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- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- Johnson, JE and Molnar, PH
- Description:
- This IF compilation was assembled from the existing literature to understand if preservation biases affected the record of iron formations.
- Keyword:
- Archean ocean chemistry, temporal record of iron formations, and early Earth iron cycle
- Citation to related publication:
- Johnson, J. E., & Molnar, P. H. ( 2019). Widespread and persistent deposition of iron formations for two billion years. Geophysical Research Letters, 46, 3327– 3339. https://doi.org/10.1029/2019GL081970
- 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:
- Wang, Yi and Hendy, Ingrid
- Description:
- This collection represents various raw data and analysis of cores extracted during the January 2009 mission of the research vessel Sproul in the Santa Barbara Basin., Cores included: box core SPR0901-04BC, box core SPR0901-unnamed, and Kasten core SPR0901-03KC. Core photos, physical properties and magnetic susceptibility from the multisensor track (MST), and the scanning X-ray fluorescence (XRF) data are included in the collection., and Cruise DOI: 10.7284/901089 This research is funded by NSF-OCE 0752093.
- Keyword:
- Santa Barbara Basin, Southern California, core photos, physical properties, scanning XRF, SPR0901, and Earth Science
- Discipline:
- Science
8Works -
- 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:
- 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
-
R/V Melville Core Retrieval Campaign (MV0811), November 2008
User Collection- Creator:
- Wang, Yi and Hendy, Ingrid
- Description:
- This collection represents various raw data and analysis of cores extracted during the November 2008 mission of R/V Melville in the Santa Barbara Basin., The core included is the jumbo piston core MV0811-14JC. Core photos, physical properties and magnetic susceptibility from the multisensor track (MST), and the scanning X-ray fluorescence (XRF) data are included in the collection., and Cruise DOI: 10.7284/903459 The research is funded by NSF OCE-1304327.
- Keyword:
- Santa Barbara Basin, Southern California, core photos, physical properties, scanning XRF, MV0811, and Earth Science
- Discipline:
- Science
3Works -
- Creator:
- Nasser, Ahmad and Gumise, Wonder
- Description:
- The work on accelerating authenticated boot for embedded system resulted in designing an algorithm in python to perform the random address generation and cryptographic MAC calculation. The Sampled Boot schemes implemented in this package allow a significant reduction of the time needed to authenticate firmware images during startup, while still retaining a high degree of trust. This is particularly useful for automotive applications in which startup time constraints make secure boot a time prohibitive process. and Citation for this dataset: Nasser, A., Gumise, W. (2019). Authenticated Boot Acceleration Algorithm [Code and data]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/yeh1-1x17
- Keyword:
- Trusted Computing, IOT security, Embedded Security, and Cyber Physical Systems
- Citation to related publication:
- Nasser, A., Gumise, W., and Ma, D., "Accelerated Secure Boot for Real-Time Embedded Safety Systems," SAE Int. J. Transp. Cyber. & Privacy 2(1) : 35-48, 2019, https://doi.org/10.4271/11-02-01-0003
- 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:
- 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:
- Linyan, Xiang and Oleg, Zikanov
- Description:
- The Liquid Metal Battery (LMB), a promising energy-storage device that contains liquid-metal interior, is studied numerically in the paper. The metal pad roll instability was modeled based on the open-source CFD software, OpenFOAM. It's based on the solver for simulations of incompressible multiphase flows multiphaseInterFoam modified to include the electromagnetic fields and account for the sharp variations of the electrical conductivity.
- Keyword:
- Liquid metal battery, Interfacial waves, Instability, and OpenFOAM
- Citation to related publication:
- Linyan Xiang (相林言) and Oleg Zikanov, “Numerical simulation of rolling pad instability in cuboid liquid metal batteries,” Physics of Fluids, vol. 31, no. 12, p. 124104, 2019, https://doi.org/10.1063/1.5123170 and Oleg Zikanov, "Shallow water modeling of rolling pad instability in liquid metal batteries." Theoretical and Computational Fluid Dynamics, 32, 325–347, 2018, https://doi.org/10.1007/s00162-018-0456-2
- Discipline:
- Science
-
- Creator:
- Tronson, Natalie C and Tchessalova, Daria
- Description:
- The main goal of this research was to identify potential molecular pathways that contribute to memory dysregulation and decline that persists long after illness or inflammation. We have previously established a subchronic immune challenge model that results in memory impairments months after the inflammatory challenge. This project aimed to determine whether memory impairments were accompanied by transcriptional dysregulation in memory related brain region (the hippocampus). These data show the differential gene expression as log2fold change (and p-value) in males and females 3 months after immune challenge (Supp Tables 1 and 2); after a subsequent immune challenge (Supp Tables 3 and 4); the differential regulation of genes in males and females (Supp Table 5); genes differentially expressed in the hippocampus of males and females at baseline (Supp Table 6) and the differential regulation of those genes in males and females after immune challenge (Supp Tables 7,8).
