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- Creator:
- University of Michigan, Division of Herpetology, Davis Rabosky, Alison R, Larson, Joanna G, Moore, Talia Y, and Curlis, John David
- Description:
- This dataset includes dorsal and ventral photographs of Neotropical snakes collected in the Peruvian Amazon. These data were collected to survey and examine the diversity in color pattern evolution in Neotropical snakes.
- Keyword:
- snake, color, serpentes, and Peru
- Citation to related publication:
- (work in progress, not yet submitted)
- Discipline:
- Science
-
- Creator:
- Davis Rabosky, Alison R. and Jantzi, Adrian
- Description:
- Video documentation of natural behavior in wild snakes is very rare, so film from opportunistic encounters of snake interactions is very valuable to scientific researchers. Our research team includes leading experts on this species of snake (the Western Groundsnake, Sonora semiannulata), so we worked with the observer to submit a formal description of the encounter to a peer-reviewed journal and make the information available to the broader research community.
- Keyword:
- Sonora semiannulata, ground snake, animal behavior, and male-male combat
- Citation to related publication:
- Jantzi A, CL Cox, AR Davis Rabosky, AT Holycross. 2021. SONORA SEMIANNULATA (Western Groundsnake). COMBAT. Herpetological Review 52(2): pg 434.
- Discipline:
- Science
-
- Creator:
- Davis Rabosky, Alison R., Moore, Talia Y., Sánchez-Paredes, Ciara M., Westeen, Erin P., Larson, Joanna G., Sealey, Briana A., and Balinski, Bailey A.
- Description:
- Animals in nature use diverse strategies to evade or deter their predators, including many vivid behavioural displays only qualitatively described from field encounters with natural predators or humans. Within venomous snake mimicry, stereotyped anti-predator displays are suggested to be a critical component of the warning signal given by toxic models and thus under strong selection for independent convergence in mimetic species. However, no studies have systematically quantified variation in snake anti-predator displays across taxonomically broad clades to test how these behaviours evolve across species within a phylogenetic comparative methods framework. Here we describe a new, high-throughput approach for collecting and scoring snake anti-predator displays in the field that demonstrates both low observer bias and infinite extension across any species. Then, we show our method's utility in quantitatively comparing the behaviour of 20 highly-divergent snake species from the Amazonian lowlands of Peru. We found that a simple experimental setup varying simulated predator cues was very successful in eliciting anti-predator displays across species and that high-speed videography captured a greater diversity of behavioural responses than described in the literature. We also found that although different display components evolve at different rates with complicated patterns of covariance, there is clear evidence of evolutionary convergence in anti-predator displays among distantly related elapid coral snakes and their colubrid mimics. We conclude that our approach significantly advances opportunity for future analyses of snake behaviour, kinematics, and the evolution of anti-predator signals more generally, especially macroevolutionary analyses across clades with similarly intractable behavioural diversity.
- Keyword:
- Batesian mimicry, phylogenetic comparative methods, signal evolution, aposematism, simulated predator cues, coral snakes, and Peruvian Amazon
- Citation to related publication:
- Alison R. Davis Rabosky, Talia Y. Moore, Ciara M. Sanchez-Paredes, Erin P. Westeen, Joanna G. Larson, Briana A. Sealey, Bailey A. Balinski (2020) Convergence and divergence in anti-predator displays: A novel approach to quantitative behavioural comparison in snakes. Biological Journal of the Linnean Society http://dx.doi.org/10.1093/biolinnean/blaa222
- Discipline:
- Science
-
- Creator:
- Lyons, Michael A, Malhotra, Rumaan, and Thompson, Cody W
- Description:
- Free-roaming domestic dogs (Canis lupus familiaris) pose major conservation and public health risks worldwide. To better understand the threat of domestic dogs to wildlife and people and add to the growing literature on free-roaming dog ecology, a study was conducted to estimate the dog population in Tulum, Mexico. A modified mark-recapture technique and program MARK were used to obtain dog population estimates along six different transects dividing the city.
- Keyword:
- Canis lupus familiaris, MARK, McMaster, parasite load, population estimation, zoonoses
- Discipline:
- Science
-
- Creator:
- Gliske, Stephen V and Stacey, William C
- Description:
- This data repository includes the quantitative features of high frequency, intracranial EEG along with all necessary scripts to reproduce the figures of the accompanying manuscript.
- Keyword:
- high frequency oscillation, HFO, high frequency activity, and epilepsy
- Citation to related publication:
- (under review)
- Discipline:
- Science, Engineering, and Health Sciences
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right astragalar [astragalus] body of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81827), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
-
- Creator:
- Xiantong Wang
- Description:
- Magnetospheric sawtooth oscillations are observed during strong and steady solar wind driving conditions. The simulation results of our global MHD model with embedded kinetic physics show that when the total magnetic flux carried by constant solar wind exceeds a threshold, sawtooth-like magnetospheric oscillations are generated. Different from previous works, this result is obtained without involving time-varying ionospheric outflow in the model. The oscillation period and amplitude agree well with observations. The simulated oscillations cover a wide range of local times, although the distribution of magnitude as a function of longitude is different from observations. Our comparative simulations using ideal or Hall MHD models do not produce global time-varying features, which suggests that kinetic reconnection physics in the magnetotail is a major contributing factor to sawtooth oscillations.
- Discipline:
- Science
-
- Creator:
- Ding, J, Moore, TY, and Gan, Z
- Description:
- Jerboas (Jaculus jaculus) are bipedal hopping rodents that frequently transition between gaits (running, hopping, and skipping) throughout their entire speed range. It has been hypothesized that these non-cursorial bipedal gait transitions are likely to enhance their maneuverability and predator evasion ability. However, it is difficult to use the underlying dynamics of these locomotion patterns to predict gait transitions due to the large number of degrees of freedom expressed by the animals. To this end, we used empirical jerboa kinematics and dynamics to develop a unified Spring Loaded Inverted Pendulum model with defined passive swing leg motions. The simulated trajectories from the model precisely matched the experimental data. Jerboas were observed to apply different neutral swing leg angles during locomotion. By investigating the gait structure of the model with coupled and uncoupled neutral swing leg, we found two set of mechanism may explain the frequent gait transitions of jerboas.
- Keyword:
- jerboa, legged locomotion, gait transition, Legged Robots, Dynamics, Bipedal locomotion, and Non-cursorial locomotion
- Citation to related publication:
- Ding, Moore, Gan (submitted) A template model explains jerboa gait transitions across a broad range of speeds. Frontiers in Bioengineering And Biotechnology
- Discipline:
- Science and Engineering
-
- Creator:
- Al Shidi, Q. and Pulkkinen, T.
- Description:
- Provided are the resultant and processed data.
