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- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for vertebrae of Phenacolemur (University of Michigan Museum of Paleontology catalog number UMMP VP 94723) as a series of TIFF images. Raw projections are not included in this dataset. The reconstructed slice data from the scan are offered here as a series of unsigned 16-bit integer TIFF images. The upper left corner of the first image (*_0000.tif) is the XYZ origin.
- Keyword:
- Paleontology, Fossil, CT, Paromomyidae, UMMP, University of Michigan Museum of Paleontology, Eocene, CTEES, and 31cf6e4a-86dd-9452-49f4-c5ce0d946613
- Discipline:
- Science
-
- Creator:
- Yang, Bing and Wittkopp, Patricia J
- Description:
- Datafiles and code described in accompanying MS, currently in review
- Keyword:
- regulatory network evolution
- Discipline:
- Science
-
- 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:
- Engineering and Science
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- 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 and Jiao, Z., Chen, Y., Manchester, W. (2020). Data for Solar Flare Intensity Prediction with Machine Learning Models [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/b07j-bj08
- Discipline:
- Engineering and Science
-
- Creator:
- Gultekin, Kayhan, Nyland, Kristina, Gray, Nichole, Fehmer, Greg , Huang, Tianchi, Sparkman, Matthew, Reines, Amy E., Greene, Jenny E., Cackett, Edward M., and Baldassare, Vivienne
- Description:
- The data were processed using the scripted VLA calibration pipeline ( https://science.nrao.edu/facilities/vla/data-processing/pipeline/scripted-pipeline) for the Common Astronomy Software Applications (CASA) package version 5.3.0. Imaging was performed using the TCLEAN task in CASA with standard parameters appropriate for broadband data with point-source emissison. We used Briggs weighting with robust parameters between 0 and 1. Self calibration was implemented manually on an as-needed basis for sufficiently bright sources with evidence for residual phase errors in the image plane.
- Keyword:
- active galactic nuclei, radio galaxies, fundamental plane, and intermediate-mass black holes
- Citation to related publication:
- Gultekin et al. (2022) MNRAS, in press
- Discipline:
- Science
-
- Creator:
- Katz, Sarah A., Levin, Naomi E., Abbott, Mark B., Rodbell, Donald T., Passey, Benjamin H., DeLuca, Nicole N., Larsen, Darren J., and Woods, Arielle
- Description:
- This dataset presents stable isotope data (d13C, d18O, D47, D17O) from Holocene lake cores from three lakes in the Peruvian Andes (Lakes Junin, Pumacocha, and Mehcocha). We also present new radiocarbon (14C) data and core age models for Lakes Junin and Mehcocha. We use these data to explore trends in lake water temperatures and evaporative state (i.e., water balance) over the Holocene. Our clumped isotope (D47) results suggest lake water temperatures at all three lakes were stable over the Holocene and similar to present day lake temperatures. Our triple oxygen isotope (D’17O) results illustrate that lake water balance at all three lakes was variable over the Holocene and tracks changes in austral summertime insolation, suggesting a connection between central Andean water balance and the South American summer monsoon (SASM).
- Keyword:
- Holocene, Andes, temperature, water balance, lacustrine carbonate, lake hydrology, triple oxygen isotopes, and clumped isotopes
- Citation to related publication:
- Katz, S.A., Levin, N.E., Abbott, M.B., Rodbell, D.T., Passey, B.H., DeLuca, N.M., Larsen, D.J., Woods, A. "Holocene temperature and water stress in the Peruvian Andes: insights from lake carbonate clumped and triple oxygen isotopes," in review. and Katz, S.A., (2024) Andean interglacial climate and hydrology over the last 650,000 years. [PhD Thesis, University of Michigan]
- Discipline:
- Science
-
- Creator:
- Carson, William F., IV
- Description:
- Transcriptional accessibility of chromatin is central to guiding CD4+ T cell function through regulation of lineage specific gene expression. Myst1 is a histone acetyltransferase responsible for acetylation of the protein tail of histone 4 at lysine residue 16 (H416ac), resulting in increased transcriptional accessibility and activation of gene transcription. Previous studies have described a role for Myst1 in governing lymphocyte development in the thymus, however the role of Myst1 and H4K16ac in guiding activation of peripheral CD4+ T cells has not been studied. Activation of human and murine CD4+ T cells resulted in upregulation of Myst1 expression, and deletion of Myst1 resulted in changes in proliferative responses to both polyclonal stimulus and exogenous cytokines. Myst1-deficient T cells also exhibited modulations in lineage commitment, with decreased function in TH1/TH2 skewing conditions and increased function in response to TH17-promoting conditions. Regulation of Myst1 function in CD4+ T cells appears governed at least in part by STAT5, as Myst1 expression is regulated by STAT5 expression and DNA binding, and modulations in H4K16ac in Myst1-deficient CD4+ T cells is observable at sites in the promoter regions of lineage specific genes following skewing to the TH1 or TH2 lineage in vitro. Taken together, these results indicate an important role for the STAT5-Myst1 epigenetic axis in governing the activation and effector function of CD4+ T cells.
- Discipline:
- Science
-
- Creator:
- Attari, Ali
- Description:
- Please refer to the "README.txt" for more details., MATLAB R2018a (Mathworks, Natick, MA, USA) was used to process this data., and Excel (Microsoft Office) was used to store survey data on the comfort of both systems and also to provide absolute and relative intraobserver variablities for the DM device.
- Keyword:
- Digital Manometry
- Citation to related publication:
- Comparison of anorectal function measured using wearable digital manometry and a high resolution manometry system Attari A, Chey WD, Baker JR, Ashton-Miller JA (2020) Comparison of anorectal function measured using wearable digital manometry and a high resolution manometry system. PLOS ONE 15(9): e0228761. https://doi.org/10.1371/journal.pone.0228761
- Discipline:
- Engineering, Science, and Health Sciences
-
- Creator:
- Wozniak, Matthew C. and Dos Santos, Thiago
- Description:
- Data and Code are divided into separate folders. Data is given for all simulations of all 3 models included in manuscript, as well as the FLUXNET data processed into monthly NetCDF files.
- Citation to related publication:
- Wozniak, M. C., Bonan, G. B., Keppel-Aleks, G., & Steiner, A. L. (2020). Influence of Vertical Heterogeneities in the Canopy Microenvironment on Interannual Variability of Carbon Uptake in Temperate Deciduous Forests. Journal of Geophysical Research: Biogeosciences, 125(8), e2020JG005658. https://doi.org/10.1029/2020JG005658
- Discipline:
- Science
-
- Creator:
- Wozniak, Matthew C., Steiner, Allison L., and Solmon, Fabien
- Description:
- Pollen grains emitted from vegetation can rupture, releasing subpollen particles (SPPs) as fine atmospheric particulates. Previous laboratory research demonstrates potential for SPPs as efficient cloud condensation nuclei (CCN). We develop the first model of atmospheric pollen grain rupture, and implement the mechanism in regional climate model simulations over spring pollen season in the United States with a CCN-dependent moisture scheme. The source of SPPs (surface or in-atmosphere) depends on region and sometimes season, due to the distribution of relative humidity and rain. Simulated concentrations of SPPs are approximately 1-10 or 1-1,000 cm-3, depending on the number of SPPs produced per pollen grain (nspg). Lower nspg (103) produces a negligible effect on precipitation, but high nspg (106) in clean continental CCN background concentrations (100 CCN cm-3) shows SPPs suppress average seasonal precipitation by 32% and shift rates from heavy to light while increasing dry days. This effect is likely smaller for polluted air. pollen_rupture_precipitation_BASE_ensemble_daily.nc - data for BASE ensemble average pollen_rupture_precipitation_SPPHIGH_ensemble_daily.nc - data for SPPHIGH ensemble average pollen_rupture_precipitation_SPPLIT_ensemble_daily.nc - data for SPPLIT ensemble average
- Discipline:
- Science
-
- Creator:
- Liemohn, Michael W, Adam, Joshua G, and Ganushkina, Natalia Y
- Description:
- Many statistical tools have been developed to aid in the assessment of a numerical model’s quality at reproducing observations. Some of these techniques focus on the identification of events within the data set, times when the observed value is beyond some threshold value that defines it as a value of keen interest. An example of this is whether it will rain, in which events are defined as any precipitation above some defined amount. A method called the sliding threshold of observation for numeric evaluation (STONE) curve sweeps the event definition threshold of both the model output and the observations, resulting in the identification of threshold intervals for which the model does well at sorting the observations into events and nonevents. An excellent data-model comparison will have a smooth STONE curve, but the STONE curve can have wiggles and ripples in it. These features reveal clusters when the model systematically overestimates or underestimates the observations. This study establishes the connection between features in the STONE curve and attributes of the data-model relationship. The method is applied to a space weather example.
- Keyword:
- space physics, statistical methods, and STONE curve
- Citation to related publication:
- Liemohn, M. W., Adam, J. G., & Ganushkina, N. Y. (2022). Analysis of features in a sliding threshold of observation for numeric evaluation (STONE) curve. Space Weather, 20, e2022SW003102. https://doi.org/10.1029/2022SW003102
- Discipline:
- Science
-
- Creator:
- Nelson, Arin D.
- Description:
- These MATLAB data files contain all the observations and model output used in the article Improved Internal Gravity Wave Spectral Continuum in a Regional Ocean Model by Nelson et al., recently submitted to Journal of Geophysical Research: Oceans.
- Keyword:
- Ocean, Ocean Mooring, Ocean Modeling, and Internal Waves
- Citation to related publication:
- Nelson, A. D., Arbic, B. K., Menemenlis, D., Peltier, W. R., Alford, M. H., Grisouard, N., & Klymak, J. M. (2020). Improved Internal Wave Spectral Continuum in a Regional Ocean Model. Journal of Geophysical Research: Oceans, 125(5), e2019JC015974. https://doi.org/10.1029/2019JC015974
- Discipline:
- Science
-
- Creator:
- Folz, Jeff
- Description:
- Data consists largely of UV-VIs spectra, both raw and analyzed, that were used to calibrate the relevant sensor. A more detailed description of individual files' contents can be found in the ReadMe word document.
- Discipline:
- Science
-
- Creator:
- Wittkopp, Patricia J and Metzger, Brian P H
- Description:
- .zip file includes data files and R code used for analysis.
- Citation to related publication:
- Metzger, B. P. H., & Wittkopp, P. J. (2019). Compensatory trans-regulatory alleles minimizing variation in TDH3 expression are common within Saccharomyces cerevisiae. Evolution Letters, 3(5), 448–461. https://doi.org/10.1002/evl3.137 and http://biorxiv.org/cgi/content/short/566653v1
- Discipline:
- Science
-
- Creator:
- Liemohn, Michael W
- Description:
- The editorial decision process for the Journal of Geophysics Research Space Physics is assisted by over 1,000 scientists every year, providing over 3,000 reviews per year. These statistics are presented for the years 2013 through 2018, showing some fluctuations but, overall, consistency in the response of the space physics research community to requests to serve as manuscript reviewers. Over half of these reviews are submitted on time, and the average time to review actually dropped as the load increased. This is greatly appreciated and the community is to be commended and thanked for their willingness to help make this journal thrive and remain a premiere publication in the field.
- Keyword:
- Editorial and reviewer statistics
- Citation to related publication:
- Liemohn, M. W. (2020). Editorial: Multiyear analysis of JGR Space Physics reviewing statistics. Journal of Geophysical Research Space Physics, 125, e2019JA027719. https://doi.org/10.1029/2019JA027719
- Discipline:
- Science
-
- Creator:
- Dewey, Ryan M, Livi, Stefano, Lepri, Susan T, Raines, Jim M, Ploof, Keeling, and The HIS Science Team
- Description:
- The data contained within the archive are for analysis and replication of Figure 2 in Livi et al. (2023), First Results from the Solar Orbiter Heavy Ion Sensor, Astronomy & Astrophysics. The readme.txt file contains more details on the contents of the archive and its files. Livi et al. (2023) reports the first solar wind composition measurements collected from the Heavy Ion Sensor (HIS) on the Solar Orbiter spacecraft. The period of study spans January-June 2022 during with the spacecraft completed nearly a full orbit about the Sun, from 0.3 AU to 1.0 AU. The solar wind composition within this publication are the first within the inner heliosphere. This paper describes the data and its processing from raw measurements (e.g., the data contained within this archive) to derived composition data products, and examines these composition data products about an interplanetary shock and interplanetary coronal mass ejection. Finally, these composition data are examined statistically and compared to historical data sets.
