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- Creator:
- Howard, Cecilia M., Sheldon, Nathan D., Loveall, Zachary, Keating, Katarina A., Hong, Jungpyo, Smith, Selena Y., and Passey, Benjamin H.
- Description:
- This study uses an array of stratigraphic, morphological, and geochemical tools to investigate lateral and temporal variability in environmental records preserved by microbialites during a global hothouse environment. It also inverts tools for reconstructing environmental conditions to elucidate ancient microbial processes. Key Points: - The Green River Basin, WY, USA preserves lacustrine microbialites deposited during the Early Eocene Climatic Optimum, a period of high CO2 and temperatures - Morphological and geochemical analyses of these microbialites preserve variable local, regional, and global environmental conditions - Measurements of environmental conditions can be inverted to understand ancient microbial processes, which could be used to inform modeling of microbial influences on carbon cycling and Abstract: The Green River Basin, WY, USA, contains extensive lacustrine microbialite beds that formed during the hothouse Early Eocene Climatic Optimum (53–49 Ma). The records of biological, chemical, and physical processes preserved in these microbialites can inform our understanding of terrestrial conditions in this warm climate, but separating the competing signals of local, regional and global changes is difficult. Studies focusing on individual localities may miss spatial drivers of differences in microbialites. In this study, we used stratigraphic, morphological, and geochemical techniques to study microbialites deposited in the Green River Basin across three million years spanning the peak of the EECO, including samples from two beds covering 13–25 km of lateral extent. These samples cover a broad set of lake conditions as well as local differences such as spring deposits. We found that these microbialites preserved a mixture of conditions such as global hothouse temperatures, regional shifts in lake level, and local variability from sediment and water sources. Morphological and elemental variability were driven primarily by local and regional conditions such as stream, spring, and clastic inputs and water depth. Isotopic data preserved these local and regional changes as well as evidence of global hothouse conditions. Comparison of past [CO2] estimates to reconstructions using organic and inorganic carbon isotopes with clumped isotope-derived temperatures provides evidence for low to moderate microbial growth rates in these microbialite building communities, demonstrating that environmental tools can be inverted to better understand ancient microbial processes. A diverse toolkit was necessary to isolate the individual controls on microbialite records, and comparing across both space and time enabled us to identify local drivers that lead to significant differences from the expected regional signal.
- Keyword:
- Geosciences, Paleoclimate, Microbialite, Stromatolite, Eocene, Paleolake, and Green River Basin
- Discipline:
- Science
-
- Creator:
- Howard, Cecilia M., Velazquez, Diana, Rico, Kathryn I., and Sheldon, Nathan D.
- Description:
- This study combines a field survey time series with analysis of remotely and locally sensed environmental and climate data. Field survey data consists of sediment chemistry from hand-push cores, and includes %Corg, %N, δ13Corg, Corg:N, collection month and year, and depth in sediment. Climate and environmental data for the region around Middle Island Sinkhole was pulled from publicly available NOAA databases (ERDDAP, National Data Buoy Center, NWS) for as much of the same time period as the sediment data as was available. These data included general weather information from the NDBC and NWS (air temperature, wind speed, wind direction, gust speed, monthly precipitation totals), as well as satellite-derived environmental data from a 0.25° area centered on MIS (ice cover, lake surface temperature, CDOM, DOC, Chlorophyll, suspended minerals). Data were processed to monthly and annual averages as described below in order to compare to sinkhole sediment chemistry. Abstract: Records of recent past climate provide an essential window into understanding how changing climate influences environments and ecosystems such as lakes. Sediment carbon and nitrogen chemistry can offer insight into productivity and biochemistry, and anoxic sediments can often preserve short-term changes in these signals. We found that seasonal and annual changes in local ice season, chlorophyll, and precipitation influenced the amount and isotopic composition of carbon reaching the sediments of Middle Island Sinkhole, an anoxic sinkhole in Lake Huron. Carbon and nitrogen signals reflected the year or season of sample collection in sediments as deep as 12 cm. Our findings demonstrate that declining ice cover in this part of the Great Lakes is leading to increased export of organic carbon into sediments, but that in situ sediment processes may make teasing out short-term changes from sediment cores difficult even in an anoxic setting.
- Keyword:
- Carbon burial, Great Lakes, Ice cover, Sediment carbon, Sediment nitrogen, Anoxia, and Geosciences
- Discipline:
- Science
-
- Creator:
- Howard, Cecilia M. and Sheldon, Nathan D.
- Description:
- This study uses a compilation of microbialite occurrences in the Archean and Paleoproterozoic from the literature to investigate how depositional environment changed across environmental shifts such as the Great Oxidation Event and the Huronian Glaciations. Key Points: - We compiled microbialite occurrences from the Archean and Paleoproterozoic with broad depositional environment information, which has not previously been incorporated in larger compilations of occurrences. - Tidal and other terrestrially-influenced settings comprise the majority of the early microbialite record, even across major environmental shifts and Abstract: Changes in microbialite abundance during the Archean and Paleoproterozoic have been attributed to a variety of environmental and biological factors. Past work looking at large-scale patterns of microbialite abundance generally assumes shallow marine deposition rather than incorporating specific settings, however, there is significant variance in conditions that might impact microbialite formation and preservation between marine, tidal, and terrestrial environments. We compiled microbialite occurrences from the Archean and Paleoproterozoic with integrated depositional environment information in order to assess how microbialite development and preservation changed across different settings. Microbially induced sedimentary structures formed a significant part of the record, but their identification primarily in conjunction with stromatolites rather than independently suggests that they may be undercounted. Broad trends in abundance were similar to previous compilations, but critically, we found that the majority of microbialites from this period formed in tidal environments. The proportion of terrestrially-influenced (including tidal) microbialites increased during periods of craton development in the Neoarchean and mid-Paleoproterozoic, with increases in marine microbialite abundance trailing. Tidal microbialite abundance also recovered more quickly than marine abundance following the Great Oxidation Event and Huronian Glaciations.
- Keyword:
- Microbialite, Stromatolite, Archean, Paleoproterozoic, Geosciences, and Tidal
- Discipline:
- Science
-
- Creator:
- Zetterberg, Daniel S., Huang, Xianglei, Hörner, Johannes, Voigt, Aiko, and Chen, Xiuhong
- Description:
- The data and code stored in this repository present the results of the paper "Instantaneous radiative effect of surface long wave spectral emissivity in a Snowball Earth simulation." In this paper, we calculate the instantaneous radiative effects of surface spectral emissivity for a Snowball Earth simulation, and find that including surface spectral emissivity has a moderate effect on the radiation budget. For clear-sky conditions, using ice or snow spectral emissivity can decrease outgoing long wave radiation by 2.9 or 1.0 W/m^2, respectively, globally averaged. This large effect could impact the simulated climate state of a Snowball Earth and potentially strengthen the Jormungand mechanism. Additionally, the large difference between ice and snow highlights the importance of precipitation processes in Snowball modeling. , This repository contains the results of the calculations and the data and code needed to recreate the manuscript figures. It contains atmospheric conditions from the simulations run by JH and AV that were processed by DSZ. It also contains emissivity datasets that were compiled by Huang et al. 2016 ("A global data set of surface spectral emissivity for GCM and NWP use"). MODTRAN calculations of the outgoing longwave radiation were processed by DSZ, XLH, and XC. The results of the study are contained in netcdf files. The README file offers a description, and the Jupyter notebook demonstrates how to access, use, and plot the calculations. , and ***Changes on 10 June, 2025*** New data files contain the outgoing longwave radiation from MODTRAN calculations, but with multiple scattering enabled in MODTRAN. The result is that downward atmospheric radiation can reflect off the surface back to the top of the atmosphere. The result is that the effect of surface emissivity is slightly decreased, though the conclusions and discussion remain unchanged. Additionally, Xiuhong Chen was added as an author, as her expertise in MODTRAN aided in resolving this issue. Data for a plot of a sample emission spectrum was also added, as this was used in the revised manuscript. Key points were updated to match those in the related article.
- Keyword:
- Spectral surface emissivity, Snowball Earth, paleoclimate modeling
- Citation to related publication:
- Zetterberg, D.S., Huang, X.L., Hörner, J., & Voigt, A. Instantaneous radiative effect of surface long wave spectral emissivity in a Snowball Earth simulation. Submitted to Journal of Geophysical Research: Atmospheres, February 2025
- Discipline:
- Science
-
- Creator:
- Colón-Rodríguez, Stephanie, Liemohn, Michael, Raines, Jim, and Lepri, Susan T.
