Award Abstract # 1840265
RTG: Data-Intensive Research and Computing at the University of California, Merced
NSF Org: |
DMS
Division Of Mathematical Sciences
|
Recipient: |
UNIVERSITY OF CALIFORNIA, MERCED
|
Initial Amendment Date:
|
May 28, 2019 |
Latest Amendment Date:
|
May 19, 2023 |
Award Number: |
1840265 |
Award Instrument: |
Continuing Grant |
Program Manager: |
Stacey Levine
slevine@nsf.gov
(703)292-2948
DMS
Division Of Mathematical Sciences
MPS
Directorate for Mathematical and Physical Sciences
|
Start Date: |
June 1, 2019 |
End Date: |
May 31, 2026 (Estimated) |
Total Intended Award
Amount: |
$2,092,605.00 |
Total Awarded Amount to
Date: |
$2,092,605.00 |
Funds Obligated to Date:
|
FY 2019 = $1,422,971.00
FY 2020 = $167,408.00
FY 2021 = $167,408.00
FY 2022 = $167,408.00
FY 2023 = $167,410.00
|
History of Investigator:
|
-
Arnold
Kim
(Principal Investigator)
adkim@ucmerced.edu
-
Francois
Blanchette
(Co-Principal Investigator)
-
Roummel
Marcia
(Co-Principal Investigator)
|
Recipient Sponsored Research
Office: |
University of California - Merced
5200 N LAKE RD
MERCED
CA
US
95343-5001
(209)201-2039
|
Sponsor Congressional
District: |
13
|
Primary Place of
Performance: |
University of California - Merced
CA
US
95343-5001
|
Primary Place of
Performance Congressional District: |
13
|
Unique Entity Identifier
(UEI): |
FFM7VPAG8P92
|
Parent UEI: |
|
NSF Program(s): |
APPLIED MATHEMATICS, COMPUTATIONAL MATHEMATICS, WORKFORCE IN THE MATHEMAT SCI
|
Primary Program Source:
|
01001920DB NSF RESEARCH & RELATED ACTIVIT
01002021DB NSF RESEARCH & RELATED ACTIVIT
01002122DB NSF RESEARCH & RELATED ACTIVIT
01002223DB NSF RESEARCH & RELATED ACTIVIT
01002324DB NSF RESEARCH & RELATED ACTIVIT
|
Program Reference
Code(s): |
7301,
9263
|
Program Element Code(s):
|
126600,
127100,
733500
|
Award Agency Code: |
4900
|
Fund Agency Code: |
4900
|
Assistance Listing
Number(s): |
47.049
|
ABSTRACT

The overarching objective of this program is to address the national need to train the next-generation workforce to be highly skilled in the field of computational and data-enabled sciences. To achieve this objective, we propose to establish the Data-Intensive Research And Computing (DIRAC) Research Training Group (RTG). The DIRAC RTG leverages strengths of the UC Merced Applied Mathematics faculty to provide undergraduate and graduate students, and postdoctoral researchers a training experience that prepares them for careers in academia, industry, and government. A key challenge is that computational and data-enabled sciences involve inextricable ties between mathematics, science, technology, and engineering. UC Merced Applied Mathematics is well positioned to address this challenge because of its three main approaches to science that will be at the core of this RTG: (1) modeling of physical and biological systems, (2) scientific computing, and (3) data analysis. To provide its trainees a collaborative training experience in computational and data-enabled sciences, the DIRAC RTG will foster Small Mentoring and Research Training (SMaRT) teams, which are vertically integrated, community-based mentoring structures, each centered on one of four research themes: (I) energy and the environment, (II) sensing and imaging, (III) mathematical biology, and (IV) numerical analysis. These SMaRT teams will provide support to individuals, guide their training, and produce a well-trained, nimble workforce that can contribute to the fast-paced modern computational research. Additionally, the DIRAC RTG is committed to serving the underrepresented and first-generation students that UC Merced Applied Mathematics actively recruits into its undergraduate and graduate programs. Built into each SMaRT Team are active measures for recruiting inclusive teams of trainees, providing continuous mentorship and support to retain these trainees, and developing the professional skills of trainees needed to succeed upon completion of this training program.
