Bioengineering/Physiology 6000: System Physiology I: Cardiovascular, Respiratory, and Renal Systems Spring of 2014 Edition Note: this class makes heavy use of Canvas for submission of all assignments.

Spring 2014 Deadlines and Dates

• Monday, January 6: first day of class
• Friday, January 10 and Monday, January 13: first lab days
• Monday, January 20: Martin Luther King Holiday
• Friday, January 24 5:00 PM: Lab report #1 (dissection) due
• Friday, February 7: Resubmission of Lab report #1 due (on Canvas)
• Friday, February 15: Homework #1 (Membrane Simulation) due (5:00 pm on Canvas)
• Monday, February 17: Presidents' Day Holiday
• Friday, Feb 21: Lab report #2 (frog lab) due (on Canvas)
• Friday, March 7: Lab report #3 (ECG lab) due
• Monday, March 17: Midterm #1 (in class)
• Monday, March 24: Lab report #4 (Simulation) due
• Monday, March 31: Optional resubmission of Lab report #2
• Wednesday, April 2: Lab #5 protocol #5 (BP and Exercise) due
• Wednesday, April 9: Midterm #2
• Monday, April 14: Proposal for term project due
• Friday, April 18: Lab report #5 (BP and Exercise) due
• Friday, May 2: Lab report #6 (Control of Respiration) due
• Wednesday, May 7: Term paper due
• Thursday, April 24, 8:00-10:00 Final Exam (in regular classroom)

Important Course Information

• The late submission penalty on lab reports is 1 point (out of 10) for each day late. If you have truly unusual circumstances, you may apply for additional time but this has to happen by email to the instructors BEFORE the submission deadline.
• Note: this class makes heavy use of Canvas for submission of all assignments.
• Still slightly tentative but always-dynamic Course Syllabus ,(PDF Acrobat format).
• Class schedule (also subject to change) .
• Doodle poll for signing up for lab days. Please check here to see which day you signed up for which lab.
• A LaTeX template for lab reports, included as a zipped archive file that will create a LaTeX subdirectory with all the files necessary.
• College of Engineering Course Guidelines.
• College of Engineering Academic Affairs
• Test/exam information
• The Healthline Body Maps, a set of amazing, interactive anatomical descriptions coupled with lots of background information. Definitely a nice resource to use for exploring the human body.

Course Lecture Notes

• Lecture block 1 (Rob MacLeod): Introduction
  • Lecture slides in PDF format (7 MB)
• Lecture block 2 (Rob MacLeod): Experimental Methods
  • Lecture slides in PDF format (3 MB)
  • Virtual Physiological Human position supporting use of animals in research.
• Lecture block 3/4 (Rob): Cardiac Cellular Electrophysiology
  • Cellular electrophysiology Slides in PDF (13 MB)
  • Derivation of Hodgkin-Huxley formalism for cardiac cells.
• Lecture block 5 (Rob): Cadiac Tissue Structure and Function and Arrhythmias
  • Lecture slides in PDF format (11 MB)
  • Living Arrhythmias movie (45MB)
• Lecture block 6: (Rob) the ECG
  • Lecture slides in PDF format (12 MB)
  • Taccardi streaming video (224 MB)
• Lecture block 7 (Rob MacLeod): Cardiac Mechanics
  • Cardiac mechanics (9 MB)
  • Review article on EC Coupling by Don Bers.
  • Video: Cellular Calcium and sparks
  • Video: Normal cardiac structure and EC coupling (5.2 MB)
  • Video: Effect of hypertension on EC coupling (3.4 MB)
  • Video: Effect of dilated cardiomypoathy on EC coupling (3.4 MB)
• Lecture block 8 (Rob and Jess): Intro to Circulation System
  • Lecture slides in PDF format (1.6 MB)
• Lecture block 9: (Rob and Kedar) Hemodynamics
  • Lecture slides in PDF format (1.5 MB)
• Lecture block 10: (Rob and Brett) Arteries and Veins
  • Lecture slides in PDF format (3 MB)
• Lecture block 11: Microcirculation (Rob)
  • Lecture slides in PDF format (4.3 MB)
• Lecture block 12: Control of circulation
  • Lecture slides in PDF format (2 MB)
• Lecture block 13: Gases and Gas Transport
  • Lecture slides in PDF format (7 MB)
  • Movie of RBC flow through the body
• Lecture block 15: Lung structure and function
  • Lecture slides in PDF format (7 MB)
• Lecture block 16: Control of Ventilation
  • Lecture slides in PDF format (10 MB)
  • Paper from J.B. West on respiratory control and climbing Everest.
  • National Geographic story on the physioligy of altitude, highlighting the question of genetics vs. preparation in the human capacity to be at high altitudes.
• Lecture block 17: Osmotic Balance
  • Lecture slides in PDF (9 MB)
• Lecture block 18: The Kidney
  • Lecture slides in PDF (11 MB)

