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- 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
- 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
- Discipline:
- Other, Science, and Engineering
-
- 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
- Discipline:
- Science
-
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:
- Crisp, Dakota N., Cheung, Warwick, Gliske, Stephen V., Lai, Alan, Freestone, Dean R., Grayden, David B., Cook, Mark J., and Stacey, William C.
- Description:
- The data and the scripts are to show that seizure onset dynamics and evoked responses change over the progression of epileptogenesis defined in this intrahippocampal tetanus toxin rat model. All tests explored in this study can be repeated with the data and scripts included in this repository. and Dataset citation: Crisp, D.N., Cheung, W., Gliske, S.V., Lai, A., Freestone, D.R., Grayden, D.B., Cook, MJ., Stacey, W.C. (2019). Epileptogenesis modulates spontaneous and responsive brain state dynamics [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/r6vg-9658
- Keyword:
- evoked response, stimulation, bifurcation, epilepsy, seizure, divergence, and dynamics
- Discipline:
- Health Sciences, Science, and Engineering
-
- 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
- Discipline:
- Health Sciences, Engineering, and Science
-
- 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:
- 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
- Discipline:
- Science and Engineering
-
- 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
- Discipline:
- Science
-
- 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
- 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:
- 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:
- 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:
- 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
- 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:
- 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:
- 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
- Discipline:
- Science
-
- 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:
- Mirshams Shahshahani, Payam
- Description:
- Investigating minimum human reaction times is often confounded by the motivation, training, and state of arousal of the subjects. We used the reaction times of athletes competing in the shorter sprint events in the Athletics competitions in recent Olympics (2004-2016) to determine minimum human reaction times because there's little question as to their motivation, training, or state of arousal. The reaction times of sprinters however are only available on the IAAF web page for each individual heat, in each event, at each Olympic. Therefore we compiled all these data into two separate excel sheets which can be used for further analyses.
- Keyword:
- minimum reaction time, sprinter, Olympics, Athletics, sex difference, starting block, and false start
- Discipline:
- Health Sciences, Engineering, Other, Science, and General Information Sources
-
- Creator:
- Bemmels, Jordan B. and Dick, Christopher W.
- Description:
- Raw SNP genotypes are provided in STRUCTURE format, with a maximum of one SNP reported per ddRAD locus. The files "caryco_SNP.str" and "caryov_SNP.str" are genotypes for Carya cordiformis and Carya ovata, respectively. The first column of each file is the individual name, the second column is the population (see original publication for information on population locations), and the remaining columns are genotypes of individual SNPs. Rows represent individuals, with the diploid genotypes contained on two lines per individual. Missing data are entered as "0" (zero). The first row is a header with a unique identifier for each SNP. and Occurrence records for each species are provided in the file "occs_carya.csv" and contain the latitude and longitude of each record.
- Keyword:
- eastern North America, glacial refugia, phylogeography, temperate trees, and single nucleotide polymorphisms
- Discipline:
- Science
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