- Description:
- During its trajectory, Wind spent a significant amount of time in the magnetotail, where its SupraThermal Ion Composition Spectrometer (STICS) measured the mass and mass per charge of protons, alpha particles, and heavy ions with an energy/charge ratio up to 226 keV/e. Although STICS originally aimed to measure the abundance of these ion species in the solar wind, its measurements within the magnetosphere from 1995 to 2002 help us identify preferential entry between the different solar wind ion species. This study statistically analyzes how the ratio between solar wind heavy ions and alpha particles (Heavies Solar Wind / He2+) varies for different upstream conditions and locations within the magnetosphere: northward vs. southward Interplanetary Magnetic Field (IMF), low vs. high solar wind density (Nsw), low vs. high solar wind dynamic pressure (PDyn), slow vs. fast solar wind (Vsw), and dawn vs. dusk. Our results indicate that the HeaviesSolar Wind enter the magnetosphere more efficiently than He2+ during northward IMF and that the Heavies Solar Wind / He2+ ratios decrease during high PDyn. In addition, the Heavies Solar Wind / He2+ ratios exhibit a dawn-dusk asymmetry, highly skewed towards the dawn side for all upstream cases likely due to charge-exchange processes.
- Keyword:
- Magnetosphere, Wind STICS, Solar wind heavy ions, Alpha particles, and dawn-dusk asymmetry
- Citation to related publication:
- Colón-Rodríguez, S., Liemohn, M. W., Raines, J. M, & Lepri, S.T. (2024). Solar wind heavy ions and alpha particles within Earth’s magnetosphere and their variability with upstream conditions. Journal of Geophysical Research Space Physics. In preparation.
- Discipline:
- Science
-
Publicly available repository for "Polariton Chern Bands in 2D Photonic Crystals beyond Dirac Cones"
- Creator:
- Xie, Xin, Sun, Kai, and Deng, Hui
- Description:
- This study explores new platforms for realizing polariton Chern bands in 2D photonic crystals (PhCs) by moving beyond the traditional Dirac cone framework. It focuses on band structures with symmetry-protected bound states in the continuum and Γ-point degeneracies, enabling larger topological gaps, higher Chern numbers, and more uniform Berry curvature—features crucial for experiments and device applications. Eigenvalue and Berry curvature calculations were performed using MATLAB and Mathematica, while Lumerical FDTD was used to simulate photonic and polaritonic band structures in realistic TMD-PhC systems, as well as edge-state dispersion. Reproducing the data requires access to these software tools.
- Keyword:
- Topological photonics, Topological polariton, Topological insulator, and Chern insulator
- Citation to related publication:
- Xie, Xin, Sun, Kai, Deng, Hui. Polariton Chern Bands in 2D Photonic Crystals beyond Dirac Cones. Phys. Rev. X, 15(2), 021061 (2025). https://doi.org/10.1103/PhysRevX.15.021061
- Discipline:
- Science
-
- Creator:
- Gergely Koban, Judit Szente, Bart van der Holst, Gabor Toth, and Enrico Landi
- Description:
- This study aims to assess the performance of coronal models across multiple solar cycles and to analyze long-term variations in solar coronal structures observed in multiple EUV channels. To achieve this, we developed a comprehensive database of solar corona (data cubes) and inner heliosphere simulation outputs using the Alfvén Wave Solar atmosphere Model (AWSoM) within the Space Weather Modeling Framework (SWMF) for Solar Cycles 24 and 25 (SC24 and SC25). This database enables us to investigate the temporal evolution of solar wind source regions—Coronal Holes (CH) and Active Regions (AR). Model accuracy was assessed by comparing synthetic images with concurrent AIA observations in six EUV channels (94, 131, 171, 193, 211, and 335 Å). Additionally, we evaluated the reliability of AWSoM’s solar wind plasma outputs at 1 AU by comparing them with OMNI data for each Carrington Rotation (CR).
- Keyword:
- Solar Corona, SWMF, Solar Physics, Solar Cycle, and MHD Modelling
- Citation to related publication:
- Koban et al. (2025). Validation of Long-Term Solar Coronal Modeling Using FORWARD (Under review).
- Discipline:
- Science
-
- Creator:
- Haynes, Laura M, Holding, Matthew L, Woodard, Jaie, Siemieniak, David, and Ginsburg, David
- Description:
- A phage displayed amino acid site-saturated variant library of plasminogen activator inhibitor (PAI-1) was screened for thermodynamic functional stability. The data are interpreted in the context of protein evolution and computational variant effect/protein stability predictors. This data set contains FASTQ files of the PAI-1 sequence variants that affect its thermodynamic stability, as well as scripts needed to analyze these files.
- Keyword:
- serpins, deep mutational scanning, thermodynamics, metastable proteins, and purifying selection
- Citation to related publication:
- Haynes LM, Holding ML,Woodard J, Siemieniak D, Ginsburg D. Thermodynamics and selection of the plasminogen activator inhibitor-1 latency transition. bioRxiv [Preprint]. 2025.06.03.655624; doi: https://doi.org/10.1101/2025.06.03.655624
- Discipline:
- Science
-
- Creator:
- Wittkopp, Patricia J and Massey, Jonathan H
- Description:
- Data provided in this record were collected in the course of studying the genetic basis of differences in wing pigmentation and wing display between Drosophila elegans and Drosophila gunungcola.
- Citation to related publication:
- Massey, J. H., Rice, G. R., Firdaus, A. S., Chen, C.-Y., Yeh, S.-D., Stern, D. L., & Wittkopp, P. J. (2020). Co-evolving wing spots and mating displays are genetically separable traits in Drosophila. Evolution, 74(6), 1098–1111. https://doi.org/10.1111/evo.13990
- Discipline:
- Science
-
- Creator:
- Moore, Talia Y., Danforth, Shannon M., Larson, Joanna G., and Davis Rabosky, Alison R.
- Description:
- Warning signals in chemically defended organisms are critical components of predator-prey interactions, often requiring multiple coordinated display components for a signal to be effective. When threatened by a predator, venomous coral snakes (genus Micrurus) display a vigorous, non-locomotory thrashing behaviour that has been only qualitatively described. Given the high-contrast and often colourful banding patterns of these snakes, this thrashing display is hypothesized to be a key component of a complex aposematic signal under strong stabilizing selection across species in a mimicry system. By experimentally testing snake response across simulated predator cues, we analysed variation in the presence and expression of a thrashing display across five species of South American coral snakes. Although the major features of the thrash display were conserved across species, we found significant variation in the propensity to perform a display at all, the duration of thrashing, and the curvature of snake bodies that was mediated by predator cue type, snake body size, and species identity. We also found an interaction between curve magnitude and body location that clearly shows which parts of the display vary most across individuals and species. Our results suggest that contrary to the assumption in the literature that all species and individuals perform the same display, a high degree of variation persists in thrashing behaviour exhibited by Micrurus coral snakes despite presumably strong selection to converge on a common signal. This quantitative behavioural characterization presents a new framework for analysing the non-locomotory motions displayed by snakes in a broader ecological context, especially for signalling systems with complex interaction across multiple modalities.
- Keyword:
- aposematism, biomechanics, coral snake mimicry, curvature, Elapidae, non-locomotory motion, Peruvian Amazon, and snake behaviour
- Citation to related publication:
- Moore, T. Y., Danforth, S. M., Larson, J. G., & Davis Rabosky, A. R. (2020). A Quantitative Analysis of Micrurus Coral Snakes Reveals Unexpected Variation in Stereotyped Anti-Predator Displays Within a Mimicry System. Integrative Organismal Biology, 2(1). https://doi.org/10.1093/iob/obaa006
- Discipline:
- Science
-
- Creator:
- Ridley, Aaron and Cnossen, Ingrid
- Description:
- These are modeling results of the thermospheric and ionospheric response to the solar eclipse of August 21, 2017. The results are discussed in a research paper published in the Journal of Geophysical Research (doi: 10.1029/2018JA026402) .
- Citation to related publication:
- Cnossen, I., Ridley, A. J., Goncharenko, L. P., and Harding, B. J.. ( 2019), The response of the ionosphere‐thermosphere system to the August 21, 2017 solar eclipse. J. Geophys. Res. Space Physics, 124. https://doi.org/10.1029/2018JA026402
- Discipline:
- Science
-
- Creator:
- dos Santos, Thiago, Steiner, Allison, Keppel-Aleks, Gretchen, and De Roo, Roger
- Description:
- Model simulations were conducted to investigate the role of soil moisture on the terrestrial carbon and water cycles. The data are composed of NetCDF files generated by the simulations that contain the data variables analyzed in the paper. and CLM5 Documentation - http://www.cesm.ucar.edu/models/cesm2/land/.
