September 2009

September, 2009 The Pioneer Newsletter is brought to you by the students, faculty, and staff of the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University. The newsletter staff and its collaborators strive to bring you the latest news from all aspects of the BME community. To submit articles, opinions, ideas, or events for publication and for more information about the newsletter, please visit: www.bmes.gatech.edu/newsletter

Inside this issue: The Successful BME Student: Tips From Paul Fincannon

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Pre-Health Column: Your Monthly Advice From Jennifer Kimble

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Student Spotlight: Abhay Kulkarni

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caCORRECT and 9 omniBioMarker: Cancer Biomarker Identification Software Tools Earn Certification The Biotechnology Career Fair: An Inside Scoop

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Faculty Spotlight: Stephen DeWeerth

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And More !

Volume IV, Issue 1

Biomedicine in Beijing An Adventure in Peking University

By Rosemary Song

M

y summer in Beijing can be summed up in four words: food, music, shopping and research. While most of my days were spent conducting biomedical research at Peking University (PKU), I was still able to explore Beijing and immerse myself in the culture of a capital city thousands of years old.

As a first year from Augusta, Georgia, this was my first time researching abroad. But I was not alone. Fellow Coulter Department students Helen Xu, Joseph Abrahamson and Nikolaus Shrum joined me for my summer adventure.

Upon our arrival in Beijing, we jumped into collaborative Georgia Tech/PKU laboratories. I explored methods for improving the healing time of bone defects in a joint laboratory led

by Coulter Department professor Barbara Boyan and PKU research professor Haifen Chen. More specifically, I investigated osteoblast proliferation and differentiation via different materials. Graduate student Wang Xiaokun taught me the elec- The Great Wall of China. (Photo: Rosemary Song) trospinning process, which I needed to use to …

Continued on page 8!

MRI Simulation of Blood Flow GT & Children’s Hospital of Philadelphia Develop Virtual Surgery Tool

By Abby Vogel

R

esearchers at the Georgia Institute of Technology, collaborating with pediatric cardiologists and surgeons at The Children’s Hospital of Philadelphia, have developed a tool for virtual surgery that allows heart surgeons to view the predicted effects of different surgical approaches. By manipulating three-dimensional cardiac magnetic resonance images of a patient’s specific anatomy, physicians can compare how alternative approaches affect blood flow and expected outcomes, and …

The Children’s Hospital of Philadelphia.

Continued on page 4!

The Successful BME Student

By Paul Fincannon

Another List from Paul

I

love to make lists. I just burned a CD of 54 songs, all under two minutes. I also recently emailed my “Top Ten” list to the BME undergraduates. Reading my email the last few days, I realized that many students do not share my fondness for lists, as they asked me many questions that would have been answered had they read my email.

But I am not writing to complain about that. I am forging forward with another list.

I call this one “The Successful BME Student”.

Communication Skills Writing well and speaking clearly are essential tools for our students. Employers, grad schools, and professional schools are looking for students who can easily communicate what they know and what they can do for their organization. Team building skills and communication skills are crucial for students trying to get into the workforce. Keep reading, writing critically, doing presentations and practicing these skills. Participate in a mock interview.

Write emails that mimic an office setting: clear, succinct, professional.

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Healthy Living Eat healthy food, exercise to reduce stress, sleep as much as you can, make time for friends. Jim Valvano, the NC State basketball coach who lost his battle with cancer, said: “To me, there are three things we all should do every day. We should do this every day of our lives. Number one is laugh. You should laugh every day. Number two is think. You should spend some time in thought. And Number three is, you should have your emotions moved to tears, could be happiness or joy… You do that seven days a week, you're going to have something special.”

Respect for Your Fellow Students at Georgia Tech My father always told me that anyone we meet can teach us something. Give your fellow students the benefit of the doubt.

Treat each other with respect and an open mind.

Preparation and Flexibility The Boy Scout motto is still a good one.

Be prepared for your classes, your meetings with professors, meetings with myself, Kim and Sally, meetings with your teams in your BME courses, and meetings with student groups you join. It will reduce stress greatly, and position you to be known as a dependable person. Practice being on time for everything, it is a stress reducer and shows others that you care about their time. Be flexible and adaptable to your professors and any situation you face. This mirrors the real world.

Concern About the World At Georgia Tech, where grade inflation is a myth, and you all feel like you have to keep you with the Jones, it’s easy to become egocentric. Fight this. The rest of the world is still out there. Know what’s going on in the news, in the world and in your community. Think about how you can make a difference in your small part of the world. Read a diversity of opinions from a variety of sources. Challenge your solidified beliefs. Don’t be a student who can’t talk about world issues. It’s not all about you.

Experiential Learning Do something besides take classes. Participate in research, internships, co-op, or just volunteer somewhere. Go hear the speakers the BMES brings to campus. Get involved in small ways to better yourself. Be more concerned with learning than grades.

No Freaking Out One of my mottos is that no one has the right to freak out about their life until they are 30 years old. If, by 30, you don’t have any idea what to do with your life, I give you permission to freak out. Until then, chill. Understand the big picture of your life. Many things that happen to you aren’t really as important as you might think in the grand context of your long life. Learn to relax and enjoy everyday. Another motto is “It can always be worse”. As long as you are walking the planet, whatever bad is happening to you can always be worse. There are always people in worse shape than you. Embrace your life as it is and be happy to wake up each day.

