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- 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
- Title:
- Mars Dayside Closed Crustal Field Electron Pitch Angle Distributions Data and Ephemeris Info
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- 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
- Discipline:
- Health Sciences and Engineering
- Title:
- CRIMSON open source project - Flow Solver Source Code for PLOS Computational Biology
-
- 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 well as three applications examples 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/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
- Discipline:
- Health Sciences and Engineering
- Title:
- CRIMSON open source project - Graphical User Interface (GUI) Source Code and Application Examples for PLOS Computational Biology
-
- 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
- Title:
- Pere language lexical datasheets and audio files
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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
- Discipline:
- Science
- Title:
- Profiles of near-surface rock mass strength across gradients in erosion, burial, and time [Data set]
-
- Creator:
- McCuen, Brett A.
- Description:
- This data are TIC 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, TIC, and dB/dt search algorithm
- Discipline:
- Science
- Title:
- 2015 Transient Induced Current (TIC) Events
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- 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., et al. (2020). Global Magnetohydrodynamic Simulations: Performance Quantification of Magnetopause Distances and Convection Potential Predictions. Forthcoming.
- Discipline:
- Engineering and Science
- Title:
- Dataset Containing Global Modeling Results Comparing Magnetopause Distances and CPCP
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- 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:
- Kaihua, Zhang (2020) "Development and Experimental Validation of Dynamic Bayesian Networks for System Reliability Prediction" Doctoral Dissertation, University of Michigan. Deep Blue. http://hdl.handle.net/2027.42/155231, "Evaluating Crack Growth Prediction in Structural Systems with Dynamic Bayesian Networks", submitted to Computers and Structure, and "Experimental Investigation of Structural System Capacity with Multiple Fatigue Cracks", submitted to Marine Structures
- Discipline:
- Engineering
- Title:
- Dataset for thesis "Development and Experimental Validation of Dynamic Bayesian Networks for System Reliability Prediction"
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- 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
- Title:
- Analyzing Reviewer Responses to Systematic Review Search Methodology through Open Peer Review
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- 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
- Discipline:
- Science
- Title:
- Application of the Monte Carlo method in modeling dusty gas, dust in plasma, and energetic ions in planetary and magnetospheric applications
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- 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
- Title:
- CT Data of UMMP VP 81820, Cantius mckennai right medial cuneiform (entocuneiform)
-
- 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
- Title:
- CT Data of UMMP VP 81831, Cantius mckennai right navicular
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- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right astragalar [astragalus] body of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81827), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
- Title:
- CT Data of UMMP VP 81827, Cantius mckennai right astragalar body
-
- 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
- Title:
- CT Data of UMMP VP 81825, Cantius mckennai right calcaneum
-
- 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
- Title:
- CT Data of UMMP VP 81823, Cantius mckennai right cuboid
-
- 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
- Title:
- CT Data of UMMP VP 81822, Cantius trigonodus right proximal metatarsal 1
-
- 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
- Title:
- Connecting Concepts in the Brain by Mapping Cortical Representations of Semantic Relations
-
- 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
- Title:
- CT Data of UMMP VP 81821, Cantius mckennai right distal tibia
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- 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. 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). 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. Detailed documentation of how the data is generated can be found in: https://afcoe.engin.umich.edu/benchmark-data
- Citation to related publication:
- Huang, C., Duraisamy, K., and Merkle, C.L., Investigations and Improvement of Robustness of Reduced-Order Models of Reacting Flow, AIAA Journal, 2019., Swischuk, R., Kramer, B., Huang, C., and Willcox, K., Learning Physics-Based Reduced-Order Models for a Single-Injector Combustion Process , AIAA Journal, 2020., and Harvazinski, M.E., Huang, C., Sankaran, V., Feldman, T.W., Anderson, W.E., Merkle, C.L., and Talley, D.G., Coupling between hydrodynamics, acoustics, and heat release in a self-excited unstable combustor, Physics of Fluids, 2015.