- Keyword:
- space physics, ground magnetometers, magnetosphere, numerical space physics, solar wind, numerical space physics, and ionosphere
- Discipline:
- Science
-
- Creator:
- Iong, Daniel, Chen, Yang, Toth, Gabor, Zou, Shasha, Pulkkinen, Tuija I., Ren, Jiaen, Camporeale, Enrico, and Gombosi, Tamas I. I.
- Description:
- In this work, we trained gradient boosted trees using XGBoost to predict the SYM-H forecasting using different combinations of solar wind and interplanetary magnetic field (IMF) parameters. Data are in csv and Python pickle formats.
- Keyword:
- SYM-H forecasting
- Citation to related publication:
- Iong, D., Y. Chen, G. Toth, S. Zou, T. I. Pulkkinen, J. Ren, E. Camporeale, and T. I. Gombosi, New Findings from Explainable SYM-H Forecasting using Gradient Boosting Machines, Space Weather,11, accepted, 2022. https://doi.org/10.1002/essoar.10508063.3
- Discipline:
- Science
-
- Creator:
- Hodgins-Davis, Andrea, Duveau, Fabien, Walker, Elizabeth, and Wittkopp, Patricia J
- Description:
- Understanding how phenotypes evolve requires disentangling the effects of mutation generating new variation from the effects of selection filtering it. Tests for selection frequently assume that mutation introduces phenotypic variation symmetrically around the population mean, yet few studies have tested this assumption by deeply sampling the distributions of mutational effects for particular traits. Here, we examine distributions of mutational effects for gene expression in the budding yeast Saccharomyces cerevisiae by measuring the effects of thousands of point mutations introduced randomly throughout the genome. We find that the distributions of mutational effects differ for the ten genes surveyed and are inconsistent with normality. For example, all ten distributions of mutational effects included more mutations with large effects than expected for normally distributed phenotypes. In addition, some genes also showed asymmetries in their distribution of mutational effects, with new mutations more likely to increase than decrease the gene’s expression or vice versa. Neutral models of regulatory evolution that take these empirically determined distributions into account suggest that neutral processes may explain more expression variation within natural populations than currently appreciated.
- Keyword:
- gene expression, evolution, mutation, mutagenesis, regulatory evolution, YFP, reporter construct, yeast, TDH1, TDH2, TDH3, GPD1, OST1, PFY1, STM1, RNR1, and RNR2
- Citation to related publication:
- Hodgins-Davis, A., Duveau, F., Walker, E. A., & Wittkopp, P. J. (2019). Empirical measures of mutational effects define neutral models of regulatory evolution in Saccharomyces cerevisiae. BioRxiv, 551804. https://doi.org/10.1101/551804
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right distal tibia of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81821), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
-
- Creator:
- MacEachern, Mark P; Sun, Gordon H; Chen, Stephanie W; Wang, Jing
- Description:
- The dataset includes all citations considered for inclusion in the systematic review. The citations are accessible in Endnote (Clarivate), as well as through the primary citation export files from each database. The literature search strategies are included for reproducibility and transparency purposes. See the published methods for more information.
- Keyword:
- Tracheostomy, Decannulation, Spinal Cord Injury, Scoping Review, and Literature Searches
- Citation to related publication:
- Gordon H. Sun, Stephanie W. Chen, Mark P. MacEachern & Jing Wang (2020) Successful decannulation of patients with traumatic spinal cord injury: A scoping review, The Journal of Spinal Cord Medicine, DOI: 10.1080/10790268.2020.1832397
- Discipline:
- Health Sciences
-
- Creator:
- Wu, Ziyou, Brunton, Steven L, and Revzen, Shai
- Description:
- These codes were produced as part of the Army Research Office Multi-University Research Initiative ARO MURI W911NF-17-1-0306 "From Data-Driven Operator Theoretic Schemes to Prediction, Inference, and Control of Systems" The code can be run using the runAll.sh shell script (in Linux and OS-X); code should work similarly under windows.
- Keyword:
- DMD, dimensionality reduction, dynamical systems, and nonlinear dynamics
- Discipline:
- Engineering and Science
-
- Creator:
- Schöpke-Gonzalez, Angela M., Thomer, Andrea K., and Conway, Paul
- Description:
- This interview protocol was designed to investigate the research question: How do self-identified refugees in the receiving societies of Greece and Germany engage with information spaces to navigate identity during liminal and post-liminal portions of their refugee experiences?
- Keyword:
- information space, identity, liminality, and migration
- Citation to related publication:
- Schöpke-Gonzalez, A., Thomer, A., & Conway, P. (2020). Identity Navigation During Refugee Experiences: The International Journal of Information, Diversity, & Inclusion (IJIDI), 4(2), 36–67. https://doi.org/10.33137/ijidi.v4i2.33151
- Discipline:
- Social Sciences
-
- Creator:
- Huang, Cheng MI
- Description:
- A 2D planar representation of a generic laboratory-scale combustor is established to assess the capabilities of ROMs for representing realistic combustion flowfields. The purpose of this dataset is to provide a testbed to build reduced model for relevant challenging reacting flow problems using different methods. The dataset was generated under the Air Force Center of Excellence on Multi-Fidelity Modeling of Rocket Combustion Dynamics and the goal of the center is to advance the state-of-the-art in Reduced Order Models (ROMs) and enable efficient prediction of instabilities in liquid fueled rocket combustion systems., Instrument and/or Software specifications: - recommendation: Matlab and Tecplot, 1. Data_150000to159999.tar: the unsteady flow field data from time step 150000 to 159999 (time increment, dt, between each time step is 1E-7 sec). - Data_160000to169999.tar: the unsteady flow field data from time step 160000 to 169999 (time increment, dt, between each time step is 1E-7 sec). 2. Data_170000to179999.tar: the unsteady flow field data from time step 170000 to 179999 (time increment, dt, between each time step is 1E-7 sec). 3. grid.dat: the topology of the CFD mesh used to generate this data (can be directly loaded in Tecplot). 4. the file "sample_code.zip" contains the sample Matlab scripts to load and output the .dat files to help the researchers to get started. To run the script, the software Matlab is required and the researchers can simply run sampleIO.m script in Matlab to test the code. , and Detailed documentation of how the data is generated can be found in: https://afcoe.engin.umich.edu/benchmark-data
- Citation to related publication:
- Huang, C., Duraisamy, K., and Merkle, C.L., Investigations and Improvement of Robustness of Reduced-Order Models of Reacting Flow, AIAA Journal, 2019., Swischuk, R., Kramer, B., Huang, C., and Willcox, K., Learning Physics-Based Reduced-Order Models for a Single-Injector Combustion Process , AIAA Journal, 2020., and Harvazinski, M.E., Huang, C., Sankaran, V., Feldman, T.W., Anderson, W.E., Merkle, C.L., and Talley, D.G., Coupling between hydrodynamics, acoustics, and heat release in a self-excited unstable combustor, Physics of Fluids, 2015.