Computational and data sciences are new paradigms for scientific inquiry and discovery that incorporate mathematics, statistics, computer science, and domain-specific knowledge. Since computational and data-enabled sciences are relatively new, their natural and effective integration into existing training programs in mathematics remains to be perfected. This RTG project brings together the entire Applied Mathematics faculty of UC Merced with the common goal of developing a modernized and comprehensive training program for undergraduate and graduate students, and postdoctoral associates that integrates these subjects in a natural and effective way and prepares the trainees for successful careers in academia, government, and industry in a broad range of fields. The proposed RTG project has three major components: (1) a balanced curriculum tightly integrated with research which is modernized to reflect the current needs in computational and data-enabled sciences; (2) a vertically integrated mentoring program that engages undergraduate, graduate, postdoctoral associates, and faculty participants; and (3) the development of extensive, dynamic, and supportive communities focused on education, research, and professional development. The thematic research areas considered focus on timely and important issues and are divided into (I) energy and the environment, (II) sensing and imaging, (III) mathematical biology, and (IV) numerical analysis. This training program focuses on enhancing each trainee's skills and experience in the process of research (as opposed to just the products of research) and provides practical teaching training, communication skills, and professional development. The activities in this RTG are crucial to making systematic improvements to the existing training program at UC Merced, which can then serve as a model for other programs. These institutional changes will profoundly transform mathematics programs and have long-lasting impact on training the future generations of computational and data-enabled scientists.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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(Showing: 1 - 10 of 62)
(Showing: 1 - 62 of 62)
A. Ali Heydari, Oscar A.
"N-ACT: An Interpretable Deep Learning Model for Automatic Cell Type and Salient Gene Identification"
The Proceedings of the 2022 International Conference on Machine Learning Workshop on Computational Biology
, 2022
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Aburidi, Mohammed and Banuelos, Mario and Sindi, Suzanne and Marcia, Roummel
"Genetic Variant Detection Over Generations: Sparsity-Constrained Optimization Using Block-Coordinate Descent"
2023 IEEE Conference on Medical Measurements and Applications (MeMeA)
, 2023
https://doi.org/10.1109/MeMeA57477.2023.10171853
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Bhat, Harish S and Bassi, Hardeep and Ranka, Karnamohit and Isborn, Christine M
"Incorporating memory into propagation of 1-electron reduced density matrices"
Journal of Mathematical Physics
, v.66
, 2025
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Blanchette, François
"Shallow-water equations and box model simulations of turbidity currents from a moving source"
Physical Review Fluids
, v.7
, 2022
https://doi.org/10.1103/PhysRevFluids.7.084301
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Blanchette, François and Montroy, Sydney and Patris, Sharon and Dawson, Michael N.
"Marine lakes as biogeographical islands: a physical model for ecological dynamics in an insular marine lake, Palau"
Frontiers of Biogeography
, v.12
, 2020
https://doi.org/10.21425/F5FBG47736
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Blomquist, Matthew and West, Scott R. and Binswanger, Adam L. and Theillard, Maxime
"Stable nodal projection method on octree grids"
Journal of Computational Physics
, v.499
, 2024
https://doi.org/10.1016/j.jcp.2023.112695
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Carvalho, Camille and Kim, Arnold and Lewis, Lori and Moitier, Zoïs
"Quadrature by Parity Asymptotic eXpansions (QPAX) for Scattering by High Aspect Ratio Particles"
Multiscale Modeling & Simulation
, v.19
, 2021
https://doi.org/10.1137/21M1416801
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Derakhshani, Afshin and Asadzadeh, Zahra and Safarpour, Hossein and Leone, Patrizia and Shadbad, Mahdi Abdoli and Heydari, Ali and Baradaran, Behzad and Racanelli, Vito
"Regulation of CTLA-4 and PD-L1 Expression in Relapsing-Remitting Multiple Sclerosis Patients after Treatment with Fingolimod, IFN-1, Glatiramer Acetate, and Dimethyl Fumarate Drugs"
Journal of Personalized Medicine
, v.11
, 2021
https://doi.org/10.3390/jpm11080721
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González-Rodríguez, Pedro and Kim, Arnold D. and Tsogka, Chrysoula
"Quantitative signal subspace imaging"
Inverse Problems
, v.37
, 2021
https://doi.org/10.1088/1361-6420/ac349b
Citation
Details
Hartland, Tucker and Stadler, Georg and Perego, Mauro and Liegeois, Kim and Petra, Noémi
"Hierarchical off-diagonal low-rank approximation of Hessians in inverse problems, with application to ice sheet model initialization"
Inverse Problems
, v.39
, 2023
https://doi.org/10.1088/1361-6420/acd719
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Details
Heydari, A. Ali and Davalos, Oscar A. and Zhao, Lihong and Hoyer, Katrina K. and Sindi, Suzanne S. and Mathelier, ed., Anthony
"ACTIVA : realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational autoencoders"
Bioinformatics
, v.38
, 2022
https://doi.org/10.1093/bioinformatics/btac095
Citation
Details
Heydari, A. Ali and Sindi, Suzanne S.