- Keyword:
- Solar Orbiter, Solar wind, Heavy ions, and Heavy Ion Sensor
- Citation to related publication:
- Livi, S., et al. (2023), First Results from the Solar Orbiter Heavy Ion Sensor, Astronomy & Astrophysics. https://doi.org/10.1051/0004-6361/202346304 and Owen, C., et al. (2020), The Solar Orbiter Solar Wind Analyser (SWA) suite, Astronomy & Astrophysics, 642. https://doi.org/10.1051/0004-6361/201937259
- Discipline:
- Science
-
- Creator:
- Malhotra, Garima and Ridley, Aaron
- Description:
- This research aims to understand the importance of lower thermospheric atomic oxygen on the upper thermosphere. O number densities between 95-100 km from WACCM-X are much closer to the observations from SABER instrument on TIMED satellite as compared to those from MSIS. We show in this study that the correction of the lower boundary atomic oxygen yields better agreement between GITM and GUVI O/N2 in the upper thermosphere .
- Keyword:
- Lower Thermosphere Atomic Oxygen, Thermospheric Dynamics, Thermospheric composition and mixing, Lower-Upper Thermosphere Vertical Coupling, GITM - WACCMX coupling, and Global Ionosphere Thermosphere Model
- Citation to related publication:
- Malhotra, G., Ridley, A. J., Marsh, D. R., Wu, C., Paxton, L. J., & Mlynczak, M. G. (2020). Impacts of Lower Thermospheric Atomic Oxygen on Thermospheric Dynamics and Composition Using the Global Ionosphere Thermosphere Model. Journal of Geophysical Research: Space Physics, e2020JA027877. https://doi.org/10.1029/2020JA027877
- Discipline:
- Science
-
- 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., Liemohn, M. W., & Ganushkina, N. Y. (2020). Improvement of Plasma Sheet Neural Network Accuracy With Inclusion of Physical Information. Frontiers in Astronomy and Space Sciences, 7. https://doi.org/10.3389/fspas.2020.00042
- Discipline:
- Science and Engineering
-
Data for Macroscopic Transition Metal Dichalcogenides Monolayers with Uniformly High Optical Quality
- Creator:
- Li, Qiuyang, Alfrey, Adam, Hu, Jiaqi, Lydick, Nathanial, Paik, Eunice, Liu, Bin, Sun, Haiping, Lu, Yang, Wang, Ruoyu, Forrest, Stephen, and Deng, Hui
- Description:
- This dataset contains raw and source data for all figures generated in the manuscript "Macroscopic Transition Metal Dichalcogenides Monolayers with Uniformly High Optical Quality" The raw data files include '.spe' data, which are spectral data collected by LightField Sofware, and '.dset' and '.vms' files, which are X-ray photoelectron spectroscopy (XPS) data and require CasaXPS to access. The source data files include the processed data that can be directly used for generating the corresponding figures in the manuscript.
- Keyword:
- 2D materials, Exciton-polaritons, and Photonics
- Discipline:
- Science
-
- Creator:
- Young, Lauren, Ferrari, Fabienne, Kelly, Lisa, Martin, Tara, Thompson-Iritani, Sally , and LaFollette, Megan R
- Description:
- This dataset contains the results of a survey about professional quality of life for individuals working in animal research facilities. The survey included questions about professional quality of life, job satisfaction, retention, and other factors influencing compassion fatigue resiliency. Data was collected via Qualtrics survey as described in the methodology section. This dataset is associated with the following publication, accepted by PLOS One: PONE-D-23-17551R2 Professional quality of life in animal research personnel is linked to retention & job satisfaction: A mixed-methods cross-sectional survey on compassion fatigue in the USA by Lauren Young, Fabienne Ferrari, Lisa Kelly, Tara Martin, Sally Thompson-Iritani, and Megan R LaFollette
- Keyword:
- compassion fatigue, culture of care, mental health, retention, job satisfaction, animal research, institutional culture, resiliency, and professional quality of life
- Citation to related publication:
- PONE-D-23-17551R2 Professional quality of life in animal research personnel is linked to retention & job satisfaction: A mixed-methods cross-sectional survey on compassion fatigue in the USA by Lauren Young, Fabienne Ferrari, Lisa Kelly, Tara Martin, Sally Thompson-Iritani, and Megan R LaFollette
- Discipline:
- Science
-
- Creator:
- Liemohn, Michael W
- Description:
- Earth’s upper atmosphere above 500 km altitude constantly loses charged particles to outer space in a process called ionospheric outflow. This outflow is important for the dynamics of the near-Earth space environment (“space weather”) yet is poorly understood on a global scale. A mission is needed to observe the global patterns of ionospheric outflow and its relation to space weather driving conditions. The science objectives of such a mission could include not only the reconstruction of global outflow patterns but also the relation of these patterns to geomagnetic activity and the spatial and temporal nature of outflow composition. A study is presented to show that four well-placed spacecraft would be sufficient for reasonable outflow reconstructions.
- Keyword:
- ionosphere, magnetosphere, satellite mission concept, and space weather
- Citation to related publication:
- Liemohn, M. W., Jörg-Micha Jahn, Raluca Ilie, Natalia Y. Ganushkina, Daniel T. Welling, Heather Elliott, Meghan Burleigh, Kaitlin Doublestein, Stephanie Colon-Rodriguez, Pauline Dredger, & Philip Valek (2024). Reconstruction analysis of global ionospheric outflow patterns. Journal of Geophysical Research Space Physics, 129, e2023JA032238. https://doi/org/10.1029/2024JA032238
- Discipline:
- Science
-
- 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. (2020). Solar Flare Intensity Prediction With Machine Learning Models. Space Weather, 18(7), e2020SW002440. https://doi.org/10.1029/2020SW002440 and Chen, Y., & Manchester, W. (2019). Data and Data products for machine learning applied to solar flares [Data set], University of Michigan - Deep Blue. https://doi.org/10.7302/qnsq-cs38
- Discipline:
- Engineering and Science
-
- Creator:
- Liemohn, Michael W, Azari, Abigail R, Ganushkina, Natalia Yu, and Rastätter, Lutz
- Description:
- Scientists often try to reproduce observations with a model, helping them explain the observations by adjusting known and controllable features within the model. They then use a large variety of metrics for assessing the ability of a model to reproduce the observations. One such metric is called the relative operating characteristic (ROC) curve, a tool that assesses a model’s ability to predict events within the data. The ROC curve is made by sliding the event-definition threshold in the model output, calculating certain metrics and making a graph of the results. Here, a new model assessment tool is introduced, called the sliding threshold of observation for numeric evaluation (STONE) curve. The STONE curve is created by sliding the event definition threshold not only for the model output but also simultaneously for the data values. This is applicable when the model output is trying to reproduce the exact values of a particular data set. While the ROC curve is still a highly valuable tool for optimizing the prediction of known and pre-classified events, it is argued here that the STONE curve is better for assessing model prediction of a continuous-valued data set. and Data and code were created using IDL, but can also be accessed with the open-source Gnu Data Language (GDL; see https://github.com/gnudatalanguage/gdl)
- Keyword:
- ROC curve, STONE curve, data-model comparison, model validation, forecasting, and statistical methods
- Citation to related publication:
- Liemohn, M. W., Azari, A. R., Ganushkina, N. Yu., & Rastätter, L. (2020). The STONE curve: A ROC-derived model performance assessment tool. Earth and Space Science, 7, e2020EA001106. https://doi.org/10.2019/2020EA001106
- Discipline:
- Science
-
- Creator:
- Sergio E. Vidal-Luengo and Mark B. Moldwin
- Description:
- Multi-satellite tracking of solar wind dynamic pressure pulse observations through the Earth's magnetosphere enables us to distinguish local changes with propagation signatures.
- Keyword:
- Heliophysics, Magnetosphere, Dynamic pressure pulse, Magnetosphere, THEMIS, MMS, Cluster, SuperMag, and Heliophysics System Observatory
- Citation to related publication:
- Vidal-Luengo, S. E., & Moldwin, M. B. (2021). Global magnetosphere response to solar wind dynamic pressure pulses during northward IMF using the heliophysics system observatory. Journal of Geophysical Research: Space Physics, 126, e2020JA028587. https://doi.org/10.1029/2020JA028587
- Discipline:
- Science
-
- Creator:
- Bemmels, Jordan B. and Dick, Christopher W.
- Description:
- Raw SNP genotypes are provided in STRUCTURE format, with a maximum of one SNP reported per ddRAD locus. The files "caryco_SNP.str" and "caryov_SNP.str" are genotypes for Carya cordiformis and Carya ovata, respectively. The first column of each file is the individual name, the second column is the population (see original publication for information on population locations), and the remaining columns are genotypes of individual SNPs. Rows represent individuals, with the diploid genotypes contained on two lines per individual. Missing data are entered as "0" (zero). The first row is a header with a unique identifier for each SNP. and Occurrence records for each species are provided in the file "occs_carya.csv" and contain the latitude and longitude of each record.
- Keyword:
- eastern North America, glacial refugia, phylogeography, temperate trees, and single nucleotide polymorphisms
- Discipline:
- Science
-
- Creator:
- Liemohn, Michael W and Wooden, Paige
- Description:
- Journals sometimes focus the attention of the research community by having a special collection, sometimes an entire special issue, devoted to a single topic. A reasonable question to ask is whether the extra effort of organizing, promoting, and maintaining the special collection is worthwhile. The paper that this data set accompanies examines paper impact in the Journal of Geophysical Research Space Physics, separating the special collection papers from the non-special-collection submissions. The conclusion is that special collections are worth the extra work.
- Keyword:
- journal special collections, bibliometrics, citations, and downloads
- Citation to related publication:
- Liemohn, M. W., & Wooden, P. (2019). Editorial: Impact of special collections in JGR Space Physics. Journal of Geophysical Research Space Physics. https://doi.org/10.1002/essoar.10501036.2
- Discipline:
- Science
-
- Creator:
- Liemohn, Michael W, McCollough, James P, Engel, Miles A, Jordanova, Vania K, and Morley, Steven K
- Description:
- There is a directory tree inside this zipped file. The main directory has the Adobe Illustrator plots of the figures in the paper, Space Weather journal manuscript # 2018SW002067, "Model evaluation guidelines for geomagnetic index predictions" by M. W. Liemohn and coauthors. The three subdirectories have the files for the individual models, the data to which they are compared, and the IDL code used to create the figure plots and metrics calculations. and Date coverage is specific to each model. The RAMSCB model covers January 2005, the WINDMI model all of 2014, and the UPOS model 1.5 solar cycles, from 1 October 2001 through 29 July 2013.
- Keyword:
- space weather, model assessment, time series metrics, and geomagnetic indices
- Discipline:
- Science
-
- Creator:
- R Paul Drake
- Description:
- The specific focus of the project was radiative shocks, which develop when shock waves become so fast and hot that the radiation from the shocked matter dominates the energy transport. This in turn leads to changes in the shock structure. Radiative shocks are challenging to simulate, as they include phenomena on a range of spatial and temporal scales and involve two types of nonlinear physics Ð- hydrodynamics and radiation transport. Even so, the range of physics involved is narrow enough that one can hope to model all of it with sufficient fidelity to reproduce the data. CRASH was focused on developing predictions for a sequence of experiments performed in Project Year 5, in which those experiments represented an extrapolation from all previously available data. The previous data involved driving radiative shocks within cylindrical structures, and mainly straight tubes. The Year 5 experiments drove a radiative shock down an elliptical tube. Our long-stated goal for these predictions was that the distribution of predicted values would overlap significantly with the observed distribution. We achieved this goal. Achieving our goal required the conversion of an established space-weather code to model radiative shocks at high energy density. To obtain reasonable fidelity with respect to the experimental data required implementing a laser absorption package, in addition to a hydrodynamic solver, electron physics and heat conduction, and multigroup diffusive radiation transport. The dedicated experiments provided evidence of experimental variability, validation of the calculation of initial shock wave behavior, and validation data at many observation times using cylindrical shock tubes. Following this were preparatory experiments for and finally the execution of the Year 5 experiments. The predictive science research included a wide range of sensitivity studies to determine which variables were important and a sequence of predictive studies focused on specific issues and sets of data. This led ultimately to predictions of shock location for the Year 5 experiments. A conclusion from this project is that the serious quantification of uncertainty in simulations is a dauntingly difficult and expensive prospect. Pre-existing codes are unlikely to have been built with attention to what will be needed to quantify their uncertainty. Pre-existing experimental results are even more unlikely to include a sufficiently detailed analysis of the experimental uncertainties. And this will also be true of most experiments that might be used to validate components of the simulation. The analysis of uncertainty in any one of the physical processes (and related physical constants) is a major effort. And addressing model form uncertainty is an even bigger challenge, that may in principle require development of complete, alternative simulation models. We made a start at all of this, and completed almost none of it. But by the end of a project, we finally had all the pieces in place and working that would have enabled a range of important studies and advances in relatively near-term years. But the sponsor terminated the program after only five years. For most of the participants this was a relatively minor development, although for a few of them it proved to be enormously disruptive. We believe that the cost to the nation, in work that was ready be done but now will not be, was much much larger. The sketch of the target was produced using a drawing program based on the experimental dimensions. The annotated photograph of the target was obtained using a visible-light camera. The colorized radiographs were obtained via backilit-pinhole radiography of a radiative shock propagating down an elliptical tube, at 26 ns after the lasers driving the shock tube fired. The graph showing lines and circles was produced by running many computer models, analyzing their statistical distribution, and measuring actual shock positions in the experiment.
