BME 244L: Quantitative Physiology with Biostatistical Applications

Fall 2014

Course Description: An examination of the importance of mass and energy balances,

transport processes, mechanics, energetics, and electrical activity in physiological systems.
Lectures cover cellular physiology, cardiovascular system, nervous system, muscle
physiology, and renal physiology. Labs complement lecture topics and introduce statistical
methods related to the measurement and analysis of physiological data. Statistical topics
include: descriptive statistics; hypothesis testing; correlation, regression, and goodness-of-fit;
ANOVA and post-hoc tests; power analysis and experimental design.
Textbook: Guyton and Hall Textbook of Medical Physiology, 12th edition
John E. Hall PhD (Author)
ISBN-10: 1416045740 | ISBN-13: 978-1416045748
We will use i>Clicker2 for in-class problems. Please purchase the i>Clicker2 from the
bookstore, online, or from another student before the 2nd week of classes (September 2rd). We
will practice using it in the second class, so go ahead and get it ASAP please.
You can find Duke many former BME 244L students looking to sell their iClicker2 here:
https://docs.google.com/spreadsheet/ccc?key=0Aoccvx25YI6YdGh3Q1FZeHkwMGJiZHROdlI4YS
1UM2c&usp=drive_web#gid=0
Here is another google doc from last fall that includes students from a STA class as well as
BME 244L. I am not sure if these students are still looking to sell or not since it is an older
google doc.
https://docs.google.com/spreadsheet/ccc?key=0AkY2lFgS9uiDdE1fMkZUZnp6alJDSG9tYlIwT
FJWdnc#gid=0
Instructors
Charles (Steve) Wallace, PhD
steve.wallace@duke.edu
Office Hours: T 10:00-11:00am
1131 CIEMAS
Other times by appointment

Christine Mulvey, PhD

christine.mulvey@duke.edu
Office Hours: M 9:00-11:00am
369 Gross Hall
Other times by appointment

Teaching Assistants:
TBA
Student Outcomes
After completion of this course, the successful student should be able to:
1. Describe how function affects the structural design and molecular mechanisms of key
tissues and organ systems
2. Identify and apply key unifying principles (conservation laws, transport processes,
mechanics, and electrical activity) that govern the function and regulation of the human
body.
3. Ability to use proper statistical methods to draw conclusions from physiological
measurements.

4. Use experimental outcomes and mathematical models to identify and/or describe key
underlying mechanisms within the physiological system
Course Website
A website (http://sites.duke.edu/bme244l/) for the course has been developed to facilitate
learning of the course topics. The website lists all of the topics within the course. Each topic
has its own webpage that lists specific chapters/page numbers within the textbook that cover
the topic, expectations for the student, and supplemental learning materials in the form of
readings or online videos. Homework assignments, lab assignments, and exams will target
the student outcomes listed within each topic page. NOTE: The top scorers on the exams
from the previous semester found it very helpful to print off all student outcomes from this
website, and attempt to write a few sentences about each outcome without looking in their
notes. After completing this exercise, they would then know what they needed to further study
to be fully prepared for the exams.
Piazza
This term we will be using Piazza for class discussion. The system is highly catered to getting
you help fast and efficiently from classmates, the TAs, and the instructors. Rather than
emailing questions to the teaching staff, we encourage you to post your questions on Piazza.
Logistic questions or questions about possible typos within assignments will be answered
immediately by the TAs or Instructors. All other questions will not be addressed by the TA or
instructors until another student has attempted to answer the question. This rule is to
encourage student discussion rather than only student-instructor interactions on Piazza.
If you have any problems or feedback for the developers, email team@piazza.com.
Find our class page at: https://piazza.com/duke/fall2014/bme244l/home
Grading
1. Homework assignments (10%)
2. Lab assignments (16%)
3. In class participation (4%)
4. Statistics Sakai Review Problems (3%)
5. Statistics Quizzes (7%)
6. Exams (60%, 3 exams @ 20% each)
Exams (60%)
Exams represent individual work. You are allowed to create your own equation sheet for the
exam. The equation sheet is limited to equations and physical, chemical, and mathematical
constants that were presented in the notes, textbook, labs, statistics modules, or homeworks.
You may have definitions (5 words or less) to the variables within the equation. The equation
sheet must be the size of one sheet of paper (8.5x11in), and only one side of the sheet can be
used. Equation sheets must be submitted with the exam. Any equation sheet that does not
meet these guidelines will result in a substantial deduction of exam points. Calculators may be
used for the exam. Use of any other information during the exam is strictly prohibited.

