Difference between revisions of "2019-2020 AMS-532 Fall-Spring"

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(Created page with "=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> === <br> {| align="center" border="2" cellpadding="8" cellspacing="0" style="back...")
 
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| 2018.08.29 Wed || Rizzo, Robert || -- || -- || Organizational Meeting
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| 2018.08.28 Wed || Rizzo, Robert || -- || -- || Organizational Meeting
 
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| 201809.05 Wed || Mudiyansel, Lakshan || -- || -- || Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. ''J Phys Chem B'' '''2018''', ''122'', 5657-5665.
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| 201809.04 Wed || Ashizawa, Ryota || -- || -- || Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. ''J Phys Chem B'' '''2018''', ''122'', 5657-5665.
 
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| 2018.09.12 Wed || -- || -- || -- || AMS Grad Student BBQ
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| 201809.11 Wed || Crosser, Jacob || -- || -- || Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. ''J Phys Chem B'' '''2018''', ''122'', 5657-5665.
 
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| 2018.09.19 Wed || Talis, Emma || -- || -- || Rietkerk et al; Regular pattern formation in real ecosystems. ''Trends in Ecology & Evolution'' '''2008''', ''23'', 169-175.
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| 2018.09.18 Wed || Kotelnikov, Sergei || -- || -- || Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. ''J Phys Chem B'' '''2018''', ''122'', 5657-5665.
 
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| 2018.09.26 Wed || Singh, Niven || -- || -- || Jiang et al; Cholinergic Signaling Controls Conditioned Fear Behaviors and Enhances Plasticity of Cortical-Amygdala Circuits. ''Neuron'' '''2016''', ''90'', 1057-1070.
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| 2018.09.25 Wed || Arachchi, Kalani || -- || -- || Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. ''J Phys Chem B'' '''2018''', ''122'', 5657-5665.
 
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| 2018.10.03 Wed || Liang, Tong || -- || -- || Schneidman et al; Weak pairwise correlations imply strongly correlated network states in a neural population. ''Nature'' '''2016''', ''440'', 1007-1012.
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| 2018.10.02 Wed || Samoilova, Khristina || -- || -- || Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. ''J Phys Chem B'' '''2018''', ''122'', 5657-5665.
 
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| 2018.10.10 Wed || Kotelnikov, Sergei || -- || -- || Cai et al; A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation. ''J Comput Phys'' '''2008''', ''227'', 10162-10177.
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| 2018.10.09 Wed || Stepanenko, Darya || -- || -- || Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. ''J Phys Chem B'' '''2018''', ''122'', 5657-5665.
 
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| 2018.10.17 Wed || Bickel, John || -- || -- || Miller et al; Molecular dynamics study of the opening mechanism for DNA polymerase I. ''PLOS Comp Bio'' '''2014''', ''10'', e1003961.
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| 2018.10.16 Wed || Earlie, Ethan || -- || -- || Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. ''J Phys Chem B'' '''2018''', ''122'', 5657-5665.
 
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| 2018.10.24 Wed || Crosser, Jacob || -- || -- || Boerlin et al; Predicting Coding of Dynamic Variables in Balanced Spiking Networks. ''PLOS Comp Bio'' '''2013''', ''9'', e1003258.
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| 2018.10.23 Wed || Lin, Lu || -- || -- || Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. ''J Phys Chem B'' '''2018''', ''122'', 5657-5665.
 