Be Honest with Your Parents Always. About as much as you can. No matter how bad it is, being truthful is better than living a lie. And less stressful. They may be disappointed sometimes, but they still love you first and foremost.

Embrace Faculty Faculty are here to teach and guide you.

They enjoy working with students or they would not be here. Yes, many of them are research driven, but they are ambitious, just like you. Getting a job with BME at Georgia Tech means that they are among the top in their profession. They love students who match their enthusiasm and interest for their work. Approach them, use them, listen to them.

In class, adapt to what they want, get out of your box. It may not always be a warm and fuzzy relationship, but interaction with faculty will greatly enhance your time here at Tech and could influence your future as well. Remember, they were in your position not long ago!

Get Out of Your Comfort Zone, Face Challenges Study abroad. Do internships and co-ops outside of Georgia, or your home state.

Join a club you know nothing about. Make yourself do things that make you uncomfortable. Join Toastmasters. Look at the global job market.

Practice Reality Therapy Reality Therapy, as developed by Dr. William Glazer, essentially says that we are all responsible for our own choices. The past may influence us, but we aren’t victims of our past unless we choose to be. Constantly ask yourself these three questions: What do I want? What am I’m doing to help me get what I want? Is it working?

Stay in touch with the academic office. Sally, Shannon, Kim and I are here to serve you. Come see us often.

THWG Start and end each day saying: “To Hell with Georgia”

Pre-Health Column This Month’s General Advice for All Pre-Health Students

W

elcome to Georgia Tech! I hope this semester goes very well for you!

As the Director of the Office of Pre-health Advising, I meet many successful pre-health students each year. One of the common traits of these students is that they are proactive. They do not sit back and wait for opportunities to fall into their laps; they go out and try to make opportunities happen. One of my favorite aspects of engineering education is the problem solving skills that are the cornerstone of the experience. So, combining that with the proactive nature of successful prehealth students, I expect great things from you during your time at Tech!

This fall, set some personal goals for you to accomplish. One of these goals should be to get your academic house in order. Make it a goal to have a minimum term GPA of a 3.6. To accomplish this, you may need to take advantage of the Academic Support programming offered. Go to office hours and start a study group.

There are some great workshops scheduled: time management, study skills, test taking, for example. In addition, they also offer one-on-one tutoring.

Get to know your faculty members. If you add the “Office of Prehealth”

to your T-Square account, you can read a tip sheet that your faculty helped me craft with tips to have them get to know you. I cannot tell you how many students over the years have done really well in the classroom, went to collect letters of evaluation from professors, and received weak letters. Not bad letters, but letters that basically said “Susie was a student in my class.

She made an ‘A’ and seemed nice. Let me know if you have any questions.” The student never allowed the faculty the opportunity to get to know her. Considering how competitive professional school is, a letter like this could very well prevent a student from being accepted.

If you are pre-health and not connected with my office, please do so ASAP! To register for the listserv, please go to the listserv website and sign up for the pre -health mailing list. You might want to join the American Medical Student Association (AMSA) if you are not already a member.

We also have a Pre-Dental Society and a Pre-Pharmacy Student Association. In order to make an individual appointment with me, you need to have attended a Mandatory Pre-Health Workshop. If you attended one last year or attended my FASET session, you are cleared for the remainder of your time. The next work-

By Jennifer Kimble shop will be Monday, September 21st at 5:00 PM in the Festival Level (Basement) of the Student Success Center. I do walk-ins for quick questions and do not require that you attend a workshop. You can come to walk-ins on Wednesdays from 1:00-3:00 PM and Fridays from 3:00-5:00 PM. Please contact me if you have any questions! My information, along with other important links, can be found below: Academic Support www.success.gatech.edu Listserv http://lists.gatech.edu/sympa Pre-health Mailing list pre-health@lists.gatech.edu AMSA Website www.amsa.gatech.edu Pre-Dental Society Email abhatnagar@gatech.edu Pre-Pharmacy Student Association http://cyberbuzz.gatech.edu/ppsa/ index.html Jennifer Kimble jennifer.kimble@carnegie.gatech.edu 404-385-2475

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MRI Simulation of Blood Flow ... can select the best approach for each patient before entering the operating room.

“This tool helps us to get the best result for each patient,” said co-author Mark A. Fogel, M.D., an associate professor of cardiology and radiology, and director of Cardiac MRI at The Children’s Hospital of Philadelphia. “The team can assess the different surgical options to achieve the best blood flow and the optimum mixture of blood, so we can maximize the heart’s energy efficiency.”

In the August issue of the Journal of the American College of Cardiology: Cardiovascular Imaging, the researchers describe the surgical planning methodology, detailing how the tool helped them to plan the surgery of a four-year-old girl who was born with just one functional ventricle, or pumping chamber, instead of two.

From Page 1

gen-rich and oxygen-poor blood mix in their one functional ventricle before being redistributed to their lungs and body.

To correct this, the children undergo a series of three open-heart surgeries—called the staged Fontan reconstruction—to reshape the circulation in a way that allows oxygen-poor blood to flow from the limbs directly to the lungs without going through the heart. While these vascular modifications can eliminate blood mixing and restore normal oxygenation levels, surgeons and cardiologists must ensure that the lungs will receive proper amounts of blood and nutrients after the surgery so that normal development occurs.

