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769 results for “Clock”
Linked collectors and determiners for: Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea).
Natural history specimen data linked to collectors and determiners held within, "Fossil butterflies, calibration points and the molecular clock (Lepidoptera: Papilionoidea)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/6c479acc-8b18-4f0b-a6e5-85bcd6d7b6b7">https://bionomia.net/dataset/6c479acc-8b18-4f0b-a6e5-85bcd6d7b6b7</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/6c479acc-8b18-4f0b-a6e5-85bcd6d7b6b7">https://gbif.org/dataset/6c479acc-8b18-4f0b-a6e5-85bcd6d7b6b7</a>. Formatted as a Frictionless Data package.
Absolute units in Arabidopsis clock models up to U2020.3
<p>The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant <em>Arabidopsis thaliana.</em> The work is published in Urquiza-Garcia and Millar, <strong>Testing the inferred transcription rates of a dynamic, gene network model in absolute units</strong>, In Silico Plants, 2021.</p> <p>Starting from the P2011 model, this project corrects theoretical issues (EC steady state binding assumption) to form an intermediate model (published as U2019.1), rescales parameters to match absolute RNA levels from the TiMet WP1a RNA dataset of Flis et al. 2015 in U2019.2, then reoptimises globally to match RNA timeseries, period and amplitude constraints to produce the U2019.3 model.</p> <p>This project then replaces regulation of the PRRs with repression by later-expressed genes (instead of activation by earlier ones, as in P2011/P2012/U2019) in the U2019.1 model, to create the U2020.1 model, then also rescales to match the RNA levels in the U2020.2 model, and performs a global reoptimisation as above to form U2020.3.</p> <p>The input data files, the computational environment for model development (a Docker image in the 'Reproducibility Toolset' assay) and the relevant model files are included here, as published in Urquiza and Millar, In Silico Plants, 2021. The biorXiv preprint version of the publication is linked inside the archive structure. The DOI for the publication was not yet available but is now: 10.1093/insilicoplants/diab022.</p> <p>This version 3 replaces 10.5281/zenodo.5150823 (version 2), as model files for the earlier KF2014 models were omitted in error from versions 1 and 2. There are no other changes.</p>
Dataset for 'Intercontinental comparison of optical atomic clocks through very long baseline interferometry'
<p>Dataset for the international comparison of optical atomic clocks using Very Long Baseline Interferometry (VLBI) and Global Positioning System (GPS) precise point positioning solution with integer ambiguity (IPPP) techniques appeared in <em>Nature Physics, <strong> 17</strong></em>, 223-227 (2021). The dataset is also available at <a href="https://doi.org/10.1038/s41567-020-01038-6">https://doi.org/10.1038/s41567-020-01038-6</a></p>
Data from: Biological clocks as age estimation markers in animals: a review and meta-analysis
<p>Complete dataset of Methylation and Telomere studies searched, retrieved, analysed, extracted and compared in the review and meta-analysis "<strong>Biological clocks as age estimation markers in animals: a review and meta-analysis".</strong></p>
FIGURE 2 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 2 Opening of Tasman Sea; Pal., Paleocene; P, Pliocene; Pe, Pelomedusa; Pel, Pelusios; Pelt, Peltocephalus; (cont.) Ph, Phrynops; Pl, Platemys; Ple, Pleurodira; Po, Podocnemis; Ps, Pseudemydura; Q, Quaternary; R, Rheodytes; Rh, Rhinemys. *, constrained nodes based on the TE MP topology; †, extinct taxa; ↑, origin of total groups Pan-Chelidae and Pan-Pelomedusioides. Downloaded from Brill.com10/07/2022 07:36:56PM via free access
FIGURE 3 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 3 Comparison of the three dating analyses performed in this study (simplified trees). Node number as in table 2. Abbreviations of analyses as in table 1. Abbreviations of geological events as in fig. 2. Abbrevia- tions of genera as in figs. 1 and 2. * constrained nodes based on the MP topologies; ↑, origin of total groups Pan-Chelidae and Pan- Pelomedusioides.
FIGURE 4 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 4 Comparison of dates produced by the three analyses of this study and four previous molecular clock studies. Abbreviations: Dea (2011), Dornburg et al. (2011); Jea (2013), Joyce et al. (2013); Pea (2017), Pereira et al. (2017); TS-M TD, This study morphological tip-dating; TS- ND, This study node-dating; TS-TE TD, This study total-evidence tip- dating; R&DF (2016), Rodrigues & Diniz-Filho (2016). Node numbers as in table 2.
Reprogramming feedback strength in gibberellin biosynthesis highlights conditional regulation by the circadian clock and carbon dioxide
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Clockor2: Inferring global and local strict molecular clocks using root-to-tip regression
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Designing epigenetic clocks for wildlife research
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Independent avian epigenetic clocks for aging and development
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Anabaena circadian clock behavior under nitrogen-poor conditions from single-cell measurements of fluorescence intensity
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Data from: Spatial and environmental influences on selection in a clock gene coding trinucleotide repeat in Canada lynx (Lynx canadensis)
Clock genes exhibit substantial control over gene expression and ultimately life-histories using external cues such as photoperiod, and are thus likely to be critical for adaptation to shifting seasonal conditions and novel environments as species redistribute their ranges under climate change. Coding trinucleotide repeats (cTNRs) are found within several clock genes, and may be interesting targets of selection due to their containment within exonic regions and elevated mutation rates. Here, we conduct inter-specific characterization of the NR1D1 cTNR between Canada lynx and bobcat, and intra-specific spatial and environmental association analyses of neutral microsatellites and our functional cTNR marker, to investigate the role of selection on this locus in Canada lynx. We report signatures of divergent selection between lynx and bobcat, with the potential for hybrid-mediated gene flow in the area of range overlap. We also provide evidence that this locus is under selection across Canada lynx in eastern Canada, with both spatial and environmental variables significantly contributing to the explained variation, after controlling for neutral population structure. These results suggest that cTNRs may play an important role in the generation of functional diversity within some mammal species, and allow for contemporary rates of adaptation in wild populations in response to environmental change. We encourage continued investment into the study of cTNR markers to better understand their broader relevance to the evolution and adaptation of mammals.
