University of Arizona College of Engineering University of Arizona College of Engineering University of Arizona College of Engineering University of Arizona College of Engineering University of Arizona College of Engineering

Welcome to the Department of Biomedical Engineering!

Established in 2009 by the Arizona Board of Regents, the newest Engineering department reflects a University of Arizona tradition of interdisciplinary research at the intersection of medicine, science, and engineering that is more than 50 years old.
Faculty in the Department of Biomedical Engineering have a variety of backgrounds and research areas, but all are dedicated to improving human health through the application of engineering and scientific principles.
The undergraduate program in Biomedical Engineering has graduated its first class of 27 students in 2013 with a BME’s Bachelor of Science. It is expected to grow to a size of 200-250 students by 2015.
The Graduate Interdisciplinary Program in Biomedical Engineering capitalizes on the research and teaching expertise of more than 60 faculty in Biomedical Engineering and 16 other departments into one exciting graduate education program.

BME News

UA Biomedical Engineering Student Earns SynCardi Scholarship

Jill Goetz • 12/18/2014 


Justine Bacchus is the second UA biomedical engineering student to receive the engineering scholarship from SynCardia Systems Inc.

Justine Bacchus, a junior studying biomedical engineering at the University of Arizona College of Engineering, has received the 2014 Anna Salazar Memorial Engineering Scholarship for Women from SynCardia Systems Inc. 

The scholarship was created in honor of Anna Salazar, a senior quality engineer who joined SynCardia in 2012 and made a lasting impression on her colleagues at the company before her death later that year at the age of 49. 

In presenting the $5,000 award to Bacchus on Nov. 12, SynCardia CEO and President Michael Garippa said, “We hope that this scholarship will allow outstanding women engineering students to reach their academic and professional goals and, like Anna, contribute to society in astounding ways.”

Tucson is the international headquarters of SynCardia, which owns and manufactures the only total artificial heart in the world approved by the Food and Drug Administration, Health Canada and CE (European Union).

The company was co-founded by Dr. Marvin J. Slepian, director of interventional cardiology and professor of medicine at the UA Sarver Heart Center, who holds a joint appointment in the biomedical engineering department in the College of Engineering.

Hometown Pride

Bacchus learned of SynCardia while attending a biomedical engineering colloquium as a UA student. 

“I thought it was really neat that synthetic hearts were manufactured in Tucson and are used around the world today,” she said. “I’m from Sahuarita, which is just a half-hour away, so I feel a sense of hometown pride in knowing this technology comes from Tucson.”

Bacchus, who has been fascinated with biomedical engineering since high school said, “I considered many options for majors during my first few semesters in college, but my heart is truly with the medical side of engineering. I want to help people directly with their health.”

In particular, she wants to help people through genetic counseling. 

“I’ve always found genetics fascinating and want to pursue genetic counseling for my advanced degree,” she said. “I want to help people understand their genetic makeup and how they can have healthy and happy lives, even while having a genetic disorder.”

Over the last year, Bacchus has gained research experience in the lab of UA associate professor of physics Charles Wolgemuth, where she is studying motility of Borrelia, the bacteria that causes Lyme disease.

“Justine is one of the best undergraduate students I have had work for me,” Wolgemuth said. “She is highly motivated and talented, and we have loved having her in the lab.” 

Exploring Science in the Czech Republic

Bacchus will broaden her research and global perspectives this summer while attending Prozkoumat! In the Czech Republic. 

Sponsored by the UA Office of Global Initiatives and offered through the UA Undergraduate Biology Research Program, the 10-week program (its name means “explore” in Czech) enables UA undergraduates to conduct research under the guidance of scientists at the Institute of Parasitology at the Czech Academy of Sciences. 

Bacchus’s interests and aspirations extend beyond biology and biomedical engineering. She is honing her leadership skills as philanthropy chair of the Honors Student Council and as a participant in the UA Blue Chip Leadership Program. She is also studying ballet in Sahuarita.

“Genetic counseling is my goal, but I see that there are so many different paths my life could take,” she said. “As long as I am working with and helping people, I will consider myself successful.”

Bacchus Is Second UA Student to Receive SynCardia Scholarship

SynCardia awarded its first Anna Salazar Memorial Engineering Scholarship for Women in 2013, to Sandra Gonzalez, then a senior in the UA biomedical engineering department.

The first member of her family to graduate from high school, Gonzalez is now a National Academy of Sciences Ford Foundation Fellow, pursuing her doctorate in biomedical engineering through a joint program between Georgia Tech and Emory University. She is conducting research on biological pacemakers, in which genetic material is transplanted into patients to regulate heartbeat.

Top photo (courtesy of SynCardia Systems Inc.): Michael Garippa, SynCardia Systems Inc. CEO and president, presents the 2014 Anna Salazar Memorial Engineering Scholarship for Women to Justine Bacchus, a UA biomedical engineering student in her junior year.

Doctors to Get Better Access to Digital Data


Jill Goetz, UA College of Engineering
July 8, 2015

With $1.3 million and a top-priority ranking from the National Institutes of Health, UA College of Engineering researchers are developing data compression software to make biomedical big data universally available.

Ali Bilgin: “We are in the middle of a global transition to digitization of biomedical data."

The National Institutes of Health has awarded a $1.3 million grant to researchers at the University of Arizona to develop open-source software that will enable health care professionals and scientists to manage biomedical big data in digital form. 
The advanced data compression software for the first time puts digitized biomedical data in a format and size that doctors, pathologists and other health care workers with limited resources and in remote locations will be able to access, analyze and store. Usable digitized data means quicker second opinions and diagnoses for patients.
"Advances in image compression technology for biomedical big data are essential to advance biomedical diagnostics and research and to save more lives," said Ali Bilgin, UA assistant professor in the departments of Electrical and Computer Engineering and Biomedical Engineering and principal investigator of the project. "We are in the middle of a global transition to digitization of biomedical data, and there’s a lot of it out there — but in files too large to be transmitted, stored or retrieved."

