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- Creator:
- Murguia, Amaya, Swanson, Scott D., Scheven, Ulrich, Jacobson, Andrea, Nielsen, Jon-Fredrik, Fessler, Jeffrey A., and Seraji-Bozorgzad, Navid
- Description:
- Validation of quantitative MRI (qMRI) parameters with histology is often done with ex vivo fixed tissue samples. Freezing is another common form of tissue preservation, but the effects of freezing and thawing tissue on myelin-sensitive qMRI parameters and their correlation with histology require further analysis. To study the effects of freezing vs. fixing tissue on myelin-sensitive parameters, we conducted myelin water imaging, off-resonance RF saturation magnetization transfer (MT), and selective inversion recovery MT MRI experiments on 14 fresh, thawed, and fixed sheep brain tissue samples to calculate various surrogate measures of myelin content. These measures were compared with luxol fast blue (LFB) histological stain results. 14 sheep brain tissue samples were scanned fresh. Half were frozen and subsequently thawed and scanned again. The second half were fixed and scanned again. Then all samples were fixed and sent for histological processing. This folder contains the MR and histology images collected for this study. All data are stored as mat files. The top level folder sheep_data_paper has subfolders: fresh_thawed: holds the data for the samples scanned fresh and thawed (S1-S7) fresh_fixed: holds the data for the samples scanned fresh and fresh_fixed (S8-S14) Each structure variable (data.mat) holds data for a specific sample and a specific tissue preparation (fresh, thawed, or fixed). The data variable has the following fields: gre: gradient echo scan data (128 x 128 x 5) fse: fast spin echo scan data (256 x 256 x 5) mese: multi-echo spin echo scan data for MWF mapping (128 x 128 x 5 x 104) b0data: gradient echo scan data for B0 mapping (128 x 128 x 5 x 4) b1data: EPI scan data for B1 mapping (32 x 32 x 5 x 9) t1data: EPI inversion recovery data for T1 mapping (64 x 64 x 5 x 21) mtdata: gradient echo data for quantitative MT analysis (128 x 128 x 4 x nf) hist: Luxol fast blue stain / Cresyl violet counterstain (LFB) histology image
- Keyword:
- myelin, magnetic resonance imaging, histology, quantitative MRI, ex vivo tissue, myelin water imaging, magnetization transfer, and luxol fast blue
- Citation to related publication:
- Murguia, A., Swanson, S. D., Scheven, U., Jacobson, A., Nielsen, J. F., Fessler, J. A., & Seraji-Bozorgzad, N. (2025). Impact of Tissue Sample Preparation Methods on Myelin-Sensitive Quantitative MR Imaging. bioRxiv, 2025-05.
- Discipline:
- Health Sciences and Engineering
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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
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- 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
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- 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
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- 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
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- 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
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- 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
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- 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
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- 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
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- 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