- Discipline:
- Engineering
- Title:
- [Updated] 2D Benchmark Reacting Flow Dataset for Reduced Order Modeling Exploration
-
- 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
- Title:
- .stl file of Circle of Willis Benchmark geometric model for hemodynamic simulation software
-
- 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., S. W. Bougher, D. Shields, and H. Liu, Planetary-scale Wave Impacts on the Venusian Upper Mesosphere and Lower Thermosphere, Icarus, in review, (2020). doi:...
- Discipline:
- Science
- Title:
- Planetary-scale Wave Impacts on the Venusian Upper Mesosphere and Lower Thermosphere: Supporting Datasets for VTGCM Numerical Simulations
-
- 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:
- 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. PLoS Comput Biol. 2020 (under review) 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
- Title:
- Dataset for calculating lattice vectors (and anisotropy) of zebrafish cone mosaic
-
- 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:
- 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. PLoS Comput Biol. 2020 (under review), 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, and 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.
- Discipline:
- Science
- Title:
- Code and accompanying input data for simulating lateral inhibition on motionless cell packing
-
- 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, radiative transfer
- Citation to related publication:
- Flanner, M. G., A. S. Gardner,S. Eckhardt, A. Stohl, and J. Perket(2014), Aerosol radiative forcing fromthe 2010 Eyjafjallajökull volcaniceruptions,J. Geophys. Res.Atmos.,119, 9481–9491,doi:10.1002/2014JD021977
- Discipline:
- Science
- Title:
- Supplementary Particle Optical Property Data for "Aerosol radiative forcing from the 2010 Eyjafjallajökull volcanic eruptions"
-
- 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:
- 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 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 PLoS Comput Biol. 2020 (under review)
- Discipline:
- Science
- Title:
- Code and example simulations of phase-field crystal model (for cone mosaic formation)
-
- 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:
- 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. PLoS Comput Biol. 2020 (under review) 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
- Title:
- Dataset for measuring tendency of Y-junctions to line up into grain boundaries during incorporation into retinae
-
- 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:
- 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. PLoS Comput Biol. 2020 (under review) 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
- Title:
- Dataset for analyzing Y-junction motion in live fish retinae
-
- 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:
- 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 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. PLoS Comput Biol. 2020 (under review)
- Discipline:
- Science
- Title:
- Set of images for Figures 1 and 2 and 6 and Supplementary Figure 7
-
- 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 is composed of eight flat-mounted (dissected and fixed) retinae from juvenile and adult zebrafish. Rows of UV cones have been traced in each retina; additionally, we have identified locations of Y-junctions (row insertions). Also included is MATLAB code for calculating which Y-junctions belong to grain boundaries. Please see the readme file for a description of included codes and image files.
- Keyword:
- zebrafish cone mosaic, topological defects, tissue patterning, and grain boundaries
- Citation to related publication:
- 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 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. PLoS Comput Biol. 2020 (under review)
- Discipline:
- Science
- Title:
- Dataset for analyzing spatial distribution of Y-junctions in flat-mounted retinae
-
- Creator:
- Brandt, Daniel, A., Bussy-Virat, Charles, D., and Ridley, Aaron, J.
- Description:
- The Multifaceted Optimization Algorithm (MOA) is a tool for generating corrected empirical model thermospheric densities during geomagnetic storms. It consists of a suite of Python functions that operate around the Spacecraft Orbit Characterization Kit (SpOCK), an orbital propagator developed by Charles D. Bussy-Virat, PhD, Joel Getchius, and Aaron J. Ridley, PhD at the University of Michigan, and it estimates new densities for the NRLMSISE-00 atmospheric model. MOA generates new model densities by estimating modifications to inputs to the NLRMSISE-00 model that minimize the orbit error between modeled spacecraft in SpOCK, and their actual altitudes as described in publicly-available Two-Line Element Sets (TLEs), made available online via Space-track.org. MOA consists of three sub-process: (1) The Area Optimization Algorithm (AROPT), (2) the F10.7 Optimization Algorithm (FOPT), and (3) the Ap Optimization Algorithm (APOPT). AROPT computes the contribution to the drag of the modeled spacecraft due to their varying projected area. FOPT estimates modifications to the 10.7 cm solar radio flux in NRLMSISE-00, and APOPT estimates modifications to the Earth's magnetic activity in NRLMSISE-00. MOA finds these modifications across many spacecraft, and the medians of those modifications are then applied in NLRMSISE-00 along the orbit of another satellite to generate new densities for verification. In this instance, modifications are applied along the orbits of the Swarm spacecraft and compared to Swarm GPS-derived densities.
