Search Constraints
Filtering by:
Language
English
Remove constraint Language: English
Resource type
Dataset
Remove constraint Resource type: Dataset
Discipline
Science
Remove constraint Discipline: Science
« Previous |
1 - 50 of 641
|
Next »
Number of results to display per page
View results as:
Search Results
-
- Creator:
- Malik, Hafiz and Khan, Muhammad Khurran, King Saud University
- Description:
- Details of the microphone used for data collection, acoustic environment in which data was collected, and naming convention used are provided here. 1 - Microphones Used: The microphones used to collect this dataset belong to 7 different trademarks. Table (1) illustrates the number of used Mics of different trademarks and models. Table 1: Trademarks and models of Mics Mic Trademark Mic Model # of Mics Shure SM-58 3 Electro-Voice RE-20 2 Sennheiser MD-421 3 AKG C 451 2 AKG C 3000 B 2 Neumann KM184 2 Coles 4038 2 The t.bone MB88U 6 Total 22 2- Environment Description: A brief description of the 6 environments in which the dataset was collected is presented here: (i) Soundproof room: a small room (nearly 1.5m × 1.5m × 2m), which is closed and completely isolated. With an exception of a small window in the front side of the room which is made of glass, all the walls of the room are made of wood and covered by a layer of sponge from the inner side, and the floor is covered by carpet. (ii) Class room: standard class room (6m × 5m × 3m). (iii) Lab: small lab (4m × 4m × 3m). All the walls are made of glasses and the floor is covered by carpet. The lab contains 9 computers. (iv) Stairs: is in the second floor. The place of recording is 3m × 5m (v) Parking: is the college parking. (vi) Garden: is an open space outside the buildings. 3- Naming Convention: This set of rules were followed as a naming convention to give each file in the dataset a unique name: (i) The file name is 19 characters long, and consists of 5 sections separated by underscores. (ii) The first section is of 3 characters indicates the Microphone trademark. (iii) The second section of 4 characters indicates the microphone model as in table (2). (iv) The third section of 2 characters indicates a specific microphone within a set of microphones of the same trademark and model, since we have more than one microphone of the same trademark and model. (v) The fourth section of 2 characters indicates the environment, where Soundproof room --> 01 Class room --> 02 Lab --> 03 Stairs --> 04 Parking --> 05 Garden --> 06 (vi) The fifth section of 2 characters indicates the language, where Arabic --> 01 English --> 02 Chinese --> 03 Indonesian --> 04 (vii) The sixth section of 2 characters indicates the speaker. Table 2: Microphones Naming Criteria Original Mic Trademark and model --> Naming Convenient Shure SM-58 --> SHU_0058 Electro-Voice RE-20 --> ELE_0020 Sennheiser MD-421 --> SEN_0421 AKG C 451 --> AKG_0451 AKG C 3000 B --> AKG_3000 Neumann KM184 --> NEU_0184 Coles 4038 --> COL_4038 The t.bone MB88U --> TBO_0088 For example: SEN_0421_02_01_02_03 is an English file recorded by speaker number 3 in the soundproof room using microphone number 2 of Sennheiser MD-421
- Keyword:
- audio forensic, multimedia forensics, microphone identification, tamper detection, splicing detection, and codec identification
- Citation to related publication:
- Muhammad Khurram Khan, Mohammed Zakariah, Hafiz Malik & Kim-Kwang Raymond Choo (2018). A novel audio forensic data-set for digital multimedia forensics, Australian Journal of Forensic Sciences, 50:5, 525-542, http://dx.doi.org/10.1080/00450618.2017.1296186
- Discipline:
- Engineering, Government, Politics and Law, and Science
-
- Creator:
- Steiner, Allison and Bryan, Alex
- Description:
- Included are RegCM simulations driven by three different types of boundary conditions 1. ERA - present day only (1979-2005) 2. GFDL - present day (1978-2005) and future (2041-2065) 3. HadGEM - present day (1978-2005) and future (2041-2065) Each directory has three files with monthly averaged values: ATM: includes 4D (t,z,y,x) atmospheric fields (pressure, winds, temperature, specific humidity, cloud water) and some 3D fields (t,y,x) precipitation, soil temperature, soil water SRF: includes 3D (t,y,x) surface variables (surface pressure, 10m winds, drag coefficient, surface temperature, 2m air temperature, soil moisture, precipitation, runoff, snow, sensible heat flux, latent heat flux, surface radiation components (SW, LW), PBL height, albedo, sunshine duration) RAD: includes 4D radiative transfer variables (SW and LW heating, TOA fluxes, cloud fraction, ice water content) clm_h0 files: CLM land surface files, includes canopy variables, surface fluxes, soil moisture by layers, etc. "
- Keyword:
- climate
- Citation to related publication:
- Bryan, A. M., A. L. Steiner, and D. J. Posselt (2015), Regional modeling of surface-atmosphere interactions and their impact on Great Lakes hydroclimate, J. Geophys. Res. Atmos., 120, 1044–1064. https://doi.org/10.1002/2014JD022316
- Discipline:
- Science
-
- Creator:
- Hayward, Stephen L. , Lund, Paul E., Kang, Qing, Johnson-Buck, Alexander , Tewari, Muneesh, and Walter, Nils G.
- Description:
- This work contains the experimental data and associated analysis that are described in the research publication entitled "Ultra-specific and Amplification-free Quantification of Mutant DNA by Single-molecule Kinetic Fingerprinting". This work contains multiple zip files, each of which represents one of the principal experiment groups presented in the publication. Each experiment group contains movie and analysis files corresponding to various experimental conditions related to that experiment group.