- Keyword:
- hippocampus, lipopolysaccharide, differential gene expression, RNA sequencing, neuroimmune, sex differences, learning and memory, and inflammation
- Citation to related publication:
- Tchessalova, D., & Tronson, N. C. (2019). Enduring and sex-specific changes in hippocampal gene expression after a subchronic immune challenge. BioRxiv, 566570. https://doi.org/10.1101/566570
- Discipline:
- Science and Health Sciences
-
- 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:
- Moore, Talia Y., Danforth, Shannon M., Larson, Joanna G., and Davis Rabosky, Alison R.
- Description:
- Warning signals in chemically defended organisms are critical components of predator-prey interactions, often requiring multiple coordinated display components for a signal to be effective. When threatened by a predator, venomous coral snakes (genus Micrurus) display a vigorous, non-locomotory thrashing behaviour that has been only qualitatively described. Given the high-contrast and often colourful banding patterns of these snakes, this thrashing display is hypothesized to be a key component of a complex aposematic signal under strong stabilizing selection across species in a mimicry system. By experimentally testing snake response across simulated predator cues, we analysed variation in the presence and expression of a thrashing display across five species of South American coral snakes. Although the major features of the thrash display were conserved across species, we found significant variation in the propensity to perform a display at all, the duration of thrashing, and the curvature of snake bodies that was mediated by predator cue type, snake body size, and species identity. We also found an interaction between curve magnitude and body location that clearly shows which parts of the display vary most across individuals and species. Our results suggest that contrary to the assumption in the literature that all species and individuals perform the same display, a high degree of variation persists in thrashing behaviour exhibited by Micrurus coral snakes despite presumably strong selection to converge on a common signal. This quantitative behavioural characterization presents a new framework for analysing the non-locomotory motions displayed by snakes in a broader ecological context, especially for signalling systems with complex interaction across multiple modalities.
- Keyword:
- aposematism, biomechanics, coral snake mimicry, curvature, Elapidae, non-locomotory motion, Peruvian Amazon, and snake behaviour
- Citation to related publication:
- Moore, T. Y., Danforth, S. M., Larson, J. G., & Davis Rabosky, A. R. (2020). A Quantitative Analysis of Micrurus Coral Snakes Reveals Unexpected Variation in Stereotyped Anti-Predator Displays Within a Mimicry System. Integrative Organismal Biology, 2(1). https://doi.org/10.1093/iob/obaa006
- Discipline:
- Science
-
- Creator:
- Bougher, S. W. (CLaSP Department, U. of Michigan), Roeten, K. J. (CLaSP Department, U. of Michigan), and Sharrar, R. (Astronomy Department, U. of Michigan)
- Description:
- The NASA MAVEN (Mars Atmosphere and Volatile Evolution) spacecraft, which is currently in orbit around Mars, has been taking daily (systematic) measurements of the densities and temperatures in the upper atmosphere of Mars between about 140 to 240 km above the surface. Wind measurement campaigns are also conducted once per month for 5-10 orbits. These densities, temperatures and winds change with time (e.g. 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. Such global dust storm period measurements can be 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 detailed comparison between direct global dust storm period measurements in the upper atmosphere of Mars and simulated MGITM fields and is important because it can help to inform us what physical processes are acting on the upper atmosphere during such large dust events. 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 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 4 months of Neutral Gas and Ion Mass Spectrometer (NGIMS) measurements of densities and winds have been made by the MAVEN team during the summer of 2018 (Elrod et al., 2019). Nine reference measurement intervals during this global dust storm (1-June through 30-August 2018) are selected for detailed study (Elrod et al. 2019). The Mars conditions for these nine intervals have been used to launch corresponding M-GITM code simulations, yielding 3-D neutral density, temperature and wind fields for comparison to these NGIMS measurements. The M-GITM datacubes used to extract the density, temperature and 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 Dust Storm of 2018
- Citation to related publication:
- Elrod, M. K., S. W. Bougher, K. Roeten, R. Sharrar, J. Murphy, Structural and Compositional Changes in the Upper Atmosphere related to the PEDE-2018 Dust Event on Mars as Observed by MAVEN NGIMS, Geophys. Res. Lett., (2019). doi: 10.1029/2019GL084378. and Jain, S. K., Bougher, S. W., Deighan, J., Schneider, N. M., Gonzalez‐Galindo, F., Stewart, A. I. F., et al. ( 2020). Martian thermospheric warming associated with the Planet Encircling Dust Event of 2018. Geophysical Research Letters, 47, e2019GL085302. https://doi.org/10.1029/2019GL085302
- Discipline:
- Engineering and 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:
- Gebarski, Benjamin B. and Becker, Udo
- Description:
- Files are uploaded as crystallographic information files (.cif), the standard text file format for representing crystallographic information. These files contain the optimized molecular models for pentavalent plutonium incorporation reactions into/onto barite, anglesite, celestine, anhydrite, aragonite, and calcite host minerals.
