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33 results on '"Lee, Diana Y."'

1. Learning to fail: Predicting fracture evolution in brittle material models using recurrent graph convolutional neural networks

Author

Schwarzer, Max, Rogan, Bryce, Ruan, Yadong, Song, Zhengming, Lee, Diana Y., Percus, Allon G., Chau, Viet T., Moore, Bryan A., Rougier, Esteban, Viswanathan, Hari S., and Srinivasan, Gowri

Subjects
Condensed Matter - Materials Science, Computer Science - Machine Learning, Physics - Data Analysis, Statistics and Probability, Statistics - Machine Learning
Abstract

We propose a machine learning approach to address a key challenge in materials science: predicting how fractures propagate in brittle materials under stress, and how these materials ultimately fail. Our methods use deep learning and train on simulation data from high-fidelity models, emulating the results of these models while avoiding the overwhelming computational demands associated with running a statistically significant sample of simulations. We employ a graph convolutional network that recognizes features of the fracturing material and a recurrent neural network that models the evolution of these features, along with a novel form of data augmentation that compensates for the modest size of our training data. We simultaneously generate predictions for qualitatively distinct material properties. Results on fracture damage and length are within 3% of their simulated values, and results on time to material failure, which is notoriously difficult to predict even with high-fidelity models, are within approximately 15% of simulated values. Once trained, our neural networks generate predictions within seconds, rather than the hours needed to run a single simulation.

Published
2018
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6. Supplementary Table 1 from Differential Gene Expression Analysis Reveals Generation of an Autocrine Loop by a Mutant Epidermal Growth Factor Receptor in Glioma Cells

Author

Ramnarain, Deepti B., primary, Park, Seongmi, primary, Lee, Diana Y., primary, Hatanpaa, Kimmo J., primary, Scoggin, Shane O., primary, Otu, Hasan, primary, Libermann, Towia A., primary, Raisanen, Jack M., primary, Ashfaq, Raheela, primary, Wong, Eric T., primary, Wu, Julian, primary, Elliott, Robert, primary, and Habib, Amyn A., primary

Published
2023
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7. Supplementary Figure 2 from Elevated CRAF as a Potential Mechanism of Acquired Resistance to BRAF Inhibition in Melanoma

Author

Montagut, Clara, primary, Sharma, Sreenath V., primary, Shioda, Toshi, primary, McDermott, Ultan, primary, Ulman, Matthew, primary, Ulkus, Lindsey E., primary, Dias-Santagata, Dora, primary, Stubbs, Hannah, primary, Lee, Diana Y., primary, Singh, Anurag, primary, Drew, Lisa, primary, Haber, Daniel A., primary, and Settleman, Jeffrey, primary

Published
2023
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8. Supplementary Figure 4 from Ligand-Dependent Platelet-Derived Growth Factor Receptor (PDGFR)-α Activation Sensitizes Rare Lung Cancer and Sarcoma Cells to PDGFR Kinase Inhibitors

Author

McDermott, Ultan, primary, Ames, Rachel Y., primary, Iafrate, A. John, primary, Maheswaran, Shyamala, primary, Stubbs, Hannah, primary, Greninger, Patricia, primary, McCutcheon, Kaitlin, primary, Milano, Randy, primary, Tam, Angela, primary, Lee, Diana Y., primary, Lucien, Laury, primary, Brannigan, Brian W., primary, Ulkus, Lindsey E., primary, Ma, Xiao-Jun, primary, Erlander, Mark G., primary, Haber, Daniel A., primary, Sharma, Sreenath V., primary, and Settleman, Jeffrey, primary

Published
2023
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9. Supplementary Figure 3 from Elevated CRAF as a Potential Mechanism of Acquired Resistance to BRAF Inhibition in Melanoma

Author

Montagut, Clara, primary, Sharma, Sreenath V., primary, Shioda, Toshi, primary, McDermott, Ultan, primary, Ulman, Matthew, primary, Ulkus, Lindsey E., primary, Dias-Santagata, Dora, primary, Stubbs, Hannah, primary, Lee, Diana Y., primary, Singh, Anurag, primary, Drew, Lisa, primary, Haber, Daniel A., primary, and Settleman, Jeffrey, primary

Published
2023
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10. Supplementary Table 1 from Elevated CRAF as a Potential Mechanism of Acquired Resistance to BRAF Inhibition in Melanoma

