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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:
- Gerber, Elisabeth R., Morenoff, Jeffrey D., Ostfeld, Mara C. , Sand, Sharon L., and Fan, Yucheng
- Description:
- Survey topics included: Household Composition, Residence and Housing Status; Health, Social Determinants of Health, Long COVID, Mental Health; Disability; Perceptions of Neighborhood; Transportation mode; Financial Precarity; Perception of Control; Voting; Employment; Demographics. This data file contains 1,379 Grand Rapids residents' close-ended responses. The full dataset will be published on ICPSR.
- Keyword:
- Grand Rapids, MI, Household composition , Housing status , Health , Long COVID symptom, Mental health , Disability , Perceptions of neighborhood , Transportation mode , Perceptions of control , Voting , Financial precarity , Employment , and Demographics
- Discipline:
- News and Current Events and Social Sciences
-
- 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:
- Delacroix, Emerson, Austin, Sarah, Bacon, Elizabeth, Rice, John, Hanson, Erika N., Stoffel, Elena Martinez, Roberts, Scott, Ulhmann, Wendy, Griggs, Jennifer J., Koeppe, Erika, and Resnicow, Ken
- Description:
- Participant-reported results from the MiGHT study Baseline Survey, including knowledge, motivators, and barriers for hereditary cancer genetic testing uptake. This is raw dataset is saved in comma separated value (.csv) format.
- Keyword:
- Hereditary Genetic Testing, Genetic Testing, NCCN Guidelines, and Genetic Counseling
- Discipline:
- Social Sciences and Health Sciences
-
- 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:
- Burgin, Tucker and Mayes, Heather B.
- Description:
- This project aimed to discover and analyze the molecular mechanism of synthesis of two particular fucosylated oligosaccharide products in a mutant enzyme, Thermatoga maratima Alpha-L-Fucosidase D224G, whose wild type performs the opposite reaction (cleavage of fucosyl glycosidic bonds). Discovery of the mechanism was performed using an unbiased simulations method known as aimless shooting, whereas analysis of the mechanism in terms of the energy profile was performed using a separate method known as equilibrium path sampling. The data here concerns the latter method. and The contents of the atesa_master.zip are the ATESA GitHub project. A Python program for automating transition path sampling with aimless shooting using Amber. https://github.com/team-mayes/atesa
- Keyword:
- Equilibrium Path Sampling, Transition Path Sampling, Enzymatic Mechanism, and GH29
- Citation to related publication:
- Burgin, T., & Mayes, H. B. (2019). Mechanism of oligosaccharide synthesis via a mutant GH29 fucosidase. Reaction Chemistry & Engineering, 4(2), 402–409. https://doi.org/10.1039/C8RE00240A
- Discipline:
- Engineering
-
- 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:
- Ruas, Terry, Grosky, William, and Aizawa, Akiko
- Description:
- This data set is a collection of word similarity benchmarks (RG65, MEN3K, Wordsim 353, simlex999, SCWS, yp130, simverb3500) in their original format and converted into a cosine similarity scale. In addition, we have two Wikpedia Dumps from 2010 (April) and 2018 (January) in which we provide the original format (raw words), converted using the techniques described in the paper (MSSA, MSSA-D and MSSA-NR) (title in this repository), and also the word embeddings models for 300d and 1000d using a word2vec implementation. A readme.txt is provided with more details for each file.
- Keyword:
- multi-sense embeddings, MSSA, word2vec, wikipedia dump, synset, and natural language processing
- Citation to related publication:
- https://doi.org/10.1016/j.eswa.2019.06.026
- Discipline:
- Other
-
- 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:
- Gerber, Elisabeth R., Morenoff, Jeffrey D., Ostfeld, Mara C., Sand, Sharon L., and Fan, Yucheng
- Description:
- Survey topics included: Household Composition, Residence and Housing Status; Health, Social Determinants of Health, Long COVID, Mental Health; Disability; Perceptions of Neighborhood; Transportation mode; Financial Precarity; Perception of Control; Voting; Employment; Demographics. This data file contains 673 Ypsilanti residents' close-ended responses. The full dataset will be published on ICPSR.