Test Information

• Sample test, just to view the test format. A real mid term will include more questions.
• Sample test with sample answers.
• Two general slides to comment on the sample test.
• Midterm #1 study topics in PDF format (Exam is March 17, 2014).
• Midterm #1 Comments
• Midterm #2 study topics in PDF format (April 9, 2014).
• Midterm #2 Comments
• Final study topics in PDF format (Apr 24, 2014).

Laboratory Exercises

• The late submission penalty on lab reports is 1 point (out of 10) for each day late. If you have truly unusual circumstances, you may apply for additional time but this has to happen by email to the instructors BEFORE the submission deadline.
• Note: all lab assignments and grading will take place using Canvas .
• Doodle poll to sign up for lab days (on which there are two days available).
• Lab report general guidelines.
• Lab #1 report specific guidelines.
• A LaTeX template for lab reports, included as a zipped archive file that will create a LaTeX subdirectory with all the files necessary.
• Lab grading rubric . Please use this to make sure lab reports contains all the essentials. We will grade the reports based on this rubric. Note that not each item in the list will receive equal value in computing the total grade.
• And did we mention that Canvas is important to pay attention to?

Lab #	Date	Topic/Description	Links/Data/Comments
1	Friday/Monday, Jan 10/13	Dissection of bovine heart/lungs (in pdf version)	Comments on lab reports (pdf)
2	Friday/Monday, Feb 7/10	Regulation of heart rate and contraction (frog)	Comments on lab reports (pdf)
3	Friday/Monday, Feb 21/24	ECG lab	Lab notes
4	Friday, March 7 in HSEB 3100C	Simulation Lab, ECG simulation
5	Friday/Monday, April 4/7	Exercise and blood pressure	Lab explanation slides
6	Friday/Monday, April 18/21	Pulmonary function	Lab notes

Homework/Lab Assignments

Link to MATLAB information

The Assignments

1. Homework Assignment #1 Simulation of cardiac action potentials.
   • Instructions for the assignment.
   • Background information in PDF format.
   • Zipped archive file for the Matlab code for Homework Assignment.
   • Links to the original Hodgkin and Huxley paper and also a tribute to this research.
   • Comments on the assignment

Semester Project

1. There is a term project (PDF) for the course that is due at the end of the semester (see deadline list , above). Note that the proposal/outline for the project is due beforehand. Please feel free to contact RSM for questions as you develop the outline and ideas for the paper.
   • Tips for the term paper
   • Sample outline #1. This is a nice example of a well detailed outline for the paper.
   • Sample outline #2. Another example of an outline, this one more compact but still covering the essential elements.
2. There is a new assignment for this year based on the CircAdapt simulator. As this new, there is not so much in the way of background material available. So please ask the instructor for more information after we have discussed this option in class.

MATLAB Info

• General information
• Shibaji's MATLAB presentation (from 2005)
• Accompanying m-files:
  • myfile.m the main program file.
  • chkevod.m
  • getrslt.m
  • plotter.m

Additional background information.

Please do visit this link as it contains lots of related resources to cardiac physiology.

Previous Year's Notes

Note: these are pdf files from the previous year's edition of the course. They will change at least slightly from year to year so use the current versions (above) if you are taking the class!