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565 results for “escapement”
Normative behavioral data from the novel One Trail Trace escape reaction task (OTTER)
<p><span>We designed a behavioral task where rats learn to associate two temporally distinct but close-in-time events by means of incidental one-trial learning. </span><span>The task takes advantage of two competing motivations - to avoid light places and to avoid painful stimuli (foot shock) predicted by an acoustic signal. Motivation to avoid a bright light is constant throughout the experiment and is manifested by rats preferring a dark compartment in a light/dark shuttle box. Motivation to stay in the dark is overridden (1) during the training session: when foot-shock (US) (preceded by the acoustic stimulus (CS)) is presented; and (2) during the testing session: when CS, that predicts US, is presented. The latter case occurs when rats successfully form an association between CS and US in the training session and the rat escapes into the light compartment ('responders'). The rats that do not escape ('non-responders' appear to lack this memory as even non-specific fear response (freezing) was absent.</span></p> <p><span>Generally, >50% of rats escape into the lit compartments following CS on the testing day. Importantly, rats do not show a contextual association measured by freezing behavior and preference for a light compartment on the testing day. Moreover, we observed that several putative details in the setup affect the probability of the successful formation of a one-trial trace association. </span><span>Compared to similar tasks, the OTTER task tests incidental learning with no requirement for pre-training. Moreover, the memory formed in the OTTER task consists of two events that do not overlap in time: a characteristic of many episodic memories. The OTTER task presents high-throughput means to study neuronal substrates of incidental temporal binding.</span></p> <p><span></span></p>
Nowhere to escape: The cross-age avian haemosporidian exposure of migrants in Northeast China
<p>Pathogen infection has been progressively recognized as a potential driver of animal migration, and the infection pattern in a certain host may be related to its migration status. Nestling viability can be a crucial life stage in the evolution of the migration cycle but has been irregularly studied to date. In this study, we tested the 'migratory exposure' hypothesis by comparing the prevalence and diversity of avian haemosporidian parasites in the breeding area between two dominant species including adults and nestlings: yellow-rumped flycatcher (<em>Ficedula zanthopygia</em>), which is a summer migratory species, and Japanese tit (<em>Parus minor</em>), which is a local resident species. The yellow-rumped flycatcher harboured more diverse parasite lineages than the Japanese tit, which is in line with the expectation of the 'migratory exposure' hypothesis, while nestlings present a similar but more applicable pattern. Among the 40 unique identified parasite lineages, only one was shared between host species and three between age classes. Nestlings suffered a high parasite diversity with plenty of age-specific lineages in the breeding area, mainly Leucocytozoon, which may suggest an extraordinary selection pressure in the life-stages not just for adults during migration. However, the most common lineages in adults were not detected in nestlings, and the prevalence of infection is significantly lower in nestlings than in adults. Our results suggest that migratory birds may have suffered from more frequent parasite infections during migration, but escaped from more virulent lineages at the same time. The difference in susceptibility and parasite assembly between adults and nestlings in migrants may result from an intricate interaction along the evolution of life history. Our investigations have revealed the significance of avian haemosporidian parasite infection patterns in nestlings in breeding areas, and provide a novel insight into the driving forces of migration.</p>
Developmental changes in red-eyed treefrog embryo behavior increase escape-hatching success in wasp attacks
