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- Creator:
- Brian C. Weeks
- Description:
- Description: Each folder contains all of the data for a specific specimen; the folder names correspond to the University of Michigan Museum of Zoology catalog number for the specimen. Folders with a “-“ in the name are individual specimens that were photographed multiple independent times; the number following the “-“ indicates the repetition number (i.e. the folder named “UMMZ_242382-10” contains the tenth set of photographs for specimen UMMZ 242382). The photographs are necessary to train and test the Skelevision model, which is a computer vision approach to identifying and measuring elements of the skeleton (length of the tibiotarsus, tarsometatarsus, femur, humerus, ulna, radius, carpometacarpus, 2nd digit 1st phalanx, skull, and keel; the outer diameter of the sclerotic ring at its widest point; and the distance from the back of the skull to the tip of the bill). The data span 115 species of passerines across 79 genera from 59 families.
- Keyword:
- Bird skeleton, neural network, and functional traits
- Citation to related publication:
- Weeks, B.C., Zhou, Z., O’Brien, B., Darling, R., Dean, M., Dias, T., Hassena, G., Zhang, M., and Fouhey, D.F. 2022. A deep neural network for high throughput measurement of functional traits on museum skeletal specimens. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210X.13864
- Discipline:
- Science
-
- Creator:
- Surajit Chatterjee, Adrien Chauvier, Shiba S. Dandpat, Irina Artsimovitch, and Nils G. Walter
- Description:
- These data were generated to study the dynamics of RNAP-ribosome interactions on a nascent mRNA with a preQ1-sensing translational riboswitch in its 5’ untranslated region (UTR). Using single-molecule fluorescence co-localization, we monitored direct transient binding of 30S ribosomal subunit to the individual nascent mRNA molecules in surface-immobilized paused elongation complexes (PECs). Also, using a novel protein-induced fluorescence enhancement assay we monitored the real-time transcription rate of RNA polymerase (RNAP) under different experimental conditions. The DNA template including the preQ1 riboswitch from B. anthracis under the control of the T7A1 promoter was cloned into pUC19 plasmid. Transcription templates for in vitro transcription were generated by PCR.
- Citation to related publication:
- Chatterjee, S., Chauvier, A., Dandpat, S.S., Artsimovitch, I., & Walter, N.G. (2021). A translational riboswitch coordinates nascent transcription-translation coupling. Proc. Natl. Acad. Sci., 118 (16), e2023426118; DOI: 10.1073/pnas.2023426118
- Discipline:
- Science
-
- Creator:
- Hayward, Stephen L. , Lund, Paul E., Kang, Qing, Johnson-Buck, Alexander , Tewari, Muneesh, and Walter, Nils G.
- Description:
- This work contains the experimental data and associated analysis that are described in the research publication entitled "Ultra-specific and Amplification-free Quantification of Mutant DNA by Single-molecule Kinetic Fingerprinting". This work contains multiple zip files, each of which represents one of the principal experiment groups presented in the publication. Each experiment group contains movie and analysis files corresponding to various experimental conditions related to that experiment group.
- Keyword:
- Single Molecule Fluorescence, Super-Resolution Microscopy, Nucleic Acid Hybridization, T790M Mutation, Cytosine Deamination, SiMREPS, and single molecule kinetic fingerprinting
- Citation to related publication:
- https://pubs.acs.org/doi/10.1021/jacs.8b06685
- Discipline:
- Science
-
- Creator:
- Hou, Qian, Chatterjee, Surajit, Lund, Paul E., Suddala, Krishna C., and Walter, Nils G.