"Deep learning in spatial transcriptomics: Learning from the next next-generation sequencing"
Biophysics Reviews
, v.4
, 2023
https://doi.org/10.1063/5.0091135
Citation
Details
Heydari, A. Ali and Sindi, Suzanne S. and Theillard, Maxime
"Conservative finite volume method on deforming geometries: The case of protein aggregation in dividing yeast cells"
Journal of Computational Physics
, v.448
, 2022
https://doi.org/10.1016/j.jcp.2021.110755
Citation
Details
Ho, Alex and Alvarez, Jacqueline and Marcia, Roummel F.
"Convolution Padding in Recurrent Neural Networks for Image Denoising with Limited Data"
2021 55th Asilomar Conference on Signals, Systems, and Computers
, 2021
https://doi.org/10.1109/IEEECONF53345.2021.9723313
Citation
Details
Ilan, Boaz and Kim, Arnold_D
"Asymptotic behavior of the reflectance of a narrow beam by a plane-parallel slab"
Journal of the Optical Society of America A
, v.41
, 2024
https://doi.org/10.1364/JOSAA.544227
Citation
Details
Ilan, Boaz and Kim, Arnold_D and Venugopalan, Vasan
"Radiance backscattered by a strongly scattering medium in the high spatial frequency limit"
Journal of the Optical Society of America A
, v.39
, 2022
https://doi.org/10.1364/JOSAA.462683
Citation
Details
Khan, Md_Imran and Ghosh, Sayantani and Baxter, Ryan and Kim, Arnold_D
"Modeling broadband cloaking using 3D nano-assembled plasmonic meta-structures"
Optics Express
, v.28
, 2020
https://doi.org/10.1364/OE.395840
Citation
Details
Kim, Arnold and Tsogka, Chrysoula
"Imaging in lossy media"
Inverse Problems
, v.39
, 2023
https://doi.org/10.1088/1361-6420/acc2b4
Citation
Details
Kim, Arnold D and Tsogka, Chrysoula
"Spectral Classification of Targets Below a Random Rough AirSoil Interface"
IEEE Geoscience and Remote Sensing Letters
, v.22
, 2025
https://doi.org/10.1109/LGRS.2024.3521342
Citation
Details
Kim, Arnold D. and Tsogka, Chrysoula
"High-Resolution, Quantitative Signal Subspace Imaging for Synthetic Aperture Radar"
SIAM Journal on Imaging Sciences
, v.15
, 2022
https://doi.org/10.1137/21M1467109
Citation
Details
Kim, Arnold D. and Tsogka, Chrysoula
"Synthetic Aperture Imaging of Dispersive Targets"
IEEE Transactions on Computational Imaging
, v.9
, 2023
https://doi.org/10.1109/TCI.2023.3326090
Citation
Details
Kim, Arnold D. and Tsogka, Chrysoula
"Synthetic Aperture Radar Imaging Below a Random Rough Surface"
Radio Science
, v.58
, 2023
https://doi.org/10.1029/2023RS007712
Citation
Details
Kim, Arnold D. and Tsogka, Chrysoula
"Tunable HighResolution Synthetic Aperture Radar Imaging"
Radio Science
, v.57
, 2022
https://doi.org/10.1029/2022RS007572
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Details
Lee, Jane HyoJin and Kim, Changho and Colvin, Michael E.
"Molecular Dynamics Studies of the Melting Kinetics of Superheated Crystals"
The Journal of Physical Chemistry C
, v.126
, 2022
https://doi.org/10.1021/acs.jpcc.1c10392
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Details
Lu, Yu and Bui, Kevin and Marcia, Roummel F
"Alternating Direction Method of Multipliers for Negative Binomial Model with the Weighted Difference of Anisotropic and Isotropic Total Variation"
, 2024
https://doi.org/10.1109/ICME57554.2024.10687632
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Details
Lu, Yu and Bui, Kevin and Marcia, Roummel F
"Negative Binomial Matrix Completion"
, 2024
https://doi.org/10.1109/MLSP58920.2024.10734831
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Details
Lu, Yu and Marcia, Roummel F.
