Difference between revisions of "2014-2015 AMS-532 Fall-Spring"

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| '''2013 Fall
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| '''2014 Fall
 
| '''Participant'''  
 
| '''Participant'''  
 
| '''Rotations or Research Group'''
 
| '''Rotations or Research Group'''
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|-
 
|-
  
−
| 2013.08.28 Wed || Last name, First name || -- || Topic || paper
+
| 2014.08.27 Wed || Last name, First name || -- || Topic || Organizational Meeting
 
|-
 
|-
  
−
| 2013.09.04 Wed || Krantsevich, Nikolay || Green || topic || Travers, SA. Conservation, compensation, and evolution of N-linked glycansin the HIV-1 group M subtypes and circulating recombinant forms. ''ISRN AIDS.'' '''2012 Nov'''.
+
| 2014.09.03 Wed || Kennedy, Chelsea || Green || topic || Alberts, B. ''et al''. Rescuing US biomedical research from its systemic flaws. ''PNAS''. '''2014 March'''. ''111(16)''. 5773-5777.
 
|-
 
|-
  
−
| 2013.09.11 Wed || Yuan, Chaohui || MacCarthy || topic || Oprea, M. and Perelson, AS. Somatic mutation leads to efficient affinity maturation when centrocytes recycle back to centroblasts. ''J Immunology''. '''1997 Jun'''. ''158(11)''. 5155-5162.
+
| 2014.09.10 Wed || Zou, Junjie || Raleigh || topic || Xiao, S. ''et al''. Rational modification of protein stability by targeting surface sites leads to complicated results. ''PNAS''. '''2013 July'''. ''110(28)''. 11337-11342
 
|-
 
|-
  
−
| 2013.09.18 Wed || Lee, Xindi (Cindy) || Green || topic || Eklund, R. and Widmalm, G. Molecular dynamics simulations of an oligosaccharide using a force field modified for carbohydrates. ''Carbohydrate Reasearch''. '''2002 Nov'''. ''338(2003)''. 393-398.
+
| 2014.09.17 Wed || - || -- || -- || AMS party
 
|-
 
|-
  
−
| 2013.09.25 Wed || Last name, First name || -- || topic || paper
+
| 2014.09.24 Wed || Yu, Bihau || Vageli || topic || Munson, P. J. and Singh, P. K. Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment. ''Protein Science''. '''1997 March'''. ''6''. 1467-1481
 
|-
 
|-
  
−
| 2013.10.02 Wed || Krantsevich, Artem || Green || topic || Kim, Pan-Jun. ''et al.'' Centralized modularity of N-linked glycosylation pathways in mammalian cells. ''PLoS ONE''. '''2009 Oct'''. ''4(10)''. e7317.
+
| 2014.10.01 Wed || Santos, Ruda || Green || topic || Fujimoto, Y. K. ''et al''. Computational models explain the oligosaccharide specificity of cyanovirin-N. ''Protein Science''. '''2008 July'''. ''17''. 2008-2014
 
|-
 
|-
  
−
| 2013.10.09 Wed || Amgalan, Anar || Dill || topic || Pang, Tin Yau. and Maslov, Sergei. Universal distribution of component frequencies in biological and technological systems. ''P.N.A.S.'' '''2013 Feb'''. ''110(52)''. 21054-21058.
+
| 2014.10.08 Wed || Cortes, Michael || Rizzo || topic || Jiang, M. ''et al''. A combined experimental and computational study of Vam3, a derivative of resveratrol, and syk interaction. ''Int. J. Mol. Sci''. '''2014 September'''. ''15''. 17188-17203
 
|-
 
|-
  
−
| 2013.10.16 Wed || Shan, Jiahui (Emma) || -- || topic || Alexandrov, LB. ''et al.'' Signatures of mutational processes in human cancer. ''Nature''. '''2013 Aug'''. ''500''. 415-421.
+
| 2014.10.15 Wed || Belfon, Kellon || Simmerling || topic || Nguyen, H. ''et al''. Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent. ''JACS''. '''2014 September'''. ''136''. 13959-13962
 
