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- Creator:
- Sealey, Briana A., Larson, Joanna G., Westeen, Erin P., Sánchez-Paredes, Ciara M., Moore, Talia Y., and Davis Rabosky, Alison R.
- Description:
- In this study, we experimentally tested for the effects of four simulated predator cues on defensive displays in two species of South American calico snakes (genus Oxyrhopus). We found that juvenile snakes were both more likely to respond and to respond more strongly than adults and that displays were most common in response to tactile stimuli than to other treatments. However, we also found broad similarity across both simulated predator treatments and species in the components used in each snake’s defensive display, suggesting a high degree of stereotyping. This research suggests an important role for both ontogeny and intensity of predation risk in structuring variation in defensive behavior in Neotropical snakes and emphasizes the foundational importance of context dependence in conceptual frameworks for understanding predator-prey interactions. and *On January 4, 2024, “Supplementary_material.pdf” was replaced with an updated version that has slightly different versions of Figures S4 and S8 after an error in code was corrected. Within “HeatmapFigures.zip,” two code files, “IndividualHeatmaps_matrices.R” and “FigureS4_S8_averagedHeatmaps.R” were updated to correct the code error. Three additional files were added to both the “figures” and “matrices” folders within the subfolder “heatmaps.” These files represent the correlation matrices, by body part, and graphical representation of the matrices for one experimental trial that had previously been excluded due to the code error.
- Keyword:
- context-dependence, anti-predator behavior, Peruvian Amazon, ontogeny, coral snake mimicry, Colubridae
- Citation to related publication:
- Sealey, B.A.*, Larson, J.G.*, Westeen, E.P., Sanchez-Paredes, C.M., Moore, T.Y., Davis Rabosky, A.R. Body size and predator cues structure variation in defensive displays of Neotropical calico snakes (Oxyrhopus spp.). Ethology. In press. *Authors contributed equally
- Discipline:
- Science
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- Creator:
- Gebarski, Benjamin B. and Becker, Udo
- Description:
- Files are uploaded as text or crystallographic information files (.cif), the standard text file format for representing crystallographic information. These files contain the results for cyclic voltammetry, x-ray absorption spectroscopy, and optimized molecular models for uranium-60 nanocluster (U60) fragments, UO2 complexes, and adsorbates.
- Keyword:
- uranium, U60, electrochemistry, computational, molecular model, and adsorption
- Citation to related publication:
- Electrochemical and computational analysis of the thermodynamics of oxidation/reduction reactions of uranyl peroxide clusters (U60), and the derivation of Pourbaix diagrams for structural and adsorbed species. In process.
- Discipline:
- Science
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- Creator:
- Elvati, Paolo, Luyet, Chloe, Wang, Yichun, Liu, Changjiang, VanEpps, J. Scott, Kotov, Nicholas A., and Violi, Angela
- Description:
- Amyloid nanofibers are abundant in microorganisms and are integral components of many biofilms, serving various purposes, from virulent to structural. Nonetheless, the precise characterization of bacterial amyloid nanofibers has been elusive, with incomplete and contradicting results. The present work focuses on the molecular details and characteristics of PSMa1-derived functional amyloids present in Staphylococcus aureus biofilms, using a combination of computational and experimental techniques, to develop a model that can aid the design of compounds to control amyloid formation. Results from molecular dynamics simulations, guided and supported by spectroscopy and microscopy, show that PSMa1 amyloid nanofibers present a helical structure formed by two protofilaments, have an average diameter of about 12 nm, and adopt a left-handed helicity with a periodicity of approximately 72 nm. The chirality of the self-assembled nanofibers, an intrinsic geometric property of its constituent peptides, is central to determining the fibers' lateral growth.