“Preoperatively determining the Fontan configuration that will achieve balanced blood flow to the lungs is very difficult and the wide variety and complexity of Georgia Tech Regents’ Professor Ajit Yoganathan led an effort to develop a surgical planning framework that allows surgeons to virtually perform surgeries, assess the predicted outcomes and select the best approach for each patient.

(Top) 3D model of hepatic flow distribution pre-surgery. (Bottom) Post-surgery hepatic flow distribution options. The surgeon ultimately selected the third option. (Image courtesy of Ajit Yoganathan)

Two in every 1,000 babies in the United States are born with this type of single ventricle heart defect. These children typically suffer from low levels of oxygen in their tissues because their oxy-

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patients’ anatomies requires an approach that is very specific and personalized,” said Ajit Yoganathan, Ph.D., Regents’ Professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech

and Emory University. “With our surgical planning framework, the physicians gain a better understanding of each child’s unique heart defect, thus improving the surgery outcome and recovery time.”

The patient described in this article, Amanda Mayer, age four, of Staten Island, N.Y., had previously undergone all three stages of the Fontan procedure at The Children’s Hospital of Philadelphia, but developed severe complications. Her oxygen saturation was very low—only 72 percent, compared to normal levels of at least 95 percent—which indicated the possibility of abnormal connections between the veins and arteries in one of her lungs.

Normally, the liver releases hormonal factors that prevent these abnormal connections, so the presence of the malformations indicated a low supply of hepatic blood to the lung.

To improve the distribution of these hormonal factors to both lungs, the surgeons needed to re-operate and reconfigure the patient’s cardiovascular anatomy.

Georgia Tech’s surgical planning framework helped Thomas L. Spray, M.D., chief of the Division of Cardiothoracic Surgery at Children’s Hospital, to determine the optimal surgical option.

“MRI acquires images of the child’s heart without using radiation,” said Spray. “Then we use the computerized technology to model different connections to simulate optimum blood flow characteristics, before we perform the surgery.”

The image-based surgical planning consisted of five major steps: acquiring magnetic resonance images of the child’s heart at different times in the cardiac cycle, modeling the preoperative heart anatomy and blood flow, performing virtual surgeries, using computational fluid dynamics to model the proposed postoperative flow, and measuring the distribution of liver-derived hormonal factors and other clinically relevant parameters as feedback to the surgeon.

Fogel collected three different types of magnetic resonance images, and Yoganathan, along with graduate students Kartik Sundareswaran and Diane de Zélicourt, generated a three-dimensional model of the child’s cardiovascular anatomy. From the model they reconstructed the three-dimensional pre-operative flow fields to understand the underlying causes of the malformations.

For this particular patient, the team saw a highly uneven flow distribution—the left lung was receiving about 70 percent of the blood pumped out by the heart, but only five percent of the hepatic blood. Both observations suggested left

lung malformations, but closer examination of the flow structures in that particular patient revealed that the competition between different vessels at the center of the original Fontan connection effectively forced all hepatic factors into the right lung even though a vast majority of total cardiac

lations on all three options to investigate for each how well blood would flow to the lungs and the amount of energy required to drive blood through each connection design. These measures of clinical performance allowed the cardiologists and surgeons to conduct a risk/benefit analysis, which also included factors such as difficulty of completion and potential complications.

Of the three choices, Spray favored the option that showed a slightly higher energy cost but exhibited the best performance with regards to hepatic factor distribution to the left and right lungs. Five months after the surgery, Mayer showed a dramatic improvement in her overall clinical condition and oxygen saturation levels, which increased from 72 to 94 percent. Mayer is breathing easier and is now able to play actively like other children, according to her cardiologist, Donald Putman, M.D., of Staten Island, N.Y. “The ability to perform this work is a team effort,” Fogel added. “State-of-the -art three-dimensional cardiac MRI married to modern biomedical engineering and applied anatomy and physiology enabled this approach. With the advanced pediatric cardiothoracic surgery we have here at The Children’s Hospital of Philadelphia, patients can benefit from this new method.”

“ The ability to perform this work

is a team effort… State-of-the-art cardiac MRI married to modern biomedical engineering enabled this approach.

”

output went to the left lung.

To facilitate the design of the surgical options that would correct this problem, Jarek Rossignac, Ph.D., a professor in Georgia Tech’s School of Interactive Computing, developed Surgem, an interactive geometric modeling environment that allowed the surgeon to use both hands and natural gestures in three-dimensions to grab, pull, twist and bend a threedimensional computer representation of the patient’s anatomy. After analyzing the three-dimensional reconstruction of the failing cardiovascular geometry, the team considered three surgical options.

The research team then performed computational fluid dynamics simu-

Student Spotlight: Abhay Kulkarni SURFing His Way Through Mayo Clinic

S

enior Abhay Kulkarni is a busy guy. As team leader for GT 1000 and vice president of youth outreach, he still took time out from his busy schedule this summer to conduct biomedical engineering-related research at the Mayo Clinic in Rochester, Minnesota.