- Keyword:
- Radiative shock
- Discipline:
- Science
-
- Creator:
- Bressler, Alison and Blesh, Jennifer
- Description:
- This dataset contains three data files and three corresponding metadata files used in Bressler, A., and J. Blesh. 2023. A grass-legume cover crop maintains nitrogen inputs and nitrous oxide fluxes from an organic agroecosystem. Ecosphere. The file “N2O_Flux.xls” contains daily nitrous oxide data organized by replicate block, treatment, and date. The file “Soil_N.xls” contains nitrate and ammonium data organized by replicate block, treatment, and date. The file “Cover_crop_corn_soil.xls” contains baseline soil fertility characteristics, cover crop and corn biomass, nitrogen and carbon content, legume BNF, and cumulative N2O content organized by replicate block and treatment. The corresponding metadata files: “N2O_Flux_metadata.xls”, “Soil_N_metadata.xls”, and “Cover_crop_corn_soil_metadata.xls” provide detailed descriptions of all variables in each data set and any abbreviations used.
- Keyword:
- cover crops, nitrous oxide, corn, biological nitrogen fixation, and legume-grass mixtures
- Citation to related publication:
- Bressler, A., and J. Blesh. 2023. A grass-legume cover crop maintains nitrogen inputs and nitrous oxide fluxes from an organic agroecosystem. Ecosphere. 14(2): e4428. https://doi.org/10.1002/ecs2.4428
- Discipline:
- Science
-
- Creator:
- Bressler, Alison and Blesh, Jennifer
- Description:
- This dataset contains three data files and three corresponding metadata files used in Bressler, A., and J. Blesh. 2022. Episodic N2O emissions following tillage of a legume-grass cover crop mixture. Biogeosciences. The file “Cover_crop_soil_N2O.xls” contains data organized by site, replicate block, and treatment for spring cover crop biomass, nitrogen and carbon content, and legume BNF; soil fertility characteristics including potentially mineralizable nitrogen, particulate organic matter stocks, concentrations, and nitrogen content; and cumulative nitrous oxide data. The file “Soil_properties.xls” contains baseline soil data organized by site and replicate block. The file “Daily_N2O.xls” contains daily nitrous oxide data organized by site, replicate block, treatment, and date. The corresponding metadata files: “Cover_crop_soil_N2O_metadata.xls”, and “Soil_properties_metadata.xls”, and “Daily_N2O_metadata.xls” provided detailed descriptions of all variables in each data set and any abbreviations used.
- Keyword:
- cover crops, legume-grass mixtures, nitrous oxide, particulate organic matter, soil organic matter.
- Citation to related publication:
- Bressler, A., and J. Blesh. 2022. Episodic N2O emissions following tillage of a legume-grass cover crop mixture. Biogeosciences.
- Discipline:
- Science
-
- Creator:
- Surdoval, Alison, Jain, Meha, Wang, Haoyu, and Blesh, Jennifer
- Description:
- We conducted a mixed-methods study to understand how financial incentive programs impact transitions to cover cropping in Michigan. Michigan farms span a wide range of soil types, climate conditions, and cropping systems that create opportunities for cover crop adoption in the state. We tested the relationship between Environmental Quality Incentives Program (EQIP) payments for cover crops and cover crop adoption between 2008-2019, as measured by remote sensing. Panel fixed effects regressions showed that EQIP increased winter cover crop presence. Every EQIP dollar for cover crops was associated with a 0.01 hectare increase in winter cover, while each hectare enrolled in an EQIP contract for cover crops was associated with a 0.86 – 0.93 hectare increase in winter cover.
- Keyword:
- adoption, cover crop, Environmental Quality Incentives Program, financial incentive program, Michigan, remote sensing
- Citation to related publication:
- Surdoval, A., Jain, M., Blair, E., Wang, H., and J. Blesh. In press. Financial incentive programs and farm diversification with cover crops: Assessing opportunities and challenges.
- Discipline:
- Science
-
- Creator:
- Blesh, Jennifer
- Description:
- This dataset contains three data files used in: Blesh, J. 2017. Functional traits in cover crop mixtures: biological nitrogen fixation and multifunctionality. Journal of Applied Ecology. There are also three corresponding metadata files. The file “Ecosystem_functions_soil_species.csv” contains data organized by farm, treatment, replicate block, and species combining the fall and spring sampling time points. These data include aboveground biomass, nitrogen and carbon content, and biological nitrogen fixation for the plant species. The dataset also includes measured soil characteristics for each farm site. The file “Ecosystem_functions_soil_treatment.csv” contains data organized by farm, treatment, and replicate block for the fall and spring sampling time points combined. These data include aboveground biomass, nitrogen and carbon content, and biological nitrogen fixation aggregated by treatment. The dataset also includes measured soil characteristics for each farm site. The file “Traits_unstandardized.csv” contains individual plant trait data, a subset of which were used to calculate an index of functional diversity after they were standardized to have zero mean and unit variance. These data are organized by farm, treatment, replicate block, and species. The corresponding metadata files: “Ecosystem_functions_soil_species_metadata.csv”, “Ecosystem_functions_soil_treatment_metadata.csv”, and “Traits_unstandardized_metadata.csv” provide a detailed description of all variables in each dataset and any abbreviations used. Note: On Dec 19th 2017, the format of the files was changed to csv to aid preservation. The following information was added to the three metadata files: the name of the data file the metadata refers to, an explanation as to the meaning of blank cells in the data file, a full citation to the paper where the author describes her findings and contact information for the author.
- Keyword:
- agroecology, biological nitrogen fixation, functional diversity, and cover crop
- Discipline:
- Science
-
- 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
- Discipline:
- Science
-
- 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
- Discipline:
- Science
-
- Creator:
- Yang, Emily G, Kort, Eric A, Wu, Dien, Lin, John C, Oda, Tomohiro, Ye, Xinxin, and Lauvaux, Thomas
- Description:
- This data set supports a study that seeks to evaluate global fossil fuel CO2 emissions inventory representations of CO2 emissions of five cities in the Middle East, and assess the ability of satellite observations to inform this evaluation. Improved observational understanding of urban CO2 emissions, a large and dynamic global source of fossil CO2, can provide essential insights for both carbon cycle science and mitigation decision making. In this study we compare three distinct global CO2 emissions inventory representations of urban CO2 emissions for five Middle Eastern cities (Riyadh, Mecca, Tabuk, Jeddah, and Baghdad) and use independent satellite observations from the Orbiting Carbon Observatory-2 (OCO-2) satellite to evaluate the inventory representations of afternoon emissions. We use the column version of the Stochastic Time-Inverted Lagrangian Transport (X-STILT) model to account for atmospheric transport and link emissions to observations. We compare XCO2 simulations with observations to determine optimum inventory scaling factors. Applying these factors, we find that the average summed emissions for all five cities are 100 MtC/y (50-151, 90% CI), which is 2.0 (1.0, 3.0) times the average prior inventory magnitudes. The total adjustment of the emissions of these cities comes out to ~7% (0%, 14%) of total Middle Eastern emissions (~700 MtC/y). We find our results to be insensitive to the prior spatial distributions in inventories of the cities’ emissions, facilitating robust quantitative assessments of urban emission magnitudes without accurate high-resolution gridded inventories. and There are three files included in this data set, and all data are in tab-delimited form. The first file, xco2_lat.zip, contains 26 separate text files, each named by the city and date of the corresponding OCO-2 overpass. Each of these 26 files includes overpass-specific data, with modeled and observed XCO2 values binned by 0.1 degree of latitude. The file overpass_scaling_factors.txt provides the scaling factors for each overpass used in this study. The file city_estimates.txt provides the scaled emissions estimates for each city (or sum of cities) as well as the lower and upper bounds of the 90% confidence intervals, for each inventory.
- Keyword:
- greenhouse gases, carbon dioxide, urban, cities, satellite, remote sensing, Lagrangian modeling, emissions inventories, carbon cycle, and climate
- Citation to related publication:
- Yang, E. G., Kort, E. A., Wu, D., Lin, J. C., Oda, T., Ye, X., & Lauvaux, T. (2020). Using space‐based observations and Lagrangian modeling to evaluate urban carbon dioxide emissions in the Middle East. Journal of Geophysical Research: Atmospheres, 125, e2019JD031922. https://doi.org/10.1029/2019JD031922
- Discipline:
- Science
-
- Creator:
- Su, Xue, Zhang, Youxue, Liu, Yang, and Holder, Robert M.
- Description:
- It is commonly thought that volcanic glass only records volatile loss during the eruptions in the Moon. However, our recent work shows that Na, K and Cu (moderately volatile elements) in lunar 74220 orange glass beads are enriched near the bead surfaces and depleted in the bead interiors, forming an overall “U-shaped” profile. The “U-shaped” profile means that rather than being “lost” into space, Na, K and Cu were “gained” into the volcanic glass during the eruption, which is contrary to the “volatile loss” story. Three different instruments (EMP, SIMS and LA-ICP-MS) were used to verify the discovery. We propose that such U-shaped Na, K and Cu profiles were formed by initial outgassing and subsequent in-gassing of Na, K and Cu when the beads were flying from the vent onto the surface through the cooling volcanic gas plume. Hence, in-gassing and the formation of surface coatings are two processes that are genetically linked during the pyroclastic eruption and evolution of the gas cloud. To quantify the processes that formed the U-shaped profiles, we developed a diffusion and surface-equilibrium model using available literature data on Na and Cu diffusivity in basaltic melts. The model reproduced U-shaped Na and Cu concentration profiles with outgassing at high temperature and subsequent in-gassing as beads cooled. By fitting the measured Na and Cu profiles, we found that the cooling time scales of individual orange glass beads range from 48 to 179 s. This is the first time that both outgassing and in-gassing were modeled and the cooling time scales of individual 74220 volcanic orange glass beads were estimated. The discovery of the U-shaped profiles of moderately volatile elements inside volcanic beads provides significant constraints on partial pressures of relevant volcanic gas species in the eruption plume.
- Keyword:
- Moon, Volcanic orange glass beads, Moderately volatile elements, Outgassing and in-gassing, and Cooling time scales
- Citation to related publication:
- Su, X., Zhang, Y., Liu, Y. and Holder, R.M. (2023) Outgassing and in-gassing of Na, K and Cu in lunar 74220 orange glass beads. Earth and Planetary Science Letters 602. https://doi.org/10.1016/j.epsl.2022.117924
- Discipline:
- Science
-
- Creator:
- Su, Xue and Zhang, Youxue
- Description:
- The H2O concentration and H2O/Ce ratio in olivine-hosted melt inclusions are high (H2O up to 1410 ppm; H2O/Ce up to 77) in lunar sample 74220 but lower (H2O up to 430 ppm; H2O/Ce up to 9.4) in all other lunar samples studied before this work. This difference is absent for other volatiles (F, S, and Cl) in melt inclusions in 74220 and other lunar samples. Because H2O (or H) is a critical volatile component with significant ramifications on the origin and evolution of the Moon, it is important to understand what causes such a large gap in H2O/Ce ratio between 74220 and other lunar samples. Two explanations have been advanced. One is that volcanic product in sample 74220 has the highest cooling rate and thus best preserved H2O in melt inclusions compared to melt inclusions in other samples. The other explanation is that sample 74220 is a localized heterogeneity enriched in some volatiles. To distinguish the two possibilities, here we present new data from three rapidly cooled lunar samples: olivine-hosted glassy melt inclusions (OHMIs) in 74220 regolith and 79135 regolith breccia, and pyroxene-hosted glassy melt inclusions (PHMIs) in 15597 pigeonite basalts. If the gap is due to the difference in cooling rates, samples with cooling rates between 74220 and other studied lunar samples should have preserved intermediate H2O concentrations and H2O/Ce ratios. Our results show that melt inclusions in 79135 and 15597 contain high H2O concentrations (up to 969 ppm in 79135 and up to 793 ppm in 15597) and high H2O/Ce ratios (up to 21 in 79135 and up to 13 in 15997). Combined with literature data, we confirm that H2O/Ce ratios of different lunar samples are positively correlated to the cooling rates and independent of the type of mare basalts. Our work bridges the big gap in H2O/Ce ratio among 74220 and other lunar samples. We hence reinforce the interpretation that the lunar sample with the highest cooling rate best represents pre-eruptive volatiles in lunar basalts due to the least degassing. H2O, F, P, S and Cl concentrations in the lunar primitive mantle are also estimated in this work. and *** 2024-03-19: In addition to the files in the previous version, this updated deposit contains more data files as the supplementary files of the paper. For example, we added a summary excel file containing data that are used for figures in the paper, and an excel file contains data in the tables of the paper for easy use by readers. See ReadMe.txt for changes.
