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| − | | '''2018 Fall | + | | '''2019 Fall |
| | | '''Participant''' | | | '''Participant''' |
| | | '''Rotations or Research Group''' | | | '''Rotations or Research Group''' |
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| − | | 2018.08.28 Wed || Rizzo, Robert || -- || -- || Organizational Meeting | + | | 2019.08.28 Wed || Rizzo, Robert || -- || -- || Organizational Meeting |
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| − | | 201809.04 Wed || Ashizawa, Ryota || -- || -- || Guney et al; Network-based in silico drug efficacy screening. ''Nature Comm'' '''2016''', ''7'', 10331. | + | | 2019.09.04 Wed || Ashizawa, Ryota || -- || -- || Guney et al; Network-based in silico drug efficacy screening. ''Nature Comm'' '''2016''', ''7'', 10331. |
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| − | | 201809.11 Wed || Crosser, Jacob || -- || -- || Brunel et al; Effects of Neuromodulation in a Cortical Network Model of Object Working memory Dominated by Recurrent Inhibition. ''J Comput Neuro'' '''2001''', ''11'', 63-85. | + | | 2019.09.11 Wed || Crosser, Jacob || -- || -- || Brunel et al; Effects of Neuromodulation in a Cortical Network Model of Object Working memory Dominated by Recurrent Inhibition. ''J Comput Neuro'' '''2001''', ''11'', 63-85. |
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| − | | 2018.09.18 Wed || Kotelnikov, Sergei || -- || -- || Ekeberg; Improved contact predictions in proteins: Using pseudolikelihoods to infer Potts models. ''Phys Rev E'' '''2013''', ''87'', 012707. | + | | 2019.09.18 Wed || Kotelnikov, Sergei || -- || -- || Ekeberg; Improved contact predictions in proteins: Using pseudolikelihoods to infer Potts models. ''Phys Rev E'' '''2013''', ''87'', 012707. |
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| − | | 2018.09.25 Wed || Stepanenko, Darya || -- || -- || Peterson et al; Simulated Evolution of Protein-Protein Interaction Networks wtih Realistic Topology. ''PLOS ONE'' '''2012''', ''7'', e39052. | + | | 2019.09.25 Wed || Stepanenko, Darya || -- || -- || Peterson et al; Simulated Evolution of Protein-Protein Interaction Networks wtih Realistic Topology. ''PLOS ONE'' '''2012''', ''7'', e39052. |
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| − | | 2018.10.02 Wed || Samoilova, Khristina || -- || -- || Butler et al; Evolutionary constraints on visual cortex architecture from the dynamics of hallucinations. ''PNAS'' '''2012''', ''109'' 606-609. | + | | 2019.10.02 Wed || Samoilova, Khristina || -- || -- || Butler et al; Evolutionary constraints on visual cortex architecture from the dynamics of hallucinations. ''PNAS'' '''2012''', ''109'' 606-609. |
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| − | | 2018.10.09 Wed || Arachchi, Kalani || -- || -- || Kong et al; Molecular determinants for ligand binding at Nav1.4 and Nav1.7 channels: Experimental affinity results analyzed by molecular modeling. ''Computational Biology and Chemistry'' '''2019''', ''83'', 107132. | + | | 2019.10.09 Wed || Arachchi, Kalani || -- || -- || Kong et al; Molecular determinants for ligand binding at Nav1.4 and Nav1.7 channels: Experimental affinity results analyzed by molecular modeling. ''Computational Biology and Chemistry'' '''2019''', ''83'', 107132. |
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| − | | 2018.10.16 Wed || Earlie, Ethan || -- || -- || Nimwegen et al; Neutral evolution of mutational robustness. ''PNAS'' '''1999''', ''96'', 9716-9720. | + | | 2019.10.16 Wed || Earlie, Ethan || -- || -- || Nimwegen et al; Neutral evolution of mutational robustness. ''PNAS'' '''1999''', ''96'', 9716-9720. |
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| − | | 2018.10.23 Wed || Ashizawa, Ryota || -- || -- || Research Presentation | + | | 2019.10.23 Wed || Ashizawa, Ryota || -- || -- || Research Presentation |
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| − | | 2018.10.30 Wed || Crosser, Jacob || -- || -- || Rotation Presentation | + | | 2019.10.30 Wed || Crosser, Jacob || -- || -- || Rotation Presentation |
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| − | | 2018.11.06 Wed || Kotelnikov, Sergei || -- || -- || Rotation Presentation | + | | 2019.11.06 Wed || Kotelnikov, Sergei || -- || -- || Rotation Presentation |
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| − | | 2018.11.13 Wed || Stepanenko, Darya and Samoilova, Khristina|| -- || -- || Lab Rotation Presentations | + | | 2019.11.13 Wed || Stepanenko, Darya and Samoilova, Khristina|| -- || -- || Lab Rotation Presentations |
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| − | | 2018.11.20 Wed || Arachchi, Kalani and Earlie, Ethan || -- || -- || Lab Rotation Presentations | + | | 2019.11.20 Wed || Arachchi, Kalani and Earlie, Ethan || -- || -- || Lab Rotation Presentations |
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| − | | 2018.11.27 Wed || -- || -- || -- || THANKSGIVING BREAK | + | | 2019.11.27 Wed || -- || -- || -- || THANKSGIVING BREAK |
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| − | | 2018.12.04 Wed || Last, First || -- || -- || Lab Rotation Presentations
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| | |- style="background:lightgreen" | | |- style="background:lightgreen" |
| − | | '''2019 Spring''' | + | | '''2020 Spring''' |
| | | '''Participant''' | | | '''Participant''' |
| | | '''Rotations or Research Group''' | | | '''Rotations or Research Group''' |
| | | '''Topic''' | | | '''Topic''' |
| − | | '''References | + | | '''This semester (Spring 2020) students will take RCR training under AMS-500 and follow that schedule:''' |
| − | SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH'''
| + | https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500 |