- Keyword:
- Ypsilanti, MI, Household composition, Housing status, Health, Long COVID symptom, Mental health, Disability, Perceptions of neighborhood, Transportation mode, Perceptions of control, Voting, Financial precarity, Employment, and Demographics
- Discipline:
- News and Current Events and Social Sciences
-
- 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:
- Heath, Jeffrey
- Description:
- lexical spreadsheet, pdf of additional notes, and audio recordings. The pdf of additional notes is organized around subsections of the chapter I am writing on "eastern Songhay", part of a book co-authored by Lameen Souag on the Songhay language family. Marense was previously known to Songhay specialists only from a paper by Robert Nicolai on "Songhay central," comparing two Marense dialects with the Songhay of Hombori and that of Tinié village. Nicolai's paper was almost entirely about vocalic and consonantal systems and tonal distinctions and had essentially no material on morphosyntax. This work also includes a spreadsheet with the Marense words gleaned from Nicolai's paper. I note that Nicolai's tapes for this and many other Songhay varieties are being processed for archiving at the Bibliothèque Nationale de France. and The recordings have not been transcribed and I have no plans to transcribe them. They should be partially intelligible to speakers of eastern Songhay languages. The topics of the individual audio files are: 0930 agriculture 1 0931 marriage 0932 life in the old days 0933 education of children 0934 travels 0935 taxes 0936 hunting 0937 circumcision 0938 agriculture 2 (crop pests) 0939 indigo dye-ing 0940 riddles
- Keyword:
- Marense and Songhay languages
- Discipline:
- Humanities
-
- 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:
- Heath, Jeffrey
- Description:
- Documentary fieldwork on Tebul Ure and other Dogon languages (grammars, lexicons, texts, audio, video). This deposit contains only audio recordings but links out to other pieces of the work.
- Keyword:
- Tebul Ure, Dogon, and Audio
- Discipline:
- Humanities
-
- 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:
- Heath, Jeffrey
- Description:
- lexical spreadsheets. One .xlsx spreadsheet with separate pages for nouns, numerals, adjectives, verbs, places, and "other" (including adverbs and grammatical morphemes). Each page is also copied as a .csv file, with one additional .csv containing Tiefo-D vocabulary gleaned from K. Winkelmann's German-language dissertation, Die Sprache der Cefo von Daramandugu (Burkina Faso). Previously "published" at Zenodo. , Jinejan, Flaso, Biton, and Masaso are village-like settlements, geographically apart but administratively part of Daramandougou. In sheets with a fifth column "Tiefo-D", this is a compromise form mainly useful for sorting and navigation. , and Tiefo-D is related to Tiefo-N but the two are quite different, mutually unintelligible languages. They are spoken in southwestern Burkina Faso.
- Keyword:
- Tiefo-D language
- Citation to related publication:
- Heath, J., & Ouattara, A. (2021). A Grammar of Tiefo-D of Daramandugu. Zenodo. https://doi.org/10.5281/zenodo.4715103, Heath, J., & Ouattara, A. (2021). Tiefo-D Texts from Daramandugu. Zenodo. https://doi.org/10.5281/zenodo.4715132, and Heath, J., & Ouattara, A. (2021). Tiefo-D lexicon [Data set]. Zenodo. https://doi.org/10.5281/zenodo.4715136
- Discipline:
- Humanities
-
- 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:
- Heath, Jeffrey
- Description:
- These recordings have not been transcribed but are made available to native speakers and to linguists. Tiéyaxo is the sister dialect to Tigemaxo, which together form a language within the Bozo family. The author has completed a study of Tigemaxo but has done no work specifically on Tiéyaxo. Other works in this collection contain Tigemaxo audio files, and one such work contains a Tigemaxo and a Tieyaxo recording from 1989.
- Keyword:
- Bozo language and Tiéyaxo
- Discipline:
- Humanities
-
- Creator:
- Heath, Jeffrey
- Description:
- Recordings in Tigemaxo from 2022 in Dia village have been transcribed and the audio files are in a separate work ( https://doi.org/10.7302/hagd-xe26). The present work is a much larger set of audio recordings, also in Tigemaxo and from Dia village, but recorded in 2024. It includes ethnohistory and tales. , The ethnohistorical texts are with one main speaker (Mama Sienta), interviewed by Oumar Dienta, both male. The tales are told by a range of male and female speakers, with light backchannel accompaniment by the audience. Each tale in Tigemaxo is accompanied by a repetition or summary in French by Oumar Dienta in a separate file. The author has no plans to transcribe the 2024 recordings and is depositing this audio library for future use by native speakers and/or by linguists. The same is true of the 2019 Tigemaxo/Tiéyaxo recordings ( https://dx.doi.org/10.7302/6632), and the 2021 Tiéyaxo recordings ( https://doi.org/10.7302/2e0d-xk52), which are in two other works in this collection. , and A short catalog of the files in this work, without transcription or translation, appears in J. Heath, "Tigemaxo (Bozo) texts of 2022 in Dia village (Mali)" in Zenodo, of which a backup copy is in Deep Blue Documents (see below).
