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- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset contains images of dissected and fixed retinae in which cones of specific subtypes are labeled either by transgenic expression of a fluorescent reporter or by antibody staining (Figures 1 and 2 and 6A and Supplementary Figure 7A). This dataset also contains images of dissected and fixed retinae in ZO1 is immunostained (Figure 6C-E and Supplementary Figure 7B). Please see the readme file for which files correspond to which figures.
- Keyword:
- zebrafish cone mosaic, topological defects, and tissue patterning
- Citation to related publication:
- Nunley, H., Nagashima, M., Martin, K., Gonzalez, A. L., Suzuki, S. C., Norton, D. A., Wong, R. O. L., Raymond, P. A., & Lubensky, D. K. (2020). Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation. PLOS Computational Biology, 16(12), e1008437. https://doi.org/10.1371/journal.pcbi.1008437 and Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679
- Discipline:
- Science
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset contains images of UV cone nuclei (labelled by transgenic expression of a photoconvertible fluorescent protein) near the retinal margin in live fish. The most important images in the dataset are the following: 1. Images (at 4X magnification) of UV cones immediately after photoconversion of a patch near the retinal margin 2. Images (at 4X magnification) of UV cones 2-4 days after photoconversion of a patch near the retinal margin Also, included is code for calculating triangulations (which connect UV cone nuclei which are nearest neighbors). This code allows us to check for motion of UV cones relative to each other between the time of photoconversion and subsequent imaging.
- Keyword:
- zebrafish cone mosaic, topological defects, tissue patterning, grain boundaries, photoconversion, and defect motion
- Citation to related publication:
- Nunley, H., Nagashima, M., Martin, K., Gonzalez, A. L., Suzuki, S. C., Norton, D. A., Wong, R. O. L., Raymond, P. A., & Lubensky, D. K. (2020). Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation. PLOS Computational Biology, 16(12), e1008437. https://doi.org/10.1371/journal.pcbi.1008437 and Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679
- Discipline:
- Science
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset contains images of UV cone nuclei near the retinal margin in live fish. These UV cones express a transgenic fluorescent reporter (that is nuclear-localized and photoconvertible). The most important images in this dataset are: Zoomed-out (1X magnification) images immediately after photoconversion Zoomed-out (1X magnification) images two to four days after photoconversion In the images immediately after photoconversion, we check if the row orientation rotates by more than a certain amount (10 degrees, 12 degrees, 14 degrees, etc.) at the retinal margin. If so, we call the region coinciding with this domain rotation an existing grain boundary. We, then, check where new Y-junctions are incorporated (by the time of later imaging) to see if they are preferentially incorporated near existing grain boundaries.
- Keyword:
- zebrafish cone mosaic, topological defects, tissue patterning, grain boundaries, and photoconversion
- Citation to related publication:
- Nunley, H., Nagashima, M., Martin, K., Gonzalez, A. L., Suzuki, S. C., Norton, D. A., Wong, R. O. L., Raymond, P. A., & Lubensky, D. K. (2020). Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation. PLOS Computational Biology, 16(12), e1008437. https://doi.org/10.1371/journal.pcbi.1008437 and Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679
- Discipline:
- Science
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- The most important part of this deposit is the code necessary for simulating the anisotropic phase-field crystal on a cone geometry. The second most important is the code for analyzing the simulation results, including the spatial distribution of Y-junctions in the simulated retinae. Included are simulation results in which we systematically scan both the undercooling parameters and the strength of noise in the initial conditions. Finally, we include an additional simulation example (as in Figure 7D). Please see readme file for description of main (MATLAB) functions used for simulating and analyzing simulations.
- Keyword:
- zebrafish cone mosaic, topological defects, grain boundaries, and phase-field crystal model
- Citation to related publication:
- Nunley, H., Nagashima, M., Martin, K., Gonzalez, A. L., Suzuki, S. C., Norton, D. A., Wong, R. O. L., Raymond, P. A., & Lubensky, D. K. (2020). Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation. PLOS Computational Biology, 16(12), e1008437. https://doi.org/10.1371/journal.pcbi.1008437 and Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky bioRxiv 806679; doi: https://doi.org/10.1101/806679
- Discipline:
- Science
-
- 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:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset includes an example cell packing (containing ~20,000 cells). This example cell packing is the same cell packing in Supplementary Figure 11. The Corson_PBC_Square_Sweep_func.m is the main function for simulating lateral inhibition on this (and other) example packings. Please see readme for which simulation parameters may be tuned within this lateral inhibition function.
- Keyword:
- tissue patterning, lateral inhibition, and topological defect
- Citation to related publication:
- Nunley, H., Nagashima, M., Martin, K., Gonzalez, A. L., Suzuki, S. C., Norton, D. A., Wong, R. O. L., Raymond, P. A., & Lubensky, D. K. (2020). Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation. PLOS Computational Biology, 16(12), e1008437. https://doi.org/10.1371/journal.pcbi.1008437 , Corson F, Couturier L, Rouault H, Mazouni K, Schweisguth F. Self-organized Notch dynamics generate stereotyped sensory organ patterns in Drosophila. Science. 2017 May 5;356(6337):eaai7407. doi: 10.1126/science.aai7407. Epub 2017 Apr 6. PMID: 28386027., and Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679
- Discipline:
- Science
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset contains images of UV cone nuclei near the retinal margin in live zebrafish. These UV cone nuclei are labelled by transgenic expression of a fluorescent reporter (that is photoconvertible). The most important data are: 1. The zoomed-in (4X magnification) images of UV cone nuclei immediately after photoconversion 2. The zoomed-in (4X magnification) images of UV cone nuclei 2-4 days after photoconversion Also included is code for segmenting UV cone nuclei (both in image from immediately after photoconversion and in image from days later) and for shifting and rotating the two images to maximally align corresponding UV cone nuclei. After aligning corresponding UV cones, we compute triangulations over UV cone nuclei positions (for both images) and identify bonds that are common to both images. We use these common bonds to calculate the lattice vectors for the UV cone lattice.
- Keyword:
- zebrafish cone mosaic, tissue patterning, lattice vectors, and photoconversion
- Citation to related publication:
- Nunley, H., Nagashima, M., Martin, K., Gonzalez, A. L., Suzuki, S. C., Norton, D. A., Wong, R. O. L., Raymond, P. A., & Lubensky, D. K. (2020). Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation. PLOS Computational Biology, 16(12), e1008437. https://doi.org/10.1371/journal.pcbi.1008437 and Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679
- Discipline:
- Science
-
- Creator:
- Huang, Cheng MI
- Description:
- This collection contains a hierarchy of test problems for turbulent reacting flow simulations. It is meant to provide a testbed to build reduced model for relevant challenging reacting flow problems using different methods. In addition, this collection also serves to engage a broad community of experts in computational science and the field of engineering to address certain challenges in constructing reduced models for reacting flow simulations. All the datasets in this collection were generated under the Air Force Center of Excellence on Multi-Fidelity Modeling of Rocket Combustion Dynamics and the goal of the center is to advance the state-of-the-art in Reduced Order Models (ROMs) and enable efficient and accurate prediction of instabilities in liquid fueled rocket combustion systems.
- Discipline:
- Engineering
2Works -
Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation
User Collection- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- The outer epithelial layer of zebrafish retinae contains a crystalline array of cone photoreceptors, called the cone mosaic. As this mosaic grows by mitotic addition of new photoreceptors at the rim of the hemispheric retina, topological defects, called “Y-Junctions”, form to maintain approximately constant cell spacing. The generation of topological defects due to growth on a curved surface is a distinct feature of the cone mosaic not seen in other well-studied biological patterns like the R8 photoreceptor array in the _ Drosophila compound eye. Since defects can provide insight into cell-cell interactions responsible for pattern formation, here we characterize the arrangement of cones in individual Y-Junction cores (see Set of images for Figures 1 and 2 and 6 and Supplementary Figure 7) as well as the spatial distribution of Y-junctions across entire retinae (see Dataset for analyzing spatial distribution of Y-junctions in flat-mounted retinae). We find that for individual Y-junctions, the distribution of cones near the core corresponds closely to structures observed in physical crystals (see Set of images for Figures 1 and 2 and 6 and Supplementary Figure 7). In addition, Y-Junctions are organized into lines, called grain boundaries, from the retinal center to the periphery (see Dataset for analyzing spatial distribution of Y-junctions in flat-mounted retinae and Dataset for measuring tendency of Y-junctions to line up into grain boundaries during incorporation into retinae). In physical crystals, regardless of the initial distribution of defects, defects can coalesce into grain boundaries via the mobility of individual particles. By imaging in live fish, we demonstrate that grain boundaries in the cone mosaic instead appear during initial mosaic formation, without requiring defect motion (see Dataset for measuring tendency of Y-junctions to line up into grain boundaries during incorporation into retinae and Dataset for analyzing Y-junction motion in live fish retinae). Motivated by this observation, we show that a computational model of repulsive cell-cell interactions generates a mosaic with grain boundaries (see Code and example simulations of phase-field crystal model (for cone mosaic formation)). In contrast to paradigmatic models of fate specification in mostly motionless cell packings (see Code and accompanying input data for simulating lateral inhibition on motionless cell packing), this finding emphasizes the role of cell motion, guided by cell-cell interactions during differentiation, in forming biological crystals. Such a route to the formation of regular patterns may be especially valuable in situations, like growth on a curved surface, where the resulting long-ranged, elastic, effective interactions between defects can help to group them into grain boundaries.
- Keyword:
- zebrafish cone mosaic, lattice vectors, topological defects, tissue patterning, grain boundaries, lateral inhibition, photoconversion, phase-field crystal model, and defect motion
- Discipline:
- Science
7Works -
- Creator:
- Bougher, S. W. (University of Michigan) and Brecht, A. S. (NASA Ames Research Center)
- Description:
- This work examines the planetary wave-induced variability within the upper mesosphere/lower thermosphere of Venus by utilizing the Venus Thermospheric General Circulation Model (VTGCM). Rossby and Kelvin wave perturbations are driven by variations in the geopotential height of the VTGCM lower boundary (~70 km). A suite of simulations was conducted to examine the impact of the individual and combined waves propagating from two different lower boundary conditions (uniform and varying). The Kelvin wave is the more dominant wave which produces the most variability, as was shown in Hoshino et al., 2012. The combination of the Kelvin and Rossby waves provides a maximum temperature amplitude of 13 K at 92 km and maximum zonal wind amplitude of 23 m/s at 102 km. The combined waves overall are able to propagate up to 125 km. Most of the variation within the temperature, winds, and composition occurs between 70 km and 110 km. The varying lower boundary increases the magnitude of the wave deposition but weakly changes the propagation altitude. The thermal variation due to the planetary waves does not reproduce most observed variations. The simulated O2 IR nightglow emission is sensitive to the waves with respect to intensity and local time, but lacks latitudinal variation. The integrated intensity ranges from 1.2 MR to 1.65 MR and the local time ranges from 0.33 local time to 23.6 local time. Overall, planetary waves do affect the atmospheric structure, but there are still observed large variations that planetary waves alone cannot explain (i.e. thermal structure).