- Keyword:
- Water in the Moon, volatiles in the Moon, olivine-hosted melt inclusions, pyroxene-hosted melt inclusions, F/P ratio, S/Dy ratio, Cl/Ba ratio
- Discipline:
- Science
-
- Creator:
- Mukhopadhyay, Agnit, Daniel T Welling, Michael W Liemohn, Aaron J Ridley, Shibaji Chakrabarty, and Brian J Anderson
- Description:
- An updated auroral conductance module is built for global models, using nonlinear regression & empirical adjustments to span extreme events., Expanded dataset raises the ceiling of conductance values, impacting the ionospheric potential dB/dt & dB predictions during extreme events., and Application of the expanded model with empirical adjustments refines the conductance pattern, and improves dB/dt predictions significantly.
- Keyword:
- Space Weather Forecasting, Extreme Weather, Ionosphere, Magnetosphere, MI Coupling, Ionospheric Conductance, Auroral Conductance, Aurora, SWMF, SWPC, Nonlinear Regression, and dB/dt
- Citation to related publication:
- Mukhopadhyay, A., Welling, D. T., Liemohn, M. W., Ridley, A. J., Chakraborty, S., & Anderson, B. J. (2020). Conductance Model for Extreme Events: Impact of Auroral Conductance on Space Weather Forecasts. Space Weather, 18(11), e2020SW002551. https://doi.org/10.1029/2020SW002551
- Discipline:
- Engineering and Science
-
- Creator:
- Agnit Mukhopadhyay
- Description:
- - A semi-physical global modeling approach is used to estimate diffuse & discrete sources of auroral precipitation during the Galaxy15 event. - Diffuse sources contribute 74% of the total auroral power. Discrete sources are strongly driven by activity and can contribute up to 61%. - Broadband precipitation contributes 31% of the auroral Pedersen conductance playing a significant role in ionospheric electrodynamics.
- Discipline:
- Science and Engineering
-
- Creator:
- Agnit Mukhopadhyay, Sanja Panovska, Raven Garvey, Michael Liemohn, Natalia Ganjushkina, Austin Brenner, Ilya Usoskin, Michael Balikhin, and Daniel Welling
- Description:
- In the recent geological past, Earth’s magnetic field reduced to 4% of the modern values and the magnetic poles moved severely apart from the geographic poles causing the Laschamps geomagnetic excursion, which happened about 41 millennia ago. The excursion lasted for about two millennia, with the peak strength reduction and dipole tilting lasting for a shorter period of 300 years. During this period, the geomagnetic field exhibited significant differences from the modern nearly-aligned dipolar field, causing non-dipole variables to mimic a magnetic field akin to the outer planets while displaying a significantly reduced magnetic strength. However, the precise magnetospheric configuration and their electrodynamic coupling with the atmosphere have remained critically understudied. This dataset contains the first space plasma investigation of the exact geomagnetic conditions in the near-Earth space environment during the excursion. The study contains a full 3D reconstruction and analysis of the geospace system including the intrinsic geomagnetic field, magnetospheric system and the upper atmosphere, linked in sequence using feedback channels for distinct temporal epochs. The reconstruction was conducted using the LSMOD.2 model, Block Adaptive Tree Solar wind-Roe-Upwind Scheme (BATS-R-US) Model and the MAGnetosphere-Ionosphere-Thermosphere (MAGNIT) Auroral Precipitation Model, all of which are publicly-available models. The dataset contains the raw data from each of these models, in addition to the images/post-processing results generated using these models. Paleomagnetic data produced by LSMOD.2 can be visualized using a combination of linear plotting and contour plotting tools available commonly in visualization software like Python (e.g. Python/Matplotlib) or MATLAB. Standard tools to read and visualize BATS-R-US and MAGNIT output are already publicly available using IDL and Python (see SpacePy/PyBats - https://spacepy.github.io/pybats.html). For information and details about the post-processed data, visualization and analysis, please contact the authors for details. The anthropological dataset can be visualized using a shape file reader (e.g. Python/GeoPandas) and a linear plotting tool (e.g. Python/Matplotlib).
- Discipline:
- Engineering and Science
-
- Creator:
- Penner-Hahn, James, Sension, Roseanne, McClain, Taylor, Lamb, Ryan, Alonso-Mori, Roberto, Lima, Frederico, Ardana-Lamas, Fernando, Biednov, Mykola, Chollet, Matthieu, Chung, Taewon, Deb, Aniruddha, Dewan, Paul, Gee, Leland, Huang, Joel, Yifeng, Khakhulin, Dmitry, Li, Jianhao, Michocki, Lindsay, Miller, Nicholas, Otte, Florian, Uemura, Yohei, and van Driel, Tim
- Description:
- UV-visible, X-ray absorption, and X-ray emission data used to characterize the dynamics of aquo and hydroxo cobalamin. Details of data collection and reduction are provided in the associated manuscript. Data files are all text files which contain tab-delimited columns of data corresponding to each figure in the manuscript.
- Keyword:
- Ultrafast, X-ray, Transient absorption, cobalamin, vitamin B12, XAS, XES, and XANES
- Citation to related publication:
- Sension, R.J., et al. (2023). Watching Excited State Dynamics with Optical and X-ray Probes: The Excited State Dynamics of Aquocobalamin and Hydroxocobalamin. J. Am. Chem. Soc. in press. and https://doi.org/10.1021/jacs.3c04099
- Discipline:
- Science
-
- Creator:
- Sergio E. Vidal-Luengo
- Description:
- This database contains spacecraft and ground-based magnetic field observations made to study the propagation of the preliminary impulse triggered by interplanetary shocks with different inclinations in the XZ plane.
- Keyword:
- Cluster, Dynamic pressure pulse, THEMIS, SuperMag, Magnetosphere, MMS, and Intermagnet
- Citation to related publication:
- (to be submitted) Vidal-Luengo, S. E., Moldwin, M. B. (2021). Shock Inclination Effects in Preliminary Impulse Propagation Observed by Ground-Based Magnetometers and the Heliophysics System Observatory
- Discipline:
- Science
-
- Creator:
- Toth, Gabor, Velli, Marco, and van der Holst, Bart
- Description:
- Data used in the paper "Theory of Magnetic Switchbacks Fully Supported by Parker Solar Probe Observations" by G. Toth, M. Velli and B. van der Holst, ApJ 2023. The Observations directory contains the PSP observations as simple text files that can be easily read by the IDL macros in the BATSRUS/share/IDL/General/ or any other plotting software. The Simulations directory contains BATSRUS simulations including input and output files. The runlog files show the Git references. The output files are in binary format that can be read by the IDL macros in the BATSRUS/share/IDL/General/ or with the SpacePy software. The BATSRUS directory contains the source code that can be used to reproduce the simulations.
- Keyword:
- solar wind, magnetohydrodynamics, Alfven waves, and switchback
- Citation to related publication:
- G. Toth, M. Velli, B. van der Holst, 2023, Theory of Magnetic Switchbacks Fully Supported by Parker Solar Probe Observations, The Astrophysical Journal, in press
- Discipline:
- Science
-
- Creator:
- Khabiri, Morteza and Freddolino, Peter L.
- Description:
- Genome-wide predictions of all transcription factor binding sites on the D. melanogaster genome were developed for use in predicting the locations of Polycomb response elements, as described in https://doi.org/10.1101/516500
- Keyword:
- Systems Biology and Drosophila
- Citation to related publication:
- Khabiri, M., & Freddolino, P. L. (2019). Genome-wide Prediction of Potential Polycomb Response Elements and their Functions. Preprint. BioRxiv, 516500. https://doi.org/10.1101/516500
- Discipline:
- Science
-
- Creator:
- Chatterjee, Tanmay, Knappik, Achim, Sandford, Erin, Tewari, Muneesh, Choi, Sung Won, Strong, William B., Thrush, Evan P., Oh, Kenneth J., Liu, Ning, Walter, Nils G., and Johnson-Buck, Alexander
- Description:
- The sensitive measurement of specific protein biomarkers is important for medical diagnostics and research. However, existing methods for quantifying proteins use antibody probes that cannot distinguish between specific and nonspecific binding, limiting their sensitivity and specificity. This work establishes a method for distinguishing between specific binding to the target protein and nonspecific binding to assay surfaces using single-molecule kinetic measurements with dynamically binding probes. This is significant because it permits extremely sensitive protein measurements without requiring a high-affinity detection antibody or any washing steps, enabling streamlined and sensitive quantification of proteins even when no pair of high-quality, tightly binding antibodies is available.
- Keyword:
- biomarker detection, single molecule fluorescence, kinetic fingerprinting, total internal reflection microscopy, and super resolution microscopy
- Citation to related publication:
- Chatterjee, T., et al. Direct kinetic fingerprinting and digital counting of single protein molecules. Proc Natl Acad Sci USA, In Press.
- Discipline:
- Science
-
- Creator:
- Liu, Meichen
- Description:
- The raw seismic records are downloaded from Incorporated Research Institutions for Seismology. The facilities of IRIS Data Services, and specifically the IRIS Data Management Center, were used for access to waveforms, related metadata, and/or derived products used in this study. The synthetic seismograms are generated by SPECMFEM3D_Globe software which was downloaded from the Computational Infrastructure for Geodynamics ( https://geodynamics.org/).
- Keyword:
- Composition and structure of the mantle, Phase transitions, North America, Body waves, and Computational seismology
- Discipline:
- Science
-
- Creator:
- Agnit Mukhopadhyay
- Description:
- Conducting quantitative metrics-based performance analysis of first-principles-based global magnetosphere models is an essential step in understanding their capabilities and limitations, and providing scope for improvements in order to enhance their space weather prediction capabilities for a range of solar conditions. In this study, a detailed comparison of the performance of three global magnetohydrodynamic (MHD) models in predicting the Earth’s magnetopause location and ionospheric cross polar cap potential (CPCP) has been presented. Using the Community Coordinated Modeling Center’s Run-on-Request system and extensive database on results from various magnetospheric scenarios simulated for a variety of solar wind conditions, the aforementioned model predictions have been compared for magnetopause standoff distance estimations obtained from six empirical models, and with cross polar cap potential estimations obtained from the Assimmilative Mapping of Ionospheric Electrodynamics (AMIE) Model and the Super Dual Auroral Radar Network (SuperDARN) observations. We have considered a range of events spanning different space weather activity to analyze the performance of these models. Using a fit performance metric analysis for each event, we have quantified the models’ reproducibility of magnetopause standoff distances and CPCP against empirically-predicted observations, and identified salient features that govern the performance characteristics of the modeled magnetospheric and ionospheric quantities.
- Citation to related publication:
- Mukhopadhyay, A., Jia, X., Welling, D. T., & Liemohn, M. W. (2021). Global Magnetohydrodynamic Simulations: Performance Quantification of Magnetopause Distances and Convection Potential Predictions. Frontiers in Astronomy and Space Sciences, 8. https://doi.org/10.3389/fspas.2021.637197
- Discipline:
- Engineering and Science
-
- Creator:
- Fuller, Jennifer, Rowan, Erin, Landgraf, Ava, Alofs, Karen, Foufopoulos, Johannes, and Gronewold, Andrew
- Description:
- This study investigates the rapid decline of black tern (Chlidonias niger) over eight years in one of Michigan’s largest colonies, Lake St. Clair. 1. Nesting Success Model: A multiple logistic regression with a binomial (logit-link) fit using the glm() function from the ‘stats’ package in R (55) to determine the influence of habitat and biological predictors on nesting survival. 2. ArcMap visualization of Nesting Success: To visualize the geographic extent of the habitat’s potential to predispose nests’ vulnerability, the coefficients and intercept from our selected GLM were applied to raster layers in ArcMap using the Raster Calculator Tool. 3. Population Change & Habitat Extent: To quantify sub-colony breeding pair population size and their response to changes in sub-colony habitat in the geospatial model, we applied a general linear mixed model (GLMM) using the lmer() function from the ‘lme4’ package in R (55). Predictor variables were chosen a priori, and included the area of open water, uninhabitable vegetation (NDVI>0.72), any habitable area, and area with >50% hatch success.
- Keyword:
- black terns, wetlands, ecology, climate change, lake levels, Great Lakes, waterbirds, ornithology, general linear model, geospatial, GIS, nesting success, avian, and breeding
- Citation to related publication:
- Fuller, J., Rowan, E., Landgraf, A., Alofs, K., Foufopoulos, J., Gronewold, A., (2021). Collapse of a Black Tern Colony (Chlidonias niger) as a Result of Climate Change Driven Lake-Level Extremes and Anthropogenic Habitat Alteration [Data set]. University of Michigan - Deep Blue. and Fuller, J., et al. (2021). Shorebird colony collapses under climate driven lake-level rise and anthropogenic stressors. Forthcoming.