- Keyword:
- Soil moisture, Community Land Model 5, Latent heat, GPP, Gross primary productivity, and Fluxnet
- Citation to related publication:
- Santos, T. dos, Keppel-Aleks, G., Roo, R. D., & Steiner, A. L. (2021). Can Land Surface Models Capture the Observed Soil Moisture Control of Water and Carbon Fluxes in Temperate-To-Boreal Forests? Journal of Geophysical Research: Biogeosciences, 126(4), e2020JG005999. https://doi.org/10.1029/2020JG005999
- Discipline:
- Science
-
- Creator:
- Ruas, Terry, Ferreira, Charles H. P., Grosky, William, França, Fabrício O., and Medeiros, Débora M. R,
- Description:
- The relationship between words in a sentence often tell us more about the underlying semantic content of a document than its actual words, individually. Recent publications in the natural language processing arena, more specifically using word embeddings, try to incorporate semantic aspects into their word vector representation by considering the context of words and how they are distributed in a document collection. In this work, we propose two novel algorithms, called Flexible Lexical Chain II and Fixed Lexical Chain II that combine the semantic relations derived from lexical chains, prior knowledge from lexical databases, and the robustness of the distributional hypothesis in word embeddings into a single decoupled system. In short, our approach has three main contributions: (i) unsupervised techniques that fully integrate word embeddings and lexical chains; (ii) a more solid semantic representation that considers the latent relation between words in a document; and (iii) lightweight word embeddings models that can be extended to any natural language task. Knowledge-based systems that use natural language text can benefit from our approach to mitigate ambiguous semantic representations provided by traditional statistical approaches. The proposed techniques are tested against seven word embeddings algorithms using five different machine learning classifiers over six scenarios in the document classification task. Our results show that the integration between lexical chains and word embeddings representations sustain state-of-the-art results, even against more complex systems. Github: https://github.com/truas/LexicalChain_Builder
- Keyword:
- document classification, lexical chains, word embeddings, synset embeddings, chain2vec, and natural language processing
- Citation to related publication:
- Terry Ruas, Charles Henrique Porto Ferreira, William Grosky, Fabrício Olivetti de França, Débora Maria Rossi de Medeiros, "Enhanced word embeddings using multi-semantic representation through lexical chains", Information Sciences, 2020, https://doi.org/10.1016/j.ins.2020.04.048
- Discipline:
- Other, Science, and Engineering
-
- Creator:
- Trung, Huy-Sinh, Liemohn, Michael W, and Ilie, Raluca
- Description:
- The goal of this research was to understand structures where the solar wind plasma contribution to the total plasma was equal to the ionospheric plasma. This simulation was performed over a simulation time of 12 hours for 4 different plasma compositions for 2 different solar wind profiles., The SWMF used the Block Adaptive Tree Solar wind Roe-type Upwind Scheme version 9.20. It can be found at http://csem.engin.umich.edu/tools/swmf/downloads.php. These data can be processed using the simulation code deposited at the Deep Blue Data record indicated in the "Citation to related material" field., and To cite this data set: Trung, H.-S., Liemohn, M., W., Ilie, R. (2019). 12 hour data for magnetospheric simulations for a multifluid plasma for 8 different configurations [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/fwq2-ey41
- Keyword:
- Space Physics, Magnetospheres, and 3D
- Citation to related publication:
- Trung, H.-S., Liemohn, M.W. Ilie, R. (2019). Steady State Characteristics of the Terrestrial Geopause [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/7w13-kq27
- Discipline:
- Science
-
- Creator:
- Li, Yang and Steiner, Allison
- Description:
- WRF-Chem simulation with 1.33 km resolution using the MYJ PBL scheme over the Baltimore-Washington region and WRF-Chem simulation with 1.33 km resolution using the YSU PBL scheme over the Baltimore-Washington region
- Keyword:
- LES, WRF-Chem, vertical mixing, oxidants, boundary layer dynamics
- Citation to related publication:
- Li, Y., Barth, M. C., and Steiner, A. L.: Comparing turbulent mixing of atmospheric oxidants across model scales, Atmospheric Environment, 199, 88-101, https://doi.org/10.1016/j.atmosenv.2018.11.004, 2018.
- Discipline:
- Science
-
- Creator:
- Morales, Annareli
- Description:
- The research that produced this data involves exploring the sensitivity of orographic precipitation to changes in microphysical parameters found in the Morrison microphysics scheme within CM1 model. These microphysical sensitivities are also tested within different environments. The tests can be described as "one-at-a-time" experiments, i.e., an individual parameter is perturbed while keeping the rest constant. Annareli Morales conducted this research for her PhD research while working at the Mesoscale and Microscale Meteorology lab at NCAR in Boulder, CO.
- Keyword:
- Orographic precipitation
- Citation to related publication:
- Morales, A., H. Morrison, and D. Posselt, 2018: Orographic precipitation response to microphysical parameter perturbations for idealized moist nearly neutral flow. Journal of Atmospheric Science, 75, 1933-1953, https://doi.org/10.1175/JAS-D-17-0389.1
- Discipline:
- Science
-
- Creator:
- Burleigh, M.
- Description:
- Brightness from an all-sky imager has been used as a spatiotemporal constraint for auroral inputs selected from in situ rocket measurements which are used to drive the ionospheric model. This method allows for realistic ionospheric forcing that is not captured in traditional "on-off" methods of describing PMAFs. Transient forcing (simulated PMAFs) and steady forcing ("on-off") simulations have been generated for comparison.
- Keyword:
- Poleward moving auroral forms, High-latitude ionosphere, Ionospheric modeling, Transient forcing, PMAF, GEMINI-TIA, and RENU2
- Citation to related publication:
- Burleigh, M., Zettergren, M., Lynch, K., Lessard, M., Moen, J., Clausen, L., Kenward, D., Hysell, D., and Liemohn, M. (2019). Transient ionospheric upflow driven by poleward moving auroral forms observed during the Rocket Experiment for Neutral Upwelling 2 (RENU2) campaign. Geophysical Research Letters. (Submitted).
- Discipline:
- Science
-
Galaxy Shape Catalogs for Dark Energy Survey Science Verification (DES-SV) Data - Additional Regions
- Creator:
- Das, Rutuparna and Dark Energy Survey (DES)
- Description:
- This dataset is associated with the University of Michigan Dept. of Physics dissertation titled "Shedding Light on the Dark: Exploring the Relation Between Galaxy Cluster Mass and Temperature Through Weak Gravitational Lensing" by Rutuparna Das. It is also associated with a paper, currently in preparation, by Das et al (details to be added once paper is submitted/accepted)., This work contains information about shapes of galaxies observed by the Dark Energy Survey (DES) during its Science Verification (SV) run. The official DES SV shape catalog has already been released to the public (see details in Jarvis et al. (2016), henceforth called "J16"). This work follows the methods presented in J16, and contains shapes from areas of the sky that were not processed as part of the official DES-SV catalog but were necessary for the work presented in the aforementioned dissertation. Each catalog contains information for galaxies in a 80′ × 80′ cutout centered at a given galaxy cluster., Note that these catalogs are not entirely analogous to the official DES-SV catalog. For one, we only measure shapes for galaxies, as stars and other objects were not needed for the dissertation. Our catalogs also only extend to a magnitude of 24 in r-band, whereas a small fraction of the objects in the official Im3shape catalog are dimmer (see Figure 29 of J16)., We also include other information necessary for weak lensing studies. Aside from all fields from Im3shape and noise bias calibration (listed and described in J16), these catalogs contain columns for object positions (“ra_gold”, “dec_gold”) and magnitudes in various filters (“mag_detmodel_g”, “mag_detmodel_r”, “mag_detmodel_i”, “mag_detmodel_z”) from the SVA1-Gold catalog ( https://des.ncsa.illinois.edu/releases/sva1/docs/docs-gold). Additionally, we include mean redshift measurements from two DES photo-z measurement pipelines, TPZ and DESDM Neural Network (“z_TPZ”, “z_DESDMnn”) (more details in Sanchez et al. (2014))., and References: Jarvis, M., Sheldon, E., Zuntz, J., et al. 2016, Monthly Notices of the Royal Astronomical Society, 460, 2245. Sanchez, C., Carrasco Kind, M., Lin, H., et al. 2014, Monthly Notices of the Royal Astronomical Society, 445, 1482.