Samples from a single patient over a lifetime can add up to a terabyte of data — enough to fill an entire hard disk, a huge amount of data that most pathology labs cannot handle.

The award is one of the first of 15 research projects funded through the NIH Big Data to Knowledge, or BD2K, Initiative, the agency announced in June. The NIH identified data compression as one of the initiative’s key focus areas and gave the UA project ("Development of Software and Analysis Methods for Biomedical Big Data in Targeted Areas of High Need") an impact factor of 11, the agency’s second-highest possible ranking. 
"Data compression software has the potential to address some of the most significant data storage, computing and sharing challenges facing biomedical researchers," the NIH said in its announcement.

Task-Specific Data Compression
The UA-developed software will compress the size of slide images up to 100 times without losing any detail or resolution from the original slide images. Bilgin’s team is working with previously scanned digital images of slide samples from breast cancer patients, but the software will be applicable for a broad range of diseases.

"The medical community has been working to digitize biomedical data for some years, but to date the data has had little real effect on health care," Bilgin said. "Most labs are not equipped to receive or use the millions of gigabytes of information from data such as DNA sequence data or protein structure data. Our software will provide access to these files despite their huge size."

Perhaps most revolutionary, the new software will compress the digital images in specific ways for specific tasks.

"A pathologist may want to determine if an image indicates cancer. A research scientist might be more interested in identifying different categories of cancer cells in the sample," Bilgin explained. "Our technology will tailor the size and format of the digital image that is transmitted so a user doesn’t receive a whole lot of data they don’t need."  It should be a first, he said.

"Although it has been long recognized that image quality should be task-based, we know of no previous attempts to compress images for specific tasks," Bilgin said. "This is an entirely new way to think about image compression."

Engineering Better Biomedical Technology 
Image compression was the subject of Bilgin’s dissertation at the UA, from which he received his doctorate in electrical and computer engineering in 2002. Although he started out as an electrical engineer, he said, "I quickly realized that all of these skills I’d gained as an engineer could be applicable to problems in medicine."

Michael Marcellin was his graduate adviser and is co-investigator of the NIH-funded study. Marcellin, a Regents' Professor in the Department of Electrical and Computer Engineering and the UA College of Optical Sciences, was a major contributor to JPEG2000, the standard image compression coding system used today and the one that will be used in the biomedical image compression research.

Other participating UA researchers include Elizabeth A. Krupinski, professor and vice chair of medical imaging and associate director of the Arizona Telemedicine Program, and Amit Ashok, assistant professor of optical sciences and electrical and computer engineering. Researchers at Ohio State University, including Metin Gurcan, associate professor of biomedical informatics, also are participating.

Krupinski said the research has major implications for telemedicine, which uses electronic communications to transmit medical information, often to remote locations, to improve patient health.

"The use of telemedicine and the volume of associated digital images in health care are expanding exponentially," she said. "Many of these images, such as whole-slide pathology images, are extremely large and difficult for users to navigate through. Dr. Bilgin’s task-specific compression techniques will make navigation more efficient and diagnostic interpretation more effective."

Second Opinions in Seconds
When a patient requests a second opinion today, pathologists send the patient’s slide sample to another laboratory to prepare bioassays for the second doctor. The process can take days. The UA-developed software will transmit review-ready data in minutes or seconds, allowing users to view digital images and share information about them over vast distances in real time.
"This will help patients more quickly get second opinions and reduce the chances of diagnostic errors," Bilgin said. 
It also will advance biomedical research and discovery. 
"Let’s say a pathologist sees a large cluster of a certain type of cell in their digital image," Bilgin said. "They can use the new software to request all digital pathology samples with a similar cellular feature. This has tremendous potential for increasing our ability to quickly identify disease."

Art Gmitro Appointed Chair of Biomedical Engineering Department

Jill Goetz • 12/08/2014 - 13:19

UA medical imaging and optics researcher will build faculty and enhance cross-disciplinary research and training opportunities in College of Engineering’s newest department.

Arthur F. Gmitro, a professor and researcher in the University of Arizona colleges of medicine and optical sciences, became chair of the UA College of Engineering department of biomedical engineering, or BME, effective Nov. 24. He succeeds associate professor and interim department head Urs Utzinger.

“Strongly supported by the University of Arizona provost and vice president for research, the appointment of Arthur Gmitro as head of the BME department reflects the University’s growing recognition of biomedical engineering’s increasing importance to effective health care,” said College of Engineering dean Jeff Goldberg. “This appointment will showcase the synergies between BME and other departments on campus, not only in the College of Medicine but throughout the University.”

He added, “Art is taking over from Urs Utzinger, who has given selflessly in his role as interim head of BME. He cannot be thanked enough for what he has done over the past couple of years.”

 Art GmitroGmitro, who has been on the UA faculty since 1987 and a full professor since 1996, is known to many in the College of Engineering. Generations of students have taken his courses in medical imaging and biomedical optics in the College of Optical Sciences. Faculty members know him through research collaborations, as a member of the UA Graduate Interdisciplinary Program in Biomedical Engineering and from his service on the Graduate Interdisciplinary Program Advisory Committee, which he led from 2005 to 2006.

Man of Vision

Gmitro received a bachelor’s degree in engineering physics from the University of Illinois before earning master’s and doctoral degrees in optical sciences at the University of Arizona in 1974 and 1979, respectively.

“I have had the pleasure of watching Art Gmitro’s development since he entered the University’s optical sciences doctoral program,” said Harrison H. Barrett, Regents' Professor in the UA College of Optical Sciences and department of medical imaging. 

After finishing graduate work, Gmitro joined the faculty at Yale University, where he taught for five years and founded a program in medical imaging.