In-Class Participation (4%)

Throughout the lectures we will use the iClicker2 to answer conceptual questions about the
lecture material. These questions will be given to promote an active learning environment.
You will be graded on your performance on these questions, but its not overly strict as you can
see by the grading scheme below. In order to receive credit for the iClicker2 questions, you
must register your clicker at http://iclicker.com/support/registeryourclicker. In the Student ID
field, enter your Net ID. In the Remote ID field, enter the 8-character alphanumeric code
printed below the barcode on the back of your iClicker2. You are required to bring your
iClicker2 to every lecture. I realize that occasionally you may forget your iClicker2 (see me
before class starts if this happens) or need to miss class; therefore, up to 2 unexcused
absences will not affect your iClicker2 grade (I will drop your two lowest class scores). The
total number of correct answers will be tallied over the entire semester, and a percentage of
correct answers will be determined for the entire semester. Using more than one iClicker2
simultaneously will be considered Academic Dishonesty and a violation of the Duke
Community Standard.
75% or better = 100% credit (4 pts)
40 74% = % Score x 4pts (1.6 3 pts)
39% or worse = 0% credit
(0 pts)
Homework Assignments (10%)
Homework assignments are due within the first 15 minutes of your class (which ever one you
are registered in) on the due date. For homework assignments, you may discuss the problems
with other students in the class. Copying all or part of a solution from somewhere else
(classmate, website, textbook, previous students, etc) is not permitted and will be considered
Academic Dishonesty and a violation of the Duke Community Standard. All homework
problems within the set will be graded for completion, but only a fraction of the problems within
the set will be graded for correctness.
Late homeworks
15% penalty = TA receives the homework 15 mins after class starts, but before the class ends
25% penalty = TA receives homework after the class ends, but before 5pm on due date
50% penalty = TA receives homework between 5pm on due date and next day by noon
100% penalty = TA receives homework after noon on day after the homework was due
Lab Assignments (16%)
Attendance is required for all labs, with make-ups only permitted with an online excuse
received by the instructor before the lab time. One unexcused absence will result in 50% loss
of total lab grade (8%). Two unexcused labs will result in automatic failure of the course.
Tardiness to the labs will also not be accepted. Students that are more than 10 minutes late
will have points deducted from the corresponding lab report. The number of points deducted
will be based on the degree of tardiness.
Labs are done as a team, usually two students that are picked at random by the TAs before
each lab. You can find the lab schedule at the end of the syllabus.

The lab report is more of an extensive homework than a traditional lab report. You are only
required to thoroughly complete the answers to the analysis questions within the lab handout.
Answers to the questions within the lab handout must be completed using word processing
software. All calculations and formula manipulations can be completed by the word processing
software or neatly completed by hand and attached to the appendix of the document. Lab
assignments will be graded on the quality of the answers, the effectiveness of the presentation
of the data, and the demonstration of the proper calculations/formula manipulations. The
answers to the questions including all calculations/formula manipulations must be shown in
painstaking detail. This is really the only class in which you will have formal statistics
instruction, so we want you to have every problem worked out to a level of detail that will
enable you to come back to it in a future class and repeat similar statistical analysis strategies.
There is a PDF (Lab Submission Guidelines.pdf) in the Resources>Labs folder on Sakai that
provides information of how to prepare for the labs, what to expect in the labs, as well as
guidelines to completing the lab assignment.
Your lab assignments must be submitted as both electronic and hard copies. One hard
copy of the lab assignment (one per team) must be turned in to the physical course dropboxes
corresponding to your section time. These dropboxes are located in the 2 nd floor hallway in the
Hudson Annex. If you have never been in the Hudson Annex before, then I suggest you try
and get their a little early in case you have trouble finding it!! The electronic copy must be
submitted to the proper Assignments folder on Sakai by the due date/time. Even though team
members will submit a joint report, each student must submit their team report and their group
evaluation ELECTRONICALLY before the due date/time. This rule is to prevent one lab
member from forgetting to submit the hard copy or being tardy in the submission and costing
the other lab member a tardiness penalty.
Lab assignment grades will be based on the quality of work within the report and on the
information within the lab group evaluation form. There is a link to the form in Resources>Labs
folder on Sakai. Please read the instructions carefully and answer all questions with complete
honesty. Only the TAs and instructors will view these evaluations, unless you give us
permission to discuss it with anyone else. If a student receives a very poor evaluation from
their partner, the student may lose the ability to work in a team to complete the hands-on lab
work and lab assignments. The instructor will closely review poor evaluations and seek further
information from the students before deciding the final penalties. It is best to notify the TA
and/or instructor of a poor lab partner before submitting the lab report, so that we can help you
successfully complete the report in a timely manner.
Reports will be due by 5pm on Tuesdays (for Monday sections) and Wednesdays (for
Tuesday sections) of as indicated in the lab schedule below. Late assignments must be
submitted to the instructor through email. You are allowed to discuss the lab assignments with
classmates that are not in your lab group, but your submitted work must be completed by only
you and your group members. Copying any part of a solution from somewhere else
(classmate, website, textbook, previous students, etc) is not permitted and will be considered
Academic Dishonesty and a violation of the Duke Community Standard.
Late Lab Assignment/Group Evaluation

