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- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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
-
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:
- 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
-
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- 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:
- Kim, YoungJae, Marcano, Maria C., Kim, Sooyeon, and Becker, Udo
- Description:
- The main objective of this research is to integrate electrochemical and microscopic approaches to understand reaction mechanisms and pathways of the uranyl reduction and nucleation mediated by magnetite and ilmenite. and This experimental data reveal how natural iron minerals mediate redox reactions of redox sensitive elements. We measure electrochemical responses of dissolved uranyl ions (UO22+) to potentials in the presence of organic molecules. The atomic force microscopic (AFM) images show nucleation of reduced uranyl on ilmenite (FeTiO3) as a function of potential.
- Keyword:
- electrochemical AFM and uranium reduction
- Citation to related publication:
- Kim, Y., Marcano, M. C., Kim, S., & Becker, U. (2021). Reduction of uranyl and uranyl-organic complexes mediated by magnetite and ilmenite: A combined electrochemical AFM and DFT study. Geochimica et Cosmochimica Acta, 293, 127–141. https://doi.org/10.1016/j.gca.2020.10.016 and Walker S. M., Marcano M. C., Bender W. M. and Becker U. (2016) Imaging the reduction of chromium (VI) on magnetite surfaces using in situ electrochemical AFM. Chemical Geology 429, 60-74.
- Discipline:
- Science
-
- Creator:
- Hille, Madeline M., Clark, Marin K., Gronewold, Andrew D., West, A. Joshua, Zekkos, Dimitrios , and Chamlagain, Deepak
- Description:
- This dataset supports the findings of Hille et al. (2021, in review) in Geophysical Research Letters. In this article, we present a multivariate analysis of extreme storm events that occur during the Indian summer monsoon over the Himalayan Range in central Nepal. We resolve storm events at sub daily durations by merging NASA’s Global Precipitation Mission (GPM) Integrated Multi-satellitE Retrievals for GPM (IMERG) 30-minute, gridded 0.1x0.1-degree precipitation product with local rain gauges operated by the Nepal Department of Hydrology and Meteorology (DHM) and the International Centre for Integrated Mountain Development (ICIMOD). We quantify spatial variability in extreme rainfall by isolating storms over a specific intensity threshold and pairing a principal components analysis with a K-means clustering approach to group storms of similar characteristics. and We find that frequent and intense storms occur over the forefront of the central Himalayan range and coincide with a locus of monsoon-driven landslide density. This pattern agrees with observations of elevated annual precipitation volumes near the Himalayan physiographic transition from low to high relief (Bookhagen and Burbank, 2010), and is consistent with orographically-influenced rainfall over other mountain ranges (Marra et al., 2021). In addition to presenting novel methodology to quantifying storm variability, our results highlight the strong orographic effect on precipitation intensity and duration, as well as an association of shallow bedrock landsliding frequency with intense precipitation.
- Keyword:
- orographic rainfall, multivariate analysis, extreme rainfall events, and rainfall-triggered landslides
- Citation to related publication:
- Hille et al. (2021, in review). The orographic influence on storm variability, extreme rainfall characteristics and rainfall-triggered landsliding. Geophysical Research Letters. Forthcoming
- Discipline:
- Science
-
- Creator:
- Majeed, Tariq
- Description:
- We use our 1-D chemical diffusive model to quantify the physical processes necessary to interpret the day-side ionospheric measurements acquired with radio occultation techniques at the southern high-latitude region of Mars, where the crustal magnetic field is strong and near-vertical in orientation. To interpret the measured ionospheric structure at altitudes where plasma transport dominates, we find it is necessary to impose field-aligned vertical plasma drifts caused by the motion of neutral winds. The most interesting finding of this study is that both upward (between 110 m/s and 150 m/s) and downward (between -55 m/s and -120 m/s) drifts are required to maintain the topside Ne distribution comparable with the measured distribution. We also find that a fixed velocity boundary condition at the upper boundary with a sizeable upward ion velocity is needed to encounter any unexpected ion accumulation in the topside ionosphere to limit the Martian ion outflow. Given the complex nature of neutral dynamics and its relationship to plasma transport processes over magnetic anomalies, we consider that a simple model, such as we have developed, is still capable of yielding valuable insights relating to the neutral wind system at Mars.
- Keyword:
- Ionosphere of Mars
- Discipline:
- Science
-
- Creator:
- Vo, Thi and Glotzer, Sharon C.
- Description:
- The goal of this project is to develop a first principle driven approach for predicting the self-assembly behavior of entropically driven crystallization. We first developed a set of mean-field theoretical framework that captures the relevant energetic contributions to the assembly process and then evaluate relevant terms within our framework to determine the excess free energy of formation for each lattice (matlab/octave codes). We then validate theoretical predictions of relevant features like shape and bonding orbitals using standard MD simulations using HOOMD-Blue (simulation scripts). and This research was supported by the Office of the Undersecretary of Defense for Research and Engineering (OUSD(R&E)), Newton Award for Transformative Ideas during the COVID-19 Pandemic, Award number HQ00342010030.
- Keyword:
- Self-Assembly, Entropy, Thermodynamics, Simulations, and Theory
- Citation to related publication:
- Vo, T., & Glotzer, S. C. (2021). Microscopic Theory of Entropic Bonding for Colloidal Crystal Prediction. ArXiv:2107.02081 [Cond-Mat]. http://arxiv.org/abs/2107.02081
- Discipline:
- Science
-
- Creator:
- Bougher, S. W. (CLaSP Department, University of Michigan)
- 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 inert light species helium is used to trace the circulation patterns and constrain wind magnitudes throughout the Mars thermosphere. Presently, more than 6 years of Neutral Gas and Ion Mass Spectrometer (NGIMS) measurements of helium densities have been obtained by the MAVEN team (e.g. Elrod et al., 2017; 2021; Gupta et al., 2021). Measured helium 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 helium distributions and how the atmosphere behaves as a whole system. Three dimensional M-GITM simulations for the Mars four cardinal seasons (Ls = 0, 90, 180, 270, for Mars Year 33) were conducted for detailed comparisons with NGIMS helium and CO2 distributions (Gupta et al. 2021). The M-GITM datacubes used to extract these densities (plus winds) along the trajectory of each orbit path between 140 and 240 km, are provided in this Deep Blue Data archive. README files are also provided for each datacube, 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, MAVEN Spacecraft Mission, Mars Thermosphere, Helium Density Distributions, and Neutral Gas and Ion Mass Spectrometer (NGIMS)
- Citation to related publication:
- Gupta, N., N. V. Rao, S. W. Bougher, and M. K. Elrod, Latitudinal and Seasonal Asymmetries of the Helium Bulge in the Martian Upper Atmosphere J. Geophys. Res., 126, XXXX-XXXX. doi:10.1002/2021JEXXXXXX
- Discipline:
- Engineering and Science
-
- Creator:
- Yadav, Rajeev, Widom, Julia R, Chauvier, Adrien, and Walter, Nils G
- Description:
- These data were generated to study the conformational dynamic of fluoride riboswitch as an isolated RNA and in presence of RNA polymerase at different transcript lengths.
- Keyword:
- Fluoride riboswitch, smFRET, and conformational dynamics
- Citation to related publication:
- Yadav, R., Widom, J.R., Chauvier, A. et al. An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch. Nat Commun 13, 207 (2022). https://doi.org/10.1038/s41467-021-27827-y
- Discipline:
- Science
-
- Creator:
- Allen, David N, Vandermeer, John, Dick, Christopher W, Perfecto, Ivette, and Burnham, Robyn J
- Description:
- These data are in the standard ForestGEO format. Each of the three censuses has its own text file. Within that file each row represents a stem measured in that census. Species information can be found in the species file. The personnel responsible for this work can be found in the personnel file. See the readme file for more information.
- Keyword:
- Forest ecology, Oak-hickory forest, Mesophication, and Invasive species
- Citation to related publication:
- Allen, D, CW Dick, RJ Burnham, I Perfecto, and J Vandermeer. The Michigan Big Woods research plot at the Edwin S. George Reserve, Pinckney, MI, USA. Occasional Papers of the Museum of Zoology. In review.