- Keyword:
- Bozo language, Tigemaxo, and Dia village Mali
- Citation to related publication:
- Heath, J. (2025). A Grammar of Tigemaxo of Dia (Bozo family, Mali). Zenodo. https://doi.org/10.5281/zenodo.15160216
- Discipline:
- Humanities
-
- Creator:
- Heath, Jeffrey
- Description:
- The 2022 recordings are transcribed and translated, with further commentary, in J. Heath, "Tigemaxo (Bozo) texts of 2022 from Dia village (Mali)" in Deep Blue Documents (see below).
- Keyword:
- Bozo language, Tigemaxo, and Dia village Mali
- Citation to related publication:
- Heath, J. (2025). A Grammar of Tigemaxo of Dia (Bozo family, Mali). Zenodo. https://doi.org/10.5281/zenodo.15160216
- Discipline:
- Humanities
-
- Creator:
- Whittaker, Collin B.
- Description:
- This study follows after work conducted first for my dissertation and is presently being prepared for journal submission. The goal of our analysis was to analyze a small design space for an electrospray array thruster---varying the geometry of its emitters, the size of its extractor apertures, and its operating voltage---to determine designs robust to uncertainty. That is, we use a model for array performance whose input parameters we treat as uncertain (stemming from approximations to higher-order physics, manufacturing tolerances in fabricating a thruster, and so on). Making these predictions as a function of design, then, we can identify configurations that are performant robust to this uncertainty (i.e., still meet required performance specifications with high confidence). The data which inform this trade study are taken pricipally from our pending manuscript "Emitter Model Inference from Electrospray Array Thruster Tests", and from my thesis, "Designing Porous Electrospray Array Thrusters Under Uncertainty" (linked to the dataset as published). The analysis was conducted in January and February of 2025. This work was supported by a NASA Space Technology Graduate Research Opportunity (80NSSC21K1247). This research was also supported in part through computational resources and services provided by Advanced Research Computing, a division of Information and Technology Services at the University of Michigan, Ann Arbor.
- Keyword:
- Electrospray, Electric propulsion, Robust optimization, Bayesian inference, and Ionic liquid ion source
- Discipline:
- Engineering
-
- Creator:
- Whittaker, Collin B
- Description:
- The object of our study was to train a reduced-fidelity model for individual emitter behavior within a porous conical type electrospray array thruster on data taken over the entire array, which is the sum over all the emitters. By leveraging surface profilometry to measure the variance in geometry in the array, we then gain insight into the individual emitter dynamics. By rigorously predicating uncertainty in the predictions made by the model on uncertainty over its inputs, we can then understand the major sources of uncertainty in the system. The raw experimental data which inform this inference and prediction study were acquired in April of 2024 at the Jet Propulsion Laboratory's MicroPropulsion Laboratory, with special thanks to Colleen Marrese-Reading and Steven Arestie. These and other results are reported in a separate manuscript: C. B. Whittaker, B. A. Jorns, S. M. Arestie, and C. M. Marrese-Reading, in 38th International Electric Propulsion Conference (Electric Rocket Propulsion Society, 2024) p. 730. The thruster used in these experiments was fabricated at the University of Michigan in March of 2024. The analysis underlying this work was conducted from September of 2024 to January of 2025. This work was supported by a NASA Space Technology Graduate Research Opportunity (80NSSC21K1247). This research was also supported in part through computational resources and services provided by Advanced Research Computing, a division of Information and Technology Services at the University of Michigan, Ann Arbor. Finally, this work was performed in part at the University of Michigan Lurie Nanofabrication Facility.
