2013-2014 AMS-532 Fall-Spring

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)

2013 Fall	Participant	Rotations or Research Group	Topic	References REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT
2013.08.28 Wed	Last name, First name	--	Topic	paper
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.
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.
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.
2013.09.25 Wed	Last name, First name	--	topic	paper
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.
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.
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.
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.
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.
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.
2013.11.13 Wed	Kennedy, Chelsea	--	--	ROTATION/RESEARCH PRESENTATIONS
2013.11.20 Wed	Last name, First name	--	--	ROTATION/RESEARCH PRESENTATIONS
2013.11.27 Wed	-	--	--	THANKSGIVING BREAK
2013.12.04 Wed	Last name, First name	--	--	ROTATION/RESEARCH PRESENTATIONS
2014 Spring	Participant	Rotations or Research Group	Topic	References SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH
2014.01.29 Wed	Class discussion	Responsible Conduct of Research (RCR)	(1) Course Overview: Discussion of work to be done outside of class to fulfill RCR training	Overall Course Requirements View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou 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
2014.02.05 Wed	Class discussion	Responsible Conduct of Research (RCR)	(2) Integrity in Scholarship (Introduction to Ethics and Science)	Stony Brook Lecture Peter Williams Lecture Readings (Nature articles) Article 1 Article 2 Article 3 Discussion Why is the class important? How should we behave as scientists? How is science a social enterprise?
2014.02.12 Wed	Class discussion	Responsible Conduct of Research (RCR)	(3) Scientific Misconduct	Stony Brook Lecture Michael Hadjiargyrou Lecture Reading Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct 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?
2014.02.19 Wed	Class discussion	Responsible Conduct of Research (RCR)	(4) Mentoring	Stony Brook Lecture Clinton Rubin Lecture Readings Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring 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?
2014.02.26 Wed	Class discussion	Responsible Conduct of Research (RCR)	(5) Ownership and Authorship	Stony Brook Lecture Peter Gergen Lecture Readings Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review 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?
2014.03.05 Wed	Class discussion	Responsible Conduct of Research (RCR)	(6) Plagiarism	Stony Brook Lecture Richard Clark Lecture Readings Stony Brook's Policy on Academic Dishonesty 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?
2014.03.12 Wed	Class discussion	Responsible Conduct of Research (RCR)	(7) Data Management	Stony Brook Lecture Stefan Judex Lecture Readings Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management 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.
2014.03.19 Wed	--	--	--	SPRING BREAK
2014.03.26 Wed	Class discussion	Responsible Conduct of Research (RCR)	(8) Journalism and Science	Stony Brook Lecture Howard Schneider Lecture Readings (3 Case Studies) Scientist and Reporters handout 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?
2014.04.02 Wed	Class discussion	Responsible Conduct of Research (RCR)	(9) Responsible Conduct of Research Involving Human Subjects	Stony Brook Lecture Judy Matuk Lecture Readings: (Background Information, Case Studies, Helsinki manuscript) Human Subjects handout Helsinki manuscript Discussion From Human Subjects handout, Background History: Why does the Helsinki Declaration limit the use of Placebo's? From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not? From Helsinki manuscript: Do you agree with the authors that placebo-controlled trails are in many cases necessary ? Why ?
2014.04.09 Wed	Class discussion	Responsible Conduct of Research (RCR)	(10) Responsible Conduct of Research Involving Laboratory Animals	Stony Brook Lecture Tom Zimmerman Lecture Readings (Case Studies) Animal Subjects handout 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?
2014.04.16 Wed	Last name, First name	--	--	ROTATION/RESEARCH PRESENTATIONS
2014.04.23 Wed	Last name, First name	--	--	ROTATION/RESEARCH PRESENTATIONS
2014.04.30 Wed	Last name, First name	--	--	ROTATION/RESEARCH PRESENTATIONS
2014.05.07 Wed	Last name, First name	--	--	ROTATION/RESEARCH PRESENTATIONS