BENG 172

BENG 172 Bioengineering Laboratory

Spring Quarter, 2018

*** Remember to upload PDF copies of Labs 6 and 10 via TritonED when you turn in the hard copy ***

** Please join the BE172 instructors and TAs for a drink at RoundTable Pizza at the Price Center on Thursday June 14th at 5:00 pm **

Location

Lecture: Monday 10:00-10:50, Room: Warren Lecture Hall 2113
Laboratories: Wed 9:30-1:00 or 2:00-5:30, Room PFBH 108

Instructors

Dr. Jeff Omens, Professor of Medicine and Bioengineering
email: <jomens AT ucsd DOT edu>
Biomedical Sciences Building, room 2004
Office hours: Monday 2:00-3:30 pm

Dr. Pedro Cabrales, Professor of Bioengineering
email: <pcabrales AT ucsd DOT edu>
Powell-Focht Bioengineering Hall, room 182
Office hours: Monday 3:00-4:00 pm

Engineer

Doug Gurevitch
email: <dgurevitch AT ucsd DOT edu>
Powell-Focht Bioengineering Hall, room 112

Teaching Assistants

Gabby Colvert (gcolvert@eng.ucsd.edu)
Lauren Severance (lseveran@eng.ucsd.edu)
Office Hours: Thursdays 11:00-11:30 and Fridays 3:30-4:00, both in PFBH 108

Text Book

Webster JG. Medical Instrumentation: Application and Design, 4th ed. 2010 John Wiley & Sons: New York.

References

• Baura G, Medical Device Technologies: A System Based Overview Using Engineering Standard. 2011, Oxford: Elsevier (Academic Press).
• Chien S, et al. [editor], Clinical Hemorheology: Applications in Cardiovascular and Hematological Disease, Diabetes, Surgery, and Gynecology. 1987, Boston: M. Nijhoff.
• Cobbold RSC, Transducers for Biomedical Measurements: Principles and Applications. 1974, New York: John Wiley & Sons.
• Doebelin EO, Measurement Systems: Application & Design. 4th ed. 1990, New York: McGraw Hill.
• Fung YC, Biomechanics: Mechanical Properties of Living Tissues. 1981, NY: Springer-Verlag.
• Geddes LA, Baker LE, Principles of Applied Biomedical Instrumentation. 3rd ed. 1989, New York: John Wiley & Sons.
• Lieber RL, Skeletal muscle structure and function: implications for rehabilitation and sports medicine. 1992, Baltimore: Williams & Wilkins.

Course Objectives (the 4 D’s):

(1) Demonstrate the basic concepts of bioengineering design through experimental procedures involving humans, animals and tissues
(2) Design physiological experiments; analyze and interpret data using statistical and error analysis
(3) Develop laboratory skills including maintenance of laboratory records that are accurate and precise
(4) Develop scientific writing skills by preparing formal “brief communications” that describe experimental findings

Course Outline

Week #

Topic

Instructor

Reading

 

1 (Apr 2)

Hydraulically Coupled Blood Pressure Recording System. Dynamics of 2nd order systems, frequency response of catheters. Introduction to lab measurement techniques Lecture Notes

Omens

Sections 1.1-1.11*, 7.1-7.8*

 

2 (Apr 9)

Skeletal Muscle I Isolated frog muscle mechanics: Isometric contractions Lecture Notes

Omens

49-69†, Sections 9.1-9.6§

 

3 (Apr 16)

Skeletal Muscle II Isolated frog muscle mechanics: Isotonic contractions Lecture Notes

Omens

Sections 9.7-9.8§

 

4 (Apr 23)

Nerve Compound action potentials from the frog sciatic nerve and properties of a bioamplifier Lecture Notes

Omens

Sections 3.1-3.6*, 4.1-4.3*, 5.1-5.3*, 5.10-5.11*

 

5 (Apr 30)

Cardiac Mechanics Pressure-volume relationships in the heart. Strain softening and residual stress. Finite element modeling Lecture Notes

Omens

Chap. 10§

 

6 (May 7)

Viscoelastic Properties of Tissues Creep, stress relaxation tests; simple mathematical models Lecture Notes Please upload a PDF copy of your Lab 6 via TritonED

Omens

Sections 2.11-2.14§, 2.1-2.3*

 

7 (May 14)

Hemorheology Fluid mechanics of blood.

Cabrales

Chapter 3§, Chapters 2,4,5£

 

8 (May 21)

Human Electrocardiogram ECG recording with a instrumentation amplifier on fellow students.