- Discipline:
- Science
-
- Creator:
- Tye, Alexander R, Niemi, Nathan A, Safarov, Rafig T, Kadirov, Fakhraddin A, Babayev, Gulam R
- Description:
- The Eastern Greater Caucasus is a mountain belt in western Asia that formed as an accretionary prism above an active subduction zone. Because of the bedrock exposure in the range, it offers a unique opportunity to research deformation processes in accretionary prisms, which are ubiquitous above the Earth's many subduction zones but are typically submarine and difficult to investigate. The data presented here result from field geologic mapping in several swaths roughly perpendicular to the mountain range that together span the entire range across strike. The data serve will serve as the basis for inference of the deep structural architecture of the range and characterization of the styles of deformation present in the range.
- Keyword:
- structural geology, Greater Caucasus, tectonics, geologic mapping, and accretionary prism
- Citation to related publication:
- Tye, A. R., Niemi, N. A., Safarov, R. T., Kadirov, F. A., & Babayev, G. R. (2021). Sedimentary response to a collision orogeny recorded in detrital zircon provenance of Greater Caucasus foreland basin sediments. Basin Research, 33(2), 933–967. https://doi.org/10.1111/bre.12499
- Discipline:
- Science
-
- Creator:
- BIRDS Lab U. Michigan
- Description:
- This dataset contains the videos used for https://doi.org/10.7302/m05a-0d90 (the "raw" motion tracking dataset), and is intended to be unpacked into the same directory tree. The 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:
- BIRDS Lab U. Michigan. BIRDS Lab Multipod robot motion tracking data - RAW dataset [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/m05a-0d90, 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, and 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
- Discipline:
- Science and Engineering
-
- Creator:
- Saylor, Kate M., Arring, Noël M., Aduse-Poku, Livingstone, Jiagge, Evelyn, Walker, Eleanor, White-Perkins, Denise, Israel, Barbara, Hinebaugh, Analise, Harb, Rayya, DeWitt, Jillian, Molnar, Maxim, Wilson-Powers, Eliza, and Brush, Barbara L.
- Description:
- The search data supports a literature review project on Strategies to Increase Black Enrollment and Retention in Cancer Clinical Trials. This dataset includes the reproducible search strategies (txt file) and the exported results of all citations from all databases (txt, ris, and.nbib files). These searches and exported result files contain all citations originating from the database searches that were considered for inclusion.
- Keyword:
- African American, Cancer, Neoplasm, clinical trials, and Minority Recruitment
- Discipline:
- Health Sciences
-
- Creator:
- Attari, Ali
- Description:
- Please refer to the "README.txt" for more details., MATLAB R2018a (Mathworks, Natick, MA, USA) was used to process this data., and Excel (Microsoft Office) was used to store survey data on the comfort of both systems and also to provide absolute and relative intraobserver variablities for the DM device.
- Keyword:
- Digital Manometry
- Citation to related publication:
- Comparison of anorectal function measured using wearable digital manometry and a high resolution manometry system Attari A, Chey WD, Baker JR, Ashton-Miller JA (2020) Comparison of anorectal function measured using wearable digital manometry and a high resolution manometry system. PLOS ONE 15(9): e0228761. https://doi.org/10.1371/journal.pone.0228761
- Discipline:
- Engineering, Science, and Health Sciences
-
- Creator:
- Shane, Alexander
- Description:
- This data set was created with the purpose to study the electron pitch angle distributions on dayside closed crustal fields at Mars and to compare with theoretical predictions made by numerical modeling. Analyzing the plasma environment of the crustal fields was another point of study to determine if whistler waves can interact with high energy superthermal electrons.
- Keyword:
- Mars, superthermal electron, pitch angle distribution, and crustal magnetic field
- Discipline:
- Science
-
- Creator:
- Niemi, Nathan A. and Abbey, Alyssa L.
- Description:
- These data were produced in the scope of research into the timing, rate, and magnitude of extensional exhumation along the length of the Rio Grande Rift in Colorado and New Mexico. The low-temperature (apatite and zircon (U-Th)/He) thermochronometric ages presented in this data set are sensitive to near-surface temperatures (~80C and 180C, respectively) and record the progressive exhumation of the rock mass from which the samples were collected towards the Earth's surface. These thermochronometric ages, and the differences between them, provide insight into the absolute timing, exhumation rate and total magnitude of exhumation on the normal faults that bound the Rio Grande Rift. and The QTQt program mentioned (Version QTQt64R5.6.2a was used for the data presented in this deposit) is not openly available for download, but is described in the Gallagher 2012 publication referenced, and can be requested from its author. For more information on the request process and a user guide, see http://www.iearth.org.au/codes/QTQt/
- Keyword:
- thermochronology, helium dating, (U-Th)/He, Rio Grande Rift, New Mexico, Colorado, and extensional tectonics
- Citation to related publication:
- Abbey, A. L., & Niemi, N. A. (2020). Perspectives on Continental Rifting Processes From Spatiotemporal Patterns of Faulting and Magmatism in the Rio Grande Rift, USA. Tectonics, 39(1), e2019TC005635. https://doi.org/10.1029/2019TC005635
- Discipline:
- Science
-
- Creator:
- Hemphill, Libby
- Description:
- Social media data offer a rich resource for researchers interested in public health, labor economics, politics, social behaviors, and other topics. However, scale and anonymity mean that researchers often cannot directly get permission from users to collect and analyze their social media data. This article applies the basic ethical principle of respect for persons to consider individuals’ perceptions of acceptable uses of data. We compare individuals' perceptions of acceptable uses of other types of sensitive data, such as health records and individual identifiers, with their perceptions of acceptable uses of social media data. Our survey of 1018 people shows that individuals think of their social media data as moderately sensitive and agree that it should be protected. Respondents are generally okay with researchers using their data in social research but prefer that researchers clearly articulate benefits and seek explicit consent before conducting research. We argue that researchers must ensure that their research provides social benefits worthy of individual risks and that they must address those risks throughout the research process.
- Keyword:
- social media, data ethics, and data reuse
- Discipline:
- Social Sciences
-
- Creator:
- Malhotra, Garima and Ridley, Aaron
- Description:
- This research aims to understand the importance of lower thermospheric atomic oxygen on the upper thermosphere. O number densities between 95-100 km from WACCM-X are much closer to the observations from SABER instrument on TIMED satellite as compared to those from MSIS. We show in this study that the correction of the lower boundary atomic oxygen yields better agreement between GITM and GUVI O/N2 in the upper thermosphere .
- Keyword:
- Lower Thermosphere Atomic Oxygen, Thermospheric Dynamics, Thermospheric composition and mixing, Lower-Upper Thermosphere Vertical Coupling, GITM - WACCMX coupling, and Global Ionosphere Thermosphere Model
- Citation to related publication:
- Malhotra, G., Ridley, A. J., Marsh, D. R., Wu, C., Paxton, L. J., & Mlynczak, M. G. (2020). Impacts of Lower Thermospheric Atomic Oxygen on Thermospheric Dynamics and Composition Using the Global Ionosphere Thermosphere Model. Journal of Geophysical Research: Space Physics, e2020JA027877. https://doi.org/10.1029/2020JA027877
- Discipline:
- Science
-
Dataset: Models generated for the bioinformatic analysis of MPER/protein fusions binding to antibody
- Creator:
- Bylund, Tatsiana, Chuang, Gwo-Yu, Kwong, Peter, Lai, Yen-Ting, McIlwain, Benjamin, and Stockbridge, Randy B.
- Description:
- This project evaluated the binding of antibody fragments to membrane proteins fused to a short epitope sequence (“MPER”). This dataset includes atomic coordinates (.pdb files) for bioinformatic models of antibody fragment binding to an MPER epitope – membrane protein fusion.
- Keyword:
- MPER, cryo-EM fiducial, crystallography chaperone, and small membrane protein
- Citation to related publication:
- McIlwain, B. C., Erwin, A. L., Davis, A. R., Ben Koff, B., Chang, L., Bylund, T., Chuang, G.-Y., Kwong, P. D., Ohi, M. D., Lai, Y.-T., & Stockbridge, R. B. (2021). N-terminal Transmembrane-Helix Epitope Tag for X-ray Crystallography and Electron Microscopy of Small Membrane Proteins. Journal of Molecular Biology, 166909. https://doi.org/10.1016/j.jmb.2021.166909
- Discipline:
- Science
-
- Creator:
- MacEachern, M. P. , Woolen, S. A., Shankar, P. R., Gagnier, J. J., Singer, L., and Davenport, M. S.
- Description:
- The intent of the project 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 2700 citations after duplicates were removed in Endnote X8.
