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  • 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:
    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

  • Application of the Monte Carlo method in modeling dusty gas, dust in plasma, and energetic ions in planetary and magnetospheric applications

    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

  • Dataset for analyzing spatial distribution of Y-junctions in flat-mounted 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 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

  • 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:
    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)

  • Code and accompanying input data for simulating lateral inhibition on motionless cell packing

    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

  • 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 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

  • 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 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

  • 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 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

  • 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 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

  • 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

  • Dataset from analysis of a peat core from the Tielishahan peatland in the Xinjiang Altai Mountains, northwestern China

    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

  • High-frequency precipitation variance in high-resolution global coupled ocean-atmosphere models: Precipitation data and analysis code

    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

  • 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 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)

  • CT Data of UMMP VP 81831, Cantius mckennai right navicular

    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

  • 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 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

  • 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 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

  • 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 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

  • CT Data of UMMP VP 81822, Cantius trigonodus right proximal metatarsal 1

    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

  • CT Data of UMMP VP 81821, Cantius mckennai right distal tibia

    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

  • Centimeter-Scale Electron Diffusion in Photoactive Organic Heterostructures

    Creator:
    Forrest, Stephen R., Panda, Anurag, Qu, Yue, Che, Xiaozhou, Coburn, Caleb, and Burlingame, Quinn
    Description:
    Mathematica Diffusion Simulation: Programmed by Coburn, Caleb. Simulation of diffusion in organic heterostructures, including least square fits and statistical goodness of fit analysis. Used to calculate fits to transient data in Fig 1, 3 and Extended Data Fig.2. Example data file included for download Matlab Montecarlo simulation: Programmed by Coburn, Caleb. Montecarlo simulation of charge diffusion on a cubic lattice to determine lateral diffusion length as a function of barrier height, assuming thermionic emission over the barrier. Matlab 2D Diffusion Simulation:Programmed by Coburn, Caleb. Modified from BYU Physics 430 Course Manual. Simulates diffusion around a film discontinuity, such a cut. Used to generate fits to Extended Data Fig. 1
    Keyword:
    Organic semiconductors and Charge diffusion
    Citation to related publication:
    Burlingame, Q., Coburn, C., Che, X., Panda, A., Qu, Y., & Forrest, S. R. (2018). Centimetre-scale electron diffusion in photoactive organic heterostructures.  Nature,  554(7690), 77-80.  https://doi.org/10.1038/nature25148
    Discipline:
    Science
    Title:
    Centimeter-Scale Electron Diffusion in Photoactive Organic Heterostructures

  • Data in support of the study "Climate response to negative greenhouse gas radiative forcing in polar winter"

    Creator:
    Flanner, Mark
    Description:
    Greenhouse gas (GHG) additions to Earth’s atmosphere initially reduce global outgoing longwave radiation (OLR), thereby warming the planet. In select environments with temperature inversions, however, increased GHG concentrations can actually increase local OLR. Negative top-of-atmosphere and effective radiative forcing (ERF) from this situation give the impression that local surface temperatures could cool in response to GHG increases. Here we consider an extreme scenario in which GHG concentrations are increased only within the warmest layers of winter near-surface inversions of the Arctic and Antarctic. We find, using a fully coupled Earth system model, that the underlying surface warms despite the GHG addition exerting negative ERF and cooling the troposphere in the vicinity of the GHG increase. This unique radiative forcing and thermal response is facilitated by the high stability of the polar winter atmosphere, which inhibits thermal mixing and amplifies the impact of surface radiative forcing on surface temperature. These findings also suggest that strategies to exploit negative ERF via injections of short-lived GHGs into inversion layers would likely be unsuccessful in cooling the planetary surface. and Note: A revised data description file was added to this work on April 11, 2018 containing additional information about the data set than was provided in the original description. Additional keywords and a full citation to the related article were added as well.
    Keyword:
    climate, greenhouse gas, polar inversion layers, radiative forcing (and/or effective radiative forcing), and MODTRAN simulation
    Citation to related publication:
    Flanner, M. G., Huang, X., Chen, X.,& Krinner, G. (2018). Climate response to negative greenhouse gas radiative forcing in polar winter. Geophysical Research Letters, 45, 1997–2004.  https://doi.org/10.1002/2017GL076668
    Discipline:
    Science
    Title:
    Data in support of the study "Climate response to negative greenhouse gas radiative forcing in polar winter"

  • AutoSiM software and sample single-molecule trace data accompanying "Automatic classification and segmentation of single-molecule fluorescence time traces with deep learning"

    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"

  • Hydrologic flushing rates drive nitrogen cycling and plant invasion in a freshwater coastal wetland model Ecological Applications EAP20-0253 Reproducable Data Archive

    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

  • Magnetometer Survey Data from the Weeden Island Site (8Pi1), Florida (2013-2014)

    Creator:
    Horsley, Timothy J. and Sampson, Christina P.
    Description:
    The data (raw data, composite files [processed], and some images) can be read by the program TerraSurveyor. Version 3.0.34.10 of the software was used to create the composite files in this deposit. and The magnetometer data was the second step in a geophysical survey program that began with magnetic susceptibility survey of a portion of the Weedon Island Preserve in St. Petersburg, Florida. Geophysical survey was used to map human occupation of the study area and to guide subsequent archaeological excavations.
    Keyword:
    magnetometry, geophysical survey, remote sensing, Florida archaeology, and coastal archaeology
    Citation to related publication:
    Sampson, C. P. (2019) Safety Harbor at the Weeden Island Site: Late Pre-Columbian Craft, Community, and Complexity on Florida's Gulf Coast. PhD Dissertation, University of Michigan. and Sampson, Christina Perry and Timothy J. Horsley. Using Multi-Staged Magnetic Survey and Excavation to Assess Community Settlement Organization: A Case Study from the Central Peninsular Gulf Coast of Florida. Advances in Archaeological Practice. Cambridge University Press: 18 December 2019.  https://doi.org/10.1017/aap.2019.45
    Discipline:
    Science and Social Sciences
    Title:
    Magnetometer Survey Data from the Weeden Island Site (8Pi1), Florida (2013-2014)

