University Times

Supercomputer time awarded

Kenneth Jordan, Distinguished Professor of Computational Chemistry and director of Pitt’s Center for Molecular and Materials Simulations, and Wissam Al-Saidi, a faculty member in the Department of Chemical and Petroleum Engineering, in collaboration with materials researchers at University College London, have been awarded 17 million processor hours on a supercomputer at Oak Ridge National Laboratory as part of the Department of Energy’s Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program.

The computational resources will be used to support the project  “Quantum Monte Carlo Brings New Realism to Surface-Science Modeling.”

The binding of molecules to surfaces underpins many important processes including catalysis, corrosion, gas sensing, crystal growth and others. However, according to the researchers, the accuracy and realism of current modeling methods fall short.

The project proposes to use quantum Monte Carlo (QMC) techniques to produce accurate benchmark values for quantities such as molecule adsorption energies. The project will utilize QMC to produce highly accurate binding energy curves for water on graphite, water on the surface of magnesium oxide, water on the surface of sodium chloride and carbon monoxide on the surface of copper.

According to the researchers, the project will move the field of electronic structure theory to calculate binding energies with chemical accuracy in many other systems where such accuracy is needed to solve important scientific and technological problems.

The 2011 INCITE program awarded nearly 1.7 billion processor hours on two of the world’s fastest and most powerful supercomputers — the Cray XT5 Jaguar at Oak Ridge and the IBM Blue Gene/P Intrepid at Argonne National Laboratory — to 57 projects, the largest-ever awards of DOE supercomputing time. According to the DOE, Jaguar’s computational capacity is roughly equivalent to 109,000 laptops all working together to solve the same problem. Intrepid is roughly equivalent to 26,000 laptops.

Projects were chosen for their potential to advance scientific discoveries, speed technological innovations and strengthen industrial competitiveness. More than half of the projects are led by university researchers, with the remainder of the awards going to government and industry scientists and engineers.

Study finds local heart health rare

Only one out of more than 1,900 local people evaluated met the American Heart Association (AHA) definition of ideal cardiovascular health, according to a new study led by researchers from the School of Medicine. Their findings were published online recently in Circulation.

Ideal cardiovascular health is the combination of these seven factors: nonsmoking; a body mass index less than 25; goal-level physical activity; a healthy diet; untreated cholesterol below 200; blood pressure below 120/80, and fasting blood sugar below 100, explained senior investigator and cardiologist Steven Reis, associate vice chancellor for clinical research at Pitt.

“Of all the people we assessed, only one out of 1,900 could claim ideal heart health,” said Reis. “This tells us that the current prevalence of heart health is extremely low, and that we have a great challenge ahead of us to attain the AHA’s aim of a 20 percent improvement in cardiovascular health rates by 2020.”

As part of the Heart Strategies Concentrating on Risk Evaluation (Heart SCORE) study, the researchers evaluated 1,933 people ages 45-75 in Allegheny County with surveys, physical exams and blood tests. Less than 10 percent met five or more criteria and after adjustment for age, sex and income level, blacks had 82 percent lower odds than whites of meeting five or more criteria.

Only 2 percent met all four heart-healthy behaviors (nonsmoking, BMI below 25, goal-level activity and healthy diet); while just 1.4 percent met all three heart-healthy factors related to blood pressure, cholesterol and blood sugar levels.

A multipronged approach, including change at the individual level, the social and physical environment, policy and access to care, will be needed to help people not only avoid heart disease, but also attain heart health, Reis said.

“Many of our study participants were overweight or obese, and that likely had a powerful influence on the other behaviors and factors,” he noted. “Our next step is to analyze additional data to confirm this and, based on the results, try to develop a multifaceted approach to improve health. That could include identifying predictors of success or failure at adhering to the guidelines.”

Other Pitt researchers involved in the study were Andrea Dinga of the Cardiovascular Institute and Suresh R. Mulukutla and Aryan N. Aiyer of the Department of Medicine.

The study was funded by the National Institutes of Health and the Pennsylvania Department of Health.