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| 2018.10.31 Wed || Ashizawa, Ryota || -- || -- || Decherchi et al; The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning. ''Nature communications'' '''2015''', ''6'', 1-10.
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| 2018.10.30 Wed || Arachchi, Kalani || -- || -- || Lab Rotation Presentations
 
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| 2018.11.07 Wed || Wang, Yuzhang || -- || -- || Miao et al; Improved Reweighing of Accelerated Molecular Dynamics Simulations for Free Energy Calculations. ''JCTC'' '''2014''', ''10'', 2677-2689.
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| 2018.11.06 Wed || Samoilova, Khristina || -- || -- || Lab Rotation Presentations
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| 2018.11.14 Wed || Bickel, John & Crosser, Jacob || -- || -- || Lab Rotation Presentations
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| 2018.11.13 Wed || Last, First || -- || -- || Lab Rotation Presentations
 
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| 2018.11.21 Wed || -- || -- || -- || THANKSGIVING BREAK
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| 2018.11.20 Wed || Last, First || -- || -- || Lab Rotation Presentations
 
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| 2018.11.28 Wed || Ashizawa, Ryota & Wang, Yuzhang || -- || -- || Lab Rotation Presentations
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| 2018.11.27 Wed || -- || -- || -- || THANKSGIVING BREAK
 
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| 2018.12.05 Wed || -- || -- || -- || AMS Holiday Party
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| 2018.12.04 Wed || Stepanenko, Darya || -- || -- || Lab Rotation Presentations
 
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Revision as of 12:54, 26 August 2019

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 P122 WESTCAMPUS, 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)

2018 Fall Participant Rotations or Research Group Topic References

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

2018.08.28 Wed Rizzo, Robert -- -- Organizational Meeting
201809.04 Wed Ashizawa, Ryota -- -- Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. J Phys Chem B 2018, 122, 5657-5665.
201809.11 Wed Crosser, Jacob -- -- Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. J Phys Chem B 2018, 122, 5657-5665.
2018.09.18 Wed Kotelnikov, Sergei -- -- Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. J Phys Chem B 2018, 122, 5657-5665.
2018.09.25 Wed Arachchi, Kalani -- -- Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. J Phys Chem B 2018, 122, 5657-5665.
2018.10.02 Wed Samoilova, Khristina -- -- Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. J Phys Chem B 2018, 122, 5657-5665.
2018.10.09 Wed Stepanenko, Darya -- -- Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. J Phys Chem B 2018, 122, 5657-5665.
2018.10.16 Wed Earlie, Ethan -- -- Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. J Phys Chem B 2018, 122, 5657-5665.
2018.10.23 Wed Lin, Lu -- -- Tofoleanu et al; Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. J Phys Chem B 2018, 122, 5657-5665.
2018.10.30 Wed Arachchi, Kalani -- -- Lab Rotation Presentations
2018.11.06 Wed Samoilova, Khristina -- -- Lab Rotation Presentations
2018.11.13 Wed Last, First -- -- Lab Rotation Presentations
2018.11.20 Wed Last, First -- -- Lab Rotation Presentations
2018.11.27 Wed -- -- -- THANKSGIVING BREAK
2018.12.04 Wed Stepanenko, Darya -- -- Lab Rotation Presentations
2019 Spring Participant Rotations or Research Group Topic References

SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH

2019.01.30 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
2019.02.06 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?
2019.02.13 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?
  • Why do people commit scientific misconduct?
  • What are some consequences of committing scientific misconduct?
  • Who are some of your mentors?
2019.02.20 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?
  • What were the problems Susan encountered with Dr. Michaels and what are some steps she could have taken to mitigate the issues?
2019.02.27 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?
  • How should authorship roles be defined?
  • What are some abuses of authorship?
  • 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?
  • Why are acknowledgments so important?
2019.03.06 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?
2019.03.13 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"?
2019.03.20 Wed -- -- -- SPRING BREAK
2019.03.27 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 run hospital which might violate patients privacy?
2019.04.03 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 ?
2019.04.10 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?
  • What are some advantages of using Animals in experiments?
  • Discuss the three R's?
  • Is our class for or against Animal testing?
2019.04.17 Wed -- -- -- ROTATION/RESEARCH PRESENTATIONS
2019.04.24 Wed -- -- -- ROTATION/RESEARCH PRESENTATIONS
2019.05.01 Wed -- -- -- ROTATION/RESEARCH PRESENTATIONS
2019.05.08 Wed -- -- -- ROTATION/RESEARCH PRESENTATIONS
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