October/November 2005
Irina Conboy is also affiliated with the California Institute for Quantitative Biomedical Research (QB3). |
As we reach middle age, our body starts to fail us. Brittle bones are more susceptible to breaking. Torn muscle is much slower to mend. Organs like the liver can become diseased and stop regenerating themselves. Can our body's natural self-repair mechanisms be reset though? UC Berkeley bioengineer Irina Conboy thinks so. She and her colleagues are developing an injectable nanomaterial that could potentially spur aged organs to heal themselves again.
"The regenerative properties of organs are tied to the behavior of stem cells," she says. "So I focus on what happens to those cells with aging. Why don't they work anymore and can we fix them?"
Stem cells are undifferentiated cells that can self-renew and differentiate into specialized cells of the organ or tissue in which they're found, a liver or muscle for example. Because adult stem cells can renew themselves, they're responsible for maintaining and repairing the tissue or organ.
An electron micrograph of a stem cell. |
The problem is that as the body ages, the molecules that regulate stem cells eventually change and inhibit their regenerative properties. Simply adding a new supply of stem cells to a damaged muscle, for instance, won't work because the foreign environment will interfere with the cells' behavior.
"They'll quickly stop repairing the muscle," Conboy says. "But if you can supplement them with regulatory factors and also protect them somewhat from the aged environment, they'll behave better."
Mouse heart injected with hydrogel specially-prepared to fluoresce red. Scale bar indicates 10 microns. (courtesy Kevin Healy) |
Conboy and colleague Kevin Healy, a professor with joint appointments in Berkeley 's departments of Materials Science and Engineering and Bioengineering, and chemical engineering professor David Schaffer are working on a novel biomaterial with just those characteristics. For several years, Healy and his graduate students have been developing a hydrogel, a polymer-based matrix for directing stem cell growth. At room temperature, the material is flexible. But once it hits body temperature, it stiffens into a scaffold where the cells can grow. The scaffold eventually degrades and is absorbed by the body.
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The beauty of the gel is that various growth factors, peptide sequences, and other biomaterials can be added to the mix to encourage the growth of the stem cells. The stem cell-seeded hydrogel can then be injected directly into the body with a syringe or catheter.
"The hydrogel acts like a protective vehicle for the stem cells," Conboy says. "So for a couple of days, the stem cells are contained in an optimal environment for growth and hopefully they'll regenerate even diseased or old muscle."
Right now, the researchers are conducting in vitro experiments to study how adult muscle stem cells from a mouse behave in gels. Soon though, they hope to transplant the scaffold into young and old animals with muscle injuries in hopes that the tissue will regenerate itself.
According to Conboy, the research could potentially lead to treatments for degenerative diseases like muscular dystrophy and therapies for other tissue such as the brain or circulatory system. The long-term goal is to remove malfunctioning stem cells from an aged or diseased organ, seed them into the hydrogel, and inject the biomaterial back into the body to improve the repair process.
"Right now, our health plateaus before 40 and then begins to drop," Conboy says. "But I'm optimistic that you could actually feel pretty good until 90 or so."
Visualizing Better Human-Computer Interaction
by David Pescovitz
Prior to joining the UC Berkeley faculty, Maneesh Agrawala was a computer scientist with Microsoft Research's Document Processing and Understanding Group. |
When computers and people communicate, something is often lost in the translation. Essentially, computers don't know how we think. UC Berkeley computer scientist Maneesh Agrawala is helping bridge the gap. From designing systems that generate clearer driving maps to software that produces simpler step-by-step assembly instructions, Agrawala's research is about leveraging our understanding of how humans think.
"My interests are in computer graphics and human computer interaction, specifically perception and cognition," says Agrawala, who joined the Electrical Engineering and Computer Sciences faculty this fall.
Agrawala's aim is to tease out cognitive design principles that can be applied to computer graphics software. The key, he says, is to determine how information should be presented to us so that we can most easily perceive and understand it. For example, Agrawala's PhD thesis at Stanford involved the development of a system to draw route maps for driving directions. As soon as he began the research, he realized that a map that's drawn to scale isn't much use when you're actually driving.
"You can't see the main detail that matters to you, the turning points along the route," he says.