- Keyword:
- actinide, quantum mechanics, molecular model, plutonium, incorporation, surface, radioactive, contamination, and nuclear waste
- Citation to related publication:
- Gebarski, B. B. and Becker, U. Quantum-Mechanical Determination of the Incorporation of Pentavalent Plutonium into Carbonate and Sulfate Minerals. (2019) Geochimica et Cosmochimica Acta. https://doi.org/10.1016/j.gca.2019.10.015
- Discipline:
- Science
-
- Creator:
- Horsley, Timothy J. and Sampson, Christina P.
- Description:
- The data (raw data, composite files [processed], and some images) can be read by the program TerraSurveyor. Version 3.0.34.10 of the software was used to create the composite files in this deposit. and The magnetometer data was the second step in a geophysical survey program that began with magnetic susceptibility survey of a portion of the Weedon Island Preserve in St. Petersburg, Florida. Geophysical survey was used to map human occupation of the study area and to guide subsequent archaeological excavations.
- Keyword:
- magnetometry, geophysical survey, remote sensing, Florida archaeology, and coastal archaeology
- Citation to related publication:
- Sampson, C. P. (2019) Safety Harbor at the Weeden Island Site: Late Pre-Columbian Craft, Community, and Complexity on Florida's Gulf Coast. PhD Dissertation, University of Michigan. and Sampson, Christina Perry and Timothy J. Horsley. Using Multi-Staged Magnetic Survey and Excavation to Assess Community Settlement Organization: A Case Study from the Central Peninsular Gulf Coast of Florida. Advances in Archaeological Practice. Cambridge University Press: 18 December 2019. https://doi.org/10.1017/aap.2019.45
- Discipline:
- Science and Social Sciences
-
- 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
-
- 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:
- Liu, Meichen
- Description:
- We intend to figure out the difference of stress drops, which is a characteristic source parameter, between shallow and deep-focus earthquakes. Significant stress drop difference may shed light on the difference of physical mechanisms of shallow and deep-focus earthquakes, which has been a elusive question. We select from deep-focus earthquakes (> 400 km) in 2000-2018 and obtain their stress drops using P and S waves. We find that stress drops of deep-focus earthquakes are about one order of magnitude higher than that of shallow earthquakes, indicating about one order of magnitude higher shear strength of shallow faults than faults in the mantle. The wide range of stress drops further suggests coexistence of phase transformation and shear-induced melting mechanisms of deep-focus earthquakes.
- Citation to related publication:
- Liu, M., Huang, Y., & Ritsema, J. (2020, March 4). Stress drop variation of deep-focus earthquakes based on empirical Green's function [preprint]. Submitted to Geophysical Research Letters. https://doi.org/10.31223/osf.io/8jx6p and Liu, M., Huang, Y., & Ritsema, J. (2020). Stress Drop Variation of Deep-Focus Earthquakes Based on Empirical Green’s Functions. Geophysical Research Letters, 47(9), e2019GL086055. https://doi.org/10.1029/2019GL086055
- Discipline:
- Science
-
- Creator:
- Tye, Alexander R, Niemi, Nathan A, Safarov, Rafig T, Kadirov, Fakhraddin A, Babayev, Gulam R
- Description:
- Apatite fission track thermochronometry data were collected from the Eastern Greater Caucasus orogen, Azerbaijan. Thermochronometry data constrain the history of exhumation and deformation of rocks within the orogen, which is an active accretionary prism. Thermochronometry data record the timing of cooling of a rock sample beneath a given closure temperature. Given an assumed or inferred geothermal gradient, thermochronometric ages can be used to infer exhumation rates and make interpretations about rates of deformation in orogens. The apatite fission track data presented here are analyzed in concert with apatite (U-Th)/He and zircon (U-Th)/He ages reported in Tye et al., in prep., to characterize the exhumation history of the Eastern Greater Caucasus.
- Keyword:
- thermochronometry, apatite fission track, Caucasus
- 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:
- 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:
- Davis Rabosky, Alison R., Moore, Talia Y., Sánchez-Paredes, Ciara M., Westeen, Erin P., Larson, Joanna G., Sealey, Briana A., and Balinski, Bailey A.
- Description:
- Animals in nature use diverse strategies to evade or deter their predators, including many vivid behavioural displays only qualitatively described from field encounters with natural predators or humans. Within venomous snake mimicry, stereotyped anti-predator displays are suggested to be a critical component of the warning signal given by toxic models and thus under strong selection for independent convergence in mimetic species. However, no studies have systematically quantified variation in snake anti-predator displays across taxonomically broad clades to test how these behaviours evolve across species within a phylogenetic comparative methods framework. Here we describe a new, high-throughput approach for collecting and scoring snake anti-predator displays in the field that demonstrates both low observer bias and infinite extension across any species. Then, we show our method's utility in quantitatively comparing the behaviour of 20 highly-divergent snake species from the Amazonian lowlands of Peru. We found that a simple experimental setup varying simulated predator cues was very successful in eliciting anti-predator displays across species and that high-speed videography captured a greater diversity of behavioural responses than described in the literature. We also found that although different display components evolve at different rates with complicated patterns of covariance, there is clear evidence of evolutionary convergence in anti-predator displays among distantly related elapid coral snakes and their colubrid mimics. We conclude that our approach significantly advances opportunity for future analyses of snake behaviour, kinematics, and the evolution of anti-predator signals more generally, especially macroevolutionary analyses across clades with similarly intractable behavioural diversity.