Kulkarni was selected for the tenweek-long Mayo Summer Undergraduate Research Fellowship (SURF) program. At the Mayo Clinic, Kulkarni’s research focused on osteogenesis, which is the process of bone regeneration. Under the mentorship of spinal surgeon and biomedical researcher Michael Yaszemski, M.D., Kulkarni researched the effectiveness of polyanhyrides in delivering growth factor proteins to the site of a bone defect. Throughout his time at the Mayo Clinic, Kulkarni learned about biomedical engineering and the dynamics of working in a group com-

posed of individuals with a variety of academic and cultural backgrounds.

It’s hard to believe that a few years ago, Kulkarni was just another freshman from Alabama. Similar to many incoming biomedical engineering majors, Kulkarni believed that biomedical engineering would provide him with the best training and exposure to various principles applied in the medical field. Kulkarni took advantage of what Georgia Tech and the biomedical engineering program had to offer, leading him to opportunities he could not even imagine before he came to Georgia Tech.

He described his experience at the Mayo Clinic as “one of the most educational experiences” in his life. “I was able to take part in great biomedical research… The experience really broadened my horizons,” remarked Kulkarni.

By Nancy Kim

Kulkarni spent 10 weeks at the Mayo Clinic performing real world research under top-notch scientists.

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September Events September 1st - BMES: Fall Kickoff Join the Biomedical Engineering Society (BMES). Free pizza, games, music, and receive or renew your BMES membership! 4:30-7:00 PM, Biotechnology Courtyard behind Whitaker. st

September 1 - SABUR: Kickoff Meeting Attend the Student Activities Board for Undergraduate Research (SABUR)’s first meeting! 11.00-12.00 PM, Student Center 319. st

September 1 - Undergraduate Research Workshop Learn more about how to become involved in undergraduate research! 4:00 PM to 5:00 PM, Student Center Room 319.

September 1st - NSF Funding for Graduate Students Attend this information session to find out more about the National Science Foundation Graduate Research Fellowship! 11:00 AM, Piedmont Room, Student Center.

September 17th - BMES: Medtronic Seminar Join BMES and this Medtronic Seminar! 11:00-12:00 PM, more info at www.bmes.gatech.edu.

September 18th - BMES: FDA Seminar Join BMES and this FDA Seminar! 10:00-11:00 AM, more info at www.bmes.gatech.edu.

September 21st - Mandatory Pre-Health Workshop Attend this mandatory pre-health workshop to find out general tips and advice for applying to health-related professional schools!

5:00 PM, Festival Level (Basement) of the Student Success Center.

September 7th - Official School Holiday

September 22nd - Pre-Health Interview Workshop Applying for medical school this year? Attend Jennifer Kimble’s workshop to learn more about interviewing skills! You may also schedule a mock interview with Ms. Kimble after attending this session. 5:00 PM, Pres. Suite A in the Student Success Center.

September 8th - ChBE Seminar, Paul Doetsch, PhD Join Professor Paul Doetsch from Emory University in his seminar “A New Paradigm for Regulation of Eukaryotic DNA Base Excision Repair via Dynamic Compartmentalization.” 3:00-4:00 PM, MS&E 3201A.

September 24th - PURA Information Session Interested in being paid for research? Find out more about the President’s Undergraduate Research Award! Eligibility, timing, and application tips will be discussed. 11:00 AM to 12:00 PM, Student Center Room 301.

September 8-9th - Resume Blitz Have your resume critiqued by an experienced employer! All BMEs should bring their resumes to Whitaker Rooms 1118 & 4101 and IBB Rooms 1316 & 1317 between 10:00-3:00 PM!

September 24th - BMES: Work Abroad & Co-Op Join speakers Debbie Gulick of the GT Work Abroad Program and Rob Rogers of the GT Co-Op Program and learn about available opportunities for BMEs! Free pizza. 11:00 AM to 12:00 PM, Whitaker Room 1103.

September 10th - ChBE Seminar, Milan Mrksich, PhD Join Professor Milan Mrksich from the University of Chicago in his seminar “Tailored Substrates for Cell Biology.” 3:00-4:00 PM, MS&E 3201A. September 14th-15th - Georgia Tech Career Fair Open to Tech faculty, students, and alumni only! Attend this year’s career fair by bringing your Buzzcard to the Campus Recreation Center (CRC) between 10:00 AM and 4:00 PM! September 15th - IBB Breakfast Club: Melissa Kemp, PhD Open to all faculty, postdocs, research scientists, graduates and undergraduates. Join Melissa Kemp, PhD, from the Department of Biomedical Engineering on her seminar “Redox Regulation of Signaling Proteins: A Systems Biology Perspective” at 8.30-9.30 PM, IBB 1128.

September 16th - Edward Life Sciences Info Session Join Janine Edwards and fellow GT BME Grads in their talk about this California-based company. 5:00-6:00 PM, Suddath Seminar room (IBB 1128).

September 17th - GT Biotechnology Career Fair Located in the Molecular Science and Engineering (MS&E) building between 1:00 PM and 5:00 PM, bring your Buzzcard and attend numerous career development events, seminars, and company presentations in the biotechnology field.

September 17th - Bioengineering Seminar Please join Mahendra S. Rao, M.D., Ph.D., in his seminar entitled, “Scalable Manufacture of Stem Cells,” beginning at 11:00 AM in the Suddath Seminar room (IBB 1128).

