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- Creator:
- Davis Rabosky, Alison R. and Jantzi, Adrian
- Description:
- Video documentation of natural behavior in wild snakes is very rare, so film from opportunistic encounters of snake interactions is very valuable to scientific researchers. Our research team includes leading experts on this species of snake (the Western Groundsnake, Sonora semiannulata), so we worked with the observer to submit a formal description of the encounter to a peer-reviewed journal and make the information available to the broader research community.
- Keyword:
- Sonora semiannulata, ground snake, animal behavior, and male-male combat
- Citation to related publication:
- Jantzi A, CL Cox, AR Davis Rabosky, AT Holycross. 2021. SONORA SEMIANNULATA (Western Groundsnake). COMBAT. Herpetological Review 52(2): pg 434.
- Discipline:
- Science
-
- Creator:
- Yiwen, Mei
- Description:
- The datasets of this archive are produced for a research project on the development of an advanced hydrologic modeling system for the St. Lawrence river basin. The outputted datasets from model simulations are in Netcdf 4 format. The author recommend using the netCDF Operators (NCO) program for data processing. For visualization and plotting, the author recommend using software like MATLAB, Python or R.
- Keyword:
- Hydrologic modeling, reanalysis product, St. Lawrence river, water balance, WRF-Hydro
- Discipline:
- Science
-
- Creator:
- Sergio E. Vidal-Luengo and Mark B. Moldwin
- Description:
- Multi-satellite tracking of solar wind dynamic pressure pulse observations through the Earth's magnetosphere enables us to distinguish local changes with propagation signatures.
- Keyword:
- Heliophysics, Magnetosphere, Dynamic pressure pulse, Magnetosphere, THEMIS, MMS, Cluster, SuperMag, and Heliophysics System Observatory
- Citation to related publication:
- Vidal-Luengo, S. E., & Moldwin, M. B. (2021). Global magnetosphere response to solar wind dynamic pressure pulses during northward IMF using the heliophysics system observatory. Journal of Geophysical Research: Space Physics, 126, e2020JA028587. https://doi.org/10.1029/2020JA028587
- Discipline:
- Science
-
- Creator:
- Brasch, Jonathan M, Elipot, Shane, and Arbic, Brian
- Description:
- For Drifters, HYCOM, MITgcm: Spectra and kinetic energy files. Please see readme.txt for a description of all data and code contained here. and - Compare kinetic energies (KE) of high-resolution global ocean models estimated from rotary spectra to KE in surface drifter observations. - Near-inertial KE is closer to drifter observations in models with frequently updated wind forcing - Internal tide KE is closer to drifter observations in models with topographic wave drag
- Keyword:
- oceanography, rotary spectra, kinetic energy, sea surface velocity, and drifters
- Citation to related publication:
- Elipot, S., Lumpkin, R., Perez, R. C., Lilly, J. M., Early, J. J., & Sykulski, A. M. (2016). A global surface drifter data set at hourly resolution. Journal of Geophysical Research: Oceans, 121(5), 2937–2966. https://doi.org/10.1002/2016JC011716
- Discipline:
- Science
-
- Creator:
- Chatterjee, Tanmay, Knappik, Achim, Sandford, Erin, Tewari, Muneesh, Choi, Sung Won, Strong, William B., Thrush, Evan P., Oh, Kenneth J., Liu, Ning, Walter, Nils G., and Johnson-Buck, Alexander
- Description:
- The sensitive measurement of specific protein biomarkers is important for medical diagnostics and research. However, existing methods for quantifying proteins use antibody probes that cannot distinguish between specific and nonspecific binding, limiting their sensitivity and specificity. This work establishes a method for distinguishing between specific binding to the target protein and nonspecific binding to assay surfaces using single-molecule kinetic measurements with dynamically binding probes. This is significant because it permits extremely sensitive protein measurements without requiring a high-affinity detection antibody or any washing steps, enabling streamlined and sensitive quantification of proteins even when no pair of high-quality, tightly binding antibodies is available.
- Keyword:
- biomarker detection, single molecule fluorescence, kinetic fingerprinting, total internal reflection microscopy, and super resolution microscopy
- Citation to related publication:
- Chatterjee, T., et al. Direct kinetic fingerprinting and digital counting of single protein molecules. Proc Natl Acad Sci USA, In Press.