Barrett noted, “A few years later, after an international search, our then radiology department hired Art to establish a new program at the UA in the emerging area of magnetic resonance imaging, which he did -- with great skill and leadership.”

He added, “I was delighted when Art was designated as the next head of the BME program. His broad knowledge of biomedical engineering and medical imaging, his calm demeanor and his devotion to education make him the ideal person for the job.”

Gmitro is developing miniature endoscopic devices in the UA Biomedical Imaging Laboratory, where he also studies the tumor microenvironment using novel optical and MRI techniques. He has been a principal or co-principal investigator on more than 10 major research projects in medical imaging, with funding from the National Institutes of Health, Arizona Biomedical Research Commission, American Cancer Society, Air Force Office of Scientific Research, American Heart Association and others.

His leadership positions have included directing the Biomedical Imaging and Spectroscopy Training Grant Program and co-directing the Cancer Imaging Program in the UA Cancer Center, where he became the Fenton Maynard Endowed Chair in Cancer Imaging in 2009. A Fellow of the American Institute for Medical and Biological Engineering, Gmitro has received the Rudolph Kingslake Award from SPIE, the International Society for Optics and Photonics; and the Francois Erbsmann Prize from Information Processing in Medical Imaging.

Big Plans for Growing the Department

The department of biomedical engineering is the College’s newest, formed in 2009. In 2014 it graduated its second class with 43 bachelor’s degree recipients.

“As a young department and a relatively young discipline, BME offers opportunities for innovations not only in the curriculum but in teaching strategies,” said Gmitro. “I thoroughly enjoy interacting with and learning from my students, and I will strive to hire new faculty who view teaching not only as a major commitment, but also as something they enjoy and want to do well.”

He added, “I look forward to working with the BME faculty to build a strong department that translates engineering innovation into improved cost-effective health care and educates the workforce necessary to achieve that outcome.”

It’s an exciting time for biomedical engineering at the University of Arizona, which Gmitro believes will take an increasingly important role in biomedical research and development for improved patient care.

“The future of health care is not only in providing improved treatments for patients with injury or disease, but in providing the resources and tools required for individuals to take a more active role in monitoring and maintaining their own health. I believe the UA has the foundation of interdisciplinary research collaboration necessary to help shape that future.”


Yoon Elected President of the Institute of Biological Engineering

Jeong-Yeol Yoon will serve as the new President of the Institute of Biological Engieneering, a professional organization dedicated to integrating engineering principles with the many aspects of life sciences.

Read the Fall 2014 issue (pg 4) of Arizona Engineer for the complete article

Congratulations to Ana Lourdes Enriquez Outstanding COE Senior Fall 2014

Ana Lourdes Enriquez
UA Engineering Announces Fall 2014 Outstanding Seniors and Grad Students

The UA College of Engineering announced the outstanding seniors and graduate students of the fall 2014 semester at a commencement luncheon December 3.
Ana Lourdes Enriquez, biomedical engineering; nominated by Bijan Najafi, was named the College of Engineering Outstanding Senior Fall 2014.

To see the complete list, please read this issue of Arizona Engineer

Photo courtesy of Arizona Engineer

Wolfgang Fink Named da Vinci Fellow for 2015

Fink da Vinci Fellow
Wolfgang Fink Named da Vinci Fellow for 2015

"UA College of Engineering expert in artificial vision systems honored for his inventive and interdisciplinary research and teaching.

Like many men of science, Wolfgang Fink works in diverse disciplines and enjoys eclectic avocations. He’s a physicist, an engineer, an educator, an inventor, a licensed helicopter pilot and a classically trained pianist. You might call him a Renaissance man."

Read the article on the da Vinci Fellow in recognition of excellence in teaching or research excellence in this issue of Arizona Engineer

Photo courtesy of Arizona Engineer

Making MRI a Potent Weapon in the War on Cancer

"Marty Pagel and his multidisciplinary research team are developing MRI techniques for early detection of cancer and for monitoring effectiveness of anticancer drugs.

Time is critical when it comes to diagnosing and treating cancer.

Aggressive cancer tumor cells often produce enzymes that cut into healthy tissues surrounding the tumor, providing routes for tumor cells to escape and create new, difficult-to-treat metastatic tumors. These enzymes could be ideal targets for diagnosing and treating aggressive tumors early on, but they are seldom investigated because accurately measuring their performance has been difficult -- until now."

Read the complete story on Arizona Engineer

Photo courtesy of Arizona Engineer

UA Engineering Turns Smartphones into Eye-Screening Tools

fink smartphone

"The University of Arizona's Wolfgang Fink, whose innovations have helped restore partial sight to the blind, takes on a new challenge: creating telemedical devices that can prevent blindness."

Read the latest on Wolfgang Fink's research in this issue of Arizona Engineer

Photo courtesy of Arizona Engineering


The University of Arizona's Wolfgang Fink, whose innovations have helped restore partial sight to the blind, takes on a new challenge: creating telemedical devices that can prevent blindness. - See more at:
The University of Arizona's Wolfgang Fink, whose innovations have helped restore partial sight to the blind, takes on a new challenge: creating telemedical devices that can prevent blindness. - See more at:
The University of Arizona's Wolfgang Fink, whose innovations have helped restore partial sight to the blind, takes on a new challenge: creating telemedical devices that can prevent blindness. - See more at:

Art Gmitro Appointed Chair of Biomedical Engineering Department

"UA medical imaging and optics researcher will build faculty and enhance cross-disciplinary research and training opportunities in College of Engineering’s newest department.

Arthur F. Gmitro, a professor and researcher in the University of Arizona colleges of medicine and optical sciences, became chair of the UA College of Engineering department of biomedical engineering, or BME, effective Nov. 24. He succeeds associate professor and interim department head Urs Utzinger."

Please read the Arizona Engineer article on Art Gmitro and his plans for the Department.
Article can be found here

UA medical imaging and optics researcher will build faculty and enhance cross-disciplinary research and training opportunities in College of Engineering’s newest department.