- Keyword:
- weak lensing, galaxy clusters, galaxy shapes, cluster cosmology, Dark Energy Survey, DES, and galaxy shape catalogs
- Discipline:
- Science
-
- Creator:
- Bhattiprolu, Prudhvi N, Petrosky, Evan, and Pierce, Aaron
- Description:
- This dataset stems from research on the singlet-doublet model of dark matter, an economical model of weakly interacting dark matter. We revisit it in light of improved dark matter detection limits. We characterize the regions of parameter space that have suppressed direct detection cross sections and discuss predictions for the Large Hadron Collider.
- Keyword:
- Dark matter models
- Citation to related publication:
- Bhattiprolu, P. N., Petrosky, E., Pierce, A. Singlet-doublet dark matter revisited, https://doi.org/10.48550/arXiv.2505.11607
- Discipline:
- Science
-
- Creator:
- Banerjee, Pavel , Ray, Sujay, Dai, Liuhan, Sandford, Erin, Chatterjee, Tanmay, Mandal, Shankar, Siddiqui, Javed, Tewari, Muneesh, and Walter, Nils G
- Description:
- Early and personalized intervention in complex diseases requires robust molecular diagnostics, yet the simultaneous detection of diverse biomarkers—microRNAs (miRNAs), mutant DNAs, and proteins—remains challenging due to low abundance and preprocessing incompatibilities. We present Biomarker Single-molecule Chromato-kinetic multi-Omics Profiling and Enumeration (Bio-SCOPE), a next-generation, triple-modality, multiplexed detection platform that integrates both chromatic and kinetic fingerprinting for nanoscale molecular profiling through digital encoding. Bio-SCOPE achieves femtomolar sensitivity, single-base mismatch specificity, and minimal matrix interference, enabling precise, parallel quantification of up to six biomarkers in a single sample with single-molecule resolution. We demonstrate its versatility in accurately detecting low-abundance miRNA signatures from human tissues, identifying upregulated miRNAs in the plasma of prostate cancer patients, and measuring elevated interleukin-6 (IL-6) and hsa-miR-21 levels in cytokine release syndrome patients (the studies that collected these samples were approved by University of Michigan's Medical School Institutional Review Board HUM00043354, HUM00115179 and HUM00037879). By seamlessly integrating multiomic biomarker panels on a unified, high-precision platform, Bio-SCOPE provides a transformative tool for molecular diagnostics and precision medicine.
- Keyword:
- biomarker, fingerprinting, multiplexed detection, digital encoding, single molecule, multiomic, precision medicine
- Citation to related publication:
- Banerjee, Ray, Dai et al. Chromato-Kinetic Fingerprinting Enables Multiomic Digital Counting of Single Disease Biomarker Molecules. ACS Nano. Submitted.
- Discipline:
- Science
-
- Creator:
- Bai, Bobo and Zhang, Youxue
- Description:
- This dataset is referenced in the manuscript “Multicomponent diffusion in basaltic melts: A temperature-independent eigenvector matrix, and a multicomponent diffusion calculator”. This manuscript explores the temperature independence of diffusion eigenvectors in an 8-component basaltic melt and provides an open-access calculator for the community to compute multicomponent diffusion profiles.
- Keyword:
- Eigen-components, Multicomponent diffusion, Uphill diffusion, and Multicomponent diffusion calculator
- Discipline:
- Science
-
- Creator:
- Faulkner, Alexa
- Description:
- This study uses in vivo two-photon calcium imaging in the visual cortex of mice to demonstrate that encoding of learned environmental visual cues is flexibly represented across different task contexts. This dataset is comprised of in vivo two-photon calcium imaging from visual cortex of mice during learning and performance of a visual discrimination task. data was acquired suing Scanbox and analysis performed in Matlab and Python.
- Keyword:
- neuroscience, two photon calcium imaging, visual cortex, and mouse
- Discipline:
- Science
-
- Creator:
- Weeks, Brian C
- 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. The photographs have been used to measure skeletal traits using 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 dataset includes images of 12,421 specimens from 1,881 species of passerine birds.
- Keyword:
- Songbird skeletons, Functional traits, Comparative morphometrics, and Computer vision
- Citation to related publication:
- Weeks, B.C., Z. Zhou, C.M. Probst, J.S. Berv, B. O’Brien, B.W. Benz, H.R. Skeen, M. Ziebell, L. Bodt, and D.F. Fouhey. 2024. Skeletal trait measurements for thousands of bird species. bioRxiv. https://doi.org/10.1101/2024.12.19.629481 and Weeks, B.C., Z. Zhou, C.M. Probst, J.S. Berv, B. O’Brien, B.W. Benz, H.R. Skeen, M. Ziebell, L. Bodt, and D.F. Fouhey. 2024. Skeletal trait measurements for thousands of bird species. Scientific Data. https://doi.org/10.1038/s41597-025-05234-y
- Discipline:
- Science
-
- Creator:
- Craven, Nicholas C, Singh, Ramanish, Quach, Co D, Gilmer, Justin B, Crawford, Brad, Marin-Rimoldi, Eliseo, Smith, Ryan, DeFever, Ryan, Dyukov, Maxim, Fothergill, Jenny, Jones, Chris, Moore, Timothy, Butler, Brandon L, Anderson, Joshua A, Iacovella, Christopher, Jankowski, Eric, Maginn, Eric, Potoff, Jeffrey, Glotzer, Sharon C, McCabe, Clare, Cummings, Peter T, and Siepmann, Ilja J
- Description:
- Data are collected in 5 separate workspace, one for the main density data calculations across the space and 4 for the subproject simulations that were performed to validate and dive deeper into specific engine implementations. In order to copy the simulation trajectory and calculated averages used to generate figures, these workspace folders must be downloaded and pointed to the correct place in the GitHub Project Structure, which can be found at https://github.com/mosdef-hub/reproducibility_study and Each compressed file contains the data for a single workspace.
- Keyword:
- molecular dynamics, monte carlo, reproducibility, and replicability
- Citation to related publication:
- https://doi.org/10.1021/acs.jced.5c00010
- Discipline:
- Science
-
- Creator:
- Liu, Bin , Silori, Yogita, Li, Yongxi, Forrest, Stephen R., and Ogilvie, Jennifer P.
- Description:
- We use angle-resolved reflection measurements to characterize polariton dispersion, and use ultrafast transient absorption (TA) spectroscopy to study the influence of the “open cavity” on the charge generation dynamics of the donor-acceptor bilayer and blend systems.
- Citation to related publication:
- Yogita Silori, Bin Liu, Yongxi Li, Stephen R. Forrest, and Jennifer P. Ogilvie, "Impact of Cavity Strong Coupling on the Charge Transfer Dynamics in Organic Donor-Acceptor Heterojunctions", Phys. Rev. B. Accepted April 2025, https://doi.org/10.1103/859s-sc6n
- Discipline:
- Science
-
- Creator:
- Chen, Hongfan, Chen, Yang, Huang, Zhenguang, Zou, Shasha, Huan, Xun, and Toth, Gabor
- Description:
- Accurately predicting the horizontal component of the ground magnetic field perturbation (dBH), which can be used to calculate the Geomagnetically Induced Currents (GICs), is crucial for estimating the space weather impact of geomagnetic disturbances. In this work, we develop a new data-driven model GeoDGP using deep Gaussian process (DGP), which is a Bayesian non-parametric approach. The model provides global probabilistic forecasts of dBH at 1-minute time cadence and with arbitrary spatial resolutions. We evaluate the model comprehensively on a wide range of geomagnetic storms, including the 2024 Gannon extreme storm. The results show that GeoDGP significantly outperforms the state-of-the-art physics-based first-principles Space Weather Modeling Framework (SWMF) Michigan Geospace model and the data-driven DAGGER model.
- Keyword:
- Space Weather, Uncertainty Quantification, Machine Learning, and Bayesian Inference
- Citation to related publication:
- Chen, H., et al. (2024). GeoDGP: One-Hour Ahead Global Probabilistic Geomagnetic Perturbation Forecasting using Deep Gaussian Process.
- Discipline:
- Science and Engineering
-
- Creator:
- King, Katelyn, Fujisaki-Manome, Ayumi, Brant, Cory, and Alofs, Karen
- Description:
- Ice cover on the Great Lakes plays an important role in regional climate, supports tourism and recreation, and provides ecological habitat. As the climate warms, ice cover in the Great Lakes is expected to decline, which in turn will create more lake effect precipitation, reduce ice cover for recreation, and alter habitat for fishes. Therefore, it is important to understand historical ice patterns to better understand and predict future ice cover on the lakes. However, Great Lakes ice cover data prior to 1973 is scarce, due to the limited routine satellite observations. Our dataset aims to fill this gap by providing historical spatial ice duration layers to be used for modeling species distributions. and ArcGIS Pro ( https://www.esri.com/en-us/arcgis/products/arcgis-pro/overview), QGIS ( https://qgis.org/) or other spatial data software will be required to view this dataset.