- Discipline:
- Science
-
- Creator:
- Sean Sharp
- Description:
- Coastal wetlands intercept significant amounts of nitrogen (N) from watersheds, especially when surrounding land cover is dominated by agriculture and urban development. Through plant uptake, soil immobilization, and denitrification wetlands can remove excess N from flow through water sources and mitigate eutrophication of connected aquatic ecosystems. Excess N can also change plant community composition in wetlands, including communities threatened by invasive species. Understanding how variable hydrology and N loading impact wetland N removal and community composition can help attain desired management outcomes, including optimizing N removal and/or preventing invasion by non-natives. By using a dynamic, process-based ecosystem simulation model, we are able to simulate various levels of hydrology and N loading that would otherwise be difficult to manipulate. We investigate the effects of hydroperiod, hydrologic residence time, N loading, and the NH4+:NO3- ratio on both N removal and the invasion success of two non-native species (Typha x glauca or Phragmites australis) in temperate freshwater coastal wetlands using Mondrian, a process-based, wetland ecosystem simulation model. We found that when residence time increased, annual N removal increased up to 10-fold while longer hydroperiods also increased N removal, but only when residence time was >10 days and N loading was >30 g N m-2 y-1. N removal efficiency also increased with increasing residence time and hydroperiod, but was less affected by N loading. However, longer hydrologic residence time increased vulnerability of wetlands to invasion by both invasive plants at low to medium N loading rates where native communities are typically more resistant to invasion. This suggests a potential tradeoff between ecosystem services related to nitrogen removal and wetland invasibility. These results help elucidate complex interactions of community composition, N loading and hydrology on N removal, helping managers to prioritize N removal when N loading is high or controlling plant invasion in more vulnerable wetlands.
- Keyword:
- Mondrian, Simulation model, Coastal wetlands, Invasive species, and Ecosystem modeling
- Citation to related publication:
- Currie, W. S., Goldberg, D. E., Martina, J., Wildova, R., Farrer, E., & Elgersma, K. J. (2014). Emergence of nutrient-cycling feedbacks related to plant size and invasion success in a wetland community–ecosystem model. Ecological Modelling, 282, 69–82. https://doi.org/10.1016/j.ecolmodel.2014.01.010
- Discipline:
- Science
-
- Creator:
- Light, Charles X, Arbic, Brian K, Martin, Paige E, Brodeau, Laurent, Farrar, J Thomas, Griffies, Stephen M, Kirtman, Ben P, Laurindo, Lucas, Menemenlis, Dimitris, Molod, Andrea, Nelson, Arin D, Nyadjro, Ebenezer, O'Rourke, Amanda K, Shriver, Jay, Siqueira, Leo, Small, R Justin, and Strobach, Udi
- Description:
- The precipitation data itself is the output of the models/datasets that we analyze in our paper. Most of it is in .nc or .nc4 format, although we provide code to extract the data into time series .mat files. We used MATLAB to perform our analysis.
- Keyword:
- precipitation and power spectra
- Citation to related publication:
- Light, C.X., Arbic, B.K., Martin, P.E., Brodeau, L., Farrar, J.T., Griffies, S.M., Kirtman, B.P., Laurindo, L.C., Menemenlis, D., Molod, A., Nelson, A.D., Nyadjro, E., O'Rourke, A.K., Shriver, J.F., Siqueira, L., Small, R.J., Strobach, E. (2022). Effects of grid spacing on high-frequency precipitation variance in coupled high-resolution global ocean-atmosphere models. Climate Dynamics, https://doi.org/10.1007/s00382-022-06257-6
- Discipline:
- Science
-
- Creator:
- Li, Jieming, Zhang, Leyou, Johnson-Buck, Alexander, and Walter, Nils G.
