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Vani Region Archaeological Survey
User Collection
- Creator:
- Ratte, Christopher and Mokrisova, Jana
- Description:
- The data presented here were collected in the course of an archaeological survey of the region around Vani in the Republic of Georgia, carried out between 2009 and 2011, with follow-up visits in 2014 and 2017. The survey was sponsored by the University of Michigan, the Institute for the Study of the Ancient World at New York University, and the Otar Lordkipanidze Institute of Archaeological Research in Tbilisi. , The archaeological site of Vani lies in the territory of ancient Colchis, a triangular area bordered by the Black Sea to the west and by the greater and lesser Caucasus Mountains to the north and south – famous in Greek legend as the land of the Golden Fleece and the home of Medea. Vani itself is situated approximately 70 km inland, in the foothills of the lesser Caucasus. A regional culture recognizable on the evidence of distinctive traditions of pottery and metalworking and the appearance of a network of relatively large settlements had emerged in Colchis by the late second and early first millennia BC. , Vani is one of the most extensively studied archaeological sites in Colchis. Excavations have revealed a continuous occupation sequence extending from the 8th to the 1st centuries B.C. Especially notable are the rich and unusual graves of the Classical period (6th-4th centuries), the monumental stone architecture of the Hellenistic period (3rd to 1st centuries), especially fortifications enclosing an area of approximately 6 ha, and the extensive evidence for interaction with the Mediterranean and Near Eastern worlds, including not only commercial and luxury imports (Greek transport amphorae, fine bronze and silver utensils from both the Greek world and Persia), but also local production of bronze sculpture and one long Greek bronze inscription., In spite of the richness of the site, however, important questions about its purpose and function over time remain unresolved. How extensive was the ancient settlement? Was Vani an isolated stronghold, a regional population center, a sanctuary, or a combination of two or all three? How does it compare with other sites in Colchis? In addition to ongoing research at Vani itself, regional survey provides an obvious approach to some of these questions. In previous years, examination of a number of outlying sites had already yielded remains extending in date from the Early Bronze Age to the mediaeval period., and The purpose of the regional survey project begun in 2009 was to integrate existing knowledge about Vani and environs into the kind of technological and conceptual framework characteristic of contemporary American survey archaeology. Of particular importance was the use of Geographical Information Systems (GIS) as an organizational and analytical tool, and of geophysical prospection both in the immediate environs of Vani and at regional sites. Like all regional surveys, our project recorded evidence of all periods, from prehistory to the present day, but we were particularly interested in questions having to do with the increasing social complexity of Colchis in the mid- and later 1st millennium BC – when Greek explorers began to establish colonies on the Black Sea coast of Georgia, and the Persian empire pushed up against the mountains of the Caucasus. What was the nature of Colchian society in this period? How was it affected by interaction with the larger Greek, Persian, and Pontic worlds? And how can regional survey at Vani and throughout Colchis help us to address these questions?
- Keyword:
- Classical Archaeology, Fortifications, Churches, Sanctuaries, Quarries, Modern Settlements, Settlements, and Burials
- Discipline:
- Humanities
25Sub-collections1Works -
- Creator:
- Bradshaw, Lisa, Vernon, Julianne, Schmidt, Thomas, James, Timothy, Zhang, Jianzhi, Archbold, Hilary, Cadigan, Ken, Wolfe, John P., and Goldberg, Deborah E.
- Description:
- This is the experimental data referenced in our manuscript entitled "Influence of CUREs on STEM retention depends on demographic identities." The dataset comprises csv files with results from student surveys given to students enrolled in Biology 173 from Fall 2015 through Fall 2019 as well as institutional data of their course grades and cumulative GPA at the time they enrolled in Biology 173, and graduation and major data for student who had graduated by 2021. The survey questions used in the analysis and the IRB consent form are also included as pdfs.
- Keyword:
- undergraduate research, STEM retention, CURE, introductory biology laboratory, and education research
- Citation to related publication:
- Bradshaw, L., Vernon J., Schmidt T., James T., Zhang J., Archbold H., Cadigan K., Wolfe J.P. & Goldberg D. 2023. Research article: Influence of CUREs on STEM retention depends on demographic identities. J Microbiol Biol Educ (accepted)
- Discipline:
- Science
-
- Creator:
- Salaree, Amir, Spica, Zack, and Huang, Yihe
- Description:
- The items in this bundle are supporting videos to a study of subsea seismo-acoustics carried out regarding an earthquake in the Persian Gulf. The main data used in the study is a diver's recording of the acoustic waves from the earthquake. The epicenter and topography data used in this study are publicly available as cited in the README.txt file.
- Keyword:
- Seismo-acoustics, Persian Gulf, Divers’ Microphones, Seismic Hazard, Early Warning
- Discipline:
- Science
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- Creator:
- Limon, Garrett C.
- Description:
- The work guides the processing of CAM6 data for use in machine learning applications. We also provide workflow scripts for training both random forests and neural networks to emulate physic s schemes from the data, as well as analysis scripts written in both Python and NCL in order to process our results.
- Keyword:
- Machine Learning, Climate Modeling, and Physics Emulation
- Citation to related publication:
- Limon, G. C., Jablonowski, C. (2022) Probing the Skill of Random Forest Emulators for Physical Parameterizations via a Hierarchy of Simple CAM6 Configurations [Pre Print]. ESSOAr. https://10.1002/essoar.10512353.1
- Discipline:
- Engineering and Science
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Resources for Training Machine Learning Algorithms Using CAM6 Simple Physics Packages
User Collection
- Creator:
- Limon, Garrett
- Description:
- The collection contains the code and the data used to train machine learning algorithms to emulate simplified physical parameterizations within the Community Atmosphere Model (CAM6). CAM6 is the atmospheric general circulation model (GCM) within the Community Earth System Model (CESM) framework, developed by the National Center for Atmospheric Research (NCAR). GCMs are made up of a dynamical core, responsible for the geophysical fluid flow calculations, and physical parameterization schemes, which estimate various unresolved processes. Simple physics schemes were used to train both random forests and neural networks in the interest of exploring the feasibility of machine learning techniques being used in conjunction with the dynamical core for improved efficiency of future climate and weather models. The results of the research show that various physical forcing tendencies and precipitation rates can be effectively emulated by the machine learning models.
- Keyword:
- Machine Learning, Climate Modeling, and Physics Emulators
- Discipline:
- Science and Engineering
2Works -
- Creator:
- Limon, Garrett C.
- Description:
- The data represents weekly output from three 60-year CAM6 model runs. The output includes state (.h0. files) and tendency (.h1. files) fields for three difference model configurations of increasing complexity. State fields include temperature, surface pressure, specific humidity, among others; while tendencies include temperature tendencies, specific humidity tendencies, as well as precipitation rates. Using the state variables at a given time step, machine learning techniques can be trained to predict the following tendency field, which can then be applied to the state variables to provide the state at the next physics time step of the model.
- Keyword:
- Machine Learning, Climate Modeling, and Physics Emulation
- Citation to related publication:
- Limon, G. C., Jablonowski, C. (2022) Probing the Skill of Random Forest Emulators for Physical Parameterizations via a Hierarchy of Simple CAM6 Configurations [Preprint]. ESSOAr. https://10.1002/essoar.10512353.1
- Discipline:
- Engineering and Science
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- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for Right innominate (acetabulum region) of Remingtonocetus domandaensis (University of Michigan Museum of Paleontology catalog number GSP-UM 3408) as a series of TIFF images. Raw projections are not included in this dataset. The reconstructed slice data from the scan are offered here as a series of unsigned 16-bit integer TIFF images. The upper left corner of the first image (*_0000.tif) is the XYZ origin.
- Keyword:
- Paleontology, Fossil, CT, Remingtonocetidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and Geological Survey of Pakistan (GSP)
- Discipline:
- Science
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- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for phalanx (pathological) of phytosaur (University of Michigan Museum of Paleontology catalog number UMMP VP 13838) as a series of TIFF images. Raw projections are not included in this dataset. The reconstructed slice data from the scan are offered here as a series of unsigned 16-bit integer TIFF images. The upper left corner of the first image (*_0000.tif) is the XYZ origin.
- Keyword:
- Paleontology, Fossil, CT, Phytosauria, UMMP, University of Michigan Museum of Paleontology, Triassic, and e06c6866-4cba-4532-2a68-d8e3357a674e
- Discipline:
- Science
-
- Creator:
- Cuyler, Antonio, Carruthers, Matthew, and Imbesi, Jason
- Description:
- Building on previous research (Cuyler, A., Carruthers, M., Imbesi, J. 2023. “Cultural Policy of the Oppressed” [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/9e20-zg88), we performed a qualitative textual analysis of three related areas of oppression, colonialism, expansionism, and imperialism, and how they have been discussed within cultural policy research. The analysis focused on three major cultural policy journals, Cultural Trends, the Journal of Arts Management, Society, and Law, and the International Journal of Cultural Policy.
- Keyword:
- content analysis, cultural policy, oppression, colonialism, expansionism, and imperialism
- Discipline:
- Arts and Humanities
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- Creator:
- Bueno-Junior, Lezio S., Ruckstuhl, Maxwell S., Lim, Miranda M., and Watson, Brendon O.
- Description:
- Rapid eye movement sleep (REM) is believed to have a binary temporal structure with “phasic” and “tonic" microstates, characterized by motoric activity versus quiescence, respectively. However, we observed in mice that the frequency of theta activity (a marker of rodent REM) fluctuates in a non-binary fashion, with the extremes of that fluctuation correlating with phasic-type and tonic-type facial motricity. Thus, phasic and tonic REM may instead represent ends of a continuum. These cycles of brain physiology and facial movement occurred at 0.01-0.06 Hz, or infraslow frequencies, and affected cross-frequency coupling and neuronal activity in the neocortex, suggesting network functional impact. We then analyzed human data and observed that humans also demonstrate non-binary phasic/tonic microstates, with continuous 0.01-0.04 Hz respiratory rate cycles matching the incidence of eye movements. These fundamental properties of REM can yield new insights into our understanding of sleep health.
- Keyword:
- REM sleep, Infraslow fluctuations, Facial movements, Theta oscillations, and Respiration rate
- Citation to related publication:
- L. S. Bueno-Junior, M. S. Ruckstuhl, M. M. Lim, B. O. Watson, The temporal structure of REM sleep shows minute-scale fluctuations across brain and body in mice and humans. Proc. Natl. Acad. Sci. U. S. A. In press (2023).
- Discipline:
- Science
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Survey Data
User Collection
- Creator:
- Galaty, Michael
- Description:
- All databases, field notebooks, paper maps, GIS files, photographs, and photo descriptions related to the intensive survey, of tracts and tumuli, and the collection of sites have been made available in PASH Deep Blue Data Realm 1. The data are broadly organized by team (A-K). The surveyed land was divided up into “tracts”. Tracts are labeled with team letter and a consecutive number: e.g., A-001, A-002, B-003, C-122, D-035.
- Keyword:
- Archaeology
- Discipline:
- Science
6Works -
- Creator:
- Billings, Gideon H and Johnson-Roberson, Matthew
- Description:
- UWHandles is a dataset for 6D object pose estimation in underwater fisheye images. It provides 6D pose and 2D bounding box annotations for 3 different graspable handle objects used for ROV manipulation. The dataset consists of 28 image sequences collected in natural seafloor environments with a total of 20,427 annotated frames. and Meta repository for the dataset https://github.com/gidobot/UWHandles
- Keyword:
- Deep Learning, Pose Estimation, and Underwater Vision
- Citation to related publication:
- Billings, G., & Johnson-Roberson, M. (2020). SilhoNet-fisheye: Adaptation of a ROI based object pose estimation network to monocular fisheye images. IEEE Robotics and Automation Letters, 5(3), 4241-4248.
- Discipline:
- Engineering
-
- Creator:
- Billings, Gideon H and Johnson-Roberson, Matthew
- Description:
- UWslam is a dataset for underwater stereo and hybrid monocular fisheye + stereo SLAM in natural seafloor environments. The dataset includes a spiral survey of a shallow reef captured with a diver operated stereo rig and 4 hybrid image sequences captured with a deep ocean ROV in different deep ocean environments. Ground truth pose estimates for the spiral stereo trajectory were obtained by processing the image sequence through COLMAP. Ground truth pose estimates for the hybrid sequences were obtained by distributing fiducials on the seafloor before capturing an image sequence and processing the image sequences with the ROS based TagSLAM package.