- Keyword:
- Single Molecule Fluorescence, Super-Resolution Microscopy, Nucleic Acid Hybridization, T790M Mutation, Cytosine Deamination, SiMREPS, and single molecule kinetic fingerprinting
- Citation to related publication:
- https://pubs.acs.org/doi/10.1021/jacs.8b06685
- Discipline:
- Science
-
- Creator:
- Bougher, Stephen W. (CLaSP Department, U. of Michigan) and Roeten, Kali J. (CLaSP Department, U. of Michigan)
- Description:
- The NASA MAVEN (Mars Atmosphere and Volatile Evolution) spacecraft, which is currently in orbit around Mars, has been taking monthly measurements of the speed and direction of the winds in the upper atmosphere of Mars between about 140 to 240 km above the surface. The observed wind speeds and directions change with time and location, and sometimes fluctuate quickly. These measurements 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. This is the first comparison between direct measurements of the winds in the upper atmosphere of Mars and simulated winds and is important because it can help to inform us what physical processes are acting on the observed winds. Some wind measurements have similar wind speeds or directions to those predicted by the M-GITM model, but sometimes, there are large differences between the simulated and measured winds. The disagreements between wind observations and model simulations suggest that processes other than normal solar forcing may become relatively more important during these observations and alter the expected circulation pattern. 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 provides key context for understanding how the atmosphere behaves as a whole system. A basic version of the M-GITM code can be found on Github as follows: https:/github.com/dpawlows/MGITM and About 30 Neutral Gas and Ion Mass Spectrometer (NGIMS) wind campaigns (of 5 to 10 orbits each) have been conducted by the MAVEN team (Benna et al., 2019). Five of these campaigns are selected for detailed study (Roeten et al. 2019). The Mars conditions for these five campaigns have been used to launch corresponding M-GITM code simulations, yielding 3-D neutral wind fields for comparison to these NGIMS wind observations. The M-GITM datacubes used to extract the zonal and meridional neutral winds, along the trajectory of each orbit path between 140 and 240 km, are provided in this Deep Blue Data archive. README files are provided for each datacube, detailing the contents of each file. A general README file is also provided that summarizes the inputs and outputs of the M-GITM code simulations for this study.
- Keyword:
- Mars, MAVEN spacecraft, Mars thermosphere, and Mars global upper atmosphere winds
- Citation to related publication:
- Roeten, K. J., Bougher, S. W., Benna, M., Mahaffy, P. R., Lee, Y., Pawlowski, D., et al. (2019). MAVEN/NGIMS thermospheric neutral wind observations: Interpretation using the M‐GITM general circulation model. Journal of Geophysical Research: Planets, 124, 3283– 3303. https://doi.org/10.1029/2019JE005957
- Discipline:
- Science and Engineering
-
- Creator:
- Crisp, Dakota N., Saggio, Maria L., Scott, Jared, Stacey, William C., Nakatani, Mitsuyoshi, Gliske, Stephen V., and Lin, Jack
- Description:
- This data and scripts are meant to test and show seizure differentiation based on bifurcation theory. A zip file is included which contains real and simulated seizure waveforms, Matlab scripts, and metadata. The matlab scripts allow for visual review validation and objective feature analysis. The file “README.txt” provides more detail about each individual file within the zip file. and Data citation: Crisp, D.N., Saggio, M.L., Scott, J., Stacey, W.C., Nakatani, M., Gliske, S.F., Lin, J. (2019). Epidynamics: Navigating the map of seizure dynamics - Code & Data [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/ejhy-5h41
- Keyword:
- Bifurcation, Epilepsy, Seizure, and Divergence
- Citation to related publication:
- Saggio, M.L., Crisp, D., Scott, J., Karoly, P.J., Kuhlmann, L., Nakatani, M., Murai, T., Dümpelmann, M., Schulze-Bonhage, A., Ikeda, A., Cook, M., Gliske, S.V., Lin, J., Bernard, C., Jirsa, V., Stacey, W., 2020. In pre-print. Epidynamics characterize and navigate the map of seizure dynamics. bioRxiv 2020.02.08.940072. https://doi.org/10.1101/2020.02.08.940072
- Discipline:
- Engineering, Science, and Health Sciences
-
- 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
-
- Creator:
- Hall, Ryan J. and Larson, Ronald G.
- Description:
- This is data is a large assortment of over 50 1,4-polybutadiene star-linear blends that can be used for assessing and developing predictive models. The data are presented in CSV files.
- Keyword:
- polymers, rheology, star-linear polymer blends, and shear rheology
- Citation to related publication:
- Hall, R., Desai, P. S., Kang, B.-G., Huang, Q., Lee, S., Chang, T., Venerus, D. C., Mays, J., Ntetsikas, K., Polymeropoulos, G., Hadjichristidis, N., & Larson, R. G. (2019). Assessing the Range of Validity of Current Tube Models through Analysis of a Comprehensive Set of Star–Linear 1,4-Polybutadiene Polymer Blends. Macromolecules, 52(20), 7831–7846. https://doi.org/10.1021/acs.macromol.9b00642
- Discipline:
- Science and Engineering
-
- 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:
- Larson, Ronald G., Wen, Fei, Huang, Wenjun, and Huang, Ming
- Description:
- We provide the parameters used in Umbrella Sampling simulations reported in our study "Efficient Estimation of Binding Free Energies between Peptides and an MHC Class II Molecule Using Coarse-Grained Molecular Dynamics Simulations with a Weighted Histogram Analysis Method", namely the set positions and spring constants for each window in simulations. Two tables are provided. Table 1 lists the names of the peptides and their corresponding sequences. Table 2 lists the parameters. The abstract of our work is the following: We estimate the binding free energy between peptides and an MHC class II molecule using molecular dynamics (MD) simulations with Weighted Histogram Analysis Method (WHAM). We show that, owing to its more thorough sampling in the available computational time, the binding free energy obtained by pulling the whole peptide using a coarse-grained (CG) force field (MARTINI) is less prone to significant error induced by biased-sampling than using an atomistic force field (AMBER). We further demonstrate that using CG MD to pull 3-4 residue peptide segments while leaving the remain-ing peptide segments in the binding groove and adding up the binding free energies of all peptide segments gives robust binding free energy estimations, which are in good agreement with the experimentally measured binding affinities for the peptide sequences studied. Our approach thus provides a promising and computationally efficient way to rapidly and relia-bly estimate the binding free energy between an arbitrary peptide and an MHC class II molecule.