|-
 
|-
  
−
| 2013.10.23 Wed || Zou, Junjie || -- || topic || Lill, MA. Efficient incorporation of protein flexibility and dynamics into molecular docking simulations. ''Biochemistry''. '''2011 Jun'''. ''50''. 6157-6169.
+
| 2014.10.22 Wed || Hassan, Mosserval || Seeliger || topic || Rezai, T. ''et al''. Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: successful in silico prediction of the relative permeabilities of cyclic peptides. ''JACS''. '''2006 May'''. ''128''. 14073-14080
 
|-
 
|-
  
−
| 2013.10.30 Wed || Li, Fangfei || -- || topic || Forli, S. and Olson, AJ. A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking. ''J Med Chem''. '''2012'''. ''55''. 623-638.
+
| 2014.10.29 Wed || Lee, Stella || Levy || topic || Tarassov, K. ''et al''. An in vivo map of the yeast protein interactome. ''Science''. '''2008 June'''. ''320''. 1465-1470
 
|-
 
|-
  
−
| 2013.11.06 Wed || Yu, Bihua || -- || topic || Green, DF. A statistical framework for hierarchical methods in molecular simulation and design. ''J Chem Theory Comput''. '''2010 Apr'''. ''6''. 1682-1697.
+
| 2014.11.05 Wed || Tian, Chuan || Dill || topic || Dominguez, C. ''et al''. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. ''JACS''. '''2013 May'''. ''125''. 1731-1737
 
|-
 
|-
  
−
| 2013.11.13 Wed || Kennedy, Chelsea || -- || -- || ROTATION/RESEARCH PRESENTATIONS
+
| 2014.11.12 Wed || Elkin, Rena || MacCarthy || topic || Payne, J. L. and Wagner, A. The robustness and evolvability of transcription factor binding sites. ''Science''. '''2014 February'''. ''343''. 875-877
 
|-
 
|-
  
−
| 2013.11.20 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS
+
| 2014.11.19 Wed || Sam-Ang, Panu || Balazsi || topic || Nevozhay. D. ''et al''. Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. ''PNAS''. '''2009 March'''. ''106(13)''. 5123-5128
 
|-
 
|-
  
−
| 2013.11.27 Wed || - || -- || -- || THANKSGIVING BREAK
+
| 2014.11.26 Wed || - || -- || -- || THANKSGIVING BREAK
−
|-
 
−
 
 
−
| 2013.12.04 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 
 
|-
 
|-
 
|- style="background:lightgreen"
 
|- style="background:lightgreen"
−
| '''2014 Spring'''
+
| '''2015 Spring'''
 
| '''Participant'''  
 
| '''Participant'''  
 
| '''Rotations or Research Group'''
 
| '''Rotations or Research Group'''
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SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH'''
 
SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH'''
 
|-
 
|-
−
| 2014.01.29 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||
+
| 2015.01.28 Wed || -- || SNOW DAY || SNOW DAY || SNOW DAY
 +
|-
 +
| 2015.02.04 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||
  
 
Discussion of Overall Course Requirements which include:  
 
Discussion of Overall Course Requirements which include:  
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|-
 
|-
  
−
| 2014.02.05 Wed || - || -- || -- || SNOW STORM, CLASS CANCELLED
+
| 2015.02.11 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||
−
|-
 
−
 
 
−
| 2014.02.12 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||
 
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p42411560 Peter Williams Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p42411560 Peter Williams Lecture]
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|-
 
|-
  
−
| 2014.02.19 Wed || Class discussion  || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||
+
| 2015.02.18 Wed || Class discussion  || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p30629381 Michael Hadjiargyrou Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p30629381 Michael Hadjiargyrou Lecture]
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|-
 
|-
  
−
| 2014.02.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring ||  
+
| 2015.02.25 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring ||  
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p20134531 Clinton Rubin Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p20134531 Clinton Rubin Lecture]
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|-
 
|-
  
−
| 2014.03.05 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||
+
| 2015.03.04 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p32819600 Peter Gergen Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p32819600 Peter Gergen Lecture]
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|-
 
|-
  
−
| 2014.03.12 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||
+
| 2015.03.11 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p41971516 Richard Clark Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p41971516 Richard Clark Lecture]
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|-
 
|-
  
−
| 2014.03.19 Wed || -- || -- || -- || SPRING BREAK
+
 
 +
| 2015.03.18 Wed || -- || -- || -- || SPRING BREAK
 
|-
 
|-
−
 
+
| 2015.03.25 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||
−
| 2014.03.26 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||
 
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p68134598 Stefan Judex Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p68134598 Stefan Judex Lecture]
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*How many years past a publication, if asked, should a researcher be able provide "raw data"?   
 