Cabrales

Sections 4.6*, 6.1-6.8*

 

9 (May 28)

No Monday Lecture. Mechanical Testing of Biocompatible Materials Compressive, tensile and shear tests of implantable materials.

Cabrales

Chap. 12§

 

10 (Jun 4)

Experimental design Use techniques learned throughout the quarter. Determine mechanical properties of arteries Please upload a PDF copy of your Lab 10 via TritonED

Omens

Chap. 8§

 

Final (June 11)

2 hours only. Bring pencil, eraser and calculator 9:00 am – 11:00 am

* Webster † Lieber § Fung £ Chien

Grading

75% Lab reports (10% of each report is for the pre-laboratory section)
25% Final Exam
Do not expect a passing grade in the course if you do not turn in 2 or more lab reports.

Grading Policies

Group study and discussion of assignments is allowed and encouraged. Each person in the group is responsible for turning in their own pre-lab, data analysis and lab report for each week; raw data needs to be copied for each person’s report since only one set will exist. If duplicate documents (except raw data) are turned in by members of the group, the grade will be divided by the number of students with the same report. In cases of suspected academic dishonesty, the student will be given a copy of the academic conduct code, and the case referred to the appropriate Dean. Generally, the penalty for academic dishonesty is a failing grade.

Roll will be taken each lab session; you cannot turn in a lab report if you did not participate in the lab experiments.

Lab Day Assignments

Each student is enrolled in a lab section on Wednesday. You will need to show up to the lab at that time for the entire quarter, and cannot switch sections.

You should divide into working groups of 3 people maximum since there are 8 lab stations. You will work at the same lab station, with the same group, each lab session.

Pre-laboratory Preparation

The purpose of the required pre-laboratory preparation is to allow you to become familiar with the experimental techniques to be used and with the concepts underlying the laboratory investigation, and to enable you to conduct the experiment and learn as efficiently as possible during the valuable laboratory time period. At the beginning of the laboratory period, a TA will check your prelab, and then it will be turned in at the end of the lab session for grading. Anyone who has not demonstrated adequate preparation for the laboratory will not be allowed to participate. It is important to be familiar with the lab exercises before the actual lab, so pre-labs are taken seriously. They will also count for part of the lab write-up score (10% unless otherwise noted). The pre-lab assignment consists of 2 parts: the protocol summary and questions, as described below.

Pre-laboratory Protocol Preparation

Bioengineering experiments usually involve studies on living cells, tissues, or animals. By its very nature, such experimentation is a perturbation of the living preparation from its normal environment. This is quite different from a typical “engineering” or “computational” experiment where the test sample may be, for example, an “inert” metal bar or computer program. In addition, many bioengineering experiments require carefully timed procedures. Thus, it is critically important that the conduct of an experiment is efficient and precise.

Good laboratory technique therefore starts with the preparation of a clear laboratory protocol. Accurate record keeping of daily activities, including the date and time of procedures, is essential in an academic or industrial environment, where, for example, you may later desire to lay claim to an important discovery. The protocol should consist of a title, brief introduction (2-3 sentences), followed by a step-by-step protocol. This protocol can be outline or bullet form, and should list all of the steps that will be followed in the lab session. Formulating a step-by-step protocol allows you to plan things more efficiently. For example, if dissection of a tissue takes 30 minutes, that step should be done early to minimize its potential to be a “rate-limiting” step. The protocol may be typed or hand-written.

Pre-laboratory Exercises/Questions

These questions review some of the basic concepts and techniques that will be needed for the lab. Each lab has some form of pre-lab questions. Most are clearly labeled in the weekly handout, otherwise specific instructions will be given. The questions must be completed by each person individually in the group and turned in as part of the pre-lab report. TAs will check the pre-labs at the beginning of the lab session. The entire pre-lab assignment, which includes the pre-lab questions and protocol summary, should be 1-2 pages (1-2 sides of a piece of paper) long. Remember to turn in your pre-lab before you leave that day.

Lab Equipment and Supplies

All of the necessary equipment, materials, and supplies will be provided, either in the station cabinet or on the counter. You are responsible for this material and it should be returned at the end of the lab in good condition to the location you found it. If there is anything necessary that is not supplied by the TA at the start of the lab, ask the TA to get it for you. Do not go scrounging around in any of the equipment cabinets. If any equipment or part appears to be malfunctioning, notify a TA.