Arthur F. Gmitro, a professor and researcher in the University of Arizona colleges of medicine and optical sciences, became chair of the UA College of Engineering department of biomedical engineering, or BME, effective Nov. 24. He succeeds associate professor and interim department head Urs Utzinger.

- See more at:
UA medical imaging and optics researcher will build faculty and enhance cross-disciplinary research and training opportunities in College of Engineering’s newest department.

Arthur F. Gmitro, a professor and researcher in the University of Arizona colleges of medicine and optical sciences, became chair of the UA College of Engineering department of biomedical engineering, or BME, effective Nov. 24. He succeeds associate professor and interim department head Urs Utzinger.

- See more at:

Jeong-Yeol Yoon is Editor-In- Chief

Jeong-Yeol Yoon is Editor-In- Chief

Jeong-Yeol Yoon has been selected as Editor-in-Chief for
Journal of Biological Engineering, starting in January 1, 2014.
This is an official journal of Institute of Biological Engineering, published by BioMed Central, a part of Springer

Check out the Journal of Biological Engineering at

Grad Students Honored for Food-Related Research

Grad Students Honored for Food-Related Research

"Pei-Shih Liang, who received her PhD in agricultural and biosystems engineering and is now a post-doctoral fellow at the University of California, Davis, was recognized for her research on “Optofluidic Lab-on-a-Chip Monitoring of Subsurface Bacterial Transport.” Jeong-Yeol Yoon, president of the Institute of Biological Engineering and UA associate professor, co-authored the paper, which focused on advancing the use of lab-on-a-chip to quickly detect food contaminants, such as E. coli."

Full article found here

National Champions!

The UA chapter of the National Society of Black Engineers,
or NSBE, had only two months to prepare -- and the team went on to win
the 2014 NSBE Undergraduate Technical Research Competition in March at the NSBE 40th Annual Convention in Nashville, Tenn.
Wolfgang Fink is the mentor for this team.

To learn more, please click on the link here.

Professors Team Up to Make Implanted Devices 'Sticky'

UA researchers are testing nanotechnology to improve how cardiovascular implant devices are attached in the body.

Jeong-Yeol Yoon, associate professor of agricultural and biosystems engineering, and Dr. Marvin Slepian, professor of cardiology and biomedical engineering, collaborated to test how nanotechnology-based techniques can be used to better facilitate adhesion between tissue and implanted devices.

Please click on the link below to learn more

Driver-less Cars About a Decade Away

Autonomous vehicles can control and navigate themselves, "in the absence of a human being," said Wolfgang Fink, an associate professor in Biomedical Engineering and Keonjian chair at the UA's Department of Electrical and Computer Engineering

"Fink has been developing an autonomous rover, which can be controlled with an iPhone or iPad. The vehicle can also use LiDAR, a kind of laser sensor, to recognize obstacles or to follow someone around. The vehicle is further equipped with cameras, which use algorithms to determine what items within range are of interest to the rover."

Full article can be found here

Ariana Nicolini Awarded Dept of Defense 2014 SMART Scholarship

Ariana Nicolini, a doctoral student in the Biomedical Engineering program of the UA Graduate Interdisciplinary Programs, has been awarded a 2014 Science, Mathematics and Research for Transformation (SMART) Scholarship from the U.S. Department of Defense (DoD). The extremely competitive scholarship is awarded to only 6 percent of total applicants, and aims to increase the number of civilian scientists and engineers working in DoD laboratories.

Full article here

Giving Sight Back to the Blind


Wolfgang Fink is giving sight back to those who once saw.

"Since 2002, Dr. Wolfgang Fink, an associate professor in the UA Departments of Electrical and Computer Engineering and Biomedical Engineering, and colleagues have been working on a new way to give sight to those whose vision has been damaged from age-related macular degeneration or retinitis pigmentosa, both are conditions that result in visual impairment and ultimately total blindness."

Full article found here

Engineering Senior Design Day

View Event Details
It is Engineering Senior Design Day!
May 6
10am to 3pm
North Ballroom AND The Mall!
Awards at 4pm.

Jeong-Yeol Yoon Elected President of the Institute of Biological Engineering

Lab-on-a-chip developer with multiple UA appointments will lead bioengineering society. Associate professor Jeong-Yeol Yoon holds so many appointments across the UA campus that people often ask him which college he is with and where they can find him. (If they can find him, he jokes.)
Read the article from Arizona Engineer here

Wolfgang Fink in the News

Wolfgang Fink has been in the news a lot lately.
Please check out the various articles on his latest work.

Arizona Public Media TV Interview can be viewed here.

UA News article can be viewed here.

Tucson News Now interview can be viewed here.

KOLD 13 Interview can be viewed here.

Phoenix CBS Channel 5 Interview can be viewed here.

Listen to the Nov 22, 2013 interview here.

The Daily Wildcat article can be viewed here.

A New Tool in the Search for Extraterrestrial
Life: A Tricked-Out Point and Shoot
Can be viewed here.

Also featured in the Arizona Daily Wildcat
article: "Say 'CHEESE' Mars!
The Arizona daily Wildcat article
can be viewed here

Arizona Public Media interview can be viewed here.

Jennifer Barton is one woman who wears many hats at UA

Jennifer Barton, professor and head of the UA department of biomedical engineering and assistant director of the BIO5 Institute.The University of Arizona's Jennifer Barton is the assistant director and No. 3 person at Bio5 Institute, she is the department head of the newly established Department of Biomedical Engineering, chair of the Biomedical Engineering Graduate Interdisciplinary Program, and she is a researcher and teaches classes within optics, electrical and computer engineering and biomedical engineering.

"Most faculty members end up teaching, doing research and some sort of service," said Barton, who is also a Arizona Cancer Center member. "My service just happens to be more administrative. It seems like a lot but although I wear a lot of different hats, they're all the same color. It's really synergistic work."