Author

Montagut, Clara, primary, Sharma, Sreenath V., primary, Shioda, Toshi, primary, McDermott, Ultan, primary, Ulman, Matthew, primary, Ulkus, Lindsey E., primary, Dias-Santagata, Dora, primary, Stubbs, Hannah, primary, Lee, Diana Y., primary, Singh, Anurag, primary, Drew, Lisa, primary, Haber, Daniel A., primary, and Settleman, Jeffrey, primary

Published
2023
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11. Supplementary Figures 1-2 from Ligand-Dependent Platelet-Derived Growth Factor Receptor (PDGFR)-α Activation Sensitizes Rare Lung Cancer and Sarcoma Cells to PDGFR Kinase Inhibitors

Author

McDermott, Ultan, primary, Ames, Rachel Y., primary, Iafrate, A. John, primary, Maheswaran, Shyamala, primary, Stubbs, Hannah, primary, Greninger, Patricia, primary, McCutcheon, Kaitlin, primary, Milano, Randy, primary, Tam, Angela, primary, Lee, Diana Y., primary, Lucien, Laury, primary, Brannigan, Brian W., primary, Ulkus, Lindsey E., primary, Ma, Xiao-Jun, primary, Erlander, Mark G., primary, Haber, Daniel A., primary, Sharma, Sreenath V., primary, and Settleman, Jeffrey, primary

Published
2023
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12. Supplementary Figure Legends 1-3, Table 1 from Elevated CRAF as a Potential Mechanism of Acquired Resistance to BRAF Inhibition in Melanoma

Author

Montagut, Clara, primary, Sharma, Sreenath V., primary, Shioda, Toshi, primary, McDermott, Ultan, primary, Ulman, Matthew, primary, Ulkus, Lindsey E., primary, Dias-Santagata, Dora, primary, Stubbs, Hannah, primary, Lee, Diana Y., primary, Singh, Anurag, primary, Drew, Lisa, primary, Haber, Daniel A., primary, and Settleman, Jeffrey, primary

Published
2023
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13. Supplementary Figure 7 from Ligand-Dependent Platelet-Derived Growth Factor Receptor (PDGFR)-α Activation Sensitizes Rare Lung Cancer and Sarcoma Cells to PDGFR Kinase Inhibitors

Author

McDermott, Ultan, primary, Ames, Rachel Y., primary, Iafrate, A. John, primary, Maheswaran, Shyamala, primary, Stubbs, Hannah, primary, Greninger, Patricia, primary, McCutcheon, Kaitlin, primary, Milano, Randy, primary, Tam, Angela, primary, Lee, Diana Y., primary, Lucien, Laury, primary, Brannigan, Brian W., primary, Ulkus, Lindsey E., primary, Ma, Xiao-Jun, primary, Erlander, Mark G., primary, Haber, Daniel A., primary, Sharma, Sreenath V., primary, and Settleman, Jeffrey, primary

Published
2023
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14. Data from Ligand-Dependent Platelet-Derived Growth Factor Receptor (PDGFR)-α Activation Sensitizes Rare Lung Cancer and Sarcoma Cells to PDGFR Kinase Inhibitors

Author

McDermott, Ultan, primary, Ames, Rachel Y., primary, Iafrate, A. John, primary, Maheswaran, Shyamala, primary, Stubbs, Hannah, primary, Greninger, Patricia, primary, McCutcheon, Kaitlin, primary, Milano, Randy, primary, Tam, Angela, primary, Lee, Diana Y., primary, Lucien, Laury, primary, Brannigan, Brian W., primary, Ulkus, Lindsey E., primary, Ma, Xiao-Jun, primary, Erlander, Mark G., primary, Haber, Daniel A., primary, Sharma, Sreenath V., primary, and Settleman, Jeffrey, primary

Published
2023
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15. Supplementary Figure 6 from Ligand-Dependent Platelet-Derived Growth Factor Receptor (PDGFR)-α Activation Sensitizes Rare Lung Cancer and Sarcoma Cells to PDGFR Kinase Inhibitors