"Negative Binomial Optimization for Low-Count Overdispersed Sparse Signal Reconstruction"
2023 European Signal Processing Conference (EUSIPCO)
, 2023
https://doi.org/10.23919/EUSIPCO58844.2023.10289862
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Details
Lu, Yu and Marcia, Roummel F.
"Overdispersed Photon-Limited Sparse Signal Recovery Using Nonconvex Regularization"
2023 IEEE 9th International Workshop on Computational Advances in Multi-Sensor Adaptive Processing (CAMSAP)
, 2023
https://doi.org/10.1109/CAMSAP58249.2023.10403416
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Details
Lu, Yu and Marcia, Roummel F.
"Sparse Overdispersed Photon-Limited Signal Recovery with Upper and Lower Bounds"
2023 IEEE 9th International Workshop on Computational Advances in Multi-Sensor Adaptive Processing (CAMSAP)
, 2023
https://doi.org/10.1109/CAMSAP58249.2023.10403449
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Details
Malone, Sarah and Aburidi, Mohammed and Marcia, Roummel F
"Wasserstein-Based Similarity Constrained Matrix Factorization for Drug-Drug Interaction Prediction"
, 2024
https://doi.org/10.1109/SiPS62058.2024.00017
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Details
Marquard, Dillon and Wright, Kyle and Marcia, Roummel F.
"Image classification and training with severe data loss"
SPIE Optical Engineering + Applications, 2022
, v.12227
, 2022
https://doi.org/10.1117/12.2633172
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Martin, David W. and Blanchette, François
"Film evolution of a spherical soap bubble"
Journal of Engineering Mathematics
, v.137
, 2022
https://doi.org/10.1007/s10665-022-10241-8
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Details
Meacham, Natalie and Rutter, Erica_M
"Estimating treatment sensitivity in synthetic and in vitro tumors using a random differential equation model"
npj Systems Biology and Applications
, v.11
, 2025
https://doi.org/10.1038/s41540-025-00530-0
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Mercado, Enrique and Jung, Hyun_Tae and Kim, Changho and Garcia, Alejandro_L and Nonaka, Andy_J and Bell, John_B
"Surface coverage dynamics for reversible dissociative adsorption on finite linear lattices"
The Journal of Chemical Physics
, v.159
, 2023
https://doi.org/10.1063/5.0171207
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Meyer, Tim and Kim, Arnold D. and Spivey, Michael and Yoshimi, Jeff
"Mouse tracking performance: A new approach to analyzing continuous mouse tracking data"
Behavior Research Methods
, 2023
https://doi.org/10.3758/s13428-023-02210-5
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Munoz, Jocelyn Ornelas and Rutter, Erica M and Banuelos, Mario and Sindi, Suzanne S and Marcia, Roummel F
"Sparse Negative Binomial Signal Recovery for Genomic Variant Prediction in Diploid Species"
, 2024
https://doi.org/10.1109/EMBC53108.2024.10782090
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Details
Munoz, Jocelyn Ornelas and Rutter, Erica M and Marcia, Roummel F
"From Observations to Theoretical Consistency: Decoder Recovery in Coded Aperture Imaging Using Convolutional Neural Networks"
, 2024
https://doi.org/10.1109/CISA60639.2024.10576438
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Details
Munoz, Jocelyn Ornelas and Rutter, Erica M. and Marcia, Roummel F.