Barton never saw herself going down this path. She worked with McDonnell Douglas Aerospace for six years, part of that time on the international space station program before returning to the University of Texas at Austin for her PhD in biomedical engineering.

"I never envisioned myself becoming a faculty member. I was quite sure when I went back to graduate school that I was going to go right back into industry," she said. "But life pulls you in interesting directions. It's like research, you start working on a problem and you see possibilities from it and you follow the possibilities."

Barton was drawn to the UA 12 years ago when the school was putting together a graduate degree program in biomedical engineering.

"I had the opportunity to get in on the ground floor of a program and help design that degree and that was really appealing to me,” she said. "I had never done anything like that before, but it was new and exciting."

This spring, the college of engineering announced there would be a department of biomedical engineering and they tapped Barton to be the new department head.

"We did not want to start an undergraduate program until a few things happened," she said. "There was a period of time that this field wasn't very well established and people in industry were slightly leery of hiring graduates from that field because they didn't know what to expect. We also needed more demand from the students and we are seeing that now."

She said the department was announced in March and they had 15 freshmen transfer into it and another 35 sign up for it for the fall.

"The response has been great," Barton said. "It looks like we'll have our goal of 60 students per year in just a year or two."

The department was developed to focus on three main areas of biomedical engineering: bio-imaging, cardiovascular engineering and nano medicine.

In addition to being department head, Barton teaches a class within the department titled "Challenges in Biomedical Engineering."

"It's the best class because I get to go in there every week and talk about a different challenge like diabetes or heart failure and then talk about what biomedical engineers are doing in order to address those challenges," she said. "I get to slip some of my own research in as well as the research of some of my colleagues which keeps me fresh on what’s going on in the field."

Barton's research focuses on optical imaging as she is developing the technology and potential applications of cancer detection utilizing optical coherence tomography, OCT, a noninvasive technique that directs a beam of near-infrared light on tissue. The light penetrates a few millimeters and is reflected back. The resulting image is similar to an ultrasound with light. She also combines OCT with other imaging methods.

"OCT can be used for a variety of organs, but ovarian cancer caught my attention because it is such a devastating disease," Barton said. "It is a challenge because the ovaries are inside the body and there is no screening technique that works well and most women don't have any symptoms until it is very advanced.

"So if we want to look at them with OCT you would have to get right up against the ovary. That won't work in the general population, but there is a group of women who have high risk of ovarian cancer doctors often recommend removing them. Now that might not be a difficult decision to make in your 60s but that is a terrible decision to have to make in your 20s. Our idea is that if we could tell with certainty the ovaries were normal then that woman could keep her ovaries and just be screened every couple of years."

She is also looking at applying the technique to colon cancer and skin cancer.

Part of this work involves developing the tools that will be used for the screenings - something she is known for around the world.

"In order to get to the organ of interest we need to build miniature endoscopes and that's really what my lab does well," she said. "We can stay at the cutting edge by doing what we're good at here which is optical design and biomedical design and working on these endoscopes mainly."

In the early days to image blood vessels a probe would have to be held up to the skin for around a minute, today the devices can render three dimensional volumes in close to real time.

"We can get images pretty well, but the next step is finding out what those images mean," she said. "We work a lot with pathologists and surgeons to review the bright spots and dark spots on an OCT image and to tell us what those correspond to and are those features diagnostically interesting."

Part of that has meant learning new languages because pathologists, biologists, oncologists and engineers don't speak the same technical language.

"That's why I spent part of my sabbatical sitting in on biochemistry classes so I could learn some of this basic information," she said. "I also purposely choose students to come into the lab who know more than I do about an area because I tell them that one of the things they have to do is teach me. It's a two way street."

In the future Barton wants to push the limits of resolution on her devices and eventually work toward more human trials.

"They are a lot of work and a definite challenge, but that's what's necessary to verify a technique is going to be useful in a patient," she said. "Making something a technological success is one thing, but making it a clinical success and a success for human health is a higher bar than that."

Contact reporter Joe Pangburn at or (520) 295-4259.

A mechanical engineer's view of the human body

Like any operating machine, the human body is made up of a series of systems. Each component in the system serves a specific function to keep the system operating. There are biological pumps, valves, pipes, filters, wiring, as well as contents under pressure. And, just like a mechanical system, if the stress on the components is high enough, those parts can fail.

“Many of the answers to medical problems are often similar to answers to engineering problems,” said Jonathan Vande Geest, 32, assistant professor at the University of Arizona. “I love that you can utilize tools and expertise that’s been developed over the last 100-plus years in mechanical engineering to solve problems related to human health.”

Vande Geest is a mechanical engineer turned biomechanical engineer and was largely responsible for establishing the curriculum of the biomedical engineering degree program the UA just established this year.

“Having a degree in biomedical engineering, it made perfect sense for me to be involved in the development of the curriculum and the future of that department,” he said. He was hired in 2005 and was originally 100 percent in the College of Aerospace and Mechanical Engineering. “But so much in mechanical engineering is leaning the way of biomedical engineering these days that last year I moved half my appointments to biomedical engineering.”

In his Soft Tissue Biomechanics Laboratory, Vande Geest applies engineering testing and analysis to human biological systems. His lab has two main research focus areas: identifying and studying relationships between structure and function in soft tissues and improving medical device design.

Vande Geest is working to grow proteins that are molded into replacement blood vessels. The work is being done in partnership with Sedona-based Protein Genomic Inc.

For his part, Vande Geest tests the man-made blood vessels to determine their maximum pressure ratings, strength and mechanical properties. Even though the blood vessels are constructed from biological materials, the U.S. Food and Drug Administration considers them to be medical devices, according to Vande Geest.

