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- Creator:
- Bai, Bobo and Zhang, Youxue
- Description:
- This dataset is referenced in the manuscript “Multicomponent diffusion in basaltic melts: A temperature-independent eigenvector matrix, and a multicomponent diffusion calculator”. This manuscript explores the temperature independence of diffusion eigenvectors in an 8-component basaltic melt and provides an open-access calculator for the community to compute multicomponent diffusion profiles.
- Keyword:
- Eigen-components, Multicomponent diffusion, Uphill diffusion, and Multicomponent diffusion calculator
- Discipline:
- Science
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- Creator:
- Faulkner, Alexa
- Description:
- This study uses in vivo two-photon calcium imaging in the visual cortex of mice to demonstrate that encoding of learned environmental visual cues is flexibly represented across different task contexts. This dataset is comprised of in vivo two-photon calcium imaging from visual cortex of mice during learning and performance of a visual discrimination task. data was acquired suing Scanbox and analysis performed in Matlab and Python.
- Keyword:
- neuroscience, two photon calcium imaging, visual cortex, and mouse
- Discipline:
- Science
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- Creator:
- Weeks, Brian C
- Description:
- Each folder contains all of the data for a specific specimen; the folder names correspond to the University of Michigan Museum of Zoology catalog number for the specimen. The photographs have been used to measure skeletal traits using the Skelevision model, which is a computer vision approach to identifying and measuring elements of the skeleton (length of the tibiotarsus, tarsometatarsus, femur, humerus, ulna, radius, carpometacarpus, 2nd digit 1st phalanx, skull, and keel; the outer diameter of the sclerotic ring at its widest point; and the distance from the back of the skull to the tip of the bill). The dataset includes images of 12,421 specimens from 1,881 species of passerine birds.
- Keyword:
- Songbird skeletons, Functional traits, Comparative morphometrics, and Computer vision
- Citation to related publication:
- Weeks, B.C., Z. Zhou, C.M. Probst, J.S. Berv, B. O’Brien, B.W. Benz, H.R. Skeen, M. Ziebell, L. Bodt, and D.F. Fouhey. 2024. Skeletal trait measurements for thousands of bird species. bioRxiv. https://doi.org/10.1101/2024.12.19.629481 and Weeks, B.C., Z. Zhou, C.M. Probst, J.S. Berv, B. O’Brien, B.W. Benz, H.R. Skeen, M. Ziebell, L. Bodt, and D.F. Fouhey. 2024. Skeletal trait measurements for thousands of bird species. Scientific Data. https://doi.org/10.1038/s41597-025-05234-y
- Discipline:
- Science
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- Creator:
- Craven, Nicholas C, Singh, Ramanish, Quach, Co D, Gilmer, Justin B, Crawford, Brad, Marin-Rimoldi, Eliseo, Smith, Ryan, DeFever, Ryan, Dyukov, Maxim, Fothergill, Jenny, Jones, Chris, Moore, Timothy, Butler, Brandon L, Anderson, Joshua A, Iacovella, Christopher, Jankowski, Eric, Maginn, Eric, Potoff, Jeffrey, Glotzer, Sharon C, McCabe, Clare, Cummings, Peter T, and Siepmann, Ilja J
- Description:
- Data are collected in 5 separate workspace, one for the main density data calculations across the space and 4 for the subproject simulations that were performed to validate and dive deeper into specific engine implementations. In order to copy the simulation trajectory and calculated averages used to generate figures, these workspace folders must be downloaded and pointed to the correct place in the GitHub Project Structure, which can be found at https://github.com/mosdef-hub/reproducibility_study and Each compressed file contains the data for a single workspace.
- Keyword:
- molecular dynamics, monte carlo, reproducibility, and replicability
- Citation to related publication:
- https://doi.org/10.1021/acs.jced.5c00010
- Discipline:
- Science
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- Creator:
- Liu, Bin , Silori, Yogita, Li, Yongxi, Forrest, Stephen R., and Ogilvie, Jennifer P.