- Keyword:
- molecular self-assembly, computational nanotechnology, nanobiotechnology, and structural properties
- Citation to related publication:
- Paolo Elvati, Chloe Luyet, Yichun Wang, Changjiang Liu, J. Scott VanEpps, Nicholas A. Kotov, and Angela Violi ACS Applied Nano Materials 2023 6 (8), 6594-6604 DOI: 10.1021/acsanm.3c00174
- Discipline:
- Engineering and Science
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- Creator:
- Penner-Hahn, James, Sension, Roseanne, McClain, Taylor, Lamb, Ryan, Alonso-Mori, Roberto, Lima, Frederico, Ardana-Lamas, Fernando, Biednov, Mykola, Chollet, Matthieu, Chung, Taewon, Deb, Aniruddha, Dewan, Paul, Gee, Leland, Huang, Joel, Yifeng, Khakhulin, Dmitry, Li, Jianhao, Michocki, Lindsay, Miller, Nicholas, Otte, Florian, Uemura, Yohei, and van Driel, Tim
- Description:
- UV-visible, X-ray absorption, and X-ray emission data used to characterize the dynamics of aquo and hydroxo cobalamin. Details of data collection and reduction are provided in the associated manuscript. Data files are all text files which contain tab-delimited columns of data corresponding to each figure in the manuscript.
- Keyword:
- Ultrafast, X-ray, Transient absorption, cobalamin, vitamin B12, XAS, XES, and XANES
- Citation to related publication:
- Sension, R.J., et al. (2023). Watching Excited State Dynamics with Optical and X-ray Probes: The Excited State Dynamics of Aquocobalamin and Hydroxocobalamin. J. Am. Chem. Soc. in press. and https://doi.org/10.1021/jacs.3c04099
- Discipline:
- Science
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- Creator:
- Wallace, Dylan M, Benyamini, Miri, Nason-Tomaszewski, Samuel R, Costello, Joseph T, Cubillos, Luis H, Mender, Matthew J, Temmar, Hisham, Willsey, Matthew S, Patil, Parag P, Chestek, Cynthia A, and Zacksenhouse, Miriam
- Description:
- This is data from Wallace, Benyamini et al., 2023, Journal of Neural Engineering. There are two sets of data included: 1. Neural features and error labels used to train error classifiers for each day used in the study 2. Trial data from an example experiment day (Monkey N, Day 6), with runs for offline calibration, online brain control, error monitoring, and error correction. The purpose of this study was to investigate the use of error signals in motor cortex to improve brain-machine interface (BMI) performance for control of two finger groups. All data is contained in .mat files, which can be opened using MATLAB or the Python SciPy library.
- Keyword:
- Brain-machine interface (BMI), Error detection, and Neural recording
- Citation to related publication:
- Wallace, D. M., Benyamini, M., Nason-Tomaszewski, S. R., Costello, J. T., Cubillos, L. H., Mender, M. J., Temmar, H., Willsey, M. S., Patil, P. G., Chestek, C. A., & Zacksenhouse, M. (2023). Error detection and correction in intracortical brain–machine interfaces controlling two finger groups. Journal of Neural Engineering, 20(4), 046037. https://doi.org/10.1088/1741-2552/acef95
- Discipline:
- Engineering, Science, and Health Sciences
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- Creator:
- Sun, Hu, Ren, Jiaen, Chen, Yang, Zou, Shasha, Chang, Yurui, Wang, Zihan, and Coster, Anthea
- Description:
- Our research focuses on providing a fully-imputed map of the worldwide total electron content with high resolution and spatial-temporal smoothness. We fill in the missing values of the original Madrigal TEC maps via estimating the latent feature of each latitude and local time along the 2-D grid and give initial guess of the missing regions based on pre-computed spherical harmonics map. The resulting TEC map has high imputation accuracy and the ease of reproducing. All data are in HDF5 format and are easy to read using the h5py package in Python. The TEC map is grouped in folders based on years and each file contains a single-day data of 5-min cadence. Each individual TEC map is of size 181*361. and WARNING: 2023-12-01 the data file for 2019-Jan-03 has badly fitted values. Please avoid using it. All other days' files are ready to use.