Dynamic physiological and transcriptome changes reveal a po-tential relationship between the circadian clock and salt stress response in Ulmus pumila
<p>Despite the important role the circadian clock plays in numerous critical physiological responses in plants, such as hypocotyl elongation, leaf movement, stomatal opening, flowering, and stress responses, there have been no investigations into the effect of the circadian clock on physiological and transcriptional networks under salt stress. <em>Ulmus pumila</em> L.—a major tree species used for timber, shelter, food, medicine, fodder, and ecological protection—has been reported to tolerate 100~150 mM NaCl treatment. We performed a time-course physiological and transcriptome analysis of 2-years-old <em>U. pumila</em> seedlings under salt treatment to dissect the physiological regulation and potential relationship between the circadian clock and the salt stress response. Seedlings in 150 mM NaCl treatment exhibited salt-induced physiological enhancement compared to the control group. A total of 7,009 unigenes were identified under salt stress, of which 283 unigenes were identified as circadian rhythm genes and 16 unigenes were differentially expressed (circadian rhythm-related DEGs). Further analysis of dynamic expression changes revealed that DEGs involved in four crucial pathways—photosynthesis, thiamine metabolism, abscisic acid synthesis and metabolism, and the hormone-MAPK signal crosstalk pathway—are closely related to the circadian clock. Finally, we constructed a co-expression network between the circadian clock and these four crucial pathways. Our results help shed light on the molecular link between the circadian clock and salt stress tolerance in <em>U. pumila</em>.</p>
Insights from empirical analyses and simulations on using multiple fossil calibrations with relaxed clocks to estimate divergence times
<p>Relaxed clock methods account for among-branch-rate-variation when estimating divergence times by inferring different rates for individual branches. In order to infer different rates for individual branches, important assumptions are required. This is because molecular sequence data does not provide direct information about rates, but instead provides direct information about the total number of substitutions along any branch, which is a product of the rate and time for that branch. Often, the assumptions required for estimating rates for individual branches depend heavily on the implementation of multiple fossil calibrations in a single phylogeny. Here, we show that the basis of these assumptions is often critically undermined. First, we highlight that the temporal distribution of the fossil record often violates key assumptions of methods that use multiple fossil calibrations with relaxed clocks. With respect to "node calibration" methods, this conclusion is based on our inference that different fossil calibrations are unlikely to reflect the relative ages of different clades. With respect to the fossilised-birth-death-process, this conclusion is based on our inference that the fossil recovery rate is often highly heterogeneous. We then demonstrate that methods of divergence time estimation that use multiple fossil calibrations are highly sensitive to assumptions about the fossil record and among-branch-rate-variation. Given the problems associated with these assumptions, our results highlight that using multiple fossil calibrations with relaxed clocks often does little to improve the accuracy of divergence time estimates.</p> <p> </p>
Lion Table Clock
This automated clock is one half of a pair, the other one is a female lion.  When the clock strikes inside the lion its eyes start rolling, the jaws open and close. The skin covering the machinery has become worn over the years. We will have to imagine a thick mane and a golden fur on the lion. To modern eyes the clock looks like a toy. To the 17th century spectator, it was a precious little miracle and a display of human progress. The lion was a symbol of Africa, a continent that the Europeans had recently started discovering. The clock work was a result of the human efforts to control time and the machinery showed the new mechanical knowledge. The drawer in the clock once contained a key to the clock work, possibly a description of it and, perhaps, remains of a real lion. It was typical for the 17th century thinking that the lion clocks were a pair. Two halves forming a whole was an important concept. Text: Sara Dixon Scan: Erik Lernestål Source: Objaverse 1.0 / Sketchfab
Custom Astronomical Clock
Small prop I created for my 4th-year project in ISART School of Game, 3D Animation & VFX Playing with constraints is fun :) Source: Objaverse 1.0 / Sketchfab
Low Poly, Old-Style Wall Clock
A simple, yet stylized free wall clock. This is a static model, a version meant for moveable hands and pendulum can also be found on my page. note: the clock face appears upside down in the model preview, but appears as it should in blender. Source: Objaverse 1.0 / Sketchfab
Table clock with shape of Hungarian hussar
ID no.: MHK 883/II Museum: Historical Museum of the City of Kraków https://muzea.malopolska.pl/en/objects-list/37 Digitalisation: RDW MIC, Małopolska's Virtual Museums project Source: Objaverse 1.0 / Sketchfab
A Clock Work Orange
A novel by Anthony Burgess. https://en.wikipedia.org/wiki/A_Clockwork_Orange_(novel) Source: Objaverse 1.0 / Sketchfab
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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.