- Discipline:
- Engineering
-
- Creator:
- Smith, Joeseph P., Gronewold, Andrew D., Read, Laura, Crooks, James L., School for Environment and Sustainability, University of Michigan, Department of Civil and Environmental Engineering, University of Michigan, and Cooperative Institute for Great Lakes Research
- Description:
- Using the statistical programming package R ( https://cran.r-project.org/), and JAGS (Just Another Gibbs Sampler, http://mcmc-jags.sourceforge.net/), we processed multiple estimates of the Laurentian Great Lakes water balance components -- over-lake precipitation, evaporation, lateral tributary runoff, connecting channel flows, and diversions -- feeding them into prior distributions (using data from 1950 through 1979), and likelihood functions. The Bayesian Network is coded in the BUGS language. Water balance computations assume that monthly change in storage for a given lake is the difference between beginning of month water levels surrounding each month. For example, the change in storage for June 2015 is the difference between the beginning of month water level for July 2015 and that for June 2015., More details on the model can be found in the following summary report for the International Watersheds Initiative of the International Joint Commission, where the model was used to generate a new water balance historical record from 1950 through 2015: https://www.glerl.noaa.gov/pubs/fulltext/2018/20180021.pdf. Large Lake Statistical Water Balance Model (L2SWBM): https://www.glerl.noaa.gov/data/WaterBalanceModel/ , and This data set has a shorter timespan to accommodate a prior which uses data not used in the likelihood functions.
- Keyword:
- Water, Balance, Great Lakes, Laurentian, Machine, Learning, Lakes, Bayesian, and Network
- Citation to related publication:
- Smith, J., Gronewald, A. et al. Summary Report: Development of the Large Lake Statistical Water Balance Model for Constructing a New Historical Record of the Great Lakes Water Balance. Submitted to: The International Watersheds Initiative of the International Joint Commission. Accessible at https://www.glerl.noaa.gov/pubs/fulltext/2018/20180021.pdf, Large Lake Statistical Water Balance Model (L2SWBM). https://www.glerl.noaa.gov/data/WaterBalanceModel/, and Gronewold, A.D., Smith, J.P., Read, L. and Crooks, J.L., 2020. Reconciling the water balance of large lake systems. Advances in Water Resources, p.103505.
- Discipline:
- Science and Engineering
-
- Creator:
- Danforth, Shannon M.
- Description:
- This dataset includes three MATLAB data files for each subject: raw motion capture and force plate data, processed motion capture and force plate data, and sagittal-plane data segmented into individual trials labeled “nominal” or “tripped.” We include two example scripts for using the segmented trial data to tabulate trip recovery strategies across subjects and plot the sorted recovery strategies.
- Keyword:
- Trip recovery, Biomechanics, and Human locomotion
- Citation to related publication:
- S. M. Danforth, X. Liu, M. J. Ward, P.D. Holmes, and R. Vasudevan, "Predicting sagittal-plane swing hip kinematics in response to trips," IEEE Robotics and Automation Letters, 2022.
- Discipline:
- Engineering
-
- Creator:
- Budak, Ceren, Goel, Sharad, and Rao, Justin M
- Description:
- Our primary analysis is based on articles published in 2013 by the top thirteen US news outlets and two popular political blogs. To compile the set of articles published by these outlets, we first examined the complete web-browsing records for US-located users who installed the Bing Toolbar, an optional add-on application for the Internet Explorer web browser. For each of the fifteen news sites, we recorded all unique URLs that were visited by at least ten toolbar users, and we then crawled the news sites to obtain the full article title and text. This process resulted in a corpus of 803,146 articles published on the fifteen news sites over the course of a year, with each article annotated with its relative popularity. , Next, we built two binary classifiers using large-scale logistic regression. The first classifier—which we refer to as the news classifier —identifies “news” articles (i.e., articles that would typically appear in the front section of a traditional newspaper). The second classifier—the politics classifier —identifies political news from the subset of articles identified as news by the first classifier. 340,191 (42 percent) were classified as news. On the set of 340,191 news articles, 114,814 (34 percent) were classified as political. , Having identified approximately 115,000 political news articles, we next seek to categorize the articles by topic (e.g., gay rights, healthcare, etc.), and to quantify the political slant of the article. To do so, we turn to human judges recruited via Mechanical Turk to analyze the articles. For every day in 2013, we randomly selected two political articles, when available, from each of the 15 outlets we study, with sampling weights equal to the number of times the article was visited by our panel of toolbar users., Amazon Mechanical Turk Labeling task: To detect and control for possible preconceptions of an outlet’s ideological slant, workers, upon first entering the experiment, were randomly assigned to either a blinded or unblinded condition. In the blinded condition, workers were presented with only the article’s title and text, whereas in the unblinded condition, they were additionally shown the name of the outlet in which the article was published. Each article was then analyzed by two workers, one each from the sets of workers in the two conditions. For each article, each worker completed the following three tasks. First, they provided primary and secondary article classifications from a list of fifteen topics: (1) civil rights; (2) Democrat scandals; (3) drugs; (4) economy; (5) education; (6) elections; (7) environment; (8) gay rights; (9) gun-related crimes; (10) gun rights/regulation; (11) healthcare; (12) international news; (13) national security; (14) Republican scandals; and (15) other. , and Second, workers determined whether the article was descriptive news or opinion. Third, to measure ideological slant, workers were asked, “Is the article generally positive, neutral, or negative toward members of the Democratic Party?” and separately, “Is the article generally positive, neutral, or negative toward members of the Republican Party?” Choices for these last two questions were provided on a five-point scale: very positive, somewhat positive, neutral, somewhat negative, and very negative. To mitigate question-ordering effects, workers were initially randomly assigned to being asked either the Democratic or Republican party question first; the question order remained the same for any subsequent articles the worker rated. Finally, we assigned each article a partisanship score between –1 and 1, where a negative rating indicates that the article is net left-leaning and a positive rating indicates that it is net right-leaning. Specifically, for an article’s depiction of the Democratic Party, the five-point scale from very positive to very negative is encoded as –1, –0.5, 0, 0.5, 1. Analogously, for an article’s depiction of the Republican Party, the scale is encoded as 1, 0.5, 0, –.0.5, –1. The score for each article is defined as the average over these two ratings. Thus, an average score of –1, for example, indicates that the article is very positive toward Democrats and very negative toward Republicans. The result of this procedure is a large, representative sample of political news articles, with direct human judgments on partisanship and article topic.