- Keyword:
- Systematic review, Meta-analysis, Radiology, Gadolinium, Chronic kidney disease, and Literature searches
- Citation to related publication:
- Woolen, S. A., Shankar, P. R., Gagnier, J. J., MacEachern, M. P., Singer, L., & Davenport, M. S. (2020). Risk of Nephrogenic Systemic Fibrosis in Patients With Stage 4 or 5 Chronic Kidney Disease Receiving a Group II Gadolinium-Based Contrast Agent: A Systematic Review and Meta-analysis. JAMA internal medicine, 180(2), 223–230. https://doi.org/10.1001/jamainternmed.2019.5284
- Discipline:
- Health Sciences
-
- Creator:
- Agnit Mukhopadhyay
- Description:
- - A semi-physical global modeling approach is used to estimate diffuse & discrete sources of auroral precipitation during the Galaxy15 event. - Diffuse sources contribute 74% of the total auroral power. Discrete sources are strongly driven by activity and can contribute up to 61%. - Broadband precipitation contributes 31% of the auroral Pedersen conductance playing a significant role in ionospheric electrodynamics.
- Discipline:
- Science and Engineering
-
- 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 of Multipod robots with 6,8,10 and 12 legs. The data is stored in .csv.gz files, one file for each robot morphology. Details of how to run the processing code on the raw dataset to generate the processed files found here, as well as example code for loading the data found here, are in the README. This dataset is self contained and can be used on its own without running any of the provided code.
- 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, 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, and BIRDS Lab Multipod robot motion tracking data - RAW data, doi:10.7302/m05a-0d90
- Discipline:
- Engineering and Science
-
- Creator:
- Sean Sharp
- Description:
- Coastal wetlands intercept significant amounts of nitrogen (N) from watersheds, especially when surrounding land cover is dominated by agriculture and urban development. Through plant uptake, soil immobilization, and denitrification wetlands can remove excess N from flow through water sources and mitigate eutrophication of connected aquatic ecosystems. Excess N can also change plant community composition in wetlands, including communities threatened by invasive species. Understanding how variable hydrology and N loading impact wetland N removal and community composition can help attain desired management outcomes, including optimizing N removal and/or preventing invasion by non-natives. By using a dynamic, process-based ecosystem simulation model, we are able to simulate various levels of hydrology and N loading that would otherwise be difficult to manipulate. We investigate the effects of hydroperiod, hydrologic residence time, N loading, and the NH4+:NO3- ratio on both N removal and the invasion success of two non-native species (Typha x glauca or Phragmites australis) in temperate freshwater coastal wetlands using Mondrian, a process-based, wetland ecosystem simulation model. We found that when residence time increased, annual N removal increased up to 10-fold while longer hydroperiods also increased N removal, but only when residence time was >10 days and N loading was >30 g N m-2 y-1. N removal efficiency also increased with increasing residence time and hydroperiod, but was less affected by N loading. However, longer hydrologic residence time increased vulnerability of wetlands to invasion by both invasive plants at low to medium N loading rates where native communities are typically more resistant to invasion. This suggests a potential tradeoff between ecosystem services related to nitrogen removal and wetland invasibility. These results help elucidate complex interactions of community composition, N loading and hydrology on N removal, helping managers to prioritize N removal when N loading is high or controlling plant invasion in more vulnerable wetlands.
- Keyword:
- Mondrian, Simulation model, Coastal wetlands, Invasive species, and Ecosystem modeling
- Citation to related publication:
- Currie, W. S., Goldberg, D. E., Martina, J., Wildova, R., Farrer, E., & Elgersma, K. J. (2014). Emergence of nutrient-cycling feedbacks related to plant size and invasion success in a wetland community–ecosystem model. Ecological Modelling, 282, 69–82. https://doi.org/10.1016/j.ecolmodel.2014.01.010
- Discipline:
- Science
-
- Creator:
- Saylor, Kate M., Sirihorachai, Rattima , and Manojlovich, Milisa
- Description:
- The search data supports a literature review project on counting interventions to reduce the incidence of retained surgical instruments. The data included in the dataset are the reproducible search strategies (txt file) and the exported results of all citations from all databases (txt, ris, and.nbib files). These searches and exported result files contain all citations originating from the database searches that were considered for inclusion.
- Keyword:
- literature search , retained surgical instruments, counting, and nursing
- Discipline:
- Health Sciences
-
- Creator:
- Regoli, Leonardo H.
- Description:
- The research analyzed the response of nine PNI RM3100 magnetometers to radiation doses expected during a Europa lander mission. The radiation levels are drawn from the Europa Lander Science Definition Team report ( https://europa.nasa.gov/resources/58/europa-lander-study-2016-report). The sensors were tested up to a total ionization dose (TID) level of 500 kRad.
- Keyword:
- Magnetometer, Magneto-inductive, Europa, and Radiation
- Citation to related publication:
- Regoli, L. H., Moldwin, M. B., Raines, C., Nordheim, T. A., Miller, C. A., Carts, M., and Pozzi, S. A.: Radiation tolerance of the PNI RM3100 magnetometer for a Europa lander mission, Geosci. Instrum. Method. Data Syst., 9, 499–507, https://doi.org/10.5194/gi-9-499-2020, 2020.
- Discipline:
- Science and Engineering
-
- Creator:
- Lori, Jody r, Moyer, Cheryl A, Perosky, Joseph E, and University of Michigan, School of Nursing
- Description:
- This study used a convergent parallel mixed methods design that included qualitative data in the form of focus group discussions (FGDs), individual interviews, quantitative data retrieved from logbook reviews, and geo-location data collected through geographic information systems (GIS). Focus group discussions were conducted with community members, including chiefs, community leaders, women of reproductive age, traditional birth attendants (TBAs), women currently staying at a MWH, and male partners. Individual interviews were conducted with healthcare providers (midwives, registered nurses, and officers in charge) providing services at the rural primary healthcare facilities associated with a MWH. Logbook registries at rural health facilities with a MWH were reviewed to capture MWH usage. Additionally, each MWH was geo-located for purposes of geo-visualization.
- Keyword:
- Maternity Waiting Homes and Liberia
- Citation to related publication:
- James, K.H., Perosky, J.E., McLean, K. et al. Protocol for geolocating rural villages of women in Liberia utilizing a maternity waiting home. BMC Res Notes 12, 196 (2019). https://doi.org/10.1186/s13104-019-4224-1 and Coley, KM, Perosky, JE, Nyanplu, A, et al. Acceptability and feasibility of insect consumption among pregnant women in Liberia. Matern Child Nutr. 2020; 16:e12990. https://doi.org/10.1111/mcn.12990
- Discipline:
- International Studies
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset is composed of eight flat-mounted (dissected and fixed) retinae from juvenile and adult zebrafish. Rows of UV cones have been traced in each retina; additionally, we have identified locations of Y-junctions (row insertions). Also included is MATLAB code for calculating which Y-junctions belong to grain boundaries. Please see the readme file for a description of included codes and image files.
- Keyword:
- zebrafish cone mosaic, topological defects, tissue patterning, and grain boundaries
- Citation to related publication:
- Nunley, H., Nagashima, M., Martin, K., Gonzalez, A. L., Suzuki, S. C., Norton, D. A., Wong, R. O. L., Raymond, P. A., & Lubensky, D. K. (2020). Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation. PLOS Computational Biology, 16(12), e1008437. https://doi.org/10.1371/journal.pcbi.1008437 and Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679
- Discipline:
- Science
-
- Creator:
- Saylor, Kate M., Hicks, Patrice M., Kang, Linda, Stagg, Brian C., Newman-Casey, Paula-Anne, and Woodward, Maria A.
- Description:
- The search data supports a scoping literature review project on Loss to follow-up barriers in care for Cornea Ulcers and Glaucoma. 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:
- Cornea, Glaucoma, Loss to follow, and ophthalmology
- Discipline:
- Health Sciences
-
- Creator:
- Liu, Meichen
- Description:
- The Brune source model is widely used in studies of complex earthquakes with multiple episodes of high moment release (i.e., multiple subevents). In this study, we investigate how corner frequency estimates of earthquakes with multiple subevents are biased if they are based on the Brune source model. By assuming complex sources as a sum of multiple Brune sources, we analyze 1,640 source time functions (STFs) of Mw 5.5-8.0 earthquakes in the SCARDEC catalog to estimate the corner frequencies, onset times, and seismic moments of subevents. We identify more subevents for strike-slip earthquakes than dip-slip earthquakes, and the number of resolvable subevents increases with magnitude. We find that earthquake corner frequency correlates best with the corner frequency of the subevent with the highest moment release (i.e., the largest subevent). This suggests that, when the Brune model is used, the estimated corner frequency and therefore the stress drop of a complex earthquake is determined primarily by the largest subevent rather than the total rupture area. and Our results imply that the stress variation of asperities, rather than the average stress change of the whole fault, contributes to the large variance of stress drop estimates.
