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769 results for “Clock”
Temperature-dependent fold-switching mechanism of the circadian clock protein KaiB
<p>Derived data accompanying publication of <em>Temperature-dependent fold-switching mechanism of the circadian clock protein KaiB</em> (Zhang et al., PNAS 2024).</p> <p> </p> <p>This dataset contains data for fold-switching of KaiB from simulations performed using the Upside coarse-grained model (Jumper et al. PLoS Comput. Bio 2017). Files contained include collective variables, kinetic quantities (committors), and initial structures used to seed unbiased simulations. These data should be sufficient recreate the analysis shown in the associated publicaion. Raw trajectory files have not been deposited due to their size; contact the author (Spencer Guo) to request.</p>
Prediction and analysis of phenotypes in the Arabidopsis clock mutant prr7prr9 using the Framework Model v2 (FMv2)
<p>This upload contains or links to the biological data, FMv2 model and simulations for the Chew et al. 2017 paper (bioRxiv <a href="https://doi.org/10.1101/105437">https://doi.org/10.1101/105437</a> ), updated 2022 as bioRxiv <a href="https://doi.org/10.1101/105437v2">https://doi.org/10.1101/105437v2</a>, mostly testing and simulating the effect of a slow circadian clock in the <em>prr7prr9 </em>double mutant compared to the Col wild type plants, with controls in <em>lsf1 </em>and <em>prr7 </em>single mutants. This is one of the outputs from the EU TiMet project, <a href="https://fairdomhub.org/projects/92">https://fairdomhub.org/projects/92</a>.</p> <p>Several data files contain results generated in the same studies, but not covered by the publication. For example, additional time points (18 or 21 days of growth), many additional metabolites, and additional genotypes including <em>pgm</em>, <em>lhy cca1, </em>and in one case, <em>toc1 </em>and <em>gi</em>.</p> <p>This data archive was updated during submisson to the journal _in Silico _Plants in 2022, and is formatted as a Research Object, generated by the Snapshot function of FairdomHub, based on <a href="https://fairdomhub.org/investigations/123">Investigation https://fairdomhub.org/investigations/123.</a> The same Snapshot is shared on FairdomHub and will be from the University of Edinburgh Datashare.</p> <p>We request that users gives appropriate credit to the authors of any data released here, as a norm of academic practice, including data released under CC-0 licence on the FairdomHub.</p>
Dataset for Clock drift corrections for large aperture ocean bottom seismometer arrays: application to the UPFLOW array in the mid-Atlantic Ocean
<p>Dataset from Clock drift corrections for large aperture ocean bottom seismometer arrays: application to the UPFLOW array in the mid-Atlantic Ocean DOI: 10.1093/gji/ggae354.</p> <p>This dataset includes the clock drift polynoms refered to jthe deployment date (jul day from 2022) and consecutive days up to the recovery date. Two types of formats.</p> <ol> <li>Txt files</li> <li>Python Pickle files with a Dictionary containing the NumPY polynom1D and additional information.</li> </ol>
Multi-omic analysis of the Arabidopsis clock activator mutant rve 4 6 8 reveals connections to carbohydrate metabolism and proteasome regulation
<p>Plants are able to sense changes in their light environments, such as the onset of day and night, as well as anticipate these changes in order to adapt and survive. Central to this ability is the plant circadian clock, a molecular circuit that precisely orchestrates plant cell processes over the course of a day. REVEILLE proteins (RVEs) are recently discovered members of the plant circadian circuitry that activate the evening complex and PRR genes to maintain regular circadian oscillation. The RVE 8 protein and its two homologs, RVE 4 and 6, have been shown to limit the length of the circadian period, with rve 4 6 8 triple-knockout plants possessing an elongated period along with increased leaf surface area, biomass, cell size and delayed flowering relative to wild-type Col-0 plants. Here, using a multi-omics approach consisting of phenomics, transcriptomics, proteomics, and metabolomics we draw novel connections between RVE8-like proteins and a number of core plant cell processes. In particular, we reveal that loss of RVE8-like proteins results in altered carbohydrate, organic acid and lipid metabolism, including a starch excess phenotype at dawn. We further demonstrate that rve 4 6 8 plants have lower levels of 20S proteasome subunits and possess significantly reduced proteasome activity, potentially explaining the increase in cell-size observed in RVE8-like mutants. Overall, this robust, multi-omic dataset, provides substantial new insights into the far reaching impact RVE8-like proteins have on the diel plant cell environment.<br> <br> This dataset has the raw search outputs for the mass-spec analysis for this manuscript. </p>
