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Dataset results
94 results for “Activation loop”
implementation of an in-line Kerr active cavity equipped with a loop mirror
<p>This dataset includes the measurements of the resonances collected at the through port of an active fiber cavity (in in-line configuration) of 5 meters of length based on a step index silica fiber and including a loop mirror and a fiberized mirror at the two ends of the cavity. The dataset includes also the measurement of the effective losses of the in-line active cavity vs. the intracavity power. </p>
Data for manuscript: The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops is Determined by Ligand Binding and Interprotomer Allostery
<div>The data is provided as a part of the manuscript "<strong>The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops is Determined by Ligand Binding and Interprotomer Allostery</strong>". This repository includes an archive with folders:</div> <div> </div> <div><strong>md_data </strong></div> <div> <ul> <li>a directory with MD data for all simulation systems considered in the manuscript. Initial and final conformations are provided.</li> </ul> </div> <div> </div> <div><strong>fig_data</strong></div> <div> <ul> <li>a directory with the data underlying all the main text in the manuscript. </li> </ul> </div> <div> </div> <div>Videos S1-S3 are also included.</div>
Data from: Non-breeding sites, loop migration and activity patterns over the annual cycle in the Lesser Grey Shrike Lanius minor from a western edge of its range
<p>Raw data from three tracked individuals. Two were tracked with light geolocators (22UL and an incomplete track of 22UH) and one (16KN) with GDL3-PAM multi-sensor logger. All produced by Swisss Ornithological Insitute.</p>
Datasets for Insights into prismatic loop formation in irradiated Fe-Cr alloys from hypothesis-driven active learning and causal analysis
<p>Datasets for irradiated Fe-Cr alloys are collected from the experimental reports on dislocation loop type and dislocation density. We have constructed a data set from experimental literature containing 182 data points. To address such challenges to predict dislocation density, we have implemented a three-step ML approach as listed in the following:</p> <div> <div> <div> <ul> <li> <p>impute dataset to fill in the missing data to construct a predictive model using the RF regression algorithm. </p> </li> <li> <p>generate functionalized features and evaluate feature importance using the predictive model</p> </li> <li> <p>use the physics-based important functionalized features as hypotheses (physics-augmented GP models) in a hypothesis-driven active learning scheme to learn and predict dislocation density for all alloys. </p> </li> </ul> </div> </div> </div>
STORM Data: Transcriptionally active chromatin loops contain both 'active' and 'inactive' histone modifications that exhibit exclusivity at the level of nucleosome clusters
<p>The dataset underlying the SMLM STORM super-resolution images of 'Transcriptionally active chromatin loops contain both ‘active’ and ‘inactive’ histone modifications that exhibit exclusivity at the level of nucleosome clusters'. See Biorxiv paper for details on sample preparation: <a href="https://www.biorxiv.org/content/10.1101/2023.09.03.555774v1.full.pdf">https://www.biorxiv.org/content/10.1101/2023.09.03.555774v1.full.pdf</a>, Pyranose Oxidase STORM buffer on Elyra 7 Zeiss Microscope, processed with Zen Black. Samples are named according to which figures they occur in the above paper.</p>
Data from: Seamounts generate efficient active transport loops to nourish the twilight ecosystem
<p>Seamounts are ecological oases nurturing abundant fisheries resources and epibenthic megafauna in the vast oligotrophic ocean. Despite their significance, the formation mechanisms underlying these seamount ecological oases remain uncertain. To shed light on this phenomenon, this study conducted interdisciplinary <em>in-situ</em> observations focusing on a shallow seamount in the oligotrophic ocean. In this dataset, we report high-resolution hydrographic and biochemical observational data from both sectional observations and time-series stations observations.</p>
Dual loop active learning of hydrophobicity of patterned SAMs
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Data from: Seamounts generate efficient active transport loops to nourish the twilight ecosystem
Open the record for dataset details and reuse information.