- Keyword:
- Orbit, Satellite, Two-line Element Set, Thermosphere, and Drag
- Discipline:
- Engineering
- Title:
- A Simple Method for Correcting Empirical Model Densities during Geomagnetic Storms Using Satellite Orbit Data
-
- Creator:
- Attari, Ali
- Description:
- Please refer to the "README.txt" for more details., MATLAB R2018a (Mathworks, Natick, MA, USA) was used to process this data., and Excel (Microsoft Office) was used to store survey data on the comfort of both systems and also to provide absolute and relative intraobserver variablities for the DM device.
- Keyword:
- Digital Manometry
- Citation to related publication:
- Comparison of anorectal function measured using wearable digital manometry and a high resolution manometry system Attari A, Chey WD, Baker JR, Ashton-Miller JA (2020) Comparison of anorectal function measured using wearable digital manometry and a high resolution manometry system. PLOS ONE 15(9): e0228761. https://doi.org/10.1371/journal.pone.0228761
- Discipline:
- Engineering, Science, and Health Sciences
- Title:
- Data for "Comparison of Anorectal Function Measured using Wearable Digital Manometry and a High Resolution Manometry System." article (PLOS ONE) PONE-D-20-01826R1
-
- Creator:
- Li, Jieming, Zhang, Leyou, Johnson-Buck, Alexander, and Walter, Nils G.
- Description:
- Traces from single-molecule fluorescence microscopy (SMFM) experiments exhibit photophysical artifacts that typically necessitate human expert screening, which is time-consuming and introduces potential for user-dependent expectation bias. Here, we have used deep learning to develop a rapid, automatic SMFM trace selector, termed AutoSiM, that improves the sensitivity and specificity of an assay for a DNA point mutation based on single-molecule recognition through equilibrium Poisson sampling (SiMREPS). The improved performance of AutoSiM is based on accepting both more true positives and fewer false positives than the conventional approach of hidden Markov modeling (HMM) followed by thresholding. As a second application, the selector was used for automated screening of single-molecule Förster resonance energy transfer (smFRET) data to identify high-quality traces for further analysis, and achieves ~90% concordance with manual selection while requiring less processing time. AutoSiM can be adapted readily to novel datasets, requiring only modest Transfer Learning.
- Keyword:
- deep learning, single-molecule fluorescence, total internal reflection microscopy, SiMREPS, smFRET, and Forster resonance energy transfer
- Citation to related publication:
- Jieming Li, Leyou Zhang, Alexander Johnson-Buck, Nils G. Walter. (2020) Automatic classification and segmentation of single-molecule fluorescence time traces with deep learning. Nature Communications, In Press. and Hayward, S., Lund, P., Kang, Q., Johnson-Buck, A., Tewari, M., Walter, N. (2018). Single-molecule microscopy image data and analysis files for "Ultra-specific and Amplification-free Quantification of Mutant DNA by Single-molecule Kinetic Fingerprinting" [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/Z2CZ35DF
- Discipline:
- Science
- Title:
- AutoSiM software and sample single-molecule trace data accompanying "Automatic classification and segmentation of single-molecule fluorescence time traces with deep learning"
-
- Creator:
- Zhang, Yan, Fujian Normal University, Yang, Ping, Fujian Normal University, Tong, Chuan, Fujian Normal University, Zhang, Xinyan, Chinese Academy of Sciences, Changchun, Liu, Xingtu, Chinese Academy of Sciences, Changchun, Zhang, Shaoqing, Chinese Academy of Sciences, Changchun, Meyers, Philip. University of Michigan, and Gao, Chuanyu , Chinese Academy of Sciences, Changchun
- Description:
- A high-resolution study of bulk properties in a peat sequence from the Xinjiang Altai Mountains of northwestern China, has allowed reconstruction of local variations in peat properties and peat C and N accumulation rates (CAR and NAR) during the Holocene. Analyses of peat bulk density, loss on ignition, and concentrations of TOC and TN and their elemental ratios and stable isotopic values suggest that changes in peat-forming vegetation types during different parts of this epoch are the major factors responsible for the variations of peat properties in this sequence.