- Keyword:
- Electrospray, Electric propulsion, Ionic liquid ion source, Bayesian inference, and Profilometry
- Discipline:
- Engineering
-
- Creator:
- Heath, Jeffrey
- Description:
- Tebul Ure is a language of the Dogon language family in east central Mali. It is spoken in a few villages on the heights overlooking the towns of Bamba and Yanda on the eastern cliffs of the Dogon plateau. The lexicon was compiled as part of a broader three-part grammar-texts-lexicon study of this language. and Columns from left to right (omitting blanks) are: Tebul Ure (transcription) finder (English finder list, i.e. usually one-word glosses) recherche (finder list in French), English (full English gloss), français (full French gloss), domain (for types of plant or fauna, e.g. snake), species (genus-species binomials), order/family (for flora-fauna terms); and synonymy (alternative or former species binomials)
- Keyword:
- Tebul Ure
- Discipline:
- Humanities
-
- Creator:
- Heath, Jeffrey
- Description:
- Tebul Ure is a Dogon language spoken on the heights in a horseshoe valley between Bamba and Yanda on the eastern edge of the Dogon (Bandiagara) plateau in central Mali. A grammar is drafted but incomplete as of May 2018. Texts were transcribed from dictation in 2012 in the Tebul area, and others were recorded digitally in 2015 at a nearby town on the plateau. Six of the 2015 texts have been transcribed. The texts are included at the end of the grammar. I grant permission to other linguists to transcribe, translate, or analyse any texts that remain untranscribed beginning 2022.
- Keyword:
- Tebul Ure, Dogon, Mali, Audio, and Recording
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
-
- 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:
- Chen, Hongfan, Sachdeva, Nishtha, Huang, Zhenguang, van der Holst, Bart, Manchester, Ward, Jivani, Aniket, Zou, Shasha, Chen, Yang, Huan, Xun, and Toth, Gabor
- Description:
- In this study, we show that coronal mass ejection (CME) simulations conducted with the Space Weather Modeling Framework (SWMF) can be assimilated with SOHO LASCO white-light (WL) coronagraph observations and solar wind observations at L1 prior to the CME eruption to improve the prediction of CME arrival time. L1 observations are used to constrain the background solar wind, while LASCO coronagraph observations filter the initial ensemble simulations by constraining the simulated CME propagation speed. We then construct probabilistic predictions for CME arrival time using the data-assimilated ensemble. Scripts in this work are written in R, Python and Julia.
- Keyword:
- Data Assimilation, Uncertainty Quantification, and Space Weather
- Citation to related publication:
- https://doi.org/10.1029/2024SW004165
- Discipline:
- Engineering
-
- Creator:
- Cevidanes, Lucia
- Description:
- Image Pre-Processing To allow reliable detection and comparison of changes between several individuals or within the same individual at different time points, before extracting the quantitative bone texture/morphometry features, all hr-CBCT scans were pre-processed using validated protocols. Extraction of Trabecular Bone Texture-based and Morphometry Imaging Features Using the “crop-volume” tool in 3D Slicer, a rectangular shaped volume of interest (VOI) was cropped from the trabecular bone in the mandibular condyles and the articular fossa. Then, using the average minimum and maximum intensity values of all VOIs, we standardized the grey level intensities of the VOIs to eliminate inaccuracies of textural features calculation and possible dependency on the global characteristics of the images. Lastly, imaging markers were extracted from the standardized VOIs using “BoneTexture” module in 3D-slicer. Measurement of the 3D Articular Joint Space To assess the progression/improvement of osteoarthritic changes in the affected individuals, we measured the 3D superior joint space. We pre-labelled two landmarks in the sagittal view of the oriented CBCT scans: on the most superior point of the condyle and on the opposing surface of the articular fossa. To avoid biasing the landmarks’ placements, pre-labelling was performed simultaneously on T1 and T2 scans, using two independent windows in ITK-SNAP. After the volumetric reconstruction of the identified landmarks, linear measurements were obtained in millimeters using the Q3DC tool in 3D Slicer. Three-dimensional Shape Analyses and Quantification of Remodeling in the Condyles SPHARM-PDM software was used to compute the correspondence across 4002 surface points among all condyles. The output point-based models displayed color-coded maps that enabled visual evaluation of consistent parametrization of all condyles. An average condyle shape for the TMJ OA and control groups was calculated through propagation of original surface point correspondences across all stages of deformations and averaging the condyle surface meshes. For visualization of the 3D qualitative changes of the average models within the same group at different time points or among different groups, semi-transparent overlays were created using 3D Slicer software. The vector differences were presented on the condyle surfaces, scaled according to the magnitude of difference, and pointing towards the direction of bone change. For quantification of remodeling in the condyles, calculation of signed distances across condyles surface meshes reflected the quantitative bone changes in the TMJ OA and control samples. To quantify regional bone changes across the lateral and anterior surfaces of the condyles, we used the Pick ‘n Paint tool in 3D Slicer to propagate regional surface points to the corresponding regions of shapes across all subjects and time points.
