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Find out how Berkeley professors and researchers are in the forefront of cutting-edge research and promising new discoveries. In ScienceMatters@Berkeley, we showcase scientific research taking place in the College of Letters & Science and the College of Chemistry.
Pulling a Voice out of a Crowd
You’re walking down a city street, and the din is deafening. Car engines roar, bus brakes shriek, and pedestrians are shouting just to be heard. Then, amid the racket, you hear it: someone speaking your name. Berkeley professor of physics Michael DeWeese is studying this remarkable ability to pay attention to certain sounds. His findings promise to improve both hearing aids and hands-free device interfaces in the future.
Michael DeWeese is also a member of the Helen Wills Neuroscience Institute. Photo credit: Vivek AyerThe next time you attend a packed party, take a moment to appreciate the brain’s remarkable listening powers. Its ability to focus in on a particular conversation, while tuning out the surrounding din, is something no artificial device can emulate.
“It’s like when you focus on one voice at a cocktail party,” says Michael DeWeese, a Berkeley professor of physics. “Your brain has top-down executive control that can direct your attention to sounds you want to focus on despite all the distracting sounds in your environment.” DeWeese is working out the neurological mechanisms behind selective auditory attention. His findings could someday generate hearing aids that filter out noise efficiently, but also inspire a whole new generation of voice activated devices.Trained in particle physics, DeWeese might seem an unlikely sort of brain researcher. He chose to study neuroscience, he says, because “I could do both theory and experiments in the same laboratory; it doesn’t require hundreds of people to do a single cutting edge experiment as it often does in particle physics. Also, the questions to me are the most compelling in all of science: discovering how the brain works.”
Auditory attention research, says DeWeese, offers an extraordinary window into the mind. “Attention is probably the best experimental handle we’ve got on consciousness. If I can get some behavioral readout that tells me an animal is paying attention to something, and I can see how its neurons are processing that signal, I can hope to figure out what the neural substrate is for our conscious experience,” DeWeese says.
In his laboratory, DeWeese trains rats to listen for certain sounds while disregarding others. Each subject rat is placed in a chamber punctuated by a row of three small portholes. Then it must respond to sounds such as a high tone versus a low one, or noise from the left hand speaker versus from the right.
Photo courtesy Wikipedia
DeWeese might reward the rat for poking its nose into the right hand porthole when it hears a high tone, and into a left hand porthole when it hears a low tone. In the first set of trials, most of the sounds might come from a speaker placed over the rat’s head, with sounds coming from a speaker behind the animal on a few rare trials. Rats that don’t pay attention to the right location in space are more likely to err and get a “time out,” forcing them to wait before they can initiate the next trail. For the next set of trials, most sounds might come from the speaker placed behind the rat’s head, requiring the animal to shift its focus of attention to a different location in its environment. “That way we can see changes in the way the brain processes the same sounds coming from the same location in space depending on whether it’s paying attention to them or ignoring them,” DeWeese says.
The brain is thought to modulate attention by altering neural behavior. Just as aspirin can increase the amount of stimulus required to make a neuron pass along pain messages, neuromodulator molecules such as acetylcholine can make some neurons more or less likely to relay information about sound stimuli. “There is some change in the internal cell processing of signals,” DeWeese says. “In addition, the transmission of sensory information is gated at the circuit level.” These changes likely occur within many of the neurons in a given circuit, and to different degrees in different brain regions.DeWeese records from neurons that are part of these circuits to determine the roles they play in propagating information. Eventually he plans to observe how such single neurons react during behaviors requiring shifts in attention.
The theoretical arm of DeWeese’s research program includes determining what aspects of sounds are most important to the brain, and how that information is encoded. For example, he is investigating how the mathematical structure of sounds recorded in nature differs from unstructured white noise. With this information, he seeks to predict what types of sounds should elicit the strongest responses from auditory cortical neurons, in a manner analogous to the way some neurons in the visual cortex respond most strongly to seeing edges. His group is also developing powerful machine learning algorithms to fit mathematical models of his neural data and testing whether they emulate actual brain behavior.
Encoding sound efficiently, and ignoring those deemed unimportant, offers strong evolutionary advantages. “It allows the brain to use those operations in a dynamical, smart way. You don’t want to waste your sensory processing resources on sounds that don’t matter,” DeWeese says.
