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- 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
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- Creator:
- Ding, J, Moore, TY, and Gan, Z
- Description:
- Jerboas (Jaculus jaculus) are bipedal hopping rodents that frequently transition between gaits (running, hopping, and skipping) throughout their entire speed range. It has been hypothesized that these non-cursorial bipedal gait transitions are likely to enhance their maneuverability and predator evasion ability. However, it is difficult to use the underlying dynamics of these locomotion patterns to predict gait transitions due to the large number of degrees of freedom expressed by the animals. To this end, we used empirical jerboa kinematics and dynamics to develop a unified Spring Loaded Inverted Pendulum model with defined passive swing leg motions. The simulated trajectories from the model precisely matched the experimental data. Jerboas were observed to apply different neutral swing leg angles during locomotion. By investigating the gait structure of the model with coupled and uncoupled neutral swing leg, we found two set of mechanism may explain the frequent gait transitions of jerboas.
- Keyword:
- jerboa, legged locomotion, gait transition, Legged Robots, Dynamics, Bipedal locomotion, and Non-cursorial locomotion
- Citation to related publication:
- Ding, Moore, Gan (submitted) A template model explains jerboa gait transitions across a broad range of speeds. Frontiers in Bioengineering And Biotechnology
- Discipline:
- Science and Engineering
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- Creator:
- Al Shidi, Q. and Pulkkinen, T.
- Description:
- Provided are the resultant and processed data.
- Keyword:
- space physics, ground magnetometers, magnetosphere, numerical space physics, solar wind, numerical space physics, and ionosphere
- Discipline:
- Science
-
- Creator:
- Iong, Daniel, Chen, Yang, Toth, Gabor, Zou, Shasha, Pulkkinen, Tuija I., Ren, Jiaen, Camporeale, Enrico, and Gombosi, Tamas I. I.
- Description:
- In this work, we trained gradient boosted trees using XGBoost to predict the SYM-H forecasting using different combinations of solar wind and interplanetary magnetic field (IMF) parameters. Data are in csv and Python pickle formats.
- Keyword:
- SYM-H forecasting
- Citation to related publication:
- Iong, D., Y. Chen, G. Toth, S. Zou, T. I. Pulkkinen, J. Ren, E. Camporeale, and T. I. Gombosi, New Findings from Explainable SYM-H Forecasting using Gradient Boosting Machines, Space Weather,11, accepted, 2022. https://doi.org/10.1002/essoar.10508063.3
- Discipline:
- Science
-
- Creator:
- Hodgins-Davis, Andrea, Duveau, Fabien, Walker, Elizabeth, and Wittkopp, Patricia J
- Description:
- Understanding how phenotypes evolve requires disentangling the effects of mutation generating new variation from the effects of selection filtering it. Tests for selection frequently assume that mutation introduces phenotypic variation symmetrically around the population mean, yet few studies have tested this assumption by deeply sampling the distributions of mutational effects for particular traits. Here, we examine distributions of mutational effects for gene expression in the budding yeast Saccharomyces cerevisiae by measuring the effects of thousands of point mutations introduced randomly throughout the genome. We find that the distributions of mutational effects differ for the ten genes surveyed and are inconsistent with normality. For example, all ten distributions of mutational effects included more mutations with large effects than expected for normally distributed phenotypes. In addition, some genes also showed asymmetries in their distribution of mutational effects, with new mutations more likely to increase than decrease the gene’s expression or vice versa. Neutral models of regulatory evolution that take these empirically determined distributions into account suggest that neutral processes may explain more expression variation within natural populations than currently appreciated.
- Keyword:
- gene expression, evolution, mutation, mutagenesis, regulatory evolution, YFP, reporter construct, yeast, TDH1, TDH2, TDH3, GPD1, OST1, PFY1, STM1, RNR1, and RNR2
- Citation to related publication:
- Hodgins-Davis, A., Duveau, F., Walker, E. A., & Wittkopp, P. J. (2019). Empirical measures of mutational effects define neutral models of regulatory evolution in Saccharomyces cerevisiae. BioRxiv, 551804. https://doi.org/10.1101/551804
- Discipline:
- Science
-
- Creator:
- Wu, Ziyou, Brunton, Steven L, and Revzen, Shai
- Description:
- These codes were produced as part of the Army Research Office Multi-University Research Initiative ARO MURI W911NF-17-1-0306 "From Data-Driven Operator Theoretic Schemes to Prediction, Inference, and Control of Systems" The code can be run using the runAll.sh shell script (in Linux and OS-X); code should work similarly under windows.