- Keyword:
- SLAM, Simultaneous Localization and Mapping, Visual Reconstruction, and Underwater
- Citation to related publication:
- G. Billings, R. Camilli and M. Johnson-Roberson, "Hybrid Visual SLAM for Underwater Vehicle Manipulator Systems," in IEEE Robotics and Automation Letters, vol. 7, no. 3, pp. 6798-6805, July 2022, doi: 10.1109/LRA.2022.3176448.
- Discipline:
- Engineering
-
- Creator:
- Sun, Hu
- Description:
- Complete Global Total Electron Content Database based on the VISTA Algorithm
- Keyword:
- Total Electron Content, Matrix Completion, VISTA, Spherical Harmonics, and Spatial-Temporal Smoothing
- Discipline:
- Engineering
2Works -
F3UEL: Flaring & Fossil Fuels: Uncovering Emissions & Losses
User Collection
- Creator:
- Kort, Eric and Plant, Genevieve
- Description:
- Fossil energy production, processing, flaring, and transmission all can harm climate and air quality by emitting greenhouse gases and air pollutants. Studies now show that onshore oil and gas production emit much more methane than what is inventoried, and that local air quality impacts can be significant, however, natural gas flaring and offshore systems have been largely overlooked. The F3UEL (Flaring & Fossil Fuels: Uncovering Emissions & Losses) project aims to address these gaps by improving our understanding of offshore emissions, characterizing how flares behave in the real world, identifying what portion of the offshore system is responsible for emissions, and determining how such systems can be monitored. Spanning three years (2020-2022), the project employed an aircraft platform to measure including both greenhouse gas and air quality measurements. To sample the largest regions of current and potential future offshore production and flaring, airborne measurements targeted the Gulf of Mexico, offshore California and Alaska, the Bakken Formation (North Dakota) and the Permian and Eagle Ford Basins (Texas). Data provided here includes the airborne measurements collected using Scientific Aviation’s Mooney aircraft platform, equipped with spectroscopic instrumentation to measure methane, carbon dioxide, water vapor, nitrous oxide, and nitrogen oxide, in addition to meteorological variables such as wind speed and direction. Data products from our analysis of these airborne measurements are also provided, including estimated flare destruction removal efficiency for the Bakken, Eagle Ford, and Permian basins. Each data file is in .csv format and is accompanied by a readme file with further information and descriptors of the variables included. All users should cite the papers and datasets provided in the readme files for each individual dataset. Website: https://graham.umich.edu/f3uel This project is funded by the Alfred P. Sloan Foundation with additional support from the Environmental Defense Fund, Scientific Aviation, and University of Michigan (College of Engineering, Climate and Space Sciences and Engineering; Graham Sustainability Institute).
- Keyword:
- offshore oil & gas, flaring, methane, Nitrogen oxides, natural gas flaring, and oil & gas
- Discipline:
- Science
4Works -
- Creator:
- Kort, Eric A., Plant, Genevieve, Brandt, Adam R., Chen, Yuanlei, Gorchov Negron, Alan M., Schwietzke, Stefan, Smith, Mackenzie L., and Zavala-Araiza, Daniel
- Description:
- As part of the Flaring & Fossil Fuels: Uncovering Emissions & Losses (F3UEL) project, in 2021 the aircraft measurement platform sampled offshore oil & gas facilities in Alaska and California to quantify facility-level emissions using the approach detailed in Conley et al. (2017). Onshore, the aircraft sampled downwind of flare combustion plumes in the Bakken region of North Dakota. Vertical profiles were conducted on each flight to capture the vertical structure and mixing depths of the atmosphere. The data file contains all merged flight data from each flight day. and Reference: Conley, S., Faloona, I., Mehrotra, S., Suard, M., Lenschow, D. H., Sweeney, C., Herndon, S., Schwietzke, S., Pétron, G., Pifer, J., Kort, E. A., and Schnell, R.: Application of Gauss’s theorem to quantify localized surface emissions from airborne measurements of wind and trace gases, Atmos. Meas. Tech., 10, 3345 – 3358, 2017.
- Keyword:
- Offshore Oil & Gas, Flaring, Methane, and Nitrogen Dioxides
- Discipline:
- Science
-
- Creator:
- Kort, Eric A., Plant, Genevieve, Smith, Mackenzie L., Brandt, Adam R., Chen, Yuanlei, Gorchov Negron, Alan M., Schwietzke, Stefan, and Zavala-Araiza, Daniel
- Description:
- As part of the Flaring & Fossil Fuels: Uncovering Emissions & Losses (F3UEL) project, in 2020 the aircraft measurement platform sampled offshore oil & gas facilities in the Gulf of Mexico to quantify facility-level emissions using the approach detailed in Conley et al. (2017). Onshore, the aircraft sampled downwind of flare combustion plumes in the Permian and Eagle Ford regions of Texas. Vertical profiles were conducted on each flight to capture the vertical structure and mixing depths of the atmosphere. The data file contains all merged flight data from each flight day. and Reference: Conley, S., Faloona, I., Mehrotra, S., Suard, M., Lenschow, D. H., Sweeney, C., Herndon, S., Schwietzke, S., Pétron, G., Pifer, J., Kort, E. A., and Schnell, R.: Application of Gauss’s theorem to quantify localized surface emissions from airborne measurements of wind and trace gases, Atmos. Meas. Tech., 10, 3345 – 3358, 2017.
- Keyword:
- Offshore Oil & Gas, Flaring, Methane, and Nitrogen Oxides
- Discipline:
- Science
-
- Creator:
- Engebretson, Mark J.
- Description:
- Large geomagnetic disturbances (GMDs, also denoted as MPEs - magnetic perturbation events) have sufficient amplitude to cause geomagnetically induced currents (GICs) that can damage technical infrastructure. In this study we present occurrence statistics for GMD / MPE events with derivatives ≥ 6 nT/s and ≥ 20 nT/s from five stations in the MACCS and AUTUMNX magnetometer arrays in Arctic Canada at magnetic latitudes ranging from 65° to 75°. Earlier studies using data from these arrays (Engebretson et al., 2019a,b, 2021a,b) covered only two years (2015 and 2017) and focused on latitude- and local time-dependent occurrence patterns and short-term dependencies on solar wind/IMF parameters and magnetospheric activity indices. This study presents all available data from these stations from 2011 through 2022 to analyze variations of GMD activity over a full solar cycle. Intense GMD activity did not closely follow the sunspot cycle, but instead was lowest during its rising phase and maximum (2011-2014), was highest during the early declining phase (2015-2017), and reached a subsequent minimum early in the following sunspot cycle (2020). GMDs with amplitude >20 nT/s followed the same yearly pattern but peaked even more strongly during 2015-2017. Most of these GMDs were associated with high-speed solar wind streams (Vsw > 600 km/s), but not with strongly negative values of the SYM/H index. The majority of these GMDs, irrespective of the Vsw value, were accompanied within 10 min (and most often less) by other events with amplitude ≥ 6 nT/s and showed a mostly poleward progression. These results show that large amplitude but spatially localized nighttime GMDs are primarily associated with high-speed stream geomagnetic drivers during the declining phase of the solar cycle. This indicates that large GIC hazard conditions can occur for a variety of solar wind drivers and geomagnetic conditions and not only for fast-coronal mass ejection driven storms.
- Keyword:
- geomagnetic disturbance events, geomagnetically induced currents
- Citation to related publication:
- Engebretson, M. J., Steinmetz, Yang, L., Pilipenko, V. A., Moldwin, M. B., McCuen, B. A., Connors, M. G., Weygand, J. M., Waters, C. L., Lyons, L. R., Nishimura, Y., Russell, C. T. (2023) Solar Cycle Dependence of Very Large Nighttime Geomagnetic Disturbances (GMDs) Observed in Eastern Arctic Canada. Journal of Geophysical Research – Space Physics
- Discipline:
- Science
-
Supporting data: Domain-agnostic predictions of nanoscale interactions in proteins and nanoparticles
- Creator:
- Saldinger, Jacob, Raymond, Matt , Elvati, Paolo, and Violi, Angela
- Description:
- The accurate and rapid prediction of generic nanoscale interactions is a challenging problem with broad applications. Much of biology functions at the nanoscale, and our ability to manipulate materials and purposefully engage biological machinery requires knowledge of nano-bio interfaces. While several protein-protein interaction models are available, they leverage protein-specific information, limiting their abstraction to other structures. Here, we present NeCLAS, a general, and rapid machine learning pipeline that predicts the location of nanoscale interactions, providing human-intelligible predictions. Two key aspects distinguish NeCLAS: coarse-grained representations, and the use of environmental features to encode the chemical neighborhood. We showcase NeCLAS with challenges for protein-protein, protein-nanoparticle and nanoparticle-nanoparticle systems, demonstrating that NeCLAS replicates computationally- and experimentally-observed interactions. NeCLAS outperforms current nanoscale prediction models, and it shows cross-domain validity, qualifying as a tool for basic research, rapid prototyping, and design of nanostructures., Software: - To reproduce all-atom molecular dynamics (MD) NAMD is required (version 2.14 or later is suggested). NAMD software and documentation can be found at https://www.ks.uiuc.edu/Research/namd/, - To reproduce coarse-grained MD simulations, LAMMPS (version 29 Sep 2021 - Update 2 or later is suggested). LAMMPS software and documentation can be found at https://www.lammps.org, - To rebuild free energy profiles, the PLUMED plugin (version 2.6) was used. PLUMED software and documentation can be found at https://www.plumed.org/ , and - To generate force matching potentials, the was used the OpenMSCG software was used. OpenMSCG software and documentation can be found at https://software.rcc.uchicago.edu/mscg/
- Keyword:
- Neural Networks, Proteins, Dimensionality Reduction, Nanoparticles, and Coarse-Graining
- Citation to related publication:
- https://www.biorxiv.org/content/10.1101/2022.08.09.503361v2
- Discipline:
- Science
-
- Creator:
- Walker, Logan A, Li, Ye, McGlothlin, Maggie, and Cai, Dawen
- Description:
- These are datasets released from our manuscript "A Comparison of Lossless Compression Methods in Microscopy Data Storage Applications". Included in this data release are: `noise16.tif`: a file containing background noise collected from a 1000-frame acquisition of a ORCA-Fusion camera; `noise8.tif`: a file containing the 16-bit data collective above converted into a 8-bit form; `brainbow.tif`: This is a mouse Brainbow image originally published and described in Roossien, et al. Bioinformatics 2019; `bead.tif`: This is a 3D image of 100nm Invitrogen TetraSpeck fluorescent microspheres imaged in a blue channel using a custom microscope; `fly.tif`: This is a 3D image of a fly Bitbow brain collected as described in Li, et al. Front. Neural Circuits 2021; and `neurite.tif`: This is a 3D image of DiD-labeled mouse V1 tissue, collected using a custom microscope.
- Keyword:
- neuroscience, microscopy, and Bitbow
- Discipline:
- Health Sciences
-
- Creator:
- Sun, Hu, Ren, Jiaen, Chen, Yang, and Zou, Shasha
- Description:
- Our research focuses on providing a fully-imputed map of the worldwide total electron content with high resolution and spatial-temporal smoothness. We fill in the missing values of the original Madrigal TEC maps via estimating the latent feature of each latitude and local time along the 2-D grid and give initial guess of the missing regions based on pre-computed spherical harmonics map. The resulting TEC map has high imputation accuracy and the ease of reproducing. and All data are in HDF5 format and are easy to read using the h5py package in Python. The TEC map is grouped in folders based on years and each file contains a single-day data of 5-min cadence. Each individual TEC map is of size 181*361.
- Keyword:
- Total Electron Content, Matrix Completion, VISTA, Spherical Harmonics, and Spatial-Temporal Smoothing
- Citation to related publication:
- Sun, H., Hua, Z., Ren, J., Zou, S., Sun, Y., & Chen, Y. (2020). Matrix Completion Methods for the Total Electron Content Video Reconstruction. arXiv preprint arXiv:2012.01618. and Zou, S., Ren, J., Wang, Z., Sun, H., & Chen, Y. (2021). Impact of Storm-Enhanced Density (SED) on Ion Upflow Fluxes During Geomagnetic Storm. Frontiers in Astronomy and Space Sciences, 162.