- Keyword:
- Venus, planetary waves, upper mesophere, lower thermosphere, and O2 nightglow
- Citation to related publication:
- Brecht, A. S., Bougher, S. W., Shields, D., & Liu, H.-L. (2021). Planetary-scale wave impacts on the Venusian upper mesosphere and lower thermosphere. Journal of Geophysical Research: Planets, 126, e2020JE006587. https://doi.org/10.1029/2020JE006587
- Discipline:
- Science
-
- Creator:
- Figueroa, C. Alberto
- Description:
- This .stl file represents the largest vessels of the cerebral circulation, specifically around the Circle of Willis. The file was created from a Computed Tomography Angiography (CTA) of a relatively healthy patient. It consisted of a 512 x 512 x 709 voxel image with a resolution of 0:35 mm x 0:35 mm x 0:5 mm. The model includes the basilar artery (1), left and right internal carotid arteries (2, and 3), left and right anterior cerebral arteries (4, and 5), left and right middle cerebral arteries (6, and 7), left and right posterior cerebral arteries (8, and 9), and various communicating arteries (10, 11, and 12).
- Keyword:
- Circle of Willis, Blood flow simulation, Hemodynamics, and Benchmarking blood flow
- Citation to related publication:
- N. Wilson, K. Wang, R. Dutton, C.A. Taylor, "A software framework for creating patient specific geometric models from medical imaging data for simulation based medical planning of vascular surgery", Medical Image Computing and Computer-Assisted Intervention MICCAI 2001, Springer, 2001, pp. 449–456. doi: 10.1007/3-540-45468-3_54 and N. Xiao, J.D. Humphrey, C.A. Figueroa, "Multi-Scale Computational Model of Three-Dimensional Hemodynamics within a Deformable Full-Body Arterial Network”, Journal of Computational Physics, 2013, Vol 244, pp. 22-40. doi: 10.1016/j.jcp.2012.09.016
- Discipline:
- Engineering and Health Sciences
-
- Creator:
- Huang, Cheng MI
- Description:
- A 2D planar representation of a generic laboratory-scale combustor is established to assess the capabilities of ROMs for representing realistic combustion flowfields. The purpose of this dataset is to provide a testbed to build reduced model for relevant challenging reacting flow problems using different methods. The dataset was generated under the Air Force Center of Excellence on Multi-Fidelity Modeling of Rocket Combustion Dynamics and the goal of the center is to advance the state-of-the-art in Reduced Order Models (ROMs) and enable efficient prediction of instabilities in liquid fueled rocket combustion systems., Detailed documentation of how the data is generated can be found in: https://afcoe.engin.umich.edu/benchmark-data. Instrument and/or Software specifications: - recommendation: Matlab and Tecplot. , 1. Data_150000to159999.tar: the unsteady flow field data from time step 150000 to 159999 (time increment, dt, between each time step is 1E-7 sec). 2. Data_160000to169999.tar: the unsteady flow field data from time step 160000 to 169999 (time increment, dt, between each time step is 1E-7 sec). , 3. Data_170000to179999.tar: the unsteady flow field data from time step 170000 to 179999 (time increment, dt, between each time step is 1E-7 sec). 4. Data_180000to189999.tar: the unsteady flow field data from time step 180000 to 189999 (time increment, dt, between each time step is 1E-7 sec)., 5. Data_190000to199999.tar: the unsteady flow field data from time step 190000 to 199999 (time increment, dt, between each time step is 1E-7 sec). 6. Data_200000to209999.tar: the unsteady flow field data from time step 200000 to 209999 (time increment, dt, between each time step is 1E-7 sec). , 7. Data_210000to219999.tar: the unsteady flow field data from time step 210000 to 219999 (time increment, dt, between each time step is 1E-7 sec). 8. Data_220000to229999.tar: the unsteady flow field data from time step 220000 to 229999 (time increment, dt, between each time step is 1E-7 sec). , and 9. grid.dat: the topology of the CFD mesh used to generate this data (can be directly loaded in Tecplot). 10. the file "sample_code.zip" contains the sample Matlab scripts to load and output the .dat files to help the researchers to get started. To run the script, the software Matlab is required and the researchers can simply run sampleIO.m script in Matlab to test the code.
- Citation to related publication:
- McQuarrie, S., Huang, C., and Willcox, K., Data-driven reduced-order models via regularised Operator Inference for a single-injector combustion process, Journal of the Royal Society of New Zealand, 2021. (code available: https://github.com/Willcox-Research-Group/ROM-OpInf-Combustion-2D)., McQuarrie, S. A., Huang, C., & Willcox, K. E. (2021). Data-driven reduced-order models via regularised Operator Inference for a single-injector combustion process. Journal of the Royal Society of New Zealand, 51(2), 194–211. https://doi.org/10.1080/03036758.2020.1863237 , Swischuk, R., Kramer, B., Huang, C., & Willcox, K. (2020). Learning Physics-Based Reduced-Order Models for a Single-Injector Combustion Process. AIAA Journal, 58(6), 2658–2672. https://doi.org/10.2514/1.J058943, Huang, C., Duraisamy, K., & Merkle, C. L. (2019). Investigations and Improvement of Robustness of Reduced-Order Models of Reacting Flow. AIAA Journal, 57(12), 5377–5389. https://doi.org/10.2514/1.J058392 , and Harvazinski, M. E., Huang, C., Sankaran, V., Feldman, T. W., Anderson, W. E., Merkle, C. L., & Talley, D. G. (2015). Coupling between hydrodynamics, acoustics, and heat release in a self-excited unstable combustor. Physics of Fluids, 27(4), 045102. https://doi.org/10.1063/1.4916673
- Discipline:
- Engineering
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right distal tibia 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:
- 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:
- Valeriy Tenishev
- Description:
- This data represents examples of some applications of AMPS and illustrates the potential of the code for modeling various physical phenomena.
- Keyword:
- Monte Carlo, DSMC
- Citation to related publication:
- Tenishev, V., Shou, Y., Borovikov, D., Lee, Y., Fougere, N., Michael, A., & Combi, M. R. (2021). Application of the Monte Carlo Method in Modeling Dusty Gas, Dust in Plasma, and Energetic Ions in Planetary, Magnetospheric, and Heliospheric Environments. Journal of Geophysical Research: Space Physics, 126(2), e2020JA028242. https://doi.org/10.1029/2020JA028242
- Discipline:
- Science
-
Division of Fishes
User Collection- Creator:
- University of Michigan Museum of Zoology
- Description:
- Division of Fishes
- Discipline:
- Science
48Works -
- Creator:
- Townsend, Whitney A, MacEachern, Mark P, and Song, Jean
- Description:
- We conducted a search through BioMed Central's 54 medicine and public health journals that provide OPR documentation in order to identify systematic review papers published in 2017. For each article we determined if OPR data, reviewer and author comments, were accessible. If so, we assessed the search methodology and reporting quality of the search process with a grading rubric based on PRISMA and PRESS standards, and then mined peer reviewer comments for references to the search methodology.
- Keyword:
- Systematic Reviews, Peer Review, Open Peer Review, Methodology, Research Methods, and Reporting
- Discipline:
- Health Sciences
-
- Creator:
- Zhang, Kaihua and Collette, Matthew D.
- Description:
- This Ph.D. research focuses on two subject areas: experimental and numerical model, which serves as two essential parts of a digital twin. A digital twin contains models of real-world structures and fuses data from observations of the structures and scale experiment to pull the models into better agreement with the real world. Digital twin models have the promise of representing complex marine structures and providing enhanced lifecycle performance and risk forecasts. Experimentally verifying the updating approaches is necessary but rarely performed. Thus, the proposed work is designing an experiment and developing a numerical model updated by the experimental data. The dataset contains all the data collected in the experiment of a four-crack hexagon- shaped specimen is presented, designed to mimic many of the properties of complex degrading marine structural systems, such as crack interaction, component inter- dependence, redundant load path, and non-binary failure.
- Keyword:
- System Reliability, Dynamic Bayesian Networks, Fatigue Experiment, Crack Length Measurement, Experimental Validation, Reliability Prediction
- Citation to related publication:
- "Evaluating Crack Growth Prediction in Structural Systems with Dynamic Bayesian Networks", submitted to Computers and Structure and Zhang, K., & Collette, M. (2021). Experimental investigation of structural system capacity with multiple fatigue cracks. Marine Structures, 78, 102943. https://doi.org/10.1016/j.marstruc.2021.102943
- Discipline:
- Engineering
-
- Creator:
- Robert Buckley, Grace O'Brien, and Zoe Zhou
- Description:
- The purpose of the research is to better understand and approximate the Thurston Set. This project was computational in nature and Python was used to collect our data. The data set contains encoded itineraries that can be used to compute values that are elements of the Thurston Set. A visual approximation of the Thurston Set can be found here ( https://arxiv.org/abs/1402.2008), on the first page Thurston’s own paper. The data can also be used to study the distribution of superattracting beta values within the interval (1, 2] and to explore an analogous Mandelbrot-Julia Correspondence. This research was conducted through the Lab of Geometry at Michigan under the advisement of Harrison Bray during the Fall semester of 2019. , The Python 3.x scripts in this deposit are the exact versions used to created the *.txt files that are in the zip archive. As the project continues, any expansion to the work, such as further analysis or visualization scripts, will be posted to the project's GitHub https://github.com/Tent-Maps-Team/Thurston-Set. Also, a user can reproduce our results and generate bigger datasets on machines with large amounts of memory. , and The data consists of zipper folders representing tent map itinerary orbit lengths. These orbit files can be used to create visualizations, create and explore conjectures such as refining proposed bounds on the Thurston Set and supporting an analogous Mandelbrot-Julia Correspondence. Within these zipped folders are .txt files in CSV format with the naming structure of xx_y of admissible itineraries up to the length indicated by the folder name where xx is the length of the encoded itineraries included. The txt's have a single column and each line(row) is an array representing an encoding of an itinerary. Some of the txt's have been split into multiple parts (whenever there are more than 200 MB of itinerary data) and these txt's have been numbered using the y after the underscore. As we exclude the degenerate tent map (where β = 1), we cannot have orbit length 1 or 2 and this is why the orbits start with length 3 (i.e. start with 3.zip).
- Keyword:
- Math, mathematics, tent maps, thurston, milnor, Milnor-Thurston, supperattracting, entropy, orbit, and itineraries
- Citation to related publication:
- Buckley R, O’Brien G, Zhou Z (2021). On Itineraries of Tent Maps. Forthcoming.
- Discipline:
- Other
-
- 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
-
- Creator:
- Pine, Alexandra F and Love, Brian J
- Description:
- This data is from a project concerned with dehydrating samples of saturated superabsorbent polymer using a centrifuge. The goal was to consider centrifugation as an energy efficient scheme to dehydrate SAP with the notion of reusing it. The data provided contains mass fractions of solvent removed through centrifugation with varied parameters.
- Keyword:
- Superabsorbent Polymer
- Citation to related publication:
- Pine, A., Wu, C. C., Raghavan, S., & Love, B. (2021). The efficiency of dehydrating desiccants by centrifugation: An assessment of superabsorbent polymers. Drying Technology, 0(0), 1–8. https://doi.org/10.1080/07373937.2021.1939710
- Discipline:
- Engineering
-
Profiles of near-surface rock mass strength across gradients in erosion, burial, and time [Data set]
- Creator:
- Townsend, Kirk F, Clark, Marin K, and Zekkos, Dimitrios
- Description:
- These datasets support the findings of Townsend et al. (2020). In this article, we project profiles of rock mass shear strength into the shallow subsurface (~30 m depth) using the Hoek and Brown criterion with Geological Strength Index (GSI) observations of outcrop structure and surface conditions, and Schmidt hammer rebound values of intact (unfractured) rock hardness. We compare these projected rock mass shear strength profiles to shear-wave velocity profiles collected using shallow geophysical arrays. We evaluate our methods in the Western Transverse Ranges of southern California, which exhibit strong gradients in the depth of latest-Mesozoic through Cenozoic sedimentary rocks exposed at the surface today, and in erosion rates quantified from catchment-average cosmogenic radionuclide concentrations and low-temperature apatite and zircon (U-Th)/He thermochronometry. We find that stratigraphic age and burial depth exerts the strongest apparent control on rock strength and S-wave velocities, likely due to diagenetic changes associated with burial. For rocks of the same age and inferred burial history, we observe that shear strength and S-wave velocities are positively correlated with erosion rate. We suggest that increasing erosion rates cause decreased residence time of rock masses within the critical zone, resulting in less weathered rocks.