  • JGR-Space-2012-Data

    Creator:
    Moldwin, Mark B
    Description:
    Tab delimited file containing the records of all papers published in JGR-Space Physics in 2012. The records were pulled from Thomsen-Reuters ISI-Web-of-Science on June 3, 2016 including citations. Gender was identified independently by the creator of the file.
    Keyword:
    Gender and Nationality Bias, Space Physics, and Bibliometrics
    Citation to related publication:
    Moldwin, M. B., & Liemohn, M. W. (2018). High‐citation papers in space physics: examination of gender, country, and paper characteristics. Journal of Geophysical Research: Space Physics, 123.  https://doi.org/10.1002/2018JA025291
    Discipline:
    Science
    Title:
    JGR-Space-2012-Data

  • Predicting Crystal Structures using Digital Alchemy Inverse Materials Design and the Random Forest Technique of Machine Learning

    Creator:
    Geng, Yina, Van Anders, Greg, and Glotzer, Sharon C.
    Description:
    The data are the 13 target structures used in developing our model for predicting colloidal crystal structures from the geometries of particular shapes. The target structures are: simple cubic (SC), body-centered cubic (BCC), face-centered cubic (FCC), simple chiral cubic (SCC), hexagonal (HEX-1-0.6), diamond (D), graphite (G), honeycomb (H), body-centered tetragonal (BCT-1-1-2.4), high-pressure Lithium (Li), Manganese (beta-Mn), Uranium (beta-U), Tungsten (beta-W). At least nine simulations were run on each of the target structures. All of the data are formatted as .pos files.
    Keyword:
    Inverse Design and Machine Learning
    Citation to related publication:
    " Yina Geng, Greg van Anders, Sharon C. Glotzer, ""Predicting colloidal crystals from shapes via inverse design and machine learning [pre-print]""  https://arxiv.org/pdf/1801.06219.pdf"
    Discipline:
    Science
    Title:
    Predicting Crystal Structures using Digital Alchemy Inverse Materials Design and the Random Forest Technique of Machine Learning

  • The Bird's Ear View of Space Physics: Audification as a Tool for the Spectral Analysis of Time Series Data

    Creator:
    Zurbuchen, Thomas H.
    Description:
    Audification Routines in MATLAB and IDL
    Citation to related publication:
    Alexander, Robert L., Sile O’Modhrain, D. Aaron Roberts, Jason A. Gilbert, and Thomas H. Zurbuchen. “The Bird’s Ear View of Space Physics: Audification as a Tool for the Spectral Analysis of Time Series Data.” Journal of Geophysical Research: Space Physics 119, no. 7 (2014): 5259–71.  https://doi.org/10.1002/2014JA020025
    Discipline:
    Science
    Title:
    The Bird's Ear View of Space Physics: Audification as a Tool for the Spectral Analysis of Time Series Data

  • MHD-EPIC simulation data of the GEM dayside kinetic processes challenge event

    Creator:
    Chen, Yuxi
    Description:
    We use the MHD with embedded particle-in-cell model (MHD-EPIC) to study the Geospace Environment Modeling (GEM) dayside kinetic processes challenge event at 01:50-03:00 UT on 2015-11-18, when the magnetosphere was driven by a steady southward IMF. In the MHD-EPIC simulation, the dayside magnetopause is covered by a PIC code so that the dayside reconnection is properly handled. We compare the magnetic fields and the plasma profiles of the magnetopause crossing with the MMS3 spacecraft observations. Most variables match the observations well in the magnetosphere, in the magnetosheath, and also during the current sheet crossing. The MHD-EPIC simulation produces flux ropes, and we demonstrate that some magnetic field and plasma features observed by the MMS3 spacecraft can be reproduced by a flux rope crossing event. We use an algorithm to automatically identify the reconnection sites from the simulation results. It turns out that there are usually multiple X-lines at the magnetopause. By tracing the locations of the X-lines, we find the typical moving speed of the X-line endpoints is about 70~km/s, which is higher than but still comparable with the ground-based observations.
    Keyword:
    MHD, PIC, and simulation
    Citation to related publication:
    Chen, Yuxi, et al. "Magnetohydrodynamic with embedded particle-in-cell simulation of the Geospace Environment Modeling dayside kinetic processes challenge event." arXiv preprint arXiv:2001.04563 (2020).  https://arxiv.org/abs/2001.04563
    Discipline:
    Science
    Title:
    MHD-EPIC simulation data of the GEM dayside kinetic processes challenge event