“With something like this, we have two options,” he said. “We can take the native sample and try and design something that matches its look, functions and design or we can look at the function of the object and design something on the basis of optimizing the functionality of it, which may or may not look like the native tissue.”

The other portion of his work involves developing patient-specific device for abdominal aneurysms formed in the aorta where it splits to go into the legs.

“My dissertation was on aneurysms so it seemed a natural fit to continue research in that area,” he said.

An aneurysm is created when the area of the split becomes filled with blood and begins to bulge. This condition is more prevalent in men over the age of 50 and in smokers. The bulge generally goes without presenting symptoms of its existence until it ruptures which is most often fatal. The device is designed to ease the pressure on the walls of the aorta as it starts to bulge.

“I hypothesized we could build a patient-specific device that could be more efficient than current devices,” Vande Geest said.

The device is made up of a smart polymer that is thin, yet very strong. Through his process, it can be created for each patient-specific aneurysm by taking the shape information from the CT scan the patient would have already had done. It is considered “smart” because once the device is inserted into the aneurysm, it is heat inflated to fit snugly inside.

“From that CT scan, we can get the exact shape of the aneurysm,” Vande Geest said. “We run an algorithm that fills the shape of it and the device is printed on a 3D printer. This process is much cheaper and will be a much better fit for the patient than current devices used.”

The current methods involve stints. One is tube shaped and can slip inside the aneurysm. Another involves invasive surgery. Vande Geest said the cost to make his device is around $50 and it theoretically could be delivered non-invasively.

“The proof of concept for fabrication is done,” he said. “I am very proud to have something on the table to show that is very close to what I envisioned when I wrote the grant in 2006. Now we are looking for the proof in functionality of the device, which is what the research will focus on next.”

Because the research is new, there are several pieces of equipment in Vande Geest’s lab that had to be created to serve the purpose they needed. But that is part of the freedom of an expanding field and researching at a university.

“I really like being able to attack problems that are broad,” he said. “I can look at it from many different viewpoints and find out the best way to move forward. I would not have this same freedom if I were working at a company specifically focused on a product.”

Next Generation is a monthly feature of Inside Tucson Business. If you’ve got an idea or someone you think should be profiled, contact reporter Joe Pangburn at or (520) 295-4259.

For Aspiring Undergrad Researchers, UA is the Place to Be

By Daniel Stolte, University Communications | August 30, 2010

Many opportunities are available for undergraduates who want to try their hands at research – in the natural sciences as well as in arts, humanities and the social sciences.

Physiology junior Amanda Urbina investigates ways of using adult stem cells obtained from patients to repair damaged joints.
Physiology junior Amanda Urbina investigates ways of using adult stem cells obtained from patients to repair damaged joints.

Amanda Urbina started her junior year last week, but she already finds herself at the forefront of biomedical science – not as part of a required class, but participating in an actual research project.

"My research focuses on regenerating cartilage damaged by injuries that lead to osteoarthritis," said Urbina, who since her freshman year has worked in the laboratory of John A. Szivek, director of orthopedic research at the Arizona Arthritis Center in the University of Arizona's College of Medicine.

"I work with adult stem cells derived from the fat tissue of patients, which can be transformed into cartilage cells and placed back into a patient's joint," Urbina said.

Participating in research offers many benefits, said Glenda Gentile, who heads the Office of Undergraduate Research, housed in the UA's College of Science.

"It helps students develop critical thinking and problem-solving skills, hone their team-working and communication skills and helps connect them to a network of professionals in their field," Gentile said.

"But I feel that one of the greatest rewards of undergraduate research is the opportunity to use information learned in the classroom and apply it to a real world problem and possibly discover a new piece of information," she added.

According to Carol Bender, director of the Undergraduate Biology Research Program, or UBRP, the program in which Urbina participates, the UA offers unusually good opportunities for undergraduates to get involved in cutting-edge science.

UBRP is open to students of any major, and they can apply as early as their freshman year.

"Our faculty members are exceptionally open to involving undergraduate students in research," Bender said.

How to get started

An excellent starting point is the Office of Undergraduate Research website. Not only does it provide a wealth of information and access to databases, but it also provides answers to questions such as "How do I know research is right for me?" "How can I find out about research opportunities in my department?" and "How should I contact a faculty member in whose research I'm interested?"

"Students interested in trying their hand at a research project should talk to the undergrad adviser and faculty in their major," Gentile said.

"We especially want to encourage the younger students to discover what they can do to learn a piece of knowledge no one has had before," she added.  "Many who have taken advantage of research opportunities later say this was the best experience of their undergrad years."

The website provides students with a step-by-step process to access information that will assist them in finding research opportunities, including those in science, technology, engineering and math, but also in broader university-wide programs. 

The site has a searchable database with information on UA faculty members interested in working with undergraduate students. The idea to create the database and centralize information about UA research opportunities came from Gail Burd, former associate dean of the UA College of Science and now vice provost of academic affairs and a distinguished professor of molecular and cellular biology.

The website also provides students with easy-to-use search tools to help them find research opportunities that best meet specific career goals or help them decide which discipline is right for them.

Interested students should keep in mind that most of the programs linked to the website are specific to undergrads, not for those who already have graduated.

Another good starting point is BioGate, the UA's life sciences database, which can be searched for potential faculty mentors according to research areas and keywords.

Before approaching a faculty member about research opportunities, it is necessary to do some homework, Bender said.

"Find out what faculty members are doing in their fields and identify those whose interests coincide with your interests," is her advice to undergraduates interested in spending some time doing research in addition to attending classes.

"Sending off mass e-mails won't cut it," she said. "Students need to be able to articulate their reasons for wanting a research experience. They should be able to explain how a research experience ties in with their career goals before they contact potential faculty mentors."

Opportunities open to many majors

The services offered by the Office of Undergraduate Research are available to students of any major.

Just like in the natural sciences, the first step for prospective student researchers in the arts, humanities and social sciences is to talk with their departmental advisers and faculty members, Gentile said.