- Keyword:
- peat properties, stable carbon and nitrogen isotopes, carbon and nitrogen accumulation rates, and Altai Mountains of northwestern China
- Citation to related publication:
- Peat properties and Holocene carbon and nitrogen accumulation rates in a peatland in the Xinjiang Altai Mountains, northwestern China
- Discipline:
- Science
- Title:
- Dataset from analysis of a peat core from the Tielishahan peatland in the Xinjiang Altai Mountains, northwestern China
-
- Creator:
- Light, Charles X, Arbic, Brian K, Martin, Paige E, Brodeau, Laurent, Farrar, J Thomas, Griffies, Stephen M, Kirtman, Ben P, Laurindo, Lucas, Menemenlis, Dimitris, Molod, Andrea, Nelson, Arin D, Nyadjiro, Ebenezer, O'Rourke, Amanda K, Shriver, Jay, Siqueira, Leo, Small, R Justin, and Strobach, Udi
- Description:
- The precipitation data itself is the output of the models/datasets that we analyze in our paper. Most of it is in .nc or .nc4 format, although we provide code to extract the data into time series .mat files. We used MATLAB to perform our analysis.
- Keyword:
- precipitation and power spectra
- Discipline:
- Science
- Title:
- High-frequency precipitation variance in high-resolution global coupled ocean-atmosphere models: Precipitation data and analysis code
-
- Creator:
- Sean Sharp
- Description:
- Coastal wetlands intercept significant amounts of nitrogen (N) from watersheds, especially when surrounding land cover is dominated by agriculture and urban development. Through plant uptake, soil immobilization, and denitrification wetlands can remove excess N from flow through water sources and mitigate eutrophication of connected aquatic ecosystems. Excess N can also change plant community composition in wetlands, including communities threatened by invasive species. Understanding how variable hydrology and N loading impact wetland N removal and community composition can help attain desired management outcomes, including optimizing N removal and/or preventing invasion by non-natives. By using a dynamic, process-based ecosystem simulation model, we are able to simulate various levels of hydrology and N loading that would otherwise be difficult to manipulate. We investigate the effects of hydroperiod, hydrologic residence time, N loading, and the NH4+:NO3- ratio on both N removal and the invasion success of two non-native species (Typha x glauca or Phragmites australis) in temperate freshwater coastal wetlands using Mondrian, a process-based, wetland ecosystem simulation model. We found that when residence time increased, annual N removal increased up to 10-fold while longer hydroperiods also increased N removal, but only when residence time was >10 days and N loading was >30 g N m-2 y-1. N removal efficiency also increased with increasing residence time and hydroperiod, but was less affected by N loading. However, longer hydrologic residence time increased vulnerability of wetlands to invasion by both invasive plants at low to medium N loading rates where native communities are typically more resistant to invasion. This suggests a potential tradeoff between ecosystem services related to nitrogen removal and wetland invasibility. These results help elucidate complex interactions of community composition, N loading and hydrology on N removal, helping managers to prioritize N removal when N loading is high or controlling plant invasion in more vulnerable wetlands.
- Keyword:
- Mondrian, Simulation model, Coastal wetlands, Invasive species, and Ecosystem modeling
- Citation to related publication:
- http://dx.doi.org/10.1016/j.ecolmodel.2014.01.010
- Discipline:
- Science
- Title:
- Hydrologic flushing rates drive nitrogen cycling and plant invasion in a freshwater coastal wetland model Ecological Applications EAP20-0253 Reproducable Data Archive
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- Creator:
- Chatterjee, Tanmay, Knappik, Achim, Sandford, Erin, Tewari, Muneesh, Choi, Sung Won, Strong, William B., Thrush, Evan P., Oh, Kenneth J., Liu, Ning, Walter, Nils G., and Johnson-Buck, Alexander
- Description:
- The sensitive measurement of specific protein biomarkers is important for medical diagnostics and research. However, existing methods for quantifying proteins use antibody probes that cannot distinguish between specific and nonspecific binding, limiting their sensitivity and specificity. This work establishes a method for distinguishing between specific binding to the target protein and nonspecific binding to assay surfaces using single-molecule kinetic measurements with dynamically binding probes. This is significant because it permits extremely sensitive protein measurements without requiring a high-affinity detection antibody or any washing steps, enabling streamlined and sensitive quantification of proteins even when no pair of high-quality, tightly binding antibodies is available.