  • Transcriptomic Profiles of Sepsis in the Human Brain

    Creator:
    Bustamante, Angela C., Opron, Kristopher, Ehlenbach, William J., Crane, Paul K., Keene, Dirk, Standiford, Theodore J., and Singer, Benjamin H.
    Description:
    This study was conducted to detect and analyze modules, or clusters of genes, associated with sepsis, using RNAseq data obtained from 12 participants who died of sepsis and 12 participants who died of non-infectious critical illness while hospitalized. This deposit contains the input data and parameters needed to reproduce the weighted gene co-expression network analysis (WGCNA) and gene enrichment analysis performed on this data. This analysis requires the R packages "WGCNA" version 1.68 and "DESeq2" version 1.22.2 available for download from bioconductor ( http://bioconductor.org). The external bioinformatics tool DAVID version 6.8 ( https://david.ncifcrf.gov/) was used as an additional gene enrichment analysis. Please see the supplemental methods document within this deposit and published research letter for more detailed information.
    Keyword:
    Sepsis, RNAseq, Transcriptomics, Human, and Brain
    Citation to related publication:
    Bustamante, A.C., Opron, K., Ehlenbach, W.J., Larson, E.B., Crane, P.K., Keene, C.D., Standiford, T.J., Singer, B.H., 2020. Transcriptomic Profiles of Sepsis in the Human Brain. Am J Respir Crit Care Med.  https://doi.org/10.1164/rccm.201909-1713LE
    Discipline:
    Science
    Title:
    Transcriptomic Profiles of Sepsis in the Human Brain

  • Data in support of the study "Modeled Response of Greenland Snowmelt to the Presence of Biomass Burning-Based Absorbing Aerosols in the Atmosphere and Snow"

    Creator:
    Ward, Jamie L ., Flanner, Mark G., Bergin, Mike, Dibb, Jack E., Polashenski, Chris M., Soja, Amber J., and Thomas, Jennie L.
    Description:
    Biomass burning produces smoke aerosols that are emitted into the atmosphere. Some smoke constituents, notably black carbon (BC), are highly effective light-absorbing aerosols (LAA). Emitted LAA can be transported to high albedo regions like the Greenland Ice Sheet (GrIS) and affect local snowmelt. In the summer, the effects of LAA in Greenland are uncertain. To explore how LAA affect GrIS snowmelt and surface energy flux in the summer, we conduct idealized global climate model simulations with perturbed aerosol amounts and properties in the GrIS snow and overlying atmosphere. The in-snow and atmospheric aerosol burdens we select range from background values measured on the GrIS to unrealistically high values. This helps us explore the linearity of snowmelt response and to achieve high signal-to-noise ratios. With LAA operating only in the atmosphere, we find no significant change in snowmelt due to the competing effects of surface dimming and tropospheric warming. Regardless of atmospheric LAA presence, in-snow BC-equivalent mixing ratios greater than ~60 ng/g produce statistically significant snowmelt increases over much of the GrIS. We find that net surface energy flux changes correspond well to snowmelt changes for all cases. The dominant component of surface energy flux change is solar energy flux, but sensible and longwave energy fluxes respond to temperature changes. Atmospheric LAA dampen the magnitude of solar radiation absorbed by in-snow LAA when both varieties are simulated. In general, the significant melt and surface energy flux changes we simulate occur with LAA quantities that have never been recorded in Greenland.
    Keyword:
    climate, Greenland Ice Sheet, black carbon, biomass burning, snowmelt, and surface energy balance
    Citation to related publication:
    Ward, J.L., et al. (2018). Modeled Response of Greenland Snowmelt to the Presence of Biomass Burning-Based Absorbing Aerosols in the Atmosphere and Snow. Journal of Geophysical Research: Atmospheres. 123, 6122– 6141.  https://doi.org/10.1029/2017JD027878
    Discipline:
    Science
    Title:
    Data in support of the study "Modeled Response of Greenland Snowmelt to the Presence of Biomass Burning-Based Absorbing Aerosols in the Atmosphere and Snow"

  • Prenatal androgen exposure alters the developmental trajectory of both GnRH neuron and preoptic area RNA transcripts in female mice.

    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.

  • Data for Solar Flare Intensity Prediction with Machine Learning Models

    Creator:
    Jiao, Zhenbang, Chen, Yang, and Manchester, Ward
    Description:
    GOES_flare_list: contains a list of more than 12,013 flare events. The list has 6 columns, flare classification, active region number, date, start time end time, emission peak time. SHARP_data.hdf5 files contain time series of 20 physical variables derived from the SDO/HMI SHARP data files. These data are saved at a 12 minute cadence and are used to train the LSTM model.
    Keyword:
    Solar Flare Prediction and Machine Learning
    Citation to related publication:
    Jiao, Z., Sun, H., Wang, X., Manchester, W., Gombosi, T., Hero, A., Chen, Y., Solar Flare Intensity Prediction with Machine Learning Models, 2020, Space Weather Journal, in press
    Discipline:
    Science and Engineering
    Title:
    Data for Solar Flare Intensity Prediction with Machine Learning Models

  • Data and Data products for machine learning applied to solar flares

    Creator:
    Chen, Yang and Manchester, Ward IV
    Description:
    GOES_flare_list: contains a list of more than 10,000 flare events. The list has 6 columns, flare classification, active region number, date, start time end time, emission peak time, GOES_B_flare_list: contains time series data of SDO/HMI SHARP parameters for B class solar flares , GOES_MX_flare_list: contains time series data of SDO/HMI SHARP parameters for M and X class solar flares, SHARP_B_flare_data_300.hdf5 and SHARP_MX_flare_data_300.hdf5 files contain time series more than 20 physical variables derived from the SDO/HMI SHARP data files. These data are saved at a 12 minute cadence and are used to train the LSTM model., and B_HARPs_CNNencoded_part_xxx.hdf5 and M_X HARPs_CNNencoded_part_xxx.hdf5 include neural network encoded features derived from vector magnetogram images derived from the Solar Dynamics Observatory (SDO) Helioseismic and Magnetic Imager (HMI). These data files typically contains one or two sequences of magnetograms covering an active region for a period of 24h with a 1 hour cadence. We encode each magnetogram with frames of a fixed size of 8x16 with 512 channels.
    Keyword:
    machine learning, data science, and solar flare prediction
    Citation to related publication:
    Chen, Y., Manchester, W., Hero, A., Toth, G., DuFumier, B. Zhou, T., Wang, X., Zhu, H., Sun, Zeyu, Gombosi, T., Identifying Solar Flare Precursors Using Time Series of SDO/HMI Images and SHARP Parameters, Space Weather, 17, 1404–1426.  https://doi.org/10.1029/2019SW002214
    Discipline:
    Science and Engineering
    Title:
    Data and Data products for machine learning applied to solar flares