- Keyword:
- ice, Great Lakes, Superior, Michigan, Ontario, Erie, Huron, and historical
- Citation to related publication:
- King, K., Fujisaki-Manome, A., Brant, C., Cohn, D., Peng, I., Alofs, K., Reconstructing Great Lakes air temperature and ice dynamics data back to 1897. Under Review
- Discipline:
- Science
-
- Creator:
- Aksoy, Doruk and Kim, Donghak
- Description:
- This dataset contains snapshots from simulations of a hexagonal self oscillating gel sheet defined via a triangular lattice. The lattice has stretching springs between neighboring vertices and bending springs with energy proportional to the square of the angle between neighboring traingular faces. The motion of the lattice is driven by time- and space-varying distributions of the rest lengths of the stretching springs. In the motivating experiments on thin gel sheets, there are chemical waves, radial or spiral in form, that induce local swelling of the sheets. As a simple model, this dataset considers radial or planar (unidirectional) traveling waves in the simulations. The sheet is modeled as a flat hexagon of radius 1 with an equilateral triangular triangle lattice mesh, with initially uniform mesh spacing of 1/33, resulting in 3367 mesh points. A small out-of-plane perturbation is applied and the motion evolves over the sheet over time. The sheet is modeled to have damped dynamics. However for large enough wave amplitudes, the sheet rapidly buckles into shapes with time-varying distributions of curvature, large in magnitude. For more information on the simulation that generated the data, please refer to "Semi-implicit methods for the dynamics of elastic sheets,” at Journal of Computational Physics by Alben et al. For an example SciML application that considers this dataset, please refer to "Inverse design of self-oscillatory gels through deep learning." Neural Computing and Applications by Aksoy et al.
- Keyword:
- Soft robotics, Partial Differential Equations, Scientific Simulations, and Chaotic Systems
- Citation to related publication:
- Alben, Silas, et al. "Semi-implicit methods for the dynamics of elastic sheets." Journal of Computational Physics 399 (2019): 108952., Aksoy, Doruk, et al. "Inverse design of self-oscillatory gels through deep learning." Neural Computing and Applications 34.9 (2022): 6879-6905., Aksoy, Doruk, et al. "An incremental tensor train decomposition algorithm." SIAM Journal on Scientific Computing 46.2 (2024): A1047-A1075., and Aksoy, Doruk, and Alex A. Gorodetsky. "Incremental Hierarchical Tucker Decomposition." arXiv preprint arXiv:2412.16544 (2024).
- Discipline:
- Engineering and Science
-
- Creator:
- Beletsky, Dmitry, Beletsky, R, and Rowe, M
- Description:
- Reliable prediction of hypoxic events in the coastal ocean and lakes depends to a large degree on the ability of hydrodynamic models to accurately simulate nearshore circulation and thermal structure. With focus on the hypoxia-prone south shore of Lake Erie, temperature and currents were measured in the central basin in 2017-2019. Major upwelling events along the south shore were identified and linked with occurrence of strong, sustained wind from the northeast (NE). A three-dimensional FVCOM-based hydrodynamic model was able to predict upwelling events along the south shore reasonably well but the surface mixed layer and thermocline depth were shallower than in observations. It was found that basin-scale wind stress curl (WSC) transformed canonic two-gyre circulation in the uniform NE wind case into a single gyre circulation causing both alongshore and cross-shore current reversal that modified coastal upwelling/downwelling. Observational evidence of Kelvin waves on the south shore was found for the first time. Kelvin wave speed in the model was underestimated. Model runs with enhanced vertical mixing improved predictions of mixed layer and thermocline depth and near-bottom dissolved oxygen but also caused additional diffusion of thermocline.
- Discipline:
- Science
-
- Creator:
- Ludlow, Andrew
- Description:
- Single molecule long read RNA/cDNA sequencing of TERT revealed 45 TERT mRNA variants including 13 known and 32 novel variants. Among the variants, TERT Delta 2-4, which lacks exons 2-4 but retains the original open reading frame, was selected for further study. Induced pluripotent stem cells and cancer cells express higher levels of TERT Delta 2-4 compared to primary human bronchial epithelial cells. Overexpression of TERT Delta 2-4 enhanced clonogenicity and resistance to cisplatin-induced apoptosis. Knockdown of endogenous TERT Delta 2-4 in Calu-6 cells reduced clonogenicity and resistance to cisplatin. Our results suggest that TERT Delta 2-4 enhances cancer cells’ resistance to intrinsic apoptosis. RNA sequencing following knockdown of Delta 2-4 TERT indicates that translation is downregulated and that mitochondrial related proteins are upregulated compared to controls.
- Keyword:
- TERT, Alternative splicing, Telomere, and Telomerase
- Citation to related publication:
- Kim, J.J., Ahn, A., Ying, J.Y. et al. Discovery and characterization of a novel telomerase alternative splicing isoform that protects lung cancer cells from chemotherapy induced cell death. Sci Rep 15, 6787 (2025). https://doi.org/10.1038/s41598-025-90639-3
- Discipline:
- Science
-
- Creator:
- Ludlow, Andrew and Kim, Jeongjin
- Description:
- Part of the regulation of telomerase activity includes the alternative splicing (AS) of the catalytic subunit telomerase reverse transcriptase (TERT). Although a therapeutic window for telomerase/TERT inhibition exists between cancer cells and somatic cells, stem cells express TERT and rely on telomerase activity for physiological replacement of cells. Therefore, identifying differences in TERT regulation between stem cells and cancer cells is essential for developing telomerase inhibition-based cancer therapies that reduce damage to stem cells. In this study, we measured TERT splice variant expression and telomerase activity in induced pluripotent stem cells (iPSCs), neural progenitor cells (NPCs), and non-small cell lung cancer cells (NSCLC, Calu-6 cells). We observed that a NOVA1-PTBP1-PTBP2 axis regulates TERT alternative splicing (AS) in iPSCs and their differentiation into NPCs. We also found that splice-switching of TERT, which regulates telomerase activity, is induced by different cell densities in stem cells but not cancer cells. Lastly, we identified cell type-specific splicing factors that regulate TERT AS. Overall, our findings represent an important step forward in understanding the regulation of TERT AS in stem cells and cancer cells. These data and subsequent studies may reveal a splicing factor(s) or their binding site(s) that could be targeted with small molecule drugs or antisense oligonucleotides, respectively, to reduce telomerase activity in cancer cells and promote durable cancer remissions.
- Keyword:
- Telomere, telomerase, TERT, alternative RNA splicing
- Citation to related publication:
- Kim JJ, Sayed ME, Ahn A, Slusher AL, Ying JY, et al. (2023) Dynamics of TERT regulation via alternative splicing in stem cells and cancer cells. PLOS ONE 18(8): e0289327. https://doi.org/10.1371/journal.pone.0289327
- Discipline:
- Science
-
Great Lakes Historical Ice Dynamics
User Collection
- Creator:
- King, Katelyn B., Fujisaki-Manome, Ayumi, Brant, Cory, and Alofs, Karen
- Description:
- This collection includes raster layers (as a geodatabase) with ice metrics for each of the Great Lakes representing the historical time period of 1898-1960. One metric is spatial mean ice duration (the number of days per year when the lake was frozen) and the other is coefficient of variation of ice duration (variability across years).
- Keyword:
- Great Lakes, Ice , Ice duration, Ice variability, Historical , Huron, Ontario, Erie, Michigan, and Superior
- Discipline:
- Science
1Works -
- Creator:
- King, Katelyn, Schell, Justin, Alofs, Karen, Thomer, Andrea, Wehrly, Kevin, Lenard, Michael , and Lopez-Fernandez, Hernan
- Description:
- Michigan lakes are an important resource, however, their ecosystems are declining and projected to continue to face further impacts under future land use and climate change. Understanding how lake ecosystems respond to environmental stressors and management actions is critical for identifying resilient lakes and developing adaptation strategies. However, the ability to manage lakes is hampered by a lack of historical information. Historical lake data in Michigan were originally archived as index cards at the Michigan Department of Natural Resources. All of the images of these cards are stored in this collection, Collections, Heterogeneous data, and Next Generation Ecological Studies (CHANGES) - Michigan Lake Surveys, and the images for this specific dataset are stored in the CHANGES Project- Fish Growth Analysis (GROW) dataset. The CHANGES project used a crowd sourcing platform called Zooniverse to transcribe at least basic information (i.e. dates, collected by) from all of these cards. Some of the card types, such as the one in this dataset, were prioritized to transcribe to produce a usable (i.e. machine-readable, uniform, and standardized) historical dataset. and Fish growth cards document fish that were aged and measured during fish surveys. The data that were transcribed from these cards and included in this dataset (grow_data.csv) are for each fish species: the number of fish measured in each age group, and the minimum, maximum, and average length of the fish for each age group. The final growth dataset includes length-at-age information for 36 different species (grow_species_table). For a description of all fields of this data table see grow_datadictionary.