- Keyword:
- Batesian mimicry, phylogenetic comparative methods, signal evolution, aposematism, simulated predator cues, coral snakes, and Peruvian Amazon
- Citation to related publication:
- Alison R. Davis Rabosky, Talia Y. Moore, Ciara M. Sanchez-Paredes, Erin P. Westeen, Joanna G. Larson, Briana A. Sealey, Bailey A. Balinski (2020) Convergence and divergence in anti-predator displays: A novel approach to quantitative behavioural comparison in snakes. Biological Journal of the Linnean Society http://dx.doi.org/10.1093/biolinnean/blaa222
- 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:
- Bustamante, Angela C., Opron, Kristopher, Ehlenbach, William J., Crane, Paul K., Keene, Dirk, Standiford, Theodore J., and Singer, Benjamin H.
- Description:
- This study was conducted to detect and analyze modules, or clusters of genes, associated with sepsis, using RNAseq data obtained from 12 participants who died of sepsis and 12 participants who died of non-infectious critical illness while hospitalized. This deposit contains the input data and parameters needed to reproduce the weighted gene co-expression network analysis (WGCNA) and gene enrichment analysis performed on this data. This analysis requires the R packages "WGCNA" version 1.68 and "DESeq2" version 1.22.2 available for download from bioconductor ( http://bioconductor.org). The external bioinformatics tool DAVID version 6.8 ( https://david.ncifcrf.gov/) was used as an additional gene enrichment analysis. Please see the supplemental methods document within this deposit and published research letter for more detailed information.
- Keyword:
- Sepsis, RNAseq, Transcriptomics, Human, and Brain
- Citation to related publication:
- Bustamante, A.C., Opron, K., Ehlenbach, W.J., Larson, E.B., Crane, P.K., Keene, C.D., Standiford, T.J., Singer, B.H., 2020. Transcriptomic Profiles of Sepsis in the Human Brain. Am J Respir Crit Care Med. https://doi.org/10.1164/rccm.201909-1713LE
- Discipline:
- Science
-
- 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
- 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, 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:
- 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
- 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, 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:
- 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:
- 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:
- 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:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:111984 (Handleyomys ALFAROI ALFAROI) - WholeBody. Raw Dataset includes 1601 TIF images (each 815 x 1310 x 1 voxel at 0.0421497172804555 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:111984 (Handleyomys ALFAROI ALFAROI) - WholeBody. Reconstructed Dataset includes 2000 TIF images (each 815 x 1310 x 1 voxel at 0.042150 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Rodentia, Cricetidae, Handleyomys ALFAROI ALFAROI, 1987286466, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987286466
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:mammals:123037 (Tscherskia TRITON) - WholeBody. Raw Dataset includes 1601 TIF images (each 715 x 1288 x 1 voxel at 0.0493711582967448 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:mammals:123037 (Tscherskia TRITON) - WholeBody. Reconstructed Dataset includes 2000 TIF images (each 715 x 1288 x 1 voxel at 0.049371 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Mammalia, Rodentia, Cricetidae, Tscherskia TRITON, 1987305166, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987305166
- Discipline:
- Science
-
- Creator:
- Lee, Dahee, Panicker, Veena, and Landis-Lewis, Zach
- Description:
- We use the term “performance summary display” (PSD) to mean a kind of visualization that relates performance levels to other types of information. In the context of healthcare organizations, PSDs are intended to be communicated to a healthcare professional, team, or organization. and Displays were identified, classified, and elements counted and coded. The performance summary display ontology provides a set of descriptions of components of displays that have been used to annotate performance feedback visualizations.
- Keyword:
- Performance
- Citation to related publication:
- Lee, D., Panicker, V., Gross, C., Zhang, J., & Landis-Lewis, Z. (2020). What was visualized? A method for describing content of performance summary displays in feedback interventions. BMC medical research methodology, 20(1), 90. https://doi.org/10.1186/s12874-020-00951-x
- Discipline:
- Health Sciences and Science
-
- Creator:
- Yue, Min, Kim, Jae Hyun, Evans, Charles R. , Kachman, Maureen, Erb-Downward, John R., D’Souza, Jennifer , Foxman, Betsy, Adar, Sara D. , Curtis, Jeffrey L. , and Stringer, Kathleen A.
- Description:
- This was a small descriptive study to determine whether short chain fatty acids (SCFAs) are detectable in water. It is part of a larger study that assessed the utility of exhaled breath condensate (EBC) as a biofluid for microbiome assays.