Computers/Software

PC computers running Windows with UCSD active directory are available at each lab station in PFBH 108. The software is continually being upgraded, so be patient with updates and other software issues (but be happy they are relatively new computers!). Computers are used for data acquisition in most of the weekly labs, and may be used for data processing and analysis. They may also be used for making spread sheets, preparing lab reports, network access, etc. Please be a responsible computer user as other students and researchers in the Department share these machines. The computers are maintained by ACS. The keyboards and mice are spray disinfected every week before our class, so gloves are not needed. They have free printing access to the black and white laser printer in the adjacent room (laser11@pfbh-108); please only print BE172 related work. There is also a color ink jet printer with a limited number of printed pages for each user. This printer is called HP Office Jet 6100. Color printing should be restricted to the final version of a lab report or plots for a report, and obviously only if they contain color.

There are other classes using the lab at other hours (Monday and Tuesday), please do not come into the lab when another class is using the lab, or during BE172 hours when other sections are in session. Printing and computer use are OK during off-hours, Thursday and Friday would be the best days. The lab will be locked at night and weekends. If it is open and not being used, you are welcome to use the computers and printers for BE172 work. Experimental equipment and supplied are only available during your lab session. There are also computers with similar software available in the PFBH Multimedia lab, Room 161.

The PC’s are refreshed to a clean image periodically. This means that you should not leave your data outside of your account, and then logout! To login to Windows (active directory), use your UCSD account (e-mail/username). You can save files in your active directory account, but do not save them only on the hard drive on the lab computers. Make sure to copy your files (or print them) before you leave for the day. “Computer failure” or “No USB thumb drive” are not good justifications for missing data. It is always a good idea to leave your lab session with a hard copy of your data taken on the computer just in case. You will typically need a hard copy of your raw data to have it signed by a TA before you leave the lab.

► Labview for data acquisition
The computers in our lab will be used for data acquisition with National Instruments Labview software, and an internal acquisition card via the grey break-out box at each station. You will need to download the Labview VI to run the BE172 program. You should leave the downloaded Labview vi file (Bioeng Lab.llb) in your UCSD account to access for the entire quarter. Note that our software only runs in Labview 2014. If you run the 2017 version, quit, and run “NI 2014 LabVIEW 2014 (32-bit)” from the start menu, then open “Bioeng Lab.LLB” from your hard drive as an existing vi.

  • Download the Zip File containing the BE172 Labview VI and associated files: Labview Files
    Instructions for using Labview in the BE172 lab for data acquisition: Labview Acq Primer
    Instructions for using Labview in the BE172 lab for ECG generation: Labview ECG Primer

► Sigmaplot graphing software
Sigmaplot is a plotting/curve-fitting program available in Rooms 108 and 161. It is very useful for data plotting and curve fitting for this course.

  • Instructions for using Sigmaplot in the BE172 lab.

► Digitial cameras in PFBH 108
USB-connected digital cameras, or close-focus “microscopes”, are available for imaging and image acquisition during the quarter. Interface software is call “amcap”.

  • Instructions for using digital Cameras in the lab.

► ImageJ analysis tools
ImageJ is public domain software developed at NIH for analysis of microscopic images, but can be used as a powerful tool for many image analysis procedures. In this course you can use it to measure dimensions and orientation in images that are saved on the computer.

Matlab, Labview and other software packages are available to UCSD students for personal use. See “Access Campus License Software” in your TritonEd account.

Laboratory Reports

All reports must be typewritten (12 pt font minimum size) and submitted in the appropriate format in order to be graded. Each person in the group should write their own report. None of the text in the report should be the same as anyone else’s. Reports are based on data acquired by the group, but plots/figures etc. should be created separately. The complete report should include the 2-page lab report, followed by the raw data (or a copy of it) taken the day of the lab, co-signed and dated by a TA on the day of the lab. Other pages may be requested for particular labs, and should be attached as appropriate.

All pages of the report must be stapled together. Reports held together with paper clips, scotch tape, spit, or similar devices are not acceptable and will not be graded. Reports are due one week after the actual lab as shown on the schedule. Turn in your lab report on your lab day 1 week after the appropriate lab session. Late reports will not be accepted.

The Brief Communication One form of scientific report is a two-page brief communication. This is the style of lab report we will be using in this course. This format is longer than many abstracts submitted for scientific meetings; a brief communication contains a bit more detail regarding the scientific methods as well as a larger body of data, and a more in-depth discussion of the results and their implications, and may include figures. A typical example of this form of report can be found in Biophysical Journal or the Journal of Biomechanical Engineering. A sample can be found on the course web page, with extra information on the formatting, figures, etc. Only the first page of this type of report should have the title, names and group header.