- Keyword:
- fish, lake, growth, length, and Michigan
- Citation to related publication:
- King, K.B.S., Schell, J, Wehrly, K.E., Lenard, M., Singer, R., López-Fernández, H., Thomer, A.K., & Alofs, K.M. Community science helps digitize 78 years of fish and habitat data for thousands of lakes in Michigan, USA. under review and Grabda, E.E., Flood, P.J., King, K.B.S., Breck, J.E., Wehrly, K.E., and Alofs, K.M. 2025. Mismatch between climate-based bioenergetics model of fish growth and long-term and regional-scale empirical data. Canadian Journal of Fisheries and Aquatic Sciences. 82: 1-15. https://doi.org/10.1139/cjfas-2024-0266
- Discipline:
- Science
-
- Creator:
- King, Katelyn , Schell, Justin, Alofs, Karen, Thomer, Andrea, Wehrly, Kevin, Lenard, Michael , and Lopez-Fernandez, Hernan
- Description:
- Michigan lakes are an important resource, however, their ecosystems are declining and projected to continue to face further impacts under future land use and climate change. Understanding how lake ecosystems respond to environmental stressors and management actions is critical for identifying resilient lakes and developing adaptation strategies. However, the ability to manage lakes is hampered by a lack of historical information. Historical lake data in Michigan were originally archived as index cards at the Michigan Department of Natural Resources. All of the images of these cards are stored in this collection, Collections, Heterogeneous data, and Next Generation Ecological Studies (CHANGES) - Michigan Lake Surveys, and the images for this specific dataset are stored in the CHANGES Project- Lake Summary (SUMM) dataset. The CHANGES project used a crowd sourcing platform called Zooniverse to transcribe at least basic information (i.e. dates, collected by) from all of these cards. Some of the card types, such as the one in this dataset, were prioritized to transcribe to produce a usable (i.e. machine-readable, uniform, and standardized) historical dataset. and Lake summary cards that we transcribed and curated include habitat information for a lake as well as observed fish species (summ_data.csv). These variables include anthropogenic lake characteristics such as fishing intensity, shoreline structures, and dams; lake morphometric characteristics like depth and area; as well as in situ measures of temperature, dissolved oxygen, and Secchi depth. Many of the characteristics were listed as a range, and therefore, have a column for minimum and maximum in the data file (e.g. temp_surface_min_c and temp_surface_max_c). In addition, the lake summary cards listed the fish species present, so the csv file includes columns with the fish species common name (summ_species_table) and corresponding values are either a ‘1’ representing presence of a species or ‘0’ representing absence. For a full description of all the fields of this data table see summ_datadictionary.
- Keyword:
- lake, fish, Secchi, temperature, nutrients, oxygen, shoreline, habitat, dams, lake depth, lake area, and fishing intensity
- Citation to related publication:
- King, K.B.S., Schell, J, Wehrly, K.E., Lenard, M., Singer, R., López-Fernández, H., Thomer, A.K., & Alofs, K.M. Community science helps digitize 78 years of fish and habitat data for thousands of lakes in Michigan, USA. under review
- Discipline:
- Science
-
- Creator:
- King, Katelyn, Schell, Justin, Alofs, Karen, Thomer, Andrea, Wehrly, Kevin, Lenard, Michael, and Lopez-Fernandez, Hernan
- Description:
- Michigan lakes are an important resource, however, their ecosystems are declining and projected to continue to face further impacts under future land use and climate change. Understanding how lake ecosystems respond to environmental stressors and management actions is critical for identifying resilient lakes and developing adaptation strategies. However, the ability to manage lakes is hampered by a lack of historical information. Historical lake data in Michigan were originally archived as index cards at the Michigan Department of Natural Resources. All of the images of these cards are stored in this collection, Collections, Heterogeneous data, and Next Generation Ecological Studies (CHANGES) - Michigan Lake Surveys, and the images for this specific dataset are stored in the CHANGES Project- Fish Collection (FISHc) dataset. The CHANGES project used a crowd sourcing platform called Zooniverse to transcribe at least basic information (i.e. dates, collected by) from all of these cards. Some of the card types, such as the one in this dataset, were prioritized to transcribe to produce a usable (i.e. machine-readable, uniform, and standardized) historical dataset. and Fish collection card types include targeted and non-targeted fisheries surveys by the Department of Natural Resources and this information was transcribed and curated into a csv file (fishc_data.csv). These records include information on the gear types used, the area surveyed and the length and mesh size of nets fished. The number and common name of fish species caught were recorded as well and included in a species table (fishc_species_table). A description of all data fields can be found in the fishc_datadictionary.
- Keyword:
- lake , fish, gear, abundance, and Michigan
- Citation to related publication:
- King, K.B.S., Schell, J, Wehrly, K.E., Lenard, M., Singer, R., López-Fernández, H., Thomer, A.K., & Alofs, K.M. Community science helps digitize 78 years of fish and habitat data for thousands of lakes in Michigan, USA. under review and King, K.B.S, Giacomini, H.C., Wehrly, K., López-Fernández, H., Thomer, A.K., & Alofs, K.M. (2023). Using historical fish catch data to evaluate predicted changes in relative abundance in response to a warming climate. Ecography. 2023:8. https://doi.org/10.1111/ecog.06798
- Discipline:
- Science
-
- Creator:
- Sutton, Etienne, Snapp, Sieglinde, Morrone, Vicki, and Blesh, Jennifer
- Description:
- Cover crops support ecosystem services in agroecosystems, but their performance can be highly variable. Functional trait ecology provides a useful framework for understanding variation in cover crop performance across different growing conditions. However, trait variation within species remains understudied compared to variation between species. In a two-year experiment, we measured nine functional traits for three cover crop species across 13 fields on working farms that spanned a gradient of soil health. Each field contained three cover crop treatments: a functionally diverse mixture of cereal rye (Secale cereale), crimson clover (Trifolium incarnatum), and dwarf-essex rapeseed (Brassica napus), and rye and clover monocrops. We evaluated i) the magnitude and relative importance of intraspecific and interspecific trait variation; ii) which soil health indicators best explained trait variation; and iii) whether interspecific interactions in mixture induced trait plasticity. Despite strong trait contrasts between species, intraspecific trait variation comprised 50% of total trait variation, on average. Trait variation was best explained by particulate organic matter nitrogen (POM N), soil phosphorus, pH, and permanganate oxidizable carbon for clover; by POM N and soil phosphorus for rye; and by POM N for dwarf essex. Rye and clover also showed significant trait plasticity in mixture relative to monocrop treatments. Our study demonstrates that intraspecific and interspecific trait variation are equally important, and that examining trait variation within species can improve the ability to predict cover crop outcomes. This information can inform cropping system design in distinct contexts to promote success of component species and complementary ecosystem functions.