- Keyword:
- rock strength, seismic, and erosion rate
- Citation to related publication:
- Townsend, K. F., Clark, M. K., & Zekkos, D. (2021). Profiles of Near-Surface Rock Mass Strength Across Gradients in Burial, Erosion, and Time. Journal of Geophysical Research: Earth Surface, 126(4), e2020JF005694. https://doi.org/10.1029/2020JF005694
- Discipline:
- Science
-
- Creator:
- Zhang, Yan, Gao, Chuanyu, Zhang, Shaoqing, Yang, Ping, Meyers, Philip A, and Wang, Guoping
- Description:
- The study focuses on reconstructing the histories of peat deposition using n-alkane biomarkers in peat cores and associated modern plant communities from four sites around a shallow maar lake in the Changbai Mountains of northeastern China. Peat development patterns in the four sites are not concordant although the sites experienced the same paleoclimate histories. Evidently, lava flows and tephra deposits produced an uneven topography of the volcanogenic lake basin that controls the water depths at the four lake edge locations, thereby leading to differences in peat-forming plant communities and peat deposition among the four sites.
- Keyword:
- peat deposition, n-alkanes, volcanic eruptions, and Changbai Lake
- Citation to related publication:
- Zhang, Y., Gao, C., Zhang, S., Yang, P., Meyers, P. A., & Wang, G. (2020). N-Alkane-based reconstructions of peat accumulations and depositional conditions at four locations around a shallow maar lake in the Changbai Mountains, northeastern China (world) [Preprint]. Earth and Space Science Open Archive; Earth and Space Science Open Archive. https://doi.org/10.1002/essoar.10505381.1
- Discipline:
- Science
-
- Creator:
- Moldwin, Mark B. and O'Brien, Paul
- Description:
- A new empirical model of the plasmapause location has been developed using density data from the plasma wave receiver onboard the CRRES spacecraft for nearly 1000 orbits. The “plasmapause” is identified here as the innermost sharp gradient in density (change of a factor of 5 in <0.5 L). Such a sharp gradient was observed on 73% of the CRRES inbound and outbound orbits that returned data. The plasmapause location is expressed as a linear function of Kp (previous 12 hour maximum) and local time. The model gives the linear best fit location of the plasmapause as well as the standard deviations of the model parameters.
- Keyword:
- Plasmapause and Plasmasphere
- Citation to related publication:
- Moldwin, M. B., Downward, L., Rassoul, H. K., Amin, R., and Anderson, R. R. (2002), A new model of the location of the plasmapause: CRRES results, J. Geophys. Res., 107( A11), 1339, doi:10.1029/2001JA009211 and O'Brien, T. P., and Moldwin, M. B. (2003), Empirical plasmapause models from magnetic indices, Geophys. Res. Lett., 30, 4, 1152. doi:10.1029/2002GL016007
- Discipline:
- Science
-
- Creator:
- Dewaraja, Yuni K and Van, Benjamin J
- Description:
- This publication contains anonymized diagnostic imaging scans of two patients. The images provided are pre-therapy scans used by clinicians for diagnosis and for selecting patients for treatment with Lu-177 DOTATATE. Multiple imaging modalities are present including diagnostic CT, MRI, and Ga68 PET, depending on the selected patient. All images are in DICOM format.
- Keyword:
- Lu-177, Lutathera, Dosimetry, Radionuclide, CT, MRI, and PET
- Discipline:
- Health Sciences
-
- Creator:
- Dewaraja, Yuni K and Van, Benjamin J
- Description:
- This publication contains anonymized planar whole body images of two patients. Patient scans were taken at 4 different time points in the week following a therapeutic dose of Lu-177 DOTATATE. Both anterior and posterior views are provided. All images are in DICOM format.
- Keyword:
- Lu-177, Lutathera, Dosimetry, Radionuclide, and Planar
- Discipline:
- Health Sciences
-
- Creator:
- Dewaraja, Yuni K and Van, Benjamin J
- Description:
- This publication contains anonymized SPECT/CT scans of two patients. Patient scans were taken at 4 different time points in the week following a therapeutic dose of Lu-177 DOTATATE. Both the SPECT and the co-registered CT are provided. All images are in DICOM format.
- Keyword:
- Lu-177, Dosimetry, Radionuclide, SPECT, and CT
- Discipline:
- Health Sciences
-
- Creator:
- Dewaraja, Yuni K and Van, Benjamin J
- Description:
- This publication contains anonymized time integrated activity maps for two patients. SPECT/CT scans were taken at 4 different time points in the week following a therapeutic dose of Lu-177 DOTATATE and combined into a single activity map for each patient. All images are in DICOM format.
- Keyword:
- Lu-177, Dosimetry, Radionuclide, SPECT, and CT
- Discipline:
- Health Sciences
-
- Creator:
- Dewaraja, Yuni K and Van, Benjamin J
- Description:
- This publication contains anonymized DICOM structure files that were outlined on SPECT/CT scans for two patients. Organ contours include the liver, right and left kidneys, and spleen when present. Two to four lesions were outlined for each patient.
- Keyword:
- Lu-177, Dosimetry, Radionuclide, SPECT, and Contour
- Discipline:
- Health Sciences
-
- Creator:
- Jeffrey Heath
- Description:
- fieldwork in Bonosso village, Côte d’Ivoire, chiefly 2016-19. See "readme" file for description of the materials.
- Keyword:
- Pere language
- Citation to related publication:
- Heath, Jeffrey, & Tioté, Brahima. (2019). A grammar of Pere (Bere, Mbre) of Côte d'Ivoire. Zenodo. http://doi.org/10.5281/zenodo.3346581
- Discipline:
- Humanities
-
Lu-177 DOTATATE Anonymized Patient Datasets
User Collection- Creator:
- Dewaraja, Yuni K and Van, Benjamin J
- Description:
- This collection is comprised of a number of works that collectively represent the imaging studies and information necessary for dosimetric analysis of a patient treated with Lutathera. All works may be used as standalone datasets or in conjunction with the others in this collection depending on the analysis performed. Files are stored using the DICOM standard widely accepted for storage and transmission of medical images and related information. All patient private information has been anonymized using MIM commercial software (MIM Software Inc.). Data from 2 patients, referred to as patient 4 and patient 6, has been provided in this collection and is divided among 6 works as outlined below:, 1) Pre-Therapy Diagnostic Images. Description: Patient diagnostic scans performed prior to Lutathera treatment. Used for identifying lesions and measuring progression. Note that the date of the baseline scan may be several months before the Lutathera treatment and changes in the anatomy are possible. Files: (1) Ga68 Dotatate PET/CT, Either: (1) MRI, (1) standalone diagnostic CT, 2) Planar Whole Body Scans. Description: Planar whole body Lu-177 scans taken at 4 time points within a week after treatment. Two views (Anterior and Posterior) and 3 energy windows (one main window at 208 keV and 2 adjacent scatter windows) are available for each time point. The units of this image is counts. Energy window information, acquisition data/time and duration can be found in DICOM header. Files: (6) individual images at each time point (24 total images per patient) , 3) SPECT/CT Scans. Description: Lu-177 SPECT/CT scans at 4 time points within a week after treatment (same time points as the planar scans). Images were acquired on a Siemens Intevo system and reconstructed using xSPECT Quant. The units of this image is Bq/mL. Information on the reconstruction, acquisition date/time, duration, Lu-177 administration time and activity can be found in the DICOM header. Files: (1) Folder with reconstructed SPECT slices per time point (4 folders total per patient), (1) Folder containing co-registered CT slices per time point (4 folders total per patient), 4) Lesion and Organ Volumes of Interest. Description: DICOM RT structure files containing organ and lesion volumes of interest (VOI) that were defined on the CT of the scan1 SPECT/CT in 3). Organs were defined using semi-automatic tools (atlas based and CNN-based) while lesions were defined manually by a radiologist guided by baseline scans. Only lesions >2 cc were defined. Files: (1) File containing organ contours, (1) File containing lesion contours, 5) Time Integrated Activity Maps. Description: A DICOM file containing the time-integrated activity map over all 4 time points within a week after treatment. This combines the SPECT/CT scans provided in 3) into a single integrated activity map. This map was generated via the MIM MRT Dosimetry package: The 4 time points were registered to the reference SPECT scan (time point 1) using a contour intensity based SPECT alignment and the voxel-level time-activity data was fit using exponential functions. Voxel-level integration was performed to generate the TIA map. The units of this image is Bq/mL * sec. Files: (1) Folder with Time-integrated activity image per patient, and 6) Projection Data and CT based Attenuation Coefficient Maps. Description: SPECT projection data for each of the 4 Lutathera scans taken within a week after treatment is provided in 3 forms: unaltered, Siemens [Reformatted], and Siemens [Advanced]. The difference between the Projections and the [Advanced] Projections is that the [Advanced] consists of uncorrected raw projection data and the other the corrected projection data (e.g. camera uniformity corrections). The [Advanced] projections are used in xSPECT reconstruction (where all corrections are done during the reconstruction), while the other is used in Flash 3D reconstruction. CT-based attenuation coefficient maps (mumaps) are provided for each of the 4 scans taken within a week after treatment. Two methods are provided for each mumap: xSPECT and F3D as the matrix size is different for the 2 cases (256 x 256 for xSPECT and 128 x 128 for Flash3D). Files: (3) Folders containing raw SPECT projections, (2) Folders containing CT attenuation coefficient maps (mumaps)
- Keyword:
- Lu-177, Lutathera, Dosimetry, Radionuclide, and CTMRIPET
- Discipline:
- Health Sciences
6Works -
- Creator:
- Arthurs, Christopher J., Khlebnikov, Rostislav, Melville, Alexander, Marčan, Marija, Gomez, Alberto, Dillon-Murphy, Desmond, Cuomo, Federica, Vieira, Miguel, Schollenberger, Jonas, Lynch, Sabrina, Tossas-Betancourt, Christopher, Iyer, Kritika, Hopper, Sara, Livingston, Elizabeth, Youssefi, Pouya, Noorani, Alia, Ben Ahmed, Sabrina, Nauta, Foeke J.N., van Bakel, Theodorus M.J., Ahmed, Yunus, van Bakel, Petrus A.J., Mynard, Jonathan, Di Achille, Paolo, Gharahi, Hamid, Lau, Kevin D., Filonova, Vasilina, Aguirre, Miquel, Nama, Nitesh, Xiao, Nan, Baek, Seungik, Garikipati, Krishna, Sahni, Onkar, Nordsletten, David, and Figueroa, Carlos A.
- Description:
- This repository contains the source code for the CRIMSON GUI, as required in the PLOS Computational Biology publication: CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation by the same authors., This is a snapshot of the software; build dependencies can be found at https://doi.org/10.7302/ssj9-n788. Please visit https://github.com/carthurs/CRIMSONGUI/releases/tag/PLOS_Comp_Bio & www.crimson.software for more general information and the most up to date version of the software., and Software can be compiled in Windows.