A Miniature Shielded-loop Active H-field Probe Design for Near-field Measurement
<p>In the "A Miniature Shielded-loop Active H-field Probe Design for Near-field Measurement", this includes all the figures.</p>
Plasma parameters and geometry of cool and warm active region loops
<p>Additional plots for the paper "Plasma parameters and geometry of cool and warm active region loops", 2017, ApJ</p>
ARID1A suppresses R-loop mediated STING-Type I Interferon pathway activation of anti-tumor immunity
<p>Clinical trials have identified ARID1A mutations as enriched among patients who respond favorably to Immune Checkpoint Blockade (ICB) in several solid tumor types independent of microsatellite instability. We show that ARID1A loss in murine models is sufficient to induce anti-tumor immune phenotypes observed in ARID1A mutant human cancers, including increased CD8+ T cell infiltration and cytolytic activity. ARID1A deficient cancers upregulated an interferon (IFN) gene expression signature, the ARID1A-IFN signature, associated with increased R-loops and cytosolic single stranded DNA (ssDNA). Overexpression of the R-loop resolving enzyme, RNASEH2B, or cytosolic DNase, TREX1, in ARID1A deficient cells prevented cytosolic ssDNA accumulation and ARID1A-IFN gene upregulation. Further, the ARID1A-IFN signature and anti-tumor immunity were driven by STING dependent Type I IFN signaling, which was required for improved responsiveness of ARID1A mutant tumors to ICB treatment. These findings define a molecular mechanism underlying anti-tumor immunity in ARID1A mutant cancers.</p>
All data support the published articel "Loop-optimization of Trichoderma reesei endoglucanases for balancing the activity–stability trade-off through cross-strategy between machine learning and the B-factor analysis"
<p><em>Trichoderma reesei</em> endoglucanases (EGs) have limited industrial applications due to its low thermostability and activity. Here, we aimed to improve the thermostability of EGs from<em> T.reesei</em> without reducing its activity counteracting the activity-stability trade-off. A cross-strategy combination of machine learning and B-factor analysis was used to predict beneficial amino acid substitution in EG loop optimization. Experimental validation showed single-site mutated EG concomitantly improved enzymatic activity and thermal properties by 17.21%–18.06% and 49.85%–62.90%, respectively, compared with wild-type EGs. Furthermore, the mechanism explained mutant variants had lower RMSD values and a more stable overall structure than the wild type. According to this study, EGs loop optimization is crucial for balancing the activity-stability trade-off, which may provide new insights into how loop region function interacts with enzymatic characteristics. Moreover, the cross-strategy between machine learning and B-factor analysis improved superior enzyme activity-stability performance, which integrated structure-dependent and sequence-dependent information.</p>
ADAR1 Links R-Loop Homeostasis to ATR Activation in Replication Stress Response
<p>Unscheduled R-loops are a major source of replication stress and DNA damage. R-loop-induced replication defects are sensed and suppressed by ATR kinase, whereas it is not known whether R-loop itself is actively involved in ATR activation and, if so, how this is achieved. Here, we report that the nuclear form of RNA-editing enzyme ADAR1 promotes ATR activation and resolves genome-wide R-loops, a process that requires its double-stranded RNA-binding domains. Mechanistically, ADAR1 interacts with TOPBP1 and facilitates its loading on perturbed replication forks by enhancing the association of TOPBP1 with RAD9 of the 9-1-1 complex. When replication is inhibited, DNA-RNA hybrid competes with TOPBP1 for ADAR1 binding to promote the translocation of ADAR1 from damaged fork to R-loop region. There, ADAR1 recruits RNA helicases DHX9 and DDX21 to unwind R-loops, simultaneously allowing TOPBP1 to stimulate ATR more efficiently. Collectively, we propose that the tempo-spatially regulated assembly of ADAR1-nucleated protein complexes link R-loop clearance and ATR activation, while R-loops crosstalk with blocked replication forks by transposing ADAR1 to finetune ATR activity and safeguard the genome.</p>
A Closed Loop Neural Activity Triggered Stroke Rehabilitation Device
ClinicalTrials.gov study NCT02098265. IPD Sharing: NO. Countries: 1. Publications: 7.
Modulation of Sleep Perception Through Auditory Closed-loop Stimulation of Brain Oscillatory Activity
ClinicalTrials.gov study NCT04276064. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
L-Cell Activity in Small Intestine as Biliopancreatic Loop in Obese Patients With DM2 Submitted to RYGBP
ClinicalTrials.gov study NCT05446415. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Real-life Follow-up of the Physical Activity in Type 1 Diabetes Participants Equipped With an Insulin Pump With Hybrid Closed Loop
ClinicalTrials.gov study NCT07015970. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Active site loop conformation regulates promiscuous activity in a lactonase from Geobacillus kaustophilus HTA426
Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a "hot spot" in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ~6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity.
Fig 2 eYFP closed loop activation controls, in Regulation of REM Sleep by Inhibitory Neurons in the Dorsomedial Medulla
<p>Sleep recording data for closed loop eYFP controls. Associated with Figure 2C,E.</p>
Data from: Active site loop conformation regulates promiscuous activity in a lactonase from Geobacillus kaustophilus HTA426
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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.