  • The KSU-UMD Dataset for Benchmarking for Audio Forensic Algorithms

    Creator:
    Malik, Hafiz and Khan, Muhammad Khurran, King Saud University
    Description:
    Details of the microphone used for data collection, acoustic environment in which data was collected, and naming convention used are provided here. 1 - Microphones Used: The microphones used to collect this dataset belong to 7 different trademarks. Table (1) illustrates the number of used Mics of different trademarks and models. Table 1: Trademarks and models of Mics Mic Trademark Mic Model # of Mics Shure SM-58 3 Electro-Voice RE-20 2 Sennheiser MD-421 3 AKG C 451 2 AKG C 3000 B 2 Neumann KM184 2 Coles 4038 2 The t.bone MB88U 6 Total 22 2- Environment Description: A brief description of the 6 environments in which the dataset was collected is presented here: (i) Soundproof room: a small room (nearly 1.5m × 1.5m × 2m), which is closed and completely isolated. With an exception of a small window in the front side of the room which is made of glass, all the walls of the room are made of wood and covered by a layer of sponge from the inner side, and the floor is covered by carpet. (ii) Class room: standard class room (6m × 5m × 3m). (iii) Lab: small lab (4m × 4m × 3m). All the walls are made of glasses and the floor is covered by carpet. The lab contains 9 computers. (iv) Stairs: is in the second floor. The place of recording is 3m × 5m (v) Parking: is the college parking. (vi) Garden: is an open space outside the buildings. 3- Naming Convention: This set of rules were followed as a naming convention to give each file in the dataset a unique name: (i) The file name is 19 characters long, and consists of 5 sections separated by underscores. (ii) The first section is of 3 characters indicates the Microphone trademark. (iii) The second section of 4 characters indicates the microphone model as in table (2). (iv) The third section of 2 characters indicates a specific microphone within a set of microphones of the same trademark and model, since we have more than one microphone of the same trademark and model. (v) The fourth section of 2 characters indicates the environment, where Soundproof room --> 01 Class room --> 02 Lab --> 03 Stairs --> 04 Parking --> 05 Garden --> 06 (vi) The fifth section of 2 characters indicates the language, where Arabic --> 01 English --> 02 Chinese --> 03 Indonesian --> 04 (vii) The sixth section of 2 characters indicates the speaker. Table 2: Microphones Naming Criteria Original Mic Trademark and model --> Naming Convenient Shure SM-58 --> SHU_0058 Electro-Voice RE-20 --> ELE_0020 Sennheiser MD-421 --> SEN_0421 AKG C 451 --> AKG_0451 AKG C 3000 B --> AKG_3000 Neumann KM184 --> NEU_0184 Coles 4038 --> COL_4038 The t.bone MB88U --> TBO_0088 For example: SEN_0421_02_01_02_03 is an English file recorded by speaker number 3 in the soundproof room using microphone number 2 of Sennheiser MD-421
    Keyword:
    audio forensic, multimedia forensics, microphone identification, tamper detection, splicing detection, and codec identification
    Citation to related publication:
    Muhammad Khurram Khan, Mohammed Zakariah, Hafiz Malik & Kim-Kwang Raymond Choo (2018). A novel audio forensic data-set for digital multimedia forensics, Australian Journal of Forensic Sciences, 50:5, 525-542,  http://dx.doi.org/10.1080/00450618.2017.1296186
    Discipline:
    Government, Politics and Law, Science, and Engineering
    Title:
    The KSU-UMD Dataset for Benchmarking for Audio Forensic Algorithms

  • Results from Morales et al. 2018 (JAS) - Orographic precipitation sensitivity analysis

    Creator:
    Morales, Annareli
    Description:
    The research that produced this data involves exploring the sensitivity of orographic precipitation to changes in microphysical parameters found in the Morrison microphysics scheme within CM1 model. These microphysical sensitivities are also tested within different environments. The tests can be described as "one-at-a-time" experiments, i.e., an individual parameter is perturbed while keeping the rest constant. Annareli Morales conducted this research for her PhD research while working at the Mesoscale and Microscale Meteorology lab at NCAR in Boulder, CO.
    Keyword:
    Orographic precipitation
    Citation to related publication:
    Morales, A., H. Morrison, and D. Posselt, 2018: Orographic precipitation response to microphysical parameter perturbations for idealized moist nearly neutral flow. Journal of Atmospheric Science, 75, 1933-1953,  https://doi.org/10.1175/JAS-D-17-0389.1
    Discipline:
    Science
    Title:
    Results from Morales et al. 2018 (JAS) - Orographic precipitation sensitivity analysis

  • Dataset for Modeling Reconnection-driven Dynamics at Ganymede's Upstream Magnetosphere