- Keyword:
- news media, media bias, crowdsourcing, and machine learning
- Citation to related publication:
- https://academic.oup.com/poq/article-abstract/80/S1/250/2223443/?redirectedFrom=fulltext and Ceren Budak, Sharad Goel, Justin M. Rao, Fair and Balanced? Quantifying Media Bias through Crowdsourced Content Analysis, Public Opinion Quarterly, Volume 80, Issue S1, 2016, Pages 250–271, https://doi.org/10.1093/poq/nfw007
- Discipline:
- Social Sciences
-
- Creator:
- Anahita, Amiri Farahani
- Description:
- this dataset is the output of WRF-Chem model for several simulations.
- Keyword:
- Lake spray aerosol
- Citation to related publication:
- Amiri-Farahani, A., Olson, N. E., Neubauer, D., Roozitalab, B., Ault, A. P., & Steiner, A. L. (2021). Lake Spray Aerosol Emissions Alter Nitrogen Partitioning in the Great Lakes Region. Geophysical Research Letters, 48(12), e2021GL093727. https://doi.org/10.1029/2021GL093727
- Discipline:
- Science
-
- Creator:
- McSherry, Sean
- Description:
- This repository includes the analysis code and raw data for a paper titled "Nanophotonic control of thermal emission under extreme temperatures in air, " in Nature Nanotechnology (see citation). In our work, well defined structure-color effects guided the design of a nanostructure containing stratified layers of two oxides, magnesium oxide (MgO) and barium zirco-hafnate (BaZr0.5Hf0.5O3 or BZHO). The repeating layers were tuned in such a way to manipulate incident infrared wavelengths. The infrared is the spectral range in which heat (in the form of electromagnetic radiation) is emitted from objects. Therefore, the nanostructure serves as a way to alter the thermal emission spectrum of hot objects, controlling how much heat can flow. This can have significant impacts on a range of technologies, such as thermal photovoltaics (TPVs), which generate electricity from the infrared light emission of hot objects (compared to visible light emission from the sun in solar photovoltaics). We envision that our MgO/BZHO nanostructure can be paired with a thermal emitter in TPV systems to beneficially manipulate the flow of infrared light, leading to more efficient electricity production. To characterize the thermal stability of this structure, we had to characterize the thermal stability and optical performance at room temperature and at 1100 °C. This lead us to conduct several experiments using ellipsometry, TEM, EDS, and FTIR.
- Keyword:
- FTIR, Infrared, Photonic Crystal, MgO, Refractory , Ellipsometry, Spectroscopy, Superlattice, and Thermal Emission
- Citation to related publication:
- McSherry et al. Nature Nanotechnology (In Press). 2022
- Discipline:
- Engineering
-
- Creator:
- Baskar, Deepika and Gorodetsky, Alex
- Description:
- Studying the effect of wind on urban air mobility typically requires comprehensive fluid dynamics simulations in a realistic urban geometry. Motivated to enable wide-spread autonomous drone activity in urban centers, such studies have indeed been considered by several authors in the recent literature. However, the accessibility of these approaches to those with less fluid dynamics experience and/or without access to purpose built simulation tools has limited validation and application of the resulting path planning strategies. and The .dat files contain the flow variables for each of the 402240 points sampled from the region under study. For flow visualization purposes, the .dat files are readable using Tecplot Software.
- Keyword:
- UAM, Energy efficient path planning , CFD, and City of Boston
- Citation to related publication:
- Baskar, D., & Gorodetsky, A. (2020). A Simulated Wind-field Dataset for Testing Energy Efficient Path-Planning Algorithms for UAVs in Urban Environment. In AIAA AVIATION 2020 FORUM. American Institute of Aeronautics and Astronautics. https://doi.org/10.2514/6.2020-2920
- Discipline:
- Other and Engineering
-
- Creator:
- Dewaraja, Yuni K and Van, Benjamin J
- Description:
- This publication contains anonymized planar whole body images of two patients. Patient scans were taken at 4 different time points in the week following a therapeutic dose of Lu-177 DOTATATE. Both anterior and posterior views are provided. All images are in DICOM format.
- Keyword:
- Lu-177, Lutathera, Dosimetry, Radionuclide, and Planar
- Discipline:
- Health Sciences
-
- Creator:
- Dewaraja, Yuni, K and Van, Benjamin J
- Description:
- This publication contains the anonymized SPECT/CT scans of two patients. Patient scans were taken at 4 different time points in the week following a therapeutic dose of Lu-177 DOTATATE. Each of the scans contains 5 subfolders, 3 of which contain SPECT projection data used for reconstructing SPECT images, and 2 contain the linear attenuation coefficient maps for the CT scans that correspond to each patients SPECT projections. All images are in DICOM format.
- Keyword:
- Lu-177, Dosimetry, Radionuclide, SPECT, and CT
- Discipline:
- Health Sciences
-
Bounce-Averaged Quasi-Linear Diffusion Model Simulation Input/Output on Mars’ Crustal Magnetic Field
- Creator:
- Alexander Shane
- Description:
- To study the effect of whistler mode waves on the superthermal electron velocity space at Mars, a numerical model was built to solve the bounce-averaged quasi-linear diffusion equation on a crustal field. This dataset includes the input and output variables to this model for the simulations performed in Shane and Liemohn, 2022. The studies using this dataset were conducted by Alex Shane in the Climate and Space Sciences and Engineering Department at the University of Michigan. This research was supported by the National Aeronautics and Space Administration (NASA) Grant NNX16AQ04G to the University of Michigan and the Rackham Predoctoral Fellowship.
- Keyword:
- Mars, Electron, and Crustal Fields
- Citation to related publication:
- Shane, A. D., & Liemohn, M. W. (2022). Modeling wave-particle interactions with photoelectrons on the dayside crustal fields of Mars. Geophysical Research Letters, 49, e2021GL096941. https://doi.org/10.1029/2021GL096941
- Discipline:
- Science
-
- Creator:
- Payam Mirshams Shahshahani
- Description:
- The two R codes are related to the feasible balance region calculations for Figures 2, 3, and 4 in the paper. The MATLAB codes are related to the simulations of the recoverable initial quasi-static states, the results of which are shown in Figure 5 of the paper.
- Keyword:
- One-legged balance, Biomechanics, Hip Abductor, and Unipedal Stance
- Citation to related publication:
- Shahshahani, P. M., & Ashton-Miller, J. A. (2020). On the importance of the hip abductors during a clinical one legged balance test: A theoretical study. PLOS ONE, 15(11), e0242454. https://doi.org/10.1371/journal.pone.0242454
- Discipline:
- Health Sciences and Engineering
-
- Creator:
- Bustamante, Angela C., Opron, Kristopher, Ehlenbach, William J., Crane, Paul K., Keene, Dirk, Standiford, Theodore J., and Singer, Benjamin H.