- Discipline:
- Science
-
- Creator:
- Hodgins-Davis, Andrea, Duveau, Fabien, Walker, Elizabeth, and Wittkopp, Patricia J
- Description:
- Understanding how phenotypes evolve requires disentangling the effects of mutation generating new variation from the effects of selection filtering it. Tests for selection frequently assume that mutation introduces phenotypic variation symmetrically around the population mean, yet few studies have tested this assumption by deeply sampling the distributions of mutational effects for particular traits. Here, we examine distributions of mutational effects for gene expression in the budding yeast Saccharomyces cerevisiae by measuring the effects of thousands of point mutations introduced randomly throughout the genome. We find that the distributions of mutational effects differ for the ten genes surveyed and are inconsistent with normality. For example, all ten distributions of mutational effects included more mutations with large effects than expected for normally distributed phenotypes. In addition, some genes also showed asymmetries in their distribution of mutational effects, with new mutations more likely to increase than decrease the gene’s expression or vice versa. Neutral models of regulatory evolution that take these empirically determined distributions into account suggest that neutral processes may explain more expression variation within natural populations than currently appreciated.
- Keyword:
- gene expression, evolution, mutation, mutagenesis, regulatory evolution, YFP, reporter construct, yeast, TDH1, TDH2, TDH3, GPD1, OST1, PFY1, STM1, RNR1, and RNR2
- Citation to related publication:
- Hodgins-Davis, A., Duveau, F., Walker, E. A., & Wittkopp, P. J. (2019). Empirical measures of mutational effects define neutral models of regulatory evolution in Saccharomyces cerevisiae. BioRxiv, 551804. https://doi.org/10.1101/551804
- Discipline:
- Science
-
- Creator:
- Swiger, Brian M, Liemohn, Liemohn W, Ganushkina, Natalia Y, and Dubyagin, Stepan V
- Description:
- The data included are those that were used in the creation of a model described in the manuscript titled "Predictions of Electron Flux in the near-Earth Plasma Sheet from Solar Wind Driving" by Swiger et al., 2022, published in the Space Weather Journal. doi: pending, TBD and The manuscript describes the development and assessment of a model that predicts electron flux (from 83 eV to 93 keV energies) in a region of Earth's magnetosphere called the plasma sheet. The model uses inputs of solar wind parameters including, but not limited, to solar wind speed and the interplanetary magnetic field.
- Keyword:
- magnetosphere plasma, machine learning, neural network, space weather forecasting, electrons in space, Earth's plasma sheet, and solar wind driving of magnetosphere
- Citation to related publication:
- Swiger, B. M., Liemohn, M. W., Ganushkina, N. Y., & Dubyagin, S. V. (2022). Energetic electron flux predictions in the near-Earth plasma sheet from solar wind driving. Space Weather, 20, e2022SW003150. https://doi.org/10.1029/2022SW003150
- Discipline:
- Science
-
- Creator:
- Wallace, Dylan M, Benyamini, Miri, Nason-Tomaszewski, Samuel R, Costello, Joseph T, Cubillos, Luis H, Mender, Matthew J, Temmar, Hisham, Willsey, Matthew S, Patil, Parag P, Chestek, Cynthia A, and Zacksenhouse, Miriam
- Description:
- This is data from Wallace, Benyamini et al., 2023, Journal of Neural Engineering. There are two sets of data included: 1. Neural features and error labels used to train error classifiers for each day used in the study 2. Trial data from an example experiment day (Monkey N, Day 6), with runs for offline calibration, online brain control, error monitoring, and error correction. The purpose of this study was to investigate the use of error signals in motor cortex to improve brain-machine interface (BMI) performance for control of two finger groups. All data is contained in .mat files, which can be opened using MATLAB or the Python SciPy library.
- Keyword:
- Brain-machine interface (BMI), Error detection, and Neural recording
- Citation to related publication:
- Wallace, D. M., Benyamini, M., Nason-Tomaszewski, S. R., Costello, J. T., Cubillos, L. H., Mender, M. J., Temmar, H., Willsey, M. S., Patil, P. G., Chestek, C. A., & Zacksenhouse, M. (2023). Error detection and correction in intracortical brain–machine interfaces controlling two finger groups. Journal of Neural Engineering, 20(4), 046037. https://doi.org/10.1088/1741-2552/acef95
- Discipline:
- Engineering, Science, and Health Sciences
-
- Creator:
- Mitchell, R.L. and Sheldon, Nathan D.
- Description:
- Samples from a road cut section were analyzed. New paleosols were discovered.
- Keyword:
- Paleosols, Precambrian, Keweenawan, Paleoenvironments, and Midcontinental Rift
- Citation to related publication:
- Mitchell, R.L., Sheldon, N.D., 2009, Weathering and paleosol formation in the 1.1. Ga Keweenawan Rift: Precambrian Research 168, p. 271–283. https://doi.org/10.1016/j.precamres.2008.09.013
- Discipline:
- Science
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset 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:
- Nunley, H., Nagashima, M., Martin, K., Gonzalez, A. L., Suzuki, S. C., Norton, D. A., Wong, R. O. L., Raymond, P. A., & Lubensky, D. K. (2020). Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation. PLOS Computational Biology, 16(12), e1008437. https://doi.org/10.1371/journal.pcbi.1008437 and Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679
- Discipline:
- Science
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset contains images of UV cone nuclei (labelled by transgenic expression of a photoconvertible fluorescent protein) near the retinal margin in live fish. The most important images in the dataset are the following: 1. Images (at 4X magnification) of UV cones immediately after photoconversion of a patch near the retinal margin 2. Images (at 4X magnification) of UV cones 2-4 days after photoconversion of a patch near the retinal margin Also, included is code for calculating triangulations (which connect UV cone nuclei which are nearest neighbors). This code allows us to check for motion of UV cones relative to each other between the time of photoconversion and subsequent imaging.
- Keyword:
- zebrafish cone mosaic, topological defects, tissue patterning, grain boundaries, photoconversion, and defect motion
- Citation to related publication:
- Nunley, H., Nagashima, M., Martin, K., Gonzalez, A. L., Suzuki, S. C., Norton, D. A., Wong, R. O. L., Raymond, P. A., & Lubensky, D. K. (2020). Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation. PLOS Computational Biology, 16(12), e1008437. https://doi.org/10.1371/journal.pcbi.1008437 and Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679
- Discipline:
- Science
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset contains images of UV cone nuclei near the retinal margin in live zebrafish. These UV cone nuclei are labelled by transgenic expression of a fluorescent reporter (that is photoconvertible). The most important data are: 1. The zoomed-in (4X magnification) images of UV cone nuclei immediately after photoconversion 2. The zoomed-in (4X magnification) images of UV cone nuclei 2-4 days after photoconversion Also included is code for segmenting UV cone nuclei (both in image from immediately after photoconversion and in image from days later) and for shifting and rotating the two images to maximally align corresponding UV cone nuclei. After aligning corresponding UV cones, we compute triangulations over UV cone nuclei positions (for both images) and identify bonds that are common to both images. We use these common bonds to calculate the lattice vectors for the UV cone lattice.
- Keyword:
- zebrafish cone mosaic, tissue patterning, lattice vectors, and photoconversion
- Citation to related publication:
- Nunley, H., Nagashima, M., Martin, K., Gonzalez, A. L., Suzuki, S. C., Norton, D. A., Wong, R. O. L., Raymond, P. A., & Lubensky, D. K. (2020). Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation. PLOS Computational Biology, 16(12), e1008437. https://doi.org/10.1371/journal.pcbi.1008437 and Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679
- Discipline:
- Science
-
- Creator:
- Zelditch, Miriam L. and Swiderski, Donald L.
- Description:
- Each row in the file contains the museum ID (museum where the specimen is located and the accession number), the species name, and the values for centroid size, followed by the x,y coordinates for each landmark. Any program that can read in a csv file can read this file.
- Keyword:
- Shape, Sciuridae, mandibles
- Citation to related publication:
- Zelditch, M.L., Swiderski, D.L. The Predictable Complexity of Evolutionary Allometry. Evol Biol (2022). https://doi.org/10.1007/s11692-022-09581-1
- Discipline:
- Science
-
- Creator:
- Cole, Shannon L
- Description:
- The nucleus accumbens (NAc) contains multiple subpopulations of medium spiny neurons (MSNs): one subpopulation expresses D1-type dopamine receptors, another expresses D2-type receptors, and a third expresses both. The relative roles in NAc of D1 neurons versus D2 neurons in appetitive motivation were assessed here. Specifically, we asked whether D1-Cre mice or D2-Cre mice would instrumentally seek optogenetic self-stimulation of those respective subpopulations in NAc, or instead avoid NAc laser stimulation. and Some statistical forms have been exported from SPSS for the purposes of accessibility to viewers. Please see the "readme" text for descriptions of each individual excel file.
- Keyword:
- Motivation Striatum Optogenetics
- Discipline:
- Science
-
- Creator:
- Malhotra, Garima and Ridley, Aaron J.
- Description:
- The goal of this research study is to understand the sensitivity of the IT region to the spatial variation of Kzz. This is done using the IT model, GITM, with different settings and spatial distributions for Kzz. We introduce latitudinal bands (longitudinally uniform) of 30 degrees width at equatorial and polar latitudes during different seasons similar to the previous observations in literature. We investigate the mechanisms through which a non-uniform global distribution of Kzz can alter the dynamics and thermal structure of the thermosphere, and how these effects compare to when a globally uniform value of Kzz is used.
- Keyword:
- Mesosphere and Lower Thermosphere, Eddy Diffusion, Thermospheric Dynamics, Thermospheric composition and mixing, Lower-Upper Thermosphere Vertical Coupling, Global Ionosphere Thermosphere Model, and Eddy Mixing
- Citation to related publication:
- Malhotra, G., Ridley, A.J. (2021). Impacts of Spatially Varying Eddy Diffusion in the Lower Thermosphere on the Ionosphere and Thermosphere using GITM - Sensitivity Study. and A.J. Ridley, Y. Deng, G. Tóth, The global ionosphere–thermosphere model, Journal of Atmospheric and Solar-Terrestrial Physics, Volume 68, Issue 8, 2006, Pages 839-864, ISSN 1364-6826, https://doi.org/10.1016/j.jastp.2006.01.008.
- Discipline:
- Science
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset contains images of UV cone nuclei near the retinal margin in live fish. These UV cones express a transgenic fluorescent reporter (that is nuclear-localized and photoconvertible). The most important images in this dataset are: Zoomed-out (1X magnification) images immediately after photoconversion Zoomed-out (1X magnification) images two to four days after photoconversion In the images immediately after photoconversion, we check if the row orientation rotates by more than a certain amount (10 degrees, 12 degrees, 14 degrees, etc.) at the retinal margin. If so, we call the region coinciding with this domain rotation an existing grain boundary. We, then, check where new Y-junctions are incorporated (by the time of later imaging) to see if they are preferentially incorporated near existing grain boundaries.
- Keyword:
- zebrafish cone mosaic, topological defects, tissue patterning, grain boundaries, and photoconversion
- Citation to related publication:
- Nunley, H., Nagashima, M., Martin, K., Gonzalez, A. L., Suzuki, S. C., Norton, D. A., Wong, R. O. L., Raymond, P. A., & Lubensky, D. K. (2020). Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation. PLOS Computational Biology, 16(12), e1008437. https://doi.org/10.1371/journal.pcbi.1008437 and Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679
- Discipline:
- Science
-
- Creator:
- 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:
- Zhou, H., Tóth, G., Jia, X., & Chen, Y. (2020). Reconnection-Driven Dynamics at Ganymede’s Upstream Magnetosphere: 3-D Global Hall MHD and MHD-EPIC Simulations. Journal of Geophysical Research: Space Physics, 125(8), e2020JA028162. https://doi.org/10.1029/2020JA028162
- Discipline:
- Science
-
- Creator:
- Ozturk, Dogacan S
- Description:
- The modeling research conducted to produce this dataset focuses on the solar wind dynamic pressure drop events and how they affect the Earth's intrinsically coupled Magnetosphere, Ionosphere and Thermosphere systems. This study specifically focuses on the 11 June 2017 event, where the solar wind dynamic pressure dropped significantly following a period of higher pressure. We model the response to this pressure drop using University of Michigan Space Weather Modeling Framework ( http://csem.engin.umich.edu/tools/swmf/). The simulation results were created using BATS-R-US and GITM models. The observational data required for model comparisons were taken from OMNI ( https://omniweb.gsfc.nasa.gov) and CDAWeb ( https://cdaweb.gsfc.nasa.gov/sp_phys/) Databases.
- Keyword:
- GITM, BATS-R-US, Solar wind dynamic pressure, Magnetosphere-Ionosphere-Thermosphere, and MHD
- Citation to related publication:
- Ozturk, D. S., Zou, S., Slavin, J. A., & Ridley, A. J. ( 2019). Response of the geospace system to the solar wind dynamic pressure decrease on 11 June 2017: Numerical models and observations. Journal of Geophysical Research: Space Physics, 124, 2613– 2627. https://doi.org/10.1029/2018JA026315
- Discipline:
- Science
-
- Creator:
- Moldwin, Mark B
- Description:
- The database was constructed by using the archived monthly newsletters of SPA and SPD. Duplicate job ads (those in both data sets and those posted over multiple months) were eliminated. The comma delimited raw data files of the job postings and the compilation of the numbers by year and job type and provided. A summary of the results is deposited in Deep Blue Documents.