- Description:
- Traces from single-molecule fluorescence microscopy (SMFM) experiments exhibit photophysical artifacts that typically necessitate human expert screening, which is time-consuming and introduces potential for user-dependent expectation bias. Here, we have used deep learning to develop a rapid, automatic SMFM trace selector, termed AutoSiM, that improves the sensitivity and specificity of an assay for a DNA point mutation based on single-molecule recognition through equilibrium Poisson sampling (SiMREPS). The improved performance of AutoSiM is based on accepting both more true positives and fewer false positives than the conventional approach of hidden Markov modeling (HMM) followed by thresholding. As a second application, the selector was used for automated screening of single-molecule Förster resonance energy transfer (smFRET) data to identify high-quality traces for further analysis, and achieves ~90% concordance with manual selection while requiring less processing time. AutoSiM can be adapted readily to novel datasets, requiring only modest Transfer Learning.
- Keyword:
- deep learning, single-molecule fluorescence, total internal reflection microscopy, SiMREPS, smFRET, and Forster resonance energy transfer
- Citation to related publication:
- Li, J., Zhang, L., Johnson-Buck, A., & Walter, N. G. (2020). Automatic classification and segmentation of single-molecule fluorescence time traces with deep learning. Nature Communications, 11(1), 5833. https://doi.org/10.1038/s41467-020-19673-1 and Hayward, S., Lund, P., Kang, Q., Johnson-Buck, A., Tewari, M., Walter, N. (2018). Single-molecule microscopy image data and analysis files for "Ultra-specific and Amplification-free Quantification of Mutant DNA by Single-molecule Kinetic Fingerprinting" [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/Z2CZ35DF
- Discipline:
- Science
-
Dataset: Models generated for the bioinformatic analysis of MPER/protein fusions binding to antibody
- Creator:
- Bylund, Tatsiana, Chuang, Gwo-Yu, Kwong, Peter, Lai, Yen-Ting, McIlwain, Benjamin, and Stockbridge, Randy B.
- Description:
- This project evaluated the binding of antibody fragments to membrane proteins fused to a short epitope sequence (“MPER”). This dataset includes atomic coordinates (.pdb files) for bioinformatic models of antibody fragment binding to an MPER epitope – membrane protein fusion.
- Keyword:
- MPER, cryo-EM fiducial, crystallography chaperone, and small membrane protein
- Citation to related publication:
- McIlwain, B. C., Erwin, A. L., Davis, A. R., Ben Koff, B., Chang, L., Bylund, T., Chuang, G.-Y., Kwong, P. D., Ohi, M. D., Lai, Y.-T., & Stockbridge, R. B. (2021). N-terminal Transmembrane-Helix Epitope Tag for X-ray Crystallography and Electron Microscopy of Small Membrane Proteins. Journal of Molecular Biology, 166909. https://doi.org/10.1016/j.jmb.2021.166909
- Discipline:
- Science
-
- Creator:
- Attari, Ali
- Description:
- Please refer to the "README.txt" for more details., MATLAB R2018a (Mathworks, Natick, MA, USA) was used to process this data., and Excel (Microsoft Office) was used to store survey data on the comfort of both systems and also to provide absolute and relative intraobserver variablities for the DM device.
- Keyword:
- Digital Manometry
- Citation to related publication:
- Comparison of anorectal function measured using wearable digital manometry and a high resolution manometry system Attari A, Chey WD, Baker JR, Ashton-Miller JA (2020) Comparison of anorectal function measured using wearable digital manometry and a high resolution manometry system. PLOS ONE 15(9): e0228761. https://doi.org/10.1371/journal.pone.0228761
- Discipline:
- Engineering, Science, and Health Sciences
-
- Creator:
- Mark Flanner
- Description:
- This dataset includes spectrally-resolved optical properties for volcanic ash particles from the 2010 Eyjafjallajökull volcanic eruptions. These properties were used in the climate simulations described by Flanner et al. (2014, doi:10.1002/2014JD021977) to quantify ash radiative forcing from the eruptions.
- Keyword:
- ash, volcano, aerosols, Eyjafjallajökull, climate, and radiative transfer
- Citation to related publication:
- Flanner, M.G., Gardner, A.S., Eckhardt, S., Stohl, A., & Perket, J. (2014). Aerosol radiative forcing from the 2010 Eyjafjallajökull volcanic eruptions. Journal of Geophysical Research: Atmospheres. https://doi.org/10.1002/2014JD021977
- Discipline:
- Science
-
- Creator:
- Zhang, Yizhen
- Description:
- We collected hours of functional magnetic resonance imaging data from human subjects listening to natural stories. We developed a predictive model of the voxel-wise response and further applied it to thousands of new words to understand how the brain stores and connects different concepts. and This is a dataset for the paper: Zhang, Y., Han, K., Worth, R., & Liu, Z. (2020). Connecting concepts in the brain by mapping cortical representations of semantic relations. Nature communications, 11(1), 1-13. https://doi.org/10.1038/s41467-020-15804-w. This project is also documented at https://osf.io/eq2ba/.