- Citation to related publication:
- Meichen Liu, Yihe Huang, Jeroen Ritsema. 2021. Characterizing Multi-Subevent Earthquakes Using the Brune Source Model [Preprint]. https://essoar.org (2021) DOI: doi.org/10.1002/essoar.10507564.1
- Discipline:
- Science
-
- Creator:
- Jeffrey Heath
- Description:
- fieldwork in Bonosso village, Côte d’Ivoire, chiefly 2016-19. See "readme" file for description of the materials.
- Keyword:
- Pere language
- Citation to related publication:
- Heath, Jeffrey, & Tioté, Brahima. (2019). A grammar of Pere (Bere, Mbre) of Côte d'Ivoire. Zenodo. http://doi.org/10.5281/zenodo.3346581
- Discipline:
- Humanities
-
- Creator:
- Boyle, Kyle, University of Michigan Transportation Research Institute and Hu, Jingwen, University of Michigan Transportation Research Institute
- Description:
- This set of Madymo models were setup with a convertible seat and the HIII 3YO child ATD model. Both FMVSS 213 and captain chair were simulated with varied vehicle interior (sedan vs. minivan) and car seat installation methods (LATCH vs. 3pt belt). Although the models provided here only represent the frontal crash condition, simulations with a wide range of impact directions can be simulated.
- Keyword:
- Occupant protection, Child passenger safety, and Child seat model
- Discipline:
- Engineering
-
An analysis of recorded and simulated SH wave reverberations in the upper mantle beneath the USArray
- Creator:
- Meichen Liu
- Description:
- We use waveform data from the USArray and spectral-element method synthetics for 3-D seismic models. The recorded waveform data are downloaded from Incorporated Research Institutions for Seismology (IRIS) which is open to everyone. The synthetic waveform data are generated by the SPECMFEM3D_Globe software that was downloaded from the Computational Infrastructure for Geodynamics ( https://geodynamics.org/). This dataset includes the scripts we use to automatically download data from IRIS, the selection of data, and the application of the CRP method. In doing this, we use the TauP toolkit which is free to download ( https://www.seis.sc.edu/taup/) to compute the travel time.
- Keyword:
- seismology
- Discipline:
- Science
-
- Creator:
- Crisp, Dakota N., Parent, Rachel, Nakatani, Mitsuyoshi, Murphy, Geoffrey G. , and Stacey, William C.
- Description:
- This data and scripts are meant to test and show that seizure onset dynamics can be modulated using anti-epileptic drugs. A zip file is included that contains all waveform data, MATLAB processing scripts, and metadata. The MATLAB scripts allow for visual review validation and objective feature analysis. The file includes various README files explaining the scripts and their relationships in greater detail.
- Keyword:
- Bifurcation, Epilepsy, Seizure, and Electrophysiology
- Discipline:
- Health Sciences, Engineering, and Science
-
- Creator:
- Nikolov, Denislav P, Srivastava, Siddhartha, Abeid, Bachir A, Scheven, Ulrich M, Arruda, Ellen M, Garikipati, Krishna, and Estrada, Jonathan B
- Description:
- Contemporary material characterisation techniques that leverage deformation fields and the weak form of the equilibrium equations face challenges in the numerical solution procedure of the inverse characterisation problem. As material models and descriptions differ, so too must the approaches for identifying parameters and their corresponding mechanisms. The widely-used Ogden material model can be comprised of a chosen number of terms of the same mathematical form, which presents challenges of parsimonious representation, interpretability, and stability. Robust techniques for system identification of any material model are important to assess and improve experimental design, in addition to their centrality to forward computations. Using fully 3D displacement fields acquired in silicone elastomers with our recently-developed magnetic resonance cartography (MR-u) technique on the order of ~20,000 points per sample, we leverage PDE-constrained optimisation as the basis of variational system identification of our material parameters. We incorporate the statistical F-test to maintain parsimony of representation. Using a new, local deformation decomposition locally into mixtures of biaxial and uniaxial tensile states, we evaluate experiments based on an analytical sensitivity metric, and discuss the implications for experimental design. This repository contains the acquired data and MRI processing code used in this work.
- Keyword:
- continuum mechanics, magnetic resonance, sensitivity, full-field deformations, physics inference, mechanics, mechanical engineering, and computational mechanics
- Citation to related publication:
- https://doi.org/10.48550/arXiv.2204.03122
- Discipline:
- Engineering
-
- Creator:
- Hinz, Isaac and Johnson, Jena
- Description:
- Laboratory experiments were conducted to compare iron precipitation under completely ferruginous conditions with solutions that contain a low amount of oxidized iron, which can be seen as a proxy for iron oxidation in the environment. and Some XRD files are from a copper source (Cu_XRD) and others are from a cobalt source (Co_XRD).
- Keyword:
- Iron silicates, Greenalite, and Archean
- Citation to related publication:
- Isaac L. Hinz, Christine Nims, Samantha Theuer, Alexis S. Templeton, Jena E. Johnson; Ferric iron triggers greenalite formation in simulated Archean seawater. Geology 2021; doi: https://doi.org/10.1130/G48495.1
- 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. All the data is provided in a single, large .csv.gz file (416256 rows); additional details and example code in the README
- Keyword:
- robot, multilegged, and steering
- Citation to related publication:
- BIRDS Lab, U. BigAnt v6 robot motion tracking data - RAW dataset [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/024q-kk06, Revzen, S., & Guckenheimer, J. (2008). Estimating the phase of synchronized oscillators. Phys. Rev. E, 78, 051907. http://dx.doi.org/10.1103/PhysRevE.78.051907, and Dan Zhao and Shai Revzen 2020 Bioinspir. Biomim. 15 045001 https://doi.org/10.1088/1748-3190/ab84c0
- Discipline:
- Engineering
-
- Creator:
- Lamb, Abigail M.
- Description:
- This Work contains Supplemental File S3-1, Supplemental File S3-2, Supplemental Table S4-1, Supplemental Table S4-2, and Supplemental Table S4-3 from the dissertation entitled "Genetic Determinants of the Development and Evolution of Drosophila Pigmentation" by Abigail M. Lamb. Supplemental File S3-1 is entitled "Raw data measuring CHC abundance" and contains the measurements of cuticular hydrocarbons used for analysis in Chapter 3 of the dissertation. These data are meant to be read into the R code contained in Supplemental File S3-2, "R code used for analyzing CHC data" to reproduce the results reported in Chapter 3 of the dissertation. Supplemental Tables S4-1, S4-2, and S4-3 contain original phenotyping data, notes, and summary data from the miRNA overexpression and competitive inhibition experiments described in Chapter 4 of the dissertation.
- Citation to related publication:
- Lamb, A. M., Wang, Z., Simmer, P., Chung, H., & Wittkopp, P. J. (2020). Ebony Affects Pigmentation Divergence and Cuticular Hydrocarbons in Drosophila americana and D. novamexicana. Frontiers in Ecology and Evolution, 8. https://doi.org/10.3389/fevo.2020.00184
- Discipline:
- Science
-
- Creator:
- Zhou, Hongyang
- Description:
- The largest moon in the solar system, Ganymede, is the only moon known to possess a strong intrinsic magnetic field and a corresponding magnetosphere. Using the latest version of Space Weather Modeling Framework (SWMF), we study the upstream plasma interactions and dynamics in this sub-Alfvenic system. Results from the Hall MHD and the coupled MHD with embedded Particle-in-Cell (MHD-EPIC) models are compared. We find that under steady upstream conditions, magnetopause reconnection occurs in a non-steady manner. Flux ropes of Ganymede's radius in length form on the magnetopause at a rate about 2/minute and create spatiotemporal variations in plasma and field properties. Upon reaching proper grid resolutions, the MHD-EPIC model can resolve both electron and ion kinetics at the magnetopause and show localized non-gyrotropic behavior inside the diffusion region. The estimated global reconnection rate from the models is about 80 kV with 60% efficiency, and there is weak evidence of about 1 minute periodicity in the temporal variations due to the dynamic reconnection process.