Understanding how the brain normally focuses on sounds could help scientists identify anomalies in those who have difficulty focusing their attention, such as patients with schizophrenia and attention deficit hyperactivity disorder (ADHD). DeWeese’s findings could also contribute to the design of hearing aids and hands-free devices that will respond to nearby voices, and deemphasize background noise. In this way, his work could help even the hard of hearing appreciate a rousing party again.
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A Taste of Andean Culture
Of all of the advances people have developed over the millennia, food plants may be the most important. Humans domesticated wheat, rice, and potatoes; learned to cook and store them; and shipped these staples far and wide to enrich themselves and extend cultural influence. By examining the plant remains on early settlements, Berkeley professor of anthropology Christine Hastorf pieces together how ancient peoples worked, ate, traded and worshiped.
The Jekyll and Hyde Act of Oncogenes
Pull one strand of a spider’s web, and the rest of the silken construction will flex and shake with the strain. The same effect can be seen in the network of genes involved with cancer, says Kunxin Luo, a Berkeley professor of cell and developmental biology. Her work with the protein TGF-beta is laying bare pathways to some of cancer’s biggest culprits.
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Pull one strand of a spider’s web, and the rest of the silken construction will flex and shake with the strain. The same effect can be seen in the network of genes involved with cancer, says Kunxin Luo, a Berkeley professor of cell and developmental biology. Her work with the protein TGF-beta is laying bare pathways to some of cancer’s biggest culprits.
The Jekyll and Hyde Act of Oncogenes
Kunxin Luo is also a cell biologist with Lawrence Berkeley National Laboratory’s Life Sciences Division. Photo courtesy LBNL
In cancer, the protein known as TGF-beta is both a blessing and a curse. Among cells just beginning to turn malignant, it acts as a tumor suppressor, inhibiting their growth. But among later stage cancers, this protein that also regulates wound healing and cellular growth becomes a tumor promoter that provokes metastasis.
How can a single molecule trigger exert such contradictory effects? In fact, genes with such dual roles in cancer may be the rule rather than the exception. “When you inhibit a tumor suppressor, you encourage cancer,” explains Kunxin Luo, “That poses a challenge for treatment.”
A Berkeley professor of cell and developmental biology, Luo studies the cellular signaling pathways turned on by TGF-beta. From the moment this protein binds to a cell, it triggers a number of biochemical changes that have a fundamental effect on cancer protection and promotion. “We study in TFG-beta the complexity of these regulatory processes to develop better means of treating cancer,” Luo says.
TGF-beta receptors interact with intracellular molecules called Smad. When Luo went fishing for molecules that bind to Smad, she netted two proteins of particular note: Ski (named for the Sloan-Kettering Institute, where it was first identified) and its relative, SnoN (Ski-related novel protein N). “They seem to be gold mines of new effects,” Luo says.
Since their discovery some 25 years ago, both have been considered cancer-promoting, or oncogenic. They inhibit TGF-beta’s tumor suppressing qualities, and are expressed in substantial amounts by breast, ovarian, and lung cancer cell lines. Yet when Luo tweaked normal cells to overproduce SnoN and Ski, these changes were insufficient to turn cells malignant.
Realizing the story must be more complicated, Luo shifted gears. She made a version of SnoN unable to interact with Smad, and inserted it into mice. The mutant mice possessed an odd combination of traits: premature aging, cancer resistance, and embryonic brain and blood vessel defects. Some of these features likely stem from a severed connection to TGF-beta activity.
TGF-beta communicates with the cells via receptors and several signaling molecules such as Smad and Sno. These pathways can promote cell proliferation and cancer, or cause premature aging (senescence), inhibiting tumor formation. Image courtesy LBNL
In culture, Luo found, cells from the mutant mice divided only six times rather than the usual ten. This explained the source of the accelerated aging. The cells also churned out high levels of a potent tumor suppressor called p53, which produced cancer resistance.
This was the discovery Luo had been hoping for. It explained how SnoN could both hasten cancer, by inactivating TGF-beta, and check cancer growth, via p53. “What we end up with is a molecule with two different functions,” Luo says.
The finding also helps illuminate the route to malignancy. To develop into full-blown cancer, cells must sustain multiple mutations to overcome the body’s many anti-cancer mechanisms. Luo thinks SnoN serves as one such early-stage defense.
Cells that have just started to become cancerous likely upregulate SnoN, which in turn activates p53. As in the mutant mice, p53 limits the spread of cancer. “The goal of cancers is to get rid of this pathway. And in 60 percent of human cancers, one of those mutations is in p53,” Luo says.