- Discipline:
- Science
-
- Creator:
- Reynolds, Mack B., Hong, Hanna S., Zhang, Li, Lyssiotis, Costas A., and O'Riordan, Mary X.
- Description:
- Untargeted lipidomics (Data S1) and targeted metabolomics (Data S2) analysis from in vitro culture of a murine macrophage cell line expressing shRNA targeted to Cardiolipin synthase (CRLS1), referred to as CRLS1 knockdown (KD), or a paired non-target shRNA-expressing (NT-Control). CRLS1 KD and NT-Control macrophages were either directly analyzed (untargeted lipidomics) or stimulated with lipopolysaccharide for a variety of timepoints and then analyzed (targeted metabolomics). Datasets are available as .csv files.
- Keyword:
- Lipidomics, Metabolomics, Cardiolipin, Macrophage, CRLS1, lipopolysaccharide, and LPS
- Citation to related publication:
- Reynolds M.B. et al. (2023). Cardiolipin coordinates inflammatory metabolic reprogramming through regulation of Complex II disassembly and degradation. Science Advances, 9(5). DOI: 10.1126/sciadv.ade8701
- Discipline:
- Health Sciences
-
Data for Macroscopic Transition Metal Dichalcogenides Monolayers with Uniformly High Optical Quality
- Creator:
- Li, Qiuyang, Alfrey, Adam, Hu, Jiaqi, Lydick, Nathanial, Paik, Eunice, Liu, Bin, Sun, Haiping, Lu, Yang, Wang, Ruoyu, Forrest, Stephen, and Deng, Hui
- Description:
- This dataset contains raw and source data for all figures generated in the manuscript "Macroscopic Transition Metal Dichalcogenides Monolayers with Uniformly High Optical Quality" The raw data files include '.spe' data, which are spectral data collected by LightField Sofware, and '.dset' and '.vms' files, which are X-ray photoelectron spectroscopy (XPS) data and require CasaXPS to access. The source data files include the processed data that can be directly used for generating the corresponding figures in the manuscript.
- Keyword:
- 2D materials, Exciton-polaritons, and Photonics
- Discipline:
- Science
-
- Creator:
- Bougher, Stephen W. and Roeten, Kali J.
- 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 an ongoing 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 [less] 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; Roeten et al 2022). For this specialized archive (Elrod et al. 2023), one reference measurement interval during this 2018 global dust storm (30-31 August 2018) is selected for detailed study of helium distributions (Elrod et al. 2023). The Mars conditions for this last of 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. This last interval is used to provide M-GITM datacubes to explicitly extract the helium density (plus corresponding temperatures and neutral winds) along the trajectory of each orbit path between 140 and 240 km . A general README file is also provided for this Deep Blue Data archive detailing the contents of each file, while also summarizing the inputs and outputs of the M-GITM code simulations for this study.
- Keyword:
- Mars , NASA MAVEN spacecraft, Mars Thermosphere, Global Dust Strom of 2018, and Helium distribution
- 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 Elrod, M. K., S. W. Bougher, K. Roeten and K. Arnold, Surprising Decrease in the Martian He Bulge during PEDE-2018 and Changes in Upper Atmospheric Circulation, J. Geophysical Research, (2023), doi:XXX
- Discipline:
- Science
-
- Creator:
- Zelditch, Miriam L. and Swiderski, Donald L.
- Description:
- Each row in the file contains the museum ID (museum where the specimen is located and the accession number), the species name, and the values for centroid size, followed by the x,y coordinates for each landmark. Any program that can read in a csv file can read this file.
- Keyword:
- Shape, Sciuridae, mandibles
- Citation to related publication:
- Zelditch, M.L., Swiderski, D.L. The Predictable Complexity of Evolutionary Allometry. Evol Biol (2022). https://doi.org/10.1007/s11692-022-09581-1
- Discipline:
- Science
-
- Creator:
- Szuromi, Matthew P. and Stacey, William C.
- Description:
- The data and scripts are meant to show how burster dynamics determine response to a single biphasic stimulus. The files include data which show trends in the propensity of termination for different burster types and the MATLAB scripts used to generate this data. The MATLAB scripts also allow the user to generate their own data sets for alternative bursting paths and stimulus parameter combinations. Furthermore, they allow the user to visually examine the effects of single stimuli in the voltage timeseries and in state space. How the user can access these features of the script is described in the file "ReadMe.pdf."
- Keyword:
- Epilepsy, Stimulation, Modelling, Dynamics, Seizure, and Dynamotype
- Citation to related publication:
- (PROVISIONAL) Optimization of Ictal Aborting Stimulation Using the Dynamotype Taxonomy
- Discipline:
- Health Sciences, Engineering, and Science
-
- Creator:
- Jivani, Aniket, Sachdeva, Nishtha, Huang, Zhenguang, Chen, Yang, van der Holst, Bart, Manchester, Ward, Iong, Daniel, Chen, Hongfan, Zou, Shasha, Huan, Xun, and Toth, Gabor
- Description:
- In this work, we perform Global Sensitivity Analysis (GSA) for the background solar wind in order to quantify contributions from uncertainty of different model parameters to the variability of in-situ solar wind speed and density at 1au, both of which have a major impact on CME propagation and strength. Scripts written in the Julia language are used to build the PCE and calculate the sensitivity results. Data is available in csv, NetCDF and JLD files. A `Project.toml` file is included to activate and install all required dependencies (See README for details).
- Keyword:
- Uncertainty Quantification, Space Weather, and Global Sensitivity Analysis
- Discipline:
- Engineering
-
- Creator:
- Huber, Daniel E
- Description:
- The files here provide monthly averaged soil NOx emissions (units of ng N m^-2 s^-1) for the contiguous United States on a 0.25 degree x 0.25 degree grid for the years 2011-2020 .
- Keyword:
- soil NOx, soil emissions, biogenic emissions, and agricultural emissions
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology, Nondestructive Evaluation Laboratory, Ford Motor Company, and Jones, Martin
- Description:
- Reconstructed CT slices for a right tusk of Loxodonta africana (University of Michigan Museum of Paleontology catalog number UMMP_VP_118186) as a series of TIFF images. Raw projections are not included in this dataset. The reconstructed slice data from the scan are offered here as a series of unsigned 16-bit integer TIFF images. The upper left corner of the first image (*_000.tif) is the XYZ origin. Metadata as produced by the Aracor system are included in *.IM$LA text files in IM$LA.zip.
- Keyword:
- Paleontology, CT, Elephantidae, UMMP, University of Michigan Museum of Paleontology, and a4f83cc6-09f2-0032-8a09-60ea798f787c
- Citation to related publication:
- Cherney, M., et al. (in prep)
- Discipline:
- Science
-
- Creator:
- Bressler, Alison and Blesh, Jennifer
- Description:
- This dataset contains three data files and three corresponding metadata files used in Bressler, A., and J. Blesh. 2023. A grass-legume cover crop maintains nitrogen inputs and nitrous oxide fluxes from an organic agroecosystem. Ecosphere. The file “N2O_Flux.xls” contains daily nitrous oxide data organized by replicate block, treatment, and date. The file “Soil_N.xls” contains nitrate and ammonium data organized by replicate block, treatment, and date. The file “Cover_crop_corn_soil.xls” contains baseline soil fertility characteristics, cover crop and corn biomass, nitrogen and carbon content, legume BNF, and cumulative N2O content organized by replicate block and treatment. The corresponding metadata files: “N2O_Flux_metadata.xls”, “Soil_N_metadata.xls”, and “Cover_crop_corn_soil_metadata.xls” provide detailed descriptions of all variables in each data set and any abbreviations used.
- Keyword:
- cover crops, nitrous oxide, corn, biological nitrogen fixation, and legume-grass mixtures
- Citation to related publication:
- Bressler, A., and J. Blesh. 2023. A grass-legume cover crop maintains nitrogen inputs and nitrous oxide fluxes from an organic agroecosystem. Ecosphere. 14(2): e4428. https://doi.org/10.1002/ecs2.4428
- Discipline:
- Science
-
- Creator:
- Su, Xue, Zhang, Youxue, Liu, Yang, and Holder, Robert M.
- Description:
- It is commonly thought that volcanic glass only records volatile loss during the eruptions in the Moon. However, our recent work shows that Na, K and Cu (moderately volatile elements) in lunar 74220 orange glass beads are enriched near the bead surfaces and depleted in the bead interiors, forming an overall “U-shaped” profile. The “U-shaped” profile means that rather than being “lost” into space, Na, K and Cu were “gained” into the volcanic glass during the eruption, which is contrary to the “volatile loss” story. Three different instruments (EMP, SIMS and LA-ICP-MS) were used to verify the discovery. We propose that such U-shaped Na, K and Cu profiles were formed by initial outgassing and subsequent in-gassing of Na, K and Cu when the beads were flying from the vent onto the surface through the cooling volcanic gas plume. Hence, in-gassing and the formation of surface coatings are two processes that are genetically linked during the pyroclastic eruption and evolution of the gas cloud. To quantify the processes that formed the U-shaped profiles, we developed a diffusion and surface-equilibrium model using available literature data on Na and Cu diffusivity in basaltic melts. The model reproduced U-shaped Na and Cu concentration profiles with outgassing at high temperature and subsequent in-gassing as beads cooled. By fitting the measured Na and Cu profiles, we found that the cooling time scales of individual orange glass beads range from 48 to 179 s. This is the first time that both outgassing and in-gassing were modeled and the cooling time scales of individual 74220 volcanic orange glass beads were estimated. The discovery of the U-shaped profiles of moderately volatile elements inside volcanic beads provides significant constraints on partial pressures of relevant volcanic gas species in the eruption plume.
- Keyword:
- Moon, Volcanic orange glass beads, Moderately volatile elements, Outgassing and in-gassing, and Cooling time scales
- Citation to related publication:
- Su, X., Zhang, Y., Liu, Y. and Holder, R.M. (2023) Outgassing and in-gassing of Na, K and Cu in lunar 74220 orange glass beads. Earth and Planetary Science Letters 602. https://doi.org/10.1016/j.epsl.2022.117924
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and Micro and Nano CT Advanced Imaging Core, Orthopaedic Research Laboratories, University of Michigan
- Description:
- Reconstructed CT slices for UMMP VP 118710 Mammuthus primigenius proximal tusk segment as a series of TIFF images. Raw projections are not included in this dataset. The reconstructed slice data from the scan are offered here as a series of unsigned 16-bit integer TIFF images. The upper left corner of the first image (*_0000.tif) is the XYZ origin.
- Keyword:
- Paleontology, Fossil, CT, Elephantidae, UMMP, University of Michigan Museum of Paleontology, and 4760d0fa-a763-23d2-1be9-89bb1aaf711c
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology, University of Michigan School of Dentostry MicroCT Core, and Lynch, Michelle
- Description:
- Reconstructed CT slices for UMMP VP 118186 Loxodonta africana tusk core as a series of TIFF images. Raw projections are not included in this dataset. The reconstructed slice data from the scan are offered here as a series of unsigned 16-bit integer TIFF images. The upper left corner of the first image (*_0000.tif) is the XYZ origin.
- Keyword:
- Paleontology, CT, Elephantidae, UMMP, University of Michigan Museum of Paleontology, and a4f83cc6-09f2-0032-8a09-60ea798f787c
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for tusk block number 2 of Mammuthus primigenius (University of Michigan Museum of Paleontology catalog number UMMP VP 118711) as a series of TIFF images. Raw projections are not included in this dataset. The reconstructed slice data from the scan are offered here as a series of unsigned 16-bit integer TIFF images. The upper left corner of the first image (*_0000.tif) is the XYZ origin.
- Keyword:
- Paleontology, Fossil, CT, Elephantidae, UMMP, University of Michigan Museum of Paleontology, Pleistocene, and eb7acb05-b8b5-9642-b90a-b7d49a83de4d
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology, University of Michigan School of Dentistry MicroCT Core, and Lynch, Michelle
- Description:
- Reconstructed CT slices for UMMP VP 118711 Mammuthus primigenius block number 10 (distalmost) removed from tusk as a series of TIFF images. Raw projections are not included in this dataset. The reconstructed slice data from the scan are offered here as a series of unsigned 16-bit integer TIFF images. The upper left corner of the first image (*_0000.tif) is the XYZ origin.