Three route maps for the same route rendered by (left) a standard computer-mapping system, (middle) a person, and (right) LineDrive. Note that the handdrawn map was created without seeing either the standard computer-generated map or the LineDrive map. (courtesy the researchers) [view larger image] |
To find out how humans prefer to read a route map, he asked a friend to draw him directions from his house to work. Agrawala immediately noticed that hand-drawn maps are never drawn to scale and that the turning points are very carefully identified. Meanwhile, the lengths of short roads are exaggerated so as not to be missed, and unnecessary information and streets aren't included at all.
After a number of in-depth user studies, Agrawala designed a software package that automatically designs and renders route maps with a distinctly hand-drawn feel to them. The resulting system, called LineDrive, is now implemented on the Microsoft Network's Maps & Directions site.
"LineDrive was designed to show how to get from one place to another, but people want other kinds of maps too," he says. "If I'm going to have a party, I want to show everyone I've invited how to get to my house from all over the city."
At left, a set of TV stand assembly instructions drawn by a participant in Agrawala's study. At right, the assembly instructions generated by the automated system. (courtesy the researchers) |
Agrawala is now working on a system that shows these multiple routes or approaches to a location on a single LineDrive map. The difficulty is that each individual route on a single map can't be rescaled separately from the others.
"The program has to consider all of the routes together in the graphic representation it generates," he says. "That's a much harder problem."
In another project, Agrawala and his colleagues examined the difficulty of assembling consumer products like furniture and toys. The included instructions are often tough to follow. That's because designers lack a set of design principles for producing them, Agrawala says. The researchers' goal was to create algorithms that a manufacturer could use to automatically generate clear assembly instructions. As with LineDrive, the first step was to determine what kind of instructions that humans prefer.
"We gave people a TV stand assemble but did not provide instructions," Agrawala says. "Once they assembled it, we asked to draw a set of instructions that would show another person how to build it."
It turned out that rather than present someone with an "exploded view" showing how an entire TV stand comes together, most people prefer step-by-step instructions with a single part added in each step.
Armed with that information, the researchers implemented the design principles in an automated system. The manufacturer need only enter a limited amount of data such as the geometry of each part, assembly orientation, and the sequence of the steps. The instructions are then automatically rendered in structural or action diagrams. A user study showed that the computer-generated instructions reduced assembly time by an average of 35 percent and cut the number of errors by half.
"With LineDrive and the assembly instructions project, we ask people to draw what's in their heads," Agrawala says. "Then we analyze the drawings to see how people cognitively understand information."
S. Shankar Sastry is the NEC Distinguished Professor of Engineering (Peg Skorpinski photo) |
On a sunny August day at UC Berkeley's secluded Richmond Field Station, several graduate students are erratically running back and forth through an overgrown field. Meanwhile, small unmanned aerial vehicles buzz overhead. The students are playing a game but it's not football, soccer, or some other college sport. They're playing Multiple Target Tracking and Pursuit Evasion Games, and it's serious business. The engineering students and faculty are demonstrating a massive wireless sensor network that's the end result of a multi-year Defense Advanced Research Projects Agency research contract.
"We think that the infrastructure of tomorrow involves large, self-configuring wireless sensor networks for everything from environmental monitoring to the control and security of electric power, water, petroleum, and natural gas systems," says principal investigator Shankar Sastry, director of the Center for Information Technology Research in the Interest of Society (CITRIS).
Launched in 2001, the aim of the Network Embedded Systems Technology (NEST) project was to build an experimental platform to speed the development of sensor network technology. The project is a collaboration between Sastry and electrical engineering and computer sciences professors David Culler, Eric Brewer, Kris Pister, and David Wagner. The research team also included graduate students Songhwai Oh, Phoebus Chen, Shawn Shaffert, Bruno Sinopoli, Jaein Jong, Sukun Kim, Prabal Dutta, Kamin Whitehouse, Gilman Tolle, Jonathan Hui, Jay Taneja, Tanya Roosta, and Bonnie Zhu. Research staff members Mike Manzo and Cory Sharp contributed too.
An "evader" traverses the field of sensors. (Songhwai Oh photo) |
At the heart of NEST are "motes," wireless sensors invented at UC Berkeley that keep a constant vigil on temperature, light, motion, and myriad other factors. Once deployed, the motes self-organize into networks that pass along data, bucket-brigade style, in short hops until the information reaches a central computer for processing. If a mote breaks down, the network routes around it.
In recent years, UC Berkeley engineers have experimented with a wide variety sensor network applications, from smart energy monitoring in homes to detecting the seismic stability of buildings to studying an elusive species of seabirds in their natural habitat. According to Sastry though, the only way the motes will move into mainstream use is if they're "robust, easy to program, and simple to deploy."