- Keyword:
- MHD, PIC, Ganymede, and magnetosphere
- Citation to related publication:
- Zhou, H., Tóth, G., Jia, X., & Chen, Y. (2020). Reconnection-Driven Dynamics at Ganymede’s Upstream Magnetosphere: 3-D Global Hall MHD and MHD-EPIC Simulations. Journal of Geophysical Research: Space Physics, 125(8), e2020JA028162. https://doi.org/10.1029/2020JA028162
- Discipline:
- Science
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset contains images of UV cone nuclei near the retinal margin in live fish. These UV cones express a transgenic fluorescent reporter (that is nuclear-localized and photoconvertible). The most important images in this dataset are: Zoomed-out (1X magnification) images immediately after photoconversion Zoomed-out (1X magnification) images two to four days after photoconversion In the images immediately after photoconversion, we check if the row orientation rotates by more than a certain amount (10 degrees, 12 degrees, 14 degrees, etc.) at the retinal margin. If so, we call the region coinciding with this domain rotation an existing grain boundary. We, then, check where new Y-junctions are incorporated (by the time of later imaging) to see if they are preferentially incorporated near existing grain boundaries.
- Keyword:
- zebrafish cone mosaic, topological defects, tissue patterning, grain boundaries, and photoconversion
- Citation to related publication:
- Nunley, H., Nagashima, M., Martin, K., Gonzalez, A. L., Suzuki, S. C., Norton, D. A., Wong, R. O. L., Raymond, P. A., & Lubensky, D. K. (2020). Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation. PLOS Computational Biology, 16(12), e1008437. https://doi.org/10.1371/journal.pcbi.1008437 and Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679
- Discipline:
- Science
-
- Creator:
- Umaña, María Natalia, Zambrano, Jenny, Weemstra, Monique, and Allen, Dave
- Description:
- The objective of this research was to improve our understanding of tree growth from underlying variation in leaf and root functional traits. This knowledge ultimately enhances our knowledge of the above- and belowground processes that are involved in structuring forest communities. To this end, we determine which, how and to what degree (combinations of) leaf and root traits influence growth rates across ten temperate tree species along a soil carbon (C) and N gradient growing at the Big Woods plot at the E.S. George Reserve, Pickney, MI. This plot is part of the Smithsonian Institution's Forest Global Earth Observatory (ForestGEO) global network of forest research sites. https://forestgeo.si.edu/ and This dataset contains data on the leaf and root traits of several individuals from tree species, as well as on the soil properties at the Big Woods plots at the E.S. George Reserve, Pickney, MI. Data were collected in June 2019, and used to explain and predict the growth rates of the trees at Big Woods. [Growth data were obtained from Allen et al., 2019, https://doi.org/10.7302/wx55-kt18]. Each file contains data on leaf traits, root traits, and soil properties. Trait data are presented per individual tree for each of the 10 study species. Soil data are represented per soil sample, with four soil samples collected per subplot throughout the Big Woods plot (see legend, and publication for explanation). Descriptions and units per variable/column are provided in the legend tab in each file.
- Keyword:
- ecology, forests, Michigan, ForestGEO, Big Woods, Roots, Leaves, Tree growth, and Forest soils
- Citation to related publication:
- M. Weemstra, J. Zambrano, D. Allen, MN Umaña. (In press) Tree growth increases through opposing above- and belowground resource strategies. Journal of Ecology. https://doi.org/10.1111/1365-2745.13729
- Discipline:
- Science
-
- Creator:
- R. Paul Acosta
- Description:
- In this study, the state-of-the-art isotope-enable global climate model (iCESM1.2) simulations of the middle Miocene and the early Eocene and Cenomanian were used to comprehensively investigate the climate forcing of paleogeography, Andean paleoelevation, global pCO2, and vegetation on the South American continent.
- Keyword:
- South America , Hydroclimate, Water isotope system, and Global climate modeling
- Discipline:
- Science
-
- Creator:
- Mukhopadhyay, Agnit, Daniel T Welling, Michael W Liemohn, Aaron J Ridley, Shibaji Chakrabarty, and Brian J Anderson
- Description:
- An updated auroral conductance module is built for global models, using nonlinear regression & empirical adjustments to span extreme events., Expanded dataset raises the ceiling of conductance values, impacting the ionospheric potential dB/dt & dB predictions during extreme events., and Application of the expanded model with empirical adjustments refines the conductance pattern, and improves dB/dt predictions significantly.
- Keyword:
- Space Weather Forecasting, Extreme Weather, Ionosphere, Magnetosphere, MI Coupling, Ionospheric Conductance, Auroral Conductance, Aurora, SWMF, SWPC, Nonlinear Regression, and dB/dt
- Citation to related publication:
- Mukhopadhyay, A., Welling, D. T., Liemohn, M. W., Ridley, A. J., Chakraborty, S., & Anderson, B. J. (2020). Conductance Model for Extreme Events: Impact of Auroral Conductance on Space Weather Forecasts. Space Weather, 18(11), e2020SW002551. https://doi.org/10.1029/2020SW002551
- Discipline:
- Engineering and Science
-
- Creator:
- Gradwohl, Kelsey M.
- Description:
- The data set includes one file: Dermatology Clerkship Chalk Talks Raw Dataset which is the raw data collected from the surveys. This raw data was then coded and scored with the following analysis. Objective knowledge questions were asked for each chalk talk which was scored by authors. A knowledge assessment score was calculated by adding the total number of points accumulated by the student, dividing it by the total number of points possible, and summarizing the score as a percentage. Pre- and post-talk knowledge assessment scores were compared for each chalk talk and for the entire curriculum using 2-tailed paired sample t-tests with statistical significance if p<0.05., Before and after each talk, students were asked how confident they felt differentiating conditions within each disease group. For the erythroderma and immunobullous talks, students were also asked how confident they felt working up the conditions. Answer choices were on a Likert scale ranging from 1 (not at all confident) to 5 (extremely confident). Pre- and post-chalk talk scores were summarized as means with standard deviations and compared using 2-tailed paired sample t-tests with statistical significance if p<0.05. , After each talk, students were asked about its efficacy in terms of enhancing their understanding of the diseases, providing a framework or approach to work-up, and facilitating interaction between student and teacher. Answer choices were on a Likert scale ranging from 1 (not at all effective) to 5 (extremely effective), and summarized as means with standard deviations. Students were asked for written feedback regarding what they liked about the talk and suggestions for improvement. Qualitative data were sorted into categories and scored by two independent raters (cohen's kappa =0.8)., and In the response Likert scale, "Not at all"=1, "Not so (much)"=2, "Somewhat"=3, "Very"=4, and "Extremely"=5.
- Keyword:
- Chalk talk, Dermatology clerkship, Dermatology education, Virtual learning, and Online learning
- Discipline:
- Health Sciences
-
- Creator:
- Valeriy Tenishev
- Description:
- This data represents examples of some applications of AMPS and illustrates the potential of the code for modeling various physical phenomena.
- Keyword:
- Monte Carlo, DSMC
- Citation to related publication:
- Tenishev, V., Shou, Y., Borovikov, D., Lee, Y., Fougere, N., Michael, A., & Combi, M. R. (2021). Application of the Monte Carlo Method in Modeling Dusty Gas, Dust in Plasma, and Energetic Ions in Planetary, Magnetospheric, and Heliospheric Environments. Journal of Geophysical Research: Space Physics, 126(2), e2020JA028242. https://doi.org/10.1029/2020JA028242
- Discipline:
- Science
-
- Creator:
- MacEachern, Mark P, Marti, Kyriaki C, Mylonas, Anastassios I, and Gruppen, Larry
- Description:
- The dataset includes most citations considered for inclusion in the scoping review. The citations are accessible in the Endnote (enlx) file, as well as the primary citation export files from each database. The literature search strategies are included for reproducibility and transparency purposes. See the methods of the article for more information.
- Keyword:
- Dental Education, Dentistry, Education, Humanities, and Scoping Review
- Citation to related publication:
- Marti KC, Mylonas AI, MacEachern M, Gruppen L. (2019). Humanities in predoctoral dental education: A scoping review. Journal of Dental Education, 83(10), 1174-1198. DOI: 10.21815/JDE.019.126, http://www.jdentaled.org/content/83/10/1174.long, and https://doi.org/10.21815/JDE.019.126
- Discipline:
- Health Sciences
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a series of vertebrae from the second lumbar through first sacral of Sifrhippus grangeri (University of Michigan Museum of Paleontology catalog number UMMP VP 115547) 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. In some publications this species is referred to as Hyracotherium grangeri.