- Keyword:
- Blood Flow Simulation, Patient-specific, Open-source Software, Image-based simulation, Cardiovascular Medical Image, Segmentation, and Finite Element Simulation
- Citation to related publication:
- CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation C.J. Arthurs, R. Khlebnikov, A. Melville, M. Marčan, A. Gomez, D. Dillon-Murphy, F. Cuomo, M.S. Vieira, J. Schollenberger, S.R. Lynch, C. Tossas-Betancourt, K. Iyer, S. Hopper, E. Livingston, P. Youssefi, A. Noorani, S. Ben Ahmed, F.J.H. Nauta, T.M.J. van Bakel, Y. Ahmed, P.A.J. van Bakel, J. Mynard, P. Di Achille, H. Gharahi, K. D. Lau, V. Filonova, M. Aguirre, N. Nama, N. Xiao, S. Baek, K. Garikipati, O. Sahni, D. Nordsletten, C.A. Figueroa bioRxiv 2020.10.14.339960; doi: https://doi.org/10.1101/2020.10.14.339960 and Computational Vascular Biomechanics Lab @ the University of Michigan and other collaborators, The Qt Company, NSIS Team and contributors, PostgreSQL Global Development Group, Oracle Corporation, Kitware. CRIMSON open source project - Build Dependencies [Data set], (2021). University of Michigan - Deep Blue. https://doi.org/10.7302/ssj9-n788
- Discipline:
- Health Sciences and Engineering
-
- Creator:
- Arthurs, Christopher J., Khlebnikov, Rostislav, Melville, Alexander, Marčan, Marija, Gomez, Alberto, Dillon-Murphy, Desmond, Cuomo, Federica, Vieira, Miguel, Schollenberger, Jonas, Lynch, Sabrina, Tossas-Betancourt, Christopher, Iyer, Kritika, Hopper, Sara, Livingston, Elizabeth, Youssefi, Pouya, Noorani, Alia, Ben Ahmed, Sabrina, Nauta, Foeke J.N., van Bakel, Theodorus M.J., Ahmed, Yunus, van Bakel, Petrus A.J., Mynard, Jonathan, Di Achille, Paolo, Gharahi, Hamid, Lau, Kevin D., Filonova, Vasilina, Aguirre, Miquel, Nama, Nitesh, Xiao, Nan, Baek, Seungik, Garikipati, Krishna, Sahni, Onkar, Nordsletten, David, and Figueroa, Carlos A.
- Description:
- This repository contains the source code for the CRIMSON Flow Solver as required in the PLOS Computational Biology publication: CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation by the same authors., This is a snapshot of the software. Please visit https://github.com/carthurs/CRIMSONFlowsolver/releases/tag/PLOS_Comp_Bio & www.crimson.software for more general information and the most up to date version of the software. , and Software can be compiled in Cygwin and Linux.
- Keyword:
- Blood Flow Simulation, Patient-specific, Open-source Software, Image-based simulation, Cardiovascular Medical Image, Segmentation, and Finite Element Simulation
- Citation to related publication:
- CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation C.J. Arthurs, R. Khlebnikov, A. Melville, M. Marčan, A. Gomez, D. Dillon-Murphy, F. Cuomo, M.S. Vieira, J. Schollenberger, S.R. Lynch, C. Tossas-Betancourt, K. Iyer, S. Hopper, E. Livingston, P. Youssefi, A. Noorani, S. Ben Ahmed, F.J.H. Nauta, T.M.J. van Bakel, Y. Ahmed, P.A.J. van Bakel, J. Mynard, P. Di Achille, H. Gharahi, K. D. Lau, V. Filonova, M. Aguirre, N. Nama, N. Xiao, S. Baek, K. Garikipati, O. Sahni, D. Nordsletten, C.A. Figueroa bioRxiv 2020.10.14.339960; doi: https://doi.org/10.1101/2020.10.14.339960 and Arthurs, C., Khlebnikov, R., Melville, A., Marčan, M., Gomez, A., Dillon-Murphy, D., Cuomo, F., Vieira, M., Schollenberger, J., Lynch, S., Tossas-Betancourt, C., Iyer, K., Hopper, S., Livingston, E., Youssefi, P., Noorani, A., Ben Ahmed, S., Nauta, F., van Bakel, T., Ahmed, Y., van Bakel, P., Mynard, J., Di Achille, P., Gharahi, H., Lau, K., Filonova, V., Aguirre, M., Nama, N., Xiao, N., Baek, S., Garikipati, K., Sahni, O., Nordsletten, D., Figueroa, C. (2021). CRIMSON open source project - Graphical User Interface (GUI) Source Code for PLOS Computational Biology [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/679b-dw96
- Discipline:
- Engineering and Health Sciences
-
- Creator:
- Anahita, Amiri Farahani
- Description:
- this dataset is the output of WRF-Chem model for several simulations.
- Keyword:
- Lake spray aerosol
- Citation to related publication:
- Amiri-Farahani, A., Olson, N. E., Neubauer, D., Roozitalab, B., Ault, A. P., & Steiner, A. L. (2021). Lake Spray Aerosol Emissions Alter Nitrogen Partitioning in the Great Lakes Region. Geophysical Research Letters, 48(12), e2021GL093727. https://doi.org/10.1029/2021GL093727
- Discipline:
- Science
-
- Creator:
- Shane, Alexander
- Description:
- This data set was created with the purpose to study the electron pitch angle distributions on dayside closed crustal fields at Mars and to compare with theoretical predictions made by numerical modeling. Analyzing the plasma environment of the crustal fields was another point of study to determine if whistler waves can interact with high energy superthermal electrons.
- Keyword:
- Mars, superthermal electron, pitch angle distribution, and crustal magnetic field
- Discipline:
- Science
-
- Creator:
- Stringer, Kathleen A.
- Description:
- These data were produced from the survival analysis of the pre-treatment metabolomics data generated from the Phase II clinical trial of L-carnitine treatment for septic shock (the RACE trial - see https://clinicaltrials.gov/ct2/show/NCT01665092). The results based on respective acetylcarnitine or valine concentration are presented (pdf). The csv files contain the at risk numbers from the Kaplan-Meier survival analysis. These findings described in our manuscript: Pharmacometabolomics Identifies Candidate Predictor Metabolites of an L-carnitine Treatment Mortality Benefit in Septic Shock. and All of the metabolomics data are available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org which is supported by NIH grant U2C-DK119886 and where it has been assigned Project ID (accession number ST001319). The data can be accessed directly via its Project DOIs: (DOI: http://dx.doi.org/10.21228/M8VX0Z).
- Keyword:
- sepsis, septic shock, survival, mortality, metabolomics, and pharmacometabolomics
- Citation to related publication:
- Puskarich, M. A., Jennaro, T. S., Gillies, C. E., Evans, C. R., Karnovsky, A., McHugh, C. E., Flott, T. L., Jones, A. E., Stringer, K. A., & Investigators, O. behalf of the R. T. (2021). Pharmacometabolomics Identifies Candidate Predictor Metabolites of an L-carnitine Treatment Mortality Benefit in Septic Shock. (Preprint) https://doi.org/10.1101/2021.01.28.21250687
- Discipline:
- Health Sciences
-
Computed tomography voxel dataset for ummz:mammals:154693-Blarina brevicauda brevicauda-Skull-DiceCT
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:154693 (Blarina brevicauda brevicauda) - Skull. Reconstructed Dataset includes 1219 TIF images (each 1013 x 1693 x 1 voxel at 0.033795 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:154693 (Blarina brevicauda brevicauda) - Skull. Raw Dataset includes 3141 TIF images (each 1013 x 1693 x 1 voxel at 0.03379497 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Soricomorpha, Soricidae, Blarina brevicauda brevicauda, 1987337719, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987337719
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:166889 (Blarina brevicauda kirtlandi) - WholeBody. Raw Dataset includes 3141 TIF images (each 877 x 1047 x 1 voxel at 0.03681702 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:166889 (Blarina brevicauda kirtlandi) - WholeBody. Reconstructed Dataset includes 1882 TIF images (each 877 x 1047 x 1 voxel at 0.036817 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Soricomorpha, Soricidae, Blarina brevicauda kirtlandi, 1987233799, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987233799
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:166889 (Blarina brevicauda kirtlandi) - Skull. Raw Dataset includes 3141 TIF images (each 1570 x 1531 x 1 voxel at 0.01919876 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:166889 (Blarina brevicauda kirtlandi) - Skull. Reconstructed Dataset includes 1978 TIF images (each 1570 x 1531 x 1 voxel at 0.019199 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Soricomorpha, Soricidae, Blarina brevicauda kirtlandi, 1987233799, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987233799
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:154691 (Blarina brevicauda brevicauda) - WholeBody. Raw Dataset includes 3141 TIF images (each 1187 x 834 x 1 voxel at 0.03976336 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:154691 (Blarina brevicauda brevicauda) - WholeBody. Reconstructed Dataset includes 2000 TIF images (each 1187 x 834 x 1 voxel at 0.039763 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Soricomorpha, Soricidae, Blarina brevicauda brevicauda, 1987241426, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987241426
- Discipline:
- Science
-
Computed tomography voxel dataset for ummz:mammals:154691-Blarina brevicauda brevicauda-Skull-DiceCT
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:154691 (Blarina brevicauda brevicauda) - Skull. Reconstructed Dataset includes 1035 TIF images (each 1322 x 910 x 1 voxel at 0.027133 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:154691 (Blarina brevicauda brevicauda) - Skull. Raw Dataset includes 3141 TIF images (each 1322 x 910 x 1 voxel at 0.02713322 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Soricomorpha, Soricidae, Blarina brevicauda brevicauda, 1987241426, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987241426
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen UMMZ:herps:130609 (PHAEOGNATHUS HUBRICHTI) - WholeBody. Raw Dataset includes 1601 TIF images (each 373 x 372 x 1 voxel at 0.1000025 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen UMMZ:herps:130609 (PHAEOGNATHUS HUBRICHTI) - WholeBody. Reconstructed Dataset includes 2000 TIF images (each 373 x 372 x 1 voxel at 0.100002 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Amphibia, CAUDATA, PLETHODONTIDAE, PHAEOGNATHUS HUBRICHTI, 1987157237, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987157237
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen UMMZ:mammals:112964 (Desmodus rotundus) - WholeBody. Raw Dataset includes 3141 TIF images (each 1047 x 1326 x 1 voxel at 0.04145749 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen UMMZ:mammals:112964 (Desmodus rotundus) - WholeBody. Reconstructed Dataset includes 2000 TIF images (each 1047 x 1326 x 1 voxel at 0.041457 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Chiroptera, Phyllostomidae, Desmodus rotundus, 1987291741, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987291741
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen UMMZ:herps:130609 (PHAEOGNATHUS HUBRICHTI) - Skull. Raw Dataset includes 1601 TIF images (each 1324 x 1087 x 1 voxel at 0.01110375 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen UMMZ:herps:130609 (PHAEOGNATHUS HUBRICHTI) - Skull. Reconstructed Dataset includes 1951 TIF images (each 1324 x 1087 x 1 voxel at 0.011104 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Amphibia, CAUDATA, PLETHODONTIDAE, PHAEOGNATHUS HUBRICHTI, 1987157237, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987157237
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen UMMZ:mammals:112964 (Desmodus rotundus) - Skull. Raw Dataset includes 3141 TIF images (each 1554 x 1520 x 1 voxel at 0.02332415 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen UMMZ:mammals:112964 (Desmodus rotundus) - Skull. Reconstructed Dataset includes 1656 TIF images (each 1554 x 1520 x 1 voxel at 0.023324 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Chiroptera, Phyllostomidae, Desmodus rotundus, 1987291741, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987291741