- Keyword:
- fMRI, natural story comprehension, neural encoding, semantic processing, word relations, and naturalistic stimuli
- Citation to related publication:
- Zhang, Y., Han, K., Worth, R., & Liu, Z. (2020). Connecting concepts in the brain by mapping cortical representations of semantic relations. Nature communications, 11(1), 1-13. https://doi.org/10.1038/s41467-020-15804-w
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right proximal metatarsal 1 of the Cantius trigonodus (University of Michigan Museum of Paleontology catalog number UMMP VP 81822), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right cuboid of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81823), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right calcaneum of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81821), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right astragalar [astragalus] body of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81827), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right navicular of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81831), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right medial cuneiform (entocuneiform) of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81820), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
-
- Creator:
- Agnit Mukhopadhyay
- Description:
- Conducting quantitative metrics-based performance analysis of first-principles-based global magnetosphere models is an essential step in understanding their capabilities and limitations, and providing scope for improvements in order to enhance their space weather prediction capabilities for a range of solar conditions. In this study, a detailed comparison of the performance of three global magnetohydrodynamic (MHD) models in predicting the Earth’s magnetopause location and ionospheric cross polar cap potential (CPCP) has been presented. Using the Community Coordinated Modeling Center’s Run-on-Request system and extensive database on results from various magnetospheric scenarios simulated for a variety of solar wind conditions, the aforementioned model predictions have been compared for magnetopause standoff distance estimations obtained from six empirical models, and with cross polar cap potential estimations obtained from the Assimmilative Mapping of Ionospheric Electrodynamics (AMIE) Model and the Super Dual Auroral Radar Network (SuperDARN) observations. We have considered a range of events spanning different space weather activity to analyze the performance of these models. Using a fit performance metric analysis for each event, we have quantified the models’ reproducibility of magnetopause standoff distances and CPCP against empirically-predicted observations, and identified salient features that govern the performance characteristics of the modeled magnetospheric and ionospheric quantities.
- Citation to related publication:
- Mukhopadhyay, A., Jia, X., Welling, D. T., & Liemohn, M. W. (2021). Global Magnetohydrodynamic Simulations: Performance Quantification of Magnetopause Distances and Convection Potential Predictions. Frontiers in Astronomy and Space Sciences, 8. https://doi.org/10.3389/fspas.2021.637197
- Discipline:
- Engineering and Science
-
- Creator:
- McCuen, Brett A.
- Description:
- These data are TLA events identified in MACCS magnetometer data throughout 2015. These events are short-timescale (< 60 s), large -amplitude (> 6 nT/s) magnetic disturbances measured at Earth's surface that are analyzed for space weather research purposes. and The events were identified in a year's worth of magnetic field data using an algorithm developed in the MATLAB platform. The algorithm dBdt_main.m can be run using the associated scripts (clean_maccs.m, simple_dbdt.m, extremes1.m, newdbdt.m) to return the events in the 2015_AllEvents.csv file. The substorm onset delays of each event are determined with the onset_delays.m script and the substorm event list 20191127-15-56-substorms.csv (both included).
- Keyword:
- space weather impacts, geomagnetically induced currents, GIC, transient induced currents, transient large amplitude, dB/dt search algorithm, and TLA
- Citation to related publication:
- Engebretson, M. J., Pilipenko, V. A., Ahmed, L. Y., Posch, J. L., Steinmetz, E. S., Moldwin, M. B., … Vorobev, A. V. (2019). Nighttime Magnetic Perturbation Events Observed in Arctic Canada: 1. Survey and Statistical Analysis. Journal of Geophysical Research: Space Physics, 124(9), 7442–7458. https://doi.org/10.1029/2019JA026794
- Discipline:
- Science