"Decoding the Hidden: Direct Image Classification Using Coded Aperture Imaging"
2023 IEEE 9th International Workshop on Computational Advances in Multi-Sensor Adaptive Processing (CAMSAP)
, 2023
https://doi.org/10.1109/CAMSAP58249.2023.10403419
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Details
Nap, Ronald and Aburidi, Mohammed and Marcia, Roummel
"Contrastive Pre-Training and Multiple Instance Learning for Predicting Tumor Microsatellite Instability"
, 2024
https://doi.org/10.1109/EMBC53108.2024.10782037
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Details
Ornelas-Munoz, Jocelyn and Terasaki, Gbocho M and Ranganath, Aditya and DeGuchy, Omar and Marcia, Roummel F
"Signal Reconstructions for ECG-Transmembrane Voltage Potentials Using Transformers"
, 2025
https://doi.org/10.1109/ISBI60581.2025.10981210
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Details
Polimeno, Matteo and Kim, Changho and Blanchette, François
"Toward a Realistic Model of Diffusion-Limited Aggregation: Rotation, Size-Dependent Diffusivities, and Settling"
ACS Omega
, v.7
, 2022
https://doi.org/10.1021/acsomega.2c03547
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Polimeno, Matteo and Kim, Changho and Blanchette, François and Srivastava, Ishan and Garcia, Alejandro_L and Nonaka, Andy_J and Bell, John_B
"Thermodynamic consistency and fluctuations in mesoscopic stochastic simulations of reactive gas mixtures"
The Journal of Chemical Physics
, v.162
, 2025
https://doi.org/10.1063/5.0251770
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Powell, Maia and Kim, Arnold D. and Smaldino, Paul E.
"Hashtags as signals of political identity: #BlackLivesMatter and #AllLivesMatter"
PLOS ONE
, v.18
, 2023
https://doi.org/10.1371/journal.pone.0286524
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Details
Qu, Zhuolin and Patterson, Denis and Childs, Lauren M. and Edholm, Christina J. and Ponce, Joan and Prosper, Olivia and Zhao, Lihong
"Modeling Immunity to Malaria with an Age-Structured PDE Framework"
SIAM Journal on Applied Mathematics
, v.83
, 2023
https://doi.org/10.1137/21M1464427
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Details
Ranganath, Aditya and Muñoz, Jocelyn Ornelas and Smith, Robert and Singhal, Mukesh and Marcia, Roummel
"Image Separation Using Transformer Attention Models"
, 2024
https://doi.org/10.1109/FMLDS63805.2024.00066
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Details
Ranganath, Aditya and Ruiz, Irabiel Romero and Singhal, Mukesh and Marcia, Roummel
"Quasi-Adam: Accelerating Adam Using Quasi-Newton Approximations"
, 2024
https://doi.org/10.1109/ICMLA61862.2024.00107
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Details
Santiago, Matea and Mitchell, Kevin A. and Khatri, Shilpa
"Numerical method for modeling photosynthesis of algae on pulsing soft corals"
Physical Review Fluids
, v.7
, 2022
https://doi.org/10.1103/PhysRevFluids.7.033102
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Details
St. Clair, Nicholas and Davenport, Dominique and Kim, Arnold D. and Kleckner, Dustin
"Dynamics of acoustically bound particles"
Physical Review Research
, v.5
, 2023
https://doi.org/10.1103/PhysRevResearch.5.013051
Citation
Details
Wright, Kyle and Marcia, Roummel and Scheibner, Michael and Ilan, Boaz
"Parameterized Inverse Eigenvalue Problem for Quantum Sensing"
2023 IEEE 9th International Workshop on Computational Advances in Multi-Sensor Adaptive Processing (CAMSAP)
, 2023
https://doi.org/10.1109/CAMSAP58249.2023.10403442
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Details
Wright, Kyle and Marcia, Roummel and Scheibner, Michael and Ilan, Boaz
"Towards Motion Sensing Using Asymmetric Coupled Quantum Dots"
, 2025
https://doi.org/10.1109/QCNC64685.2025.00090
Citation
Details
Yoo, Eunji and Khatri, Shilpa and Blanchette, François
"Hydrodynamic forces on randomly formed marine aggregates"
Physical Review Fluids
, v.5
, 2020
10.1103/PhysRevFluids.5.044305
Citation
Details
Zhao, Lihong and Lundy, Stephanie R. and Eko, Francis O. and Igietseme, Joeseph U. and Omosun, Yusuf O.
"Genital tract microbiome dynamics are associated with time of Chlamydia infection in mice"
Scientific Reports
, v.13
, 2023
https://doi.org/10.1038/s41598-023-36130-3
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Details
Zhao, Lihong and Santiago, Fabian and Rutter, Erica_M and Khatri, Shilpa and Sindi, Suzanne_S
"Modeling and Global Sensitivity Analysis of Strategies to Mitigate Covid-19 Transmission on a Structured College Campus"
Bulletin of Mathematical Biology
, v.85
, 2023
https://doi.org/10.1007/s11538-022-01107-2
Citation
Details
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(Showing: 1 - 62 of 62)
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