- Keyword:
- Paleontology, Fossil, CT, Equidae, UMMP, University of Michigan Museum of Paleontology, Eocene, CTEES, and ef48281d-2984-86f2-2bee-052b26cf8da9
- Discipline:
- Science
-
- Creator:
- Smith, Joeseph P., Gronewold, Andrew D., Read, Laura, Crooks, James L., School for Environment and Sustainability, University of Michigan, Department of Civil and Environmental Engineering, University of Michigan, and Cooperative Institute for Great Lakes Research
- Description:
- Using the statistical programming package R ( https://cran.r-project.org/), and JAGS (Just Another Gibbs Sampler, http://mcmc-jags.sourceforge.net/), we processed multiple estimates of the Laurentian Great Lakes water balance components -- over-lake precipitation, evaporation, lateral tributary runoff, connecting channel flows, and diversions -- feeding them into prior distributions (using data from 1950 through 1979), and likelihood functions. The Bayesian Network is coded in the BUGS language. Water balance computations assume that monthly change in storage for a given lake is the difference between beginning of month water levels surrounding each month. For example, the change in storage for June 2015 is the difference between the beginning of month water level for July 2015 and that for June 2015., More details on the model can be found in the following summary report for the International Watersheds Initiative of the International Joint Commission, where the model was used to generate a new water balance historical record from 1950 through 2015: https://www.glerl.noaa.gov/pubs/fulltext/2018/20180021.pdf. Large Lake Statistical Water Balance Model (L2SWBM): https://www.glerl.noaa.gov/data/WaterBalanceModel/, and This data set has a shorter timespan to accommodate a prior which uses data not used in the likelihood functions.
- Keyword:
- Water, Balance, Great Lakes, Laurentian, Machine, Learning, Lakes, Bayesian, and Network
- Citation to related publication:
- Smith, J., Gronewald, A. et al. Summary Report: Development of the Large Lake Statistical Water Balance Model for Constructing a New Historical Record of the Great Lakes Water Balance. Submitted to: The International Watersheds Initiative of the International Joint Commission. Accessible at https://www.glerl.noaa.gov/pubs/fulltext/2018/20180021.pdf, Large Lake Statistical Water Balance Model (L2SWBM). https://www.glerl.noaa.gov/data/WaterBalanceModel/, and Gronewold, A.D., Smith, J.P., Read, L. and Crooks, J.L., 2020. Reconciling the water balance of large lake systems. Advances in Water Resources, p.103505.
- Discipline:
- Science and Engineering
-
- Creator:
- Burger, Laura L , Wagenmaker, Elizabeth R., Phumsatitpong, Chayarndorn , Olson, David P., and Moenter, Suzanne M.
- Description:
- Polycystic ovary syndrome (PCOS) is the most common form of infertility in women. The causes of PCOS are not yet understood and both genetics and early-life exposure have been considered as candidates. With regard to the latter, circulating androgens are elevated in mid-late gestation in women with PCOS, potentially exposing offspring to elevated androgens in utero; daughters of women with PCOS are at increased risk for developing this disorder. Consistent with these clinical observations, prenatal androgenization (PNA) of several species recapitulates many phenotypes observed in PCOS. There is increasing evidence that symptoms associated with PCOS, including elevated luteinizing hormone (LH) (and presumably gonadotropin-releasing hormone (GnRH)) pulse frequency emerge during the pubertal transition. We utilized translating ribosomal affinity purification coupled with RNA sequencing to examine GnRH neuron mRNAs from prepubertal (3wk) and adult female control and PNA mice. Prominent in GnRH neurons were transcripts associated with protein synthesis and cellular energetics, in particular oxidative phosphorylation. The GnRH neuron transcript profile was affected more by the transition from prepuberty to adulthood than by PNA treatment, however PNA did change the developmental trajectory of GnRH neurons. This included families of transcripts related to both protein synthesis and oxidative phosphorylation, which were more prevalent in adults than in prepubertal mice but were blunted in PNA adults. These findings suggest that prenatal androgen exposure can program alterations in the translatome of GnRH neurons, providing a mechanism independent of changes in the genetic code for altered expression. These are Microsoft Excel Files
- Keyword:
- GnRH Neuron TRAP Seq
- Citation to related publication:
- Unprocessed RNASeq data is available at Gene Expression Omnibus ( https://www.ncbi.nlm.nih.gov/gds) accession GSE155314.
- Discipline:
- Science
-
- Creator:
- Carlson, Zachary
- Description:
- Data repository for supplemental data for manuscript. Article and data set are currently under review by publisher. Email for more information.
- Citation to related publication:
- Carlson, Z., Hafner, H., Mulcahy, M., Bullock, K., Zhu, A., Bridges, D., Bernal-Mizrachi, E., & Gregg, B. (2020). Lactational metformin exposure programs offspring white adipose tissue glucose homeostasis and resilience to metabolic stress in a sex-dependent manner. American Journal of Physiology-Endocrinology and Metabolism, 318(5), E600–E612. https://doi.org/10.1152/ajpendo.00473.2019
- Discipline:
- Science
-
- Creator:
- van Velden, Grace and Reddy, Raghav
- Description:
- A household survey was developed to capture household perceptions and behaviors around drinking water use. It consisted of several modules: key informant and household demographics, household assets and consumption, water use behaviors in the dry season, water use behaviors during the rest of the year, and water supply maintenance and repair. Intervention and safe water device surveys were also developed; the household and intervention surveys were administered via Qualtrics. and This record consists of several survey instruments, exported where appropriate from Qualtrics into PDF and .qsf.
- Keyword:
- Bangladesh, arsenic, sustainability, survey
- Discipline:
- Engineering
-
- Creator:
- Pasquinelli, Rennie, Hu, Xiaosu, Tessier, Anne-Michelle, Kovelman, Ioulia, Zwolan, Terry A., Karas, Zachary E., and Wagley, Neelima
- Description:
- This data is from a project examining prosodic processing in children and adults using functional near-infrared spectroscopy (fNIRS) neuroimaging. fNIRS data is optical data collected using a cap with an array of source and detector fibers that emit and detect infrared light, respectively. We used fNIRS neuroimaging to explore prosodic processing, rhyme judgement, and the "oddball" paradigm in children, adults, and a small sample of children with cochlear implants. Matlab scripts, including Ted Huppert's Nirs Toolbox, were used to process the neuroimaging data. The children also took a battery of behavioral assessments (OWLS, Digit Span, PPVT, CTOPP).
- Keyword:
- Prosodic Processing, fNIRS neuroimaging, Development, Cochlear Implants, and Rhyming
- Discipline:
- Science
-
- Creator:
- Liu, Meichen
- Description:
- We intend to figure out the difference of stress drops, which is a characteristic source parameter, between shallow and deep-focus earthquakes. Significant stress drop difference may shed light on the difference of physical mechanisms of shallow and deep-focus earthquakes, which has been a elusive question. We select from deep-focus earthquakes (> 400 km) in 2000-2018 and obtain their stress drops using P and S waves. We find that stress drops of deep-focus earthquakes are about one order of magnitude higher than that of shallow earthquakes, indicating about one order of magnitude higher shear strength of shallow faults than faults in the mantle. The wide range of stress drops further suggests coexistence of phase transformation and shear-induced melting mechanisms of deep-focus earthquakes.
- Citation to related publication:
- Liu, M., Huang, Y., & Ritsema, J. (2020, March 4). Stress drop variation of deep-focus earthquakes based on empirical Green's function [preprint]. Submitted to Geophysical Research Letters. https://doi.org/10.31223/osf.io/8jx6p and Liu, M., Huang, Y., & Ritsema, J. (2020). Stress Drop Variation of Deep-Focus Earthquakes Based on Empirical Green’s Functions. Geophysical Research Letters, 47(9), e2019GL086055. https://doi.org/10.1029/2019GL086055
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for vertebrae of Hyopsodus (University of Michigan Museum of Paleontology catalog number UMMP_VP_102495) 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, Hyopsodontidae, UMMP, University of Michigan Museum of Paleontology, Eocene, CTEES, and 01ee73fb-6b53-fe52-3a01-2857be88a65e
- Discipline:
- Science
-
- Creator:
- Harper Diane M
- Description:
- Patients included in this study were all males with no prior HIV diagnosis between 18 and 45 years who had at least one primary care encounter between March 2016 and March 2019. We chose 2016 as the index year because the question of the sexual partners’ gender became coded data elements with the clinic contact. Eligible patients were grouped based on reported sexual partners at the most recent disclosure. Individuals who reported having a male sexual partner or both a male and female partner were included in the MSM group. The non-MSM group included individuals who reported only a female partner or no partner. Patients who did not answer the question were excluded from the study. The study proposal was submitted to the Institutional Review Boards of the University of Michigan Medical School and was exempted from ongoing IRB review (HUM00155091). Individual consent was waived for this study.