BCI initiatives funded

Funding has been awarded for two projects that will place brain-computer interfaces (BCI) in patients with spinal cord injuries to test if it is possible for them to control external devices such as a computer cursor or a prosthetic limb with their thoughts.

The projects build upon ongoing research conducted in epilepsy patients who were able to move cursors and play computer games after having the interfaces temporarily placed on their brains, as well as in monkeys that through BCI guided a robotic arm to feed themselves marshmallows and turn a doorknob.

In one project, funded by an $800,000 grant from the National Institutes of Health, a BCI based on electrocorticography will be placed on the motor cortex surface of a spinal cord injury patient’s brain for up to 29 days. The neural activity picked up by the BCI will be translated through a computer processor, allowing the patient to learn to control computer cursors, virtual hands, computer games and assistive devices such as a prosthetic hand or a wheelchair.

The second project, funded by the Defense Advanced Research Projects Agency for up to $6 million over three years, is part of a program led by the Johns Hopkins University Applied Physics Laboratory. It will develop technology tested in monkeys by Pitt neurobiology faculty member Andrew Schwartz, who is a senior investigator on both projects.

It uses an interface that is a tiny 10-by-10 array of electrodes implanted on the surface of the brain to read activity from individual neurons. Those signals will be processed and relayed to maneuver a sophisticated prosthetic arm.

Schwartz said, “Our animal studies have shown that we can interpret the messages the brain sends to make a simple robotic arm reach for an object and turn a mechanical wrist. The next step is to see not only if we can make these techniques work for people, but also if we can make the movements more complex.”

In the study, which is expected to begin by late 2011, participants will get two separate electrodes. In future research efforts, the technology may be enhanced with an innovative telemetry system that would allow wireless control of a prosthetic arm, as well as a sensory component.

Michael L. Boninger, chair of the School of Medicine’s Department of Physical Medicine and Rehabilitation and director of the UPMC Rehabilitation Institute, said, “Our ultimate aim is to develop technologies that can give patients with physical disabilities control of assistive devices that will help restore their independence.”

Boninger, a senior scientist on both projects, added, “We are now ready to begin testing BCI technology in the patients who might benefit from it the most, namely those who have lost the ability to move their upper limbs due to a spinal cord injury. It’s particularly exciting for us to be able to test two types of interfaces within the brain.”

Elizabeth Tyler-Kabara, a faculty member in neurological surgery and bioengineering, said, “By expanding our research from the laboratory to clinical settings, we hope to gain a better understanding of how to train and motivate patients who will benefit from BCI technology.”

Tyler-Kabara, a UPMC neurosurgeon, is the lead surgeon on both projects.

Poor sleep affects arthritis patients

Poor sleep quality correlates with higher levels of depressive symptoms, more severe pain, increased fatigue and greater functional disability in patients with rheumatoid arthritis (RA), according to a study by School of Nursing researchers recently published in the Journal of Clinical Sleep Medicine. The study suggests that addressing sleep problems may have a critical impact on the health and quality of life of patients with RA.

Nursing faculty member Faith S. Luyster led the study that surveyed 162 patients with RA about their sleep quality, depression, fatigue, functional disability and pain severity.

Results showed that sleep quality had an indirect effect on functional disability after controlling for age, gender and number of co-morbidities. One index found that 61 percent of patients were poor sleepers and 33 percent reported pain that disturbed their sleep three or more times per week.

“Not sleeping well at night can contribute to greater pain sensitivity and fatigue during the day, which in turn can limit a patient’s ability to engage in activities of daily living and discretionary activities,” Luyster said. “These results highlight the importance of addressing sleep complaints among patients with RA.”

Collaborators on the study were nursing school Dean Jacqueline Dunbar-Jacob and faculty member Eileen Chasens.

The study was funded by the National Institutes of Health.

Drier Northwest predicted

A multi-university team led by Pitt researchers extracted a 6,000-year climate record from a Washington lake that shows the famously rain-soaked Pacific Northwest not only could be in for longer dry seasons, but also is unlikely to see a period as wet as the 20th century any time soon.