- Description:
- This study was conducted to detect and analyze modules, or clusters of genes, associated with sepsis, using RNAseq data obtained from 12 participants who died of sepsis and 12 participants who died of non-infectious critical illness while hospitalized. This deposit contains the input data and parameters needed to reproduce the weighted gene co-expression network analysis (WGCNA) and gene enrichment analysis performed on this data. This analysis requires the R packages "WGCNA" version 1.68 and "DESeq2" version 1.22.2 available for download from bioconductor ( http://bioconductor.org). The external bioinformatics tool DAVID version 6.8 ( https://david.ncifcrf.gov/) was used as an additional gene enrichment analysis. Please see the supplemental methods document within this deposit and published research letter for more detailed information.
- Keyword:
- Sepsis, RNAseq, Transcriptomics, Human, and Brain
- Citation to related publication:
- Bustamante, A.C., Opron, K., Ehlenbach, W.J., Larson, E.B., Crane, P.K., Keene, C.D., Standiford, T.J., Singer, B.H., 2020. Transcriptomic Profiles of Sepsis in the Human Brain. Am J Respir Crit Care Med. https://doi.org/10.1164/rccm.201909-1713LE
- Discipline:
- Science
-
- Creator:
- Chatterjee, Tanmay, Knappik, Achim, Sandford, Erin, Tewari, Muneesh, Choi, Sung Won, Strong, William B., Thrush, Evan P., Oh, Kenneth J., Liu, Ning, Walter, Nils G., and Johnson-Buck, Alexander
- Description:
- The sensitive measurement of specific protein biomarkers is important for medical diagnostics and research. However, existing methods for quantifying proteins use antibody probes that cannot distinguish between specific and nonspecific binding, limiting their sensitivity and specificity. This work establishes a method for distinguishing between specific binding to the target protein and nonspecific binding to assay surfaces using single-molecule kinetic measurements with dynamically binding probes. This is significant because it permits extremely sensitive protein measurements without requiring a high-affinity detection antibody or any washing steps, enabling streamlined and sensitive quantification of proteins even when no pair of high-quality, tightly binding antibodies is available.
- Keyword:
- biomarker detection, single molecule fluorescence, kinetic fingerprinting, total internal reflection microscopy, and super resolution microscopy
- Citation to related publication:
- Chatterjee, T., et al. Direct kinetic fingerprinting and digital counting of single protein molecules. Proc Natl Acad Sci USA, In Press.
- Discipline:
- Science
-
- Creator:
- Zhang, Yan, Fujian Normal University, Yang, Ping, Fujian Normal University, Tong, Chuan, Fujian Normal University, Zhang, Xinyan, Chinese Academy of Sciences, Changchun, Liu, Xingtu, Chinese Academy of Sciences, Changchun, Zhang, Shaoqing, Chinese Academy of Sciences, Changchun, Meyers, Philip. University of Michigan, and Gao, Chuanyu , Chinese Academy of Sciences, Changchun
- Description:
- A high-resolution study of bulk properties in a peat sequence from the Xinjiang Altai Mountains of northwestern China, has allowed reconstruction of local variations in peat properties and peat C and N accumulation rates (CAR and NAR) during the Holocene. Analyses of peat bulk density, loss on ignition, and concentrations of TOC and TN and their elemental ratios and stable isotopic values suggest that changes in peat-forming vegetation types during different parts of this epoch are the major factors responsible for the variations of peat properties in this sequence.
- Keyword:
- peat properties, stable carbon and nitrogen isotopes, carbon and nitrogen accumulation rates, and Altai Mountains of northwestern China
- Citation to related publication:
- Zhang, Y., Yang, P., Gao, C., Tong, C., Zhang, X., Liu, X., Zhang, S., & Meyers, P. A. (2020). Peat Properties and Holocene Carbon and Nitrogen Accumulation Rates in a Peatland in the Xinjiang Altai Mountains, Northwestern China. Journal of Geophysical Research: Biogeosciences, 125(12), e2019JG005615. https://doi.org/10.1029/2019JG005615
- Discipline:
- Science
-
- Creator:
- Dulka, Eden A
- Description:
- This data is a subset of that originally produced as part of an effort to characterize GnRH neuron activity during prepubertal development in control and PNA mice and investigate the potential influences of sex and PNA treatment on this process (1). It was later used in (2) to further investigate the firing patterns of GnRH neurons in these categories of mice and determine how these patterns might differ based on age and treatment condition. The data files can be opened and examined using Wavemetric's Igor Pro software. Code used to further examine and visualize the data can be found at https://gitlab.com/um-mip/mc-project-code. This research was supported by National Institute of Health/Eunice Kennedy Shriver National Institute of Child Health and Human Development R01 HD34860 and P50 HD28934. (1) Dulka EA, Moenter SM. Prepubertal development of gonadotropin-releasing hormone (GnRH) neuron activity is altered by sex, age and prenatal androgen exposure. Endocrinology 2017; 158:3941-3953 (2) Penix JJ, DeFazio RA, Dulka EA, Schnell S, Moenter SM. Firing patterns of gonadotropin-releasing hormone (GnRH) neurons are sculpted by their biology. Pending.
- Keyword:
- action potential, Monte Carlo, polycystic ovary syndrome, puberty, and androgen
- Citation to related publication:
- Dulka EA, Moenter SM. Prepubertal development of gonadotropin-releasing hormone neuron activity is altered by sex, age and prenatal androgen exposure. Endocrinology 2017; 158:3943-3953. https://dx.doi.org/10.1210%2Fen.2017-00768 and Penix JJ, DeFazio RA, Dulka EA, Schnell S, Moenter SM. Firing patterns of gonadotropin-releasing hormone (GnRH) neurons are sculpted by their biology. Pending.
- Discipline:
- Health Sciences
-
- Creator:
- Arbic, B.K., Elipot, S., Menemenlis, D., and Shriver, J.F.
- Description:
- The datafiles and Matlab code files in this repository contain the information needed to produce the figures in the paper. We also include the code used to process the raw model output files into spectra.
- Citation to related publication:
- B.K. Arbic, S. Elipot, J.M. Brasch, D. Menemenlis, A.L. Ponte, J.F. Shriver, X. Yu, E.D. Zaron, M.H. Alford, M.C. Buijsman, R. Abernathey, D. Garcia, L. Guan, P.E. Martin, and A.D. Nelson (2022), Near-surface oceanic kinetic energy distributions from drifter observations and numerical models. In review.
- Discipline:
- Science
-
- Creator:
- Light, Charles X, Arbic, Brian K, Martin, Paige E, Brodeau, Laurent, Farrar, J Thomas, Griffies, Stephen M, Kirtman, Ben P, Laurindo, Lucas, Menemenlis, Dimitris, Molod, Andrea, Nelson, Arin D, Nyadjro, Ebenezer, O'Rourke, Amanda K, Shriver, Jay, Siqueira, Leo, Small, R Justin, and Strobach, Udi
- Description:
- The precipitation data itself is the output of the models/datasets that we analyze in our paper. Most of it is in .nc or .nc4 format, although we provide code to extract the data into time series .mat files. We used MATLAB to perform our analysis.