- Description:
- We use angle-resolved reflection measurements to characterize polariton dispersion, and use ultrafast transient absorption (TA) spectroscopy to study the influence of the “open cavity” on the charge generation dynamics of the donor-acceptor bilayer and blend systems.
- Citation to related publication:
- Yogita Silori, Bin Liu, Yongxi Li, Stephen R. Forrest, and Jennifer P. Ogilvie, "Impact of Cavity Strong Coupling on the Charge Transfer Dynamics in Organic Donor-Acceptor Heterojunctions", Phys. Rev. B. Accepted April 2025, https://doi.org/10.1103/859s-sc6n
- Discipline:
- Science
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- Creator:
- Chen, Hongfan, Chen, Yang, Huang, Zhenguang, Zou, Shasha, Huan, Xun, and Toth, Gabor
- Description:
- Accurately predicting the horizontal component of the ground magnetic field perturbation (dBH), which can be used to calculate the Geomagnetically Induced Currents (GICs), is crucial for estimating the space weather impact of geomagnetic disturbances. In this work, we develop a new data-driven model GeoDGP using deep Gaussian process (DGP), which is a Bayesian non-parametric approach. The model provides global probabilistic forecasts of dBH at 1-minute time cadence and with arbitrary spatial resolutions. We evaluate the model comprehensively on a wide range of geomagnetic storms, including the 2024 Gannon extreme storm. The results show that GeoDGP significantly outperforms the state-of-the-art physics-based first-principles Space Weather Modeling Framework (SWMF) Michigan Geospace model and the data-driven DAGGER model.
- Keyword:
- Space Weather, Uncertainty Quantification, Machine Learning, and Bayesian Inference
- Citation to related publication:
- Chen, H., et al. (2024). GeoDGP: One-Hour Ahead Global Probabilistic Geomagnetic Perturbation Forecasting using Deep Gaussian Process.
- Discipline:
- Science and Engineering
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- Creator:
- King, Katelyn, Fujisaki-Manome, Ayumi, Brant, Cory, and Alofs, Karen
- Description:
- Ice cover on the Great Lakes plays an important role in regional climate, supports tourism and recreation, and provides ecological habitat. As the climate warms, ice cover in the Great Lakes is expected to decline, which in turn will create more lake effect precipitation, reduce ice cover for recreation, and alter habitat for fishes. Therefore, it is important to understand historical ice patterns to better understand and predict future ice cover on the lakes. However, Great Lakes ice cover data prior to 1973 is scarce, due to the limited routine satellite observations. Our dataset aims to fill this gap by providing historical spatial ice duration layers to be used for modeling species distributions. and ArcGIS Pro ( https://www.esri.com/en-us/arcgis/products/arcgis-pro/overview), QGIS ( https://qgis.org/) or other spatial data software will be required to view this dataset.
- Keyword:
- ice, Great Lakes, Superior, Michigan, Ontario, Erie, Huron, and historical
- Citation to related publication:
- King, K., Fujisaki-Manome, A., Brant, C., Cohn, D., Peng, I., Alofs, K., Reconstructing Great Lakes air temperature and ice dynamics data back to 1897. Under Review
- Discipline:
- Science
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- Creator:
- Aksoy, Doruk and Kim, Donghak
- Description:
- This dataset contains snapshots from simulations of a hexagonal self oscillating gel sheet defined via a triangular lattice. The lattice has stretching springs between neighboring vertices and bending springs with energy proportional to the square of the angle between neighboring traingular faces. The motion of the lattice is driven by time- and space-varying distributions of the rest lengths of the stretching springs. In the motivating experiments on thin gel sheets, there are chemical waves, radial or spiral in form, that induce local swelling of the sheets. As a simple model, this dataset considers radial or planar (unidirectional) traveling waves in the simulations. The sheet is modeled as a flat hexagon of radius 1 with an equilateral triangular triangle lattice mesh, with initially uniform mesh spacing of 1/33, resulting in 3367 mesh points. A small out-of-plane perturbation is applied and the motion evolves over the sheet over time. The sheet is modeled to have damped dynamics. However for large enough wave amplitudes, the sheet rapidly buckles into shapes with time-varying distributions of curvature, large in magnitude. For more information on the simulation that generated the data, please refer to "Semi-implicit methods for the dynamics of elastic sheets,” at Journal of Computational Physics by Alben et al. For an example SciML application that considers this dataset, please refer to "Inverse design of self-oscillatory gels through deep learning." Neural Computing and Applications by Aksoy et al.
