trafficking and 65% of these trafficking defective variants exerted a dominant-negative effect when co-expressed with a WT <em>KCNH2</em> allele as assessed using a calibrated patch clamp electrophysiology assay. The massively parallel trafficking assay was more accurate (AUC of 0.94) than bioinformatic prediction tools (REVEL and CardioBoost, AUC of 0.81) in discriminating between functionally normal and abnormal variants. Interestingly, over half of variants in exon 2 were found to be functionally normal, suggesting a nuanced interpretation of variants in this 'hotspot' domain is necessary. Our massively parallel trafficking assay can provide this information prospectively.</span></p>
[3/3] Patch clamp of a Purkinje cell in a simulated cerebellar cortex model during single impulse stimulation
<p>Patch clamp of a Purkinje cell in a simulated cerebellar cortex model during single impulse stimulation</p>
[2/3] Patch clamp of a Purkinje cell in a simulated cerebellar cortex model during single impulse stimulation
<p>Patch clamp of a Purkinje cell in a simulated cerebellar cortex model during single impulse stimulation</p>
[1/3] Patch clamp of a Purkinje cell in a simulated cerebellar cortex model during single impulse stimulation
<p>Patch clamp of a Purkinje cell in a simulated cerebellar cortex model during single impulse stimulation</p>
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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.