- Description:
- Bacteria live in a broad range of environmental temperatures that require adaptations of their RNA sequences to maintain function. Riboswitches are regulatory RNAs that change conformation upon binding of typical metabolite ligands to control bacterial gene expression. The paradigmatic small class-I preQ1 riboswitches from the mesophile Bacillus subtilis (Bsu) and the thermophile Thermoanaerobacter tengcongensis (Tte) adopt similar pseudoknot structures when bound to preQ1. Here, we use single-molecule detected chemical denaturation by urea to compare the thermodynamic and kinetic folding properties of the two riboswitches, and the urea-countering effects of trimethylamine N-oxide (TMAO). This data includes the experimental findings and associated analyses detailed in the research article titled "Single-molecule FRET observes opposing effects of urea and TMAO on structurally similar meso- and thermophilic riboswitch RNAs". The data consists of multiple zip files, each representing an experiment that corresponds to the key results in the publication. Each experiment includes movies, qualifying smFRET trajectories, and analysis files related to various conditions within that experimental group.
- Keyword:
- Riboswitch, Single molecule FRET, RNA folding, UV-melting, Osmolyte, Urea, and Trimethylamine N-oxide
- Citation to related publication:
- https://doi.org/10.1093/nar/gkad866
- Discipline:
- 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:
- Ray, Sujay
- Description:
- Single molecule data and analysis code for Figure4 in the paper titled: "A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower". Follow the readme file for deiails.
- Discipline:
- Science
-
- Creator:
- Larson, Ronald G., Wen, Fei, Huang, Wenjun, and Huang, Ming
- Description:
- We provide the parameters used in Umbrella Sampling simulations reported in our study "Efficient Estimation of Binding Free Energies between Peptides and an MHC Class II Molecule Using Coarse-Grained Molecular Dynamics Simulations with a Weighted Histogram Analysis Method", namely the set positions and spring constants for each window in simulations. Two tables are provided. Table 1 lists the names of the peptides and their corresponding sequences. Table 2 lists the parameters. The abstract of our work is the following: We estimate the binding free energy between peptides and an MHC class II molecule using molecular dynamics (MD) simulations with Weighted Histogram Analysis Method (WHAM). We show that, owing to its more thorough sampling in the available computational time, the binding free energy obtained by pulling the whole peptide using a coarse-grained (CG) force field (MARTINI) is less prone to significant error induced by biased-sampling than using an atomistic force field (AMBER). We further demonstrate that using CG MD to pull 3-4 residue peptide segments while leaving the remain-ing peptide segments in the binding groove and adding up the binding free energies of all peptide segments gives robust binding free energy estimations, which are in good agreement with the experimentally measured binding affinities for the peptide sequences studied. Our approach thus provides a promising and computationally efficient way to rapidly and relia-bly estimate the binding free energy between an arbitrary peptide and an MHC class II molecule.
- Keyword:
- Molecular Dynamics, Binding Free Energy, Protein, MHC, and Coarse-Grained
- Discipline:
- Science and Engineering
-
- Creator:
- Ramasubramani, Vyas
- Description:
- The goal of the work is to elucidate the stability of a complex experimentally observed structure of proteins. We found that supercharged GFP molecules spontaneously assemble into a complex 16-mer structure that we term a protomer, and that under the right conditions an even larger assembly is observed. The protomer structure is very well defined, and we performed simulations to try and understand the mechanics underlying its behavior. In particular, we focused on understanding the role of electrostatics in this system and how varying salt concentrations would alter the stability of the structure, with the ultimate goal of predicting the effects of various mutations on the stability of the structure. There are two separate projects included in this repository, but the two are closely linked. One, the candidate_structures folder, contains the atomistic outputs used to generate coarse-grained configurations. The actual coarse-grained simulations are in the rigid_protein folder, which pulls the atomistic coordinates from the other folder. All data is managed by signac and lives in the workspace directories, which contain various folders corresponding to different parameter combinations. The parameters associated with a given folder are stored in the signac_statepoint.json files within each subdirectory. The atomistic data uses experimentally determined protein structures as a starting point; all of these are stored in the ConfigFiles folder. The primary output is the topology files generated from the PDBs by GROMACS; these topologies are then used to parametrize the Monte Carlo simulations. In some cases, atomistic simulations were actually run as well, and the outputs are stored alongside the topology files. In the rigid_protein folder, the ConfigFiles folder contains MSMS, the software used to generate polyhedral representations of proteins from the PDBs in the candidate_structures folder. All of the actual polyhedral structures are also stored in the ConfigFiles folder. The actual simulation trajectories are stored as general simulation data (GSD) files within each subdirectory of the workspace, along with a single .pos file that contains the shape definition of the (nonconvex) polyhedron used to represent a protein. The logged quantities, such as energies and MC move sizes, are stored in .log files. The logic for the simulations in the candidate_structures project is in the Python scripts project.py, operations.py, and scripts/init.py. The rigid_protein folder also includes the notebooks directory, which contains Jupyter notebooks used to perform analyses, as well as the Python scripts used to actually perform the simulations and manage the data space. In particular, the project.py, operations.py and scripts/init.py scripts contain most of the logic associated with the simulations.