- Keyword:
- precipitation and power spectra
- Citation to related publication:
- Light, C.X., Arbic, B.K., Martin, P.E., Brodeau, L., Farrar, J.T., Griffies, S.M., Kirtman, B.P., Laurindo, L.C., Menemenlis, D., Molod, A., Nelson, A.D., Nyadjro, E., O'Rourke, A.K., Shriver, J.F., Siqueira, L., Small, R.J., Strobach, E. (2022). Effects of grid spacing on high-frequency precipitation variance in coupled high-resolution global ocean-atmosphere models. Climate Dynamics, https://doi.org/10.1007/s00382-022-06257-6
- Discipline:
- Science
-
- Creator:
- Townsend, Whitney A, MacEachern, Mark P, and Song, Jean
- Description:
- We conducted a search through BioMed Central's 54 medicine and public health journals that provide OPR documentation in order to identify systematic review papers published in 2017. For each article we determined if OPR data, reviewer and author comments, were accessible. If so, we assessed the search methodology and reporting quality of the search process with a grading rubric based on PRISMA and PRESS standards, and then mined peer reviewer comments for references to the search methodology.
- Keyword:
- Systematic Reviews, Peer Review, Open Peer Review, Methodology, Research Methods, and Reporting
- Discipline:
- Health Sciences
-
- Creator:
- Huffaker, Jordan S., Kummerfeld, Jonathan K., Lasecki, Walter S., and Ackerman, Mark S.
- Description:
- The following files include supplementary materials for our CHI 2020 paper "Crowdsourced Detection of Emotionally Manipulative Language". Namely, these materials include the dataset that was used in the evaluation. See the paper for more details.
- Keyword:
- Crowdsourcing, Media Manipulation, Rhetoric, and Emotion
- Citation to related publication:
- J.S. Huffaker, J.K. Kummerfeld, W.S. Lasecki, M.S. Ackerman. Crowdsourced Detection of Emotionally Manipulative Language. In Proceedings of the ACM Conference on Human Factors in Computing Systems (CHI 2020). Honolulu, HI. 2020.
- Discipline:
- Engineering
-
- Creator:
- Jiao, Zhenbang, Chen, Yang, and Manchester, Ward
- Description:
- GOES_flare_list: contains a list of more than 12,013 flare events. The list has 6 columns, flare classification, active region number, date, start time end time, emission peak time. SHARP_data.hdf5 files contain time series of 20 physical variables derived from the SDO/HMI SHARP data files. These data are saved at a 12 minute cadence and are used to train the LSTM model.
- Keyword:
- Solar Flare Prediction and Machine Learning
- Citation to related publication:
- Jiao, Z., Sun, H., Wang, X., Manchester, W., Gombosi, T., Hero, A., & Chen, Y. (2020). Solar Flare Intensity Prediction With Machine Learning Models. Space Weather, 18(7), e2020SW002440. https://doi.org/10.1029/2020SW002440 and Chen, Y., & Manchester, W. (2019). Data and Data products for machine learning applied to solar flares [Data set], University of Michigan - Deep Blue. https://doi.org/10.7302/qnsq-cs38
- Discipline:
- Engineering and Science
-
- Creator:
- BIRDS Lab U. Michigan
- Description:
- These data were produced for ARO W911NF-14-1-0573 "Morphologically Modulated Dynamics" and ARO MURI W911NF-17-1-0306 "From Data-Driven Operator Theoretic Schemes to Prediction, Inference, and Control of Systems" to explore the trade-offs between various oscillator coupling models in modeling multilegged locomotion. The data were also used extensively in examining multi-contact slipping, in the studying the influence of number of legs on otherwise identical locomotion patterns, and in the use of geometric mechanics models for multilegged locomotion. Folder and file names encode the meta-data, with names following an informative naming convention documented in the README.
- Keyword:
- phase, multilegged, robot, and locomotion
- Citation to related publication:
- Zhao, D. & Revzen, S. Multi-legged steering and slipping with low DoF hexapod robots Bioinspiration & biomimetics, 2020, 15, 045001 https://doi.org/10.1088/1748-3190/ab84c0 and Zhao, D. Ph.D. Thesis "Locomotion of low-DOF multi-legged robots" University of Michigan 2021 https://deepblue.lib.umich.edu/handle/2027.42/169985
- Discipline:
- Science and Engineering
-
- Creator:
- Foltynek, Tomas, Ruas, Terry, Scharpf, Philipp , Meuschke, Norman, Schubotz, Moritz , Grosky, William , and Gipp, Bela
- Description:
- This data set is comprised of multiple folders. The corpus folder contains raw text used for training and testing in two splits, "document" and "paragraph". The Spun documents and paragraphs are generated using the SpinBot tool ( https://spinbot.com/API). The paragraph split is generated by only selecting paragraphs with 3 or more sentences in the document split. Each folder is divided in mg (i.e., machine generated through SpinBot) and og (i.e., original generated file), The human judgement folder contains the human evaluation between original and spun documents (sample). It also contains the answers (keys) and survey results. , The models folder contains the machine learning classifier models for each word embedding technique used (only for document split training). The models were exported using pickle (Python 3.6). The grid search for hyperparameter adjustments is described in the paper. , and The vector folders (train and test) contains the average of all word vectors for each document and paragraph. Each line has the number of dimensions of the word embeddings technique used (see paper for more details) followed by its respective class (i.e, label mg or og). Each file belong to one class, either "mg" or "og". The values are comma-separated (.csv). The extension is .arff can be read as a normal .txt file.