Frequency ratio of the Ar13+ clock transition and the 171Yb+ ocutpole transition
<p>Measured and corrected frequency ratio between the optical clock transition in Ar<sup>13+</sup> and the octupole transition in <sup>171</sup>Yb<sup>+</sup>. Data is provided for the two isotopes <sup>40</sup>Ar<sup>13+</sup> and <sup>36</sup>Ar<sup>13+</sup>.</p>
Atomic clock dataset for 'Coherent Optical-Fiber Link Across Italy and France'
<p>Dataset of the comparison of the atomic clocks at LNE-SYRTE and INRIM via optical fibre link between October 2021 and February 2022. Results discussed in Clivati et al., Coherent Optical-Fiber Link Across Italy and France, <em>Phys. Rev. Applied, American Physical Society, </em><em> 18</em>, 054009, <strong>202<em>2</em></strong>.</p> <p>The involved atomic clocks are the Cs fountains SYRTE-F02Cs, IT-CsF2, the Rb fountain SYRTE-F02Rb and the Yb optical lattice clock IT-Yb1.</p> <p>Data is organized in folders, one for each comparison. In the folders data is separated is one file per day. Data is reported as fractional frequency ratios in bins of 864 s. Timetags are reported in modified Julian date (MJD). A validity flag is given where 0 = invalid, valid otherwise. Each folder includes a yaml file with metadata required for generalized data processing as in [Lodewyck et al., 2020]. The Python package used for data processing can be found on <a href="https://github.com/INRIM/tintervals">github.</a></p> <p> </p>
Two metabolomics data sets (mouse kidney, mouse plasma), generated for the publication Bignon et al., 2023: "Multiomics reveals multilevel control of renal and systemic metabolism by the renal tubular circadian clock".
<p><strong>Publication: </strong>Bignon Y, Wigger L, Ansermet C, Weger BD, Lagarrigue S, Centeno G, Durussel F, Götz L, Ibberson M, Pradervand S, Quadroni M, Weger M, Amati F, Gachon F, Firsov D. Multiomics reveals multilevel control of renal and systemic metabolism by the renal tubular circadian clock. J Clin Invest. 2023 Mar 2:e167133. doi: 10.1172/JCI167133. Epub ahead of print. PMID: 36862511.</p> <p> </p> <p><strong>Abstract: </strong> Circadian rhythmicity in renal function suggests rhythmic adaptations in renal metabolism. To decipher the role of the circadian clock in renal metabolism, we studied diurnal changes in renal metabolic pathways using integrated transcriptomic, proteomic, and metabolomic analysis performed on control mice and mice with inducible deletion of the circadian clock regulator Bmal1 in the renal tubule (cKOt). With this unique resource, we demonstrated that ~30% RNAs, ~20% proteins and ~20% metabolites are rhythmic in kidneys of control mice. Several key metabolic pathways including NAD+ biosynthesis, fatty acid transport, carnitine shuttle,and b-oxidation displayed impairments in kidneys of cKOt, resulting in a perturbed mitochondrial activity. Carnitine reabsorption from the primary urine was one of the most impacted processes with a ~50% reduction in plasma carnitine levels and a parallel systemic decrease in tissues carnitine content. This suggests that the circadian clock in the renal tubule controls both kidney and systemic physiology.</p> <p> </p> <p><strong>This record contains two separate mass-spectrometry metabolomics data sets associated with this study:</strong></p> <ol> <li>Metabolic profile of renal tubules, MS/MS data, Metabolon, Morrisville, NC (N=60)</li> <li>Metabolic profile of blood plasma, MS/MS data, Biocrates, Innsbruck, Austria (N=60)</li> </ol> <p>For each data set, original data as received from the platforms and processed data as used in the data analysis are provided. Preprocessing of kidney data included removal of metabolites with more than 80% missing data values, median normalization, imputation and glog2 transformation. Preprocessing of plasma data included filtering of metabolites with any missing data and log2 transformation. Details of data processing are available in the STAR*methods of the publication.</p> <p> </p> <p><strong>Data sets in other repositories associated with the same study:</strong></p> <p>Additional data sets (transcriptomics, proteomics) pertaining to the same study have been deposited in public repositories:</p> <ul> <li>Gene Expression Omnibus (NCBI GEO), GSE216252</li> <li>PRIDE Archive (EMBL-EBI), PXD036803</li> </ul> <p> </p>
Data for "Noise-induced servo errors in optical clocks utilizing Rabi interrogation"