- Keyword:
- Molecular Dynamics, Binding Free Energy, Protein, MHC, and Coarse-Grained
- Discipline:
- Science and Engineering
-
- Creator:
- Okullo, Dolorence, Gomez-Lopez, Iris N., Goodspeed, Robert, Reddy, Shruthi, Veinot, Tiffany C, Clarke, Phillipa J., and Data Driven Detroit
- Description:
- The information and education environment refers to: 1) the presence of information infrastructures such as broadband Internet access and public libraries in a location; 2) a person’s proximity to information infrastructures and sources; 3) the distribution of information infrastructures, sources and in a specific location; and 4) exposure to specific messages (information content) within a specific location. Coverage for all data: 10-county Detroit-Warren-Ann Arbor Combined Statistical Area.
- Keyword:
- Residential Broadband Data Adoption Rates, Census tract level, Broadband Internet Access and Speed, Colleges and Universities, Public Libraries, Spatial Measures, and Schools
- Discipline:
- Science, Social Sciences, and Health Sciences
-
- Creator:
- Keppel-Aleks, Gretchen and Liptak, Jessica
- Description:
- -CESM_bdrd _NEP_pulse_response_CO2.nc contains time series from the ‘FullyCoupled’ simulation -CESM_bdrcs_NEP_pulse_response_CO2.nc contains time series from the ‘NoRad’ simulation -CESM_bdrd_pftcon_NEP_pulse_response_CO2.nc contains data from the ‘NoLUC’ simulation -CESM_bdrd_Regional_Fluxes_NEP.nc contains NEP time series for each terrestrial source region from the FullyCoupled simulation - CESM_bdrcs_Regional_Fluxes_NEP.nc contains NEP time series for each terrestrial source region from the CESM ‘NoRad’ simulation - CESM_bdrd_pftcon_Regional_Fluxes_NEP.nc contains NEP time series for each terrestrial source region from the CESM ‘NoLUC’ simulation The 3-letter station IDs, latitudes, and longitudes of the sample locations are: ID Latitude (ºN) Longitude (ºE) 1. BRW 71.3 203.4 2. ZEP 78.9 11.9 3. SHM 52.7 174.1 4. THD 41.1 235.8 5. TAP 36.7 126.1 6. BMW 32.3 295.1 7. MLO 19.5 204.4 8. POCN15 15.0 215.0 9. ALT 82.5 297.5 10. BHD -41.4 174.9 11. EIC -27.2 250.6 12. GMI 13.4 144.7 13. HUN 47.0 16.7 14. IZO 28.3 343.5 15. LLN 23.5 120.9 16. NAT -5.8 324.7 17. WLG 36.3 100.9 18. HBA -75.6 333.8 19. BKT -0.20 100.3 20. UUM 44.5 111.1 21. CGO -40.7 144.5 22. SDZ 40.7 117.1 23. ASC -8.0 345.6 24. SEY -4.7 55.5 25. POCS20 -20.0 186.0 26. POCS35 -35.0 180.0 27. PSA -64.9 296.0 28. SYO -69.0 39.6 29. CHR 1.7 202.8 30. KEY 25.7 279.8 31. BAL 55.4 17.2 32. HPB 47.8 11.0 33. LMP 35.5 12.6 34. NMB -23.6 15.0 35. RPB 13.2 300.2 36. WIS 30.0 35.1 37. POCS10 -10.0 199.0 38. POCN10 10.0 211.0 39. MID 28.2 182.6 40. SMO -14.2 189.4 41. SPO -90.0 335.2 The terrestrial CO2 source region abbreviations are: 1. NBNA 2. SBNA 3. ETNA 4. WTNA 5. CNAM 6. AMZN 7. EASA 8. WESA 9. EURO 10. SAME 11. MDAF 12. AFRF 13. SOAF 14. EABA 15. WEBA 16. SOBA 17. CNAS 18. SEAS 19. EQAS 20. AUST 21. GNLD 22. ATCA
- Keyword:
- atmospheric CO2 annual cycle amplitude and CESM extended concentration pathway
- Citation to related publication:
- Hornick, T., Bach, L. T., Crawfurd, K. J., Spilling, K., Achterberg, E. P., Woodhouse, J. N., Schulz, K. G., Brussaard, C. P. D., Riebesell, U., & Grossart, H.-P. (2017). Ocean acidification impacts bacteria–phytoplankton coupling at low-nutrient conditions. Biogeosciences, 14(1), 1–15. https://doi.org/10.5194/bg-14-1-2017
- Discipline:
- Science
-
- Creator:
- Singh, Deepak
- Description:
- This includes data for all the plots and maps I created for my paper publication entitled "Improvement of Mars surface snow albedo modeling in LMD Mars GCM with SNICAR".
- 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
- Citation to related publication:
- Blesh J. Functional traits in cover crop mixtures: Biological nitrogen fixation and multifunctionality. J Appl Ecol. 2018;55:38–48. https://doi.org/10.1111/1365-2664.13011
- Discipline:
- Science
-
- Creator:
- Engel, Daniel D. , Evans, Mary Anne, Low, Bobbi S., and Schaeffer, Jeff
- Description:
- This dataset was compiled as an attempt to understand how natural resource managers and research ecologists in the Great Lakes region integrate the ecosystem services (ES) paradigm into their work. The following text is the adapted abstract from a thesis associated with this data. Ecosystem services, or the benefits people obtain from ecosystems, have gained much momentum in natural resource management in recent decades as a relatively comprehensive approach to provide quantitative tools for improving decision-making and policy design. However, to date we know little about whether and how natural resource practitioners, from natural resource managers to research ecologists (hereafter managers and ecologists respectively), have adopted the ES paradigm into their respective work. Here, we addressed this knowledge gap by asking managers and ecologists about whether and how they have adopted the ES paradigm into their respective work. First, we surveyed federal, state, provincial and tribal managers in the Great Lakes region about their perception and use of ES as well as the relevance of specific services to their work. Although results indicate that fewer than 31% of the managers said they currently consider economic values of ES, 79% of managers said they would use economic information on ES if they had access to it. Additionally, managers reported that ES-related information was generally inadequate for their resource management needs. We also assessed managers by dividing them into identifiable groups (e.g. managers working in different types of government agencies or administrative levels) to evaluate differential ES integration. Overall, results suggest a desire among managers to transition from considering ES concepts in their management practices to quantifying economic metrics, indicating a need for practical and accessible valuation techniques. Due to a sample of opportunity at the USGS Great Lakes Science Center (GLSC), we also evaluated GLSC research ecologists’ integration of the ES paradigm because they play an important role by contributing requisite ecological knowledge for ES models. Managers and ecologists almost unanimously agreed that it was appropriate to consider ES in resource management and also showed convergence on the high priority ES. However, ecologists appeared to overestimate the adequacy of ES-related information they provide as managers reported the information was inadequate for their needs. This divergence may reflect an underrepresentation of ecological economists in this system who can aid in translating ecological models into estimates of human well-being. As a note, the dataset for the research ecologists has had some data removed as it could be considered personally identifiable information due to the small sample size in that population. The surveys associated with both datasets have also been included in PDF format. Curation Notes: Three files were added to the data set on Dec 21, 2017. Two csv files: "Ecosystem services and Research Ecologists - Data Index.csv" and "Ecosystem services and Research Managers - Data Index.csv" and one text file: "Ecosystem Services Adoption Readme.txt". The file names of the original four files were altered to replace an ampersand with the word "and".