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen UMMZ:mammals:99103 (Desmodus rotundus) - WholeBody. Reconstructed Dataset includes 2000 TIF images (each 881 x 1326 x 1 voxel at 0.041457 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen UMMZ:mammals:99103 (Desmodus rotundus) - WholeBody. Raw Dataset includes 3141 TIF images (each 881 x 1326 x 1 voxel at 0.04145749 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Chiroptera, Phyllostomidae, Desmodus rotundus, 1987245972, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987245972
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen UMMZ:mammals:99103 (Desmodus rotundus) - Skull. Reconstructed Dataset includes 1464 TIF images (each 1443 x 1496 x 1 voxel at 0.023324 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen UMMZ:mammals:99103 (Desmodus rotundus) - Skull. Raw Dataset includes 3141 TIF images (each 1443 x 1496 x 1 voxel at 0.02332415 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Chiroptera, Phyllostomidae, Desmodus rotundus, 1987245972, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987245972
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:90288 (SEPSINA TETRADACTYLA) - WholeBody. Reconstructed Dataset includes 1983 TIF images (each 241 x 360 x 1 voxel at 0.053454 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:90288 (SEPSINA TETRADACTYLA) - WholeBody. Raw Dataset includes 1601 TIF images (each 241 x 360 x 1 voxel at 0.05345412 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Reptilia, SAURIA, SCINCIDAE, SEPSINA TETRADACTYLA, 1987065539, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987065539
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:90288 (SEPSINA TETRADACTYLA) - Skull. Reconstructed Dataset includes 1479 TIF images (each 687 x 924 x 1 voxel at 0.010001 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:90288 (SEPSINA TETRADACTYLA) - Skull. Raw Dataset includes 1601 TIF images (each 687 x 924 x 1 voxel at 0.01000145 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Reptilia, SAURIA, SCINCIDAE, SEPSINA TETRADACTYLA, 1987065539, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987065539
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:116965 (CHRYSOPELEA PARADISI) - WholeBody. Reconstructed Dataset includes 2000 TIF images (each 2000 x 846 x 1 voxel at 0.049512 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:116965 (CHRYSOPELEA PARADISI) - WholeBody. Raw Dataset includes 1601 TIF images (each 2000 x 846 x 1 voxel at 0.04951242 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Reptilia, OPHIDIA, COLUBRIDAE, CHRYSOPELEA PARADISI, 1987085793, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987085793
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:116965 (CHRYSOPELEA PARADISI) - Skull. Raw Dataset includes 1601 TIF images (each 760 x 1231 x 1 voxel at 0.01844824 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:116965 (CHRYSOPELEA PARADISI) - Skull. Reconstructed Dataset includes 751 TIF images (each 760 x 1231 x 1 voxel at 0.018448 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Reptilia, OPHIDIA, COLUBRIDAE, CHRYSOPELEA PARADISI, 1987085793, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987085793
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:154693 (Blarina brevicauda brevicauda) - WholeBody. Raw Dataset includes 3141 TIF images (each 1611 x 1121 x 1 voxel at 0.03882457 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:154693 (Blarina brevicauda brevicauda) - WholeBody. Reconstructed Dataset includes 1959 TIF images (each 1611 x 1121 x 1 voxel at 0.038825 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Soricomorpha, Soricidae, Blarina brevicauda brevicauda, 1987337719, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987337719
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:181698 (CHRYSOPELEA PARADISI) - WholeBody. Raw Dataset includes 1601 TIF images (each 1703 x 1701 x 1 voxel at 0.03202086 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:181698 (CHRYSOPELEA PARADISI) - WholeBody. Reconstructed Dataset includes 1402 TIF images (each 1703 x 1701 x 1 voxel at 0.032021 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Reptilia, OPHIDIA, COLUBRIDAE, CHRYSOPELEA PARADISI, 1987124862, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987124862
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:181698 (CHRYSOPELEA PARADISI) - Skull. Raw Dataset includes 1601 TIF images (each 378 x 682 x 1 voxel at 0.01542104 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:181698 (CHRYSOPELEA PARADISI) - Skull. Reconstructed Dataset includes 927 TIF images (each 378 x 682 x 1 voxel at 0.015421 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Reptilia, OPHIDIA, COLUBRIDAE, CHRYSOPELEA PARADISI, 1987124862, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987124862
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:246849 (THAMNODYNASTES PALLIDUS) - Skull. Raw Dataset includes 1601 TIF images (each 1416 x 914 x 1 voxel at 0.0150099083890765 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:246849 (THAMNODYNASTES PALLIDUS) - Skull. Reconstructed Dataset includes 654 TIF images (each 1416 x 914 x 1 voxel at 0.015010 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Reptilia, OPHIDIA, COLUBRIDAE, THAMNODYNASTES PALLIDUS, 1987213257, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987213257
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:246849 (THAMNODYNASTES PALLIDUS) - WholeBody. Raw Dataset includes 1601 TIF images (each 2000 x 2000 x 1 voxel at 0.0327439804971583 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:246849 (THAMNODYNASTES PALLIDUS) - WholeBody. Reconstructed Dataset includes 1240 TIF images (each 2000 x 2000 x 1 voxel at 0.032744 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Reptilia, OPHIDIA, COLUBRIDAE, THAMNODYNASTES PALLIDUS, 1987213257, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987213257
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:177463 (LEIOPELMA HOCHSTETTERI) - WholeBody. Reconstructed Dataset includes 2000 TIF images (each 506 x 1232 x 1 voxel at 0.026167 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:177463 (LEIOPELMA HOCHSTETTERI) - WholeBody. Raw Dataset includes 3141 TIF images (each 506 x 1232 x 1 voxel at 0.02616705 mm resolution, derived from 3141 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Amphibia, ANURA, LEIOPELMATIDAE, LEIOPELMA HOCHSTETTERI, 1987038228, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987038228
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:177463 (LEIOPELMA HOCHSTETTERI) - WholeBody. Reconstructed Dataset includes 2000 TIF images (each 659 x 1423 x 1 voxel at 0.023619 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:177463 (LEIOPELMA HOCHSTETTERI) - WholeBody. Raw Dataset includes 1601 TIF images (each 659 x 1423 x 1 voxel at 0.02361855 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Amphibia, ANURA, LEIOPELMATIDAE, LEIOPELMA HOCHSTETTERI, 1987038228, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987038228
- Discipline:
- Science
-
- Creator:
- Lamb, Abigail M.
- Description:
- This Work contains Supplemental File S3-1, Supplemental File S3-2, Supplemental Table S4-1, Supplemental Table S4-2, and Supplemental Table S4-3 from the dissertation entitled "Genetic Determinants of the Development and Evolution of Drosophila Pigmentation" by Abigail M. Lamb. Supplemental File S3-1 is entitled "Raw data measuring CHC abundance" and contains the measurements of cuticular hydrocarbons used for analysis in Chapter 3 of the dissertation. These data are meant to be read into the R code contained in Supplemental File S3-2, "R code used for analyzing CHC data" to reproduce the results reported in Chapter 3 of the dissertation. Supplemental Tables S4-1, S4-2, and S4-3 contain original phenotyping data, notes, and summary data from the miRNA overexpression and competitive inhibition experiments described in Chapter 4 of the dissertation.
- Citation to related publication:
- Lamb, A. M., Wang, Z., Simmer, P., Chung, H., & Wittkopp, P. J. (2020). Ebony Affects Pigmentation Divergence and Cuticular Hydrocarbons in Drosophila americana and D. novamexicana. Frontiers in Ecology and Evolution, 8. https://doi.org/10.3389/fevo.2020.00184
- Discipline:
- Science
-
- Creator:
- Dewaraja, Yuni, K and Van, Benjamin J
- Description:
- This publication contains the anonymized SPECT/CT scans of two patients. Patient scans were taken at 4 different time points in the week following a therapeutic dose of Lu-177 DOTATATE. Each of the scans contains 5 subfolders, 3 of which contain SPECT projection data used for reconstructing SPECT images, and 2 contain the linear attenuation coefficient maps for the CT scans that correspond to each patients SPECT projections. All images are in DICOM format.
- Keyword:
- Lu-177, Dosimetry, Radionuclide, SPECT, and CT
- Discipline:
- Health Sciences
-
- Creator:
- University of Michigan, Division of Herpetology, Davis Rabosky, Alison R, Larson, Joanna G, Moore, Talia Y, and Curlis, John David
- Description:
- This dataset includes dorsal and ventral photographs of Neotropical snakes collected in the Peruvian Amazon. These data were collected to survey and examine the diversity in color pattern evolution in Neotropical snakes.
- Keyword:
- snake, color, serpentes, and Peru
- Citation to related publication:
- (work in progress, not yet submitted)
- Discipline:
- Science
-
- Creator:
- Computational Vascular Biomechanics Lab @ the University of Michigan and other collaborators, The Qt Company, NSIS Team and contributors, PostgreSQL Global Development Group, Oracle Corporation, and Kitware
- Description:
- This repository contains several open-source components as well as software developed by our own lab that are required to build the GUI of the open source CRIMSON software from scratch using Visual Studio 2013 update 5:, cmake-3.13.5-win64-x64.zip: build tool; nsis-3.05-setup.exe: packaging tool; postgresql-9.5.21-1-windows-x64-binaries.zip: Qt dependency; presolver_win.zip: windows binary for CRIMSON Presolver built using MinGW; qt-opensource-windows-x86-msvc2013_64-5.7.0.exe: Qt GUI library; mysql-5.7.29-winx64.zip: Qt dependencies, Software in this repository is a snapshot; please visit https://github.com/carthurs/CRIMSONGUI & www.crimson.software for more general information and the most up to date version of the software., and This repository completes the following Deep Blue repository: GUI repository: https://doi.org/10.7302/679b-dw96
- Citation to related publication:
- CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation C.J. Arthurs, R. Khlebnikov, A. Melville, M. Marčan, A. Gomez, D. Dillon-Murphy, F. Cuomo, M.S. Vieira, J. Schollenberger, S.R. Lynch, C. Tossas-Betancourt, K. Iyer, S. Hopper, E. Livingston, P. Youssefi, A. Noorani, S. Ben Ahmed, F.J.H. Nauta, T.M.J. van Bakel, Y. Ahmed, P.A.J. van Bakel, J. Mynard, P. Di Achille, H. Gharahi, K. D. Lau, V. Filonova, M. Aguirre, N. Nama, N. Xiao, S. Baek, K. Garikipati, O. Sahni, D. Nordsletten, C.A. Figueroa bioRxiv 2020.10.14.339960; doi: https://doi.org/10.1101/2020.10.14.339960 and Arthurs, C., Khlebnikov, R., Melville, A., Marčan, M., Gomez, A., Dillon-Murphy, D., Cuomo, F., Vieira, M., Schollenberger, J., Lynch, S., Tossas-Betancourt, C., Iyer, K., Hopper, S., Livingston, E., Youssefi, P., Noorani, A., Ben Ahmed, S., Nauta, F., van Bakel, T., Ahmed, Y., van Bakel, P., Mynard, J., Di Achille, P., Gharahi, H., Lau, K., Filonova, V., Aguirre, M., Nama, N., Xiao, N., Baek, S., Garikipati, K., Sahni, O., Nordsletten, D., Figueroa, C. (2021). CRIMSON open source project - Graphical User Interface (GUI) Source Code for PLOS Computational Biology [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/679b-dw96
- Discipline:
- Health Sciences and Engineering
-
- Creator:
- Figueroa, Carlos A., Computational Vascular Biomechanics Lab, University of Michigan, and et al.