5% penalty = Received within 1 hour after time due

20% penalty = Received 1 hour after time due, but by midnight of due date
50% penalty = Received by 5pm one day after the assignment was due
100% penalty = Received after 5pm on day after the homework was due
Statistics
The lab periods will be used for the statistics modules and the labs. A schedule is presented
at the end of the syllabus. There is some online reading associated with each stats module
that must be completed prior to each statistics session. The readings can be found in the BME
244L section of the BOSS BME Online Statistics Source. There is a link to the BOSS
(http://sites.duke.edu/boss/) in the Resources tool of the BME 244L Lecture Sakai Site. After
completing the readings within the statistic module, the student must complete the
corresponding Statistics Module Review Problems located in the Tests and Quizzes tool on the
BME 244L Lecture Sakai Site. Students are NOT allowed to discuss these review
problems or their solutions with anyone other than the course instructors or TAs before
the solutions are made public. Failure to meet this criteria or copying any part of a solution
from somewhere else (website, textbook, previous students, etc) is not permitted and will be
considered Academic Dishonesty and a violation of the Duke Community Standard. Your
answers to the assignments must be submitted 2 hours before your statistics session begins.
Late submissions will be rejected. Only one submission allowed.
During the first 15 minutes of the statistics session, students will individually (closed book)
complete 1 to 3 problems directly from the Online Sakai Statistics Module Review Problems.
These quizzes will account for 2 of the 7% associated with the Statistics Quizzes outlined in
the grading scheme above. We hope that by successfully completing this quiz, students will
be better prepared to complete the group work. Students can use their computers, notes, and
peers to complete the group work in the statistics session. Group work will not be collected,
but is used to help you understand the material through further discussion of the topic. At the
end of each statistics session, students will complete a short individual quiz on the statistical
topics covered that week. Students can use any notes within their group work packet to aid in
the completion of this individual stats quiz.
One unexcused absence from the statistics session will result in a 50% deduction from the
total statistics quiz grade (3.5 points). A second unexcused absence from a statistics session
will result in a deduction of 5 points from your final course grade. If a student misses a
statistics session (excused or unexcused), then the quiz can be made-up orally with the
instructor. Tardiness to the statistics session will also not be accepted. Students will have
only until 15 minutes past the start of the section to work on the pre-quiz. Students who arrive
after pre-quizzes are collected will not be allowed to make them up and will forfeit those points.

Academic Integrity
Education and research depend upon high standards of integrity to be successful. Such
standards are embodied in the Duke Community standard
(http://www.integrity.duke.edu/new.html).
Duke University is a community dedicated to scholarship, leadership, and service and to the
principles of honesty, fairness, respect, and accountability. Citizens of this community commit
to reflect upon and uphold these principles in all academic and non-academic endeavors, and
to protect and promote a culture of integrity.
To uphold the Duke Community Standard:
1. I will not lie, cheat, or steal in my academic endeavors.
2. I will conduct myself honorably in all my endeavors.
3. I will act if the Standard is compromised.
At the same time, instructors have an obligation to be clear about their expectations with
respect to collaboration. The sections above contain the policies for BME 244L. If you have
questions about the policies or their implications, please contact the instructors.
Dukes Punishment for Academic Dishonesty
Penalty in the course and consequences with the Student Conduct Office, which could
impact the students status as a student at Duke
In addition, students also note the following common consequences of academic dishonesty:
Stress of being accused of cheating
Sleepless nights over whether you will remain a student at Duke
Fear of having to report the incident to an employer or graduate/professional school
Embarrassment of sharing the incident with ones family
Visa implications for international students
What should I do if I witness a violation of the academic integrity policy?
Under the Duke Community Standard, you are obligated to act when you witness a
violation
One course of action is anonymously reporting the incident to student affairs
o http://studentaffairs.duke.edu/conduct/report-incident
What should I do if I am concerned about another students well-being?
Please speak to the instructors and/or contact Duke Reach
o http://studentaffairs.duke.edu/dos/dukereach
What should I do if I am concerned about my own well-being?
Please speak to the instructors and/or contact Duke CAPs
o http://studentaffairs.duke.edu/caps

Tentative Lecture Schedule

T Aug 26

1-Introduction, Functional Organization of the Human Body,

Homeostasis, & Control Systems

Th Aug 28

2-Differential Equations, Electricity Basics, & Diffusion

T Sept 2

3-Membrane Transport

Th Sept 4

4-Resting Membrane Potential and Action Potentials

T Sept 9

5-Action Potentials

Th Sept 11

6-Propagation of Action Potential

Compound Action Potential

T Sept 16

7- Quantitative Analysis of the Action Potential:

Hodgkin-Huxley Model

Th Sept 18

8-Neuromuscular Junction
Excitation and Contraction of Skeletal Muscle

(HW 1 Due)

(HW 2 Due)

(HW 3 Due)

T Sept 23

9-Skeletal Muscle Mechanics

Th Sept 25

10-Quantitative Analysis of Muscle Contraction:

Hill Model Part 1

T Sept 30

Exam 1 Topics from Lectures 1-7, Stat Modules 1-2, and Lab 1

Th Oct 2

11-Quantitative Analysis of Muscle Contraction:

Hill Model Part 2

T Oct 7

12-Cardiac Muscle

Th Oct 9

13- Excitation and Conduction System of the Heart

T Oct 14

Fall Break

Th Oct 16

14-Heart as a Pump

T Oct 21

15-Pressure-Volume Loops

Th Oct 23

16-Cardiac Mechanics

T Oct 28

17-The Circulation

(HW 4 Due)

(HW 5 Due)

(HW 6 Due)

Th Oct 30

Exam 2 Topics from Lectures 1-16, Stat Modules 1-3, and Labs 1-2

T Nov 4

18-Blood Vessel Mechanics

Th Nov 6

19-Quantitative Analysis of the Hemodynamics

of the Arterial System: Windkessel Model

T Nov 11

20-General Blood Flow

Th Nov 13

21- Tissue Blood Flow Control

T Nov 18

22- Microcirculation

Th Nov 20

23-Cardiac Output, Venous Return and their Regulation

T Nov 25

24-Kidney Anatomy and Primary Functions

Th Nov 27

Thanksgiving

T Dec 2

25-Glomerular Filtration

Th Dec 4

Exam 3 Weighted to topics not previously tested on:

Topics from Lectures 16-25, Stat Modules 4-5, and Labs 3-4

(HW 7 Due)

(HW 8 Due)

(HW 9 Due)

Lab and Statistics Schedule

Notes:
1. A few Duke Lab Safety Modules must be completed throughout the semester. After you have completed the
module you will need to save the certificate showing that you have successfully passed the module, and then
you will need to upload it to the corresponding Sakai Assignments folder by the dates listed below. The
safety modules can be found here:
http://www.safety.duke.edu/OnlineTraining/Default.asp
1. Log in with NetID and password
2. Click on Courses Available On-line at the top of the left menu
3. Select the relevant courses, listed above
2. Students must wear closed-toe shoes for Lab 2: Frog Muscle Contraction lab. Frog skin is known to harbor
pathogenic bacteria (botulism, tetanus, salmonella, etc.) and if a student were to drop scissors onto their feet,
they risk infection from the bacteria. Long pants are not mandatory, but a good idea. No pictures, as per
OESO regulations.

Date
Aug 25/26

Statistics Topic/Lab Topic

No Meetings

Sept 1/2

Basics of Statistics & Data Presentation See ACES for Room #

*Submit Stat Module-1 Sakai Quiz 2 hours prior

Sept 8/9

Hypothesis Testing t-testing - See ACES for Room #

*Submit Stat Module-2 Sakai Quiz 2 hours prior
*Submit Laboratory Safety General & Fire/Life Safety
Safety Quiz completion documents

Sept 15/16

Lab 1. Nerve Conduction Velocity - CIEMAS 1392

Sept 22/23

Regression and Correlation See ACES for Room #

*Submit Lab 1 Report
*Submit Stat Module-3 Sakai Quiz 2 hours prior
*Submit Animal Handlers Part 1 and 2 Safety Quiz
completion document

Sept 29/30

No Meetings -- Exam on 30th

Oct 6/7

Lab 2. Muscle Contraction - CIEMAS 1392

*See Note 2 above
Graded Lab 1 available for pickup

Oct 13/14

Fall Break

Oct 20/21

One-way ANOVA and Repeated Measures ANOVA CIEMAS 1392

*Submit Lab 2 Report
*Submit Stat Module-4 Sakai Quiz 2 hours prior

Oct 27/28

Two-Way ANOVA and Post-Hoc Testing See ACES for Room #

*Submit Stat Module-6 Sakai Quiz 2 hours prior

Nov 3/4

Lab 3. Pulse wave velocity CIEMAS 1392

Nov 10/11

Power Analysis and Experimental Design See ACES for Room #

*Submit Lab 3 Report
*Submit Stat Module-6 Sakai Quiz 2 hours prior
*Submit Bloodborne Pathogens Safety Quiz
completion document

Nov 17/18

Lab 4. Renal Function Teer P015

Nov 24/25

No Meetings
*Submit Lab 4 Report

Dec 1/2

No Meetings