- Keyword:
- paraphrase detection, plagiarism detection, document classification, and word embeddings
- Citation to related publication:
- Foltýnek, T. & Ruas, T. & Scharpf, P. & Meuschke, N. & Schubotz, M. & Grosky, W. & Gipp, B., “Detecting Machine-obfuscated Plagiarism,” in Sustainable Digital Communities, vol. 12051 LNCS, Springer, 2020, pp. 816–827. https://doi.org/10.1007/978-3-030-43687-2_68
- Discipline:
- General Information Sources
-
Geotechnical observations of weathered rock across a tectonic and climatic gradient in Central Nepal
- Creator:
- Medwedeff, William, G (University of Michigan Earth & Environmental Science), Clark, Marin, K (University of Michigan Earth & Environmental Science), Zekkos, Dimitrios (University of California, Berkeley), West, A., Joshua (University of Southern California), and Chamlagain, Deepak (Tribhuvan University, Kathmandu Nepal)
- Description:
- These datasets support the findings of Medwedeff et al. (2021) in JGR: Earth Surface. In this article, we present seismic and geotechnical characterizations of the shallow subsurface across a 200 km by 50 km swath of the central Himalayan Range, in Nepal. By pairing widely-distributed 1D shear wave velocity surveys and engineering outcrop descriptions per the Geological Strength Index classification system, we evaluate landscape-scale patterns in near-surface mechanical characteristics and their relation to environmental factors known to affect rock strength. We find that near-surface strength is more dependent on the degree of weathering, rather than the mineral and textural differences between the metamorphic lithologies found in the central Himalaya. Furthermore, weathering varies systematically with topography. Bedrock ridge top sites are highly weathered and have S-wave seismic velocities and shear strength characteristics that are more typical of engineering soils, whereas sites near the bedrock channel bottom tend to be less weathered and characterized by high S-wave velocities and shear strength estimates typical of hard rock. Weathering of bedrock on hillslopes is significantly more variable, resulting in S-wave velocities that range between the ridge and channel endmembers. We hypothesize variability in the hillslope environment may be partly explained by the stochastic nature of mass wasting, which clears away weathered material where landslide scars are recent. These results underscore the mechanical heterogeneity in the shallow subsurface and highlight the need to account for bedrock weathering when estimating strength parameters for regional landslide hazard analysis.
- Keyword:
- rock strength, critical zone, shallow seismic, and chemical weathering
- Discipline:
- Science
-
- Creator:
- Gorchov Negron, Alan M., Kort, Eric A., Conley, Stephen A., and Smith, Mackenzie L.
- Description:
- This data-set contains data used in the publication "Airborne Assessment of Methane Emissions from Offshore Platforms in the U.S. Gulf of Mexico" by Gorchov Negron et al. (2020). There are 46,032 rows and 45 columns in the data. and The aircraft sampled offshore facilities with two unique sampling strategies: facility-level samples and regional box samples. Gorchov Negron et al. used facility-level samples to calculate facility-level fluxes and regional box samples, in conjunction with vertical profiles, to calculate regional-level fluxes. Meteorological parameters in the data were evaluated to discern when assumptions for each method were met. The facility-level fluxes were used to generate a facility-level aerial measurement-based inventory that was scaled up for comparison with regional-level fluxes.
- Keyword:
- Methane Emissions, Offshore Oil and Gas Platforms, Airborne Measurements, Greenhouse Gas Mitigation, and Gulf of Mexico
- Citation to related publication:
- Alan M. Gorchov Negron, Eric A. Kort, Stephen A. Conley, Mackenzie L. Smith. "Airborne Assessment of Methane Emissions from Offshore Platforms in the U.S. Gulf of Mexico". Environ. Sci. Technol. 2020. http://dx.doi.org/10.1021/acs.est.0c00179
- Discipline:
- Science
-
- Creator:
- Yiwen, Mei
- Description:
- The datasets of this archive are produced for a research project on the development of an advanced hydrologic modeling system for the St. Lawrence river basin. The outputted datasets from model simulations are in Netcdf 4 format. The author recommend using the netCDF Operators (NCO) program for data processing. For visualization and plotting, the author recommend using software like MATLAB, Python or R.
- Keyword:
- Hydrologic modeling, reanalysis product, St. Lawrence river, water balance, WRF-Hydro
- Discipline:
- Science
-
- Creator:
- Dewaraja, Yuni K and Van, Benjamin J
- Description:
- This publication contains anonymized time integrated activity maps for two patients. SPECT/CT scans were taken at 4 different time points in the week following a therapeutic dose of Lu-177 DOTATATE and combined into a single activity map for each patient. All images are in DICOM format.
- Keyword:
- Lu-177, Dosimetry, Radionuclide, SPECT, and CT
- Discipline:
- Health Sciences
-
- Creator:
- McCuen, Brett A.
- Description:
- These data are TLA events identified in MACCS magnetometer data throughout 2015. These events are short-timescale (< 60 s), large -amplitude (> 6 nT/s) magnetic disturbances measured at Earth's surface that are analyzed for space weather research purposes. and The events were identified in a year's worth of magnetic field data using an algorithm developed in the MATLAB platform. The algorithm dBdt_main.m can be run using the associated scripts (clean_maccs.m, simple_dbdt.m, extremes1.m, newdbdt.m) to return the events in the 2015_AllEvents.csv file. The substorm onset delays of each event are determined with the onset_delays.m script and the substorm event list 20191127-15-56-substorms.csv (both included).
- Keyword:
- space weather impacts, geomagnetically induced currents, GIC, transient induced currents, transient large amplitude, dB/dt search algorithm, and TLA
- Citation to related publication:
- Engebretson, M. J., Pilipenko, V. A., Ahmed, L. Y., Posch, J. L., Steinmetz, E. S., Moldwin, M. B., … Vorobev, A. V. (2019). Nighttime Magnetic Perturbation Events Observed in Arctic Canada: 1. Survey and Statistical Analysis. Journal of Geophysical Research: Space Physics, 124(9), 7442–7458. https://doi.org/10.1029/2019JA026794
- Discipline:
- Science
-
- Creator:
- Li, Jieming, Zhang, Leyou, Johnson-Buck, Alexander, and Walter, Nils G.
- Description:
- Traces from single-molecule fluorescence microscopy (SMFM) experiments exhibit photophysical artifacts that typically necessitate human expert screening, which is time-consuming and introduces potential for user-dependent expectation bias. Here, we have used deep learning to develop a rapid, automatic SMFM trace selector, termed AutoSiM, that improves the sensitivity and specificity of an assay for a DNA point mutation based on single-molecule recognition through equilibrium Poisson sampling (SiMREPS). The improved performance of AutoSiM is based on accepting both more true positives and fewer false positives than the conventional approach of hidden Markov modeling (HMM) followed by thresholding. As a second application, the selector was used for automated screening of single-molecule Förster resonance energy transfer (smFRET) data to identify high-quality traces for further analysis, and achieves ~90% concordance with manual selection while requiring less processing time. AutoSiM can be adapted readily to novel datasets, requiring only modest Transfer Learning.
- Keyword:
- deep learning, single-molecule fluorescence, total internal reflection microscopy, SiMREPS, smFRET, and Forster resonance energy transfer
- Citation to related publication:
- Li, J., Zhang, L., Johnson-Buck, A., & Walter, N. G. (2020). Automatic classification and segmentation of single-molecule fluorescence time traces with deep learning. Nature Communications, 11(1), 5833. https://doi.org/10.1038/s41467-020-19673-1 and Hayward, S., Lund, P., Kang, Q., Johnson-Buck, A., Tewari, M., Walter, N. (2018). Single-molecule microscopy image data and analysis files for "Ultra-specific and Amplification-free Quantification of Mutant DNA by Single-molecule Kinetic Fingerprinting" [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/Z2CZ35DF
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right proximal metatarsal 1 of the Cantius trigonodus (University of Michigan Museum of Paleontology catalog number UMMP VP 81822), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
-
- Creator:
- MacEachern, Mark, DeLong, M. R. , Tandon, V. J., Bertrand, A. A. , Goldberg, M. , Salibian, A. , Pusic, A. L. , Festekjian, J. H. , and Wilkins, E. G.