- Keyword:
- Workforce, Decadal Survey, and Job Ad
- Discipline:
- Science
-
- Creator:
- Chung, Taewon , McClain, Taylor P. , Alonso-Mori, Roberto , Chollet, Matthieu , Deb, Aniruddha , Garcia-Esparza, Angel T. , Huang, Joel Ze En , Lamb, Ryan M. , Michocki, Lindsay B. , Reinhard, Marco , van Driel, Tim B. , Penner-Hahn, James E. , and Sension, Roseanne J.
- Description:
- UV-visible, X-ray absorption, and X-ray emission data used to characterize the dynamics of methyl cobalamin at low pH, so called "base off" configuration. Details of data collection and reduction are provided in the associated manuscript. Data files are all text files which contain tab-delimited columns of data corresponding to each figure in the manuscript
- Keyword:
- Ultrafast, X-ray, Transient absorption, cobalamin, vitamin B12, XAS, and XANES
- Citation to related publication:
- Chung, T., et al. (2024). "Ultrafast X-ray Absorption Spectroscopy Reveals Excited State Dynamics of B12 Coenzymes Controlled by the Axial Base". J. Phys. Chem. B. 2024, in press https://pubs.acs.org/doi/10.1021/acs.jpcb.3c07779
- Discipline:
- Science
-
- Creator:
- Cotton, Jennifer M. and Sheldon, Nathan D.
- Description:
- These spreadsheets contain all data and data by diet type, meat consumption, gender, and British comparison for the classroom activity described in the accompanying paper.
- Keyword:
- Sustainable agriculture , Active learning, Stable isotopes, and Large enrollment
- Citation to related publication:
- Cotton, J.M., and Sheldon, N.D., 2013, Using stable carbon and nitrogen isotopes of hair to teach about sustainable agriculture through active learning: Journal of Geoscience Education 61, 59–67. https://doi.org/10.5408/12-309.1
- Discipline:
- Science
-
- 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:
- Zhang, Y., Yang, P., Gao, C., Tong, C., Zhang, X., Liu, X., Zhang, S., & Meyers, P. A. (2020). Peat Properties and Holocene Carbon and Nitrogen Accumulation Rates in a Peatland in the Xinjiang Altai Mountains, Northwestern China. Journal of Geophysical Research: Biogeosciences, 125(12), e2019JG005615. https://doi.org/10.1029/2019JG005615
- Discipline:
- Science
-
- Creator:
- Niemi, Nathan A. and Abbey, Alyssa L.
- Description:
- These data were produced in the scope of research into the timing, rate, and magnitude of extensional exhumation along the length of the Rio Grande Rift in Colorado and New Mexico. The low-temperature (apatite and zircon (U-Th)/He) thermochronometric ages presented in this data set are sensitive to near-surface temperatures (~80C and 180C, respectively) and record the progressive exhumation of the rock mass from which the samples were collected towards the Earth's surface. These thermochronometric ages, and the differences between them, provide insight into the absolute timing, exhumation rate and total magnitude of exhumation on the normal faults that bound the Rio Grande Rift. and The QTQt program mentioned (Version QTQt64R5.6.2a was used for the data presented in this deposit) is not openly available for download, but is described in the Gallagher 2012 publication referenced, and can be requested from its author. For more information on the request process and a user guide, see http://www.iearth.org.au/codes/QTQt/
- Keyword:
- thermochronology, helium dating, (U-Th)/He, Rio Grande Rift, New Mexico, Colorado, and extensional tectonics
- Citation to related publication:
- Abbey, A. L., & Niemi, N. A. (2020). Perspectives on Continental Rifting Processes From Spatiotemporal Patterns of Faulting and Magmatism in the Rio Grande Rift, USA. Tectonics, 39(1), e2019TC005635. https://doi.org/10.1029/2019TC005635
- Discipline:
- Science
-
- Creator:
- Auteri, Giorgia G., Knowles, L. Lacey, Marchán-Rivadeneira, Raquel M., and Olson, Deanna H.
- Description:
- This data was collected as part of a study to study population dynamics of coastal giant salamanders in Oregon. The study uses genetics to answer questions related to conservation concerns including population connectivity, sensitivity to habitat disturbances (such as logging and fires), and genetic diversity of populations.
- Keyword:
- salamander, Dicamptodon tenebrosus, conservation genetics, microsatellite , landscape genetics, population connectivity, and bottleneck
- Citation to related publication:
- Auteri, Giorgia G., M. Raquel Marchán-Rivadeneira, Deanna H. Olson, L. Lacey Knowles. Connectivity in coastal giant salamanders (Dicamptodon tenebrosus) shows no association with land-use, fire frequency, or river drainage but does not offset negative consequences of locally unstable population sizes. PLoS ONE. In review.
- Discipline:
- Science
-
- Creator:
- Isaacoff, Benjamin P., Li, Yilai, Lee, Stephen A., and Biteen, Julie S.
- Description:
- This is the experimental data referenced in our manuscript entitled “SMALL-LABS: An algorithm for measuring single molecule intensity and position in the presence of obscuring backgrounds .” These live-cell single-molecule imaging movies were used as a test of the SMALL-LABS single-molecule image analysis algorithm. The dataset comprises two movies; each one is provided both as a .tif stack and as an .avi file. The movie called “low_bg” has a standard low background, and the movie called “high_bg” includes a high fluorescent background produced by an external 488-nm laser.
- Keyword:
- single-molecule, microscopy, image analysis, mirobiology, and bacteria
- Discipline:
- Engineering and Science
-
- Creator:
- Yuan, Ye, Currie, William S., Sharp, Sean J. , Martina, Jason P. , and Elgersma, Kenneth J.
- Description:
- This archived dataset includes all of the input files that were used to run the model for all the runs in this set, including files containing model parameters and drivers. This dataset also includes all of the model output files from model runs in this set.
- Keyword:
- wetland, Great Lakes, greenhouse gas, climate change, and ecosystem model
- Citation to related publication:
- Yuan, Y., S. J. Sharp, J. P. Martina, K. J. Elgersma, and W. S. Currie. Sustained-flux global warming potential driven by nitrogen inflow and hydroperiod in a model of Great Lakes coastal wetlands. JGR Biogeosciences in review.
- Discipline:
- Science
-
- Creator:
- Bradshaw, Lisa, Vernon, Julianne, Schmidt, Thomas, James, Timothy, Zhang, Jianzhi, Archbold, Hilary, Cadigan, Ken, Wolfe, John P., and Goldberg, Deborah E.
- Description:
- This is the experimental data referenced in our manuscript entitled "Influence of CUREs on STEM retention depends on demographic identities." The dataset comprises csv files with results from student surveys given to students enrolled in Biology 173 from Fall 2015 through Fall 2019 as well as institutional data of their course grades and cumulative GPA at the time they enrolled in Biology 173, and graduation and major data for student who had graduated by 2021. The survey questions used in the analysis and the IRB consent form are also included as pdfs.
- Keyword:
- undergraduate research, STEM retention, CURE, introductory biology laboratory, and education research
- Citation to related publication:
- Bradshaw, L., Vernon J., Schmidt T., James T., Zhang J., Archbold H., Cadigan K., Wolfe J.P. & Goldberg D. 2023. Research article: Influence of CUREs on STEM retention depends on demographic identities. J Microbiol Biol Educ (accepted)
- Discipline:
- Science
-
- Creator:
- Ansong, Joseph K. and Arbic, Brian K.
- Description:
- This is the model and observational data referenced in our manuscript entitled “surface and sub-subsurface internal gravity wave kinetic energy spectra from global ocean models and observations.” The model data for the 7 regions from the two global simulations (HYCOM and MITgcm) can be found here.
- Keyword:
- vertical wavenumber spectra of internal waves, surface kinetic energy spectra, and ratio of high versus low-frequency surface kinetic energy
- Citation to related publication:
- Ansong, J.K., et al., "forthcoming", Surface and sub-subsurface internal gravity wave kinetic energy spectra in global ocean models and observations
- Discipline:
- Science
-
- Creator:
- Salaree, Amir
- Description:
- Study of the effect of various rupture scenarios in Cascadia on tsunami hazard
- Keyword:
- Earthquake, Tsunami, Simulation, and Bathymetry
- Discipline:
- Science
-
- Creator:
- Martin, Tara L, Young, LR, Goldsteen, D, Nunamaker, EA, Reynolds, P, Thompson-Iritani, S, Thurston, SE, and LaFollette, MR
- Description:
- This dataset contains the results of a survey of mouse handling methods by personnel working with laboratory mice. The survey included questions about preferred handling methods, barriers to use of refined handling methods, and a knowledge quiz about refined mouse handling. Data was collected via Qualtrics survey as described in the methodology section. This dataset is associated with the following publication, accepted by PLOS One: PONE-D-23-01633R1 Title: Using refined methods to pick up mice: A survey benchmarking prevalence & beliefs about tunnel and cup handling Authors: Lauren Young, Donna Goldsteen, Elizabeth A. Nunamaker, Mark J. Prescott, Penny Reynolds, Sally Thompson-Iritani, Sarah E. Thurston, Tara L. Martin, Megan R. LaFollette
- Keyword:
- Mouse, Refined Handling, Tunnel Handling, Cup Handling, Laboratory Animal, and Animal Care
- Citation to related publication:
- Young LR, Goldsteen D, Nunamaker EA, Prescott MJ, Reynolds P, Thompson-Iritani S, Thurston SE, Martin TL, LaFollette MR. Using refined methods to pick up mice: A survey benchmarking prevalence & beliefs about tunnel and cup handling. PLOS ONE. 2023. In Press.
- Discipline:
- Science
-
- Creator:
- Johnson, Jena E., Webb, Samuel M., Condit, Cailey B., Beukes, Nicolas J., and Fischer, Woodward W.
- Description:
- Manganese in the sedimentary record has been interpreted by many as a powerful redox proxy for paleoenvironments, and yet very little work has been done to ensure that the manganese-rich minerals in the rock record are actually recording primary signals. In the accompanying manuscript, we present an in-depth characterization of the manganese mineralogy from two correlated regions recording the Transvaal Supergroup in South Africa with markedly different alteration histories to investigate if there can be post-depositional emplacement of manganese-rich minerals. The data uploaded here are X-ray absorption spectra of (1) manganese standard minerals that were useful in our analyses and (2) minerals from an important well-characterized sample that may be useful as comparative standards in future studies.
- Keyword:
- manganese and X-ray absorption spectroscopy
- Citation to related publication:
- J.E. Johnson, S.M. Webb, C.B. Condit, N.J. Beukes, W.W. Fischer; Effects of metamorphism and metasomatism on manganese mineralogy: Examples from the Transvaal Supergroup. South African Journal of Geology doi: https://doi.org/10.25131/sajg.122.0034
- Discipline:
- Science
-
Dataset: Models generated for the bioinformatic analysis of MPER/protein fusions binding to antibody
- Creator:
- Bylund, Tatsiana, Chuang, Gwo-Yu, Kwong, Peter, Lai, Yen-Ting, McIlwain, Benjamin, and Stockbridge, Randy B.
- Description:
- This project evaluated the binding of antibody fragments to membrane proteins fused to a short epitope sequence (“MPER”). This dataset includes atomic coordinates (.pdb files) for bioinformatic models of antibody fragment binding to an MPER epitope – membrane protein fusion.
- Keyword:
- MPER, cryo-EM fiducial, crystallography chaperone, and small membrane protein
- Citation to related publication:
- McIlwain, B. C., Erwin, A. L., Davis, A. R., Ben Koff, B., Chang, L., Bylund, T., Chuang, G.-Y., Kwong, P. D., Ohi, M. D., Lai, Y.-T., & Stockbridge, R. B. (2021). N-terminal Transmembrane-Helix Epitope Tag for X-ray Crystallography and Electron Microscopy of Small Membrane Proteins. Journal of Molecular Biology, 166909. https://doi.org/10.1016/j.jmb.2021.166909
- Discipline:
- Science
-
- Creator:
- Zhu, Jialei, Penner, Joyce E., Yu, Fangqun, Sillman, Sanford, Andreae, Meinrat O., and Coe, Hugh
- Description:
- The dataset contains the Fortran programs applied in the latest CESM/IMPACT model as well as the data created from this model, which are used in the referenced paper.