- Keyword:
- Paleontology, Fossil, CT, Elephantidae, UMMP, University of Michigan Museum of Paleontology, Pleistocene, and eb7acb05-b8b5-9642-b90a-b7d49a83de4d
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology, University of Michigan School of Dentistry MicroCT Core, and Lynch, Michelle
- Description:
- Reconstructed CT slices for UMMP VP 118711 Mammuthus primigenius block number 1 (proximalmost) removed from tusk as a series of TIFF images. Raw projections are not included in this dataset. The reconstructed slice data from the scan are offered here as a series of unsigned 16-bit integer TIFF images. The upper left corner of the first image (*_0000.tif) is the XYZ origin.
- Keyword:
- Paleontology, Fossil, CT, Elephantidae, UMMP, University of Michigan Museum of Paleontology, Pleistocene, and eb7acb05-b8b5-9642-b90a-b7d49a83de4d
- Discipline:
- Science
-
- Creator:
- Lin, Jack and Stacey, William C.
- Description:
- The characterization of HFO networks through functional connectivity analysis and network centrality. Details of the code repository can be found in the README.txt file.
- Keyword:
- Epilepsy, High Frequency Oscillation, HFO, Network, and EEG
- Citation to related publication:
- Pending
- Discipline:
- Health Sciences
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for Posterior cranium fragment (juvenile) of Dorudon atrox (University of Michigan Museum of Paleontology catalog number UMMP VP 100142) as a series of TIFF images. Raw projections are not included in this dataset. The reconstructed slice data from the scan are offered here as a series of unsigned 16-bit integer TIFF images. The upper left corner of the first image (*_0000.tif) is the XYZ origin.
- Keyword:
- Paleontology, Fossil, CT, Basilosauridae, Eocene, CTEES, UMMP, University of Michigan Museum of Paleontology, and a470edbc-75b1-f352-d947-330dd1043256
- Discipline:
- Science
-
- Creator:
- Eckels, Joshua D.
- Description:
- The goal of the research was to train a surrogate model for the prediction of electric field distribution for a given electrospray emitter geometry design. The surrogate is to be used in reduced-fidelity modeling of electrospray thruster arrays. The code repository is included in the README.txt file.
- Keyword:
- Electrospray design, Martinez-Sanchez hyperboloid solution, and Electrospray engineering toolkit (ESPET)
- Citation to related publication:
- J.D. Eckels, C.B. Whittaker, B.A. Jorns, A.A. Gorodetsky, B. St. Peter, R.A. Dressler, “Simulation-based surrogate methodology of electric field for electrospray emitter geometry design and uncertainty quantification”, presented at the 37th International Electric Propulsion Conference, Boston, MA USA, June19-23, 2022 Available: https://www.electricrocket.org/IEPC_2022_Papers.html
- Discipline:
- Engineering
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for skull of Stylemys nebrascensis (University of Michigan Museum of Paleontology catalog number UMMP VP 9318) as a series of TIFF images. Raw projections are not included in this dataset. The reconstructed slice data from the scan are offered here as a series of unsigned 16-bit integer TIFF images. The upper left corner of the first image (*_0000.tif) is the XYZ origin.
- Keyword:
- Paleontology, Fossil, CT, Testudinidae, UMMP, University of Michigan Museum of Paleontology, Oligocene, CTEES, and c38728f5-6f38-d862-7bcf-9745e69db222
- Discipline:
- Science
-
- Creator:
- Kharbush, Jenan J, Carter, Susan J, and Robinson, Rebecca S
- Description:
- Nitrogen availability is hypothesized to play a central role in cyanoHAB progression, as well as production of the N-rich toxin microcystin. Recent work implicated reduced N substrates like ammonium and dissolved organic N (DON) in promoting greater bloom biomass and longevity. To examine the relative importance of oxidized and reduced N substrates to phytoplankton during different bloom stages, we measured concentrations and natural abundance δ15N isotope values of dissolved N substrates and phytoplankton biomass throughout the entirety of the 2020 cyanoHAB in Western Lake Erie. This is the first data on DON concentrations and isotope values in Western Lake Erie. We measured nitrate concentrations and isotope values to compare with DON and also with particulate organic matter (POM) 15N isotope values. This dataset is described and analyzed in the publication, "Patterns in sources and forms of nitrogen during a freshwater cyanobacterial harmful algal bloom".
- Keyword:
- Dissolved organic nitrogen, cyanobacteria, nitrate, particulate organic matter, δ15N, stable isotopes
- Citation to related publication:
- Kharbush, Jenan J., Robinson, Rebecca S., Carter, Susan J. In revision. Patterns in sources and forms of nitrogen during a freshwater cyanobacterial harmful algal bloom. Limnology and Oceanography.
- Discipline:
- Science
-
- Creator:
- Zhou, Peng and Mi, Zetian
- Description:
- Production of hydrogen fuel from sunlight and water offers one of the most promising pathways for carbon neutrality. Some solar hydrogen production approaches, e.g., photoelectrochemical water splitting, often requires corrosive electrolyte, limiting their performance stability and environmental sustainability. Alternatively, clean hydrogen can be produced directly from tap water, or seawater by wireless photocatalytic water splitting. The solar-to-hydrogen (STH) efficiency, however, is still lower than 3%. Herein, we have developed a unique strategy to overcome the efficiency bottleneck. A high STH efficiency of 9.2% was achieved by utilizing pure water, concentrated solar light, and visible-light-responsive InGaN photocatalyst. The success of this strategy was explained by the synergistic effects of promoting forward hydrogen-oxygen evolution and inhibiting the reverse hydrogen-oxygen recombination by operating at an optimal reaction temperature (~70 °C). Such an optimal temperature can be readily achieved by harvesting the previously wasted infrared light of the solar spectrum without other energy consumption. This temperature-dependent strategy also leads to the STH efficiencies of ~7% from the widely available tap water and seawater. A large-scale photocatalytic water splitting system with a natural solar light capacity of 257 W on a 4 cm × 4 cm photocatalyst wafer achieves a STH of 6.2% at ~70 oC. Our study offers a practical approach to produce hydrogen fuel efficiently from natural solar and water, overcoming some of the major barriers for green hydrogen economy.
- Keyword:
- photocatalysis, water splitting, and solar hydrogen
- Discipline:
- Science
-
- Creator:
- Krupka, Erin
- Description:
- The survey data used in this project is from two larger overarching projects titled the Rice Preferences Study and the Black Student Success Study. The Rice Preferences Study began with a sample of 661 entering undergraduates matriculating in August of 2016. This was 66.7% of the entering class, randomly selected. Of that sample, 553 completed the study with an 83.7% response rate. Prior to coming to campus in fall 2016 Rice students were given a battery of incentivized preference measures including risk aversion, loss aversion, altruism, in-group favoritism, time discounting, competitiveness, and so on. Over the subsequent four years that group was tested with new and repeated measures, in two to four tests per year. As a basis for comparison, each year a smaller sample (between 112 And 148) was drawn from incoming classes and tested with the same instruments. The remaining students from the Class of 2020 who had never been tested were invited in March 2020 to complete the initial study (259 of 376 completed the study). In March 2020, as Rice University closed, the team joined together to build a COVID module for the long-term Rice panel, as well as the other members of the Class of 2020. A total of 670 participated in this wave (67.1% of the graduating class). The Black Student Success Study recruited samples from PVAMU and TAMU in 2017 and again in 2019. This study aimed at understanding the effects of stereotype threat on Black student success in two different university environments in Texas: PVAMU, a historically Black university with about 9,000 students, 65% female, and 83% Black; and TAMU, a large state university with about 70,000 students, 47% female and 3.7% Black. That study was ongoing in 2020 when COVID struck. A total of 880 subjects responded to the initial survey out of a total of 3,709 who were contacted. Black subjects were over-sampled at TAMU, and constituted 37% of the TAMU sample. Respondents completed a one-hour survey that included measures of identity, non-cognitive skills, stereotype-threat vulnerability, and controls for economic preferences (survey measures) and family background. They were paid $20 for completing the study. In March 2020 additional funding was awarded through NSF to expand and follow the Rice, TAMU and PVAMU panels, focusing on the impact of COVID-19.
- Keyword:
- Norms, Preferences, Social Identity, COVID-19
- Discipline:
- Social Sciences
-
- Creator:
- MacEachern, Mark and Bauer, Melissa
- Description:
- The intent of the project was to identify all relevant studies and data related to the topic. There are searches for the following databases: Ovid MEDLINE, Elsevier Embase, Wiley Cochrane Central Register of Controlled Trials, and EBSCOhost CINAHL.
- Keyword:
- Health sciences, Thrombocytopenia, Literature searches, and Systematic review
- Citation to related publication:
- Bauer ME, Toledano RD, Houle T, Beilin Y, MacEachern M, McCabe M, Rector D, Cooper JP, Gernsheimer T, Landau R, Leffert L. Lumbar neuraxial procedures in thrombocytopenic patients across populations: A systematic review and meta-analysis. J Clin Anesth. 2020 May;61:109666. doi: 10.1016/j.jclinane.2019.109666. Epub 2019 Dec 4. PMID: 31810860. and Bauer ME, Arendt K, Beilin Y, Gernsheimer T, Perez Botero J, James AH, Yaghmour E, Toledano RD, Turrentine M, Houle T, MacEachern M, Madden H, Rajasekhar A, Segal S, Wu C, Cooper JP, Landau R, Leffert L. The Society for Obstetric Anesthesia and Perinatology Interdisciplinary Consensus Statement on Neuraxial Procedures in Obstetric Patients With Thrombocytopenia. Anesth Analg. 2021 Jun 1;132(6):1531-1544. doi: 10.1213/ANE.0000000000005355. PMID: 33861047.
- Discipline:
- Health Sciences
-
- Creator:
- MacEachern, Mark, Khouri, Alexander, Adidharma, Widya, Haase, Steven, Waljee, Jennifer, Cederna, Paul, and Strong, Amy
- Description:
- The intent of the project was to identify all relevant studies and data related to the topic. There are searches for the following databases: Ovid MEDLINE, Elsevier Embase, Clarivate Web of Science, and Wiley Cochrane Central Register of Controlled Trials. The searches yielded 889 citations after duplicates were removed in Endnote X8.
- Keyword:
- Fat Grafting, Surgery, Hand, Systematic Review, and Health Sciences
- Citation to related publication:
- Khouri AN, Adidharma W, MacEachern M, et al. The Current State of Fat Grafting in the Hand: A Systematic Review for Hand Diseases. HAND. February 2022. doi:10.1177/15589447211066347
- Discipline:
- Health Sciences
-
- Creator:
- Liemohn, Michael W, Adam, Joshua G, and Ganushkina, Natalia Y
- Description:
- Many statistical tools have been developed to aid in the assessment of a numerical model’s quality at reproducing observations. Some of these techniques focus on the identification of events within the data set, times when the observed value is beyond some threshold value that defines it as a value of keen interest. An example of this is whether it will rain, in which events are defined as any precipitation above some defined amount. A method called the sliding threshold of observation for numeric evaluation (STONE) curve sweeps the event definition threshold of both the model output and the observations, resulting in the identification of threshold intervals for which the model does well at sorting the observations into events and nonevents. An excellent data-model comparison will have a smooth STONE curve, but the STONE curve can have wiggles and ripples in it. These features reveal clusters when the model systematically overestimates or underestimates the observations. This study establishes the connection between features in the STONE curve and attributes of the data-model relationship. The method is applied to a space weather example.
- Keyword:
- space physics, statistical methods, and STONE curve
- Citation to related publication:
- Liemohn, M. W., Adam, J. G., & Ganushkina, N. Y. (2022). Analysis of features in a sliding threshold of observation for numeric evaluation (STONE) curve. Space Weather, 20, e2022SW003102. https://doi.org/10.1029/2022SW003102
- Discipline:
- Science
-
- Creator:
- Brian C. Weeks
- Description:
- Description: Each folder contains all of the data for a specific specimen; the folder names correspond to the University of Michigan Museum of Zoology catalog number for the specimen. Folders with a “-“ in the name are individual specimens that were photographed multiple independent times; the number following the “-“ indicates the repetition number (i.e. the folder named “UMMZ_242382-10” contains the tenth set of photographs for specimen UMMZ 242382). The photographs are necessary to train and test the Skelevision model, which is a computer vision approach to identifying and measuring elements of the skeleton (length of the tibiotarsus, tarsometatarsus, femur, humerus, ulna, radius, carpometacarpus, 2nd digit 1st phalanx, skull, and keel; the outer diameter of the sclerotic ring at its widest point; and the distance from the back of the skull to the tip of the bill). The data span 115 species of passerines across 79 genera from 59 families.