- Keyword:
- biomarker detection, single molecule fluorescence, kinetic fingerprinting, total internal reflection microscopy, and super resolution microscopy
- Citation to related publication:
- Chatterjee, T., et al. Direct kinetic fingerprinting and digital counting of single protein molecules. Proc Natl Acad Sci USA, In Press.
- Discipline:
- Science
- Title:
- Dataset (TIRF microscopy movies) for "Direct kinetic fingerprinting and digital counting of single protein molecules"
-
- Creator:
- Mohtat, Peyman, Siegel, Jason B., and Stefanopoulou, Anna G.
- Description:
- The goal here is to study the voltage and expansion response of lithium-ion batteries at different charging rates. Specifically, the goal is to capture the observation of the smoothing of the peaks in dV/dQ and retention of the peaks in d^2 \delta/dQ^2 at higher C-rates. The retention of the peaks at higher charging rates enables better estimation of the cell capacity. To achieve this goal a reduced order electrochemical and mechanical model with multiple particles with a size distribution is developed. This allows us to capture the smoothing and preservation of the phase transitions in the voltage and expansion measurements at high C-rates, respectively. The model is written in Matlab software.
- Keyword:
- Lithium-ion batteries, Modeling, Multiparticle, Mechanical response, and Electrochemical
- Citation to related publication:
- https://doi.org/10.1149/1945-7111/aba5d1
- Discipline:
- Engineering
- Title:
- UofM pouch cell voltage and expansion dataset and modeling code
-
- Creator:
- Brasch, Jonathan M, Elipot, Shane, and Arbic, Brian
- Description:
- For Drifters, HYCOM, MITgcm: Spectra and kinetic energy files. Please see readme.txt for a description of all data and code contained here. and - Compare kinetic energies (KE) of high-resolution global ocean models estimated from rotary spectra to KE in surface drifter observations. - Near-inertial KE is closer to drifter observations in models with frequently updated wind forcing - Internal tide KE is closer to drifter observations in models with topographic wave drag
- Keyword:
- oceanography, rotary spectra, kinetic energy, sea surface velocity, and drifters
- Citation to related publication:
- Elipot, S., R. Lumpkin, R. C. Perez, J. M. Lilly, J. J. Early, and A. M. Sykulski (2016), "A global surface drifter dataset at hourly resolution", J. Geophys. Res. Oceans, 121, doi:10.1002/2016JC011716.
- Discipline:
- Science
- Title:
- Rotary spectra of surface kinetic energy in drifters and high-resolution global ocean models
-
- Creator:
- Sergio E. Vidal-Luengo and Mark B. Moldwin
- Description:
- Multi-satellite tracking of solar wind dynamic pressure pulse observations through the Earth's magnetosphere enables us to distinguish local changes with propagation signatures.
- Keyword:
- Heliophysics, Magnetosphere, Dynamic pressure pulse, Magnetosphere, THEMIS, MMS, Cluster, SuperMag, and Heliophysics System Observatory
- Discipline:
- Science
- Title:
- Data for: Global Magnetosphere Response to Solar Wind Dynamic Pressure Pulses during Northward IMF Using the Heliophysics System Observatory
-
- Creator:
- Van, Benjamin J. and Dewaraja, Yuni K.