<p>Numerical simulation data used for figures in "Noise-induced servo errors in optical clocks utilizing Rabi interrogation" (Metrologia, DOI 10.1088/1681-7575/acdfd4). For some figures, also the analytical results are given. For description of data, see header rows. For details, see the corresponding figure captions in the article.</p>
Time trees and Clock genes: a Systematic Review and Comparative Analysis of Contemporary Avian Migration Genetics (Dataset)
<p>Complete dataset of <em>Clock</em> and <em>Adcyap1</em> alleles, distance matrices, and migration data used in the review and meta-analysis "<strong>Time trees and Clock genes: a Systematic Review and Comparative Analysis of Contemporary Avian Migration Genetics".</strong> </p>
Anabaena circadian clock behavior under nitrogen-poor conditions from single-cell measurements of fluorescence intensity
<p>Circadian clock arrays in multicellular filaments of the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 display remarkable spatio-temporal coherence under nitrogen-replete conditions. To shed light on the interplay between circadian clocks and the formation of developmental patterns, we followed the expression of a clock-controlled gene under nitrogen deprivation, at the level of individual cells. Our experiments showed that differentiation into heterocysts took place preferentially within a limited interval of the circadian clock cycle, that gene expression in different vegetative intervals along a developed filament was discoordinated, and that the circadian clock was active in individual heterocysts. Furthermore, Anabaena mutants lacking the kaiABC genes encoding the circadian clock core components produced heterocysts but failed in diazotrophy. Therefore, genes related to some aspect of nitrogen fixation, rather than early or mid-heterocyst differentiation genes, are likely affected by the absence of the clock. A bioinformatics analysis supports the notion that RpaA may play a role as master regulator of clock outputs in Anabaena, the temporal control of differentiation by the circadian clock and the involvement of the clock in proper diazotrophic growth. Together, these results suggest that under nitrogen-deficient conditions, the clock coherent unit in Anabaena is reduced from a full filament under nitrogen-rich conditions to the vegetative cell interval between heterocysts.</p>
The Eclipse Clock-Eclipse on a Polar Day
<p>First place winner in the 2023 IAU OAE Astrophotography Contest, category Still images of the day arc of the Sun and solargraphs: The Eclipse Clock-Eclipse on a Polar Day, by Stephanie Ziyi Ye</p> <p>Constructed by combining multiple images over the course of a 24-hour period, the image was captured in Union Glacier, Antarctica, during the total solar eclipse of 4 December 2021, and showcases the day arc of the Sun. It illustrates the unique phenomenon of a polar day, during which the Sun travels around the sky without setting. During polar days, areas within the polar circles experience 24 hours of continuous daylight, and the Sun doesn’t set for an extended period. The image also offers a rare perspective of a solar eclipse, where the Moon passes between the Sun and Earth, and as viewed from Earth. This can be seen in the lower image of the Sun, where the Moon covers the solar disc.</p> <p>Credit: Stephanie Ziyi Ye/IAU OAE (<a href="https://creativecommons.org/licenses/by/4.0/legalcode">CC BY 4.0</a>)</p>
Clockor2: Inferring global and local strict molecular clocks using root-to-tip regression
<p>Molecular sequence data from rapidly evolving organisms are often sampled at different points in time. Sampling times can then be used for molecular clock calibration. The root-to-tip (RTT) regression is an essential tool to assess the degree to which the data behave in a clock-like fashion. Here, we introduce Clockor2, a client-side web application for conducting RTT regression. Clockor2 uniquely allows users to quickly fit local and global molecular clocks, thus handling the increasing complexity of genomic datasets that sample beyond the assumption homogeneous host populations. Clockor2 is efficient, handling trees of up to the order of 10^4 tips, with significant speed increases compared to other RTT regression applications. Although clockor2 is written as a web application, all data processing happens on the client-side, meaning that data never leaves the user's computer. Clockor2 is freely available at https://clockor2.github.io/</p>
Clock Synchronization Accuracy over Mobile Networks