- Keyword:
- microbiome, short chain fatty acids, pulmonary, bronchoalveolar lavage fluid, exhaled breath condensate, and water
- Citation to related publication:
- Yue, M., Kim, J. H., Evans, C. R., Kachman, M., Erb-Downward, J. R., D’Souza, J., Foxman, B., Adar, S. D., Curtis, J. L., & Stringer, K. A. (2020). Measurement of Short-Chain Fatty Acids in Respiratory Samples: Keep Your Assay above the Water Line. American Journal of Respiratory and Critical Care Medicine, 202(4), 610–612. https://doi.org/10.1164/rccm.201909-1840LE
- Discipline:
- Science
-
- Creator:
- Gorchov Negron, Alan M., Kort, Eric A., Conley, Stephen A., and Smith, Mackenzie L.
- Description:
- This data-set contains data used in the publication "Airborne Assessment of Methane Emissions from Offshore Platforms in the U.S. Gulf of Mexico" by Gorchov Negron et al. (2020). There are 46,032 rows and 45 columns in the data. and The aircraft sampled offshore facilities with two unique sampling strategies: facility-level samples and regional box samples. Gorchov Negron et al. used facility-level samples to calculate facility-level fluxes and regional box samples, in conjunction with vertical profiles, to calculate regional-level fluxes. Meteorological parameters in the data were evaluated to discern when assumptions for each method were met. The facility-level fluxes were used to generate a facility-level aerial measurement-based inventory that was scaled up for comparison with regional-level fluxes.
- Keyword:
- Methane Emissions, Offshore Oil and Gas Platforms, Airborne Measurements, Greenhouse Gas Mitigation, and Gulf of Mexico
- Citation to related publication:
- Alan M. Gorchov Negron, Eric A. Kort, Stephen A. Conley, Mackenzie L. Smith. "Airborne Assessment of Methane Emissions from Offshore Platforms in the U.S. Gulf of Mexico". Environ. Sci. Technol. 2020. http://dx.doi.org/10.1021/acs.est.0c00179
- Discipline:
- Science
-
- 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:
- Zalmout, Iyad S, Sanders, William J, MacLatchy, Laura M, Gunnell, Gregg F, Al-Mufarreh, Yahya A, Ali, Mohammad A, Nasser, Abdul-Azziz H, Al-Masari, Abdu M, Al-Sobhi, Salih A, Nadhra, Ayman O, Matari, Adel H, Wilson, Jeffrey A, and Gingerich, Philip D
- Description:
- Reconstructed CT slices for the partial cranium of the holotype specimen of Saadanius hijazensis in DICOM format. Data supporting the publication: New Oligocene primate from Saudi Arabia and the divergence of apes and Old World monkeys, https://doi.org/10.1038/nature09094 Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, Saudi Arabia, CT, Primate, Oligocene, Hominoidea, Cercopithecoidea, University of Michigan Museum of Paleontology, and UMMP
- Citation to related publication:
- Zalmout, I., Sanders, W., MacLatchy, L. et al. New Oligocene primate from Saudi Arabia and the divergence of apes and Old World monkeys. Nature 466, 360–364 (2010). https://doi.org/10.1038/nature09094, A cast of this specimen is held by the University of Michigan Museum of Paleontology (UMMP) under catalog number 14200., and 3D surface model viewable on UMORF site : https://umorf.ummp.lsa.umich.edu/wp/specimen-data/?Model_ID=1408
- Discipline:
- Science
-
- 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:
- Kim, YoungJae, Marcano, Maria C., Kim, Sooyeon, and Becker, Udo
- Description:
- The main objective of this research is to integrate electrochemical and microscopic approaches to understand reaction mechanisms and pathways of the uranyl reduction and nucleation mediated by magnetite and ilmenite. and This experimental data reveal how natural iron minerals mediate redox reactions of redox sensitive elements. We measure electrochemical responses of dissolved uranyl ions (UO22+) to potentials in the presence of organic molecules. The atomic force microscopic (AFM) images show nucleation of reduced uranyl on ilmenite (FeTiO3) as a function of potential.
- Keyword:
- electrochemical AFM and uranium reduction
- Citation to related publication:
- Kim, Y., Marcano, M. C., Kim, S., & Becker, U. (2021). Reduction of uranyl and uranyl-organic complexes mediated by magnetite and ilmenite: A combined electrochemical AFM and DFT study. Geochimica et Cosmochimica Acta, 293, 127–141. https://doi.org/10.1016/j.gca.2020.10.016 and Walker S. M., Marcano M. C., Bender W. M. and Becker U. (2016) Imaging the reduction of chromium (VI) on magnetite surfaces using in situ electrochemical AFM. Chemical Geology 429, 60-74.