Author

McDermott, Ultan, primary, Ames, Rachel Y., primary, Iafrate, A. John, primary, Maheswaran, Shyamala, primary, Stubbs, Hannah, primary, Greninger, Patricia, primary, McCutcheon, Kaitlin, primary, Milano, Randy, primary, Tam, Angela, primary, Lee, Diana Y., primary, Lucien, Laury, primary, Brannigan, Brian W., primary, Ulkus, Lindsey E., primary, Ma, Xiao-Jun, primary, Erlander, Mark G., primary, Haber, Daniel A., primary, Sharma, Sreenath V., primary, and Settleman, Jeffrey, primary

Published
2023
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16. Data from Elevated CRAF as a Potential Mechanism of Acquired Resistance to BRAF Inhibition in Melanoma

Author

Montagut, Clara, primary, Sharma, Sreenath V., primary, Shioda, Toshi, primary, McDermott, Ultan, primary, Ulman, Matthew, primary, Ulkus, Lindsey E., primary, Dias-Santagata, Dora, primary, Stubbs, Hannah, primary, Lee, Diana Y., primary, Singh, Anurag, primary, Drew, Lisa, primary, Haber, Daniel A., primary, and Settleman, Jeffrey, primary

Published
2023
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17. Supplementary Figure 5 from Ligand-Dependent Platelet-Derived Growth Factor Receptor (PDGFR)-α Activation Sensitizes Rare Lung Cancer and Sarcoma Cells to PDGFR Kinase Inhibitors

Author

McDermott, Ultan, primary, Ames, Rachel Y., primary, Iafrate, A. John, primary, Maheswaran, Shyamala, primary, Stubbs, Hannah, primary, Greninger, Patricia, primary, McCutcheon, Kaitlin, primary, Milano, Randy, primary, Tam, Angela, primary, Lee, Diana Y., primary, Lucien, Laury, primary, Brannigan, Brian W., primary, Ulkus, Lindsey E., primary, Ma, Xiao-Jun, primary, Erlander, Mark G., primary, Haber, Daniel A., primary, Sharma, Sreenath V., primary, and Settleman, Jeffrey, primary

Published
2023
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18. Supplementary Tables 1-2 from Ligand-Dependent Platelet-Derived Growth Factor Receptor (PDGFR)-α Activation Sensitizes Rare Lung Cancer and Sarcoma Cells to PDGFR Kinase Inhibitors

Author

McDermott, Ultan, primary, Ames, Rachel Y., primary, Iafrate, A. John, primary, Maheswaran, Shyamala, primary, Stubbs, Hannah, primary, Greninger, Patricia, primary, McCutcheon, Kaitlin, primary, Milano, Randy, primary, Tam, Angela, primary, Lee, Diana Y., primary, Lucien, Laury, primary, Brannigan, Brian W., primary, Ulkus, Lindsey E., primary, Ma, Xiao-Jun, primary, Erlander, Mark G., primary, Haber, Daniel A., primary, Sharma, Sreenath V., primary, and Settleman, Jeffrey, primary

Published
2023
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19. Supplementary Figure 1 from Elevated CRAF as a Potential Mechanism of Acquired Resistance to BRAF Inhibition in Melanoma

Author

Montagut, Clara, primary, Sharma, Sreenath V., primary, Shioda, Toshi, primary, McDermott, Ultan, primary, Ulman, Matthew, primary, Ulkus, Lindsey E., primary, Dias-Santagata, Dora, primary, Stubbs, Hannah, primary, Lee, Diana Y., primary, Singh, Anurag, primary, Drew, Lisa, primary, Haber, Daniel A., primary, and Settleman, Jeffrey, primary

Published
2023
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20. Supplementary Figure 3 from Ligand-Dependent Platelet-Derived Growth Factor Receptor (PDGFR)-α Activation Sensitizes Rare Lung Cancer and Sarcoma Cells to PDGFR Kinase Inhibitors

Author

McDermott, Ultan, primary, Ames, Rachel Y., primary, Iafrate, A. John, primary, Maheswaran, Shyamala, primary, Stubbs, Hannah, primary, Greninger, Patricia, primary, McCutcheon, Kaitlin, primary, Milano, Randy, primary, Tam, Angela, primary, Lee, Diana Y., primary, Lucien, Laury, primary, Brannigan, Brian W., primary, Ulkus, Lindsey E., primary, Ma, Xiao-Jun, primary, Erlander, Mark G., primary, Haber, Daniel A., primary, Sharma, Sreenath V., primary, and Settleman, Jeffrey, primary