- Keyword:
- HIV, MSM, and annual screening
- Discipline:
- Health 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., Detailed documentation of how the data is generated can be found in: https://afcoe.engin.umich.edu/benchmark-data. 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). 2. 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). , 3. 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). 4. Data_180000to189999.tar: the unsteady flow field data from time step 180000 to 189999 (time increment, dt, between each time step is 1E-7 sec)., 5. Data_190000to199999.tar: the unsteady flow field data from time step 190000 to 199999 (time increment, dt, between each time step is 1E-7 sec). 6. Data_200000to209999.tar: the unsteady flow field data from time step 200000 to 209999 (time increment, dt, between each time step is 1E-7 sec). , 7. Data_210000to219999.tar: the unsteady flow field data from time step 210000 to 219999 (time increment, dt, between each time step is 1E-7 sec). 8. Data_220000to229999.tar: the unsteady flow field data from time step 220000 to 229999 (time increment, dt, between each time step is 1E-7 sec). , and 9. grid.dat: the topology of the CFD mesh used to generate this data (can be directly loaded in Tecplot). 10. 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.
- Citation to related publication:
- McQuarrie, S., Huang, C., and Willcox, K., Data-driven reduced-order models via regularised Operator Inference for a single-injector combustion process, Journal of the Royal Society of New Zealand, 2021. (code available: https://github.com/Willcox-Research-Group/ROM-OpInf-Combustion-2D)., McQuarrie, S. A., Huang, C., & Willcox, K. E. (2021). Data-driven reduced-order models via regularised Operator Inference for a single-injector combustion process. Journal of the Royal Society of New Zealand, 51(2), 194–211. https://doi.org/10.1080/03036758.2020.1863237 , Swischuk, R., Kramer, B., Huang, C., & Willcox, K. (2020). Learning Physics-Based Reduced-Order Models for a Single-Injector Combustion Process. AIAA Journal, 58(6), 2658–2672. https://doi.org/10.2514/1.J058943, Huang, C., Duraisamy, K., & Merkle, C. L. (2019). Investigations and Improvement of Robustness of Reduced-Order Models of Reacting Flow. AIAA Journal, 57(12), 5377–5389. https://doi.org/10.2514/1.J058392 , and Harvazinski, M. E., Huang, C., Sankaran, V., Feldman, T. W., Anderson, W. E., Merkle, C. L., & Talley, D. G. (2015). Coupling between hydrodynamics, acoustics, and heat release in a self-excited unstable combustor. Physics of Fluids, 27(4), 045102. https://doi.org/10.1063/1.4916673
- Discipline:
- Engineering
-
- Creator:
- Sergio E. Vidal-Luengo
- Description:
- This database contains spacecraft and ground-based magnetic field observations made to study the propagation of the preliminary impulse triggered by interplanetary shocks with different inclinations in the XZ plane.
- Keyword:
- Cluster, Dynamic pressure pulse, THEMIS, SuperMag, Magnetosphere, MMS, and Intermagnet
- Citation to related publication:
- (to be submitted) Vidal-Luengo, S. E., Moldwin, M. B. (2021). Shock Inclination Effects in Preliminary Impulse Propagation Observed by Ground-Based Magnetometers and the Heliophysics System Observatory
- Discipline:
- Science
-
- Creator:
- Shi, Xuetao, Elvati, Paolo, and Violi, Angela
- Description:
- Non-thermal plasma systems offer unique opportunities in the fields of bio-imaging, drug delivery, photovoltaics, microelectronics manufacturing. Such interests are largely inspired by the fact that hot plasma electrons coexist with neutral species and ions close to room-temperature under non-thermal plasma conditions. Modeling of these systems requires a deep understanding of the atomistic processes underlying the rich chemistry of the various radicals and ions with the nascent nanoparticle surface. A key parameter for determining the contribution of a certain radical/ion species to the nanoparticle surface growth, called sticking coefficient, is computed as a weighted sum from the simulated sticking outcomes with different collision velocities drawn from a Maxwell-Boltzmann distribution at certain temperatures. In this work, the collisions of SiHx (x=1-4) fragments and silicon cluster (Si4, Si2H6, and Si29H36) surfaces, responsible for the sticking coefficients, are simulated by molecular dynamics (MD) with a reactive force field. The dependence of sticking coefficients on temperature, H coverage of both silane fragments and cluster surfaces, and the size of the cluster, are systematically examined. And the mechanism underlying the sticking events, specifically the conversion of physical aggregation to chemisorption is investigated to better understand the complex interplay between factors influencing the surface growth. The detailed and multi-parameter model of sticking coefficients, accompanied by the mechanism study of physisorption to chemisorption conversion, provides a more accurate and robust approximation of surface growth rate using sticking coefficients, and a deeper understanding of surface growth processes, for the wider non-thermal plasma simulation community.
- Keyword:
- Sticking coefficients, Silanes, Molecular Dynamics, Non-equilibrium, and Aggregation mechanisms
- Citation to related publication:
- Shi, X., Elvati, P., Violi, A. (2021). On the growth of Si nanoparticles in non-thermal plasma: physisorption to chemisorption conversion. J. Phys. D. Submitted.
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for vertebrae of Phenacolemur (University of Michigan Museum of Paleontology catalog number UMMP VP 94723) 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, Paromomyidae, UMMP, University of Michigan Museum of Paleontology, Eocene, CTEES, and 31cf6e4a-86dd-9452-49f4-c5ce0d946613
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right medial cuneiform (entocuneiform) of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81820), 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:
- Lee, Joyce Y, Knauer, Heather A, Lee, Shawna J, MacEachern, Mark P, and Garfield, Craig F
- Description:
- The dataset includes all citations considered for inclusion in the systematic review. The citations are accessible in Endnote (enlx), 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:
- Systematic Review, Fathers, Education, and Perinatal
- Citation to related publication:
- Lee JY, Knauer HA, Lee SJ, MacEachern MP, Garfield CF. (2018). Father-inclusive perinatal parent education programs: A systematic review. Pediatrics, 142(1). PMID: 29903835. and https://doi.org/10.1542/peds.2018-0437
- Discipline:
- Health Sciences
-
- Creator:
- Liemohn, Michael W and Wooden, Paige
- Description:
- Journals sometimes focus the attention of the research community by having a special collection, sometimes an entire special issue, devoted to a single topic. A reasonable question to ask is whether the extra effort of organizing, promoting, and maintaining the special collection is worthwhile. The paper that this data set accompanies examines paper impact in the Journal of Geophysical Research Space Physics, separating the special collection papers from the non-special-collection submissions. The conclusion is that special collections are worth the extra work.
- Keyword:
- journal special collections, bibliometrics, citations, and downloads
- Citation to related publication:
- Liemohn, M. W., & Wooden, P. (2019). Editorial: Impact of special collections in JGR Space Physics. Journal of Geophysical Research Space Physics. https://doi.org/10.1002/essoar.10501036.2
- Discipline:
- Science
-
- Creator:
- Troesch, Armin, W. and Kang, C.-G.
- Description:
- This scaled acceleration time series has been used in the graduate class, NA540, as an example of hydrodynamic impact. For a more detailed description of the tests, please see: Troesch, A.W. and Kang, C.-G., "Hydrodynamic Impact Loads on Three Dimensional Bodies," Proceedings of the 16th Symposium on Naval Hydrodynamics, Berkeley, July 1986, National Academy Press, Washington, D.C., 1987, pp. 537-558.