- Discipline:
- Science
-
- Creator:
- Ayumi Fujisaki-Manome
- Description:
- Precipitation impacts on ice cover and water temperature in the Laurentian Great Lakes were examined using state-of-art coupled ice-hydrodynamic models. Numerical experiments were conducted for the recent anomalously cold (2014-2015) and warm (2015-2016) winters that were accompanied by high and low ice coverage over the lakes, respectively. The results of numerical experiments showed that, snow cover on the ice, which is the manifestation of winter precipitation, reduced the total ice volume (or mean ice thickness) in all of the Great Lakes, shortened the ice duration, and allowed earlier warming of water surface. The reduced ice volume was due to the thermal insulation of snow cover. The surface albedo was also increased by snow cover, but its impact on the delay the melting of ice was overcome by the thermal insulation effect. During major snowstorms, snowfall over the open lake caused notable cooling of the water surface due to latent heat absorption. Overall, the sensible heat flux from rain in spring and summer was found to have negligible impacts on the water surface temperature. Although uncertainties remain in over-lake precipitation estimates and model’s representation of snow on the ice, this study demonstrated that winter precipitation, particularly snowfall on the ice and water surfaces, is an important contributing factor in Great Lakes ice production and thermal conditions from late fall to spring.
- Keyword:
- Great Lakes, lake ice, numerical modeling, and precipitation
- Citation to related publication:
- Fujisaki-Manome, A., Anderson, E. J., Kessler, J. A., Chu, P. Y., Wang, J., & Gronewold, A. D. (2020). Simulating Impacts of Precipitation on Ice Cover and Surface Water Temperature Across Large Lakes. Journal of Geophysical Research: Oceans, 125(5), e2019JC015950. https://doi.org/10.1029/2019JC015950
- Discipline:
- Science and Engineering
-
- Creator:
- Regoli, Leonardo H.
- Description:
- The research analyzed the response of nine PNI RM3100 magnetometers to radiation doses expected during a Europa lander mission. The radiation levels are drawn from the Europa Lander Science Definition Team report ( https://europa.nasa.gov/resources/58/europa-lander-study-2016-report). The sensors were tested up to a total ionization dose (TID) level of 500 kRad.
- Keyword:
- Magnetometer, Magneto-inductive, Europa, and Radiation
- Citation to related publication:
- Regoli, L. H., Moldwin, M. B., Raines, C., Nordheim, T. A., Miller, C. A., Carts, M., and Pozzi, S. A.: Radiation tolerance of the PNI RM3100 magnetometer for a Europa lander mission, Geosci. Instrum. Method. Data Syst., 9, 499–507, https://doi.org/10.5194/gi-9-499-2020, 2020.
- Discipline:
- Science and Engineering
-
- 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:
- 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
-
- Creator:
- James, David A. and Lokam, Nikhil
- Description:
- The object of this project is to provide researchers and students with a tool to allow them to develop an intuitive understanding of singular vectors and singular values. 2x2 matrices A with real entries map circles to ellipses; in particular, unit circles centered at the origin to ellipses centered at the origin. It is known that the points on the ellipse farthest from the origin correspond to the singular vectors of A. Users can use the GUI to enter matrices of their choice and explore to visually self-determine the singular vectors/values.
- Keyword:
- SVD, Singular Value Decomposition, Singular Vector, Singular Value, and Matrix
- Discipline:
- Science and Engineering
-
Quantifying near-surface rock strength on a regional scale from hillslope stability models - dataset
- Creator:
- Townsend, Kirk F., Gallen, Sean F., and Clark, Marin K.
- Description:
- These datasets support the findings of Townsend et al. (2020). In this article, we quantify rock strength using two novel applications of hillslope stability models, resulting in estimates of cohesive and frictional strength at the spatial scale of small watersheds. We compare these results against the direct-shear test dataset here for validation of our approach. We find that cohesive strength is dependent on the original burial depth of the sedimentary rocks studied here. The low-temperature thermochronometry data was used to assess the magnitude of burial.
- Keyword:
- Thermochronology, Thermochronometry, Direct-Shear, Landslides, Rock Strength, Landscape Evolution, and Geomorphology
- Citation to related publication:
- Townsend, K.F., Gallen, S.F., & Clark, M.K., in press, Quantifying near-surface rock strength on a regional scale from hillslope stability models: Journal of Geophysical Research Earth Surface. https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020JF005665
- Discipline:
- Science
-
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:
- Do, Hong X., Smith, Joeseph P., Fry, Lauren M., and Gronewold, Andrew D.
- Description:
- This data set contains a new monthly estimate of the water balance of the Laurentian Great Lakes, the largest freshwater system on Earth, from 1950 to 2019. The source codes and inputs to derive the new estimates are also included in this dataset. and ***ADDED 2024-02-27: The component net basins supply data "*NBSC_GLWBData.csv" in "output_ts_posterior.zip" need to be revised for further applications***
- Keyword:
- Laurentian Great Lakes, Bayesian inference, water levels, data assimilation, and water balance
- Citation to related publication:
- Do, H. X., Smith, J. P., Fry, L. M., & Gronewold, A. D. (2020). Seventy-year long record of monthly water balance estimates for Earth’s largest lake system. Scientific Data, 7(1), 276. https://doi.org/10.1038/s41597-020-00613-z, 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. https://doi.org/10.1016/j.advwatres.2020.103505 , and This version replaces the following deprecated dataset: Do, H.X., Smith, J.P., Fry, L.M., Gronewold, A.D. (2020). Monthly water balance estimates for the Laurentian Great Lakes from 1950 to 2019 [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/0rsp-v195
- Discipline:
- Science
-
- Creator:
- Boles, Austin H and van der Pluijm, Ben
- Description:
- This data was generated as a chapter in the dissertation of Austin Boles.