- Keyword:
- Protein assembly, Cryo TEM, Hierarchical Assembly, Monte Carlo simulation, and Coarse-grained simulation
- Discipline:
- Science and Engineering
-
- Creator:
- Zhang, Yingxiao MI and Steiner, Allison MI
- Description:
- In the dataset, "_T" means temperature effects only, without "_T" means temperature and precipitation effects are both considered, "_co2" means CO2 effects are considered on the based of temperature and precipitation effects.
- Keyword:
- pollen emission, climate change, and public health
- Discipline:
- Science
-
- Creator:
- Zhang, Yingxiao MI and Steiner, Allison MI
- Description:
- Atmospheric aerosols are emitted from both natural and anthropogenic sources, and they play an important role in climate, impacting solar radiation and cloud formation. Compared to other types of aerosol particles, primary biological aerosol particles (PBAP, e.g., fungal spores, bacteria, pollen, virus, etc.) are relatively understudied. However, they are linked to adverse health effects and have the potential to influence ice nucleation at higher temperatures. Anemophilous (or wind-driven) pollen is one of the important PBAP, impacts cloud properties under some conditions, and triggers allergic diseases such as allergic rhinitis (also known as hay fever) and asthma. Because pollen emission is closely associated with environmental drivers, the climatic change could influence pollen emission and consequently the incidence of allergic disease. Using CMIP6 model data, our research projects continental-scale changes in pollen emissions at the end of the century, considering the effects of temperature, precipitation, CO2, and future vegetation distribution change. While prior studies have evaluated single types of pollen, we use a mechanistic model to comprehensively simulate total pollen across the United States from all sources. Similar to previous single-source pollen studies, our simulations suggest that pollen season duration will lengthen, and pollen emission will increase in the future, but in addition, we identify new synergies between different pollen types that can influence the maximum daily pollen. Our work highlights that the changes of overlap between pollen seasons of different vegetation taxa can magnify or mitigate the impacts of climate change, which addresses the importance to study all pollen emissions comprehensively. Given pollen is one of the most common triggers of seasonal allergies, our findings also provide information to evaluate global health conditions in the future. In this study, all of the pollen emission data are written in NetCDF files.
- Keyword:
- Pollen emission change, Climate change, Public health, Vegetation land cover change, and CO2 effects
- Citation to related publication:
- Zhang, Y. and Steiner, A. “Projected climate-driven changes in pollen emission season length and magnitude over the continental United States”, under review in Nature Communication, 2022. and yingxz. (2022). steiner-lab/pecm: PECM2.0 (2.0). Zenodo. https://doi.org/10.5281/zenodo.5874177
- Discipline:
- Science
-
- Creator:
- Lin, Xin, Keppel-Aleks, Gretchen, Rogers, Brendan M., and Birch, Leah
- Description:
- The data contain the daily-averaged atmospheric concentrations of CO2 tracers in the Northern Hemisphere simulated from a tagged tracer transport model GEOS-Chem v12.0.0. Thirteen land flux regions are defined and tagged in the model to separate their imprints on the long-term atmospheric CO2 seasonal amplification in Northern Hemisphere. A file describing the delineation of these land flux regions is also provided. See the README file for more details on the dataset and model configurations.
