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Year Three Appendix PHYSICAL SCIENCES-ONCOLOGY CENTER PROGRAM Appendix Fall 2012 Appendix 1 2 Physical Sciences-Oncology Center Program Table of Contents 1. Publications ...............................................................................................................................................................................1 2. Patents Disclosures/Applications ............................................................................................................................................31 3. Clinical Samples and Trials ......................................................................................................................................................35 4. Additional Center Highlights ...................................................................................................................................................41 5. Pilot Projects .............................................................................................................................................................................71 6. Trans-Network Projects ............................................................................................................................................................77 7. Young Investigator Trans-Network ...........................................................................................................................................81 8. PS-OC Cores ..............................................................................................................................................................................85 9. PS-OC Outreach Programs ........................................................................................................................................................89 10. PS-OC Courses ........................................................................................................................................................................101 11. Trainee Exchanges ..................................................................................................................................................................105 12. Trainee Transitions .................................................................................................................................................................109 13. PS-OC Investigator Interactions with the Media ..................................................................................................................115 14. PS-OC Investigator Conferences and Seminars ....................................................................................................................121 15. OPSO Staff Invited Presentations ...........................................................................................................................................159 16. OPSO Staff Symposium and Workshops ................................................................................................................................165 17. PS-OC Investigator Meeting Agendas ....................................................................................................................................169 17.1 First Annual Principal Investigator Meeting ................................................................................................................171 17.2 Second Annual Principal Investigator Meeting ...........................................................................................................183 17.3 Third Annual Principal Investigator Meeting ..............................................................................................................195 17.4 Joint Meeting of Junior Investigators .........................................................................................................................207 18. Science Technology Policy Institute Memos ..........................................................................................................................209 19. Extended Scientific Report emplateT .....................................................................................................................................223 20. Survey Questions ....................................................................................................................................................................243 21. Survey Results ........................................................................................................................................................................345 Appendix i ii Physical Sciences-Oncology Center Program 1. Publications Appendix 1 2 Physical Sciences-Oncology Center Program 1. PS-OC Peer-Reviewed Publications 1. Abaci, H.E., Devendra, R., Smith, Q., Gerecht, S. & Drazer, G. Design and development of microbioreactors for long- term cell culture in controlled oxygen microenvironments. Biomed Microdevices 14, 145-152 (2012). 2. Balzer, E.M. & Konstantopoulos, K. Intercellular adhesion: Mechanisms for growth and metastasis of epithelial cancers. Wiley Interdisciplinary Reviews-Systems Biology and Medicine 4, 171-181 (2012). 3. Barrett, L.E., et al. Self-renewal does not predict tumor growth potential in mouse models of high-grade glioma. Cancer Cell 21, 11-24 (2012). 4. Basanta, D., Gatenby, R.A. & Anderson, A.R.A. Exploiting evolution to treat drug resistance: Combination therapy and the double bind. Molecular Pharmaceutics 9, 914-921 (2012). 5. Basanta, D., et al. Investigating prostate cancer tumour-stroma interactions: Clinical and biological insights from an evolutionary game. Br J Cancer 106, 174-181 (2012). 6. Battistini, F., Hunter, C.A., Moore, I.K. & Widom, J. Structure-based identification of new high-affinity nucleosome binding sequences. Journal of Molecular Biology 420, 8-16 (2012). 7. Bergethon, K., et al. Ros1 rearrangements define a unique molecular class of lung cancers.J Clin Oncol 30, 863-870 (2012). 8. Bryan, A.K., Engler, A., Gulati, A. & Manalis, S.R. Continuous and long-term volume measurements with a commercial coulter counter. PLoS One 7, 17 (2012). 9. Carbonaro, M., Escuin, D., O’Brate, A., Thadani-Mulero, M. & Giannakakou, P. Microtubules regulate hypoxia- inducible factor-1 alpha protein trafficking and activity implications for taxane therapy.Journal of Biological Chemistry 287, 11859-11869 (2012). 10. Carey, S.P., Kraning-Rush, C.M., Williams, R.M. & Reinhart-King, C.A. Biophysical control of invasive tumor cell behavior by extracellular matrix microarchitecture. Biomaterials 33, 4157-4165 (2012). 11. Charest, J.M., Califano, J.P., Carey, S.P. & Reinhart-King, C.A. Fabrication of substrates with defined mechanical properties and topographical features for the study of cell migration. Macromol Biosci 12, 12-20 (2012). 12. Chen, S.H., Dallas, M.R., Balzer, E.M. & Konstantopoulos, K. Mucin 16 is a functional selectin ligand on pancreatic cancer cells. Faseb Journal 26, 1349-1359 (2012). 13. Cheng, Y.K., et al. A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis. PLoS Comput Biol 8, 5 (2012). 14. Chmielecki, J., et al. Egfr-mutant lung adenocarcinomas treated first-line with the novel egfr inhibitor, xl647, can subsequently retain moderate sensitivity to erlotinib. Journal of Thoracic Oncology 7, 434-442 (2012). 15. Cho, E.H., et al. Characterization of circulating tumor cell aggregates identified in patients with epithelial tumors. Phys Biol 9, 3 (2012). 16. Ciriello, G., Cerami, E., Sander, C. & Schultz, N. Mutual exclusivity analysis identifies oncogenic network modules. Genome Res 22, 398-406 (2012). 17. Damani, S., et al. Characterization of circulating endothelial cells in acute myocardial infarction. Sci Transl Med 4(2012). 18. Fraley, S.I., Feng, Y., Giri, A., Longmore, G.D. & Wirtz, D. Dimensional and temporal controls of three-dimensional cell migration by zyxin and binding partners. Nat Commun 3(2012). Appendix 3 19. Galban, S., et al. Dw-mri as a biomarker to compare therapeutic outcomes in radiotherapy regimens incorporating temozolomide or gemcitabine in glioblastoma. PLoS One 7, 20 (2012). 20. Gao, D., et al. Myeloid progenitor cells in the premetastatic lung promote metastases by inducing mesenchymal to epithelial transition. Cancer Res 72, 1384-1394 (2012). 21. Gibson, D.S., et al. Biomarkers in rheumatology, now and in the future. Rheumatology 51, 423-433 (2012). 22. Govern, C.C., Yang, M. & Chakraborty, A.K. Identifying dynamical bottlenecks of stochastic transitions in biochemical networks. Phys Rev Lett 108, 30 (2012). 23. Gu, S., et al. Applying a patient-specific bio-mathematical model of glioma growth to develop virtual [18f]-fmiso-pet images. Math Med Biol 29, 31-48 (2012). 24. Guo, W., et al. Slug and sox9 cooperatively determine the mammary stem cell state. Cell 148, 1015-1028 (2012). 25. Haeno, H., et al. Computational modeling of pancreatic cancer reveals kinetics of metastasis suggesting optimum treatment strategies. Cell 148, 362-375 (2012). 26. Hielscher, A.C., Qiu, C. & Gerecht, S. Breast cancer cell-derived matrix supports vascular morphogenesis. Am J Physiol Cell Physiol 302, 25 (2012). 27. Hughes, A.D., et al. Microtube device for selectin-mediated capture of viable circulating tumor cells from blood. Clin Chem 58, 846-853 (2012). 28. Huynh, K.A., McCaffery, J.M. & Chen, K.L. Heteroaggregation of multiwalled carbon nanotubes and hematite nanoparticles: Rates and mechanisms. Environ Sci Technol 46, 5912-5920 (2012).
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