- Keyword:
- Organic nucleation and Radiative forcing
- Citation to related publication:
- Zhu, J. et al. Decrease in radiative forcing by organic aerosol nucleation, climate, and land use change. Nature Communications 10, 423 (24 January 2019). https://doi.org/10.1038/s41467-019-08407-7
- Discipline:
- Science
-
Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation
User Collection- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- The outer epithelial layer of zebrafish retinae contains a crystalline array of cone photoreceptors, called the cone mosaic. As this mosaic grows by mitotic addition of new photoreceptors at the rim of the hemispheric retina, topological defects, called “Y-Junctions”, form to maintain approximately constant cell spacing. The generation of topological defects due to growth on a curved surface is a distinct feature of the cone mosaic not seen in other well-studied biological patterns like the R8 photoreceptor array in the _ Drosophila compound eye. Since defects can provide insight into cell-cell interactions responsible for pattern formation, here we characterize the arrangement of cones in individual Y-Junction cores (see Set of images for Figures 1 and 2 and 6 and Supplementary Figure 7) as well as the spatial distribution of Y-junctions across entire retinae (see Dataset for analyzing spatial distribution of Y-junctions in flat-mounted retinae). We find that for individual Y-junctions, the distribution of cones near the core corresponds closely to structures observed in physical crystals (see Set of images for Figures 1 and 2 and 6 and Supplementary Figure 7). In addition, Y-Junctions are organized into lines, called grain boundaries, from the retinal center to the periphery (see Dataset for analyzing spatial distribution of Y-junctions in flat-mounted retinae and Dataset for measuring tendency of Y-junctions to line up into grain boundaries during incorporation into retinae). In physical crystals, regardless of the initial distribution of defects, defects can coalesce into grain boundaries via the mobility of individual particles. By imaging in live fish, we demonstrate that grain boundaries in the cone mosaic instead appear during initial mosaic formation, without requiring defect motion (see Dataset for measuring tendency of Y-junctions to line up into grain boundaries during incorporation into retinae and Dataset for analyzing Y-junction motion in live fish retinae). Motivated by this observation, we show that a computational model of repulsive cell-cell interactions generates a mosaic with grain boundaries (see Code and example simulations of phase-field crystal model (for cone mosaic formation)). In contrast to paradigmatic models of fate specification in mostly motionless cell packings (see Code and accompanying input data for simulating lateral inhibition on motionless cell packing), this finding emphasizes the role of cell motion, guided by cell-cell interactions during differentiation, in forming biological crystals. Such a route to the formation of regular patterns may be especially valuable in situations, like growth on a curved surface, where the resulting long-ranged, elastic, effective interactions between defects can help to group them into grain boundaries.
- Keyword:
- zebrafish cone mosaic, lattice vectors, topological defects, tissue patterning, grain boundaries, lateral inhibition, photoconversion, phase-field crystal model, and defect motion
- Discipline:
- Science
7Works -
- Creator:
- Brenner, Austin M
- Description:
- Results of computer simulation of near Earth space is looked at in a new way to understand how energy moves around the global system. It is found that in addition to a pathway of energy from the outside into the system and back again there is an internal loop which recirculates energy. These new methods will greatly improve our understanding how the whole magnetosphere system evolves and will help address evolution of processes that have space weather impacts.
- Keyword:
- Energy flux, geospace, magnetopause, magnetosphere, poynting flux, and reconnection
- Citation to related publication:
- Austin Brenner, Tuija I. Pulkkinen, Qusai Al Shidi, et al. Dissecting Earth’s Magnetosphere: 3D Energy Transport in a Simulation of a Real Storm Event. ESS Open Archive . August 04, 2023.
- Discipline:
- Science and Engineering
-
Division of Birds
User Collection- Creator:
- University of Michigan Museum of Zoology
- Description:
- University of Michigan Museum of Zoology Division of Birds
- Discipline:
- Science
1Works -
Division of Fishes
User Collection- Creator:
- University of Michigan Museum of Zoology
- Description:
- Division of Fishes
- Discipline:
- Science
48Works -
Division of Mammals
User Collection- Creator:
- University of Michigan Museum of Zoology
- Description:
- The Division of Mammals at the Museum of Zoology was established in 1837, and has grown steadily to its current size, with over 150,000 specimens. An important feature of the mammal collection at the Museum of Zoology is our emphasis on non-traditional specimens.
- Discipline:
- Science
32Works -
Division of Reptiles and Amphibians
User Collection- Creator:
- University of Michigan Museum of Zoology
- Description:
- The Division of Reptiles and Amphibians maintains a collection that is worldwide in scope. The research collections contain over 200,000 catalogued lots representing approximately 435,000 individual specimens.
- Discipline:
- Science
13Works -
- Creator:
- Mirshams Shahshahani, Payam
- Description:
- Investigating minimum human reaction times is often confounded by the motivation, training, and state of arousal of the subjects. We used the reaction times of athletes competing in the shorter sprint events in the Athletics competitions in recent Olympics (2004-2016) to determine minimum human reaction times because there's little question as to their motivation, training, or state of arousal. The reaction times of sprinters however are only available on the IAAF web page for each individual heat, in each event, at each Olympic. Therefore we compiled all these data into two separate excel sheets which can be used for further analyses.
- Keyword:
- minimum reaction time, sprinter, Olympics, Athletics, sex difference, starting block, and false start
- Discipline:
- Engineering, Health Sciences, Science, Other, and General Information Sources
-
Dynamical Heating in the Martian Thermosphere: Temperatures, Winds and Thermal Balances using M-GITM
- Creator:
- Bougher, S. W. and Pilinski, M. D.
- Description:
- The NASA MAVEN (Mars Atmosphere and Volatile Evolution) spacecraft, which is currently in orbit around Mars, has been taking systematic measurements of the densities and deriving temperatures in the upper atmosphere of Mars (between about 140 to 240 km above the surface) since late 2014. Wind measurement campaigns have also been conducted once per month for 5-10 orbits since 2016. These densities, temperatures and winds change with time (e.g. solar cycle, season, local time) and location, and sometimes fluctuate quickly. Global dust storm events are also known to significantly impact these density, temperature and wind fields in the Mars thermosphere. For the current project, in-situ measured winds and corresponding argon density derived temperatures are combined to trace the circulation patterns and investigate their convergence and divergence locations and impacts throughout the Mars thermosphere. M-GITM computed thermal balance terms are subsequently extracted to investigate the processes required to maintain the temperature distribution around the planet. For this work, Mars Year #33 (MY33) Neutral Gas and Ion Mass Spectrometer (NGIMS) measurements have been obtained by the MAVEN team for this purpose (see these representative works: (Bougher et al., 2017; Stone et al., 2018; Benna et al., 2019). These temperature and wind fields are compared to simulations from a computer model of the Mars atmosphere called M-GITM (Mars Global Ionosphere-Thermosphere Model), developed at U. of Michigan. Since the global circulation plays a role in the structure, variability, and evolution of the atmosphere, understanding the processes that drive the winds in the upper atmosphere of Mars also provides the needed context for understanding temperature distributions and underlying thermal balances throughout the atmosphere. Three dimensional M-GITM simulations for three of the four Mars cardinal seasons (Ls = 0, 90, 270) for MY33 were conducted for detailed comparisons with NGIMS temperature and wind distributions (Pilinski et al. 2022). Corresponding M-GITM datacubes used to extract these temperatures (plus winds) along the trajectory of each orbit path between 140 and 240 km, are provided in this Deep Blue Data archive. A single README file is included that details the contents of each datacube file. In addition, this general README file summarizes the inputs and outputs of each M-GITM simulation interval used for this study. Finally, a basic version of the M-GITM code can be found on Github at https:/github.com/dpawlows/MGITM.
- Keyword:
- MAVEN, Mars thermosphere, global dynamics, and heat balances owing to winds
- Citation to related publication:
- Pilinski, M. D., K. J. Roeten, S. W. Bougher and M. Benna, Dynamical Heating in the Martian Thermosphere, Journal Geophysical Res., XXX, (forthcoming - 2022). doi: .....
- Discipline:
- Science
-
- Creator:
- Ludlow, Andrew and Kim, Jeongjin
- Description:
- Part of the regulation of telomerase activity includes the alternative splicing (AS) of the catalytic subunit telomerase reverse transcriptase (TERT). Although a therapeutic window for telomerase/TERT inhibition exists between cancer cells and somatic cells, stem cells express TERT and rely on telomerase activity for physiological replacement of cells. Therefore, identifying differences in TERT regulation between stem cells and cancer cells is essential for developing telomerase inhibition-based cancer therapies that reduce damage to stem cells. In this study, we measured TERT splice variant expression and telomerase activity in induced pluripotent stem cells (iPSCs), neural progenitor cells (NPCs), and non-small cell lung cancer cells (NSCLC, Calu-6 cells). We observed that a NOVA1-PTBP1-PTBP2 axis regulates TERT alternative splicing (AS) in iPSCs and their differentiation into NPCs. We also found that splice-switching of TERT, which regulates telomerase activity, is induced by different cell densities in stem cells but not cancer cells. Lastly, we identified cell type-specific splicing factors that regulate TERT AS. Overall, our findings represent an important step forward in understanding the regulation of TERT AS in stem cells and cancer cells. These data and subsequent studies may reveal a splicing factor(s) or their binding site(s) that could be targeted with small molecule drugs or antisense oligonucleotides, respectively, to reduce telomerase activity in cancer cells and promote durable cancer remissions.
- Keyword:
- Telomere, telomerase, TERT, alternative RNA splicing
- Citation to related publication:
- Dynamics of TERT Regulation via Alternative Splicing in Stem Cells and Cancer Cells. Accepted in Plos One
- Discipline:
- Science
-
- Creator:
- Tye, Alexander R, Niemi, Nathan A, Safarov, Rafig T, Kadirov, Fakhraddin A, Babayev, Gulam R
- Description:
- The Eastern Greater Caucasus is a mountain belt in western Asia that formed as an accretionary prism above an active subduction zone. Because of the bedrock exposure in the range, it offers a unique opportunity to research deformation processes in accretionary prisms, which are ubiquitous above the Earth's many subduction zones but are typically submarine and difficult to investigate. The data presented here result from field geologic mapping in several swaths roughly perpendicular to the mountain range that together span the entire range across strike. The data serve will serve as the basis for inference of the deep structural architecture of the range and characterization of the styles of deformation present in the range.
- Keyword:
- structural geology, Greater Caucasus, tectonics, geologic mapping, and accretionary prism
- Citation to related publication:
- Tye, A. R., Niemi, N. A., Safarov, R. T., Kadirov, F. A., & Babayev, G. R. (2021). Sedimentary response to a collision orogeny recorded in detrital zircon provenance of Greater Caucasus foreland basin sediments. Basin Research, 33(2), 933–967. https://doi.org/10.1111/bre.12499
- Discipline:
- Science
-
- Creator:
- Mason, Lacey A., Riseng, Catherine M., Layman, Andrew J., and Jensen, Robert
- Description:
- Wind exposure is a key physical driver of coastal systems in aquatic environments influencing circulation and wave dynamics. A measure of wind exposure is fetch, the distance over which wind can travel across open water. In large lake systems, such as the Laurentian Great Lakes, estimating fetch has proved to be difficult due to their vast size and complex topobathymetry. Here we describe the development of two spatially discrete indicators of exposure to provide a more accurate indicator of influence of wind exposure in the nearshore of the Laurentian Great Lakes. We summarized wind data from offshore buoys and leveraged existing tools to calculate effective fetch and relative exposure index (effective fetch scaled by mean wind speed) at a 30 m grid cell resolution. We validated these models by comparing our exposure maps to the U.S. Army Corps of Engineers Wave Information Studies models and found general agreement. These exposure maps are available for public download for the years 2004-2014.
- Keyword:
- GLAHF, Great Lakes, waves, fetch, REI, wind exposure, and geospatial
- Discipline:
- Science
-
- Creator:
- Zhang, Yingxiao MI
- Description:
- We developed a new model framework based on WRF-Chem, simulating primary biological aerosol particle emissions and their interaction with clouds. We have designed different sensitivity tests to evaluate the effects of pollen and sub-pollen particles (SPPs), respectively. Our results show that SPPs have a larger effect on cloud microphysics and precipitation than whole pollen grains.
- Keyword:
- Aerosol-cloud interactions, Primary biological aerosol particles, Ice nucleating particles, Microphyscis scheme, and Pollen
- Discipline:
- Science
-
- Creator:
- Gebarski, Benjamin B. and Becker, Udo
- Description:
- Files are uploaded as text or crystallographic information files (.cif), the standard text file format for representing crystallographic information. These files contain the results for cyclic voltammetry, x-ray absorption spectroscopy, and optimized molecular models for uranium-60 nanocluster (U60) fragments, UO2 complexes, and adsorbates.
- Keyword:
- uranium, U60, electrochemistry, computational, molecular model, and adsorption
- Citation to related publication:
- Electrochemical and computational analysis of the thermodynamics of oxidation/reduction reactions of uranyl peroxide clusters (U60), and the derivation of Pourbaix diagrams for structural and adsorbed species. In process.