- Keyword:
- carbon dioxide, seasonal cycle, amplification, Arctic-boreal, global change, and GEOS-Chem
- Citation to related publication:
- Lin, X., Rogers, B. M., Sweeney, C., Chevallier, F., Arshinov, M., Dlugokencky, E., Machida, T., Sasakawa, M., Tans, P., & Keppel-Aleks, G. (2020). Siberian and temperate ecosystems shape Northern Hemisphere atmospheric CO2 seasonal amplification. Proceedings of the National Academy of Sciences, 117(35), 21079–21087.
- Discipline:
- Science
-
- Creator:
- Basile, Samantha, Lin, Xin, and Keppel-Aleks, Gretchen
- Description:
- Files contain the atmospheric CO2 mole fraction responses to land flux type (HRcasa, HRcorpse, HRmimics) and land flux region (latband variable). Land flux regions are categorized as: Northern Hemisphere high latitudes (NHL; 61 to 90°N), midlatitudes (NML; 24 to 60°N), tropics (NT; 1 to 23°N), Southern Hemisphere tropics (ST; 0 to 23°S), and extratropics (SE; 24 to 90°S). See the README file for how these land flux region definitions relate to the file's latband variable. and To cite dataset: Basile, S., Lin, X., Keppel-Aleks, G. (2019). Simulated CO2 dataset using the atmospheric transport model GEOSChem v12.0.0: Response to regional land carbon fluxes [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/xjzc-xy05
- Keyword:
- carbon dioxide, soil heterotrophic respiration, GEOSChem, HR, CO2, CASA-CNP, CORPSE, and MIMICS
- Discipline:
- Science
-
- Creator:
- Limon, Garrett C.
- Description:
- The data represents weekly output from three 60-year CAM6 model runs. The output includes state (.h0. files) and tendency (.h1. files) fields for three difference model configurations of increasing complexity. State fields include temperature, surface pressure, specific humidity, among others; while tendencies include temperature tendencies, specific humidity tendencies, as well as precipitation rates. Using the state variables at a given time step, machine learning techniques can be trained to predict the following tendency field, which can then be applied to the state variables to provide the state at the next physics time step of the model.
- Keyword:
- Machine Learning, Climate Modeling, and Physics Emulation
- Citation to related publication:
- Limon, G. C., Jablonowski, C. (2022) Probing the Skill of Random Forest Emulators for Physical Parameterizations via a Hierarchy of Simple CAM6 Configurations [Preprint]. ESSOAr. https://10.1002/essoar.10512353.1
- Discipline:
- Engineering and Science
-
- Creator:
- Limon, Garrett C.
- Description:
- The work guides the processing of CAM6 data for use in machine learning applications. We also provide workflow scripts for training both random forests and neural networks to emulate physic s schemes from the data, as well as analysis scripts written in both Python and NCL in order to process our results.
- Keyword:
- Machine Learning, Climate Modeling, and Physics Emulation
- Citation to related publication:
- Limon, G. C., Jablonowski, C. (2022) Probing the Skill of Random Forest Emulators for Physical Parameterizations via a Hierarchy of Simple CAM6 Configurations [Pre Print]. ESSOAr. https://10.1002/essoar.10512353.1
- Discipline:
- Engineering and Science
-
- 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 dissected and fixed retinae in which cones of specific subtypes are labeled either by transgenic expression of a fluorescent reporter or by antibody staining (Figures 1 and 2 and 6A and Supplementary Figure 7A). This dataset also contains images of dissected and fixed retinae in ZO1 is immunostained (Figure 6C-E and Supplementary Figure 7B). Please see the readme file for which files correspond to which figures.