- Keyword:
- cover crop, functional trait, soil health, mixture, species interactions, and intraspecific trait variation
- Citation to related publication:
- Sutton, E., Snapp, S., Morrone, V., & Blesh, J. (2025). Cover crop functional trait plasticity in response to soil conditions and interspecific interactions. Plant and Soil. https://doi.org/10.1007/s11104-025-07471-x
- Discipline:
- Science
-
- Creator:
- Quartey, Nii-Boi A and Liemohn, Michael W
- Description:
- This dataset contains results from the BATS-R-US multispecies MHD code simulating the solar wind interaction at Mars at the following orbital and solar cycle locations: solar maximum at perihelion, solar maximum at aphelion, solar minimum at perihelion, solar minimum at aphelion. These simulations contain results with and without the crustal magnetic fields and includes variables such as the magnetic field and ion density., 2025-02-25: The metadata in this dataset has been updated in response to reviewer comments during the journal review process. Additional Tecplot 360 EX file containing MAVEN multifluid MHD simulation data added. The multifluid MHD simulation result from this result is from the MAVEN simulation library. The simulation result is run for 25,000 iterations., and 2025-04-28: The following files have been replaced with the following as these files contain the nominal solar wind conditions: z_0_mhd_permax.plt -> permax_3d.plt z_0_mhd_aphmax.plt -> aphmax_3d.plt z_0_mhd_permin.plt -> permin_3d.plt z_0_mhd_aphmin.plt -> aphmin_3d.plt The following file has been removed as the slice can be extracted from permax_3d.plt: x_0_mhd_permax.plt
- Keyword:
- mars, magnetosphere, magnetotail, current sheet, asymmetry, multispecies, multifluid, MHD, and MAVEN
- Citation to related publication:
- https://doi.org/10.1029/2024JA033445
- Discipline:
- Science
-
- Creator:
- Nunley, Hayden, Xue, Xufeng, Sun, Yubing, Resto-Irizarry, Agnes M, Yuan, Ye, Yong, Koh Meng Aw, Zheng, Yi, Weng, Shinuo, Shao, Yue, Lubensky, David K, Studer, Lorenz, and Fu, Jianping
- Description:
- Studies of fate patterning during development typically emphasize cell-cell communication via diffusible chemical signals. Recent experiments on stem cell colonies (see Xue et al. Nature Materials 2018), however, suggest that in some cases mechanical stresses, rather than secreted chemicals, enable long-ranged cell-cell interactions that specify positional information and pattern cell fates. The authors of this earlier publication reported a set of in vitro experiments in which uniformly supplied chemical media induced spatially patterned fates in cell colony in a disc geometry. They provided significant evidence that inter-cellular mechanical interactions, as well as mechanical interactions between cells and the substrate, play an important role in this in vitro differentiation process. As part of these experiments, they showed that the concentric width of the outer fate domain is approximately constant as the colony diameter is increased from 300 um to 800 um. In this subsequent publication, we propose a mathematical model for this fate patterning process and explore how the fate pattern depends on substrate stiffness. The experimental images of cell colonies, both for varying cell colony diameter (from Xue et al. Nature Materials 2018) and for varying substrate stiffness (data generated for the publication linked to these data), are provided here. Each example has an image for PAX3 signal (marker for outer fate domain; Paired box gene 3) and an image for DAPI signal (staining nuclei; 4′,6-diamidino-2-phenylindole).
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, Force sensing, and Vertebrate development
- Citation to related publication:
- Nunley H, Xue X, Fu, J, Lubensky, DK. Generation of fate patterns via intercellular forces. BioRxiv 442205 [Preprint]. April 30, 2021 [cited 2025 Feb 20]. Available from: doi: https://doi.org/10.1101/2021.04.30.442205 and Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9
- Discipline:
- Science and Engineering
-
- Creator:
- Nunley, Hayden and Lubensky, David K
- Description:
- In a previous study (Xue et al. Nature Materials 2018), the authors showed that a key fate patterning event in vertebrate development can be reproduced in an in vitro stem cell culture. They further showed that this in vitro fate pattern seems to depend on mechanical signals rather than secreted chemical signals. In this follow-up study, a mathematical model of this process is proposed. The code in this deposit is for the simulation of this mathematical model in various cell layer geometries and substrate geometries. These geometries include a 1D cell layer, quasi-1D stripe geometry, disc geometry (all on a very thin substrate or a substrate composed of microposts) as well as a 1D cell layer on a finite-thickness substrate. Our model implies that the width of the outer fate domain varies non-monotonically with substrate stiffness, a prediction that we confirm experimentally.
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, and Force sensing
- Citation to related publication:
- Nunley H, Xue X, Fu, J, Lubensky, DK. Generation of fate patterns via intercellular forces. BioRxiv 442205 [Preprint]. April 30, 2021 [cited 2025 Feb 20]. Available from: doi: https://doi.org/10.1101/2021.04.30.442205, Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9, Banerjee S, Marchetti MC. Substrate rigidity deforms and polarizes active gels. EPL (Europhysics Letters) 96, 28003 (2011). https://doi.org/10.1209/0295-5075/96/28003, Edwards CM, Schwarz US. Force Localization in Contracting Cell Layers, Physical Review Letters 107, 128101 (2011). https://doi.org/10.1103/PhysRevLett.107.128101, and Banerjee S, Marchetti MC. Contractile Stresses in Cohesive Cell Layers on Finite-Thickness Substrates, Physical Review Letters 109, 108101 (2012). https://doi.org/10.1103/PhysRevLett.109.108101
- Discipline:
- Engineering and Science
-
- Creator:
- Nunley, Hayden, Xue, Xufeng, Sun, Yubing, Resto-Irizarry, Agnes M, Yuan, Ye, Yong, Koh Meng Aw, Zheng, Yi, Weng, Shinuo, Shao, Yue, Lubensky, David K, Studer, Lorenz, and Fu, Jianping
- Description:
- In an earlier study (Xue et al. Nature Materials 2018), stem cells differentiated into one of two cell types, neural plate border (NPB) or neural plate (NP), in vitro. This previous study demonstrated that this differentiation is likely mechanics-guided. Part of this demonstration was measurements of the displacement of microposts under the cell layer as the cells differentiate. These measurements suggested that the NPB cells are more contractile than NP cells. In a follow-up study (linked to this dataset), we quantitatively analyzed these data to demonstrate even further that the NPB cells are mechanically different than the NP cells and that the post displacement profile is not explained by a model of a cell layer with uniform mechanical properties. This analysis motivated the mathematical model -- for this cell colony system -- that we proposed and analyzed.
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, Force sensing, and Vertebrate development
- Citation to related publication:
- Hayden Nunley, Xufeng Xue, Jianping Fu, David K. Lubensky bioRxiv 2021.04.30.442205; doi: https://doi.org/10.1101/2021.04.30.442205 and Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9
- Discipline:
- Engineering and Science
-
- Creator:
- Nunley, Hayden, Xue, Xufeng, Fu, Jianping, and Lubensky, David K
- Description:
- In an earlier publication (Xue et al. Nature Materials 2018), the authors reported a set of in vitro experiments in which uniformly supplied chemical media induced spatially patterned fates in cell colony in a disc geometry. They provided significant evidence that inter-cellular mechanical interactions, as well as mechanical interactions between cells and the substrate, play an important role in this in vitro differentiation process. In this subsequent publication, we propose a mathematical model for this fate patterning process and explore how the fate pattern depends on substrate stiffness. One ingredient of this mathematical model is that the cells at the very edge of the colony (lacking adherens junctions on one side) are geometrically different than the rest (by occupying a larger area on the micropattern). These images of DAPI (staining nuclei) and ECad (at adherens junctions) for colonies during early cell differentiation demonstrate this difference. Corresponding code for analysis is included.
- Keyword:
- Biomechanics, Cell mechanics, and Developmental pattern formation
- Citation to related publication:
- Nunley H, Xue X, Fu, J, Lubensky, DK. Generation of fate patterns via intercellular forces. BioRxiv 442205 [Preprint]. April 30, 2021 [cited 2025 Feb 20]. Available from: doi: https://doi.org/10.1101/2021.04.30.442205 and Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9
- Discipline:
- Engineering and Science
-
- Creator:
- Nunley, Hayden, Xue, Xufeng, Sun, Yubing, Resto-Irizarry, Agnes M, Yuan, Ye, Yong, Koh Meng Aw, Zheng, Yi, Weng, Shinuo, Shao, Yue, Studer, Lorenz, Fu, Jianping, and Lubensky, David K
- Description:
- In an earlier study (Xue et al. Nature Materials 2018), stem cells differentiated into one of two cell types, neural plate border (NPB) or neural plate (NP), in vitro with the NP forming a central circular domain. This previous study demonstrated that this differentiation is likely mechanics-guided. Part of this demonstration was measurements of the displacement of microposts under the cell layer as the cells differentiate. These measurements suggested that the NPB cells are more contractile than NP cells (see Dataset of cell layers on micro-patterned substrates compost of posts). The authors of the 2018 study and of a follow-up study further explored how the size of the NPB domain depends on experimental conditions (see Dataset of stem cell colonies differentiating in neural induction medium and code for analysis of resulting fate pattern). To further understand what factors could be driving NPB formation, we estimated cell area at the colony edge (see Dataset on cell areas and nuclear densities in differentiating stem cell colonies). This analysis inspired a mathematical model of mechanical patterning: fate affects cell contractility, and pressure in the cell layer biases fate. Cells at the colony edge, more contractile than cells at the center, seed a pattern that propagates via force transmission. We simulated the model in various cell geometries and for different substrates (see Code for simulating NP/NPB fate patterning in stem cell colonies). Strikingly, our model implies that the width of the outer fate domain varies non-monotonically with substrate stiffness, a prediction that we confirm experimentally. Our findings thus support the idea that mechanical stress can mediate patterning in the complete absence of chemical morphogens, even in non-motile cell layers, thus expanding the repertoire of possible roles for mechanical signals in development and morphogenesis.