- Keyword:
- Degenerative joint disease, Temporomandibular joint osteoarthritis, TMJ OA, Machine learning, and Prognosis
- Citation to related publication:
- Al Turkestani N, Li T, Bianchi J, Gurgel M, Prieto J, Shah H, Benavides E, Soki F, Mishina Y, Fontana M, Rao A, Zhu H, Cevidanes L. A comprehensive patient-specific prediction model for temporomandibular joint osteoarthritis progression. Proc Natl Acad Sci U S A. 2024 Feb 20;121(8):e2306132121. doi: 10.1073/pnas.2306132121. Epub 2024 Feb 12. PMID: 38346188; PMCID: PMC10895339.
- Discipline:
- Health Sciences
-
- Creator:
- Ludlow, Andrew and Ahn, Alexander
- Description:
- Publicly accessible short-read RNA sequencing (SRS) of clinical exercise studies were extracted from the Gene Expression Omnibus. Oxford Nanopore long-read RNA sequencing (LRS) was performed on mouse gastrocnemius before and following treadmill exercise. Differential gene expression (DGE), differential alternative splicing (DAS), and differential isoform expression (DIE) were analyzed. Gel-based/droplet digital RT-PCR and western blots were performed to validate expression changes of select genes. Both SRS and LRS illustrated significant DGE in skeletal muscle post-exercise, whereby 89 RBPs were significantly up-/down-regulated. rMATS analysis of SRS data revealed that exon-skipping and intron-retaining splicing events were the most common. Swan analysis of LRS data revealed 61 RBPs with significant isoform switching: one of these RBPs, mHnrnpa3, underwent a significant non-coding to protein-coding switch. HnRNP-A3 protein levels validated nearly two-fold increases at 1 hour and 24 hours post-exercise.
- Keyword:
- Alternative splicing and Exercise
- Citation to related publication:
- Impact of Acute Endurance Exercise on Alternative Splicing in Skeletal Muscle. Alexander Ahn, Jeongjin J. Kim, Aaron L. Slusher, Jeffrey Y. Ying, Eric Y. Zhang, Andrew T. Ludlow bioRxiv 2024.11.21.624690; doi: https://doi.org/10.1101/2024.11.21.624690
- Discipline:
- Health Sciences
-
- 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:
- Patil, Crystal
- Description:
- We conducted a hybrid effectiveness-implementation trial at seven clinics in Blantyre District, Malawi, comparing outcomes for 1887 pregnant women randomly assigned to Group ANC or Individual ANC. The seven study clinics were selected in consultation with the Blantyre District health team to represent a diversity of clinics and communities served. The catchment areas and populations served by the clinics differ socioeconomically. Three clinics serve the urban population of Blantyre city, the rapidly-growing second largest city in Malawi. Two clinics serve the peri-urban communities adjacent to metropolitan Blantyre, and two clinics primarily serve a rural and predominately agricultural community. The clinics varied in volume and number of working midwives. , To be eligible to participate in this study, participants had to be pregnant, over the age of 14, have a gestational age of less than 24 weeks, and be capable of making an informed choice about participation. Those aged 15-17 assented with consent from a legal guardian. Those who did not meet all criteria were excluded. All pregnant women presenting for their first antenatal visit received the same standard individual intake visit that included a health assessment with the midwife, laboratory tests, and HIV testing. , and After completing the intake visit, midwives directed clients to study team members so that eligibility could be assessed. Interested women then learned the information needed to give informed consent and sign a consent form. They then completed the baseline self-report survey using Audio Computer-Assisted Self-Interview software. The study statistician determined the randomization order list for each site before recruitment, and assignments were placed in order in sealed envelopes. After completing the baseline survey, the woman selected the next sealed envelope in that clinic’s box to reveal the type of ANC assignment, Group ANC or Individual ANC. Seven individual-level demographic and socioeconomic variables were treated as covariates in all analyses. Two clinic-level variables were also included as covariates, catchment area (rural, peri-urban, or urban) and midwife ANC workloads. Midwife ANC workloads were captured by a ratio of the average number of new ANC clients served each month divided by the number of midwives, with a higher ratio indicating a higher workload. The ratio was highest in two rural-serving clinics and substantially lower in peri-urban and urban communities.