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September 29th - What Makes a Great Mentor Workshop Join us as we cover the “basics” of mentoring undergraduates in research in this interactive session. We’ll discuss timely tips, provide a set of key resources, and hear directly from students and experienced mentors. 11.00 AM to 1.00 PM, Klaus Room 1116E. RSVP by 09/22: http://fall09mentoringworkshop.eventbrite.com/ September 29th - Contemporary Issues of Biomedical Informatics Join Dr. Mark Braunstein, associate director of the GT Health Systems Institute, in his talk entitled “Contemporary Issues of Biomedical Informatics.” For more information, go to: www.gatech.edu/calendar/event.html?id=4654 September 29th - NSF Funding for Graduate Students Attend this information session to find out more about the National Science Foundation Graduate Research Fellowship! 11:00 AM, Crescent Room, Student Center.

October 1st - BMES: General Meeting & Elections Come to the first BMES general meeting of the year! A special election will also be held. Free pizza. 11:00-12:00 PM, Whitaker 1103.

October 3rd-6th - Fall Student Recess

To submit events and other important dates, please email to: bmed.newsletter@gmail.com! *Events subject to change. For more information, please check www.gatech.edu/calendar, www.bme.gatech.edu/calendar, and www.ibb.gatech.edu/events.

Join the Georgia Tech Biomedical Engineering Society today! Meet new people in your department, learn about the biomedical engineering industry, and attend numerous seminars hosting BME alumni and company representatives from around the country!

Fill out an application now! More info can be found at: www.bmes.gatech.edu.

BMES T-Shirt Design Contest Design the 2009-2010 BMES T-Shirt! There will be a reward for the designer of the chosen shirt. For submissions or more information, please contact: bmes@gatech.edu!

Featured Scholarship: Petit Undergraduate Research Scholars The Petit Undergraduate Research Scholars is a competitive scholarship program that allows undergraduates to conduct independent research in the laboratories of the Parker H. Petit Institute for Bioengineering and Bioscience. The program serves to develop the next generation of leading bioengineering and bioscience researchers by providing a comprehensive research experience for an entire year. The Scholars are mentored by top graduate students and postdocs in state-of-the-art laboratories and will develop their own research project. The Petit Undergraduate Research Scholars Program runs from January to December 2010. Deadline: September 15th. For more information, please check: www.ibb.gatech.edu.

interested in a rewarding health-related career A rethatyouservices the community? Well then, the Ameri-

can Medical Student Association (AMSA) is the club for you! The GT AMSA chapter is a student-run organization that caters to the needs of pre-health students interested in pursuing a career in healthcare. With over 500 members this year, AMSA serves as one of the largest preprofessional organizations at Georgia Tech.

AMSA provides a supportive network for prehealth students by building connections in the healthcare field through personal guidance, volunteer opportunities at hospitals and other social gatherings. These events include: volunteering at Medshare, visits to medical schools, banquets, pre-health conferences, and seminars hosted by admission directors from the University of Chicago, Duke, Emory, and more!

GT AMSA is dedicated to not only meeting the needs of pre-medical students at Tech but also providing information about alternative healthcare careers. Last year, AMSA hosted admission directors from osteopathic medical schools, optometry schools, pharmacy schools, and podiatry schools.

This year, the GT AMSA chapter will be involved in planning the Regional 5, 7 & 9 Conference at Emory University held at Emory from October 17-19th. The Georgia Tech conference will be held in the spring time.

So, whether you want to become a doctor, a dentist, a pharmacist, or a vet, AMSA will be extremely beneficial to your pre-health career! To find out more information about joining AMSA, please visit: www.amsa.gatech.edu.

Interested in promoting undergraduate research on campus or in attending meetings with presentations on topics related to research? Then check out GT’s Student Activities Board for Undergraduate Research (SABUR). The group’s first meeting of the Fall ‘09 will be Tuesday, September 1st, 11:00-12:00 PM, Student Center Room 319. Pizza and Drinks will be provided! Please visit http://undergradresearch.gatech.edu/StudentAdvisoryGroup.php or contact us via email at gt.sabur@gmail.com for more information!

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Biomedicine in Beijing

From Page 1

which electrified the crowd and had us all microarrays identify bioactive cues for begging for more. diagnostics.

When we weren’t listening to Nick worked on two different great live music, Helen and I spent time projects in PKU associate professor Yanyi shopping. With the great exchange rate Huang’s laboratory. In testing the alignand street vendors pushing you to buy ment of human umbilical vein endothelial eight pairs of socks for 10 renminbi (or cells (HUVEC) under lami$1.50 U.S. dollars), shopping was one of nar and oscillatory sheer our favorite activities. We also spent time stress, he learned cell eating. Occasional Russian restaurants culturing and LabVIEW aside, my favorites were the street-side programming to create pancakes and lamb skewers. If you ever the flow conditions. Then visit Beijing, I recommend eating peking Nick independently investigated platelet and endoduck and zhajiang noodles. thelial cell interaction unAs a member of the first group of der oscillatory flow condiGeorgia Tech students to visit PKU and tions. conduct research in their laboratories, I had a fantastic experience in Beijing. I Although we caught an enticing glimpse of what the conducted a lot of research, we still found time to explore the vivacious nightlife and thriving underground music scene in Beijing.