- Description:
- Interest in quantitative imaging of Y-90 is growing because transarterial radioembolization (RE) with Y-90 loaded microspheres is a promising and minimally invasive treatment that is FDA approved for unresectable primary and metastatic liver tumors. These cancers are a leading cause of cancer mortality and morbidity. Radioembolization is a therapy that irradiates liver tumors with radioactive microspheres administered through a microcatheter placed in the hepatic arterial vasculature. Radioembolization is based on the principle that healthy liver and tumor are mainly vascularized by the portal vein and the hepatic artery respectively. As a result, radioactive microspheres are preferentially located in the lesions after they are administered via the hepatic artery.
- Keyword:
- Y-90, PET, SPECT, CT, Segmentation, Organ, Tumor, Label, Microsphere, Radioembolization, and SIRT
- Discipline:
- Health Sciences
- Title:
- Y-90 PET/CT & SPECT/CT and Corresponding Contours Dataset 31JULY2020
-
- Creator:
- Burger, Laura L , Wagenmaker, Elizabeth R., Phumsatitpong, Chayarndorn , Olson, David P., and Moenter, Suzanne M.
- Description:
- Polycystic ovary syndrome (PCOS) is the most common form of infertility in women. The causes of PCOS are not yet understood and both genetics and early-life exposure have been considered as candidates. With regard to the latter, circulating androgens are elevated in mid-late gestation in women with PCOS, potentially exposing offspring to elevated androgens in utero; daughters of women with PCOS are at increased risk for developing this disorder. Consistent with these clinical observations, prenatal androgenization (PNA) of several species recapitulates many phenotypes observed in PCOS. There is increasing evidence that symptoms associated with PCOS, including elevated luteinizing hormone (LH) (and presumably gonadotropin-releasing hormone (GnRH)) pulse frequency emerge during the pubertal transition. We utilized translating ribosomal affinity purification coupled with RNA sequencing to examine GnRH neuron mRNAs from prepubertal (3wk) and adult female control and PNA mice. Prominent in GnRH neurons were transcripts associated with protein synthesis and cellular energetics, in particular oxidative phosphorylation. The GnRH neuron transcript profile was affected more by the transition from prepuberty to adulthood than by PNA treatment, however PNA did change the developmental trajectory of GnRH neurons. This included families of transcripts related to both protein synthesis and oxidative phosphorylation, which were more prevalent in adults than in prepubertal mice but were blunted in PNA adults. These findings suggest that prenatal androgen exposure can program alterations in the translatome of GnRH neurons, providing a mechanism independent of changes in the genetic code for altered expression. These are Microsoft Excel Files
- Keyword:
- GnRH Neuron TRAP Seq
- Citation to related publication:
- Unprocessed RNASeq data is available at Gene Expression Omnibus ( https://www.ncbi.nlm.nih.gov/gds) accession GSE155314.
- Discipline:
- Science
- Title:
- Prenatal androgen exposure alters the developmental trajectory of both GnRH neuron and preoptic area RNA transcripts in female mice.
-
- Creator:
- Payam Mirshams Shahshahani
- Description:
- The two R codes are related to the feasible balance region calculations for Figures 2, 3, and 4 in the paper. The MATLAB codes are related to the simulations of the recoverable initial quasi-static states, the results of which are shown in Figure 5 of the paper.
- Keyword:
- One-legged balance, Biomechanics, Hip Abductor, and Unipedal Stance
- Citation to related publication:
- On the importance of the hip abductors during a clinical one legged balance test: a theoretical study
- Discipline:
- Engineering and Health Sciences
- Title:
- Simulation Code for "On the importance of the hip abductors during a clinical one legged balance test: a theoretical study"
-
- Creator:
- Davis Rabosky, Alison R. and Jantzi, Adrian
- Description:
- Video documentation of natural behavior in wild snakes is very rare, so film from opportunistic encounters of snake interactions is very valuable to scientific researchers. Our research team includes leading experts on this species of snake (the Western Groundsnake, Sonora semiannulata), so we worked with the observer to submit a formal description of the encounter to a peer-reviewed journal and make the information available to the broader research community.
- Keyword:
- Sonora semiannulata, ground snake, animal behavior, male-male combat
- Citation to related publication:
- Jantzi A, CL Cox, AR Davis Rabosky, AT Holycross. SONORA SEMIANNULATA (Western Groundsnake). COMBAT. Submitted, Herpetological Review.