- Keyword:
- authigenic illite, hydrogen isotopes, and 40Ar/39Ar isotopic analysis
- Citation to related publication:
- Boles, A., & Pluijm, B. van der. (2020). Locally Derived, Meteoric Fluid Infiltration Was Responsible for Widespread Late Paleozoic Illite Authigenesis in the Appalachian Basin. Tectonics, 39(7), e2020TC006137. https://doi.org/10.1029/2020TC006137
- Discipline:
- Science
-
- Creator:
- Davis Rabosky, Alison R. and Jantzi, Adrian
- Description:
- Video documentation of natural behavior in wild snakes is very rare, so film from opportunistic encounters of snake interactions is very valuable to scientific researchers. Our research team includes leading experts on this species of snake (the Western Groundsnake, Sonora semiannulata), so we worked with the observer to submit a formal description of the encounter to a peer-reviewed journal and make the information available to the broader research community.
- Keyword:
- Sonora semiannulata, ground snake, animal behavior, and male-male combat
- Citation to related publication:
- Jantzi A, CL Cox, AR Davis Rabosky, AT Holycross. 2021. SONORA SEMIANNULATA (Western Groundsnake). COMBAT. Herpetological Review 52(2): pg 434.
- Discipline:
- Science
-
- Creator:
- Yiwen, Mei
- Description:
- The datasets of this archive are produced for a research project on the development of an advanced hydrologic modeling system for the St. Lawrence river basin. The outputted datasets from model simulations are in Netcdf 4 format. The author recommend using the netCDF Operators (NCO) program for data processing. For visualization and plotting, the author recommend using software like MATLAB, Python or R.
- Keyword:
- Hydrologic modeling, reanalysis product, St. Lawrence river, water balance, WRF-Hydro
- 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:
- Brasch, Jonathan M, Elipot, Shane, and Arbic, Brian
- Description:
- For Drifters, HYCOM, MITgcm: Spectra and kinetic energy files. Please see readme.txt for a description of all data and code contained here. and - Compare kinetic energies (KE) of high-resolution global ocean models estimated from rotary spectra to KE in surface drifter observations. - Near-inertial KE is closer to drifter observations in models with frequently updated wind forcing - Internal tide KE is closer to drifter observations in models with topographic wave drag
- Keyword:
- oceanography, rotary spectra, kinetic energy, sea surface velocity, and drifters
- Citation to related publication:
- Elipot, S., Lumpkin, R., Perez, R. C., Lilly, J. M., Early, J. J., & Sykulski, A. M. (2016). A global surface drifter data set at hourly resolution. Journal of Geophysical Research: Oceans, 121(5), 2937–2966. https://doi.org/10.1002/2016JC011716
- 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:
- Sean Sharp
- Description:
- Coastal wetlands intercept significant amounts of nitrogen (N) from watersheds, especially when surrounding land cover is dominated by agriculture and urban development. Through plant uptake, soil immobilization, and denitrification wetlands can remove excess N from flow through water sources and mitigate eutrophication of connected aquatic ecosystems. Excess N can also change plant community composition in wetlands, including communities threatened by invasive species. Understanding how variable hydrology and N loading impact wetland N removal and community composition can help attain desired management outcomes, including optimizing N removal and/or preventing invasion by non-natives. By using a dynamic, process-based ecosystem simulation model, we are able to simulate various levels of hydrology and N loading that would otherwise be difficult to manipulate. We investigate the effects of hydroperiod, hydrologic residence time, N loading, and the NH4+:NO3- ratio on both N removal and the invasion success of two non-native species (Typha x glauca or Phragmites australis) in temperate freshwater coastal wetlands using Mondrian, a process-based, wetland ecosystem simulation model. We found that when residence time increased, annual N removal increased up to 10-fold while longer hydroperiods also increased N removal, but only when residence time was >10 days and N loading was >30 g N m-2 y-1. N removal efficiency also increased with increasing residence time and hydroperiod, but was less affected by N loading. However, longer hydrologic residence time increased vulnerability of wetlands to invasion by both invasive plants at low to medium N loading rates where native communities are typically more resistant to invasion. This suggests a potential tradeoff between ecosystem services related to nitrogen removal and wetland invasibility. These results help elucidate complex interactions of community composition, N loading and hydrology on N removal, helping managers to prioritize N removal when N loading is high or controlling plant invasion in more vulnerable wetlands.