The network tracks two individuals moving through the field of sensors. (courtesy the researchers) [view larger image] |
"We set up the NEST demonstration so the stakeholders, the people who would actually use sensor networks, could assess whether the technology really works," he says.
The NEST demonstration involved 573 motes outfitted with passive infrared detectors, microphones, and magnetometers. Distributed over two square kilometers outside, the sensors were solar-powered, remotely programmable, and resistant to most of what nature could throw at them.
"We had to install little protrusions on the motes to keep birds from sitting on the solar cells," Sastry says.
One of the sensor nodes mounted on a tripod. (Songhwai Oh photo) |
In the end, the winner of the Multiple Target Tracking and Pursuit Evasion Games was the network itself. As three graduate students moved through the field of motes, their paths were tracked in real time. Meanwhile, on the screen, simulated "pursuers" stayed hot on their trails. In the real world, the military might use such a network to track enemy forces. Pursuers could be people or robots, Sastry says.
As the games were played, small remote-controlled helicopters and fixed-wing unmanned aerial vehicles (UAVs) buzzed over head, collecting the data from the sensor network. Even zipping by at 55 miles per hour, the UAVs were able to receive the wireless transmissions from the motes.
"In this case, the demonstration was all about chasing people," Sastry says. 'But there is also talk about oil refineries, water supplies, and other operations using sensor networks instead of their existing supervisor control and data acquisition (SCADA) wired systems."
Quickly identifying problems in large-scale infrastructures can be quite challenging, Sastry explains, requiring complicated and expensive hardware. Distributed sensor networks may be a more secure and cost-effective solution for fault detection and diagnosis, he says.
Now that the NEST network has proven itself, Sastry is reluctant to disassemble the system. He's now planning to keep the network alive as a true test bed.
"I want people to do science rather than demos," he says. "How easy is it to reprogram the motes remotely? How will they do out in the field over long periods. We might get some rain showers soon."
Andy Schuler (Ph.D.98 CEE), an assistant professor of civil engineering at Duke University |
Hey there little buddy. If you could play a character on Gilligans Island, who would you be? The Skipper? Ginger? For Andy Schuler (Ph.D.98 CEE), an assistant professor of civil engineering at Duke University, it was the professor, of course. After a fortuitous phone call, he found himself in TBSs reality show The Real Gilligans Island on an uncharted island off Mexico. He was cast as none other than the professor, played by actor Russell Johnson in the original series which ran from 1964-1967.
"The professor really was one of my heroes growing up, and how many people get the chance to walk in their heros shoes, particularly when that hero was on a cheesy sixties sitcom?" says Schuler.
Schuler says his journey from engineering professor to TV professor and back again was a fun, but surreal experience. It all started last summer when he read an email about the shows call for auditions. It sounded interesting and I was curious, so I responded within a few minutes, he recalls. I thought it would be a fun and different thing to do. He called the phone number and was encouraged to send in digital photos and a video. They liked what they saw and heard so they flew me out to L.A. for a screen test. The next thing he knew, he had a plane ticket to Mexico and 10 days off work for the filming.
I didnt know what to expect, he says. I thought we might be shipwrecked and have to build huts and trap animals so I brushed up on my survival skills. But when we got there, theyd built a whole set just like Gilligans Island.
On the reality show, two complete sets of castaways -- two real-life skippers, first mates, millionaire couples, movie stars, farm girls, and professors -- competed as teams, then individually, to be the only castaway left on the island and the winner of a quarter million dollars.
Schuler didnt win -- he lost in a catapult game, but he says he was in it mostly for the experience. During his run, Schuler found himself in a love triangle (one of the Gilligans liked one of the Mary Anns, who liked him), and he became good friends with Gilligan Zach, one of his teammates. They hung out on the beach together and made traps to catch fish. It was a blast, he says.
It was also strange. We were all in costume walking around the set trying to act normal, but there are movie crews, cameramen, and sound guys everywhere. You have a conversation with someone, but youre miked so its all recorded. It was big brother watching you every moment. The whole reality thing is a mix of real moments and edited moments. I was pretty happy with how I was portrayed on it. At the end of the day, it is a business.
Schuler is now back on the job. He says his students and colleagues teased him a little when he got back, though most were interested in his experience. But Schuler says his flirtation with TV is probably over. I dont have an agent and am not planning to try out for anything else, he says. Being a [real] professor is one of the greatest jobs in the world.
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