- Discipline:
- Science
- Title:
- Raw video data from opportunistic observation of behavioral interaction between wild snakes (Sonora semiannulata)
-
- Creator:
- Crisp, Dakota N., Parent, Rachel, Nakatani, Mitsuyoshi, Murphy, Geoffrey G. , and Stacey, William C.
- Description:
- This data and scripts are meant to test and show that seizure onset dynamics can be modulated using anti-epileptic drugs. A zip file is included that contains all waveform data, MATLAB processing scripts, and metadata. The MATLAB scripts allow for visual review validation and objective feature analysis. The file includes various README files explaining the scripts and their relationships in greater detail.
- Keyword:
- Bifurcation, Epilepsy, Seizure, and Electrophysiology
- Discipline:
- Science, Engineering, and Health Sciences
- Title:
- Carbamazepine and GABA have distinct effects on seizure onset dynamics in mouse brain slices
-
- Creator:
- Gosner, Linda R., Nowlin, Jessica, and Smith, Alexander J.
- Description:
- Included here are 1) a detailed description of each of the dataset’s components, 2) a database of finds from the survey, 3) databases of the faunal bone studied by specialist Damià Ramis, 4) notes and documentation made in the field, 5) excavation photographs 6) artifact photographs.
- Keyword:
- Sardinia, Mediterranean archaeology, archaeological survey, excavation, and Classical archaeology
- Citation to related publication:
- Dommelen, Peter van, Enrique Díes Cusí, Linda R. Gosner, Jeremy Hayne, Guillem Pérez-Jordà, Damià Ramis, Andrea Roppa, and Alfonso Stiglitz. 2018. “Un millennio di storie: nuove notizie preliminari sul Progetto S’Urachi (San Vero Milis, OR), 2016-2018.” Quaderni. Rivista di Archeologia 29: 141–65., Gosner, Linda R., and Alexander J. Smith. 2018. “Landscape Use and Local Settlement at the Nuraghe S’Urachi (West-Central Sardinia): Results from the First Two Seasons of Site Survey.” Fasti Online Documents & Research: Survey Series, no. 7: 1–27. www.fastionline.org/docs/FOLDER-sur-2018-7.pdf., Gosner, Linda R., Jeremy Hayne, Emanuele Madrigali, Jessica Nowlin. 2020. New Evidence for Local Continuity and Phoenician Influence in the Ceramic Assemblage from Iron Age Su Padrigheddu (West-Central Sardinia). Proceedings of the IX Congreso de Estudios Fenicios y Púnicos. Myrta 5: 1649-1657., Madrigali, Emanuele, Linda R. Gosner, Jeremy Hayne, Jessica Nowlin, and Damià Ramis. 2019. “Tradizioni e interazioni nella quotidianità dell’età del ferro. nuove evidenze da Su Padrigheddu (San Vero Milis, OR).” Quaderni. Rivista di Archeologia 30: 107–26., Stiglitz, Alfonso, Enrique Díes Cusí, Damià Ramis, Andrea Roppa, and Peter van Dommelen. 2015. “Intorno al nuraghe: notizie preliminari sul Progetto S’Urachi (San Vero Milis, OR).” Quaderni. Rivista di Archeologia 26: 191–218., and Gosner, Linda R., Jessica Nowlin, and Alexander J. Smith. in preparation. Ground-truthing the Site-based Survey at S’Urachi and Su Padrigheddu (West-Central Sardinia): Results of the 2016 and 2017 Seasons.
- Discipline:
- Social Sciences
- Title:
- S’Urachi Site-Based Archaeological Survey 2016-2017
-
- Creator:
- Batterman, Stuart; University of Michigan
- Description:
- We evaluated PM levels at the Agbogbloshie e-waste and scrap yard site in Accra, Ghana, and at upwind and downwind locations. This monitoring forms part of the West Africa-Michigan Charter II for GEOHealth cohort study, which is analyzing occupational exposures and health risks at this site.