Published
2023
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27. CAT-2003: A novel sterol regulatory element-binding protein inhibitor that reduces steatohepatitis, plasma lipids, and atherosclerosis in apolipoprotein E*3-Leiden mice

Author

Zimmer, Michael, primary, Bista, Pradeep, additional, Benson, Ericka L., additional, Lee, Diana Y., additional, Liu, Feng, additional, Picarella, Dominic, additional, Vega, Rick B., additional, Vu, Chi B., additional, Yeager, Maisy, additional, Ding, Min, additional, Liang, Guosheng, additional, Horton, Jay D., additional, Kleemann, Robert, additional, Kooistra, Teake, additional, Morrison, Martine C., additional, Wielinga, Peter Y., additional, Milne, Jill C., additional, Jirousek, Michael R., additional, and Nichols, Andrew J., additional

Published
2017
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29. Ligand-Dependent Platelet-Derived Growth Factor Receptor (PDGFR)-α Activation Sensitizes Rare Lung Cancer and Sarcoma Cells to PDGFR Kinase Inhibitors

Author

McDermott, Ultan, primary, Ames, Rachel Y., additional, Iafrate, A. John, additional, Maheswaran, Shyamala, additional, Stubbs, Hannah, additional, Greninger, Patricia, additional, McCutcheon, Kaitlin, additional, Milano, Randy, additional, Tam, Angela, additional, Lee, Diana Y., additional, Lucien, Laury, additional, Brannigan, Brian W., additional, Ulkus, Lindsey E., additional, Ma, Xiao-Jun, additional, Erlander, Mark G., additional, Haber, Daniel A., additional, Sharma, Sreenath V., additional, and Settleman, Jeffrey, additional

Published
2009
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30. Elevated CRAF as a Potential Mechanism of Acquired Resistance to BRAF Inhibition in Melanoma

Author

Montagut, Clara, primary, Sharma, Sreenath V., additional, Shioda, Toshi, additional, McDermott, Ultan, additional, Ulman, Matthew, additional, Ulkus, Lindsey E., additional, Dias-Santagata, Dora, additional, Stubbs, Hannah, additional, Lee, Diana Y., additional, Singh, Anurag, additional, Drew, Lisa, additional, Haber, Daniel A., additional, and Settleman, Jeffrey, additional

Published
2008
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31. Differential Gene Expression Analysis Reveals Generation of an Autocrine Loop by a Mutant Epidermal Growth Factor Receptor in Glioma Cells

Author

Ramnarain, Deepti B., primary, Park, Seongmi, additional, Lee, Diana Y., additional, Hatanpaa, Kimmo J., additional, Scoggin, Shane O., additional, Otu, Hasan, additional, Libermann, Towia A., additional, Raisanen, Jack M., additional, Ashfaq, Raheela, additional, Wong, Eric T., additional, Wu, Julian, additional, Elliott, Robert, additional, and Habib, Amyn A., additional

Published
2006
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32. Rapid B 1 field mapping at 3 T using the 180° signal null method with extended flip angle.

Author

Rejimon AC, Lee DY, Bergeron CM, Zhuo Y, Qian W, Spencer RG, and Bouhrara M

Subjects
Adult, Aged, Algorithms, Computer Simulation, Female, Humans, Image Enhancement, Linear Models, Male, Middle Aged, Phantoms, Imaging, Brain diagnostic imaging, Image Processing, Computer-Assisted methods, Magnetic Resonance Imaging methods
Abstract