- Keyword:
- Bird skeleton, neural network, and functional traits
- Citation to related publication:
- Weeks, B.C., Zhou, Z., O’Brien, B., Darling, R., Dean, M., Dias, T., Hassena, G., Zhang, M., and Fouhey, D.F. 2022. A deep neural network for high throughput measurement of functional traits on museum skeletal specimens. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210X.13864
- Discipline:
- Science
-
- Creator:
- Benjamin Leffel
- Description:
- The three datasets provided here identify the city location of all CDM projects in China by referencing the individual Project Description Documents (via the UNFCCC) attached to each project. Through this method, all 3,764 Clean Development Mechanism projects at the city-level in China are identified out of a total of over 8,000 globally.
- Keyword:
- climate finance, carbon offset, China, urban, clean development mechanism, cities, and climate change
- Citation to related publication:
- https://escholarship.org/uc/item/3vr8850s and https://doi.org/10.1002/wcc.709
- Discipline:
- Government, Politics and Law, Social Sciences, International Studies, and Business
-
- Creator:
- Bressler, Alison and Blesh, Jennifer
- Description:
- This dataset contains three data files and three corresponding metadata files used in Bressler, A., and J. Blesh. 2022. Episodic N2O emissions following tillage of a legume-grass cover crop mixture. Biogeosciences. The file “Cover_crop_soil_N2O.xls” contains data organized by site, replicate block, and treatment for spring cover crop biomass, nitrogen and carbon content, and legume BNF; soil fertility characteristics including potentially mineralizable nitrogen, particulate organic matter stocks, concentrations, and nitrogen content; and cumulative nitrous oxide data. The file “Soil_properties.xls” contains baseline soil data organized by site and replicate block. The file “Daily_N2O.xls” contains daily nitrous oxide data organized by site, replicate block, treatment, and date. The corresponding metadata files: “Cover_crop_soil_N2O_metadata.xls”, and “Soil_properties_metadata.xls”, and “Daily_N2O_metadata.xls” provided detailed descriptions of all variables in each data set and any abbreviations used.
- Keyword:
- cover crops, legume-grass mixtures, nitrous oxide, particulate organic matter, soil organic matter.
- Citation to related publication:
- Bressler, A., and J. Blesh. 2022. Episodic N2O emissions following tillage of a legume-grass cover crop mixture. Biogeosciences.
- Discipline:
- Science
-
- Creator:
- Cody H. Pham, Jason M. Tallant, J. Jordan Price, and David N. Karowe
- Description:
- Anthropogenic climate change will dramatically alter species distributions. The rate and magnitude of range shifts, however, will differ among taxa, resulting in altered patterns of co-occurrence and interspecific interactions. We examined potential climate-mediated breeding range shifts among North American wood-warblers (Parulidae), a speciose avian family likely to be especially impacted by such changes. We used publicly available species distribution model (SDM) range outputs to compare current ranges and patterns of sympatry among warbler species to future ranges and sympatry under 1.5 °C, 2.0 °C, and 3.0 °C of average global warming. We used these outputs to calculate average breeding range area, range overlap among species, number of sympatric species, and distances of breeding range shifts. We additionally calculated the number gained and lost sympatric interactions under each warming scenario.
- Keyword:
- wood-warbler, University of Michigan Biological Station (UMBS), Research Experience for Undergraduates (REU), climate change, interspecific, range shift, species distribution models, sympatric, and student-friendly
- Discipline:
- Science
-
- Creator:
- Vaskov, Alex K, Vu, Philip P, North, Naia, Davis, Alicia J, Kung, Theodore A, Gates, Deanna H, Cederna, Paul S, and Chestek, Cynthia A
- Description:
- The data was used to calibrate and simulate pattern recognition algorithms for the following publication: Surgically Implanted Electrodes Enable Real-Time Finger and Grasp Pattern Recognition for Prosthetic Hands (medRxiv 2020, IEEE TRO in review). Each data file is named as follows Px_PostureSet.csv. Where Px is the patient number. The 1 of 10 posture set contains individual finger and intrinsic thumb movements, the grasps posture set contains a fewer number of combined finger movements. P1’s calibration data for individual fingers is labelled 1 of 12 because it also includes two grasps, which were removed for analysis in the publication. The first column of each .csv file is the experiment time in seconds. The second column is the posture of the cue hand at that timestamp. The rest of the columns are the raw EMG data in microvolts sampled at 30KSps. A legend of the movement postures, each patients EMG channels, and suggested signal processing and filtering is included in DataLabellingAndProcessing.pdf
- Keyword:
- pattern recognition, electromyography, regenerative peripheral nerve interface, intramuscular electrodes, and myoelectric prostheses
- Citation to related publication:
- Surgically Implanted Electrodes Enable Real-Time Finger and Grasp Pattern Recognition for Prosthetic Hands A. K. Vaskov, P. P. Vu, N. North, A. J. Davis, T. A. Kung, D. H. Gates, P. S. Cederna, C. A. Chestek medRxiv 2020.10.28.20217273; doi: https://doi.org/10.1101/2020.10.28.20217273
- Discipline:
- Science and Engineering
-
- Creator:
- Hawes, Jason K, Johnson, Rebecca, Payne, Lindsey, Ley, Christian, Grady, Caitlin A., Domenech, Jennifer, Evich, Carly D., Kanach, Andrew, Koeppen, Allison, Roe, Kristen, Caprio, Audrey, Puente Castro, Jessica, LeMaster, Paige, and Blatchley, Ernest R. III
- Description:
- Global service-learning brings students, instructors, and communities together to support learning and community development across borders. In doing so, global service-learning practitioners act at the intersection of two fields: service-learning and international development. Critical scholarship in all three domains has highlighted the tensions inherent in defining and tracking “success” in community development. In response, service-learning and international development have turned considerable attention to documenting project characteristics, also known as best practices or success factors, which support equitable, sustainable community development. This database accompanies the article "Global Service-Learning - A systematic review of principle and practice," which presents a systematic synthesis of these fields’ best practices in the context of global service-learning. We propose 18 guiding principles for project design which aim to support practitioners in creating and maintaining justice-oriented, stakeholder-driven projects. This database contains the necessary reference material to trace the path of our analysis from abstract review to thematic synthesis. It also contains the final results of the thematic synthesis. To respect copyright restrictions, we have not made PDFs of all articles analyzed publicly accessible. Please contact the authors of this database or of the original article if you seek to access one of the articles we reference. For more information, see: Hawes, J. K., et al. “Global Service-Learning - A Systematic Review of Principle and Practice.” International Journal of Research on Service-Learning and Community Engagement 10, no. 1 (2022).
- Keyword:
- service-learning, international development, global service-learning, best practices, equitable development, higher education, community engagement, and student-friendly
- Citation to related publication:
- Hawes, J. K. (2021). Global Service-Learning—A systematic review of principle and practice. International Journal of Research on Service-Learning and Community Engagement, 10(1). https://doi.org/10.37333/001c.31383
- Discipline:
- International Studies and Other
-
- Creator:
- Brenner, Austin, M
- Description:
- Coupling between the solar wind and magnetosphere can be expressed in terms of energy transfer through the separating boundary known as the magnetopause. Geospace simulation is performed using the Space Weather Modeling Framework (SWMF) of a multi-ICME impact event on February 18-20, 2014 in order to study the energy transfer through the magnetopause during storm conditions. The magnetopause boundary is identified using a modified plasma $\beta$ and fully closed field line criteria to a downstream distance of $-20R_{e}$. Observations from Geotail, Themis, and Cluster are used as well as the Shue 1998 model to verify the simulation field data results and magnetopause boundary location. Once the boundary is identified, energy transfer is calculated in terms of total energy flux \textbf{K}, Poynting flux \textbf{S}, and hydrodynamic flux \textbf{H}. Surface motion effects are considered and the regional distribution of energy transfer on the magnetopause surface is explored in terms of dayside $\left(X>0\right)$, flank $\left(X<0\right)$, and tail cross section $\left(X=X_{min}\right)$ regions. It is found that total integrated energy flux over the boundary is nearly balanced between injection and escape, and flank contributions dominate the Poynting flux injection. Poynting flux dominates net energy input, while hydrodynamic flux dominates energy output. Surface fluctuations contribute significantly to net energy transfer and comparison with the Shue model reveals varying levels of cylindrical asymmetry in the magnetopause flank throughout the event. Finally existing energy coupling proxies such as the Akasofu $\epsilon$ parameter and Newell coupling function are compared with the energy transfer results.
- Keyword:
- Space plasma, Magnetosphere, MHD simulations, Magnetopause, Substorm, Energy transfer, and Poynting flux
- Citation to related publication:
- Brenner A, Pulkkinen TI, Al Shidi Q and Toth G (2021) Stormtime Energetics: Energy Transport Across the Magnetopause in a Global MHD Simulation. Front. Astron. Space Sci. 8:756732. doi: 10.3389/fspas.2021.756732
- Discipline:
- Science
-
- Creator:
- Fuller, Jennifer, Rowan, Erin, Landgraf, Ava, Alofs, Karen, Foufopoulos, Johannes, and Gronewold, Andrew
- Description:
- This study investigates the rapid decline of black tern (Chlidonias niger) over eight years in one of Michigan’s largest colonies, Lake St. Clair. 1. Nesting Success Model: A multiple logistic regression with a binomial (logit-link) fit using the glm() function from the ‘stats’ package in R (55) to determine the influence of habitat and biological predictors on nesting survival. 2. ArcMap visualization of Nesting Success: To visualize the geographic extent of the habitat’s potential to predispose nests’ vulnerability, the coefficients and intercept from our selected GLM were applied to raster layers in ArcMap using the Raster Calculator Tool. 3. Population Change & Habitat Extent: To quantify sub-colony breeding pair population size and their response to changes in sub-colony habitat in the geospatial model, we applied a general linear mixed model (GLMM) using the lmer() function from the ‘lme4’ package in R (55). Predictor variables were chosen a priori, and included the area of open water, uninhabitable vegetation (NDVI>0.72), any habitable area, and area with >50% hatch success.
- Keyword:
- black terns, wetlands, ecology, climate change, lake levels, Great Lakes, waterbirds, ornithology, general linear model, geospatial, GIS, nesting success, avian, and breeding
- Citation to related publication:
- Fuller, J., Rowan, E., Landgraf, A., Alofs, K., Foufopoulos, J., Gronewold, A., (2021). Collapse of a Black Tern Colony (Chlidonias niger) as a Result of Climate Change Driven Lake-Level Extremes and Anthropogenic Habitat Alteration [Data set]. University of Michigan - Deep Blue. and Fuller, J., et al. (2021). Shorebird colony collapses under climate driven lake-level rise and anthropogenic stressors. Forthcoming.
- Discipline:
- Science
-
- Creator:
- Lynch, Erin and van der Pluijm, Ben
- Description:
- High-resolution, low-angle XRD analysis of oriented clay samples (.txt files) and TC/EA, Mass Spectronometric analysis of oxygen and hydrogen isotopes (.xslx files)
- Keyword:
- fault gouge and geofluids
- Citation to related publication:
- In submission
- Discipline:
- Science
-
- Creator:
- BIRDS Lab, U. Michigan
- Description:
- These data were produced in an attempt to characterize the turning and steering behaviors of 1-DoF multi-legged (hexpedal in this case) robots. Such turning behaviors require sliding contact points. The .tar file contains multiple trials in .csv.gz format, with names following an informative naming convention documented in the README. Additional metadata for the trials is given in the metadata.py file in both machine and human readable form.
- Keyword:
- robot, multilegged, and steering
- Citation to related publication:
- Dan Zhao and Shai Revzen 2020 Bioinspir. Biomim. 15 045001 https://doi.org/10.1088/1748-3190/ab84c0
- Discipline:
- Engineering
-
- Creator:
- Herrick, Etienne M
- Description:
- This data was produced as part of field experiment investigating the extent, drivers, and consequences of functional trait variation in cover crops. Specifically, we studied the role of intraspecific trait variation in explaining interactions between species in cover crop mixtures, and whether and how intraspecific trait variation improves understanding of relationships between functional traits and ecosystem services from cover crops.