    Creator:
    Zhou, Hongyang
    Description:
    The largest moon in the solar system, Ganymede, is the only moon known to possess a strong intrinsic magnetic field and a corresponding magnetosphere. Using the latest version of Space Weather Modeling Framework (SWMF), we study the upstream plasma interactions and dynamics in this sub-Alfvenic system. Results from the Hall MHD and the coupled MHD with embedded Particle-in-Cell (MHD-EPIC) models are compared. We find that under steady upstream conditions, magnetopause reconnection occurs in a non-steady manner. Flux ropes of Ganymede's radius in length form on the magnetopause at a rate about 2/minute and create spatiotemporal variations in plasma and field properties. Upon reaching proper grid resolutions, the MHD-EPIC model can resolve both electron and ion kinetics at the magnetopause and show localized non-gyrotropic behavior inside the diffusion region. The estimated global reconnection rate from the models is about 80 kV with 60% efficiency, and there is weak evidence of about 1 minute periodicity in the temporal variations due to the dynamic reconnection process.
    Keyword:
    MHD, PIC, Ganymede, and magnetosphere
    Citation to related publication:
    H.Zhou et al. "Reconnection-driven Dynamics at Ganymede's Upstream Magnetosphere: 3D Global Hall MHD and MHD-EPIC Simulations", Journal of Geophysical Research Space Physics, 2020.
    Discipline:
    Science
    Title:
    Dataset for Modeling Reconnection-driven Dynamics at Ganymede's Upstream Magnetosphere

  • Computer Data from Ross Thesis

    Creator:
    Mathews, Elizabeth and Verhoff, Frank
    Description:
    Each pdf is an electronic version of the paper output for each experiment. Each text file is the electronic version of the data on the computer cards for each experiment. These text files are directly readable by Excel. Once in Excel, the data can be manipulated as desired. Additional information is in the theses.
    Keyword:
    Two Liquid Phase Processes, Droplet Size and Concentration, Population Balances, and Dispersed Phase Mixing
    Citation to related publication:
    Ross, S. L. (1971). Measurements and models of the dispersed phase mixing process (Doctoral dissertation). Retrieved from  http://hdl.handle.net/2027.42/136886 and Verhoff, F. H. (1969). A study of the bivariate analysis of dispersed phase mixing (Doctoral dissertation). Retrieved from  http://hdl.handle.net/2027.42/137651
    Discipline:
    Science and Engineering
    Title:
    Computer Data from Ross Thesis

  • Event List for "Interchange Injections at Saturn: Statistical Survey of Energetic H+ Sudden Flux Intensifications"

    Creator:
    Azari, A. R.
    Description:
    ABSTRACT: We present a statistical study of interchange injections in Saturn's inner and middle magnetosphere focusing on the dependence of occurrence rate and properties on radial distance, partial pressure, and local time distribution. Events are evaluated from over the entirety of the Cassini mission’s equatorial orbits between 2005 and 2016. We identified interchange events from CHarge Energy Mass Spectrometer (CHEMS) H+ data using a trained and tested automated algorithm, which has been compared with manual event identification for optimization. We provide estimates of interchange based on intensity, which we use to investigate current inconsistencies in local time occurrence rates. This represents the first automated detection method of interchange, estimation of injection event intensity, and comparison between interchange injection survey results. We find the peak rates of interchange occur between 7 - 9 Saturn radii and that this range coincides with the most intense events as defined by H+ partial particle pressure. We determine that nightside occurrence dominates as compared to the dayside injection rate, supporting the hypothesis of an inversely dependent instability growth rate on local Pedersen ionospheric conductivity. Additionally, we observe a slight preference for intense events on the dawn side, supporting a triggering mechanism related to large-scale injections from downtail reconnection. Our observed local time dependence paints a dynamic picture of interchange triggering due to both the large-scale injection driven process and ionospheric conductivity. Within this repository we provide a readme file (description of data file and usage) and the event list provided as a .txt file. The event list includes start and stop times, comparison to previous surveys, and the average location of events identified. Additional formats are available on request. , Further details on this method can be found in "Interchange Injections at Saturn: Statistical Survey of Energetic H+ Sudden Flux Intensifications" by Azari et al., 2018 in the Journal of Geophysical Research: Space Physics.  https://doi.org/10.1029/2018JA025391. , and Curation notes: The files 'events_CORRECTED.txt' and 'readme_UPDATED.rtf' were added to this record July 31 and August 7, 2018 and supersede the previous data file 'events.txt' and readme file 'readme.rtf'. The file 'events.txt' uploaded May 9, 2018 should not be used, as this file contains a duplication error where the last column, InAllSurveys, is incorrectly presented as a duplicate of the column InAnySurvey. 'readme_UPDATED.rtf' contains additional context and updated references to the new data file.
    Keyword:
    Planetary Science, Automated Event Detection, Space Physics, Magnetospheric Physics, Interchange Injections, and Saturn
    Citation to related publication:
    Azari, A. R., Liemohn, M. W., Jia, X., Thomsen, M. F., Mitchell, D. G., Sergis, N., Rymer, A. M., Hospodarsky, G. B., Paranicas, C. , and Vandegriff, J. (2018). Interchange Injections at Saturn: Statistical Survey of Energetic H+ Sudden Flux Intensifications. Journal of Geophysical Research: Space Physics, 123.  https://doi.org/10.1029/2018JA025391
    Discipline:
    Science
    Title:
    Event List for "Interchange Injections at Saturn: Statistical Survey of Energetic H+ Sudden Flux Intensifications"

  • Epileptogenesis modulates spontaneous and responsive brain state dynamics - Code & Data