Taking the subway to Georgia Tech/Emory/PKU Biomedical Engithe liveliest street of resneering Joint Ph.D. Program will be like for taurants in Beijing, we graduate students. Based on my experience walked under hundreds of SEM image of titanium dioxide scaffold. Rosemary and her group were involved this summer, I will definitely consider that red lanterns strung across in different multidisciplinary research projects in Peking University. (Photo: Roseprogram in the future. I thank Georgia the sidewalk, while hosts mary Song) Tech for giving me this amazing opportuand waiters tried to entice nity, which opened the world to me. No us to enter their restaurants by shouting during bone development. Such a natural matter how many places I travel to, Beijing out the restaurant menus. Eventually a environment is predicted to enhance cell will always be at the top of my list of favorgreen building framed by red and yellow growth and differentiation. The titanium banisters caught our attention. It was Trakdioxide samples I created will be used in ites. tirr Pushkin, a Russian restaurant tucked professor Boyan’s lab to further investigate amongst all of the traditional Chinese the differences in osteoblast growth and restaurants. After a delicious meal of differentiation on the three-dimensional chicken kiev, steak wrapped in bacon, and two-dimensional scaffolds. With the potato pancakes and traditional Russian optimal surface and mechanical properties, ice cream for dessert, we were almost the construct can be implanted at the site too full to get up and see the concert we of a bone defect to improve healing time. planned to attend.

Helen, Nick and Joe also tackled After some directional confuresearch projects of their own. Joe consion, we spotted a couple of people with ducted research in a laboratory led by instruments heading toward a drive-in Coulter Department professor Xiaoping theater and we could hear faint music Hu and PKU associate professor Jue playing from the other side of a grove of Zhang. Joe analyzed functional MRI brain trees. Turning the corner, we headed into images in order to determine the effects of a small building surrounded by trees with acupuncture on the brain. a courtyard covered by a canopy of white For her research project, Helen Christmas lights. A packed audience created carbohydrate microarrays in Coulrocked in Chinese and English with a band ter Department associate professor Julie called DH & Chinese Hellcats. Then SUBS Babensee’s laboratory. Helen’s responsibiliscreamed their hearts out and was folties were to fabricate microarrays and lowed by Ziyo. The lead singer’s shiny learn macromolecule immobilization techmetallic leggings were only outdone by niques for future examination of dendritic the guitarist’s bell fringed cow hat. The Rosemary Song enjoys the many sights and wonders of cell responses at Georgia Tech. These band finished with the song “Take it Off,” China. Shown above is the Forbidden City located in Beijing. ...create three-dimensional titanium dioxide nanofiber scaffolds. In contrast with twodimensional surfaces, three-dimensional scaffolds allow cell growth in three dimensions, and their nanofibers mimic the natural collagen matrix osteoblasts secreted

“ Beijing will always be at

”

the top of my list of favorites.

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caCORRECT and omniBioMarker Cancer Biomarker Identification Software Tools Earn Certification

T

he explosive growth of genomic and proteomic data has ushered in a new era of molecular medicine in which cancer detection, diagnosis and treatment are tailored to each individual’s molecular profile. But this personalized medicine approach requires that researchers discover and link biomarkers—such as genes or proteins—to specific disease behaviors,

“Certification by caBIG means the tools can be easily used by everyone in the cancer community to improve approaches to cancer detection, diagnosis, treatment and prevention,” said Wang, an associate professor in the Coulter Department and a Georgia Cancer Coalition Distinguished Cancer Scholar. caBIG is a collaborative informa-

By Abby Vogel caCORRECT and omniBioMarker passed a rigorous set of requirements, ensuring the cancer research community that the software tools are high quality and interoperable with all other caBIG-certified systems for nationwide deployment. caCORRECT—chip artifact CORRECTion—is a software program that improves the quality of collected microarray data, ultimately leading to improved biomarker selection. Widely used Affymetrix microarrays contain thousands of probes, each including a 25-oligo sequence, which are used to detect mRNA expression levels.

“Once someone has collected microarray data, it is important to run quality control on it and remove any problematic points of data that could highlight incorrect biomarkers when analyzed,” explained Wang, who is also director of the biocomputing and bioinformatics core in the Emory-Georgia Tech National Cancer Institute Center for Cancer Nanotechnology Excellence (CCNE).

Associate professor May Dongmei Wang (left) recently received silver-level compatibility certification for two software programs that improve the process of identifying cancer biomarkers from gene expression data. (Photo: Gary Meek)

Richard Moffitt, Martin Ahrens, May Dongmei Wang and Todd Stokes (right) developed caCORRECT, software that improves the quality of collected microarray data, ultimately leading to improved cancer biomarker selection. (Photo: Gary Meek)

such as the rate of tumor progression and different responses to treatments.