*How many years past a publication, if asked, should a researcher be able provide "raw data"?   
 
|-
 
|-
−
 
+
| 2015.04.01 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||
−
| 2014.04.02 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||
 
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p99353453 Howard Schneider Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p99353453 Howard Schneider Lecture]
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|-
 
|-
  
−
| 2014.04.09 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||
+
| 2015.04.08 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p10813599 Judy Matuk Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p10813599 Judy Matuk Lecture]
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|-
 
|-
  
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| 2014.04.16 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||
+
| 2015.04.15 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||
 
Stony Brook Lecture
 
Stony Brook Lecture
 
*[https://meeting.sinc.stonybrook.edu/p69209438 Tom Zimmerman Lecture]
 
*[https://meeting.sinc.stonybrook.edu/p69209438 Tom Zimmerman Lecture]
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*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?
 
*From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?
 
|-
 
|-
−
 
+
| 2015.04.22 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS
−
 
 
−
| 2014.04.23 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 
 
|-
 
|-
−
 
+
| 2015.04.29 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS
−
| 2014.04.30 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 
 
|-
 
|-
−
 
+
| 2015.05.06 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS
−
| 2014.05.07 Wed || Last name, First name || -- || -- || ROTATION/RESEARCH PRESENTATIONS
 
 
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Latest revision as of 07:36, 25 March 2015

Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage


Instructor Dr. Robert C. Rizzo [631-632-9340, rizzorc@gmail.com]
Course No. AMS-532
Location/Time Physics P124 Wed 12:00PM - 12:53PM
Office Hours Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics


Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring)

2014 Fall Participant Rotations or Research Group Topic References

REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT

2014.08.27 Wed Last name, First name -- Topic Organizational Meeting
2014.09.03 Wed Kennedy, Chelsea Green topic Alberts, B. et al. Rescuing US biomedical research from its systemic flaws. PNAS. 2014 March. 111(16). 5773-5777.
2014.09.10 Wed Zou, Junjie Raleigh topic Xiao, S. et al. Rational modification of protein stability by targeting surface sites leads to complicated results. PNAS. 2013 July. 110(28). 11337-11342
2014.09.17 Wed - -- -- AMS party
2014.09.24 Wed Yu, Bihau Vageli topic Munson, P. J. and Singh, P. K. Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment. Protein Science. 1997 March. 6. 1467-1481
2014.10.01 Wed Santos, Ruda Green topic Fujimoto, Y. K. et al. Computational models explain the oligosaccharide specificity of cyanovirin-N. Protein Science. 2008 July. 17. 2008-2014
2014.10.08 Wed Cortes, Michael Rizzo topic Jiang, M. et al. A combined experimental and computational study of Vam3, a derivative of resveratrol, and syk interaction. Int. J. Mol. Sci. 2014 September. 15. 17188-17203
2014.10.15 Wed Belfon, Kellon Simmerling topic Nguyen, H. et al. Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent. JACS. 2014 September. 136. 13959-13962
2014.10.22 Wed Hassan, Mosserval Seeliger topic Rezai, T. et al. Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: successful in silico prediction of the relative permeabilities of cyclic peptides. JACS. 2006 May. 128. 14073-14080
2014.10.29 Wed Lee, Stella Levy topic Tarassov, K. et al. An in vivo map of the yeast protein interactome. Science. 2008 June. 320. 1465-1470
2014.11.05 Wed Tian, Chuan Dill topic Dominguez, C. et al. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. JACS. 2013 May. 125. 1731-1737
2014.11.12 Wed Elkin, Rena MacCarthy topic Payne, J. L. and Wagner, A. The robustness and evolvability of transcription factor binding sites. Science. 2014 February. 343. 875-877
2014.11.19 Wed Sam-Ang, Panu Balazsi topic Nevozhay. D. et al. Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. PNAS. 2009 March. 106(13). 5123-5128
2014.11.26 Wed - -- -- THANKSGIVING BREAK
2015 Spring Participant Rotations or Research Group Topic References

SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH

2015.01.28 Wed -- SNOW DAY SNOW DAY SNOW DAY
2015.02.04 Wed Class discussion Responsible Conduct of Research (RCR) (1) Course Overview: Fulfilling Responsible Conduct in Research Training

Discussion of Overall Course Requirements which include:

  • View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) 2010.06.08_hadjiargyrou.pdf
  • Complete a relevant RCR module, and achieve a 80% or higher quiz grade, within the web-based Collaborative Institutional Training Initiative located at http://www.citiprogram.org
  • Following the schedule below and prior to coming to each class: (i) view the appropriate online lecture, (ii) read additional accompanying materials, and (iii) come prepared for the days discussion topics
2015.02.11 Wed Class discussion Responsible Conduct of Research (RCR) (2) Integrity in Scholarship (Introduction to Ethics and Science)

Stony Brook Lecture


Readings (Nature articles)


Discussion

  • Why is the class important?
  • How should we behave as scientists?
  • How is science a social enterprise?
2015.02.18 Wed Class discussion Responsible Conduct of Research (RCR) (3) Scientific Misconduct

Stony Brook Lecture


Reading


Discussion

  • From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?
  • From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?
  • How can the pressure to publish influence the conduct of research?
2015.02.25 Wed Class discussion Responsible Conduct of Research (RCR) (4) Mentoring

Stony Brook Lecture


Readings


Discussion

  • What qualities do you want in a mentor?
  • What are the challenges associated with being a mentor?
  • What does Professor Rubin mean when he says it is very important not to burn bridges?
2015.03.04 Wed Class discussion Responsible Conduct of Research (RCR) (5) Ownership and Authorship

Stony Brook Lecture


Readings


Discussion (also from the above Columbia course)

  • Is it ever appropriate for authorship to change during a project or potential paper?
  • Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?
  • Did Ms. Jacobs handle the proposed changes to authorship appropriately?
2015.03.11 Wed Class discussion Responsible Conduct of Research (RCR) (6) Plagiarism

Stony Brook Lecture


Readings


Discussion

  • Is plagiarism really that bad?
  • If you copy a paragraph from another sources and modify it by say 10% is that enough to not be plagiarism ? What about 20%, or 30%, or 51% ? At what percentage is it no longer plagiarism? How many words do you need to change?
2015.03.18 Wed -- -- -- SPRING BREAK
2015.03.25 Wed Class discussion Responsible Conduct of Research (RCR) (7) Data Management

Stony Brook Lecture


Readings


Discussion

  • From Case Study 1: Why shouldn't Renee be able to use the samples since she is not studying any disease associated with the samples?
  • From Case Study 2: Under what condition is copying allowed?
  • Discuss ways to keep good records so that future researchers will be able to (A) reproduce your work and (B) re-analyze your results. Include in your discussion how you you will be able to share "raw" results.
  • How many years past a publication, if asked, should a researcher be able provide "raw data"?
2015.04.01 Wed Class discussion Responsible Conduct of Research (RCR) (8) Journalism and Science

Stony Brook Lecture


Readings (3 Case Studies)


Discussion

  • From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why?
  • From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?
  • From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly hospital which might violate patients privacy?
2015.04.08 Wed Class discussion Responsible Conduct of Research (RCR) (9) Responsible Conduct of Research Involving Human Subjects

Stony Brook Lecture


Readings: (Background Information, Case Studies, Helsinki Manuscript)

Discussion

  • From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?
  • From Human Subjects handout, Case Study 2: Was this an ethical trial? If so, why? If not, why not? Why does the Helsinki Declaration limit the use of Placebo's?
  • From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?
2015.04.15 Wed Class discussion Responsible Conduct of Research (RCR) (10) Responsible Conduct of Research Involving Laboratory Animals

Stony Brook Lecture


Readings (Case Studies)


Discussion

  • From Case Study 1: What are some of the troublesome issues associated with this set of experiments?
  • From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?
  • From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?
  • From Case Study 1: If Edith were to respond that the study could not be carried out in chimpanzees, how might it be designed instead for human subjects?
2015.04.22 Wed Last name, First name -- -- ROTATION/RESEARCH PRESENTATIONS
2015.04.29 Wed Last name, First name -- -- ROTATION/RESEARCH PRESENTATIONS
2015.05.06 Wed Last name, First name -- -- ROTATION/RESEARCH PRESENTATIONS
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