- Keyword:
- Total Electron Content, Matrix Completion, VISTA, Spherical Harmonics, and Spatial-Temporal Smoothing
- Citation to related publication:
- Sun, H., Hua, Z., Ren, J., Zou, S., Sun, Y., & Chen, Y. (2022). Matrix completion methods for the total electron content video reconstruction. The Annals of Applied Statistics, 16(3), 1333-1358., Sun, H., Chen, Y., Zou, S., Ren, J., Chang, Y., Wang, Z., & Coster, A. (2023). Complete Global Total Electron Content Map Dataset based on a Video Imputation Algorithm VISTA. Scientific Data, in press., and Zou, S., Ren, J., Wang, Z., Sun, H., & Chen, Y. (2021). Impact of storm-enhanced density (SED) on ion upflow fluxes during geomagnetic storm. Frontiers in Astronomy and Space Sciences, 8, 746429.
- Discipline:
- Science and Engineering
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- Creator:
- Brian, Chen
- Description:
- The procedure followed while creating this data is summarized in Section II of Chen, Brian, et al. "Behavioral cloning in atari games using a combined variational autoencoder and predictor model." 2021 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2021. This data is not a result of a research but an intermediate product that is used in research. This dataset is generated to train a behavioral cloning framework from gameplay screen captures and keystrokes of an "expert" player. The RL agent that is trained using "RL Baselines Zoo package" acts as the "expert" player, whose decision making process we desire to learn. In addition to behavioral cloning experiments, this dataset is further used to demonstrate the efficacy of a novel incremental tensor decomposition algorithm on image-based data streams.
- Keyword:
- Imitation Learning, Behavioral Cloning, Reinforcement Learning, Machine Learning, and Gameplay Data
- Citation to related publication:
- Chen, Brian, et al. "Behavioral cloning in atari games using a combined variational autoencoder and predictor model." 2021 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2021., Aksoy, Doruk, et al. "An Incremental Tensor Train Decomposition Algorithm." arXiv preprint arXiv:2211.12487 (2022)., and Chen, Brian, et al. "Low-Rank Tensor-Network Encodings for Video-to-Action Behavioral Cloning", forthcoming
- Discipline:
- Engineering and Science
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- Creator:
- Ponder, Brandon M., Ridley, Aaron J., Bougher, Stephen W., Pawlowski, David, and Brecht, Amanda
- Description:
- This research was completed to introduce a state-of-the-art Venus GCM to the modeling community. Validation studies were performed to give credence to the model's results. and This data set is made available under a Creative Commons Public Domain license (CC0 1.0). The python scripts contained were ran on macOS Monterey version 12.7 with Python 3.9. Numpy version: 1.19.4 Pandas version: 1.2.0
- Keyword:
- Venus, GITM, Ionosphere, Thermosphere, Solar minimum, Navier-stokes, Fluid dynamics, Shocks, V-GITM, and VGITM
- Citation to related publication:
- Ponder, Brandon & Ridley, Aaron J. & Bougher, Stephen W. & Pawlowski, D. & Brecht, A. (2023). The Venus Global Ionosphere-Thermosphere Model (V-GITM): A Coupled Thermosphere and Ionosphere Formulation. JGR Planets. In Press.
- Discipline:
- Science
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- Creator:
- Alben, Silas D
- Description:
- The research involved vortex-panel simulations of fluid-structure interactions. A file Captions_for_SpanwiseVariationsMovies.pdf is included that describes the movies.
- Discipline:
- Science
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- Creator:
- Brenner, Austin M
- Description:
- Results of computer simulation of near Earth space is looked at in a new way to understand how energy moves around the global system. It is found that in addition to a pathway of energy from the outside into the system and back again there is an internal loop which recirculates energy. These new methods will greatly improve our understanding how the whole magnetosphere system evolves and will help address evolution of processes that have space weather impacts.
- Keyword:
- Energy flux, geospace, magnetopause, magnetosphere, poynting flux, and reconnection
- Citation to related publication:
- Austin Brenner, Tuija I. Pulkkinen, Qusai Al Shidi, et al. Dissecting Earth’s Magnetosphere: 3D Energy Transport in a Simulation of a Real Storm Event. ESS Open Archive . August 04, 2023.
- Discipline:
- Science and Engineering