Two new software programs that help address that challenge have recently earned silver-level compatibility certification from the National Cancer Institute’s cancer Biomedical Informatics Grid®, also known as caBIG®. The programs improve the process of identifying cancer biomarkers from gene expression data Developed by May Dongmei Wang and her team in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University, the programs—caCORRECT and omniBioMarker—remove noise and artifacts, and identify and validate biomarkers from microarray data. Funding to develop the programs was provided by the National Institutes of Health, the Georgia Cancer Coalition, Microsoft Research and Hewlett-Packard.

tion network that enables researchers, physicians, and patients to share data, tools and knowledge to accelerate the discovery of new approaches that they hope will ultimately improve cancer patient outcomes. To become caBIG-certified,

Since each microarray chip contains thousands of spots, it is easy for a few spots to become marred by artifacts and noise. These unusable portions are typically the result of experimental variations by different laboratory technicians or er-

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rors that create scratches, edge effects and bubble effects on the data. caCORRECT removes the noise and artifacts from the data, while retaining high-quality genes on the array. The software can also effectively recover lost information that has been obscured by artifacts.

In collaboration with Andrew N. Young, an associate professor in pathology and laboratory medicine at Emory University School of Medicine and clinical laboratory director at Grady Health System, Wang and graduate students Todd Stokes, Martin Ahrens and Richard Moffitt validated the caCORRECT software. A largescale survey of public data and data from Young’s laboratory demonstrated the ability of caCORRECT to assess and improve the quality of a wide array of datasets. “caCORRECT is a quality assurance tool that allows researchers to utilize and trust imperfect experimental microarray data that they spent a tremendous amount of time and money to generate,” added Wang. “caCORRECT improves the downstream analysis of microarray data and should be used before conducting biomarker selection, therapeutic target studies, or pathway analysis studies in bioinformatics and systems biology.”

Once the quality of the data is assured with caCORRECT, researchers can use the caBIG-certified omniBioMarker software to identify and validate biomarkers from the high-throughput gene expression data.

Candidate cancer biomarkers are typically genes expressed at different levels in cancer patients compared to healthy subjects. omniBioMarker searches these groups of patient data for genes with the highest potential for accurately determining whether a patient has cancer. However, because individual genes are not expressed independently, the software also identifies groups of genes that act in concert.

The advantage of the omniBioMarker software is that it fine-tunes biomarker selection to a particular dataset or clinical problem based on prior biological knowledge. It also applies unique analysis parameters for each specific clinical problem. The parameters are optimal when the software selects genes that are known to be relevant biomarkers based on clinical observations and laboratory experiments available in literature and public databases.

Then the software finds new potential biomarkers for experimental validation.

Wang, graduate student John

Phan and Young tested the ability of the software to identify biomarkers in clinical renal cancer microarray data. The researchers selected renal cancer for study because it has several distinct subtypes, which can appear in the same person in varying degrees and must be treated according to the diagnosed subtype to maximize treatment success. The results indicate that integrating prior laboratory and clinical knowledge with the microarray data improves biomarker selection.

“Using omniBioMarker to create an optimal metric for ranking and identifying novel biomarkers reduces the number of false discoveries, increases the number of true discoveries, reduces the required time for validation and increases the overall efficiency of the process,” noted Wang.

Since receiving caBIG silver-level compatibility certification for caCORRECT and omniBioMarker, Wang and her team have been working on getting two more software programs certified—Q-IHC, a tool that analyzes and quantifies multispectral images such as quantum dotstained histopathological images, and omniVisGrid, a grid-based tool that visualizes data and analysis processes of microarrays, biological pathways and clinical outcomes.

Looking for a Job or Internship?

Hit The Georgia Tech Career Fairs

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By Sally Gerrish

th

he 5 Annual Georgia Tech Biotechnology Career Fair will be held on September 17th from 1:00 to 5:00 PM in the MS&E Building. Besides a growing line up of excellent companies, many activities, workshops and information sessions will lead up to the fair. This is an amazing chance to find out about opportunities, connect with companies, and practice that oft mentioned skill: networking. Be sure to check the Biotech Career Fair website for dates, times, and locations! http://careerfair.bme.gatech.edu Submit your Resume Online!

Show you interest, support, and most importantly, how capable and valuable BME students are. Submit your resume online to the BioTech Career Fair resume database.

Georgia Tech Career Fair Be sure to attend the GT Career Fair on September 14-15th, 10:00-4:00 PM at the CRC. For more information about the GT Career Fair and the companies attending, see: http://career.gatech.edu Are you ready to embark on your full time job or internship search? This is the time to start. Take advantage of services offered by the BME department, Career Services and the Division of Professional Practice. Regularly check their web sites for upcoming events, workshops, interviews.

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The Biotechnology Career Fair in the MS&E Building, 2008. Students wait in line with their resumes as they eagerly introduce themselves to several biotechnology company representatives.

Faculty Spotlight: Stephen DeWeerth The Unique Path of a Modern Neuroengineer

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allace H. Coulter Department professor Stephen DeWeerth started college like many students in our department — as a pre-med major. Attending “a small liberal arts college” in Iowa called Wartburg College, he planned to major in chemistry with plans for a M.D./Ph.D. But as his current occupation indicates, plans change.

One summer during his undergraduate career, DeWeerth accordingly conducted research at the Mayo Clinic in a physical biochemistry laboratory. After this summer, DeWeerth concluded that physical biochemistry was not his favorite subject, to say the least. At that time DeWeerth asked the question that all students have asked, are asking or will ask themselves: “What interests me?” For him, the answer was the “intellectual challenge of a Ph.D.” rather than an M.D./ Ph.D. So he replaced his pre-med major with mathematics for his undergraduate degree. This led him to earn a master’s degree in computer science and a Ph.D. in computational neural systems from the California Institute of Technology.