Another, lesser-known option is to pursue an undergraduate research scholarship awarded through the UA's Honors College. Students do not have to be enrolled as an honors student to be eligible.

"Our scholarships have supported classical guitar studies, history, social science and visual arts projects, social sciences, creative writing – it's really all over the map," said Karna Walter, director of nationally competitive scholarships at the Honors College. "Applications to our program are reviewed by a multidisciplinary panel of students and faculty members."

Undergraduate research scholarships through the Honors College come with a stipend of $1,500. With about one out of two applications getting funded, the odds of scoring a stipend are pretty good. Applications are due in March. Students perform their research over the summer, write up project report in the fall and present their results in the spring.

NASA's Space Grant program is another option. Its scope is not limited to astronomy and space science, but is very broadly defined and includes journalism.

Time is of the essence

"Planning is the key to success," Gentile said. "Start the process early. You can't start thinking in April about what you would like to do in the summer. Most undergraduate research program deadlines are in January or February."

Applications to UBRP's summer research program open Oct. 15 and must be made online.

"The deadline for the summer 2011 UBRP positions is Feb. 1, 2011, but don't wait until January to think about your application," Bender said.

In addition to their primary research stint over the summer, UBRP students can continue working year-round if they can spare 15 hours per week. More than 80 percent of them do, underscoring the positive experience they obtain through the program.

"It takes a while to learn the skills," Bender said, "and the longer a student does research, the more benefits he or she gains from the experience." 

Gentile reminds students wishing to gain scientific experience of a number of opportunities available outside the UA campus.

"The competition gets steeper because students apply from all over the country," she said. "But these programs can be especially rewarding, taking people to places and institutions they would have never had a chance to work at otherwise."

In addition to the programs mentioned above, many opportunities exist that cater to under-represented minority students such as the Minority Access to Research Careers, or MARC, Program. Together with UBRP, they are among those helping UA students to present their data at scientific conferences across the nation. Listings can be found on the Office of Undergraduate Research's website.

Multiple ways to get involved

Facing a jungle of programs, scholarships and initiatives, it is important to not overlook other opportunities that exist for those looking to check in with their inner scientist.

"In addition to structured undergraduate research programs, there are individual faculty members who hire undergrads to do research on a specific project," said Gentile. "Students can participate in research a number of ways. They can do it for credit or they can volunteer."

"Volunteering in a lab is a good way to get started," Bender added. "Many researchers who don't teach undergraduate classes or don't have funding available say they find mentoring a student very rewarding because it builds a relationship."

"Professors and teaching assistants have a lot of knowledge about research opportunities," is Urbina's advice to students interested in pursuing research on their own.

"Find out if they're looking for someone to join their lab. Look online at the information for different professors in your major or what you're interested in, and then write to them," she said. "The summer programs, too, have a lot to offer. UBRP provided me with a lot of resources that I wouldn't even have known about."

"I found out that I really do love research," she added, "and even though it sounds old, what drives me is that you can use it to better someone's life."


Biomedical Engineering Undergraduates Help Develop Body Worn Sensor Technology


 Biomedical Engineering Undergraduates Help Develop Body Worn Sensor Technology

BME students Pooja Rajguru and Rose Anderson spent the past summer developing sensors for gait analysis as part of their NIH-supported summer training program.

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Warp Power May Soon Add Extra Life to Your Cell Phone and iPod Batteries

Roman Lysecky is assistant professor in the Department of Electrical and Computer Engineering.

By Pete Brown - February 25, 2009, 11:04 am

Assistant Professor Roman Lysecky of the Department of Electrical and Computer Engineering has been awarded a grant of more than $400,000 by the National Science Foundation to develop high-performance customizable computer chips. 

Lysecky’s research will focus on the emerging field of warp processing, which uses high-performance computer chips called field-programmable gate arrays, or FPGAs.

Star Trek fans should note that Lysecky will not be setting up a “warp core” in his Embedded Systems Design Laboratory. Although warp processing certainly is about achieving very high speeds, it is also about achieving gains in power conservation, but exceeding the speed of light is not part of Lysecky’s research.

“The original focus of warp processing was strictly performance,” said Lysecky. “My research proposal expands warp processing into a new domain of low power.” Some systems don’t actually need to be faster. Putting a warp processor in a cell phone, for instance, would not improve call quality. “The chip in a cell phone is already fast enough,” said Lysecky. “Using a warp processor doesn’t improve the quality of the call itself, it just leaves a few idle cycles behind. However, from a power perspective, there is a noticeable impact in the form of extended battery life.”

Computer chips such as FPGAs are hardware, and hardware typically is not programmable. It just does what it was built to do. FPGAs, however, are computer chips that can be programmed after manufacture—hence “field-programmable.”

FPGAs work in a parallel fashion, which means they can execute thousands of instructions simultaneously. Software, on the other hand, works sequentially and executes instructions one after the other. “This is very efficient from a computational point of view,” said Lysecky. “We can give hardware the flexibility of software so that hardware can be programmed on the fly,” said Lysecky. “It takes a matter of seconds to configure how the chip will work.”

Warp processing allows hardware programming to be integrated into software development. This is significant because it reduces dependence on hardware designers, who are in short supply. “Warp processing hides FPGAs from software developers,” said Lysecky. “But it allows them to extract the power and performance inherent in hardware programming, which speeds up development, reduces cost, and creates better performing software that uses less energy.”

Lysecky was awarded the 5-year grant of $415,000 under the NSF’s prestigious Faculty Early Career Development (CAREER) Program. The program supports junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research.

In-Stat, a market research company based in Scottsdale, Ariz., predicted in a 2006 report that the global market for FPGAs would increase from $1.9 billion in 2005 to $2.75 billion by 2010. In-Stat estimates that communications and industrial applications will account for 77 percent of the market share.