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, Force Sensing, and Vertebrate development
- Discipline:
- Science
4Works -
- Creator:
- Phillips, Chrystian D, DeFazio, R. Anthony, and Moenter, Suzanne M.
- Description:
- Supplemental tables containing the statistical analysis for the manuscript "Sex and time of day alter the interactions between hypothalamic glia and the neural circuits controlling reproduction"
- Discipline:
- Science
-
- Creator:
- Raymond, Matt, Elvati, Paolo, Saldinger, Jacob C, Lin, Jonathan, Shi, Xuetao, and Violi, Angela
- Description:
- Nanoparticles (NPs) formed in nonthermal plasmas (NTPs) can have unique properties and applications. However, modeling their growth in these environments presents significant challenges due to the non-equilibrium nature of NTPs, making them computationally expensive to describe. In this work, we address the challenges associated with accelerating the estimation of parameters needed for these models. Specifically, we explore how different machine learning models can be tailored to improve prediction outcomes. We apply these methods to reactive classical molecular dynamics data, which capture the processes associated with colliding silane fragments in NTPs. These reactions exemplify processes where qualitative trends are clear, but their quantification is challenging, hard to generalize, and requires time-consuming simulations. Our results demonstrate that good prediction performance can be achieved when appropriate loss functions are implemented and correct invariances are imposed. While the diversity of molecules used in the training set is critical for accurate prediction, our findings indicate that only a fraction (15-25%) of the energy and temperature sampling is required to achieve high levels of accuracy. This suggests a substantial reduction in computational effort is possible for similar systems.
- Keyword:
- machine learning, molecular dynamics, nanoparticle, nonthermal plasma, silane, and sticking coefficient
- Citation to related publication:
- Raymond, M., Elvati, P., Saldinger, J. C., Lin, J., Shi, X., & Violi, A. (2025). Machine learning models for Si nanoparticle growth in nonthermal plasma. Plasma Sources Science and Technology. https://doi.org/10.1088/1361-6595/adbae1 and https://arxiv.org/abs/2501.00003
- Discipline:
- Science
-
- Creator:
- Wang, Danhao and Mi, Zetian
- Description:
- Wurtzite ferroelectrics possess transformative potential for next-generation microelectronics. A comprehensive understanding of their ferroelectric properties and domain energetics is crucial for tailoring their ferroelectric characteristics and exploiting their functional properties in practical devices. Despite burgeoning interest, the exact configurations, and electronic structures of domain walls in wurtzite ferroelectrics remain elusive. In this work, we elucidate the atomic configurations and electronic properties of electric-field-induced domain walls in ferroelectric ScGaN. By combining transmission electron microscopy and theoretical calculations, a novel charged domain wall with a buckled two-dimensional hexagonal phase is revealed. Density functional theory calculations confirm that such domain wall structures further give rise to unprecedented mid-gap states within the forbidden band. Quantitative analysis unveils a universal charge-compensation mechanism stabilizing antipolar domain walls in ferroelectric materials, wherein the polarization discontinuity at the 180º domain wall is compensated by the unbonded valence electrons. Furthermore, the reconfigurable conductivity of these domain walls is experimentally demonstrated, showcasing their potential for ultra-scaled device applications. Our findings represent a pivotal advancement in understanding the structural and electronic properties of wurtzite ferroelectric domain walls and lay the groundwork for fundamental physics studies and device applications.
- Keyword:
- Charged domain walls, Scanning transmission electron microscopy, and Density functional theory calculations
- Discipline:
- Science
-
- Creator:
- Brinkmeier, Michelle L, Wang, Su Qing, Pittman, Hannah, Cheung, Leonard Y, and Prasov, Lev
- Description:
- MYRF is a gene that regulates the development and function of the retinal pigmented epithelium (RPE), which play an important role in maintaining photoreceptor structure and function. Mutations in patients have been implicated in eye size disorders, particularly causing a small, but structurally normal eye. We have utilized a molecular technique, single cell RNA sequencing, to investigate how loss of Myrf specifically in the RPE in a mouse model impacts downstream gene expression at three developmental timepoints and used this information to define the role of Myrf in development. Our work identified key cytoskeletal structural genes specific to the RPE, Ermn and Upk3b, and a gene important for the cell survival, Sox10, as critical targets of Myrf. In addition, we have identified and confirmed that the TGFbeta signaling pathway is dysregulated when Myrf is lost during development. This pathway is particularly relevant in RPE health and eye growth. Our electron microscopy and histologic analyses also confirm a defect in RPE structure and function. We place MYRF within a hierarchy of genes involved in RPE development and introduce novel candidate genes for further study as retinal degeneration and nanophthalmos candidate genes.
- Keyword:
- ERMN, MYRF, Hypopigmentation, TMEM98, SOX10, Retinal Pigment Epithelium (RPE), and Retinal degeneration
- Discipline:
- Science
-
- Creator:
- Kersten, Roland D, Ousley, D, Wang, Xiaofeng, Chigumba, Desnor N, Davis, Dulciana, Shafiq, Khadija, McDonough, Kali, Mydy, Lisa M, and Sexton, Jonathan Z
- Description:
- Moroidins are plant ribosomally synthesized and posttranslationally modified peptides (RiPPs) called burpitides biosynthesized from copper-dependent peptide cyclases. The bicyclic structure of moroidins contains (1) a stephanotic acid scaffold with a Leu-Cꞵ-Trp-indole-C6-crosslink and (2) a C-terminal ring formed by a Trp-indole-C2-His-imidazole-N1-crosslink. Moroidin is cytotoxic to H1437 non-small cell lung adenocarcinoma cells in vitro, underscoring the potential of stephanotic acid-type burpitides as anticancer lead structures and the importance of exploring diversification strategies to discover analogs with enhanced bioactivity. We mined the transcriptome of 7579 plant species from 498 plant families to identify moroidin analogs with novel second-ring structures and the cyclases responsible for their biosynthesis. A search of >27000 candidate burpitide cyclases reveals two stephanotic acid-type burpitides in plants with new second-ring crosslinks derived from posttranslational modification: Glechomanin from ground ivy (Glechoma hederacea) with a C-C-crosslink between a C-terminal tryptophan-indole-C6 and the β-carbon of a valine, and Mercurialin from annual mercury (Mercurialis annua) featuring a C-O-crosslink between a C-terminal tyrosine-phenol hydroxy and the β-carbon of a phenylalanine, respectively. Furthermore, our transcriptomics-guided burpitide genotyping enabled isolation of a moroidin analog from water chickweed (Stellaria aquatica), which exhibits a ten-fold higher in vitro cytotoxicity than moroidin and selective toxicity against H1437 lung adenocarcinoma cells. We demonstrate that plant transcriptome mining can expand the medicinal chemistry toolbox for chemical and biological exploration of burpitide lead structures.
- Keyword:
- RNA-seq, de novo transcriptome assembly, plant peptides, natural products, and RiPP
- Citation to related publication:
- in preparation
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:238369 (NOTOTRITON PICADOI) - Limbs. Raw Dataset includes 1601 TIF images (each 461 x 741 x 1 voxel at 0.01300206 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:238369 (NOTOTRITON PICADOI) - Limbs. Reconstructed Dataset includes 0.013002 TIF images (each 461 x 741 x 1 voxel at 0.013002 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Amphibia, CAUDATA, PLETHODONTIDAE, NOTOTRITON PICADOI, 1987030882, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987030882
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:194448 (PSEUDOTRITON RUBER) - Limbs. Raw Dataset includes 1601 TIF images (each 372 x 652 x 1 voxel at 0.03100344 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:194448 (PSEUDOTRITON RUBER) - Limbs. Reconstructed Dataset includes 0.031003 TIF images (each 372 x 652 x 1 voxel at 0.031003 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Amphibia, CAUDATA, PLETHODONTIDAE, PSEUDOTRITON RUBER, 1987126336, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987126336
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:143736 (PSEUDOEURYCEA BELLII) - Limbs. Raw Dataset includes 1601 TIF images (each 642 x 2000 x 1 voxel at 0.02199678 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction., Scan of specimen ummz:herps:143736 (PSEUDOEURYCEA BELLII) - Limbs. Reconstructed Dataset includes 0.021997 TIF images (each 642 x 2000 x 1 voxel at 0.021997 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction., and Scan of specimen ummz:herps:143736 (PSEUDOEURYCEA BELLII) - Limbs. Reconstructed Dataset includes 0.021997 TIF images (each 642 x 2000 x 1 voxel at 0.021997 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Amphibia, CAUDATA, PLETHODONTIDAE, PSEUDOEURYCEA BELLII, 1987206748, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987206748
- Discipline:
- Science