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| − | | 2019.01.30 Wed || Class discussion || Responsible Conduct of Research (RCR) || (1) Course Overview: Fulfilling Responsible Conduct in Research Training ||
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| − | Discussion of Overall Course Requirements which include:
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| − | *View the Responsible Conduct of Research and Scholarship Presentation given to department chairs by professor Michael Hadjiargyrou (to be done as a group today) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2012-2011_AMS532_Fall_and_Spring/2010.06.08_hadjiargyrou.pdf 2010.06.08_hadjiargyrou.pdf]
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| − | *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
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| − | *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
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| − | | 2019.02.06 Wed || Class discussion|| Responsible Conduct of Research (RCR) || (2) Integrity in Scholarship (Introduction to Ethics and Science) ||
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| − | Stony Brook Lecture
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| − | *[https://www.youtube.com/watch?time_continue=1&v=av3P2n8t2qc&feature=emb_logo Peter Williams Lecture]
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| − | Readings (Nature articles)
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| − | *[http://www.nature.com/nature/journal/v445/n7125/pdf/445240a.pdf Article 1]
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| − | *[http://www.nature.com/nature/journal/v445/n7125/pdf/445242a.pdf Article 2]
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| − | *[http://www.nature.com/nature/journal/v445/n7125/pdf/445244a.pdf Article 3]
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| − | Discussion
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| − | *Why is the class important?
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| − | *How should we behave as scientists?
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| − | *How is science a social enterprise?
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| − | | 2019.02.13 Wed || Class discussion || Responsible Conduct of Research (RCR) || (3) Scientific Misconduct ||
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| − | Stony Brook Lecture
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| − | *[https://www.youtube.com/watch?v=RayszjsMDH8&feature=emb_logo Michael Hadjiargyrou Lecture]
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| − | Reading
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| − | *[http://ccnmtl.columbia.edu/projects/rcr/rcr_misconduct/case/index.html#1 Introduction and Case Study 1 Sections from Columbia University online RCR Website: Research Misconduct]
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| − | Discussion
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| − | *From Case Study 1: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?
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| − | *From Case Study 1: It seems clear that there is a problem with Samantha's data. What should Julio do now?
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| − | *Why do people commit scientific misconduct?
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| − | *What are some consequences of committing scientific misconduct?
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| − | *Who are some of your mentors?
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| − | | 2019.02.20 Wed || Class discussion || Responsible Conduct of Research (RCR) || (4) Mentoring ||
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| − | Stony Brook Lecture
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| − | *[https://www.youtube.com/watch?v=ko-PWjRyLEU&feature=emb_logo Clinton Rubin Lecture]
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| − | Readings
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| − | *[http://ccnmtl.columbia.edu/projects/rcr/rcr_mentoring Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Mentoring]
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| − | Discussion
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| − | *What qualities do you want in a mentor?
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| − | *What are the challenges associated with being a mentor?
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| − | *What does Professor Rubin mean when he says it is very important not to burn bridges?
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| − | *What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?
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| − | | 2019.02.27 Wed || Class discussion || Responsible Conduct of Research (RCR) || (5) Ownership and Authorship ||
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| − | Stony Brook Lecture
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| − | *[https://www.youtube.com/watch?v=7TPqqGWKjsg&feature=emb_logo Peter Gergen Lecture]
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| − | Readings
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| − | *[http://ccnmtl.columbia.edu/projects/rcr/rcr_authorship Read Introduction and Case Study 1 Sections from Columbia University online RCR Website: Responsible Authorship and Peer Review]
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| − | Discussion (also from the above Columbia course)
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| − | *Is it ever appropriate for authorship to change during a project or potential paper?