- Keyword:
- agroecology, cover crops, functional diversity, functional traits, intraspecific trait variation, ecosystem services, nitrogen, species interactions, and student-friendly
- Citation to related publication:
- Herrick, E., and Blesh, J. (2021) Intraspecific trait variation improves understanding and management of cover crop outcomes. Ecosphere.
- Discipline:
- Science
-
- Creator:
- Sun, Xin, Zhang, Kehui, Marks, Rebecca, Karas, Zachary, Eggleston, Rachel, Nickerson, Nia, Yu, Chi-Lin, Wagley, Neelima, Hu, Xiaosu, Caruso, Valeria, Tardif, Twila, Satterfield, Teresa, Chou, Tai-Li, and Kovelman, Ioulia
- Description:
- In a broad sense, this dataset explores morphological and phonological processing in English monolinguals and two bilingual populations, Chinese-English and Spanish-English, using a battery of standardized and self-developed behavioral measures, as well as fNIRS neuroimaging.
- Citation to related publication:
- Sun X, Zhang K, Marks R, Karas Z, Eggleston R, Nickerson N, Yu CL, Wagley N, Hu X, Caruso V, Chou TL, Satterfield T, Tardif T, Kovelman I. Morphological and phonological processing in English monolingual, Chinese-English bilingual, and Spanish-English bilingual children: An fNIRS neuroimaging dataset. Data Brief. 2022 Mar 12;42:108048. doi: 10.1016/j.dib.2022.108048. PMID: 35313503; PMCID: PMC8933821.
- Discipline:
- Science
-
- Creator:
- Brang, David and Karthik, Ganesan
- Description:
- Data were acquired from 21 patients with intractable epilepsy undergoing clinical evaluation using iEEG. Patients ranged in age from 15-58 years (mean = 37.1, SD = 12.8) and included 10 females. Across all patients, data was recorded from a total of 1367 electrodes. Each participant were presented with multiple trials of auditory only and congruent audio-visual stimuli. On each trial a single phoneme was presented to the participant. Three variants of the tasks were used with each variant consisting of a different set of phonemes (variant A: /ba/ /da/ /ta/ /tha/, variant B: /ba/ /da/ /ga/, variant C: /ba/ /ga/ /ka/ /pa/). Trials were presented in a random order and phonemes were distributed uniformly across conditions. While conditions were matched in terms of trial numbers, participants completed a variable number of trials (based on task variant and the number of blocks completed). All provided data has been resampled to 1024 Hz during initial stages of processing for all participants. Data has been referenced in a bipolar fashion (signals subtracted from each immediately adjacent electrode in a pairwise manner) to ensure that the observed signals were derived from maximally local neuronal populations. The preprocessing steps followed have been described in the detailed description document in the attached materials. and The dataset zip folder consists of three main sub-folders: 1) Electrodes: This folder provides details regarding the individual electrodes for each subject, their MNI coordinates as well as their MNI vertices information according to freesurfer parcellations. This folder also consists of images of the physical location of each of the electrode sets. 2) Processed: This folder contains preprocessed data in all three frequencies (theta, beta and high gamma power) for individual subjects and the corresponding vertex locations for each of the electrodes from which their data was recorded. The images subfolder also contains figures provided in the main manuscript. 3) MatlabCodes: This folder contains all the matlab scripts required to reproduce the results provided in the main manuscript. LME_AvsAV_Main_Windows.m is the main file that an user has to run to reproduce the results.
- Keyword:
- Cognitive Neuroscience, Neuroscience, Perception, and Mixed Effects Models
- Citation to related publication:
- Ganesan, K., Plass, J., Beltz, A. M., Liu, Z., Grabowecky, M., Suzuki, S., ... & Brang, D. (2020). Visual speech differentially modulates beta, theta, and high gamma bands in auditory cortex. bioRxiv. https://doi.org/10.1101/2020.09.07.284455
- Discipline:
- Science
-
- Creator:
- Saylor, Kate M., McCormick, Amanda D., Wilde, Megan M., Charpie, Christine E., Yu, Sunkyung, and Cousino, Melissa K.
- Description:
- The search data supports a literature review project on Psychological Functioning in Pediatric Patients with Single Ventricle Congenital Heart Disease. The data included are the reproducible search strategies (txt file) and the exported results of all citations from all databases (txt, ris, and.nbib files). Both the original search files and updated search files have been included in the deposit.
- Keyword:
- pediatrics, univent, Single Ventricle Congenital Heart Disease, and psychological
- Discipline:
- Health Sciences
-
- Creator:
- Umberfield, Elizabeth, Ford, Kathleen, Stansbury, Cooper, and Harris, Marcelline R.
- Description:
- Research Overview: This dataset is clinical consent forms, collected as part of Dr. Elizabeth Umberfield's dissertation research of at the University of Michigan. 134 consent forms are used in the analysis, 102 of which are shared here (not all are shared due to data protection agreements with participating sites). The research aimed to enable representation of clinical consent forms and their permissions within the Informed Consent Ontology. These efforts were supported by the Rackham Graduate Student Research Grant, and Dr. Umberfield's doctoral training was supported by the Robert Wood Johnson Foundation Future of Nursing Scholars Program.
- Keyword:
- Consent, Consent Form, Informed Consent, Health Care, and Healthcare
- Citation to related publication:
- Umberfield, E., Jiang, Y., Fenton, S., Stansbury, C., Ford, K., Crist, K., Kardia, S., Thomer, A., & Harris, M. R. (In Press). Lessons Learned for Identifying and Annotating Permissions in Clinical Consents. Applied Clinical Informatics. and Umberfield, E., Stansbury, C., Ford, K., Jiang, Y., Kardia, S. L. R., Thomer, A., & Harris, M. R. (Under Review). Evaluating and Extending the Informed Consent Ontology for Representing Permissions from the Clinical Domain.
- Discipline:
- Health Sciences
-
- Creator:
- Stringer, Kathleen A.
- Description:
- These data were produced from the survival analysis of the pre-treatment metabolomics data generated from the Phase II clinical trial of L-carnitine treatment for septic shock (the RACE trial - see https://clinicaltrials.gov/ct2/show/NCT01665092). The results based on respective acetylcarnitine or valine concentration are presented (pdf). The csv files contain the at risk numbers from the Kaplan-Meier survival analysis. These findings described in our manuscript: Pharmacometabolomics Identifies Candidate Predictor Metabolites of an L-carnitine Treatment Mortality Benefit in Septic Shock. and All of the metabolomics data are available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org which is supported by NIH grant U2C-DK119886 and where it has been assigned Project ID (accession number ST001319). The data can be accessed directly via its Project DOIs: (DOI: http://dx.doi.org/10.21228/M8VX0Z).
- Keyword:
- sepsis, septic shock, survival, mortality, metabolomics, and pharmacometabolomics
- Citation to related publication:
- Puskarich, M. A., Jennaro, T. S., Gillies, C. E., Evans, C. R., Karnovsky, A., McHugh, C. E., Flott, T. L., Jones, A. E., Stringer, K. A., & Investigators, O. behalf of the R. T. (2021). Pharmacometabolomics Identifies Candidate Predictor Metabolites of an L-carnitine Treatment Mortality Benefit in Septic Shock. (Preprint) https://doi.org/10.1101/2021.01.28.21250687
- Discipline:
- Health Sciences
-
- Creator:
- Moldwin, Mark B. and O'Brien, Paul
- Description:
- A new empirical model of the plasmapause location has been developed using density data from the plasma wave receiver onboard the CRRES spacecraft for nearly 1000 orbits. The “plasmapause” is identified here as the innermost sharp gradient in density (change of a factor of 5 in <0.5 L). Such a sharp gradient was observed on 73% of the CRRES inbound and outbound orbits that returned data. The plasmapause location is expressed as a linear function of Kp (previous 12 hour maximum) and local time. The model gives the linear best fit location of the plasmapause as well as the standard deviations of the model parameters.
- Keyword:
- Plasmapause and Plasmasphere
- Citation to related publication:
- Moldwin, M. B., Downward, L., Rassoul, H. K., Amin, R., and Anderson, R. R. (2002), A new model of the location of the plasmapause: CRRES results, J. Geophys. Res., 107( A11), 1339, doi:10.1029/2001JA009211 and O'Brien, T. P., and Moldwin, M. B. (2003), Empirical plasmapause models from magnetic indices, Geophys. Res. Lett., 30, 4, 1152. doi:10.1029/2002GL016007
- Discipline:
- Science
-
- Creator:
- Zhang, Kaihua and Collette, Matthew D.
- Description:
- This Ph.D. research focuses on two subject areas: experimental and numerical model, which serves as two essential parts of a digital twin. A digital twin contains models of real-world structures and fuses data from observations of the structures and scale experiment to pull the models into better agreement with the real world. Digital twin models have the promise of representing complex marine structures and providing enhanced lifecycle performance and risk forecasts. Experimentally verifying the updating approaches is necessary but rarely performed. Thus, the proposed work is designing an experiment and developing a numerical model updated by the experimental data. The dataset contains all the data collected in the experiment of a four-crack hexagon- shaped specimen is presented, designed to mimic many of the properties of complex degrading marine structural systems, such as crack interaction, component inter- dependence, redundant load path, and non-binary failure.
- Keyword:
- System Reliability, Dynamic Bayesian Networks, Fatigue Experiment, Crack Length Measurement, Experimental Validation, Reliability Prediction
- Citation to related publication:
- "Evaluating Crack Growth Prediction in Structural Systems with Dynamic Bayesian Networks", submitted to Computers and Structure and Zhang, K., & Collette, M. (2021). Experimental investigation of structural system capacity with multiple fatigue cracks. Marine Structures, 78, 102943. https://doi.org/10.1016/j.marstruc.2021.102943
- Discipline:
- Engineering
-
- 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:
- 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:
- 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
-
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
-
- 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
-
- 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:
- Agrawal, Mayank and Glotzer, Sharon C
- Description:
- Micron-scale robots require systems that can morph into arbitrary target configurations controlled by external agents such as heat, light, electricity, and chemical environment. Achieving this behavior using conventional approaches is challenging because the available materials at these scales are not programmable like their macroscopic counterparts. To overcome this challenge, we propose a design strategy to make a robotic machine that is both programmable and compatible with colloidal-scale physics. Our strategy uses motors in the form of active colloidal particles that constantly propel forward. We sequence these motors end-to-end in a closed chain forming a two-dimensional loop that folds under its mechanical constraints. We encode the target loop shape and its motion by regulating six design parameters, each scale-invariant and achievable at the colloidal scale. The research dataset includes simulation, visualization, and analysis scripts and results generated for the 2D chain loops of self-propelling particles. File Description:, -- arrows_folding - Contains the data for the folded chain loop shapes resembling an arrowhead., -- bending_vs_variation - Contains the data to study the stability of a particular shape in simulations as one of the segments of the shape bends and/or the distribution of propulsion on it varies., -- curved_triangle - Contains the data to study motion and bending of a triangle shape made using chain loop., -- example_shapes - Contains data for various examples of shapes that can be generated by designing the chain loops., -- nskT_vs_fakT - Contains the data for a specific shape to study the effect of scaling up the number of particles (governed by ns) and the propulsion (governed by fa) in its chain., -- stability - Contains the data and theoretical model (stability.py) to study the stability of the six different shapes., -- tuning_design_forM - Contains the data for sequential tuning the design parameters to fold the shape "M" as described in the corresponding publication., and -- two_neighboring_cds_segments_ - Contains the data to study a system of two neighboring chain segments with respect to different parameters discussed in the publication.
- Keyword:
- active particles, colloidal robotics, design, kilobots, and morphological control
- Citation to related publication:
- Agrawal, M, Glotzer SC. (2020). Scale-free, programmable design of morphable chain loops of kilobots and colloidal motors. PNAS. www.pnas.org/cgi/doi/10.1073/pnas.1922635117
- Discipline:
- Engineering
-
- Creator:
- Moser, Carol, Schoenebeck, Sarita , and Resnick, Paul
- Description:
- These data, survey instruments (including informed consent) and analysis scripts come from Carol Moser's dissertation titled, Impulse Buying: Designing for Self-Control with E-commerce.
- Keyword:
- Impulse Buying, Self-control, and Experimental Design
- Discipline:
- Social Sciences
-
- Creator:
- Moniri, Saman, Xiao, Xianghui, and Shahani, Ashwin J.