Format of Lab Reports The Brief Communication format of a lab report must include:

Header on first page only:

  • Title – The title should describe the area of investigation without necessarily giving away the results. Make it interesting enough that someone would want to read the report, but not so detailed. Most scientific publications limit the length of the title.

    Names – Include your name FIRST, followed by the other members of your group.

    Group – Under the names include your Lab day (with AM/PM) and Station number, for example: “Wednesday AM, Station 8”

Introduction – This is where the objective of the study or the hypothesis under investigation should be stated along with a short review of relevant background information (i.e., what is already known about the field). For this report it should be about 1/4 of a page of text.

Material and methods – A brief summary of the experimental techniques should be included so that the reader has some idea of how the experiment was performed. In a full-length publication, enough detail should be included so that the reader could duplicate the experiment. However, in an abstract, there is not room for such a level of detail. Assume that the reader is a specialist in the field. The lab handout may be referenced, but not without further explanation (i.e., “We did what the lab manual said” is not an acceptable method). Since this describes work that is completed, it should be worded in the past tense. This should be 1/3 of a page at most.

Results – Include a summary of the data that you obtained. This should include descriptive prose (paragraphs, also in the past tense) that contain or describe the data in graphs or tables. The data that you present should be appropriately reduced from the raw data. For example, if multiple readings were taken, it may be appropriate to determine a mean and standard deviation, or fit a hypothetical relationship. Remember that every data reading has units associated with it; be sure to include units on all plots. Data may be presented in graphical or tabular form if necessary. However, don’t include figures just because they look nice! They should demonstrate some relationship or trend. The text in the results is minimal, it should be mostly figures, tables and numbers.

Discussion and conclusion – A discussion of the data and its relevance to the objective of the lab should be included. What do your findings show and how do they relate to the function of the body? If one set of measurements is bigger, stronger, or faster than another, why are they that way, and what are the implications? Do your findings support or refute other investigators work, and can they explain differences in other experiments? The discussion is worth a large portion of your grade, and is the hardest part to write. It should be 1/2-3/4 of a page long.

References – Include and cite in the appropriate place in the report any references used in writing the report or which relate to your research findings. You should also reference raw data of other groups if you do not get data for some section of the lab and used theirs instead, with prior approval of the instructor or TA.

Page Layout – Include the line borders around the text as shown it the sample. If all else fails, draw them in by hand! The margin widths should be uniform and between 0.5 and 1″. Any color paper is acceptable. Please make plots large enough so that they are legible. Color plots can be an excellent way of getting your point across (but not required).

Grading Criteria for Lab Reports
In the absence of specific guidelines for a particular write-up, the following criteria will be used for grading of the lab reports.

Style / Grammar (15%) Poor writing reduces the effectiveness of your presentation, makes it difficult for the reader to understand what was done or what was found, and decreases the excitement of your findings. In addition, typographical errors and spelling mistakes (easily avoidable in this modern age by using the spelling and grammar checking features that are available in most word-processing programs), changes in tense, and improper punctuation all indicate oversights by the investigator.

Introduction / Content (15%) The report should convey a general understanding of subject in the introduction and how measurements relate to the topic of that week’s laboratory. The engineering and scientific background should be accurate. Overall content of the report is included here.

Data and Analysis (25%) If a measurement is requested, the relevant data should be presented. An adequate description of the data and its accuracy and repeatability should be included along with any potential sources of error. Statistical analysis should be included where appropriate. If no data was obtained, either the expected results should be discussed with an explanation of the difficulties encountered, or data from another group should be used and properly referenced.

Figures (10%) When figures are used to present data they should be clear and readable and in the appropriate style. This includes the proper use of curve fitting and error bars, along with a legible choice of tick marks and labels. Remember that if you fit a set of data to a curve, you have implied that a functional relationship exists and you should discuss this in the text. The figures should also be numbered and have short captions. Make sure that all figure legends and symbols are clear and legible in the final document.

Discussion(25%) This is where the tie between the objective of the lab and the data obtained should be made. A thorough explanation of your findings and its implications in relation to normal or abnormal function of the material is important. Show how these results do or don’t fit with the existing literature. Do they support or refute current theories?