UA Engineering Gets $2M from U.S. Army for Research into Computer Models of Unconventional Warfare


By Pete Brown - February 19, 2009, 12:55 pm

The U.S. Army has awarded another $2 million to Professor Jerzy Rozenblit to fund phase 2 of a project to design intelligent software that can analyze the behavior and customs of political and cultural groups. 

In 2007, the Army awarded Rozenblit $2 million to fund the recently completed phase 1 of the Asymmetric Threat Response and Analysis Project, known as ATRAP. Rozenblit holds the Raymond J. Oglethorpe endowed chair in electrical and computer engineering, and is head of that department. 

In the context of armed conflict, “asymmetric” describes opposing forces that differ in terms of size, strength, resources, tactics, armaments, strategy, technology or motivation. Forging peace between such disparate belligerents has confounded negotiators for centuries.  

The ATRAP software will enable intelligence analysts to build up three-dimensional maps of interactions between conflicting groups. By mapping behavior, relationships, resources, events and timelines, analysts hope to be able to predict, and therefore prevent, eruptions of violence.

A screen image from the ATRAP system shows how various relationships are rendered in the three-dimensional thoughtspace.

Can a computer model prevent a war? It is compelling to imagine what the world look like today had such software been available during historical asymmetric conflicts, such as between the Greeks and Persians at Thermopylae, or the Rebels and British during the Revolutionary War. Few would deny that war is an existential reality of the human condition, but Rozenblit acknowledges that this project is entering the realm of science fiction. “It is very intellectually stimulating and goes well beyond the normal focus of engineering,” he says. “A lot of it is discovery and creation, so it’s fun.”

The American Revolutionary War was an asymmetric conflict. The British surrender to combined French and American forces on Oct. 19, 1781, shown here in John Trumbull’s “Surrender of Cornwallis at Yorktown,” essentially ended the war.

Rozenblit envisions the ATRAP software as a tool that will allow opposing groups to sit down at the negotiating table and rationalize particular approaches to achieving peace. “I call it CPR, which in this case stands for conflict prediction and resolution,” Rozenblit says. “Ultimately, these mathematical tools are intended to generate solutions that give us equilibrium, or status quo solutions.”

Such solutions require that multiple parties sit around the negotiating table and try to reach a win-win situation, says Rozenblit. “These tools allow us to compute measures that don’t necessarily maximize reward,” he says. “Instead, the tools can be used to convince negotiating parties that it would not be in their interest to deviate from the proposed solution because they would actually lose more than they gain.”

Phase 1 of the project involved “designing the blueprints of the system,” says Rozenblit. “We assembled a very strong team of software developers, engineers and architects to set up a solid foundation on which to build the suite of software tools, and to provide a springboard from which we can do very advanced research.” This advanced research will be the focus of phase 2.

Brian Ten Eyck, director of research support in the Department of Electrical and Computer Engineering, describes the main planks of the research as “behavior modeling” and “entity extraction.”

ATRAP’s three-dimensional behavior modeling is based on maps—satellite images, for example— with two dimensions: latitude and longitude. The third dimension, time, is added to create what Ten Eyck describes as a “thought space.”

This third dimension consists of people, groups and events and their locations in time, but also more abstract entities such as relationships and affiliations. “There’s a person here, there’s an organization there, an explosion took place here,” says Ten Eyck. “These things are all connected and the thought space shows you lines that connect the place where the bomb blew up and where the bomb-maker lives, for example. And there’s a slider that lets you move back and forth through time so you can see how events unfold or change over time in a particular region.”

Creating software that can compute these abstract entities is “very, very tough,” Rozenblit adds. “How do you express the level of affinity between certain groups of people?” he asks. “If they are related, maybe that affinity stems from their blood relationship. If they are friends, maybe it’s the years that they have spent together.” To understand these group dynamics and the complexities of modeling political conflicts, which Rozenblit calls “soft factors,” the ATRAP team has enlisted help from the political science department and Eller College of Management.

“A lot of research is going into these soft factors,” says Ten Eyck. “It will enable us to overlay a sort of behavioral filter and understand these cultural affinities, and understand the technical capabilities and financial resources of different organizations.” This understanding already has created the ability, albeit rudimentary, says Ten Eyck, to predict potential courses of action.

The “entity extraction” referred to by Ten Eyck describes software that can parse text and extract meaningful information. “News bulletins, intelligence reports, e-mails—terabytes of data, more than any human can read—are constantly streamed into the database,” says Ten Eyck. “The software can pull out the name of somebody, his or her title, the fact that they work for this organization, that they were born in this location, whatever the content of the message may be. It’s not a hundred percent foolproof, which is why it’s being researched. We’re trying to improve the ways that machines can extract those entities, possibly even connect them, link them together.”

ATRAP’s potential spreads far beyond the limits of defense, says Rozenblit, into the financial world, for example, “to combat financial fraud.” He also cites disaster relief and epidemiology as areas that could benefit from ATRAP’s analytical and mapping capabilities. Ten Eyck points out that the project as a whole fulfills UA’s land-grant mission. “We are engaging software developers here in the community,” he says.

Ten Eyck is referring to Ephibian, a Tucson-based software development firm that works closely with the ATRAP research team to bring its ideas to fruition. A few College of Engineering alumni founded Ephibian after working together on highly complex multimillion-dollar software projects in the U.S. Army. Rozenblit describes Ephibian as “the Maserati of software writing” and says: “For our students, working with a professional software engineering company of this caliber is the best internship you can imagine.”

“The project represents net new dollars to the region, it’s interdisciplinary and it’s putting students in touch with corporations that can offer them jobs once they get their degrees,” Ten Eyck says. “It’s doing all the things that the university is chartered with doing.”

University of Arizona College of Engineering
Department of Biomedical Engineering 1127 E James E. Rogers Way P.O. Box 210020 Tucson, AZ 85721-0020