- Description:
- This collection concerns the CRIMSON (CardiovasculaR Integrated Modelling and SimulatiON) software environment. CRIMSON provides a powerful, customizable and user-friendly system for performing three-dimensional and reduced-order computational haemodynamics studies via a pipeline which involves: 1) segmenting vascular structures from medical images; 2) constructing analytic arterial and venous geometric models; 3) performing finite element mesh generation; 4) designing, and 5) applying boundary conditions; 6) running incompressible Navier-Stokes simulations of blood flow with fluid-structure interaction capabilities; and 7) post-processing and visualizing the results, including velocity, pressure and wall shear stress fields. , The minimum specifications to run CRIMSON are: Any AMD64 CPU (note: Intel Core i series are AMD64), Windows (only tested on Windows 10 but might work on Windows 7), 8 GB of RAM , If you are running non-trivial models you will want to have: Quad core CPU or higher, Solid state drive for storing data, Windows, 16 GB of RAM, Dedicated discrete GPU for rendering models. , and Software in this collection is a snapshot; please visit https://github.com/carthurs/CRIMSONGUI & www.crimson.software for more general information and the most up to date version of the software.
- Keyword:
- Blood Flow Simulation, Patient-specific, Open-source Software, Image-based simulation, Cardiovascular Medical Image, Segmentation, and Finite Element Simulation
- Citation to related publication:
- CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation C.J. Arthurs, R. Khlebnikov, A. Melville, et al. bioRxiv 2020.10.14.339960; doi: https://doi.org/10.1101/2020.10.14.339960
- Discipline:
- Health Sciences and Engineering
4Works -
- Creator:
- Xian Li
- Description:
- Low-velocity accretionary wedges and sedimentary layers overlaying continental plates are widely observed in the subduction zones where historical large earthquakes have occurred. It was observed that rupture of the 2011 Mw 9.0 Tohoku-Oki earthquake propagated to the trench with large coseismic slip on the shallow fault, but what caused the huge shallow slip remains a prominent problem., Here we explore how the two low-velocity structures, accretionary wedge and sedimentary layer, affect the coseismic slip and near-fault ground motions during the 2011 Tohoku-Oki earthquake. Constrained by the observed seafloor deformation, we present a 2-D dynamic rupture model of the 2011 Tohoku-Oki earthquake with an accretionary wedge and a sedimentary layer. Compared to a homogeneous model with the same friction and stress parameters on the fault, we find that the co-existence of the accretionary wedge and sedimentary layer significantly enhances the shallow coseismic slip and amplifies ground accelerations near the accretionary wedge. We then investigate a plausible scenario of a smaller Tohoku-Oki earthquake when its rupture does not reach the accretionary wedge. The sedimentary layer slightly enhances the coseismic slip while the accretionary wedge has almost no influence for the smaller earthquake scenario, but both structures significantly amplify the ground accelerations on the overriding plate. , and By simulating a suite of earthquake scenarios, we suggest that the co-existence of an accretionary wedge and sedimentary layers tend to enhance coseismic slip, but the enhancement effect decreases as the up-dip limit of rupture zones terminates at a larger depth. The numerical simulations were solved using SEM2DPACK _2.3.8 ( http://www.sourceforge.net/projects/sem2d/), and simulation results were visualized by Matlab. This folder includes the input files to reproduce our simulation results and plot scripts.
- Keyword:
- 2011 Tohoku-Oki earthquake, Dynamic rupture simulation, Accretionary wedge, and Sedimentary layer
- Citation to related publication:
- Li, X., & Huang, Y. (2021). The enhancement of coseismic slip and ground motion due to the accretionary wedge and sedimentary layer in the 2011 Tohoku-Oki earthquake (world) [Preprint]. Earth and Space Science Open Archive. https://doi.org/10.1002/essoar.10506336.1
- Discipline:
- Science
-
- Creator:
- Malhotra, Garima and Ridley, Aaron
- Description:
- This research aims to understand the influence of lower thermospheric atomic oxygen ([O]) and dynamics on the thermospheric Semi Annual Oscillation (SAO). [O] number densities between 95-100 km from WACCM-X are much closer to the observations from SABER instrument on TIMED satellite as compared to those from MSIS. We compare the phase and amplitude of SAO from different simulations with empirical models and observational datasets, and explore different mechanisms that can improve the SAO in IT models.
- Keyword:
- Semi Annual Oscillation, SAO, T-I SAO, Thermospheric Dynamics, Thermospheric Semi Annual Oscillation, WACCM-X coupling with GITM, Global Ionosphere Thermosphere Model, WACCM-X, Whole Atmosphere Model, Vertical coupling, Meridional Circulation, Annual Oscillation, Thermospheric Intra-Annual Variations, and Semiannual Oscillation
- Citation to related publication:
- Malhotra, G., Ridley, A., Jones, M., (2021) Impacts of Lower Thermospheric Atomic Oxygen and Dynamics on Thermospheric Semiannual Oscillation using GITM and WACCM-X, Journal of Geophysical Research: Space Physics
- Discipline:
- Science
-
- Creator:
- Umberfield, Elizabeth, Ford, Kathleen, Stansbury, Cooper, and Harris, Marcelline R.
- Description:
- Research Overview: This dataset is clinical consent forms, collected as part of Dr. Elizabeth Umberfield's dissertation research of at the University of Michigan. 134 consent forms are used in the analysis, 102 of which are shared here (not all are shared due to data protection agreements with participating sites). The research aimed to enable representation of clinical consent forms and their permissions within the Informed Consent Ontology. These efforts were supported by the Rackham Graduate Student Research Grant, and Dr. Umberfield's doctoral training was supported by the Robert Wood Johnson Foundation Future of Nursing Scholars Program.
- Keyword:
- Consent, Consent Form, Informed Consent, Health Care, and Healthcare
- Citation to related publication:
- Umberfield, E., Jiang, Y., Fenton, S., Stansbury, C., Ford, K., Crist, K., Kardia, S., Thomer, A., & Harris, M. R. (In Press). Lessons Learned for Identifying and Annotating Permissions in Clinical Consents. Applied Clinical Informatics. and Umberfield, E., Stansbury, C., Ford, K., Jiang, Y., Kardia, S. L. R., Thomer, A., & Harris, M. R. (Under Review). Evaluating and Extending the Informed Consent Ontology for Representing Permissions from the Clinical Domain.
- Discipline:
- Health Sciences
-
- Creator:
- Ramos, Marlon D., Yihe, H., Ulrich, T., Gabriel, A. A., and Thomas, A.
- Description:
- This study used three-dimensional, dynamic earthquake simulations to investigate how stress and friction levels on the Cascadia megathrust fault influence the final earthquake size and coastal subsidence patterns from the 1700 A.D. earthquake.
- Discipline:
- Science
-
- Creator:
- Salaree, Amir
- Description:
- Study of the effect of various rupture scenarios in Cascadia on tsunami hazard
- Keyword:
- Earthquake, Tsunami, Simulation, and Bathymetry
- Discipline:
- Science
-
- Creator:
- Chun-Seok Cho, Jingyue Xi, Hyun Min Kang, and Jun Hee Lee
- Description:
- There are three experimental outputs from Seq-Scope. (1) High definition map coordinate identifier (HDMI) sequence, tile and spatial coordinate information from 1st-Seq, (2) HDMI sequence, coupled with cDNA sequence from 2nd-Seq, and (3) Histological image obtained from Hematoxylin and Eosin (H&E) staining of the tissue slice. (1) and (2) were uploaded to GEO ( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169706). (3) is deposited here. In addition, this deposit includes the processed RDS (single R object) data files.
- Keyword:
- Seq-Scope, scRNA-seq, and spatial transcriptomics
- Citation to related publication:
- Chun-Seok Cho, Jingyue Xi, Sung-Rye Park, Jer-En Hsu, Myungjin Kim, Goo Jun, Hyun-Min Kang, Jun Hee Lee “Seq-Scope: Submicrometer-resolution spatial transcriptomics for single cell and subcellular studies” (preprint) bioRxiv https://doi.org/10.1101/2021.01.25.427807 and Related data sets in NCBI’s Gene Expression Omnibus (GEO) repository: Cho C, Xi J, Si Y, Lee JH, Kang HM, Park S, Hsu J, Kim M, Jun G “Seq-Scope: Submicrometer-resolution spatial barcoding technology that enables microscopic examination of tissue transcriptome at single cell and subcellular levels” https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169706
- Discipline:
- Health Sciences
-
- Creator:
- Saylor, Kate M., Sirihorachai, Rattima , and Manojlovich, Milisa
- Description:
- The search data supports a literature review project on counting interventions to reduce the incidence of retained surgical instruments. The data included in the dataset are the reproducible search strategies (txt file) and the exported results of all citations from all databases (txt, ris, and.nbib files). These searches and exported result files contain all citations originating from the database searches that were considered for inclusion.
- Keyword:
- literature search , retained surgical instruments, counting, and nursing
- Discipline:
- Health Sciences
-
- Creator:
- Hinz, Isaac and Johnson, Jena
- Description:
- Laboratory experiments were conducted to compare iron precipitation under completely ferruginous conditions with solutions that contain a low amount of oxidized iron, which can be seen as a proxy for iron oxidation in the environment. and Some XRD files are from a copper source (Cu_XRD) and others are from a cobalt source (Co_XRD).
- Keyword:
- Iron silicates, Greenalite, and Archean
- Citation to related publication:
- Isaac L. Hinz, Christine Nims, Samantha Theuer, Alexis S. Templeton, Jena E. Johnson; Ferric iron triggers greenalite formation in simulated Archean seawater. Geology 2021; doi: https://doi.org/10.1130/G48495.1
- Discipline:
- Science
-
- Creator:
- Surajit Chatterjee, Adrien Chauvier, Shiba S. Dandpat, Irina Artsimovitch, and Nils G. Walter
- Description:
- These data were generated to study the dynamics of RNAP-ribosome interactions on a nascent mRNA with a preQ1-sensing translational riboswitch in its 5’ untranslated region (UTR). Using single-molecule fluorescence co-localization, we monitored direct transient binding of 30S ribosomal subunit to the individual nascent mRNA molecules in surface-immobilized paused elongation complexes (PECs). Also, using a novel protein-induced fluorescence enhancement assay we monitored the real-time transcription rate of RNA polymerase (RNAP) under different experimental conditions. The DNA template including the preQ1 riboswitch from B. anthracis under the control of the T7A1 promoter was cloned into pUC19 plasmid. Transcription templates for in vitro transcription were generated by PCR.
- Citation to related publication:
- Chatterjee, S., Chauvier, A., Dandpat, S.S., Artsimovitch, I., & Walter, N.G. (2021). A translational riboswitch coordinates nascent transcription-translation coupling. Proc. Natl. Acad. Sci., 118 (16), e2023426118; DOI: 10.1073/pnas.2023426118
- Discipline:
- Science
-
- Creator:
- Saylor, Kate M., King, Wesley M., and Gamarel, Kristi E.
- Description:
- The search data supports a literature review project on Firearm violence among LGBTQ+ communities. The data included in the dataset are the reproducible search strategies (txt file) and the exported results of all citations from all databases (txt, ris, and.nbib files). These searches and exported result files contain all citations originating from the database searches that were considered for inclusion.