- Keyword:
- Research Ecologist, Decision-Making, Ecosystem Services, Natural Resource Management, Paradigm Adoption, and Ecological Economics
- Citation to related publication:
- Engel, D.D., Evans, M.A., Low, B.S., Schaeffer, J. (2017) “Understanding Ecosystem Services Adoption by Natural Resource Managers and Research Ecologists.” Journal of Great Lakes Research, 43(3), 169-179. https://doi.org/10.1016/j.jglr.2017.01.005
- Discipline:
- Science and Social Sciences
-
- Creator:
- Steiner, Allison and Kawecki, Stacey
- Description:
- WRF-Chem model
- Keyword:
- aerosols and weather
- Citation to related publication:
- Kawecki, S., Steiner, A.L., 2018. The Influence of Aerosol Hygroscopicity on Precipitation Intensity During a Mesoscale Convective Event. Journal of Geophysical Research: Atmospheres 123, 424–442. https://doi.org/10.1002/2017JD026535
- Discipline:
- Science
-
- Creator:
- Blesh, Jennifer and King, Alison E.
- Description:
- This dataset contains three data files used in: King, A.E. and J. Blesh, 2017. Crop rotations for increased soil carbon: perenniality as a guiding principle. Ecological Applications. There are also three corresponding metadata files. The file “CRMA 2017 Main.csv” contains data for the control and treatment rotations used to construct pairwise comparisons for meta-analysis, response ratios calculated for soil organic carbon concentration, and change in carbon input. The dataset also includes management, soil, and other environmental characteristics for each site. The file “CRMA 2017 Diversity x Nitrogen.csv” contains data used to test whether N fertilizer inputs mediated the effect of functional diversity on SOC concentrations. The file “CRMA Annual grain.csv” contains data used to test for effects of crop rotation species diversity (one vs. two species, or two vs. three species) on SOC concentrations and C input (i.e., for the “grain-only” rotations). The dataset also includes management, soil, and other environmental characteristics for each site. The corresponding metadata files: “CRMA 2017 Main_metadata.csv”, “CRMA 2017 Diversity x Nitrogen_metadata.csv”, and “CRMA Annual grain _metadata.csv” provide a detailed description of all variables in each dataset. Note: On Jan 12, 2018 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:
- soil carbon, functional diversity, meta-analysis, cropping system, and student-friendly
- Discipline:
- Science
-
- Creator:
- Forrest, Stephen R., Panda, Anurag, Qu, Yue, Che, Xiaozhou, Coburn, Caleb, and Burlingame, Quinn
- Description:
- Mathematica Diffusion Simulation: Programmed by Coburn, Caleb. Simulation of diffusion in organic heterostructures, including least square fits and statistical goodness of fit analysis. Used to calculate fits to transient data in Fig 1, 3 and Extended Data Fig.2. Example data file included for download Matlab Montecarlo simulation: Programmed by Coburn, Caleb. Montecarlo simulation of charge diffusion on a cubic lattice to determine lateral diffusion length as a function of barrier height, assuming thermionic emission over the barrier. Matlab 2D Diffusion Simulation:Programmed by Coburn, Caleb. Modified from BYU Physics 430 Course Manual. Simulates diffusion around a film discontinuity, such a cut. Used to generate fits to Extended Data Fig. 1
- Keyword:
- Organic semiconductors and Charge diffusion
- Citation to related publication:
- Burlingame, Q., Coburn, C., Che, X., Panda, A., Qu, Y., & Forrest, S. R. (2018). Centimetre-scale electron diffusion in photoactive organic heterostructures. Nature, 554(7690), 77-80. https://doi.org/10.1038/nature25148
- Discipline:
- Science
-
- 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:
- Johnson, Jena E.
- Description:
- Note: The "Readme_Metadata" file was updated on March 15, 2018 to include a citation to the related article making use of this data and was reformatted to be presented as a pdf file rather than as a docx file. and This data set is comprised of synchrotron-based X-ray transmission and absorption spectroscopy data as well as X-ray diffraction patterns that were performed to characterize the best-preserved examples of nanoscale iron silicate mineral inclusions from 2.5 billion-year-old Banded Iron Formations (BIFs) and ferruginous cherts.
- Keyword:
- Precambrian banded iron formations and nanoparticle inclusions of iron silicates in chert
- Citation to related publication:
- Johnson, J. E., Muhling, J. R., Cosmidis, J., Rasmussen, B. & Templeton, A. S. (2018). Low-Fe(III) Greenalite Was a Primary Mineral from Neoarchean Oceans. Geophysical Research Letters, 45. https://doi.org/10.1002/2017GL076311
- Discipline:
- Science
-
- Creator:
- Ozturk, Dogacan
- Description:
- The global magnetosphere-ionosphere-thermosphere (M-I-T) system is intrinsically coupled and susceptible to external drivers such as solar wind dynamic pressure enhancements. In order to understand the large-scale dynamic processes in the M-I-T system due to the compression from the solar wind, the 17 March 2015 sudden commencement was studied in detail using global numerical models. This data set is comprised of the simulation data generated from these models. and NOTE: The following changes were made to this dataset on March 28, 2018. First, two mp4 files were added. Second, the symbol representing "degree" was not rendering properly in the README file. The symbols were removed and replaced with the word "degree". Third, the metadata in the "methodology" and "description" fields were revised for content and clarity. On April 16, 2018 a citation to the corresponding article was added to the metadata record.