- Keyword:
- hydrodynamic impact
- Citation to related publication:
- Troesch, A.W. and Kang, C.-G., "Hydrodynamic Impact Loads on Three Dimensional Bodies," Proceedings of the 16th Symposium on Naval Hydrodynamics, Berkeley, July 1986, National Academy Press, Washington, D.C., 1987, pp. 537-558. This item is not available online due to copyright restrictions, but the text can be searched using Hathi Trust: https://babel.hathitrust.org/cgi/pt?id=mdp.39015040312475
- Discipline:
- Engineering and Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right navicular of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81831), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
-
Prescribed Burn Single-Particle Mass Spectra, University of Michigan Biological Station October 2017
- Creator:
- Pratt, Kerri
- Description:
- This dataset corresponds to 5,500 single-particle, dual-polarity mass spectra of biomass burning particles measured from a mobile laboratory during the 2017 prescribed burn at the University of Michigan Biological Station near Pellston, Michigan. Size-resolved chemical composition of individual particles, primarily ranging from 0.15 - 0.60 μm in vacuum aerodynamic diameter, was measured using an aerosol time-of-flight mass spectrometer (ATOFMS).
- Keyword:
- aerosol chemistry
- Discipline:
- Science
-
- Creator:
- MacEachern, Mark, Vitous, C Ann, Dinh, Duyhoang, Jafri, Sara, Bennett, Olivia, and Suwanabol, Pasithorn
- 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 EBSCOhost CINAHL. The searches yielded 1168 citations after duplicates were removed in Endnote X8.
- Keyword:
- Health Sciences, Systematic Review, Surgeons, Well-being, and Literature Searches
- Citation to related publication:
- Vitous, C. Ann MA, MPH*; Dinh, Duyhoang Q. BS†; Jafri, Sara M. BS‡; Bennett, Olivia M. BS†; MacEachern, Mark MLIS§; Suwanabol, Pasithorn A. MD, MS* Optimizing Surgeon Well-Being, Annals of Surgery Open: March 2021 - Volume 2 - Issue 1 - p e029 doi: 10.1097/AS9.0000000000000029
- Discipline:
- Health Sciences
-
- Creator:
- Robert Buckley, Grace O'Brien, and Zoe Zhou
- Description:
- The purpose of the research is to better understand and approximate the Thurston Set. This project was computational in nature and Python was used to collect our data. The data set contains encoded itineraries that can be used to compute values that are elements of the Thurston Set. A visual approximation of the Thurston Set can be found here ( https://arxiv.org/abs/1402.2008), on the first page Thurston’s own paper. The data can also be used to study the distribution of superattracting beta values within the interval (1, 2] and to explore an analogous Mandelbrot-Julia Correspondence. This research was conducted through the Lab of Geometry at Michigan under the advisement of Harrison Bray during the Fall semester of 2019. , The Python 3.x scripts in this deposit are the exact versions used to created the *.txt files that are in the zip archive. As the project continues, any expansion to the work, such as further analysis or visualization scripts, will be posted to the project's GitHub https://github.com/Tent-Maps-Team/Thurston-Set. Also, a user can reproduce our results and generate bigger datasets on machines with large amounts of memory. , and The data consists of zipper folders representing tent map itinerary orbit lengths. These orbit files can be used to create visualizations, create and explore conjectures such as refining proposed bounds on the Thurston Set and supporting an analogous Mandelbrot-Julia Correspondence. Within these zipped folders are .txt files in CSV format with the naming structure of xx_y of admissible itineraries up to the length indicated by the folder name where xx is the length of the encoded itineraries included. The txt's have a single column and each line(row) is an array representing an encoding of an itinerary. Some of the txt's have been split into multiple parts (whenever there are more than 200 MB of itinerary data) and these txt's have been numbered using the y after the underscore. As we exclude the degenerate tent map (where β = 1), we cannot have orbit length 1 or 2 and this is why the orbits start with length 3 (i.e. start with 3.zip).
- Keyword:
- Math, mathematics, tent maps, thurston, milnor, Milnor-Thurston, supperattracting, entropy, orbit, and itineraries
- Citation to related publication:
- Buckley R, O’Brien G, Zhou Z (2021). On Itineraries of Tent Maps. Forthcoming.
- Discipline:
- Other
-
- Creator:
- LaBarre, Jennifer L., Peterson, Karen E., Kachman, Maureen T., Perng, Wei., Tang, Lu., Hao, Wei., Zhou, Ling., Karnovsky, Alla., Cantoral, Alejandra., Téllez-Rojo, Martha María., Song, Peter XK., and Burant, Charles F.
- Description:
- Participants were enrolled in the Early Life Exposure in Mexico to ENvironmental Toxicants (ELEMENT) project which was started in 1994 and consists of three sequentially-enrolled birth cohorts from Mexico City Maternity Hospitals (20). A subset of these children, age 8-14 years, were contacted through their primary caregiver to provide urine samples, serum samples, anthropometry and complete an interview-based questionnaire (n=250). Subjects for this analysis have baseline and follow data on anthropometry, metabolic biomarkers and adequate serum volume for metabolomics analyses (n=206).
- Citation to related publication:
- LaBarre, J. L., Peterson, K. E., Kachman, M. T., Perng, W., Tang, L., Hao, W., Zhou, L., Karnovsky, A., Cantoral, A., Téllez-Rojo, M. M., Song, P. X. K., & Burant, C. F. (2020). Mitochondrial Nutrient Utilization Underlying the Association Between Metabolites and Insulin Resistance in Adolescents. The Journal of Clinical Endocrinology & Metabolism, 105(7), 2442–2455. https://doi.org/10.1210/clinem/dgaa260
- Discipline:
- Health Sciences
-
- Creator:
- Zalmout, Iyad S, Sanders, William J, MacLatchy, Laura M, Gunnell, Gregg F, Al-Mufarreh, Yahya A, Ali, Mohammad A, Nasser, Abdul-Azziz H, Al-Masari, Abdu M, Al-Sobhi, Salih A, Nadhra, Ayman O, Matari, Adel H, Wilson, Jeffrey A, and Gingerich, Philip D
- Description:
- Reconstructed CT slices for the partial cranium of the holotype specimen of Saadanius hijazensis in DICOM format. Data supporting the publication: New Oligocene primate from Saudi Arabia and the divergence of apes and Old World monkeys, https://doi.org/10.1038/nature09094 Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, Saudi Arabia, CT, Primate, Oligocene, Hominoidea, Cercopithecoidea, University of Michigan Museum of Paleontology, and UMMP
- Citation to related publication:
- Zalmout, I., Sanders, W., MacLatchy, L. et al. New Oligocene primate from Saudi Arabia and the divergence of apes and Old World monkeys. Nature 466, 360–364 (2010). https://doi.org/10.1038/nature09094, A cast of this specimen is held by the University of Michigan Museum of Paleontology (UMMP) under catalog number 14200., and 3D surface model viewable on UMORF site : https://umorf.ummp.lsa.umich.edu/wp/specimen-data/?Model_ID=1408
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right cuboid of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81823), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
-
- Creator:
- Moore, Talia Y, Villacis Nunez, C Nathaly, Ray, Andrew P, and Cooper, Kimberly L
- Description:
- Hind limbs can undergo dramatic changes in loading conditions during the transition from quadrupedal to bipedal locomotion. For example, the most early diverging bipedal jerboas (Rodentia: Dipodidae) are some of the smallest mammals in the world, with body masses that range 2-4 grams. The larger jerboa species exhibit developmental and evolutionary fusion of the central three metatarsals into a single cannon bone. We hypothesize that body size reduction and metatarsal fusion are mechanisms to maintain the safety factor of the hind limb bones despite the higher ground reaction forces associated with bipedal locomotion. Using finite element analysis to model collisions between the substrate and the metatarsals, we found that body size reduction was insufficient to reduce bone stress on unfused metatarsals, based on the scaled dynamics of larger jerboas, and that fused bones developed lower stresses than unfused bones when all metatarsals are scaled to the same size and loading conditions. Based on these results, we conclude that fusion reinforces larger jerboa metatarsals against high ground reaction forces. Because smaller jerboas with unfused metatarsals develop higher peak stresses in response to loading conditions scaled from larger jerboas, we hypothesize that smaller jerboas use alternative dynamics of bipedal locomotion that reduces the impact of collisions between the foot and substrate.
- Keyword:
- finite element, functional morphology, bipedal, jerboa, metatarsus, and bone fusion
- Citation to related publication:
- Villacis Nunez, Ray, Cooper, Moore (submitted). Body size reduction and metatarsal fusion were distinct mechanisms to resist bending as jerboas (Dipodidae) transitioned from quadrupedal to bipedal.
- Discipline:
- Science and Engineering