For a cancer cell, mutations that shut down p53 are more advantageous than those that eliminate SnoN. With SnoN intact, or even upregulated, cancers can inhibit TGF-beta’s anti-tumorigenic activity.
TGF-beta receptors interact with signaling molecules called Smad. This model depicts Smad4 interacting with the Ski protein, which in turn affects gene expression in the cell. Image courtesy Kunxin Luo
“We’re finding that such pro- and anti-cancer pathways are not linear; they are networks where many molecules regulate each other. If we want to develop better cancer therapies, we need to know more about these networks that we can selectively inhibit one pathway and not touch the other,” Luo says.
The fact that many oncogenes operate in networks highlights a potential advantage of personalized medicine. Genetic tests that reveal which oncogenes are mutated in a given cancer could identify which pathways are involved and therefore which drugs might be most effective in each case. In other words, scientists could learn how to harness the Jekyll and Hyde tendencies of oncogenes like TGF-beta for healing rather than harm.
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Earthquake simulation shows off
the potential for safer bridges
PEER shake-table demonstration subjects 30-foot span to
Loma Prieta, Northridge, Kobe and Chile temblors
| 27 May 2010
http://tek-tips.nethawk.net/a/gdfdze
With a series of computer-controlled earthquakes, simulating some of the most devastating in recent memory, Berkeley engineers Wednesday showed off new technology designed to keep bridges not just from collapsing in a catastrophic temblor but open to traffic.
A 30-foot scale-model bridge, set up on the shake table (earthquake simulator) at the Richmond Field Station, was the star of the show, put on by Berkeley’s Pacific Earthquake Engineering Research Center (PEER).
In a series of simulated quakes, which ranged from moderate to severe, the bridge trembled, shook and rocked violently— but the deck stayed intact and settled back on its supports after each event.
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Gulf oil spill
ENGINEERING
http://tek-tips.nethawk.net/a/uv3mt7
Robert Bea
Professor, Department of Civil and Environmental Engineering
Home office: (925) 631-1587
E-mail: bea@ce.berkeley.edu
Media relations contact: Sarah Yang, (510) 643-7741, scyang@berkeley.edu
Note: Bea is on sabbatical until January 2011, but he will respond to messages as soon as he can.
Expertise: Bea was a National Academy of Engineering Expert Reviewer on the Department of Interior’s May 27 report on additional safety measures needed to reduce the risk of failures from offshore oil and gas activities. In 2002, Bea and Prof. Karlene Roberts, director of the Center for Catastrophic Risk Management at UC Berkeley, authored a report for BP identifying organizational challenges within the company after a series of acquisitions.
Bea has more than 50 years of experience in engineering and management of design, construction, maintenance, operation, and decommissioning of engineered systems, including offshore platforms, pipelines and floating facilities. Before coming to UC Berkeley, he worked as a consultant with Sohio and BP on the topic of risk assessment and management of offshore oil and gas operations. He also worked with the U.S. Army Corps of Engineers, Shell Oil, Shell Development, and Royal Dutch Shell companies in a variety of engineering, construction, operations, and research assignments around the world.
Can California fix the Delta before disaster strikes?
| 20 April 2010
http://tek-tips.nethawk.net/a/cz0u0p
Sherman Island is a "chokepoint" of highways, gas and power lines typical of the Sacramento-San Joaquin River Delta. Researchers are studying the intersection of such infrastructure systems, which are protected by 1,100 miles of levees, some more than 100 years old. (Animation by Melani King, Graphics by Hulda Nelson)
BERKELEY —When visiting Sherman Island in the Sacramento-San Joaquin River Delta, it is easy to forget the region’s ever-present threat of catastrophic floods and instead revel in the West Coast’s largest estuary, which supports farmers, anglers, and more than 700 native species of plants and animals, including some that are endangered.
"You drive out there and you see that cows are grazing, birds are chirping; but it’s deceptive," said Robert Bea, professor of civil and environmental engineering at the University of California, Berkeley. "As you start to dig in, you find out how incredibly complex and vulnerable we’ve made this place."
At least 220 government agencies have jurisdiction in the Delta, which is home to half a million residents in 25 villages, towns and cities, including Sacramento, Stockton and Pittsburg. The region is under continual threat from floods, prevented only by a vast — and fragile — network of earthen levees.
Sherman Island, said Bea, is an example of a critical chokepoint in the Delta for the tangled networks of highways, railroads, and electrical, gas and telecommunication lines that serve as lifelines for the San Francisco Bay Area and large swaths of the state. The Delta also serves as the hub for aqueducts that channel drinking water for two-thirds of the state’s population — more than 23 million people — and irrigation water for 3 million acres of agriculture responsible for half the nation’s fruits and vegetables and one-quarter of its dairy products.