<pre><code><strong>Dataset: Clock Synchronization Accuracy over Mobile Networks</strong> This dataset evaluates time synchronization accuracy between two devices operating in different mobile network environments and setups. The synchronization is achieved using Precision Time Protocol (PTP) version 2 (PTPv2) over the User Plane within the mobile network. The dataset includes two types of clock offset data: <strong> Calculated Offset:</strong> This data is extracted from the PTPd software logs on the Slave device. Specifically, the "Offset From Master" section in the log files provides the value (in seconds) representing how much the Slave device's internal clock was adjusted to align with the Master clock. However, this value does not represent the exact offset from the Master clock. Instead, it is derived from the PTPv2 synchronization process and reflects the clock adjustment calculated during synchronization. <strong>Pulse-Per-Second (PPS) Offset:</strong> The PPS offset represents the most accurate measurement of clock offset between two devices. It is obtained using an Analog Discovery 2 oscilloscope, which directly compares the PPS signals generated by the Network Interface Card (NIC) timers of both devices. This method provides a high-precision measurement of the synchronization accuracy. <strong>Dataset Structure</strong> Each folder in the dataset contains: Clock offset data: Organized by type (Calculated or PPS). Setup schematics: Detailed diagrams illustrating the complete clock synchronization setup used for data collection. <strong> Additional Information</strong> The data in the folder titled "Clock offset (Pulse-per-second offset) over private 5G SA mobile network" is further described in the following scientific publication: <strong>"Clock Synchronization and Network Delay Evaluation over a Private 5G Standalone Network"</strong> Authors: Marcis Kalnins, Artis Rusins, Atis Elsts.</code></pre>
Data and Software for "Complex Dynamics in a Synchronized Cell-Free Genetic Clock"
<p>Contains raw data, analysis scripts, simulation scripts, device operation software for the publication: "Complex Dynamics in a Synchronized Cell-Free Genetic Clock".</p>
Fig. 6 in Exploring the evolution and terrestrialization of scorpions (Arachnida: Scorpiones) with rocks and clocks
Fig. 6 Time tree _or scorpions in_erred in MCMCTree under the correlated rate model (Yang 2007), using 9 so_t upper and hard lower bounded calibrations derived _rom the scorpion _ossil record (see Tables 2 and 3). Node bars = 95% HPD intervals. Gold circles represent _ossil node-calibration minima
Fig. 5 in Exploring the evolution and terrestrialization of scorpions (Arachnida: Scorpiones) with rocks and clocks
Fig. 5 Scorpion calibration _ossils, as speci_ied in Table 1. a Dolichophonus loudonensis, scale 1 cm. b Compsoscorpius buthiformis, scale 1 cm. c Electrochaerilus buckleyi, scale 1 mm. d Protoischnurus axelrodurum, scale 1 cm. e Uintascorpio halandrasi, scale 1 cm. Images a and b belong to the authors. Image c reproduced with permission _rom SantiagoBlay et al. (2004a). Image e reproduced with permission _rom Santiago-Blay et al. (2004b). Image d courtesy o_ Wilson Lourenço
Fig. 4 in Exploring the evolution and terrestrialization of scorpions (Arachnida: Scorpiones) with rocks and clocks
Fig. 4 Maximum likelihood tree in_erred in IQ-TREE under LG+F+I+G4 model (Le and Gascuel 2008). Nodal support values determined _rom 1000 ultra_ast bootstrap replicates (Minh et al. 2013; Hoang et al. 2018). Scale bar = branch length
Fig. 1 in Exploring the evolution and terrestrialization of scorpions (Arachnida: Scorpiones) with rocks and clocks
Fig. 1 General consensus of internal phylogenetic relationships of Chelicerata at present. Question marks represent uncertainty surrounding the monophyly of mites and ticks (Acari) and the unresolved marine life habit of early scorpions
Fig. 2 Optimisation o in Exploring the evolution and terrestrialization of scorpions (Arachnida: Scorpiones) with rocks and clocks
Fig. 2 Optimisation o_ book lung origin(s) on competing phylogenies o_ Chelicerata. a Scorpions as the sister group to other Arachnida (e.g. Weygoldt and Paulus 1979), implying either book lung loss in other Arachnida or book lung convergence between scorpions and tetrapulmonates. b Scorpions as sister group to Eurypterida (e.g. Dunlop and Braddy 2001), implying book lung convergence and
Fig. 3 Phylogenetic hypotheses o in Exploring the evolution and terrestrialization of scorpions (Arachnida: Scorpiones) with rocks and clocks
Fig. 3 Phylogenetic hypotheses o_ scorpion relationships, with representative taxa _or each major group. (A) Pandinus (Pandinopsis) dictator Pocock, 1888; (B) Cercophonius squama Gervais, 1844; (C) Iurus dufoureius Brullé, 1832; (D) Brotheas sp.; (E) Centruroides
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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)
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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.