- Keyword:
- LGBTQ, Transgender, Firearms
- Discipline:
- Health Sciences
-
- Creator:
- Arthurs, Christopher J., Khlebnikov, Rostislav, Melville, Alexander, Marčan, Marija, Gomez, Alberto, Dillon-Murphy, Desmond, Cuomo, Federica, Vieira, Miguel, Schollenberger, Jonas, Lynch, Sabrina, Tossas-Betancourt, Christopher, Iyer, Kritika, Hopper, Sara, Livingston, Elizabeth, Youssefi, Pouya, Noorani, Alia, Ben Ahmed, Sabrina, Nauta, Foeke J.N., van Bakel, Theodorus M.J., Ahmed, Yunus, van Bakel, Petrus A.J., Mynard, Jonathan, Di Achille, Paolo, Gharahi, Hamid, Lau, Kevin D., Filonova, Vasilina, Aguirre, Miquel, Nama, Nitesh, Xiao, Nan, Baek, Seungik, Garikipati, Krishna, Sahni, Onkar, Nordsletten, David, and Figueroa, Carlos A.
- Description:
- This repository includes the following:, - Example Case A: complete process of creating a model, running the simulation and examining the results., - Example Case B: segmenting and imposing a patient-specific aortic inflow velocity profile from a provide PC-MRI dataset., - Example Case C: simulation of a patient under rest conditions, and then of the same patient under post-liver-transplant conditions., - GUI Windows Binary Executable (version 2019.11.01), and - Flow Solver Windows Binary Executable (version 1.4.4, 2019.11.01)
- Keyword:
- Blood Flow Simulation, Patient-specific, Open-source Software, Image-based simulation, Cardiovascular Medical Image, Segmentation, and Finite Element Simulation
- Citation to related publication:
- CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation C.J. Arthurs, R. Khlebnikov, A. Melville, M. Marčan, A. Gomez, D. Dillon-Murphy, F. Cuomo, M.S. Vieira, J. Schollenberger, S.R. Lynch, C. Tossas-Betancourt, K. Iyer, S. Hopper, E. Livingston, P. Youssefi, A. Noorani, S. Ben Ahmed, F.J.H. Nauta, T.M.J. van Bakel, Y. Ahmed, P.A.J. van Bakel, J. Mynard, P. Di Achille, H. Gharahi, K. D. Lau, V. Filonova, M. Aguirre, N. Nama, N. Xiao, S. Baek, K. Garikipati, O. Sahni, D. Nordsletten, C.A. Figueroa bioRxiv 2020.10.14.339960; doi: https://doi.org/10.1101/2020.10.14.339960
- Discipline:
- Engineering and Health Sciences
-
- Creator:
- Majeed, Tariq
- Description:
- We use our 1-D chemical diffusive model to quantify the physical processes necessary to interpret the day-side ionospheric measurements acquired with radio occultation techniques at the southern high-latitude region of Mars, where the crustal magnetic field is strong and near-vertical in orientation. To interpret the measured ionospheric structure at altitudes where plasma transport dominates, we find it is necessary to impose field-aligned vertical plasma drifts caused by the motion of neutral winds. The most interesting finding of this study is that both upward (between 110 m/s and 150 m/s) and downward (between -55 m/s and -120 m/s) drifts are required to maintain the topside Ne distribution comparable with the measured distribution. We also find that a fixed velocity boundary condition at the upper boundary with a sizeable upward ion velocity is needed to encounter any unexpected ion accumulation in the topside ionosphere to limit the Martian ion outflow. Given the complex nature of neutral dynamics and its relationship to plasma transport processes over magnetic anomalies, we consider that a simple model, such as we have developed, is still capable of yielding valuable insights relating to the neutral wind system at Mars.
- Keyword:
- Ionosphere of Mars
- Discipline:
- Science
-
- Creator:
- Amir Salaree
- Description:
- We carry out a set of exploratory numerical experiments based on ocean bottom pressure and seismic data from a simulated linear array of SMART (Scientific Monitoring And Reliable Telecommunication) cable stations off the trench in the Sumatra-Java region. We use a set of earthquake rupture as well as submarine landslide scenarios to calculate tsunami propagation via hydrodynamic simulations. We also investigate the contribution of SMART stations to improvement of earthquake early warning by calculating the arrival times of seismic phases. Existing telecom cables can also contribute to the SMART network, if they are equipped with scientific sensors and repeaters. In this study we use the MOST (Method of Splitting Tsunami; Titov et al, 2016) to simulate tsunamis, and the TauP toolkit (Crotwell et al, 1999) to calculate seismic arrival times. This study was supported by grants from National Science Foundation (PREEVENTS geosciences directorate No. 1663769) and NASA JPL (Award NNN13D462T). - Crotwell, H.P., Owens, T.J. and Ritsema, J., 1999. The TauP Toolkit: Flexible seismic travel-time and ray-path utilities. Seismological Research Letters, 70(2), pp.154-160. Titov, V., Kânoğlu, U. and Synolakis, C.E., 2016, Development of MOST for real-time tsunami forecasting. J Waterw Port Coast Ocean Eng 142:03116004-1–03116004-16
- Keyword:
- SMART Cables, Tsunami, Earthquake, Landslide, Early Warning, Indian Ocean, Indonesia, Sumatra, Java, and Simulation
- Discipline:
- Science
-
- Creator:
- Mohtat, Peyman, Siegel, Jason B., Stefanopoulou, Anna G., and Lee, Suhak
- Description:
- The focus of this research effort is to systematically study the capability of aging diagnostics using cell expansion under variety of aging conditions and states. The data collection campaign is very important to cover various degradation modes to extract the degradation features that will be used to inform, parameterize, and validate the models developed earlier. In the data collection campaign, we are documenting the evolution of the electrical and mechanical characteristics and especially the reversible mechanical measurement. It is important to note that we collect data using newly developed fixtures that enables the simultaneous measurement of mechanical and electrical response under pseudo-constant pressure.
- Keyword:
- Lithium-ion batteries, Mechanical response, Aging, NMC, and Pouch cells
- Citation to related publication:
- Peyman Mohtat et al. (2021). Reversible and Irreversible Expansion of Lithium-ion Batteries Under a Wide Range of Stress Factors. J. Electrochem. Soc. 168 100520 https://doi.org/10.1149/1945-7111/ac2d3e
- Discipline:
- Engineering
-
- Creator:
- Mosley, Jennifer and Park, Sunggeun
- Description:
- This data set is comprised of publicly available data from three HUD websites and the 2014 National Continuum of Care (CoC) Survey questionnaire and protocol. The HUD data sets are comprised of Community Planning and Development (CPD) Awards information from 2005-2014, Demographic information on areas served by CoC sites (sub-region estimates from the 2006-2010 American Community Survey), and Housing Inventory Count (HIC) and Point-in-Time (PIT) counts per CoC from 2015-2007. The data are associated with the article "Service Providers' Influence in Collaborative Governance Networks: Effectiveness in Reducing Chronic Homelessness" conditionally accepted for publication in the Journal of Public Administration Research and Theory (JPART).
- Discipline:
- Social Sciences
-
Geotechnical observations of weathered rock across a tectonic and climatic gradient in Central Nepal
- Creator:
- Medwedeff, William, G (University of Michigan Earth & Environmental Science), Clark, Marin, K (University of Michigan Earth & Environmental Science), Zekkos, Dimitrios (University of California, Berkeley), West, A., Joshua (University of Southern California), and Chamlagain, Deepak (Tribhuvan University, Kathmandu Nepal)
- Description:
- These datasets support the findings of Medwedeff et al. (2021) in JGR: Earth Surface. In this article, we present seismic and geotechnical characterizations of the shallow subsurface across a 200 km by 50 km swath of the central Himalayan Range, in Nepal. By pairing widely-distributed 1D shear wave velocity surveys and engineering outcrop descriptions per the Geological Strength Index classification system, we evaluate landscape-scale patterns in near-surface mechanical characteristics and their relation to environmental factors known to affect rock strength. We find that near-surface strength is more dependent on the degree of weathering, rather than the mineral and textural differences between the metamorphic lithologies found in the central Himalaya. Furthermore, weathering varies systematically with topography. Bedrock ridge top sites are highly weathered and have S-wave seismic velocities and shear strength characteristics that are more typical of engineering soils, whereas sites near the bedrock channel bottom tend to be less weathered and characterized by high S-wave velocities and shear strength estimates typical of hard rock. Weathering of bedrock on hillslopes is significantly more variable, resulting in S-wave velocities that range between the ridge and channel endmembers. We hypothesize variability in the hillslope environment may be partly explained by the stochastic nature of mass wasting, which clears away weathered material where landslide scars are recent. These results underscore the mechanical heterogeneity in the shallow subsurface and highlight the need to account for bedrock weathering when estimating strength parameters for regional landslide hazard analysis.
- Keyword:
- rock strength, critical zone, shallow seismic, and chemical weathering
- Discipline:
- Science
-
- Creator:
- Saylor, Kate M., McCormick, Amanda D., Wilde, Megan M., Charpie, Christine E., Yu, Sunkyung, and Cousino, Melissa K.
- Description:
- The search data supports a literature review project on Psychological Functioning in Pediatric Patients with Single Ventricle Congenital Heart Disease. The data included are the reproducible search strategies (txt file) and the exported results of all citations from all databases (txt, ris, and.nbib files). Both the original search files and updated search files have been included in the deposit.
- Keyword:
- pediatrics, univent, Single Ventricle Congenital Heart Disease, and psychological
- Discipline:
- Health Sciences
-
Neotropical Snake Photo and Video Data
User Collection- Creator:
- University of Michigan, Division of Herpetology, Davis Rabosky, Alison R, Moore, Talia Y., Larson, Joanna G., Curlis, John David, Westeen, Erin P., Sealey, Briana A., and Balinski, Bailey A.
- Description:
- All animal-related procedures were approved by the University of Michigan Institutional Animal Care and Use Committee (Protocols #PRO00006234 and #PRO00008306) and the Peruvian government SERFOR (Servicio Nacional Forestal y de Fauna Silvestre. and Data were collected during five field expeditions in the Amazonian lowlands of Peru from March 2016 to December 2018.
- Keyword:
- snake behavior, coral snake mimicry, serpentes, Peruvian Amazon, and Elapidae
- Discipline:
- Science
3Works -
- Creator:
- Brang, David and Karthik, Ganesan
- Description:
- Data were acquired from 21 patients with intractable epilepsy undergoing clinical evaluation using iEEG. Patients ranged in age from 15-58 years (mean = 37.1, SD = 12.8) and included 10 females. Across all patients, data was recorded from a total of 1367 electrodes. Each participant were presented with multiple trials of auditory only and congruent audio-visual stimuli. On each trial a single phoneme was presented to the participant. Three variants of the tasks were used with each variant consisting of a different set of phonemes (variant A: /ba/ /da/ /ta/ /tha/, variant B: /ba/ /da/ /ga/, variant C: /ba/ /ga/ /ka/ /pa/). Trials were presented in a random order and phonemes were distributed uniformly across conditions. While conditions were matched in terms of trial numbers, participants completed a variable number of trials (based on task variant and the number of blocks completed). All provided data has been resampled to 1024 Hz during initial stages of processing for all participants. Data has been referenced in a bipolar fashion (signals subtracted from each immediately adjacent electrode in a pairwise manner) to ensure that the observed signals were derived from maximally local neuronal populations. The preprocessing steps followed have been described in the detailed description document in the attached materials. and The dataset zip folder consists of three main sub-folders: 1) Electrodes: This folder provides details regarding the individual electrodes for each subject, their MNI coordinates as well as their MNI vertices information according to freesurfer parcellations. This folder also consists of images of the physical location of each of the electrode sets. 2) Processed: This folder contains preprocessed data in all three frequencies (theta, beta and high gamma power) for individual subjects and the corresponding vertex locations for each of the electrodes from which their data was recorded. The images subfolder also contains figures provided in the main manuscript. 3) MatlabCodes: This folder contains all the matlab scripts required to reproduce the results provided in the main manuscript. LME_AvsAV_Main_Windows.m is the main file that an user has to run to reproduce the results.