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In an effort to help lower the cost of pumping fluids through pipelines, U.S. and German scientists have discovered an unlikely solution: adding more turbulence.
By injecting puffs of water into a water pipe, the team completely eliminated turbulence in the pipe.
Intermittent turbulence is shown receding in a simulation of water flowing through pipes as additional turbulence is added.
(Credit: Marc Avila, MPI - DS)
The research could have huge implications in a wide variety of fields. The most immediate beneficiaries could be water utilities and oil companies, but aerospace and ship engineers could use the method to make vessels more fuel efficient. Cardiologists could even tap the findings to keep arteries clear and save lives.
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Robots are great for going where humans can’t, and the cramped confines of municipal water pipes are the perfect example. A new initiative is working on building robots that can access and repair aging water pipes from the inside.
Old pipes are a pressing issue for many cities. The American Society of Civil Engineers which rates the quality of city infrastructure, including water works, estimates that 6 billion gallons of clean drinking water disappears each day, mostly due to old, leaky pipes and mains. That’s enough water to supply all the residents of California for a year.
An engineering research team at the University of California, Irvine are building a robot that can travel along water pipes and repair them from the inside. (Credit: UC Irvine)
"This is a nationwide emergency," said Maria Feng, civil & environmental engineering professor at the University of California, Irvine. "Some pipelines are nearly 100 years old, and the problem is very serious, especially in urban areas, where it’s difficult to access leaking and burst pipes."
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Bridging the gap between CAD and GIS, AutoCAD Map 3D allows engineering and GIS professionals to work with the same data, and enables design processes to integrate geospatial functions in a single environment for more efficient workflows.
This results in better designs, increased productivity, and better data quality. View this screencast to learn about the top five ways AutoCAD Map 3D can help you improve your infrastructure design process.
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Read how the Public Works Department of the City of Tacoma (Tacoma), Washington, uses its geospatial data to do everything from issuing building permits and managing waste water to maintaining streetlights. The city has prioritized the centralized storage, efficient maintenance, and real-time distribution of spatial data. Tacoma’s efforts have met with spectacular—and award-winning—success. Tacoma has been able to:
- Eliminate duplicate data entry from its design and GIS processes
- Collect and process spatial data more quickly
- Save time with instant access to maps
- Customize web applications quickly and easily with existing IT staff
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Join Autodesk and Waterworld for this short informational webcast that to learn how to quickly save time and be more efficient in planning for maintenance. This tutorial demonstrates a plan to access, record and then prioritize the maintenance of fire hydrants. See firsthand the benefits of system-wide reporting and time-savings GIS interoperability can add to your utility workflow.
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The Orange County Sanitation District, in Southern California, seamlessly integrates CAD design and geospatial data to effectively manage the collection and disposal of wastewater. They use AutoCAD® Map 3D, along with other Autodesk Solutions, to maintain asset data, update enterprise GIS datasets, and deliver better service and more accurate information to customers.
View this interactive customer video to find out more about the Orange County Sanitation District.
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Watch and see this interactive overviews to learn how the Public Works Department of the City of Tacoma (Tacoma), Washington, uses its geospatial data to do everything from issuing building permits and managing waste water to maintaining streetlights. The city has prioritized the centralized storage, efficient maintenance, and real-time distribution of spatial data. Tacoma has been able to:
- Eliminate duplicate data entry from its design and GIS processes
- Collect and process spatial data more quickly
- Save time with instant access to maps
- Customize web applications easily with existing IT staff
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Topobase is Autodesk’s platform for integrating infrastructure design and management. This study from IDC details the business benefits of using Topobase within utilities. They conducted this study using standard IDC methods for assessing business value in terms of return on investment. They also outline industry trends that drive utilities toward integrated information management platforms like Topobase. There are two case studies included. Their intent is to provide information useful to decision makers who are considering solutions for reducing costs and improving process efficiencies within their information systems.
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AutoCAD® Map 3D integrates CAD with GIS for efficiency gains during the data creation, acquisition, and consolidation phases of your utilities and public works projects.
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If you’re using AutoCAD, this video will show you why you need Map 3D.
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Hear about how the Las Vegas Valley Water District relies on CAD engineering software and 3D modeling to maintain their geospatial database for the Las Vegas water supply system.
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