<p>The arboreal embryos of red-eyed treefrogs (<em>Agalychnis</em> <em>callidryas</em>) hatch prematurely to escape from egg-predators, and escape success increases with age. We assessed developmental changes in the behavior and hatching performance of embryos attacked by wasps (<em>Polybia</em> <em>rejecta</em>) and their contributions to improved embryo survival. We recorded videos of 4- and 5-day-old embryos exposed to wasp attacks and determined each embryo's fate. For a stratified random sample of embryos that escaped and died, we determined the occurrence, sequence, and timing of events during wasp-embryo interactions. We constructed path diagrams of event sequences, tested for age effects on transition probabilities, and measured durations of periods between key events. Overall escape success was 38% higher in older embryos. They were more likely to hatch pre-emptively than younger ones, thus less likely to experience direct attacks, suggesting that developmental gains in mechanosensory sensitivity may increase hatching responses to indirect cues. During direct attacks, embryos were equally likely to be captured by wasps at both ages and hatching speed was similar, suggesting no relevant difference in escape-hatching performance. After a wasp ruptured their egg capsule, older embryos were more likely to exit and did so much sooner; younger embryos remained in ruptured capsules for longer and were more likely to be attacked again. This developmental change in embryo behavior indicates decreased tolerance for egg-stage risk as the chance of tadpole survival increases, suggesting that ontogenetic adaptation to changing risk trade-offs contributes strongly to the developmental increase in escape success.<span></span></p>
Multiplexed On-Yeast Serological Assay for Immune Escape Screening of SARS-CoV-2 Variants
<p>Experimental data and scripts used for the development of a Yeast-based serological Assay:</p> <ol> <li>The<strong> Python scripts</strong> folder includes all scripts used in this study to analyze sera titers and plotting data.</li> <li>The<strong> Raw data</strong> folder includes: <ol> <li>The Y<strong>east Immunoassay development</strong> folder includes the flow cytometric data for serum depletion and reduction of ligand depletion effects.</li> <li>The <strong>Yeast serological data folder</strong> includes the raw data of all tested sera and related data for their analyses.</li> </ol> </li> <li>The <strong>Snapgene plasmid maps </strong>folder includes the plasmid maps for the three SARS-CoV-2 VOCs for Snapgene.</li> </ol> <p> </p> <p> </p>
Giant Tidal Tails of Helium Escaping the Hot Jupiter HAT-P-32 b
<p>This dataset contains materials presented in the paper ``Giant Tidal Tails of Helium Escaping the Hot Jupiter HAT-P-32 b'' (Zhang et al. 2023) accepted for publication by Science Advances. Please cite this paper and the Zenodo repository if these data are used in your work.</p> <p>Description of these files: </p> <ul> <li><strong>HPF_data.zip</strong> includes all 77 observed HPF spectral data of HAT-P-32 A+b.</li> <li><strong>HAT-P-32b_properties.csv</strong> includes our measured spectroscopic and physical properties of the planetary system. Columns of this file are explained in a README file <strong>README_HAT-P-32b_properties.dat</strong></li> <li><strong>3d_simulation_EW_vs_orbital_phase.dat</strong> includes the helium excess equivalent widths as a function of the planet's orbital phase, as predicted by our 3D hydrodynamic simulations</li> <li><strong>3d_simulation_orbital_phase_vs_helium_central_wavelength.dat</strong> includes the central wavelength of helium excess spectral feature (in the stellar restframe) as a function of the planet's orbital phase, as predicted by our 3D hydrodynamic simulations. </li> </ul>
TRACE-Omicron: Epidemiological Counterfactuals; High Immune Escape
<p>This repository contains the simulation data corresponding to the Epidemiological Counterfactuals under the High Immune Escape baseline scenario in "TRACE-Omicron: Policy Counterfactuals to Inform Mitigation of COVID-19 Spread in the United States" published in Advanced Theory and Simulations (doi:10.1002/adts.202300147)</p>
Condition dependence of (un)predictability in escape behavior of a grasshopper species
