American ingenuity is alive and well in New Jersey. In the spirit of Thomas Edison, university researchers are linking up with practitioners and creating solutions in such areas as medicine, research methods, and carbon nanotubes.

Anant Madabhushi, director of the Laboratory for Computational Imaging and Bioinformatics at Rutgers, has developed a computerized image analysis program called Ibris, which investigates the structure of a breast cancer tumor to determine the best treatment approach.

At the New Jersey Institute of Technology, retired Bell Labs researchers have developed projects after interviewing physicians at the University of Medicine and Dentistry of New Jersey about medical needs. Gordon Thomas, an expert in optics and applied physics, met up with a doctor in glaucoma research who sent him away to create a device that could measure eye pressure at home, through a closed eyelid.

A postdoctoral fellow at Princeton University and her co-inventor, Johannes Dapprich, created a technique for quickly and cheaply marking desired pieces of DNA and then gathering them using magnetic beads.

The work of these inventors and others will be presented at the Regional Commercialization Conference on Thursday, December 9, from 8 a.m. to 3 p.m., at the Friend Center at Princeton University. The event opens with a keynote address by Sandy Wiggins, co-founder and chairman of e3bank. Cost: $80. Visit www.njtc.org.

The conference also features an investment panel on what tech transfer officers and entrepreneurs need to know, moderated by Tony Volpe, CEO of Philadelphia-based law firm Volpe and Koenig. A second panel features entrepreneurs who have successfully accessed resources. It is moderated by Stephen Tang, president and CEO of University City Science Center in Philadelphia.

At the regionalization conference, explains Carl Georgeson, manager of patents and licensing at the New Jersey Institute of Technology, his researchers will be mostly “looking for a licensee or for someone to do further funding of sponsored research as a collaborator going forward.”

The school will be presenting the personal tonometer developed by Thomas, professor of physics and bioengineering, to assess eye pressure, as well as three other projects. One is a smart shunt for the 700,000 adults and children with hydrocephalus, a buildup of spinal fluid in the brain that causes a huge headache. The only way to treat this condition is with a drain, the current version of which malfunctions frequently. The smart shunt that Thomas also developed measures flow and pressure rates in the shunt and will be able to detect problems early on without waiting for a severe headache to evolve, says Georgeson.

#b#Brest cancer detection#/b#. To develop his tumor-imaging project, Madabhushi worked with Shridar Ganesan, a breast cancer oncologist at Robert Wood Johnson Medical Center. “The two of us came up with the Ibris technology together,” says Madabhushi. “He provided the clinical domain knowledge, and I came in with the technical background.”

Currently, says Madabhushi, 200,000 women in the United States are diagnosed with breast cancer yearly. Sixty percent of these — some 120,000 women — have estrogen receptor positive breast cancer, and of that group half will need chemotherapy in addition to treatment with Tamoxifen.

The trick is to distinguish between the women who do and do not need chemotherapy. With Madabhushi’s technique he can glean information up front that allows doctors to make personalized treatment decisions, so that women can avoid the significant side effects of chemo if they don’t need it.

The decision whether to do chemotherapy requires an analysis of 21 different genes. The test, which costs $3,500 to $4,000, yields a risk score from which a physician decides whether to do chemotherapy. But this approach has two principal problems, suggests Madabhushi. The first is expense and the second is that the test requires the biopsy sample to be shipped to a specialized facility, which does the test and communicates the risk score back to the oncologist.

“Our technology involves just image analysis of the breast cancer biopsy specimen,” Madabhushi says. “Our assumption is that if we look at the arrangement of cells, glands, and nuclei, there is specific information encoded in the images of a breast cancer biopsy specimen that allows us to identify whether it is from a tumor that has a good or a bad outcome.”

Based on preliminary data from about 40 patients, Madabhushi suggests that Ibris’ quick and inexpensive process seems to offer a prediction as good as the current method. The technique is also portable and can analyze samples from anywhere in the world. Further, because the Ibris technique only requires looking at the tissue, the technology itself does not disrupt the current clinical paradigm, and clinicians don’t have to change what they do.

Ibris is in the process of generating additional data to evaluate the software’s effectiveness in predicting patient outcomes. Scientists will digitize biopsy specimens from patients whose outcome is already known. “The beauty of the technology is that we can validate it retroactively,” says Madabhushi.

Ibris has been acquiring data through partnerships with the Cancer Institute of New Jersey and the University of Pennsylvania. Already the company has data from more than 100 women and will be able to publish once it has 200, which could happen in the next three to six months.

Madabhushi and his co-founder, research professor James Monaco, are the only employees Ibris has, but if National Institutes of Health funding is confirmed, the firm will be hiring more people. Once in hiring mode, Madabhushi, as a Rutgers faculty member, will disassociate from the company. Madabhushi grew up in Bombay, where his mother, who has a Ph.D. in maternal and child nutrition, is a professor. His father trained as a mechanical engineer and owns a company that exports building materials.