- Keyword:
- MHD model, BATS'R'US, and GITM
- Citation to related publication:
- Ozturk, D. S., Zou, S., Ridley, A. J., & Slavin, J. A. (2018). Modeling study of the geospace system response to the solar wind dynamic pressure enhancement on 17 March 2015. Journal of Geophysical Research: Space Physics, 123, 2974–2989. https://doi.org/10.1002/2017JA025099
- Discipline:
- Science
-
- Creator:
- Tye, Alexander R, Wolf, Aaron S, and Niemi, Nathan A
- Description:
- Detrital zircon age distributions provide robust insights into past sedimentary systems, but these age distributions are often complex and multi-peaked, with sample sizes too small to confidently resolve population distributions. This limited sampling hinders existing quantitative methods for comparing detrital zircon age distributions, which show systematic dependence on the sizes of compared samples. The proliferation of detrital zircon studies motivates the development of more robust quantitative methods. We present the first attempt, to our knowledge, to infer probability model ensembles (PMEs) for samples of detrital zircon ages using a Bayesian method. Our method infers the parent population age distribution from which a sample is drawn, using a Monte Carlo approach to aggregate a representative set of probability models that is consistent with the constraints that the sample data provide. Using the PMEs inferred from sample data, we develop a new estimate of correspondence between detrital zircon populations called Bayesian Population Correlation (BPC). Tests of BPC on synthetic and real detrital zircon age data show that it is nearly independent from sample size bias, unlike existing correspondence metrics. Robust BPC uncertainties can be readily estimated, enhancing interpretive value. When comparing two partially overlapping zircon age populations where the shared proportion of each population is independently varied, BPC results conform almost perfectly to expected values derived analytically from probability theory. This conformity of experimental and analytical results permits direct inference of the shared proportions of two detrital zircon age populations from BPC. We provide MATLAB scripts to facilitate the procedures we describe.
- Keyword:
- provenance, statistics, zircon, Bayesian, detrital, and density estimation
- Citation to related publication:
- A.R. Tye, A.S. Wolf, N.A. Niemi, Bayesian population correlation: A probabilistic approach to inferring and comparing population distributions for detrital zircon ages, Chemical Geology, Volume 518, 2019, Pages 67-78, ISSN 0009-2541, https://doi.org/10.1016/j.chemgeo.2019.03.039
- Discipline:
- Science
-
- 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:
- 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:
- 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
- Citation to related publication:
- Cole, S. L., Robinson, M. J. F., & Berridge, K. C. (2018). Optogenetic self-stimulation in the nucleus accumbens: D1 reward versus D2 ambivalence. PLOS ONE, 13(11), e0207694. https://doi.org/10.1371/journal.pone.0207694
- Discipline:
- Science
-
- Creator:
- Gliske, Stephen V and Stacey, William C
- Description:
- This data is part of a large program to translate detection and interpretation of HFOs into clinical use. A zip file is included which contains hfo detections, metadata, and Matlab scripts. The matlab scripts analyze this input data and produce figures as in the referenced paper (note: the blind source separation method is stochastic, and so the figures may not be exactly the same). A file "README.txt" provides more detail about each individual file within the zip file.
- Keyword:
- hfo, high frequency oscillation, ripple, fast ripple, blind source separation, non-negative matrix factorization, and temporal variability
- Discipline:
- Science, Engineering, and Health Sciences
-
- Creator:
- Ward, Jamie L ., Flanner, Mark G., Bergin, Mike, Dibb, Jack E., Polashenski, Chris M., Soja, Amber J., and Thomas, Jennie L.
- Description:
- Biomass burning produces smoke aerosols that are emitted into the atmosphere. Some smoke constituents, notably black carbon (BC), are highly effective light-absorbing aerosols (LAA). Emitted LAA can be transported to high albedo regions like the Greenland Ice Sheet (GrIS) and affect local snowmelt. In the summer, the effects of LAA in Greenland are uncertain. To explore how LAA affect GrIS snowmelt and surface energy flux in the summer, we conduct idealized global climate model simulations with perturbed aerosol amounts and properties in the GrIS snow and overlying atmosphere. The in-snow and atmospheric aerosol burdens we select range from background values measured on the GrIS to unrealistically high values. This helps us explore the linearity of snowmelt response and to achieve high signal-to-noise ratios. With LAA operating only in the atmosphere, we find no significant change in snowmelt due to the competing effects of surface dimming and tropospheric warming. Regardless of atmospheric LAA presence, in-snow BC-equivalent mixing ratios greater than ~60 ng/g produce statistically significant snowmelt increases over much of the GrIS. We find that net surface energy flux changes correspond well to snowmelt changes for all cases. The dominant component of surface energy flux change is solar energy flux, but sensible and longwave energy fluxes respond to temperature changes. Atmospheric LAA dampen the magnitude of solar radiation absorbed by in-snow LAA when both varieties are simulated. In general, the significant melt and surface energy flux changes we simulate occur with LAA quantities that have never been recorded in Greenland.