<p>(Un)predictability has only recently been recognized as an important dimension of animal behavior. Currently, we neither know if (un)predictability encompasses one or multiple traits nor how (un)predictability is dependent on individual conditions. Knowledge about condition dependence, in particular, could inform us about whether predictability or unpredictability is costly in a specific context. Here, we study the condition dependence of (un)predictability in the escape behavior of the steppe grasshopper <em>Chorthippus dorsatus</em>. Predator–prey interactions represent a behavioral context in which we expect unpredictability to be particularly beneficial. By exposing grasshoppers to an immune challenge, we explore if individuals in poor condition become more or less predictable. We quantified three aspects of escape behavior (flight initiation distance, jump distance, and jump angle) in a standardized setup and analyzed the data using a multivariate double-hierarchical generalized linear model. The immune challenge did not affect (un)predictability in flight initiation distance and jump angle, but decreased unpredictability in jump distances, suggesting that unpredictability can be costly. Variance decomposition shows that 3–7% of the total phenotypic variance was explained by individual differences in (un)predictability. Covariation between traits was found both among averages and among unpredictabilities for one of the three trait pairs. The latter might suggest an (un)predictability syndrome, but the lack of (un)predictability correlation in the third trait suggests modularity. Our results indicated condition dependence of (un)predictability in grasshopper escape behavior in one of the traits, and illustrate the value of mean and residual variance decomposition for analyzing animal behavior.</p>
A Great Escape: resource availability and density-dependence shape population dynamics along trailing range edges
<p>Populations along geographical range limits are often exposed to unsuitable climate and low resource availability relative to core populations. As such, there has been a renewed focus on understanding the factors that determine range limits to better predict how species will respond to global change. Using recent theory on range limits and classical understanding of density dependence, we evaluated the influence of resource availability on the snowshoe hare Lepus americanus along its trailing range edge. We estimated variation in population density, habitat use, survival, and parasite loads to test the Great Escape Hypothesis (GEH), i.e. that density dependence determines, in part, a species' persistence along trailing edges. We found that variability in resource availability affected density and population fluctuations and led to trade-offs in survival for snowshoe hare populations in the northeastern USA. Hares living in resource-limited environments had lower and less variable population density, yet higher survival and lower parasitism compared to populations living in resource-rich environments. We suggest that density-dependent dynamics, elicited by resource availability, provide hares a unique survival advantage and partly explain persistence along their trailing edge. We hypothesize that this low-density escape from predation and parasitism occurs for other prey species along trailing edges, but the extent to which it occurs is likely conditional on the quality of matrix habitat. Our work indicates that biotic factors play an important role in shaping species' trailing edges and more detailed examination of non-climatic factors is warranted to better inform conservation and management decisions.</p>
Reproduction package for the paper "Expanding the inventory of spectral lines used to trace atmospheric escape in exoplanets"
<p>This is a basic reproduction package for the paper "Expanding the inventory of spectral lines used to trace atmospheric escape in exoplanets" by Linssen & Oklopčić (2023). It provides the full transmission spectra of all simulations presented in the paper, as well as the data products necessary to reproduce the figures of the paper.</p>
Dataset of mouse EEG and behaviors under threat-and-escape paradigm (solitary threat condition)
<p>Original publication link: <a href="https://doi.org/10.1073/pnas.2308762120">https://doi.org/10.1073/pnas.2308762120</a></p> <p>A set of mouse EEG data (raw data files in [data_EEG-BIDS.zip]) and simultaneously recorded video (raw data files and processed behavioral data in [data_behavior.zip]). A mirror of this dataset is located here: <a href="https://gin.g-node.org/hiobeen/Mouse-threat-and-escape-Han-et-al-PNAS">https://gin.g-node.org/hiobeen/Mouse-threat-and-escape-Han-et-al-PNAS</a>.