    Creator:
    Crisp, Dakota N., Cheung, Warwick, Gliske, Stephen V., Lai, Alan, Freestone, Dean R., Grayden, David B., Cook, Mark J., and Stacey, William C.
    Description:
    The data and the scripts are to show that seizure onset dynamics and evoked responses change over the progression of epileptogenesis defined in this intrahippocampal tetanus toxin rat model. All tests explored in this study can be repeated with the data and scripts included in this repository. and Dataset citation: Crisp, D.N., Cheung, W., Gliske, S.V., Lai, A., Freestone, D.R., Grayden, D.B., Cook, MJ., Stacey, W.C. (2019). Epileptogenesis modulates spontaneous and responsive brain state dynamics [Data set]. University of Michigan Deep Blue Data Repository.  https://doi.org/10.7302/r6vg-9658
    Keyword:
    evoked response, stimulation, bifurcation, epilepsy, seizure, divergence, and dynamics
    Discipline:
    Health Sciences, Science, and Engineering
    Title:
    Epileptogenesis modulates spontaneous and responsive brain state dynamics - Code & Data

  • Single-molecule microscopy image data and analysis files for "Ultra-specific and Amplification-free Quantification of Mutant DNA by Single-molecule Kinetic Fingerprinting"

    Creator:
    Hayward, Stephen L. , Lund, Paul E., Kang, Qing, Johnson-Buck, Alexander , Tewari, Muneesh, and Walter, Nils G.
    Description:
    This work contains the experimental data and associated analysis that are described in the research publication entitled "Ultra-specific and Amplification-free Quantification of Mutant DNA by Single-molecule Kinetic Fingerprinting". This work contains multiple zip files, each of which represents one of the principal experiment groups presented in the publication. Each experiment group contains movie and analysis files corresponding to various experimental conditions related to that experiment group.
    Keyword:
    Single Molecule Fluorescence, Super-Resolution Microscopy, Nucleic Acid Hybridization, T790M Mutation, Cytosine Deamination, SiMREPS, and single molecule kinetic fingerprinting
    Citation to related publication:
     https://pubs.acs.org/doi/10.1021/jacs.8b06685
    Discipline:
    Science
    Title:
    Single-molecule microscopy image data and analysis files for "Ultra-specific and Amplification-free Quantification of Mutant DNA by Single-molecule Kinetic Fingerprinting"

  • Evans Old Field Plant Database, 1948-1997

    Creator:
    Dr. Francis C. Evans
    Description:
    The Evans Old Field Plant Database contains FileMaker and Excel files of data collected by Dr. Francis C. Evans during a 50-year study on successional change on Evans Old Field on the Edwin S. George Reserve. Data include plant phenology, location, and abundances observed from 1948 to 1997.
    Discipline:
    Science
    Title:
    Evans Old Field Plant Database, 1948-1997

  • Bayesian Population Correlation: A probabilistic approach to comparing detrital zircon age distributions

    Creator:
    Tye, Alexander R, Wolf, Aaron S, and Niemi, Nathan A
    Description:
    Detrital zircon age distributions provide robust insights into past sedimentary systems, but these age distributions are often complex and multi-peaked, with sample sizes too small to confidently resolve population distributions. This limited sampling hinders existing quantitative methods for comparing detrital zircon age distributions, which show systematic dependence on the sizes of compared samples. The proliferation of detrital zircon studies motivates the development of more robust quantitative methods. We present the first attempt, to our knowledge, to infer probability model ensembles (PMEs) for samples of detrital zircon ages using a Bayesian method. Our method infers the parent population age distribution from which a sample is drawn, using a Monte Carlo approach to aggregate a representative set of probability models that is consistent with the constraints that the sample data provide. Using the PMEs inferred from sample data, we develop a new estimate of correspondence between detrital zircon populations called Bayesian Population Correlation (BPC). Tests of BPC on synthetic and real detrital zircon age data show that it is nearly independent from sample size bias, unlike existing correspondence metrics. Robust BPC uncertainties can be readily estimated, enhancing interpretive value. When comparing two partially overlapping zircon age populations where the shared proportion of each population is independently varied, BPC results conform almost perfectly to expected values derived analytically from probability theory. This conformity of experimental and analytical results permits direct inference of the shared proportions of two detrital zircon age populations from BPC. We provide MATLAB scripts to facilitate the procedures we describe.
    Keyword:
    provenance, statistics, zircon, Bayesian, detrital, and density estimation
    Citation to related publication:
    A.R. Tye, A.S. Wolf, N.A. Niemi, Bayesian population correlation: A probabilistic approach to inferring and comparing population distributions for detrital zircon ages, Chemical Geology, Volume 518, 2019, Pages 67-78, ISSN 0009-2541,  https://doi.org/10.1016/j.chemgeo.2019.03.039
    Discipline:
    Science
    Title:
    Bayesian Population Correlation: A probabilistic approach to comparing detrital zircon age distributions