- Keyword:
- climate, Greenland Ice Sheet, black carbon, biomass burning, snowmelt, and surface energy balance
- Citation to related publication:
- Ward, J.L., et al. (2018). Modeled Response of Greenland Snowmelt to the Presence of Biomass Burning-Based Absorbing Aerosols in the Atmosphere and Snow. Journal of Geophysical Research: Atmospheres. 123, 6122– 6141. https://doi.org/10.1029/2017JD027878
- Discipline:
- Science
-
- 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
- Citation to related publication:
- Bemmels, J.B., and C.W. Dick. 2018. Genomic evidence of a widespread southern distribution during the Last Glacial Maximum for two North American hickory species. Journal of Biogeography, 45: 1739– 1750. https://doi.org/10.1111/jbi.13358
- Discipline:
- Science
-
- 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
- Citation to related publication:
- Mirshams Shahshahani P, Lipps DB, Galecki AT, Ashton-Miller JA (2018) On the apparent decrease in Olympic sprinter reaction times. PLoS ONE 13(6): e0198633. https://doi.org/10.1371/journal.pone.0198633
- Discipline:
- Engineering, Health Sciences, Science, Other, and General Information Sources
-
- Creator:
- Adam Schneider and Mark Flanner
- Description:
- This dataset contains all data used to generate the figures in The Cryosphere manuscript “Measuring Snow Specific Surface Area with 1.30 and 1.55 micro-meter Bidirectional Reflectance Factors,” by Adam Schneider, Mark Flanner, and Roger De Roo. These data support the theory, calibration, and application of the Near-Infrared Emitting and Reflectance Monitoring Dome (NERD), an instrument engineered to rapidly retrieve surface snow specific surface area in the field. Note that this deposit includes a microCT scan database for natural snowfall samples collected in New Hampshire during 2015-2017, comprised of raw tiff files as well as reconstructions, binarized reconstructions, and some 3D model reconstructions. and Running python scripts generally require that the following packages are installed: NumPy, SciPy, Matplotlib, Pandas, and ipdb (for debugging).
- Keyword:
- Snow specific surface area, Monte Carlo, X-ray micro-computed tomography, SNICAR, Near-Infrared Emitting and Reflectance-Monitoring Dome, Bidirectional reflectance factor, Cryosphere, and 3D
- Discipline:
- Science
-
- Creator:
- Alsip, Peter
- Description:
- Percent Weight Change Data: The model was run continuously on a daily time step for seasonal intervals (Spring: March thru May; Summer: June thru August; Fall: September thru November) as well as contiguously from Spring to Fall to assess total growth over the likely growing season (March thru November). CSV files represent the simulated weight change (%) of Bighead and Silver Carp for the respective time periods associated with the file name. Initial fish mass for each seasonal interval and growing season was 4350 g for Silver Carp and 5480 g for Bighead Carp. Maximum and mean total weight change (%) was determined for three depth ranges (near surface depths [NS]: 0 – 10 m; deep chlorophyll layer depths [DCL]: 10 - 50 m; and whole water column [WC]). Coordinates are in decimal degrees. File naming convention: speciesSeasonWtChange (e.g. bigheadFallWtChange = % weight change of Bighead Carp from September through November) , Monthly Habitat Quality Data: Rdata files contain matrices of Bighead or Silver carp growth rate potential as represented as a mass-proportional growth rate (gram of carp/gram of carp/day [g/g/d]) for the 15th day of each month. Habitats with growth rate potential >= 0 g/g/d were deemed suitable. Matrix attributes: Rows: Row numbers refer to the spatial node with 20 equally-spaced vertical layers. Columns: Columns 1-20 refer to the growth rate potential value for each vertical layer of each node. Vertical layers are evenly spaced based on the total depth of the water column for each node. Depth for each node can be found in the grid attributes data file. Columns 21 ("meanG") and 22 ("Gmax") represent the average and maximum growth rate potential, respectively, of the fish across the whole water column for the corresponding node. File naming convention: species_MonthNumber (e.g. silver_06 = Silver carp growth rate potential in June) Spatial coordinates for each node can be found in the grid attributes data files., Grid attributes data: This Rdata file provides the spatial reference data and other grid attributes. Coordinates are provided in UTM (x & y) and latitude and longitude (decimal degrees). Depth (meters) for each node is listed in this file. , GRP Model code: Details bioenergetics equations, foraging equation, functions for running the model on a monthly time-step and daily time step, and functions for basic analyses. Model is coded in R., and The simulated input data (prey and temperature) used to run our model is not included in this data set. Instead we provide the model code, grid attributes, and outputs of the model. The readRDS() function (R Base Package v.3.5.1) is required to read in .Rdata files in R.
- Keyword:
- Asian Carp, Laurentian Great Lakes, Habitat Suitability, Invasive Species, Lake Michigan, and Ecological Modeling
- Discipline:
- Science
-
- Creator:
- Thomaz, Andréa T. (UMICH) and Knowles, L. Lacey (UMICH)
- Description:
- The eastern coastal basins of Brazil are a series of small and isolated rivers that drain directly into the Atlantic Ocean. During the Pleistocene, sea-level retreat caused by glaciations exposed the continental shelf, resulting in enlarged paleodrainages that connected rivers that are isolated today. Using Geographic Information System (GIS), we infer the distribution of these paleodrainages, and their properties for the east Brazilian coast. Here, we publicly make available the shapefiles that demonstrate the paleodrainage structure along the Brazilian coast during the largest sea-level retreats in the Pleistocene, the riverine vectors during the same period and the coastal line for a drop of -125m in the sea.
- Keyword:
- Paleodrainages, Glaciations, Pleistocene, Brazil, Neotropical, and Sea-level retreat
- Discipline:
- Science
-
- Creator:
- Kort, EA, Gvakharia, A, Smith, ML, and Conley, S
- Description:
- Data is collected from research flights based in West Memphis, Arkansas, covering the Mississippi River Valley. The data file contains all merged flight data from each flight day.