- Keyword:
- Cognitive Neuroscience, Neuroscience, Perception, and Mixed Effects Models
- Citation to related publication:
- Ganesan, K., Plass, J., Beltz, A. M., Liu, Z., Grabowecky, M., Suzuki, S., ... & Brang, D. (2020). Visual speech differentially modulates beta, theta, and high gamma bands in auditory cortex. bioRxiv. https://doi.org/10.1101/2020.09.07.284455
- Discipline:
- Science
-
- Creator:
- Pasquinelli, Rennie, Hu, Xiaosu, Tessier, Anne-Michelle, Kovelman, Ioulia, Zwolan, Terry A., Karas, Zachary E., and Wagley, Neelima
- Description:
- This data is from a project examining prosodic processing in children and adults using functional near-infrared spectroscopy (fNIRS) neuroimaging. fNIRS data is optical data collected using a cap with an array of source and detector fibers that emit and detect infrared light, respectively. We used fNIRS neuroimaging to explore prosodic processing, rhyme judgement, and the "oddball" paradigm in children, adults, and a small sample of children with cochlear implants. Matlab scripts, including Ted Huppert's Nirs Toolbox, were used to process the neuroimaging data. The children also took a battery of behavioral assessments (OWLS, Digit Span, PPVT, CTOPP).
- Keyword:
- Prosodic Processing, fNIRS neuroimaging, Development, Cochlear Implants, and Rhyming
- Discipline:
- Science
-
- Creator:
- Sun, Xin, Zhang, Kehui, Marks, Rebecca, Karas, Zachary, Eggleston, Rachel, Nickerson, Nia, Yu, Chi-Lin, Wagley, Neelima, Hu, Xiaosu, Caruso, Valeria, Tardif, Twila, Satterfield, Teresa, Chou, Tai-Li, and Kovelman, Ioulia
- Description:
- In a broad sense, this dataset explores morphological and phonological processing in English monolinguals and two bilingual populations, Chinese-English and Spanish-English, using a battery of standardized and self-developed behavioral measures, as well as fNIRS neuroimaging.
- Citation to related publication:
- Sun X, Zhang K, Marks R, Karas Z, Eggleston R, Nickerson N, Yu CL, Wagley N, Hu X, Caruso V, Chou TL, Satterfield T, Tardif T, Kovelman I. Morphological and phonological processing in English monolingual, Chinese-English bilingual, and Spanish-English bilingual children: An fNIRS neuroimaging dataset. Data Brief. 2022 Mar 12;42:108048. doi: 10.1016/j.dib.2022.108048. PMID: 35313503; PMCID: PMC8933821.
- Discipline:
- Science
-
- Creator:
- Shi, Xuetao, Elvati, Paolo, and Violi, Angela
- Description:
- Non-thermal plasma systems offer unique opportunities in the fields of bio-imaging, drug delivery, photovoltaics, microelectronics manufacturing. Such interests are largely inspired by the fact that hot plasma electrons coexist with neutral species and ions close to room-temperature under non-thermal plasma conditions. Modeling of these systems requires a deep understanding of the atomistic processes underlying the rich chemistry of the various radicals and ions with the nascent nanoparticle surface. A key parameter for determining the contribution of a certain radical/ion species to the nanoparticle surface growth, called sticking coefficient, is computed as a weighted sum from the simulated sticking outcomes with different collision velocities drawn from a Maxwell-Boltzmann distribution at certain temperatures. In this work, the collisions of SiHx (x=1-4) fragments and silicon cluster (Si4, Si2H6, and Si29H36) surfaces, responsible for the sticking coefficients, are simulated by molecular dynamics (MD) with a reactive force field. The dependence of sticking coefficients on temperature, H coverage of both silane fragments and cluster surfaces, and the size of the cluster, are systematically examined. And the mechanism underlying the sticking events, specifically the conversion of physical aggregation to chemisorption is investigated to better understand the complex interplay between factors influencing the surface growth. The detailed and multi-parameter model of sticking coefficients, accompanied by the mechanism study of physisorption to chemisorption conversion, provides a more accurate and robust approximation of surface growth rate using sticking coefficients, and a deeper understanding of surface growth processes, for the wider non-thermal plasma simulation community.
- Keyword:
- Sticking coefficients, Silanes, Molecular Dynamics, Non-equilibrium, and Aggregation mechanisms
- Citation to related publication:
- Shi, X., Elvati, P., Violi, A. (2021). On the growth of Si nanoparticles in non-thermal plasma: physisorption to chemisorption conversion. J. Phys. D. Submitted.
- Discipline:
- Science
-
- Creator:
- Sergio E. Vidal-Luengo
- Description:
- This database contains spacecraft and ground-based magnetic field observations made to study the propagation of the preliminary impulse triggered by interplanetary shocks with different inclinations in the XZ plane.
- Keyword:
- Cluster, Dynamic pressure pulse, THEMIS, SuperMag, Magnetosphere, MMS, and Intermagnet
- Citation to related publication:
- (to be submitted) Vidal-Luengo, S. E., Moldwin, M. B. (2021). Shock Inclination Effects in Preliminary Impulse Propagation Observed by Ground-Based Magnetometers and the Heliophysics System Observatory
- Discipline:
- Science
-
- Creator:
- Herrick, Etienne M
- Description:
- This data was produced as part of field experiment investigating the extent, drivers, and consequences of functional trait variation in cover crops. Specifically, we studied the role of intraspecific trait variation in explaining interactions between species in cover crop mixtures, and whether and how intraspecific trait variation improves understanding of relationships between functional traits and ecosystem services from cover crops.
- Keyword:
- agroecology, cover crops, functional diversity, functional traits, intraspecific trait variation, ecosystem services, nitrogen, species interactions, and student-friendly
- Citation to related publication:
- Herrick, E., and Blesh, J. (2021) Intraspecific trait variation improves understanding and management of cover crop outcomes. Ecosphere.
- Discipline:
- Science
-
- Creator:
- MacEachern, Mark P; Sun, Gordon H; Chen, Stephanie W; Wang, Jing
- Description:
- The dataset includes all citations considered for inclusion in the systematic review. The citations are accessible in Endnote (Clarivate), as well as through the primary citation export files from each database. The literature search strategies are included for reproducibility and transparency purposes. See the published methods for more information.
- Keyword:
- Tracheostomy, Decannulation, Spinal Cord Injury, Scoping Review, and Literature Searches
- Citation to related publication:
- Gordon H. Sun, Stephanie W. Chen, Mark P. MacEachern & Jing Wang (2020) Successful decannulation of patients with traumatic spinal cord injury: A scoping review, The Journal of Spinal Cord Medicine, DOI: 10.1080/10790268.2020.1832397
- Discipline:
- Health Sciences
-
- Creator:
- Gliske, Stephen V and Stacey, William C
- Description:
- This data repository includes the quantitative features of high frequency, intracranial EEG along with all necessary scripts to reproduce the figures of the accompanying manuscript.
- Keyword:
- high frequency oscillation, HFO, high frequency activity, and epilepsy
- Citation to related publication:
- (under review)
- Discipline:
- Science, Engineering, and Health Sciences
-
- Creator:
- Umaña, María Natalia, Zambrano, Jenny, Weemstra, Monique, and Allen, Dave
- Description:
- The objective of this research was to improve our understanding of tree growth from underlying variation in leaf and root functional traits. This knowledge ultimately enhances our knowledge of the above- and belowground processes that are involved in structuring forest communities. To this end, we determine which, how and to what degree (combinations of) leaf and root traits influence growth rates across ten temperate tree species along a soil carbon (C) and N gradient growing at the Big Woods plot at the E.S. George Reserve, Pickney, MI. This plot is part of the Smithsonian Institution's Forest Global Earth Observatory (ForestGEO) global network of forest research sites. https://forestgeo.si.edu/ and This dataset contains data on the leaf and root traits of several individuals from tree species, as well as on the soil properties at the Big Woods plots at the E.S. George Reserve, Pickney, MI. Data were collected in June 2019, and used to explain and predict the growth rates of the trees at Big Woods. [Growth data were obtained from Allen et al., 2019, https://doi.org/10.7302/wx55-kt18]. Each file contains data on leaf traits, root traits, and soil properties. Trait data are presented per individual tree for each of the 10 study species. Soil data are represented per soil sample, with four soil samples collected per subplot throughout the Big Woods plot (see legend, and publication for explanation). Descriptions and units per variable/column are provided in the legend tab in each file.
- Keyword:
- ecology, forests, Michigan, ForestGEO, Big Woods, Roots, Leaves, Tree growth, and Forest soils
- Citation to related publication:
- M. Weemstra, J. Zambrano, D. Allen, MN Umaña. (In press) Tree growth increases through opposing above- and belowground resource strategies. Journal of Ecology. https://doi.org/10.1111/1365-2745.13729
- Discipline:
- Science
-
- Creator:
- Yuan, Ye, Currie, William S., Sharp, Sean J. , Martina, Jason P. , and Elgersma, Kenneth J.
- Description:
- This archived dataset includes all of the input files that were used to run the model for all the runs in this set, including files containing model parameters and drivers. This dataset also includes all of the model output files from model runs in this set.
- Keyword:
- wetland, Great Lakes, greenhouse gas, climate change, and ecosystem model
- Citation to related publication:
- Yuan, Y., S. J. Sharp, J. P. Martina, K. J. Elgersma, and W. S. Currie. Sustained-flux global warming potential driven by nitrogen inflow and hydroperiod in a model of Great Lakes coastal wetlands. JGR Biogeosciences in review.
- Discipline:
- Science
-
- Creator:
- Vo, Thi and Glotzer, Sharon C.
- Description:
- The goal of this project is to develop a first principle driven approach for predicting the self-assembly behavior of entropically driven crystallization. We first developed a set of mean-field theoretical framework that captures the relevant energetic contributions to the assembly process and then evaluate relevant terms within our framework to determine the excess free energy of formation for each lattice (matlab/octave codes). We then validate theoretical predictions of relevant features like shape and bonding orbitals using standard MD simulations using HOOMD-Blue (simulation scripts). and This research was supported by the Office of the Undersecretary of Defense for Research and Engineering (OUSD(R&E)), Newton Award for Transformative Ideas during the COVID-19 Pandemic, Award number HQ00342010030.
- Keyword:
- Self-Assembly, Entropy, Thermodynamics, Simulations, and Theory
- Citation to related publication:
- Vo, T., & Glotzer, S. C. (2021). Microscopic Theory of Entropic Bonding for Colloidal Crystal Prediction. ArXiv:2107.02081 [Cond-Mat]. http://arxiv.org/abs/2107.02081
- Discipline:
- Science
-
- Creator:
- Weng, Andrew, Mohtat, Peyman, Attia, Peter, Less, Greg, Lee, Suhak, and Stefanopoulou, Anna
- Description:
- The goal of this research is to investigate the impact of fast formation protocol on battery lifetime. The dataset has also been used to explore data-driven approaches in battery lifetime estimation (manuscript under review). Source code used to generate the results for this work has been included. The file contents contain a detailed README.md file which describes the organization of the files.
- Citation to related publication:
- Weng et al., Predicting the impact of formation protocols on battery lifetime immediately after manufacturing, Joule (2021), https://doi.org/10.1016/j.joule.2021.09.015
- Discipline:
- Engineering