  • A taxonomy of seizure dynamotypes - Code & Data

    Creator:
    Crisp, Dakota N., Saggio, Maria L., Scott, Jared, Stacey, William C., Nakatani, Mitsuyoshi, Gliske, Stephen V., and Lin, Jack
    Description:
    This data and scripts are meant to test and show seizure differentiation based on bifurcation theory. A zip file is included which contains real and simulated seizure waveforms, Matlab scripts, and metadata. The matlab scripts allow for visual review validation and objective feature analysis. The file “README.txt” provides more detail about each individual file within the zip file. and Data citation: Crisp, D.N., Saggio, M.L., Scott, J., Stacey, W.C., Nakatani, M., Gliske, S.F., Lin, J. (2019). Epidynamics: Navigating the map of seizure dynamics - Code & Data [Data set]. University of Michigan Deep Blue Data Repository.  https://doi.org/10.7302/ejhy-5h41
    Keyword:
    Bifurcation, Epilepsy, Seizure, and Divergence
    Citation to related publication:
    Saggio, M.L., Crisp, D., Scott, J., Karoly, P.J., Kuhlmann, L., Nakatani, M., Murai, T., Dümpelmann, M., Schulze-Bonhage, A., Ikeda, A., Cook, M., Gliske, S.V., Lin, J., Bernard, C., Jirsa, V., Stacey, W., 2020. In pre-print. Epidynamics characterize and navigate the map of seizure dynamics. bioRxiv 2020.02.08.940072.  https://doi.org/10.1101/2020.02.08.940072
    Discipline:
    Health Sciences, Science, and Engineering
    Title:
    A taxonomy of seizure dynamotypes - Code & Data

  • Scanning X-ray fluorescence (XRF) for SPR0901-03KC

    Creator:
    Ingrid L. Hendy and Yi Wang
    Description:
    This dataset includes scanning X-ray fluorescence (XRF) data for the core SPR0901-03KC (34.2832°N, 120.0401°W, 586 m water depth). SPR0901-03KC was collected by the research vessel R/V Sproul off Southern California in 2009.1. The research is funded by NSF OCE-0752093.
    Keyword:
    scanning X-ray fluorescence, XRF, Santa Barbara Basin, and SPR0901-03KC
    Citation to related publication:
    "Recover MT Receivers offshore Morro Bay/Deploy and Recover EM Sensor in the San Diego Trough." Cruise ID: SP0901. 2009. Accessible at Rolling Deck to Repository at  https://doi.org/10.7284/901085
    Discipline:
    Science
    Title:
    Scanning X-ray fluorescence (XRF) for SPR0901-03KC

  • Maximum Spreading Speed for Magnetopause Reconnection: Model Dataset

    Creator:
    Welling, Daniel and Walsh, Brian
    Description:
    The goal of this simulation was to examine the spread of magnetic reconnection across the dayside magnetopause upon the arrival of a tangential discontinuity of the interplanetary magnetic field from a purely northward to southward configuration. Simple solar wind conditions were used to give us input into the system. A very high resolution grid setup was used in BATS-R-US.
    Keyword:
    space science, magnetosphere, magnetohydrodynamics, magnetopause, and magnetic reconnection
    Citation to related publication:
    Walsh, B. M., Welling, D. T.,Zou, Y., & Nishimura, Y. (2018). A maximum spreading speed for magnetopause reconnection. Geophysical Research Letters, 45, 5268–5273.  https://doi.org/10.1029/2018GL078230
    Discipline:
    Science
    Title:
    Maximum Spreading Speed for Magnetopause Reconnection: Model Dataset

  • Quantifying near-surface rock strength on a regional scale from hillslope stability models - dataset

    Creator:
    Townsend, Kirk F., Gallen, Sean F., and Clark, Marin K.
    Description:
    These datasets support the findings of Townsend et al. (2020). In this article, we quantify rock strength using two novel applications of hillslope stability models, resulting in estimates of cohesive and frictional strength at the spatial scale of small watersheds. We compare these results against the direct-shear test dataset here for validation of our approach. We find that cohesive strength is dependent on the original burial depth of the sedimentary rocks studied here. The low-temperature thermochronometry data was used to assess the magnitude of burial.
    Keyword:
    Thermochronology, Thermochronometry, Direct-Shear, Landslides, Rock Strength, Landscape Evolution, and Geomorphology
    Citation to related publication:
    Townsend, K.F., Gallen, S.F., & Clark, M.K., in press, Quantifying near-surface rock strength on a regional scale from hillslope stability models: Journal of Geophysical Research Earth Surface.  https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020JF005665
    Discipline:
    Science
    Title:
    Quantifying near-surface rock strength on a regional scale from hillslope stability models - dataset

  • Data and Code Set for "Measuring the Earth's Synchrotron Emission from Radiation Belts with a Lunar Near Side Radio Array"