- Keyword:
- Greenhouse gas
- Citation to related publication:
- Gvakharia, A., Kort, E.A., Smith, M.L., Conley, S., 2018. Testing and evaluation of a new airborne system for continuous N2O, CO2, CO, and H2O measurements: the Frequent Calibration High-performance Airborne Observation System (FCHAOS). Atmospheric Measurement Techniques; Katlenburg-Lindau 11, 6059. https://doi.org/10.5194/amt-11-6059-2018
- 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:
- Ramasubramani, Vyas
- Description:
- The goal of the work is to elucidate the stability of a complex experimentally observed structure of proteins. We found that supercharged GFP molecules spontaneously assemble into a complex 16-mer structure that we term a protomer, and that under the right conditions an even larger assembly is observed. The protomer structure is very well defined, and we performed simulations to try and understand the mechanics underlying its behavior. In particular, we focused on understanding the role of electrostatics in this system and how varying salt concentrations would alter the stability of the structure, with the ultimate goal of predicting the effects of various mutations on the stability of the structure. There are two separate projects included in this repository, but the two are closely linked. One, the candidate_structures folder, contains the atomistic outputs used to generate coarse-grained configurations. The actual coarse-grained simulations are in the rigid_protein folder, which pulls the atomistic coordinates from the other folder. All data is managed by signac and lives in the workspace directories, which contain various folders corresponding to different parameter combinations. The parameters associated with a given folder are stored in the signac_statepoint.json files within each subdirectory. The atomistic data uses experimentally determined protein structures as a starting point; all of these are stored in the ConfigFiles folder. The primary output is the topology files generated from the PDBs by GROMACS; these topologies are then used to parametrize the Monte Carlo simulations. In some cases, atomistic simulations were actually run as well, and the outputs are stored alongside the topology files. In the rigid_protein folder, the ConfigFiles folder contains MSMS, the software used to generate polyhedral representations of proteins from the PDBs in the candidate_structures folder. All of the actual polyhedral structures are also stored in the ConfigFiles folder. The actual simulation trajectories are stored as general simulation data (GSD) files within each subdirectory of the workspace, along with a single .pos file that contains the shape definition of the (nonconvex) polyhedron used to represent a protein. The logged quantities, such as energies and MC move sizes, are stored in .log files. The logic for the simulations in the candidate_structures project is in the Python scripts project.py, operations.py, and scripts/init.py. The rigid_protein folder also includes the notebooks directory, which contains Jupyter notebooks used to perform analyses, as well as the Python scripts used to actually perform the simulations and manage the data space. In particular, the project.py, operations.py and scripts/init.py scripts contain most of the logic associated with the simulations.
- Keyword:
- Protein assembly, Cryo TEM, Hierarchical Assembly, Monte Carlo simulation, and Coarse-grained simulation
- Discipline:
- Science and Engineering
-
- Creator:
- Thomaz, Andréa T. (UMICH), Carvalho, Tiago P. (UFRGS), Malabarba, Luiz R. (UFRGS), and Knowles, L. Lacey (UMICH)
- Description:
- Estimated phylogenetic relationships based on more than 18,000 loci in 93 individuals (full data) or 21 individuals (subset data) representing 19 described species and two putative undescribed species. Nine files are part of this dataset, including all input files to infer the phylogenetic reconstructions and the outputs obtained, in addition to a pruned tree used to infer the ancestral state reconstructions.
- Keyword:
- dusky millions poeciliids, sexual selection, South America, and ddRADseq
- Citation to related publication:
- Andréa T. Thomaz, Tiago P. Carvalho, Luiz R. Malabarba, L. Lacey Knowles, Geographic distributions, phenotypes, and phylogenetic relationships of Phalloceros (Cyprinodontiformes: Poeciliidae): insights about diversification among sympatric species pools, Molecular Phylogenetics and Evolution, 2018, ISSN 1055-7903, https://doi.org/10.1016/j.ympev.2018.12.008
- Discipline:
- Science
-
- Creator:
- Xiantong Wang
- Description:
- We perform a geomagnetic event simulation using a newly developed magnetohydrodynamic with adaptively embedded particle-in-cell (MHD-AEPIC) model. We have developed effective criteria to identify reconnection sites in the magnetotail and cover them with the PIC model. The MHD-AEPIC simulation results are compared with Hall MHD and ideal MHD simulations to study the impacts of kinetic reconnection at multiple physical scales. At the global scale, the three models produce very similar SYM-H and SuperMag Electrojet (SME) indexes, which indicates that the global magnetic field configurations from the three models are very close to each other. At the mesoscale we compare the simulations with in situ Geotail observations in the tail. All three models produce reasonable agreement with the Geotail observations. The MHD-AEPIC and Hall MHD models produce tailward and earthward propagating fluxropes, while the ideal MHD simulation does not generate flux ropes in the near-earth current sheet. At the kinetic scales, the MHD-AEPIC simulation can produce a crescent shape distribution of the electron velocity space at the electron diffusion region which agrees very well with MMS observations near a tail reconnection site. These electron scale kinetic features are not available in either the Hall MHD or ideal MHD models. Overall, the MHD-AEPIC model compares well with observations at all scales, it works robustly, and the computational cost is acceptable due to the adaptive adjustment of the PIC domain.
- Keyword:
- MHD, PIC, and Magnetosphere
- Discipline:
- Science
-
- Creator:
- Holmes, Iris A, Monagan Jr., Ivan V, Westphal, Michael F, and Davis Rabosky, Alison R
- Description:
- We generated these data from desert night lizards, Xantusia vigilis, from populations in central California. We performed phylogeographic analyses based on these data.
- Keyword:
- ddRADseq, phylogeography, Xantusia vigilis, lizard, and genome-scale sequencing
- Discipline:
- Science
-
- Creator:
- Zhang, Yan, Gao, Chuanyu, Zhang, Shaoqing, Yang, Ping, Meyers, Philip A, and Wang, Guoping
- Description:
- The study focuses on reconstructing the histories of peat deposition using n-alkane biomarkers in peat cores and associated modern plant communities from four sites around a shallow maar lake in the Changbai Mountains of northeastern China. Peat development patterns in the four sites are not concordant although the sites experienced the same paleoclimate histories. Evidently, lava flows and tephra deposits produced an uneven topography of the volcanogenic lake basin that controls the water depths at the four lake edge locations, thereby leading to differences in peat-forming plant communities and peat deposition among the four sites.