Madabhushi graduated in 1998 from the University of Bombay with a bachelor’s in biomedical engineering. He received a master’s in the same field from the University of Texas at Austin in 2000 and a doctorate from Penn in 2004. In 2005 he became an assistant professor in the department of biomedical engineering at Rutgers.

His decision to pursue biomedical engineering came at a juncture when he was trying to choose between medicine or engineering. “At that point, I felt I wanted to do both,” he says. “I knew if I went into just a medical track, I wasn’t going to be able to do much engineering, but by going into biomedical engineering, I thought I could have my cake and eat it too.”

Madabhushi says he always wanted to be involved in research that translates from the laboratory into making a tangible difference in people’s lives. It may originate in the laboratory, but either through startups or industrial collaboration, he says, the technology ultimately goes to people and patients who need it.

In fact, Madabhushi has been involved in two large industrial collaborations, where the National Institutes of Health funds industry to work together with researchers in academe. Both are $3.4 million, five-year projects; the first between Rutgers, Siemens, and the University of Pennsylvania, and the second between Rutgers, Riverside Research in New York City, Beth Israel Deaconess Medical Center in Boston, and General Electric.

#b#DNA research#/b#. Things have also been cooking at Princeton University. Johannes Dapprich’s research with Michele Cleary of Merck yielded a technique that allows scientists to “fish out a specific sequence from a mixed DNA sample,” Drappich says. He likened it to doing an Internet search — after typing specific search terms into Google, you pull out pages and websites and paragraphs that contain those words and phrases. “The more specific your search term is, the more specifically you can target a document or a website,” says Dapprich.

He also likened his technique to marking pages of interest in a big encyclopedia (the entire human genome) with Post-it notes. In his system these are short, artificial pieces of DNA that flag the DNA segments he wants to capture. He then uses magnetic particles to bind to the tagged DNA segments, which can then be isolated with a magnet.

The advantage of Dapprich’s technique is that it is specific and can capture larger segments of a chromosome. “The analogy for that application is that if you have a patient who has a complex disease and you need to interrogate six or seven positions on the DNA, you don’t want to have to look at the person’s entire genome.” Whereas it might take a day to read a full genome (and cost $7,000 apiece), Dapprich can barcode the desired DNA for each patient and then run 50 to 100 patients together at the same cost.

The technique’s first application was to ensure that what looks like identical tissue between bone marrow or kidney donors and receipients is indeed identical. In about 6 percent of cases, says Dapprich, the DNA looks identical but is not, and the consequences can be deadly for the recipient.

The problem is that humans have two copies of the full genome, one from each parent, and it is difficult to tell whether the tightly wound DNA strands are as alike as they seem. His technique can flag, say, the mother’s strands, gather them with the little magnetic beads, and have a robot use a magnet to pull the mother’s DNA to the side of the tube. This application was licensed to Qiagen, a life sciences reagent provider and maker of DNA-extraction robotics.

Next Dapprich will be peddling his technique to companies that do what is called “next generation sequencing,” a collection of new instruments that can do ultra-high throughput DNA sequences. Dapprich and his partner were able to develop the technology with the help of a $3 million NIH small-business research grant.

Dapprich, who grew up about an hour north of Frankfurt, where his father was a judge, received his undergraduate degee at the University of Gottingen. He earned a master’s in physics at the University of Florida in Gainesville, then a doctorate in physics and biophysics at the Max Planck Institute in Germany.

After completing a postdoctoral fellowship at the Karolinska Institute in Stockholm, he went to work for Seq, a small company that did single-molecule #b#DNA sequencing#/b#. He then moved to Orchid Biosciences, where he soon found himself on the wrong side of a layoff. At that point, the founder of Seq suggested that if he had a good idea, he should start his own company. Princeton University president Shirley Tilghman helped him out by inviting him to work for a year in her lab, where he and Cleary finalized the technology.

#b#Nanotechhnology#/b#. Another project, developed by Somenath Mitra, acting chair and professor and director of the graduate program in environmental science, involves carbon nanotubes, which must be purified and functionalized in order to be useful. Mitra came up with a way to do this using a microwave process that takes 30 minutes rather than the normal three days, and disperses the tubes evenly in a solution. Another professor has used these carbon nanotubes to make small solar cells that would usually require silicon or precious metals.

#b#Cartilage repair#/b#. The last project, developed by Treena Arinzeh, associate professor of bioengineering at NJIT, offers an approach to regenerating cartilage, which does not grow back together after it is broken.

With projects also being offered by Fox Chase Cancer Center, Temple University, the University City Science Center, and the University of Medicine and Dentistry of New Jersey, attendees at the Regional Commercialization Conference will be able to appreciate the creativity of area researchers as they push their projects into an entrepreneurial framework — in a way that would have made Thomas Edison proud.

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