    Creator:
    Hegedus, Alexander M
    Description:
    This is the README for the LunarSynchrotronArray package, maintained by Dr. Alex Hegedus  alexhege@umich.edu This code repository corresponds to the Hegedus et al. 2020 (accepted) Radio Science paper, "Measuring the Earth's Synchrotron Emission from Radiation Belts with a Lunar Near Side Radio Array". The arxiv link for the paper is  https://arxiv.org/abs/1912.04482. The DOI link is  https://doi.org/10.1029/2019RS006891 , The Earth's Ionosphere is home to a large population of energetic electrons that live in the balance of many factors including input from the Solar wind, and the influence of the Earth's magnetic field. These energetic electrons emit radio waves as they traverse Earth's magnetosphere, leading to short‐lived, strong radio emissions from local regions, as well as persistent weaker emissions that act as a global signature of the population breakdown of all the energetic electrons. Characterizing this weaker emission (Synchrotron Emission) would lead to a greater understanding of the energetic electron populations on a day to day level. A radio array on the near side of the Moon would always be facing the Earth, and would well suited for measuring its low frequency radio emissions. In this work we simulate such a radio array on the lunar near side, to image this weaker synchrotron emission. The specific geometry and location of the test array were made using the most recent lunar maps made by the Lunar Reconnaissance Orbiter. This array would give us unprecedented day to day knowledge of the electron environment around our planet, providing reports of Earth's strong and weak radio emissions, giving both local and global information. , This set of codes should guide you through making the figures in the paper, as well as hopefully being accessible enough for changing the code for your own array. I would encourage you to please reach out to collaborate if that is the case! Requirements: , and CASA 4.7.1 (or greater?) built on python 2.7 Example link for Red Hat 7  https://casa.nrao.edu/download/distro/casa/release/el7/casa-release-4.7.1-el7.tar.gz Users may follow this guide to download and install the correct version of CASA for their system  https://casa.nrao.edu/casadocs/casa-5.5.0/introduction/obtaining-and-installing CASA executables should be fairly straightforward to extract from the untarred files. gcc 4.8.5 or above (or below?) GCC installation instructions can be found here:  https://gcc.gnu.org/install/ SPICE (I use cspice here)  https://naif.jpl.nasa.gov/naif/toolkit_C.html As seen in lunar_furnsh.txt which loads the SPICE kernels, you also must download KERNELS_TO_LOAD = ( '/home/alexhege/SPICE/LunarEph/moon_pa_de421_1900-2050.bpc' '/home/alexhege/SPICE/LunarEph/moon_080317.tf' '/home/alexhege/SPICE/LunarEph/moon_assoc_me.tf' '/home/alexhege/SPICE/LunarEph/pck00010.tpc' '/home/alexhege/SPICE/LunarEph/naif0008.tls' '/home/alexhege/SPICE/LunarEph/de430.bsp' ) All of which can be found at  https://naif.jpl.nasa.gov/pub/naif/generic_kernels/ SLDEM2015_128_60S_60N_000_360_FLOAT.IMG for the lunar surface data by LRO LOLA found at  http://imbrium.mit.edu/DATA/SLDEM2015/GLOBAL/FLOAT_IMG/
    Citation to related publication:
    Hegedus, A., Nenon, Q., Brunet, A., Kasper, J., Sicard, A., Cecconi, B., MacDowall, R., & Baker, D. (2019). Measuring the Earth's Synchrotron Emission from Radiation Belts with a Lunar Near Side Radio Array.  https://arxiv.org/abs/1912.04482 and Hegedus, A., Nenon, Q., Brunet, A., Kasper, J., Sicard, A., Cecconi, B., MacDowall, R., & Baker, D. (2020). Radio Science.  https://doi.org/10.1029/2019RS006891
    Discipline:
    Science and Engineering
    Title:
    Data and Code Set for "Measuring the Earth's Synchrotron Emission from Radiation Belts with a Lunar Near Side Radio Array"

  • Data for Improvement of Plasma Sheet Neural Network Accuracy with Inclusion of Physical Information

    Creator:
    Swiger, Brian M., Liemohn, Michael W., and Ganushkina, Natalia Y.
    Description:
    We sampled the near-Earth plasma sheet using data from the NASA Time History of Events and Macroscale Interactions During Substorms mission. For the observations of the plasma sheet, we used corresponding interplanetary observations using the OMNI database. We used these data to develop a data-driven model that predicts plasma sheet electron flux from upstream solar wind variations. The model output data are included in this work, along with code for analyzing the model performance and producing figures used in the related publication. and Data files are included in hdf5 and Python pickle binary formats; scripts included are set up for use of Python 3 to access and process the pickle binary format data.
    Keyword:
    neural network, plasma sheet, solar wind, machine learning, keV electron flux, deep learning, and space weather
    Citation to related publication:
    Swiger, B. M. et al. 2020. Improvement of Plasma Sheet Neural Network Accuracy With Inclusion of Physical Information. Frontiers in Astronomy and Space Science doi:10.3389/fspas.2020.00042
    Discipline:
    Science and Engineering
    Title:
    Data for Improvement of Plasma Sheet Neural Network Accuracy with Inclusion of Physical Information

  • Supplementary Particle Optical Property Data for "Aerosol radiative forcing from the 2010 Eyjafjallajökull volcanic eruptions"

    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"

  • CT Data of the partial cranium of SGS-UM 2009-002, Saadanius hijazensis (holotype).

    Creator:
    Zalmout, Iyad S, Sanders, William J, MacLatchy, Laura M, Gunnell, Gregg F, Al-Mufarreh, Yahya A, Ali, Mohammad A, Nasser, Abdul-Azziz H, Al-Masari, Abdu M, Al-Sobhi, Salih A, Nadhra, Ayman O, Matari, Adel H, Wilson, Jeffrey A, and Gingerich, Philip D
    Description:
    Reconstructed CT slices for the partial cranium of the holotype specimen of Saadanius hijazensis in DICOM format. Data supporting the publication: New Oligocene primate from Saudi Arabia and the divergence of apes and Old World monkeys,  https://doi.org/10.1038/nature09094 Raw projections are not included in this dataset.
    Keyword:
    Paleontology, Fossil, Saudi Arabia, CT, Primate, Oligocene, Hominoidea, Cercopithecoidea, University of Michigan Museum of Paleontology, and UMMP
    Citation to related publication:
    Zalmout, I., Sanders, W., MacLatchy, L. et al. New Oligocene primate from Saudi Arabia and the divergence of apes and Old World monkeys. Nature 466, 360–364 (2010).  https://doi.org/10.1038/nature09094, A cast of this specimen is held by the University of Michigan Museum of Paleontology (UMMP) under catalog number 14200., and 3D surface model viewable on UMORF site :  https://umorf.ummp.lsa.umich.edu/wp/specimen-data/?Model_ID=1408
    Discipline:
    Science
    Title:
    CT Data of the partial cranium of SGS-UM 2009-002, Saadanius hijazensis (holotype).