In a recent report in the Proceedings of the National Academy of Sciences, the team linked the longer dry spells to the intensifying El Niño/La Niña climate pattern and concluded that western states likely will suffer severe water shortages as El Niño/La Niña wields greater influence on the region.

The researchers analyzed a sediment core from Castor Lake in north-central Washington to plot the region’s drought history since around 4000 BCE and found that wet and dry cycles during the past millennium have grown longer. The team attributed this recent deviation to the irregular pressure and temperature changes brought on by El Niño/La Niña. At the same time, they reported, the wet cycle stretching from the 1940s to approximately 2000 was the dampest in 350 years.

Lead researcher Mark Abbott, a faculty member in geology and planetary science, said those unusually wet years coincided with the period when western states developed water-use policies. “Western states happened to build dams and water systems during a period that was unusually wet compared to the past 6,000 years,” he said. “Now the cycle has changed and is trending drier, which is actually normal. It will shift back to wet eventually, but probably not to the extremes seen during most of the 20th century.”

The team produced a climate record from the lake mud by measuring the oxygen isotope ratios of calcite. The mineral precipitates from the lake water every summer and builds up in fine layers on the lake floor, accumulating more in wet years than in dry ones.

They reproduced their findings by measuring grayscale, or the color of mud based on calcite concentration, with darker mud signifying a drier year.

The record in the sediment core was then compared to the Palmer Drought Severity Index, which uses meteorological and tree-ring data to determine drought cycles dating back 1,500 years, Abbott explained. The Castor Lake core matched the Palmer Index reconstructed with tree-ring data and expanded on it by 4,500 years, suggesting that lakebeds are better records of long-term climate change, the authors contend.

Analysis of the sediment core revealed that the climate of the Pacific Northwest fluctuated more or less evenly between wet and dry periods for thousands of years. Droughts tended to be lengthier with 25 percent of dry periods during the past 6,000 years persisting for 30 years or more and the longest lingering for around 75 years. Wet periods tended to be shorter with only 19 percent lasting more than 30 years and the longest spanning 64 years.

Abbott said that since approximately 1000 AD, these periods have become longer, shifted less frequently and, most importantly, ushered in more extreme conditions.

The two driest cycles in the past 6,000 years occurred within only 400 years of each other — the first in the 1500s and the second during the Great Depression, researchers found. Wet periods showed a similar pattern shift with five very wet eras crammed into the past 900 years. The wettest cycle of the past 6,000 years began around the 1650s, and the second most sodden began a mere 300 years later, in the 1940s.

The change in cycle regularity Abbott and his colleagues found correlates with documented activity of El Niño/La Niña. When the patterns became more intense, wet and dry cycles in the Pacific Northwest became more erratic and lasted longer, Abbott said.

Abbott worked with his former graduate student, lead author and Pitt alumnus Daniel Nelson; geology and planetary science faculty member Michael Rosenmeier; Nathan Stansell, a Pitt PhD graduate now a postdoctoral researcher at Ohio State University, and Pitt geology and planetary science graduate student Byron Steinman. The team included researchers from Columbia, Kent State, Idaho State and North Cascades National Park.

A timeline of the wet and dry cycles, a graph illustrating the average duration of each cycle and a photo of the sediment core are available at www.news.pitt.edu/news/Abbott-wet-dry-cycles-American-West.

Pitt joins in new bipolar research

The Department of Psychiatry’s mood disorders treatment research program is participating in Bipolar CHOICE (Clinical Health Outcomes Initiative in Comparative Effectiveness), a 10-site nationwide trial evaluating the advantages and disadvantages of quetiapine versus lithium.

The study, funded by a $10 million grant from the Agency for Healthcare Research Quality, is being conducted locally by psychiatry faculty member Edward S. Friedman.

Friedman and his research team are seeking adults ages 18-68 with bipolar disorder who are experiencing at least mild symptoms of depression, hypomania or mania. Participants will receive either lithium or quetiapine as a mood stabilizer for six months.