</p> <p>Check this <a href="https://gin.g-node.org/hiobeen/Mouse-threat-and-escape-Han-et-al-PNAS/src/master/README.md">how-to-start guide</a> to this dataset! <br> </p> <p>1. EEG dataset</p> <p>Most of all, the overall dataset structure adheres to the BIDS-EEG format introduced by Pernet et al. (2019). Within the top-level directory 'data_EEG-BIDS/', the EEG data is organized under paths starting with 'sub-##/'. These EEG recordings (mouse n = 8) were recorded under the Threat-and-escape paradigm experiment, which involves dynamic interactions with a spider robot. This experiment was done in two separate conditions: the solitary condition, where a mouse was exposed to the robot alone in the arena (referred to as the 'Single' condition), and the group condition, where mice encountered the robot alongside other conspecifics (referred to as the 'Group' condition). This dataset only includes the data from solitary condition. CBRAIN headstage (Kim et al., 2019) was employed to record this EEG data at a sampling rate of 1024 Hz. The recordings were taken from the medial prefrontal cortex (channel 1) and the basolateral amygdala (channel 2). For a comprehensive understanding of the experimental methods and procedures, please see our original publications: Han et al. (2023), Cho et al. (2023), and Kim et al. (2020).</p> <p> </p> <p>2. Position dataset</p> <p>Another top-level directory, 'data_behavior/', contains simultaneously recorded video (in avi format) ('data_behavior/raw/') and position extracted from the video in csv format ('data_behavior/processed/'). The positions are located in the 'stimuli/position/' directory.</p> <p>Position tracking is performed using the U-Net architecture of CNN (Ronnenberger, 2015; also see, Han et al. in press for detailed procedure). This method tracks the body area's location to extract its centroid.</p> <p> </p> <p>3. References</p> <p>Han, H. B., Shin, H. S., Jeong, Y., Kim, J., Choi, J. H., (2023) Dynamic switching of neural oscillations in the prefrontal–amygdala circuit for naturalistic freeze-or-flight, <em>Proceedings of the National Academy of Sciences,</em>, <em>120</em>(37), <a href="https://doi.org/10.1073/pnas.2308762120">https://doi.org/10.1073/pnas.2308762120</a></p> <p>Pernet, C. R., Appelhoff, S., Gorgolewski, K. J., Flandin, G., Phillips, C., Delorme, A., & Oostenveld, R. (2019). EEG-BIDS, an extension to the brain imaging data structure for electroencephalography. <em>Scientific data</em>, <em>6</em>(1), 103.</p> <p>Kim, J., Kim, C., Han, H. B., Cho, C. J., Yeom, W., Lee, S. Q., & Choi, J. H. (2020). A bird’s-eye view of brain activity in socially interacting mice through mobile edge computing (MEC). <em>Science Advances</em>, <em>6</em>(49).</p> <p>Cho, S., & Choi, J. H. (2023). A guide towards optimal detection of transient oscillatory bursts with unknown parameters. <em>Journal of Neural Engineering</em>.</p> <p>Ronneberger, O., Fischer, P., & Brox, T. (2015). U-net: Convolutional networks for biomedical image segmentation. In <em>Medical Image Computing and Computer-Assisted Intervention–MICCAI 2015: 18th International Conference, Munich, Germany, October 5-9, 2015, Proceedings, Part III 18</em> (pp. 234-241). Springer International Publishing.</p> <p> </p> <p>written by Hio-Been Han, hiobeen.han@gmail.com, 2023-09-07.</p>
Evaluation of Stepped Care for Chronic Pain in Iraq/Afghanistan Veterans (ESCAPE)
ClinicalTrials.gov study NCT00386243. IPD Sharing: Not stated. Countries: 1. Publications: 3.
RHYTHM (Formerly Escape II Myocardium)
ClinicalTrials.gov study NCT01548768. IPD Sharing: NO. Countries: 1. Publications: 1.
Early Versus Delayed Cholecystectomy After Percutaneous Cholecystostomy in Moderate and Severe Cholecystitis (ESCAPE)
ClinicalTrials.gov study NCT07161960. IPD Sharing: NO. Countries: 1. Publications: 6.
Data from: Recovery from infection is more likely to favor the evolution of migration than social escape from infection
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Escape responses of terrestrial and aquatic birds to drones: towards a code of practice to minimise disturbance
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Data and code from: Spring phenological escape is critical for the survival of temperate tree seedlings
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Data and scripts from: Most mammals do not wander: few species escape continental endemism
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Condition dependence of (un)predictability in escape behavior of a grasshopper species
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Save for a rainy day? Simulating how current investment in escaping decisions may affect future reproductive success of males
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Temporal and spatial pattern analysis of escaped prescribed fires in California from 1991 to 2020
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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.