- Keyword:
- peat deposition, n-alkanes, volcanic eruptions, and Changbai Lake
- Citation to related publication:
- Zhang, Y., Gao, C., Zhang, S., Yang, P., Meyers, P. A., & Wang, G. (2020). N-Alkane-based reconstructions of peat accumulations and depositional conditions at four locations around a shallow maar lake in the Changbai Mountains, northeastern China (world) [Preprint]. Earth and Space Science Open Archive; Earth and Space Science Open Archive. https://doi.org/10.1002/essoar.10505381.1
- Discipline:
- Science
-
- Creator:
- Revzen, Shai
- Description:
- This repository contains both the data and python3 code that reads this data and reproduces the relevant figures. The code depends on NumPy >1.17 and matplotlib >3.1 and was tested on python 3.8
- Keyword:
- locomotion, slipping, low Reynolds number, walking, and slithering
- Discipline:
- Science and Engineering
-
- Creator:
- Lin, Xin, Keppel-Aleks, Gretchen, Rogers, Brendan M., and Birch, Leah
- Description:
- The data contain the daily-averaged atmospheric concentrations of CO2 tracers in the Northern Hemisphere simulated from a tagged tracer transport model GEOS-Chem v12.0.0. Thirteen land flux regions are defined and tagged in the model to separate their imprints on the long-term atmospheric CO2 seasonal amplification in Northern Hemisphere. A file describing the delineation of these land flux regions is also provided. See the README file for more details on the dataset and model configurations.
- Keyword:
- carbon dioxide, seasonal cycle, amplification, Arctic-boreal, global change, and GEOS-Chem
- Citation to related publication:
- Lin, X., Rogers, B. M., Sweeney, C., Chevallier, F., Arshinov, M., Dlugokencky, E., Machida, T., Sasakawa, M., Tans, P., & Keppel-Aleks, G. (2020). Siberian and temperate ecosystems shape Northern Hemisphere atmospheric CO2 seasonal amplification. Proceedings of the National Academy of Sciences, 117(35), 21079–21087.
- Discipline:
- Science
-
- Creator:
- Mark Flanner
- Description:
- This dataset includes spectrally-resolved optical properties for volcanic ash particles from the 2010 Eyjafjallajökull volcanic eruptions. These properties were used in the climate simulations described by Flanner et al. (2014, doi:10.1002/2014JD021977) to quantify ash radiative forcing from the eruptions.
- Keyword:
- ash, volcano, aerosols, Eyjafjallajökull, climate, and radiative transfer
- Citation to related publication:
- Flanner, M.G., Gardner, A.S., Eckhardt, S., Stohl, A., & Perket, J. (2014). Aerosol radiative forcing from the 2010 Eyjafjallajökull volcanic eruptions. Journal of Geophysical Research: Atmospheres. https://doi.org/10.1002/2014JD021977
- Discipline:
- Science
-
- Creator:
- 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:
- Smith, Joeseph P., Gronewold, Andrew D., Read, Laura, Crooks, James L., School for Environment and Sustainability, University of Michigan, Department of Civil and Environmental Engineering, University of Michigan, and Cooperative Institute for Great Lakes Research, University of Michigan
- Description:
- Using the statistical programming package R ( https://cran.r-project.org/), and JAGS (Just Another Gibbs Sampler, http://mcmc-jags.sourceforge.net/), we processed multiple estimates of the Laurentian Great Lakes water balance components -- over-lake precipitation, evaporation, lateral tributary runoff, connecting channel flows, and diversions -- feeding them into prior distributions (using data from 1950 through 1979), and likelihood functions. The Bayesian Network is coded in the BUGS language. Water balance computations assume that monthly change in storage for a given lake is the difference between beginning of month water levels surrounding each month. For example, the change in storage for June 2015 is the difference between the beginning of month water level for July 2015 and that for June 2015., More details on the model can be found in the following summary report for the International Watersheds Initiative of the International Joint Commission, where the model was used to generate a new water balance historical record from 1950 through 2015: https://www.glerl.noaa.gov/pubs/fulltext/2018/20180021.pdf. Large Lake Statistical Water Balance Model (L2SWBM): https://www.glerl.noaa.gov/data/WaterBalanceModel/, and This data set has a shorter timespan to accommodate a prior which uses data not used in the likelihood functions.
- Keyword:
- Water, Balance, Great Lakes, Laurentian, Machine Learning, Machine, Learning, Lakes, Bayesian, and Network
- Citation to related publication:
- Smith, J., Gronewald, A. et al. Summary Report: Development of the Large Lake Statistical Water Balance Model for Constructing a New Historical Record of the Great Lakes Water Balance. Submitted to: The International Watersheds Initiative of the International Joint Commission. Accessible at https://www.glerl.noaa.gov/pubs/fulltext/2018/20180021.pdf, Large Lake Statistical Water Balance Model (L2SWBM). https://www.glerl.noaa.gov/data/WaterBalanceModel/, and Gronewold, A.D., Smith, J.P., Read, L. and Crooks, J.L., 2020. Reconciling the water balance of large lake systems. Advances in Water Resources, p.103505.
- Discipline:
- Science and Engineering
-
- Creator:
- Brandt, Daniel, A. and Ridley, Aaron, J.
- Description:
- The research that produced this data focused on conducting a statistical comparison between horizontal winds modeled with GITM and those derived from the accelerometer aboard the GOCE satellite. The winds from GITM and GOCE were compared by constructing their respective probability densities under different levels of geomagnetic activity, and by distributing them as a function of geomagnetic activity, magnetic latitude, magnetic local time, day-of-the-year, and solar radio flux.
- Keyword:
- Thermosphere, GITM, GOCE, Neutral winds, and Thermospheric modeling
- Discipline:
- Science and Engineering
-
- 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:
- 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
-
- 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:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right calcaneum of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81821), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
-
- Creator:
- Tye, Alexander R, Niemi, Nathan A, Safarov, Rafig T, Kadirov, Fakhraddin A, Babayev, Gulam R
- Description:
- The dataset contains U-Pb radiometric ages of zircon grains from sedimentary rocks and modern river sands from the Caucasus region of western Asia. The data were collected as part of a research project investigating the effects of continental collision in the Caucasus region on regional erosion and sedimentary systems. The data are presented using the standard quantities reported for zircon U-Pb age analyses at the University of Arizona Laserchron Center.
- Keyword:
- detrital zircon, provenance, and U-Pb
- 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