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- 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
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- 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
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- 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
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- 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
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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
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- 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
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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:
- 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
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- 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