Purpose: To extend the null signal method (NSM) for B 1 mapping to 3 T magnetic resonance imaging (MRI)., Background: The NSM operates in the steady state regime and exploits the linearity of the spoiled gradient recalled echo (SPGR) signal around the 180° flip angle (FA). Using linear regression, B 1 maps are derived from three SPGR images acquired at different FAs with a short repetition time. While the conventional NSM allows accurate mapping of B 1 for moderate B 1 variation, we observed that this method fails for the larger B 1 variations typical of high-field MRI., Methods: We analyzed the effect of the FA range of the acquired SPGR images on B 1 determination using the NSM for 3 T MRI through extensive numerical and in vivo analyses. B 1 maps derived from the extended angle-range NSM (EA-NSM) were calculated and compared to those derived from the conventional, more restricted angle range, NSM, and to those derived from the reference, but much more time-consuming, double angle method (DAM). Furthermore, we investigated the compatibility of EA-NSM B 1 mapping and the half-scan and SENSE reconstruction methods for accelerating acquisition time., Results: Our results show that the use of the conventional FA range leads to substantial inaccuracies in B 1 determination. Both numerical and in vivo analyses demonstrate that expanding the FA range of the acquired SPGR images substantially improves the accuracy of B 1 maps. Furthermore, B 1 maps derived from EA-NSM were demonstrated to be quantitatively comparable to those derived from the lengthy DAM protocol. We also found that B 1 maps derived from SPGR images using the EA-NSM and imaging acceleration methods were comparable to those derived from images acquired without acceleration. Finally, the use of half scanning combined with SENSE reconstruction permits whole-brain B 1 mapping in ~1 min., Conclusions: The EA-NSM permits accurate, fast, and practical B 1 mapping in a 3 T clinical setting., (Published by Elsevier Inc.)

Published
2018
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33. Ligand-dependent platelet-derived growth factor receptor (PDGFR)-alpha activation sensitizes rare lung cancer and sarcoma cells to PDGFR kinase inhibitors.

Author

McDermott U, Ames RY, Iafrate AJ, Maheswaran S, Stubbs H, Greninger P, McCutcheon K, Milano R, Tam A, Lee DY, Lucien L, Brannigan BW, Ulkus LE, Ma XJ, Erlander MG, Haber DA, Sharma SV, and Settleman J

Subjects
Antibodies immunology, Antibodies pharmacology, Carcinoma, Non-Small-Cell Lung enzymology, Carcinoma, Non-Small-Cell Lung genetics, Cell Line, Tumor, Gene Amplification, Gene Expression Profiling, Humans, Ligands, Lung Neoplasms enzymology, Lung Neoplasms genetics, Lymphokines genetics, Lymphokines immunology, Platelet-Derived Growth Factor genetics, Platelet-Derived Growth Factor immunology, RNA, Small Interfering genetics, Receptor, Platelet-Derived Growth Factor alpha antagonists & inhibitors, Receptor, Platelet-Derived Growth Factor alpha genetics, Rhabdomyosarcoma enzymology, Rhabdomyosarcoma genetics, Sunitinib, Carcinoma, Non-Small-Cell Lung drug therapy, Indoles pharmacology, Lung Neoplasms drug therapy, Pyrroles pharmacology, Receptor, Platelet-Derived Growth Factor alpha metabolism, Rhabdomyosarcoma drug therapy
Abstract

Platelet-derived growth factor (PDGF) receptors (PDGFR) and their ligands play critical roles in several human malignancies. Sunitinib is a clinically approved multitargeted tyrosine kinase inhibitor that inhibits vascular endothelial growth factor receptor, c-KIT, and PDGFR, and has shown clinical activity in various solid tumors. Activation of PDGFR signaling has been described in gastrointestinal stromal tumors (PDGFRA mutations) as well as in chronic myeloid leukemia (BCR-PDGFRA translocation), and sunitinib can yield clinical benefit in both settings. However, the discovery of PDGFR activating mutations or gene rearrangements in other tumor types could reveal additional patient populations who might benefit from treatment with anti-PDGFR therapies, such as sunitinib. Using a high-throughput cancer cell line screening platform, we found that only 2 of 637 tested human tumor-derived cell lines show significant sensitivity to single-agent sunitinib exposure. These two cell lines [a non-small-cell lung cancer (NSCLC) and a rhabdomyosarcoma] showed expression of highly phosphorylated PDGFRA. In the sunitinib-sensitive adenosquamous NSCLC cell line, PDGFRA expression was associated with focal PFGRA gene amplification, which was similarly detected in a small fraction of squamous cell NSCLC primary tumor specimens. Moreover, in this NSCLC cell line, focal amplification of the gene encoding the PDGFR ligand PDGFC was also detected, and silencing PDGFRA or PDGFC expression by RNA interference inhibited proliferation. A similar codependency on PDGFRA and PDGFC was observed in the sunitinib-sensitive rhabdomyosarcoma cell line. These findings suggest that, in addition to gastrointestinal stromal tumors, rare tumors that show PDGFC-mediated PDGFRA activation may also be clinically responsive to pharmacologic PDGFRA or PDGFC inhibition.

Published
2009
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