- Keyword:
- DMD, dimensionality reduction, dynamical systems, and nonlinear dynamics
- Discipline:
- Engineering and Science
-
- Creator:
- Smith, Joeseph P., Gronewold, Andrew D., Read, Laura, Crooks, James L., School for Environment and Sustainability, University of Michigan, Department of Civil and Environmental Engineering, University of Michigan, and Cooperative Institute for Great Lakes Research
- Description:
- Using the statistical programming package R ( https://cran.r-project.org/), and JAGS (Just Another Gibbs Sampler, http://mcmc-jags.sourceforge.net/), we processed multiple estimates of the Laurentian Great Lakes water balance components -- over-lake precipitation, evaporation, lateral tributary runoff, connecting channel flows, and diversions -- feeding them into prior distributions (using data from 1950 through 1979), and likelihood functions. The Bayesian Network is coded in the BUGS language. Water balance computations assume that monthly change in storage for a given lake is the difference between beginning of month water levels surrounding each month. For example, the change in storage for June 2015 is the difference between the beginning of month water level for July 2015 and that for June 2015., More details on the model can be found in the following summary report for the International Watersheds Initiative of the International Joint Commission, where the model was used to generate a new water balance historical record from 1950 through 2015: https://www.glerl.noaa.gov/pubs/fulltext/2018/20180021.pdf. Large Lake Statistical Water Balance Model (L2SWBM): https://www.glerl.noaa.gov/data/WaterBalanceModel/ , and This data set has a shorter timespan to accommodate a prior which uses data not used in the likelihood functions.
- Keyword:
- Water, Balance, Great Lakes, Laurentian, Machine, Learning, Lakes, Bayesian, and Network
- Citation to related publication:
- Smith, J., Gronewald, A. et al. Summary Report: Development of the Large Lake Statistical Water Balance Model for Constructing a New Historical Record of the Great Lakes Water Balance. Submitted to: The International Watersheds Initiative of the International Joint Commission. Accessible at https://www.glerl.noaa.gov/pubs/fulltext/2018/20180021.pdf, Large Lake Statistical Water Balance Model (L2SWBM). https://www.glerl.noaa.gov/data/WaterBalanceModel/, and Gronewold, A.D., Smith, J.P., Read, L. and Crooks, J.L., 2020. Reconciling the water balance of large lake systems. Advances in Water Resources, p.103505.
- Discipline:
- Science and Engineering
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Bounce-Averaged Quasi-Linear Diffusion Model Simulation Input/Output on Mars’ Crustal Magnetic Field
- Creator:
- Alexander Shane
- Description:
- To study the effect of whistler mode waves on the superthermal electron velocity space at Mars, a numerical model was built to solve the bounce-averaged quasi-linear diffusion equation on a crustal field. This dataset includes the input and output variables to this model for the simulations performed in Shane and Liemohn, 2022. The studies using this dataset were conducted by Alex Shane in the Climate and Space Sciences and Engineering Department at the University of Michigan. This research was supported by the National Aeronautics and Space Administration (NASA) Grant NNX16AQ04G to the University of Michigan and the Rackham Predoctoral Fellowship.
- Keyword:
- Mars, Electron, and Crustal Fields
- Citation to related publication:
- Shane, A. D., & Liemohn, M. W. (2022). Modeling wave-particle interactions with photoelectrons on the dayside crustal fields of Mars. Geophysical Research Letters, 49, e2021GL096941. https://doi.org/10.1029/2021GL096941
- Discipline:
- Science
-
- Creator:
- Bustamante, Angela C., Opron, Kristopher, Ehlenbach, William J., Crane, Paul K., Keene, Dirk, Standiford, Theodore J., and Singer, Benjamin H.
- Description:
- This study was conducted to detect and analyze modules, or clusters of genes, associated with sepsis, using RNAseq data obtained from 12 participants who died of sepsis and 12 participants who died of non-infectious critical illness while hospitalized. This deposit contains the input data and parameters needed to reproduce the weighted gene co-expression network analysis (WGCNA) and gene enrichment analysis performed on this data. This analysis requires the R packages "WGCNA" version 1.68 and "DESeq2" version 1.22.2 available for download from bioconductor ( http://bioconductor.org). The external bioinformatics tool DAVID version 6.8 ( https://david.ncifcrf.gov/) was used as an additional gene enrichment analysis. Please see the supplemental methods document within this deposit and published research letter for more detailed information.
- Keyword:
- Sepsis, RNAseq, Transcriptomics, Human, and Brain
- Citation to related publication:
- Bustamante, A.C., Opron, K., Ehlenbach, W.J., Larson, E.B., Crane, P.K., Keene, C.D., Standiford, T.J., Singer, B.H., 2020. Transcriptomic Profiles of Sepsis in the Human Brain. Am J Respir Crit Care Med. https://doi.org/10.1164/rccm.201909-1713LE
- 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