His unusual transition “from a liberal arts with… no electrical background at all to… a Ph.D. doing electronic design” reveals what DeWeerth describes as the “breadth of opportunity” available to students in seeking a graduate degree or other academic routes. This philosophy urges students to honestly evaluate their future paths in light of their interests.

Continuing his philosophy of exploring the “breadth of opportunity,”

Stephen DeWeerth, Ph.D., professor and researcher.

DeWeerth arrived on the Georgia Tech electrical engineering scene with an interest in neuroengineering. An evaluation of neuroengineering on campus revealed very little activity. In fact, DeWeerth recalls a “barren wasteland for neuro[engineering]” at Georgia Tech. At that time, the biomedical engineering department did not even exist.

With the founding of the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University and the creation of the new biotechnology buildings, DeWeerth proposed a collaborative Laboratory for Neuroengineering (NeuroLab). Such a lab would entail shared lab space and principal investigators working together in the field of neu-

By Willa Ni roengineering. But the proposal met resistance. As DeWeerth explains, “Faculty members are used to having their own space both figuratively and literally.” But once the resistance eroded, the “unexpected and surprising” fruits of this pioneering collaboration testify to its success. Collaborative efforts between DeWeerth and Coulter Department associate professor Lena Ting led to the creation of robotic models of postural control.

DeWeerth and Coulter Department associate professor Michelle LaPlaca, a tissue engineer by trade, are even co-directors of a grant after committing to the idea of a Neurolab.

Today, neuroengineering research at Georgia Tech is rising to even greater heights. DeWeerth would like to build upon the success of NeuroLab and develop a campus-wide neurotechnology initiative in the future. A proposal and grant for an institute for neurotechnology are pending. Given the potential to involve “biomedical engineering, electrical engineering, computer engineering, mechanical engineering, applied physiology, and psychology,” DeWeerth looks to apply the same concepts seen in the Neurolabs to “develop something even bigger.”

As students, DeWeerth’s accomplishments serve to inspire and educate.

Peering behind the professor responsible for BMED 3510, students should see a path. And from this path students should take a new outlook on their academic careers and even explore their own “breadth of opportunity.”

Biotechnology Info Sessions: Novozymes Info Session Sept. 16th, 5-6 PM, IBB 1128 Edwards Lifesciences Sept. 16th, 6-7 PM, Whitaker 1103 Medtronic Info Session Sept. 17th, 11-12 PM, Whitaker 1103 FDA Info Session Sept. 18th, 10-11 AM, IBB 1128 WL Gore Info Session Sept. 18th, 11-12 PM, IBB 1128 Be sure to check the Biotech Career Fair website for more updates!

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“That’s So BME!”

By You!

Voices From The Student Body

“It was my first Friday back on campus... I spent seven hours of it befriending an exacto knife, foamboard, Bristol paper, and the senior design lab.”

- BMED 2300 Student “When it rains, I stand inside the door facing Ferst Drive and watch for Stingers. Now that the bus stop has moved, I have farther to run. Sad.” - Umbrella-less “Procrastination is the devil.”

- Regretful One “Two people just walked by with Matlab Tshirts.”

- A Tech Student “BMES meetings = my meal plan.”

- Pizza Lover

“Sorry I didn’t get your email last night…

My inbox was full.”

Staff Members Editors in Chief Chun Yong Willa Ni Staff Writers Rosemary Song Nancy Kim Editors Kanav Jain Advisory Board Rafeed Chaudhury (BMES) Joseph Mets (bmedSAB) Aakanksha Angra (AMSA) Ramya Parthasarathy (SABUR)

Photographers Kiersten Peterson Layout Editors Elysia Hwang Collaborators Paul Fincannon Sally Gerrish Megan McDevitt Jennifer Kimble Adrianne Proeller David Terraso Don Fernandez Abby Vogel John Toon Faculty Sponsor Wendy Newstetter

“The diagonal sidewalk from the entrance of IBB to the entrance of the MS&E is 100 meters. You ask: why do I know?”

- Pedometer Tester

A Couple of Words From the Editors in Chief

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he Pioneer welcomes you back to Georgia Tech and the Wallace H. Coulter Department of Biomedical Engineering. First years, welcome to innovative curriculum and exaggerated horror stories. Creator of those horror stories, welcome back to whiteboard fumes and group dynamics.

As you can see, The Pioneer underwent intensive plastic surgery this summer. And the changes cut past the surface. New features include a calendar of events for the upcoming month, faculty and student spotlights, coverage of events you may have missed, updates from student organizations, and much, much more!

To bring all these great resources together for you, The Pioneer thanks the faculty and staff that worked with the student team over this summer. The editors thank them for their support, enthusiasm, impromptu brainstorming sessions, advice, and time. And this gratitude extends to all the groundwork laid by the founding team of this department. With the innovative curriculum, dedicated professors, and eager students, we have a culture. The Pioneer not only strives to communicate this culture, but to also embrace this unique and oftentimes quirky character we know as BME. So thank you for reading and look forward to an amazing new semester!

Contribute to The Pioneer!

Submit student voices, articles, or join the staff! www.bmes.gatech.edu/newsletter

Yours sincerely,

Chun Yong and Willa Ni Editors in Chief The Pioneer

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