- Description:
- The data is comprised of 22 directories, each housing a .hdf file of the X-ray projections recorded during solidification of Al-Si-Cu-Sr. The flat and dark projections are also included as two separate .hdf files (total file count: 24). The raw data file is in .hdf format and can be reconstructed into .tiff, e.g., by using the TomoPy toolbox in Python.
- Keyword:
- Crystallization, growth modifiers, silicon, in situ, X-ray tomography
- Citation to related publication:
- Wang, Y., Gao, J., Ren, Y., De Andrade, V., & Shahani, A. J. (2020). Formation of a Three-Phase Spiral Structure Due to Competitive Growth of a Peritectic Phase with a Metastable Eutectic. JOM, 72(8), 2965–2973. https://doi.org/10.1007/s11837-020-04237-x
- Discipline:
- Engineering
-
- 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:
- Ahluwalia, Vinayak S., Steimle, Lauren N., and Denton, Brian T.
- Description:
- This repository includes test instances of infinite-horizon Markov decision processes with multiple models of parameters (i.e., "Multi-model Markov decision processes"). We generated each test instance in the dataset using a Python script. The test instances can be read in using the provided C++ and Python script. See the README for details.
- Keyword:
- Markov decision processes, mixed-integer programming, stochastic programming, and dynamic programming
- Citation to related publication:
- Ahluwalia, Steimle, and Denton. "Policy-based branch-and-bound for infinite-horizon Multi-model Markov decision processes". 2020.
- Discipline:
- Engineering
-
- Creator:
- Hatch, Nan E.
- Description:
- Crouzon FGFR2-C342Y/+ and wild type littermate pups on a C57BL/6 congenic background were injected with lentivirus expressing recombinant TNAP enzyme or phosphate buffered saline shortly after birth. Mice were euthanized 3 weeks after birth for analyses.
- Keyword:
- craniofacial, bone, craniosynotosis, FGFR2, TNAP tissue nonspecific alkaline phosphatase, mouse model, and development
- Citation to related publication:
- Nam, H. K., Vesela, I., Schutte, S. D., & Hatch, N. E. (2020). Viral delivery of tissue nonspecific alkaline phosphatase diminishes craniosynostosis in one of two FGFR2C342Y/+ mouse models of Crouzon syndrome. PLOS ONE, 15(5), e0234073. https://doi.org/10.1371/journal.pone.0234073
- Discipline:
- Health Sciences
-
- 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:
- 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:
- 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:
- 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:
- 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:
- 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
-
- 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:
- Heath, Jeffrey , Ouattara, Aminata , and Hantgan, Abbie
- Description:
- Our project, mainly on Dogon languages of Mali, has branched out to Burkina Faso with emphasis on documentation of the most endangered languages. Tiefo-N was studied on an emergency basis since it was down to two aging competent speakers. For additional comments and links to a reference grammar, see the readme file.
- Keyword:
- Gur languages, Tiefo, Tiefo-N language, and Lexicon
- Citation to related publication:
- Jeffrey Heath, Aminata Ouattara & Abbie Hantgan. Short grammar of Tiefo-N of Nyafogo (Gur, Burkina Faso). Language Description Heritage Library (MPI). http://ldh.clld.org/2017/01/01/escidoc2378140/ and A copy of this publication is also available in Deep Blue: http://dx.doi.org/10.17617/2.2378140
- Discipline:
- Humanities
-
- Creator:
- Heath, Jeffrey, Hantgan, Abbie , and Elders, Stefan
- Description:
- The work on the Bangime language, spoken by the Bangande people, was carried out as part of a larger linguistic fieldwork project focused on Dogon languages. Bangime is confirmed as a language isolate with no demonstrable linguistic relatives—possibly the only such isolate in West Africa.
- Keyword:
- Bangime, Mali, and Lexicon
- Citation to related publication:
- Heath & Hantgan. A grammar of Bangime. Berlin: de Gruyter, 2018. ISBN 978-3-11-055749-7
- Discipline:
- Humanities
-
- Creator:
- Heath, Jeffrey
- Description:
- Jalkunan is an endangered language of the Mande family, spoken in the village cluster of Blédougou in southwestern Burkina Faso. The lexical work complements a published grammar with texts. See the readme for further information.
- Keyword:
- Jalkunan, Burkina Faso, Mande languages, and Lexicon
- Citation to related publication:
- Heath, Jeffrey. A grammar of Jalkunan (Mande, Burkina Faso). 2017. http://hdl.handle.net/2027.42/139025
- Discipline:
- Humanities
-
- Creator:
- Haydar, Bishr and MacEachern, Mark
- Description:
- The research adheres to PRISMA-HARM recommendations for systematic reviews. The reproducible search strategies for all databases, the citation export files from all databases, and the eligibility screening decisions are included in the dataset.
- Keyword:
- Systematic review, Patient transportation, intrahospital, intra-hospital, and Critically ill patients
- Citation to related publication:
- Haydar B, Baetzel A, Elliott A, MacEachern M, Kamal A, Christensen R. Adverse Events During Intrahospital Transport of Critically Ill Children: A Systematic Review. Anesth Analg. 2019. http://dx.doi.org/doi:10.1213/ANE.0000000000004585
- Discipline:
- Health Sciences
-
- Creator:
- Lee, Kyu Han
- Description:
- Data include variables used to run accelerated failure time models examining the association between the nose/throat microbiome and 1) symptom duration, 2) shedding duration, and 3) time to infection. Certain individual participant data have been excluded due to identifiability concerns. Data also include the oligotype count table and taxonomic classifications.
- Keyword:
- Influenza and Microbiome
- Citation to related publication:
- Lee KH, Gordon A, Shedden K, Kuan G, Ng S, Balmaseda A, Foxman B. The respiratory microbiome and susceptibility to influenza virus infection. PloS One. 2019;14:e0207898. https://doi.org/10.1371/journal.pone.0207898
- Discipline:
- Health Sciences
-
- 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:
- Jenkins, G. J. and Bougher, S. W.
- Description:
- In early 2019, the Mars Atmosphere and Volatile Evolution (MAVEN) mission underwent an ~2-month aerobraking campaign, during which time the spacecraft periapsis altitude was lowered from its nominal altitude range of 140-160 km to as low as ~123 km. Excluding spacecraft walk-in/out maneuvers, accelerometer measurements were made along 272 orbits with coverage spanning Ls 340-3°, latitudes ~5-54°S, longitudes 0-360°, and Local Solar Time (LST) ~22-17 hours. In this study, we perform a diagnostic analysis of the full aerobraking data set by fitting 4-harmonic waves to mass densities. We then study the variations of these waves as a function of latitude with an emphasis on those observed previously in Mars’ thermosphere by MAVEN and other missions. Additionally, we utilize data collected during the same time period from the Mars Reconnaissance Orbiter’s Mars Climate Sounder to study the vertical propagation of waves originating from the middle atmosphere. Key results indicate that normalized wave amplitudes decrease with latitude, and this is consistent with the latitudinal structure of a diurnal Kelvin mode. We also observe that waves imprinted from the middle atmosphere show normalized amplitude growth with increasing altitude. A complete summary of data sets, analysis methodology, and scientific results is given. The purpose of this study is to add to the body of knowledge surrounding Martian atmospheric wave features and to provide further constraints for future numerical modeling and subsequent tidal mode identification.
- Keyword:
- MAVEN, Mars Thermosphere, Accelerometer Data Set, Global Data Set, and Wave Analysis of Tides
- Citation to related publication:
- Jenkins, G. A., Bougher, S. W., Lugo, R., Tolson, R. H., Zurek, R. W., Baird, D., Steele, L., Kass, D., Withers, P. (2023), MAVEN Accelerometer Observations of Thermospheric Densities during Aerobraking and Deep Dip 2: Wave Features and Connections to Upward Propagating Thermal Tides, Journal of Geophysical Research: Planets, xx, xx.
- Discipline:
- Science
-
- Creator:
- Walsh, Lisa L
- Description:
- Stable isotope values of carbon (δ13C) and nitrogen (δ15N) from Virginia opossum (Didelphis virginiana) guard hairs were analyzed to evaluate the ecology and winter adaptations in opossums by Dr. Lisa L. Walsh as part of her Ph.D. thesis in the Ecology and Evolutionary Biology Department. The collection of stable isotope data took place from 2017 to 2019. Guard hair was processed at the University of Michigan and analyzed by the University of New Mexico Center for Stable Isotopes (UNM-CSI, USA). Captive and wild opossums were evaluated for evidence of biannual or incomplete biannual molting, a mammalian adaptation to harsh winters. Results suggest opossums do not exhibit either winter molting strategy and that guard hairs capture the opossum’s lifetime diet (Walsh and Tucker 2021). The stable isotope values were used to test the hypothesis that a Type A generalist’s niche is positively correlated with habitat heterogeneity and to evaluate which climate variables best explained isotope values. There was a positive correlation between isotopic niche size and habitat-diversity indexes (Walsh and Tucker 2020). The δ13C values from opossums in the Midwest and Northeast to test whether opossums rely on anthropogenic trash to survive extreme winters. There was no significant relationship between δ13C and winter variables, but there was a significant increase in variance of Midwest opossums’ δ13C after the 1970 corn agricultural boom (Walsh and Tucker 2023).
- Keyword:
- stable isotope, Virginia opossum, mesopredator, ecology, and mammal
- Citation to related publication:
- Walsh, L.L. and P.K. Tucker. 2020. Habitat heterogeneity is correlated with isotopic niche breadth across the range of a mammalian generalist mesopredator. Ecosphere, 11(12): e03314. https://doi.org/10.1002/ecs2.3314, Walsh, L.L. and P.K. Tucker. 2021. Stable isotope values suggest opossums (Didelphis virginiana) at their northern edge do not seasonally molt. Northeastern Naturalist, 28(1): 1-8. https://doi.org/10.1656/045.028.0101, and Walsh, L.L., and P.K. Tucker. 2023. Evaluating anthropogenic influence on a mesopredator: Opossum (Didelphis virginiana) isotope values influenced by corn agriculture more than urbanization. Canadian Journal of Zoology, 101: https://doi.org/10.1139/cjz-2021-0172.
- Discipline:
- Science
-
- Creator:
- Bougher, Stephen W. and Roeten, Kali J.
- Description:
- The NASA MAVEN (Mars Atmosphere and Volatile Evolution) spacecraft, which is currently in orbit around Mars, has been taking systematic measurements of the densities and deriving temperatures in the upper atmosphere of Mars between about 140 to 240 km above the surface since late 2014. Wind measurement campaigns are also conducted once per month for 5-10 orbits. These densities, temperatures and winds change with time (e.g. solar cycle, season, local time) and location, and sometimes fluctuate quickly. Global dust storm events are also known to significantly impact these density, temperature and wind fields in the Mars thermosphere. For the current project, the derived temperatures and O plus CO2 densities are used to characterize the upper atmosphere dayside thermal and density structure. Presently, more than 6 years of Neutral Gas and Ion Mass Spectrometer (NGIMS) measurements of neutral densities have been obtained by the MAVEN team (e.g. Mahaffy et al. 2015; Bougher et al 2015; Elrod et al., 2017; 2021; Stone et al. 2018; Gupta et al., 2021). Measured neutral density distributions are compared to simulations from a computer model of the Mars atmosphere called M-GITM (Mars Global Ionosphere-Thermosphere Model), developed at U. of Michigan. Since the global circulation plays a role in the structure, variability, and evolution of the atmosphere, understanding the processes that drive the winds in the upper atmosphere of Mars also provides the needed context for understanding density and temperature distributions and how the atmosphere behaves as a whole system. Three dimensional M-GITM simulations for extreme Mars seasonal and solar cycle conditions were conducted for detailed comparisons with NGIMS derived temperatures and O/CO2 ratio distributions (Bougher et al. 2022). Extracted model densities and temperatures along the MAVEN inbound trajectory of each orbit path (between ~300 km and periapsis) are provided in this Deep Blue Data archive. Corresponding M-GITM heat balance terms are also provided in vertical 1-D tabulated formats. README files are included for each suite of 1-D "flythru" tables, detailing the contents of each file. In addition, a general README file is provided that summarizes the inputs and outputs of the M-GITM code simulations for this study. Finally, a basic version of the M-GITM code can be found on Github at https:/github.com/dpawlows/MGITM.