- 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 1168 citations after duplicates were removed in Endnote X8.
- Keyword:
- Literature searches, Breast reconstruction, Mesh, and Systematic review
- Citation to related publication:
- DeLong MR, Tandon VJ, Bertrand AA, MacEachern M, Goldberg M, Salibian A, Pusic AL, Festekjian JH, Wilkins EG. Review of Outcomes in Prepectoral Prosthetic Breast Reconstruction with and without Surgical Mesh Assistance. Plast Reconstr Surg. 2021 Feb 1;147(2):305-315. doi: 10.1097/PRS.0000000000007586. PMID: 33177453.
- Discipline:
- Health Sciences
-
- Creator:
- Chun-Seok Cho, Jingyue Xi, Hyun Min Kang, and Jun Hee Lee
- Description:
- There are three experimental outputs from Seq-Scope. (1) High definition map coordinate identifier (HDMI) sequence, tile and spatial coordinate information from 1st-Seq, (2) HDMI sequence, coupled with cDNA sequence from 2nd-Seq, and (3) Histological image obtained from Hematoxylin and Eosin (H&E) staining of the tissue slice. (1) and (2) were uploaded to GEO ( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169706). (3) is deposited here. In addition, this deposit includes the processed RDS (single R object) data files.
- Keyword:
- Seq-Scope, scRNA-seq, and spatial transcriptomics
- Citation to related publication:
- Chun-Seok Cho, Jingyue Xi, Sung-Rye Park, Jer-En Hsu, Myungjin Kim, Goo Jun, Hyun-Min Kang, Jun Hee Lee “Seq-Scope: Submicrometer-resolution spatial transcriptomics for single cell and subcellular studies” (preprint) bioRxiv https://doi.org/10.1101/2021.01.25.427807 and Related data sets in NCBI’s Gene Expression Omnibus (GEO) repository: Cho C, Xi J, Si Y, Lee JH, Kang HM, Park S, Hsu J, Kim M, Jun G “Seq-Scope: Submicrometer-resolution spatial barcoding technology that enables microscopic examination of tissue transcriptome at single cell and subcellular levels” https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169706
- Discipline:
- Health Sciences
-
- Creator:
- Xian Li
- Description:
- Low-velocity accretionary wedges and sedimentary layers overlaying continental plates are widely observed in the subduction zones where historical large earthquakes have occurred. It was observed that rupture of the 2011 Mw 9.0 Tohoku-Oki earthquake propagated to the trench with large coseismic slip on the shallow fault, but what caused the huge shallow slip remains a prominent problem., Here we explore how the two low-velocity structures, accretionary wedge and sedimentary layer, affect the coseismic slip and near-fault ground motions during the 2011 Tohoku-Oki earthquake. Constrained by the observed seafloor deformation, we present a 2-D dynamic rupture model of the 2011 Tohoku-Oki earthquake with an accretionary wedge and a sedimentary layer. Compared to a homogeneous model with the same friction and stress parameters on the fault, we find that the co-existence of the accretionary wedge and sedimentary layer significantly enhances the shallow coseismic slip and amplifies ground accelerations near the accretionary wedge. We then investigate a plausible scenario of a smaller Tohoku-Oki earthquake when its rupture does not reach the accretionary wedge. The sedimentary layer slightly enhances the coseismic slip while the accretionary wedge has almost no influence for the smaller earthquake scenario, but both structures significantly amplify the ground accelerations on the overriding plate. , and By simulating a suite of earthquake scenarios, we suggest that the co-existence of an accretionary wedge and sedimentary layers tend to enhance coseismic slip, but the enhancement effect decreases as the up-dip limit of rupture zones terminates at a larger depth. The numerical simulations were solved using SEM2DPACK _2.3.8 ( http://www.sourceforge.net/projects/sem2d/), and simulation results were visualized by Matlab. This folder includes the input files to reproduce our simulation results and plot scripts.
- Keyword:
- 2011 Tohoku-Oki earthquake, Dynamic rupture simulation, Accretionary wedge, and Sedimentary layer
- Citation to related publication:
- Li, X., & Huang, Y. (2021). The enhancement of coseismic slip and ground motion due to the accretionary wedge and sedimentary layer in the 2011 Tohoku-Oki earthquake (world) [Preprint]. Earth and Space Science Open Archive. https://doi.org/10.1002/essoar.10506336.1
- Discipline:
- Science
-
- Creator:
- Yuan, Ye, Currie, William S., Sharp, Sean J. , Martina, Jason P. , and Elgersma, Kenneth J.
- Description:
- This archived dataset includes all of the input files that were used to run the model for all the runs in this set, including files containing model parameters and drivers. This dataset also includes all of the model output files from model runs in this set.
- Keyword:
- wetland, Great Lakes, greenhouse gas, climate change, and ecosystem model
- Citation to related publication:
- Yuan, Y., S. J. Sharp, J. P. Martina, K. J. Elgersma, and W. S. Currie. Sustained-flux global warming potential driven by nitrogen inflow and hydroperiod in a model of Great Lakes coastal wetlands. JGR Biogeosciences in review.
- Discipline:
- Science
-
- Creator:
- Benjamin Leffel
- Description:
- Time series dataset of adoption by year of climate action plans by 177 U.S. cities, 2010-2019, with links to plans included. This dataset is intended for use by researchers and practitioners investigating both individual climate action plans and time series patterns of adoption at the municipal level.
- Keyword:
- climate change, climate action plan, municipal, and Urban Sustainability Research Group
- Discipline:
- Social Sciences and Government, Politics and Law
-
Monthly water balance estimates for the Laurentian Great Lakes from 1950 to 2019 (v1.0) [Deprecated]
- Creator:
- Do, Hong X., Smith, Joeseph P., Fry, Lauren M., and Gronewold, Andrew D.
- Description:
- This data set contains a new estimate of monthly water balance components from 1950 to 2019 for the Laurentian Great Lakes, the largest freshwater system on Earth. The source code and inputs to derive the new estimates are also included in this dataset.
- Keyword:
- Great Lakes water levels, statistical inference, water balance, and data assimilation
- Citation to related publication:
- Do, H.X., Smith, J., Fry, L.M., and Gronewold, A.D., Seventy-year long record of monthly water balance estimates for Earth’s largest lake system (pending for submission) and Version Note: This dataset is deprecated and has been replaced by version 1.1, found at https://deepblue.lib.umich.edu/data/concern/data_sets/sb3978457
- Discipline:
- Science