- Discipline:
- Science
-
- Creator:
- Brang, David and Karthik, Ganesan
- Description:
- Data were acquired from 21 patients with intractable epilepsy undergoing clinical evaluation using iEEG. Patients ranged in age from 15-58 years (mean = 37.1, SD = 12.8) and included 10 females. Across all patients, data was recorded from a total of 1367 electrodes. Each participant were presented with multiple trials of auditory only and congruent audio-visual stimuli. On each trial a single phoneme was presented to the participant. Three variants of the tasks were used with each variant consisting of a different set of phonemes (variant A: /ba/ /da/ /ta/ /tha/, variant B: /ba/ /da/ /ga/, variant C: /ba/ /ga/ /ka/ /pa/). Trials were presented in a random order and phonemes were distributed uniformly across conditions. While conditions were matched in terms of trial numbers, participants completed a variable number of trials (based on task variant and the number of blocks completed). All provided data has been resampled to 1024 Hz during initial stages of processing for all participants. Data has been referenced in a bipolar fashion (signals subtracted from each immediately adjacent electrode in a pairwise manner) to ensure that the observed signals were derived from maximally local neuronal populations. The preprocessing steps followed have been described in the detailed description document in the attached materials. and The dataset zip folder consists of three main sub-folders: 1) Electrodes: This folder provides details regarding the individual electrodes for each subject, their MNI coordinates as well as their MNI vertices information according to freesurfer parcellations. This folder also consists of images of the physical location of each of the electrode sets. 2) Processed: This folder contains preprocessed data in all three frequencies (theta, beta and high gamma power) for individual subjects and the corresponding vertex locations for each of the electrodes from which their data was recorded. The images subfolder also contains figures provided in the main manuscript. 3) MatlabCodes: This folder contains all the matlab scripts required to reproduce the results provided in the main manuscript. LME_AvsAV_Main_Windows.m is the main file that an user has to run to reproduce the results.
- Keyword:
- Cognitive Neuroscience, Neuroscience, Perception, and Mixed Effects Models
- Citation to related publication:
- Ganesan, K., Plass, J., Beltz, A. M., Liu, Z., Grabowecky, M., Suzuki, S., ... & Brang, D. (2020). Visual speech differentially modulates beta, theta, and high gamma bands in auditory cortex. bioRxiv. https://doi.org/10.1101/2020.09.07.284455
- Discipline:
- Science
-
- Creator:
- Vaskov, Alex K, Vu, Philip P, North, Naia, Davis, Alicia J, Kung, Theodore A, Gates, Deanna H, Cederna, Paul S, and Chestek, Cynthia A
- Description:
- The data was used to calibrate and simulate pattern recognition algorithms for the following publication: Surgically Implanted Electrodes Enable Real-Time Finger and Grasp Pattern Recognition for Prosthetic Hands (medRxiv 2020, IEEE TRO in review). Each data file is named as follows Px_PostureSet.csv. Where Px is the patient number. The 1 of 10 posture set contains individual finger and intrinsic thumb movements, the grasps posture set contains a fewer number of combined finger movements. P1’s calibration data for individual fingers is labelled 1 of 12 because it also includes two grasps, which were removed for analysis in the publication. The first column of each .csv file is the experiment time in seconds. The second column is the posture of the cue hand at that timestamp. The rest of the columns are the raw EMG data in microvolts sampled at 30KSps. A legend of the movement postures, each patients EMG channels, and suggested signal processing and filtering is included in DataLabellingAndProcessing.pdf
- Keyword:
- pattern recognition, electromyography, regenerative peripheral nerve interface, intramuscular electrodes, and myoelectric prostheses
- Citation to related publication:
- Surgically Implanted Electrodes Enable Real-Time Finger and Grasp Pattern Recognition for Prosthetic Hands A. K. Vaskov, P. P. Vu, N. North, A. J. Davis, T. A. Kung, D. H. Gates, P. S. Cederna, C. A. Chestek medRxiv 2020.10.28.20217273; doi: https://doi.org/10.1101/2020.10.28.20217273
- Discipline:
- Science and Engineering
-
- Creator:
- Umaña, María Natalia and Arellano, Gabriel
- Description:
- The objective of this study was to examine the existence of congruent tree growth responses to different extreme climatic events –hurricanes and drought–affecting tropical wet forests.
- Keyword:
- Dendrometers , El Niño Southern Oscillation (ENSO), Hurricane Maria, Puerto Rico, and Tropical Forests
- Citation to related publication:
- Umaña, M.N.and Arellano G. In press. Legacy effects of drought on tree growth responses to hurricanes. Ecography. https://doi.org/10.1111/ecog.05803
- Discipline:
- Science
-
- Creator:
- Ruas, Terry, Ferreira, Charles H. P., Grosky, William, França, Fabrício O., and Medeiros, Débora M. R,
- Description:
- The relationship between words in a sentence often tell us more about the underlying semantic content of a document than its actual words, individually. Recent publications in the natural language processing arena, more specifically using word embeddings, try to incorporate semantic aspects into their word vector representation by considering the context of words and how they are distributed in a document collection. In this work, we propose two novel algorithms, called Flexible Lexical Chain II and Fixed Lexical Chain II that combine the semantic relations derived from lexical chains, prior knowledge from lexical databases, and the robustness of the distributional hypothesis in word embeddings into a single decoupled system. In short, our approach has three main contributions: (i) unsupervised techniques that fully integrate word embeddings and lexical chains; (ii) a more solid semantic representation that considers the latent relation between words in a document; and (iii) lightweight word embeddings models that can be extended to any natural language task. Knowledge-based systems that use natural language text can benefit from our approach to mitigate ambiguous semantic representations provided by traditional statistical approaches. The proposed techniques are tested against seven word embeddings algorithms using five different machine learning classifiers over six scenarios in the document classification task. Our results show that the integration between lexical chains and word embeddings representations sustain state-of-the-art results, even against more complex systems. Github: https://github.com/truas/LexicalChain_Builder
- Keyword:
- document classification, lexical chains, word embeddings, synset embeddings, chain2vec, and natural language processing
- Citation to related publication:
- Terry Ruas, Charles Henrique Porto Ferreira, William Grosky, Fabrício Olivetti de França, Débora Maria Rossi de Medeiros, "Enhanced word embeddings using multi-semantic representation through lexical chains", Information Sciences, 2020, https://doi.org/10.1016/j.ins.2020.04.048
- Discipline:
- Other, Science, and Engineering
-
- Creator:
- Title, Pascal O. and Bemmels, Jordan B.
- Description:
- The ENVIREM dataset v1.0 is a set of 16 climatic and 2 topographic variables that can be used in modeling species' distributions. The strengths of this dataset include their close ties to ecological processes, and their availability at a global scale, at several spatial resolutions, and for several time periods. The underlying temperature and precipitation data that went into their construction comes from the WorldClim dataset ( www.worldclim.org), and the solar radiation data comes from the Consortium for Spatial Information ( www.cgiar-csi.org). The data are compatible with and expand the set of variables from WorldClim v1.4 ( www.worldclim.org). For more information, please visit the project website: envirem.github.io
- Keyword:
- raster, species distribution modeling, and bioclimatic
- Citation to related publication:
- Title, P. O. and Bemmels, J. B. (2018), ENVIREM: an expanded set of bioclimatic and topographic variables increases flexibility and improves performance of ecological niche modeling. Ecography, 41: 291-307. http://doi.org/10.1111/ecog.02880
- Discipline:
- Science
-
- 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
- Citation to related publication:
- Crisp, D. N., Cheung, W., Gliske, S. V., Lai, A., Freestone, D. R., Grayden, D. B., Cook, M. J., & Stacey, W. C. (2020). Quantifying epileptogenesis in rats with spontaneous and responsive brain state dynamics. Brain Communications, 2(1). https://doi.org/10.1093/braincomms/fcaa048
- Discipline:
- Science, Engineering, and Health Sciences
-
Estimates of the water balance of the Laurentian Great Lakes using the Large Lakes Statistical Water Balance Model (L2SWBM)
User Collection- Creator:
- Smith, Joeseph P., Fry, Lauren M., Do, Hong X., and Gronewold, Andrew D.
- Description:
- This collection contains estimates of the water balance of the Laurentian Great Lakes that were produced by the Large Lakes Statistical Water Balance Model (L2SWBM). Each data set has a different configuration and was used as the supplementary for a published peer-reviewed article (see "Citations to related material" section in the metadata of individual data sets). The key variables that were estimated by the L2SWBM are (1) over-lake precipitation, (2) over-lake evaporation, (3) lateral runoff, (4) connecting-channel outflows, (5) diversions, and (6) predictive changes in lake storage. and Contact: Andrew Gronewold Office: 4040 Dana Phone: (734) 764-6286 Email: drewgron@umich.edu
- Keyword:
- Great Lakes water levels, statistical inference, water balance, data assimilation, Great Lakes, Laurentian, Machine learning, Bayesian, and Network
- Citation to related publication:
- Smith, J. P., & Gronewold, A. D. (2017). Development and analysis of a Bayesian water balance model for large lake systems. arXiv preprint arXiv:1710.10161., 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 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 (under revision)
- Discipline:
- Science and Engineering
5Works -
- 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
-
- 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
- Discipline:
- Science
-
- Creator:
- Kort, Eric A., Plant, Genevieve, Brandt, Adam R., Chen, Yuanlei, Fordice, Graham, Gorchov Negron, Alan M., Schwietzke, Stefan, Smith, Mackenzie, and Zavala-Araiza, Daniel
- Description:
- As part of the Flaring & Fossil Fuels: Uncovering Emissions & Losses (F3UEL) project, the aircraft measurement platform sampled downwind of flares in the Permian and Eagle Ford regions of Texas (2020) and the Bakken in North Dakota (2021). Estimates of methane destruction removal efficiency are calculated for each airborne intercept of a flare combustion plume based on the observed enhancements of carbon dioxide and methane, along with assumptions about the flare gas composition. Locations provided are the GPS coordinates for the aircraft sampling, not of the upwind flare infrastructure on the ground. Attempts to link the airborne sampling locations to ground infrastructure using the provided wind information (measured at the aircraft), should take care to account for complexities of transport in the atmosphere.
- Keyword:
- Natural Gas Flaring, Methane, and Oil & Gas
- Citation to related publication:
- Plant, G., Kort, E. A., Brandt, A. R., Chen, Y., Fordice, G., Gorchov Negron, A. M., Schwietzke, S., Smith, M., & Zavala-Araiza, D. (2022). Inefficient and unlit natural gas flares both emit large quantities of methane. Science, 377(6614), 1566–1571. https://doi.org/10.1126/science.abq0385, Kort, E. A., Plant, G., Smith, M. L., Brandt, A. R., Chen, Y., Gorchov Negron, A. M., Schwietzke, S., Zavala-Araiza, D. (2022). Aircraft Data (2020) for Flaring & Fossil Fuels: Uncovering Emissions & Losses (F3UEL), University of Michigan - Deep Blue Data. https://doi.org/10.7302/1xjm-3v49, and Kort, E. A., Plant, G., Brandt, A. R., Chen, Y., Gorchov Negron, A. M., Schwietzke, S., Smith, M. L., Zavala-Araiza, D. (2022). Aircraft Data (2021) for Flaring & Fossil Fuels: Uncovering Emissions & Losses (F3UEL), University of Michigan - Deep Blue Data. https://doi.org/10.7302/6tgq-e116
- Discipline:
- Science
-
F3UEL: Flaring & Fossil Fuels: Uncovering Emissions & Losses
User Collection- Creator:
- Kort, Eric and Plant, Genevieve
- Description:
- Fossil energy production, processing, flaring, and transmission all can harm climate and air quality by emitting greenhouse gases and air pollutants. Studies now show that onshore oil and gas production emit much more methane than what is inventoried, and that local air quality impacts can be significant, however, natural gas flaring and offshore systems have been largely overlooked. The F3UEL (Flaring & Fossil Fuels: Uncovering Emissions & Losses) project aims to address these gaps by improving our understanding of offshore emissions, characterizing how flares behave in the real world, identifying what portion of the offshore system is responsible for emissions, and determining how such systems can be monitored. Spanning three years (2020-2022), the project employed an aircraft platform to measure including both greenhouse gas and air quality measurements. To sample the largest regions of current and potential future offshore production and flaring, airborne measurements targeted the Gulf of Mexico, offshore California and Alaska, the Bakken Formation (North Dakota) and the Permian and Eagle Ford Basins (Texas). Data provided here includes the airborne measurements collected using Scientific Aviation’s Mooney aircraft platform, equipped with spectroscopic instrumentation to measure methane, carbon dioxide, water vapor, nitrous oxide, and nitrogen oxide, in addition to meteorological variables such as wind speed and direction. Data products from our analysis of these airborne measurements are also provided, including estimated flare destruction removal efficiency for the Bakken, Eagle Ford, and Permian basins. Each data file is in .csv format and is accompanied by a readme file with further information and descriptors of the variables included. All users should cite the papers and datasets provided in the readme files for each individual dataset. Website: https://graham.umich.edu/f3uel This project is funded by the Alfred P. Sloan Foundation with additional support from the Environmental Defense Fund, Scientific Aviation, and University of Michigan (College of Engineering, Climate and Space Sciences and Engineering; Graham Sustainability Institute).
- Keyword:
- offshore oil & gas, flaring, methane, Nitrogen oxides, natural gas flaring, and oil & gas
- Discipline:
- Science
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