- Keyword:
- Air pollution, particulate matter, e-waste, Fires, and monitoring
- Discipline:
- Engineering and Health Sciences
- Title:
- Data pertaining to Article: Air Quality Impacts at an E-Waste Site in Ghana using Flexible, Low-Cost and Quality Assured Measurements
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- Creator:
- Kue, Jessie and Meurer, William
- Description:
- NHAMCS is an annual survey of emergency department visits. and SAS programs are required to read this data.
- Keyword:
- emergency department and hypertension
- Citation to related publication:
- To be published in F1000, DOI pending
- Discipline:
- Health Sciences
- Title:
- Dataset derived from 2014 National Hospital Ambulatory Care Survey - Emergency Department
-
- Creator:
- Boles, Austin H and van der Pluijm, Ben
- Description:
- This data was generated as a chapter in the dissertation of Austin Boles.
- Keyword:
- authigenic illite, hydrogen isotopes, and 40Ar/39Ar isotopic analysis
- Citation to related publication:
- Manuscript in submission to Tectonics: Boles, A., van der Pluijm, B., 2020, Locally derived, meteoric fluid infiltration was responsible for widespread Late-Paleozoic illite authigenesis in the Appalachian Basin
- Discipline:
- Science
- Title:
- Locally Derived, Meteoric Fluid Infiltration was Responsible for Widespread Late Paleozoic Illite Authigenesis in the Appalachian Basin
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- Creator:
- Lori, Jody r, Moyer, Cheryl A, Perosky, Joseph E, and University of Michigan, School of Nursing
- Description:
- This study used a convergent parallel mixed methods design that included qualitative data in the form of focus group discussions (FGDs), individual interviews, quantitative data retrieved from logbook reviews, and geo-location data collected through geographic information systems (GIS). Focus group discussions were conducted with community members, including chiefs, community leaders, women of reproductive age, traditional birth attendants (TBAs), women currently staying at a MWH, and male partners. Individual interviews were conducted with healthcare providers (midwives, registered nurses, and officers in charge) providing services at the rural primary healthcare facilities associated with a MWH. Logbook registries at rural health facilities with a MWH were reviewed to capture MWH usage. Additionally, each MWH was geo-located for purposes of geo-visualization.
- Keyword:
- Maternity Waiting Homes and Liberia
- Citation to related publication:
- James, K.H., Perosky, J.E., McLean, K. et al. Protocol for geolocating rural villages of women in Liberia utilizing a maternity waiting home. BMC Res Notes 12, 196 (2019). https://doi.org/10.1186/s13104-019-4224-1 and Coley, KM, Perosky, JE, Nyanplu, A, et al. Acceptability and feasibility of insect consumption among pregnant women in Liberia. Matern Child Nutr. 2020; 16:e12990. https://doi.org/10.1111/mcn.12990
- Discipline:
- International Studies
- Title:
- Mixed method dataset of a countrywide multi-sector scale-up of Maternity Waiting Homes in Liberia
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- Creator:
- Do, Hong X., Smith, Joeseph P., Fry, Lauren M., and Gronewold, Andrew D.
- Description:
- This data set contains a new monthly estimate of the water balance of the Laurentian Great Lakes, the largest freshwater system on Earth, from 1950 to 2019. The source codes and inputs to derive the new estimates are also included in this dataset.
- Keyword:
- Laurentian Great Lakes, Bayesian inference, water levels, data assimilation, and water balance
- Citation to related publication:
- Do, H.X., Smith, J., Fry, L.M., and Gronewold, A.D., Seventy-year long record of monthly water balance estimates for Earth’s largest lake system (submitted), Gronewold, A. D., Smith, J. P., Read, L., & Crooks, J. L. (2020). Reconciling the water balance of large lake systems. Advances in Water Resources, 103505, and This version replaces the following deprecated dataset: Do, H.X., Smith, J.P., Fry, L.M., Gronewold, A.D. (2020). Monthly water balance estimates for the Laurentian Great Lakes from 1950 to 2019 [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/0rsp-v195
- Discipline:
- Science
- Title:
- Monthly water balance estimates for the Laurentian Great Lakes from 1950 to 2019 (v1.1)