- Keyword:
- Soft robotics, Partial Differential Equations, Scientific Simulations, and Chaotic Systems
- Citation to related publication:
- Alben, Silas, et al. "Semi-implicit methods for the dynamics of elastic sheets." Journal of Computational Physics 399 (2019): 108952., Aksoy, Doruk, et al. "Inverse design of self-oscillatory gels through deep learning." Neural Computing and Applications 34.9 (2022): 6879-6905., Aksoy, Doruk, et al. "An incremental tensor train decomposition algorithm." SIAM Journal on Scientific Computing 46.2 (2024): A1047-A1075., and Aksoy, Doruk, and Alex A. Gorodetsky. "Incremental Hierarchical Tucker Decomposition." arXiv preprint arXiv:2412.16544 (2024).
- Discipline:
- Engineering and Science
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- Creator:
- Beletsky, Dmitry, Beletsky, R, and Rowe, M
- Description:
- Reliable prediction of hypoxic events in the coastal ocean and lakes depends to a large degree on the ability of hydrodynamic models to accurately simulate nearshore circulation and thermal structure. With focus on the hypoxia-prone south shore of Lake Erie, temperature and currents were measured in the central basin in 2017-2019. Major upwelling events along the south shore were identified and linked with occurrence of strong, sustained wind from the northeast (NE). A three-dimensional FVCOM-based hydrodynamic model was able to predict upwelling events along the south shore reasonably well but the surface mixed layer and thermocline depth were shallower than in observations. It was found that basin-scale wind stress curl (WSC) transformed canonic two-gyre circulation in the uniform NE wind case into a single gyre circulation causing both alongshore and cross-shore current reversal that modified coastal upwelling/downwelling. Observational evidence of Kelvin waves on the south shore was found for the first time. Kelvin wave speed in the model was underestimated. Model runs with enhanced vertical mixing improved predictions of mixed layer and thermocline depth and near-bottom dissolved oxygen but also caused additional diffusion of thermocline.
- Discipline:
- Science
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- Creator:
- Ludlow, Andrew
- Description:
- Single molecule long read RNA/cDNA sequencing of TERT revealed 45 TERT mRNA variants including 13 known and 32 novel variants. Among the variants, TERT Delta 2-4, which lacks exons 2-4 but retains the original open reading frame, was selected for further study. Induced pluripotent stem cells and cancer cells express higher levels of TERT Delta 2-4 compared to primary human bronchial epithelial cells. Overexpression of TERT Delta 2-4 enhanced clonogenicity and resistance to cisplatin-induced apoptosis. Knockdown of endogenous TERT Delta 2-4 in Calu-6 cells reduced clonogenicity and resistance to cisplatin. Our results suggest that TERT Delta 2-4 enhances cancer cells’ resistance to intrinsic apoptosis. RNA sequencing following knockdown of Delta 2-4 TERT indicates that translation is downregulated and that mitochondrial related proteins are upregulated compared to controls.
- Keyword:
- TERT, Alternative splicing, Telomere, and Telomerase
- Citation to related publication:
- Kim, J.J., Ahn, A., Ying, J.Y. et al. Discovery and characterization of a novel telomerase alternative splicing isoform that protects lung cancer cells from chemotherapy induced cell death. Sci Rep 15, 6787 (2025). https://doi.org/10.1038/s41598-025-90639-3
- Discipline:
- Science