- Keyword:
- Mondrian, Simulation model, Coastal wetlands, Invasive species, and Ecosystem modeling
- Citation to related publication:
- Currie, W. S., Goldberg, D. E., Martina, J., Wildova, R., Farrer, E., & Elgersma, K. J. (2014). Emergence of nutrient-cycling feedbacks related to plant size and invasion success in a wetland community–ecosystem model. Ecological Modelling, 282, 69–82. https://doi.org/10.1016/j.ecolmodel.2014.01.010
- Discipline:
- Science
-
- Creator:
- Light, Charles X, Arbic, Brian K, Martin, Paige E, Brodeau, Laurent, Farrar, J Thomas, Griffies, Stephen M, Kirtman, Ben P, Laurindo, Lucas, Menemenlis, Dimitris, Molod, Andrea, Nelson, Arin D, Nyadjro, Ebenezer, O'Rourke, Amanda K, Shriver, Jay, Siqueira, Leo, Small, R Justin, and Strobach, Udi
- Description:
- The precipitation data itself is the output of the models/datasets that we analyze in our paper. Most of it is in .nc or .nc4 format, although we provide code to extract the data into time series .mat files. We used MATLAB to perform our analysis.
- Keyword:
- precipitation and power spectra
- Citation to related publication:
- Light, C.X., Arbic, B.K., Martin, P.E., Brodeau, L., Farrar, J.T., Griffies, S.M., Kirtman, B.P., Laurindo, L.C., Menemenlis, D., Molod, A., Nelson, A.D., Nyadjro, E., O'Rourke, A.K., Shriver, J.F., Siqueira, L., Small, R.J., Strobach, E. (2022). Effects of grid spacing on high-frequency precipitation variance in coupled high-resolution global ocean-atmosphere models. Climate Dynamics, https://doi.org/10.1007/s00382-022-06257-6
- Discipline:
- Science
-
- Creator:
- Li, Jieming, Zhang, Leyou, Johnson-Buck, Alexander, and Walter, Nils G.
- Description:
- Traces from single-molecule fluorescence microscopy (SMFM) experiments exhibit photophysical artifacts that typically necessitate human expert screening, which is time-consuming and introduces potential for user-dependent expectation bias. Here, we have used deep learning to develop a rapid, automatic SMFM trace selector, termed AutoSiM, that improves the sensitivity and specificity of an assay for a DNA point mutation based on single-molecule recognition through equilibrium Poisson sampling (SiMREPS). The improved performance of AutoSiM is based on accepting both more true positives and fewer false positives than the conventional approach of hidden Markov modeling (HMM) followed by thresholding. As a second application, the selector was used for automated screening of single-molecule Förster resonance energy transfer (smFRET) data to identify high-quality traces for further analysis, and achieves ~90% concordance with manual selection while requiring less processing time. AutoSiM can be adapted readily to novel datasets, requiring only modest Transfer Learning.
- Keyword:
- deep learning, single-molecule fluorescence, total internal reflection microscopy, SiMREPS, smFRET, and Forster resonance energy transfer
- Citation to related publication:
- Li, J., Zhang, L., Johnson-Buck, A., & Walter, N. G. (2020). Automatic classification and segmentation of single-molecule fluorescence time traces with deep learning. Nature Communications, 11(1), 5833. https://doi.org/10.1038/s41467-020-19673-1 and Hayward, S., Lund, P., Kang, Q., Johnson-Buck, A., Tewari, M., Walter, N. (2018). Single-molecule microscopy image data and analysis files for "Ultra-specific and Amplification-free Quantification of Mutant DNA by Single-molecule Kinetic Fingerprinting" [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/Z2CZ35DF
- Discipline:
- Science
-
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:
- 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:
- 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:
- Zhang, Yizhen
- Description:
- We collected hours of functional magnetic resonance imaging data from human subjects listening to natural stories. We developed a predictive model of the voxel-wise response and further applied it to thousands of new words to understand how the brain stores and connects different concepts. and This is a dataset for the paper: Zhang, Y., Han, K., Worth, R., & Liu, Z. (2020). Connecting concepts in the brain by mapping cortical representations of semantic relations. Nature communications, 11(1), 1-13. https://doi.org/10.1038/s41467-020-15804-w. This project is also documented at https://osf.io/eq2ba/.
- Keyword:
- fMRI, natural story comprehension, neural encoding, semantic processing, word relations, and naturalistic stimuli
- Citation to related publication:
- Zhang, Y., Han, K., Worth, R., & Liu, Z. (2020). Connecting concepts in the brain by mapping cortical representations of semantic relations. Nature communications, 11(1), 1-13. https://doi.org/10.1038/s41467-020-15804-w
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right proximal metatarsal 1 of the Cantius trigonodus (University of Michigan Museum of Paleontology catalog number UMMP VP 81822), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right cuboid of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81823), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right calcaneum of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81821), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right astragalar [astragalus] body of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81827), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right navicular of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81831), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science