- Keyword:
- Mars, NASA MAVEN Mission, NGIMS instrument , and M-GITM numerical simulations
- Citation to related publication:
- Bougher, S. W., Benna, M., Elrod, M., Roeten, K., & Thiemann, E. (2023). MAVEN/NGIMS dayside exospheric temperatures over solar cycle and seasons: Role of dayside thermal balances in regulating temperatures. Journal of Geophysical Research: Planets, 128, e2022JE007475. https://doi.org/10.1029/2022JE007475
- Discipline:
- Science
-
- Creator:
- George De la Rosa, Mery Vet, Patel, Dipali, McCann, Marc R., Stringer, Kathleen A., and Rosania, Gus R.
- Description:
- These data were produced from a study that employed a database strategy to identify candidate mitochondrial metabolites that could be clinically useful to identify individuals at increased risk of mitochondrial-related ADRs. The main candidate metabolite identified by the database strategy was evaluated using a mouse model of mitochondrial drug toxicity. These findings are described in our manuscript: Database Screening as a Strategy to Identify Endogenous Candidate Metabolites to Probe and Assess Mitochondrial Drug Toxicity. Data reported was supported by funding from the National Institute of General Medical Sciences (NIGMS) at the National Institutes of Health (NIH) under award numbers R01GM127787 (GRR) & R35GM136312 (KAS).
- Keyword:
- mitochondrial-realted metabolites, adverse drug reactions, and mitochondrial drug toxicity
- Discipline:
- Health Sciences
-
- Creator:
- Bacon, Elizabeth, Hanson, Erika N., Austin, Sarah, Delacroix, Emerson, Uhlmann, Wendy, Roberts, Scott, and Resnicow, Ken
- Description:
- Survey respondents were cancer-affected patients seen at an academic medical center, and self-reported experiences with genetic testing and counseling. This is raw dataset is saved in comma separated value (.csv) format.
- Keyword:
- Genetic Testing, Clinician Recommandation , NCCN Guidelines, Hereditary Genetic Testing, and Disparities in Genetic Counseling
- Citation to related publication:
- American Association of Kidney Patients: A List of Support Groups in Michigan. https://aakp.org/wp-content/uploads/2020/06/Support-Groups-Michigan.pdf
- Discipline:
- Science and Health Sciences
-
- Creator:
- Cuyler, Antonio, Carruthers, Matthew, and Imbesi, Jason
- Description:
- we conducted an emergent qualitative systematic content analysis of scholarship published in Cultural Trends, the International Journal of Cultural Policy, and the Journal of Arts Management, Law, and Society since the peer-reviewed journals’ inceptions.
- Keyword:
- content analysis, cultural policy, and oppression
- Discipline:
- Humanities and Arts
-
- Creator:
- Gonzales, Wilkinson Daniel Wong
- Description:
- The Lannang Corpus (LanCorp) is a sociolinguistic POS-tagged 375,000-word speech-and-text corpus of Lannang languages based on audio recordings collected in metropolitan Manila between 2016 and 2020. It hopes to furnish scholars interested in Sino-Philippine (socio)linguistics with a contemporary, multilingual corpus (i.e., Hokkien, Tagalog, English, Lánnang-uè, Mandarin) compiled using recorded oral data primarily collected from a Sino-Philippine community in metropolitan Manila by the community: the Manila Lannangs. The publicly available corpus contains manual transcriptions (time-aligned to the audio), source language and part-of-speech tags derived using a mix of manual and computational methods, and a wide range of social metadata; it is also organized and stored systematically for easy data retrieval and (socio)linguistic analysis. Although there are existing sociolinguistic corpora, they are small in scale and were not released publicly due to lack of informant consent – LanCorp readily fills the gap.
- Keyword:
- Lannang, Chinese Filipino, Filipino-Chinese, Hokkien, diaspora, mixed language, recordings, oral variety, multilingual, corpus, data, dataset, databank, LanCorp, Lannang Corpus, sociolinguistics, and ELAN
- Citation to related publication:
- [1] Gonzales, Wilkinson Daniel Wong. 2021. Interactions of Sinitic languages in the Philippines: Sinicization, Filipinization, and Sino-Philippine language creation. The Palgrave handbook of Chinese language studies, ed. by Zhengdao Ye. London: Palgrave-MacMillan., [2] Gonzales, Wilkinson Daniel Wong. 2021. Filipino, Chinese, neither, or both? The Lannang identity and its relationship with language. Language & Communication 77., [3] Gonzales, Wilkinson Daniel Wong. 2022. “Truly a Language of Our Own” A Corpus-Based, Experimental, and Variationist Account of Lánnang-uè in Manila. Ann Arbor: University of Michigan Ph.D. dissertation., [4] Gonzales, Wilkinson Daniel Wong. 2022. Hybridization. Philippine English: Development, Structure, and Sociology of English in the Philippines, ed. by Ariane Macalinga Borlongan. London: Routledge., and [5] Gonzales, Wilkinson Daniel Wong. in preparation. Advancing Sino-Philippine (socio)linguistics using the Lannang Corpus (LanCorp) – a multilingual, POS-tagged, and audio-textual databank.
- Discipline:
- Social Sciences
-
Transmission of Oral microbiome and Sequencing
User Collection
- Creator:
- Lee, Kyu Han
- Description:
- De-identified participant data from household transmission study of influenza in Nicaragua Oligotype count table and taxonomic classifications
- Keyword:
- Influenza and Microbiome
- Discipline:
- Health Sciences
2Works -
- Creator:
- Yan, Xiang (Jacob), Clarke, Phillipa J., Okullo, Dolorence, Goodspeed, Robert, Data Driven Detroit, Gomez-Lopez, Iris N., and Veinot, Tiffany C
- Description:
- This collection was produced as part of the project, “A ‘Big Data’ Approach to Understanding Neighborhood Effects in Chronic Illness Disparities.” The Investigators for the project are Tiffany Veinot, Veronica Berrocal, Phillipa Clarke, Robert Goodspeed, Daniel Romero, and VG Vinod Vydiswaran from the University of Michigan. The study took place from 2015-2016, with funding from the University of Michigan’s Social Sciences Annual Institute, MCubed, and the Sloan and Moore Foundations. Contact: Tiffany Veinot, MLS, PhD Office: 3443 North Quad Phone: 734/615-8281 Email: tveinot@umich.edu MCubed project page: https://mcubed.umich.edu/projects/%E2%80%9Cbig-data%E2%80%9D-approach-understanding-neighborhood-effects-chronic-illness-disparities
- Keyword:
- Food Environment, Health Status, Employment, Health Care Resources, Neighborhood Safety, Healthcare Utilization, Transportation, Census tract level, Information and Education Environment, Spatial Measures, Detroit, Active Living Resources, Social Environment, Demographics, Community Health, Housing, and student-friendly
- Discipline:
- Social Sciences
6Works -
- Creator:
- Hero, Alfred O, Zhai, Yaya, Burke, Thomas, Doraiswamy, Murali, Ginsburg, Geoffrey S, Henao, Ricardo, Turner, Ronald B, and Woods, Christopher W
- Description:
- The data deposited here is as follows: The clinical shedding/symptom data, RNAseq, steroid, and wearable E4 data was partially presented in publications [1]-[3] and the cognitive lumos and VAFS data is presented in the paper [4], which is under review and embargoed. The data files are: subject.json, sample.json, and genematrix_TPM.csv. In addition, a copy of the blank consent form used to enroll volunteers in the study is included (17964_Adult Consent_2015Mar17-Mod 1_clean.pdf)., Clinical symptom and viral shedding data (in subject.json): reports each subject's accumulated and maximum self-reported symptom score (modified Jackson score) and shedding titrations from nasal-pharyngeal washes after inoculation. , RNAseq data (genematrix_TMP.csv): Whole blood was collected in PAXgene™ Blood RNA tubes (PreAnalytiX), and total RNA extracted using the PAXgene™ Blood miRNA Kit (QIAGEN) using the manufacturer’s recommended protocol. RNA quantity and quality were assessed using Nanodrop 2000 spectrophotometer (Thermo-Fisher) and Bioanalyzer 2100 with RNA 6000 Nano Chips (Agilent). RNA sequencing libraries were prepared using Illumina TruSeq mRNA Library Kit with RiboZero Globin depletion, and sequenced on an Illumina NextSeq sequencer with 50bp paired-end reads (target 40M reads per sample). After demultiplexing to FASTQ paired-end read counts files, the 396 samples were TPM transformed using HISAT2 software with the reference genome Homo_sapiens.GRCh38.84. Each sample corresponds to one of the 18 subjects at one of 22 time points. One of these samples was of insufficient quality to be mapped to read counts. In addition to the TPM normalized RNAseq data contained in this repository, the raw FASTQ data for the 395 samples are deposited in the GEO repository ( https://www.ncbi.nlm.nih.gov/geo), Accession # GSE215087. , Cognitive data (sample.json): Outcomes from a NeuroCognitive Performance Test (NCPT) that was taken approximately 3 time daily by all volunteers. The NCPT is a repeatable, web-based, computerized, cognitive assessment platform designed to measure subtle changes in performance across multiple cognitive domains. Subject scores along 18 cognitive variables data were collected at approximated 22 time points during the challenge study. The data structure sample.json contains the raw cognitive data and the extracted 18 cognitive scores over time for each subject. , The Visual Analog Fatigue Scale (sample.json): the VAFS is a measure of cognitive fatigue that was measured approximately 3 times per day at the same time as the NCPT and blood draw. , Wearable device data (sample.json): participants wore an Empatica E4 device for the duration of the challenge study. Summarized features are provided for each subject that include sleep duration (mean and std), sleep offset (mean and std), and temperature (mean and std). , Steroid data was also collected and is included in the sample.json. This steroid data was collected from the whole blood samples and consists of cortisol, melatonin, and DHEAS. , and See README.txt for more specific details on the data structures contained in the sample.json, subject.json, and genematrix_TPM.csv files.
- Keyword:
- human challenge study and cognitive health and immunity
- Citation to related publication:
- X She, Y Zhai, R Henao, CW Woods, C Chiu, Geoffrey S. Ginsburg, Peter X.K. Song, AO. Hero, “Adaptive multi-channel event segmentation and feature extraction for monitoring health outcomes,” IEEE Transactions on Biomedical Engineering, vol. 68, no. 8, pp. 2377-2388, Aug. 2021, doi: 10.1109/TBME.2020.3038652. Available on arxiv:2008.09215 , Emilia Grzesiak, Brinnae Bent, Micah T. McClain, Christopher W. Woods, Ephraim L. Tsalik, Bradly P. Nicholson, Timothy Veldman, Thomas W. Burke, Zoe Gardener, Emma Bergstrom, Ronald B. Turner, Christopher Chiu, P. Murali Doraiswamy, Alfred Hero, Ricardo Henao, Geoffrey S. Ginsburg, Jessilyn Dunn Assessment of the Feasibility of Using Noninvasive Wearable Biometric Monitoring Sensors to Detect Influenza and the Common Cold Before Symptom Onset. JAMA Netw Open. 2021;4(9):e2128534. doi:10.1001/jamanetworkopen.2021.28534 , E Sabeti, S Oh, PX Song, A Hero. “A Pattern Dictionary Method for Anomaly Detection,” Entropy, vol 24, pp. 1095 Aug 2022. doi: 10.3390/e24081095, and Yaya Zhai, P. Murali Doraiswamy, Christopher W. Woods, Ronald B. Turner, Thomas W. Burke, Geoffrey S. Ginsburg, Alfred O. Hero, "Pre-exposure cognitive performance variability is associated with severity of respiratory infection," manuscript under review.
- Discipline:
- Health Sciences and Social Sciences
-
- Creator:
- Yu, Chi-Lin, Eggleston, Rachel, Zhang, Kehui, Nickerson, Nia, Sun, Xin, Marks, Rebecca A., Hu, Xiaosu, Brennan, Jonathan R. , Wellman, Henry M. , and Kovelman, Ioulia
- Description:
- The dataset includes 51 children (age range = 6-12 years) who listened to the first chapter of Alice’s Adventures in Wonderland during fNIRS neuroimaging. We also provide the text of the story with several word-by-word predictors motivated by research in Theory of Mind development and language. These annotated, naturalistic datasets can be used to replicate prior work and test new hypotheses about everyday social cognition and natural language comprehension in the developing brain.
- Keyword:
- neuroimaging, fNIRS, Children, Theory of Mind, Language, Naturalistic Neuroscience, and Story Listening
- Discipline:
- Science