- Keyword:
- zebrafish cone mosaic, topological defects, and tissue patterning
- 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:
- Kim, Yongsung, Cheng, Weiqiu, Cho, Chun-Seok, Kang, Hyun Min, and Lee, Jun Hee
- Description:
- This dataset contains a typical example of Seq-Scope dataset that investigators would generate after examining the initial sequence data. If the quality of the initial Seq-Scope dataset looks great, one may decide to sequence the library much more deeply to maximize the information content. (see NovaScope tutorial at https://seqscope.github.io/NovaScope/ for more details). The spatial barcode sequences and the initial version of the sequenced cDNA library are deposited separate repository, which is described in the NovaScope documentation ( https://seqscope.github.io/NovaScope/). This data repository contains a deeper sequencing of the same library. A shallower version of sequencing, which does not have overlapping data with the current repository can be found at https://doi.org/10.5281/zenodo.10840695
- Keyword:
- Seq-Scope, Spatial Transcriptomics
- Citation to related publication:
- Yongsung Kim, Weiqiu Cheng, Chun-Seok Cho, Yongha Hwang, Yichen Si, Anna Park, Mitchell Schrank, Jer-En Hsu, Jingyue Xi, Myungjin Kim, Ellen Pedersen, Olivia I. Koues, Thomas Wilson, Goo Jun, Hyun Min Kang2, Jun Hee Lee, “Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics” (submitted)
- Discipline:
- Science
-
- 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:
- Huber, Daniel E
- Description:
- The files here provide monthly averaged soil NOx emissions (units of ng N m^-2 s^-1) for the contiguous United States on a 0.25 degree x 0.25 degree grid for the years 2011-2020 .
- Keyword:
- soil NOx, soil emissions, biogenic emissions, and agricultural emissions
- Discipline:
- Science
-
- Creator:
- James, David A. and Lokam, Nikhil
- Description:
- The object of this project is to provide researchers and students with a tool to allow them to develop an intuitive understanding of singular vectors and singular values. 2x2 matrices A with real entries map circles to ellipses; in particular, unit circles centered at the origin to ellipses centered at the origin. It is known that the points on the ellipse farthest from the origin correspond to the singular vectors of A. Users can use the GUI to enter matrices of their choice and explore to visually self-determine the singular vectors/values.
- Keyword:
- SVD, Singular Value Decomposition, Singular Vector, Singular Value, and Matrix
- Discipline:
- Science and Engineering
-
- Creator:
- Huang, Yihe (University of Michigan); De Barros, Louis (Université Côte d’Azur)
- Description:
- Numerous small and moderate injection-induced earthquakes have been recorded in North America, Europe and Asia. Here we present a detailed analysis about microearthquakes in an in-situ injection-induced earthquake experiment, which provides an unprecedented opportunity to investigate the mechanisms of induced earthquakes. Our analysis illuminates meter-scale earthquake sources distributed in a network of preexisting rock fractures. The majority of induced earthquakes in our analysis happened when injection pressure reached a peak, indicating a direct response of rock fractures to fluid pressure perturbation. But the relatively low ratio of stress drop to crustal strength reveals that a very small fraction of the crustal shear strength is released by earthquakes, supporting the previous notion that fluid injection induces large aseismic deformation during the experiment. and Citation for dataset: Huang, Y., De Barros, L. (2019). Seismograms of earthquake pairs in the injection experiment [Data set]. University of Michigan - Deep Blue.
- Keyword:
- Induced seismicity
- Citation to related publication:
- Huang, Y., De Barros, L., Cappa, F. (2019). Illuminating the Rupturing of Microseismic Sources in an Injection‐Induced Earthquake Experiment. Geophysical Research Letters, 46(16), 9563-9572. https://doi.org/10.1029/2019GL083856
- Discipline:
- Science