- Keyword:
- Group antenatal care, Malawi, pregnancy, and woman-centered
- Citation to related publication:
- Group antenatal care positively transforms the care experience: Results of an effectiveness trial in Malawi Crystal L. Patil, Kathleen F. Norr, Esnath Kapito, Li C. Liu, Xiaohan Mei, Elizabeth T. Abrams, Elizabeth Chodzaza, Genesis Chorwe-Sungani, Ursula Kafulafula, Allissa Desloge, Ashley Gresh, Rohan D. Jeremiah, Dhruvi R. Patel, Anne Batchelder, Heidy Wang, Jocelyn Faydenko, Sharon S. Rising, Ellen Chirwa medRxiv 2024.12.25.24319635; doi: https://doi.org/10.1101/2024.12.25.24319635
- Discipline:
- Health Sciences
-
- Creator:
- Steiner, Allison L., Wozniak, Matthew, Kort, Eric, and DeCola, Phil
- Description:
- Airborne pollen can impact human health by causing seasonal allergies and contribute to the total amount of particulate matter in the atmosphere. Current observations of pollen are limited in both space and time, making it is difficult to accurately forecast how pollen is released into the environment. Lidar is a ground-based remote sensing technique that can identify particles in the atmosphere, and depolarized light can identify irregularly shaped particles like pollen. We deployed a ground-based lidar with depolarization at a forested site in northern Michigan during the spring tree pollination season to understand the timing and contribution of pollen to the total amount of particulate matter in the atmosphere. We identify nine pollen events at the forested site that lead to high particulate matter in the atmosphere. This dataset includes the processed lidar data using the MiniMPL raw event count , which is calibrated and normalized to calculate the normalized relative backscatter (NRB) as a function of height (Ware et al., 2016).
- Keyword:
- lidar; University of Michigan Biological Station; aerosols; depolarization
- Citation to related publication:
- Steiner, A.L., et al. Lidar-based observations of pollen above a mixed hardwood forest in the United States. Submitted.
- Discipline:
- Engineering
-
- Creator:
- Hames, Alexandra, Tipirneni, Renuka, Switzer, Galen, Ayanian, John, Kullgren, Jeffrey, Solway, Erica, and Roberts, Eric
- Description:
- We examined whether enrollment in MA was associated with narrower racial and ethnic disparities in cost-related medical care barriers and cost-related dental care barriers as well as receipt of eye exams among near-poor Medicare beneficiaries. We further examined the extent to which racial and ethnic disparities were narrower among MA enrollees than TM enrollees who did and did not have private supplemental insurance. and This deposit includes code to process data for transparency and reproducibility purposes.
- Citation to related publication:
- Hames AG, Tipirneni R, Switzer GE, Ayanian JZ, Kullgren JT, Solway E, Roberts ET. Racial/Ethnic Disparities in Cost-Related Barriers to Care Among Near-Poor Beneficiaries in Medicare Advantage vs Traditional Medicare. Am J Manag Care. 2024;30(10):e297-e304. doi:10.37765/ajmc.2024.89622
- Discipline:
- Health Sciences
-
- 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
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- Creator:
- Diaz-Espinosa, Jennifer, Stringer, Kathleen, and Rosania, Gus
- Description:
- These data were produced from a study that assessed mitochondrial metabolic function by measuring two metabolites, l-carnitine and acetylcarnitine, to determine their effectiveness as candidate clinical biomarkers for age-related, drug-induced alterations in mitochondrial metabolism. To study age and medication-related changes in mitochondrial metabolism, we administered the FDA-approved mitochondriotropic drug, clofazimine (CFZ), or vehicle for to young and old mice. These findings are described in our manuscript: Clofazimine-Mediated, Age-Related Changes in Skeletal Muscle Mitochondrial Metabolites. Data reported was supported by funding from the National Institute of General Medical Sciences (NIGMS) at the National Institutes of Health (NIH) under award numbers R01GM127787 (GRR), R35GM136312 (KAS), P30AR069620 (K Jepsen), and T32GM140223 (L Isom).
- Keyword:
- adverse drug reactions, mitochondrial metabolism, l-carnitine, acetylcarnitine, and cardiac muscle
- Citation to related publication:
- Diaz-Espinosa J, Stringer KA, Rosania GR. Clofazimine-Mediated, Age-Related Changes in Skeletal Muscle Mitochondrial Metabolites. Metabolites. 2023 May 19;13(5):671. doi: 10.3390/metabo13050671. PMID: 37233713; PMCID: PMC10220805.
- Discipline:
- Health Sciences