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| − | *How should authorship roles be defined?
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| − | *What are some abuses of authorship?
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| − | *Describe methods/techniques you can use to be sure you are properly citing the work of others in the context of writing a paper?
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| − | *Did Ms. Jacobs handle the proposed changes to authorship appropriately?
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| − | *Why are acknowledgments so important?
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| − | | 2019.03.06 Wed || Class discussion || Responsible Conduct of Research (RCR) || (6) Plagiarism ||
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| − | Stony Brook Lecture
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| − | *[https://www.youtube.com/watch?v=wrokaKkeCw4&feature=emb_logo Richard Clark Lecture]
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| − | Readings
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| − | *[http://www.stonybrook.edu/uaa/academicjudiciary/policies.shtml Stony Brook's Policy on Academic Dishonesty]
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| − | Discussion
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| − | *Is plagiarism really that bad?
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| − | *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?
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| − | | 2019.03.13 Wed || Class discussion || Responsible Conduct of Research (RCR) || (7) Data Management ||
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| − | Stony Brook Lecture
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| − | *[https://www.youtube.com/watch?v=sIUkSVJEMus&feature=emb_logo Stefan Judex Lecture]
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| − | Readings
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| − | *[http://ccnmtl.columbia.edu/projects/rcr/rcr_data Read Introduction and Case Study 1 and 2 Sections from Columbia University online RCR Website: Data Acquisition and Management]
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| − | Discussion
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| − | *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?
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| − | *From Case Study 2: Under what condition is copying allowed?
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| − | *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.
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| − | *How many years past a publication, if asked, should a researcher be able provide "raw data"?
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| − | | 2019.03.20 Wed || -- || -- || -- || SPRING BREAK
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| − | | 2019.03.27 Wed || Class discussion || Responsible Conduct of Research (RCR) || (8) Journalism and Science ||
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| − | Stony Brook Lecture
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| − | *[https://www.youtube.com/watch?v=q5j_vqa-OI8&feature=emb_logo Howard Schneider Lecture]
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| − | Readings (3 Case Studies)
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| − | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/scientists_and_reporters.pdf Scientist and Reporters handout]
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| − | Discussion
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| − | *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?
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| − | *From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why?
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| − | *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 run hospital which might violate patients privacy?
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| − | | 2019.04.03 Wed || Class discussion || Responsible Conduct of Research (RCR) || (9) Responsible Conduct of Research Involving Human Subjects ||
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| − | Stony Brook Lecture
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| − | *[https://meeting.sinc.stonybrook.edu/p10813599 Judy Matuk Lecture]
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| − | Readings: (Background Information, Case Studies, Helsinki Manuscript)
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| − | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Human_subjects.pdf Human Subjects handout]
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| − | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/helsinki.pdf Helsinki manuscript]
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| − | Discussion
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| − | *From Human Subjects handout, Case Study 1: Was this an ethical trial? If so, why? If not, why not?
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| − | *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?
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| − | *From Helsinki Manuscript: Do you agree with the authors that placebo-controlled trial are in many cases necessary ? Why ?
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| − | | 2019.04.10 Wed || Class discussion || Responsible Conduct of Research (RCR) || (10) Responsible Conduct of Research Involving Laboratory Animals ||
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| − | Stony Brook Lecture
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| − | *[https://meeting.sinc.stonybrook.edu/p69209438 Tom Zimmerman Lecture]
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| − |
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| − |
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| − | Readings (Case Studies)
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| − | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/2014-2013_AMS531_AMS532_Fall_and_Spring/Animal_subjects.pdf Animal Subjects handout]
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| − | Discussion
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| − | *From Case Study 1: What are some of the troublesome issues associated with this set of experiments?
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| − | *From Case Study 1: Does giving an animal a fatal infection constitute cruelty, especially considering the characteristics of HIV infection in humans?
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| − | *From Case Study 1: Is it ethically appropriate to transmit intentionally a human virus in a setting that is not fully controlled?
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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?
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| − | *What are some advantages of using Animals in experiments?
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| − | *Discuss the three R's?
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| − | *Is our class for or against Animal testing?
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| − | | 2019.04.17 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
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| − | | 2019.04.24 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
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| − | | 2019.05.01 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
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| − | | 2019.05.08 Wed || -- || -- || -- || ROTATION/RESEARCH PRESENTATIONS
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| | |} | | |} |