Pre-lab write up: turn in the day of the lab (10%)

Although raw data is not graded, it must be attached behind each 2-page lab report.

Sample 2-page lab report: Sample report

Regrade Policy:
Regrades must be submitted within 1 week after returned
• A note must be attached to the cover page of the report indicating the request
• If the regrade is simply an addition error, please just write “addition error” on the first page and resubmit
• The entire lab report is subject to regrading upon any request received
• Give regrade directly to your TA, DO NOT turn in with the most recent lab reports, DO NOT give to Dr. Omens
• Regrades can be picked up within two weeks after submission from the “graded” file folder

Laboratory Procedures

Safety Guidelines The guidelines listed here should not be considered comprehensive, but rather a list of common sense rules to follow for both your safety and good scientific practice.
• Have fun, but behave responsibly.
• No eating or drinking in the labs.
• No bare feet or open sandals.
• Know where the first aid kit, eyewash station, and fire extinguisher are located
• Keep your fingers out of your face and eyes while handling the equipment or chemicals and wash your hands at the end of the lab.
• Report any accident or injury to the TA or instructor.
• Keep your work area clean. Clean up any spills or leaks, try not to spill water on electrical equipment!
• Dispose of tissue sample in the appropriate waste containers, not the sink or trash can.
• Dispose of glass, syringes, needles and razor blades in a “sharps” container.
• Remove broken glass with a dustpan and brush right away.
• THINK! It’s not just your grade.
Laboratory Safety Documentation

In Case of an Emergency, call:
(Use an on-campus phone for 911, cell phones will go to the SDPD and they are not familiar with the campus)
Fire: 911
Police: 911
Medical: 911
Poison Center 3-6000
Environmental Health & Safety 4-3660
First Aid (Student Health): 4-3300

Use and Care of Laboratory Animals

Bioengineering research frequently uses humans and animals to study physiological function. Therefore the bioengineer must face the issue of the use of animals in research. While many benefits have been derived from this type of research, not all animal experiments have necessarily yielded useful results, and cases of abuse do unfortunately exist. The use of animals in science is a controversial subject that people must decide for themselves. Listen to both sides, rather than just making a blanket assumption about the issue from one source. Alternative techniques such as mathematical, computational, or tissue culture models should always be considered whenever experiments involving animals are contemplated. Bioengineers, by way of their multidisciplinary training, are in the unique position to be able to take advantage of all of these tools in their research.

In order to safeguard the health and well being of animals used at research facilities, national guidelines have been drawn up. In addition to local and state regulations, there are several federal laws aimed at protecting animals in the United States. The Endangered Species Act of 1973 desires “to provide a means whereby the ecosystems upon which endangered species and threatened species depend may be conserved, to provide a program for the conservation of such endangered species and threatened species, and to take such steps as may be appropriate to achieve the purposes of the treaties and conservation of wild flora and fauna worldwide.” Regulatory authority is vested in the Fish and Wildlife Service.

While this act is aimed primarily at wild animals, animals used for research, exhibition, or as pets are covered under the Animal Welfare Act (AWA) which was enacted in 1966. It gave responsibility for regulating dogs, cats, hamsters, guinea pigs, rabbits, and nonhuman primates held by research facilities to the United States Department of Agriculture (USDA). The act was amended in 1970 to include other warm-blooded animals and again in 1976 to cover control of live animal transportation. The most recent revision in 1985, “Improved Standards for Laboratory Animals Act”, requires regular exercise for dogs and an appropriate environment to insure the psychological well being of both dogs and nonhuman primates. This act also mandates that each institution have an animal care committee that approves research protocols, monitors projects and enforces administration of drugs. All research facilities must have an attending veterinarian who is involved in care of the animals and must be a member of the animal care committee. Proper pre-surgical and post-surgical care must also be provided, and multiple procedures must be restricted. The USDA was further instructed to develop regulations guaranteeing humane care and treatment of animals including minimal standards of handling, housing, feeding, veterinary care, and transportation. The Regulatory Enforcement and Animal Care (REAC) unit of the Animal and Plant Health Inspection Service (APHIS) is responsible for enforcement of these standards. The REAC maintains five field offices throughout the United States and conducts regular unannounced inspections. The APHIS may issue a warning notice, offer a stipulation agreement, or prosecute the institution of any violations that are found.

Link to UCSD Institutional Animal Care and Use Committee information on possible Health Risks associated with lab animals

Excerpts from the National Institutes of Health Guide for the Care and Use of Laboratory Animals