The pharmacologic treatments for bipolar disorder have shifted away from lithium in favor of newly developed antipsychotics, such as quetiapine. Both drugs have well-documented side effects. Quetiapine may cause drowsiness and weight gain and increases the risk of cardiovascular disease. Lithium is associated with the risk of long-term thyroid and kidney problems.

“We hope this study will help us determine which medications work best for patients with bipolar disease with the least amount of side-effect burden. These results may help us to design personalized treatments,” noted Friedman.

Additional information on the study is available at www.pittsburghbipolarstudy.com.

Study looks at effects of mine subsidence

A new report from Pitt and the Department of Environmental Protection is providing information that will be used to better understand and prevent underground mine subsidence from damaging above-ground property and water supplies, which continues to be a problem in southwestern Pennsylvania.

The assessment, led by Pitt engineering faculty member Anthony Iannacchione, addresses the effects of mining in Armstrong, Beaver, Cambria, Clearfield, Elk, Greene, Indiana, Jefferson, Somerset and Washington counties, August 2003-August 2008. Pennsylvania Act 54 requires such a report to be prepared every five years.

Act 54 held deep mine operators legally responsible for surface damages caused by their mining operations for the first time in Pennsylvania’s history. Underground coal mines that operated prior to 1994 did not have a legal obligation to protect or restore surface structures or water supplies.

The study analyzed the effects of mine subsidence from 50 underground mines with data collected by DEP and through University field monitoring studies. The investigation focused on the subsidence effects to residential and commercial property as well as water sources such as wells, springs, streams and wetlands.

The report details the number of structures, water supplies and streams undermined during the five-year assessment period. It provides an overview of the type and severity of any damages to surface structures and surface features, as well as information on how long it took to resolve those issues. The report also describes and assesses the effectiveness of mitigation measures designed to minimize structural damage and damage to water resources.

Preparing the report brought together faculty and students across Pitt’s Swanson School of Engineering as well as from the geology and planetary science and biological sciences departments.

Iannacchione, director of Pitt’s mining engineering program, said, “Pitt was chosen to write this assessment for two important reasons: our expert faculty and outstanding students in all the disciplines necessary to prepare the report, and our proximity to the mines. Both were not only strengths but a necessity.”

According to the report, there were 50 underground coal mines active during the reporting period beneath 38,256 acres of land. In total, there were 1,247 different “effects,” or incidents reported to DEP during this most recent five-year period by its staff, coal companies or landowners.

Eight longwall mines in Greene and Washington counties accounted for nearly 94 percent of the incidents involving structures and 89 percent of the impacts to land.

The total number of incidents reported represents a 14 percent increase over the 1998-2003 period. DEP is examining the incident reports to determine what factors, if any, contributed to the increase and to identify trends that can be used in designing the next five-year assessment.

Other findings of the report included:

• Of the 3,735 structures inventoried in the target counties, 456 (12 percent) were impacted by mining, while 108 of the 3,587 properties (3 percent) inventoried were impacted;

• Nearly 2,800 wells, springs and ponds were undermined with 683, or 24.5 percent, reporting some impact. At the end of the assessment period, 449 of those cases had been resolved.

• The average time to resolve impacts to structures, land and water supplies was 207 days, 246 days and 321 days, respectively.

In a prepared statement, DEP Secretary John Hanger said, “Mining has been — and, for the foreseeable future, will continue to be — a part of our economy and way of life. Unfortunately, mine subsidence is often associated with the industry’s activities. While coal companies have made advances to reduce underground mining’s impact on the surface, this report gives us a chance to better understand how those incidents occur, where they’re occurring, and how we can prevent them or address them more timely.”

The full report is available at www.dep.state.pa.us/dep/deputate/minres/bmr/act54_2008_report/cover.htm.

Liver donation optimization proposed

A redesign of the nation’s donor-liver distribution network developed by Pitt researchers could result in several hundred more people each year receiving the transplants they need.

The team reported in the journal INFORMS Management Science that donor livers currently are doled out to 11 national regions that evolved with little regard for geography and demographics, an arrangement that prevents many livers from getting to prospective recipients in time.

Using an optimization model they developed, the Pitt researchers instead trimmed the network down to six regions that better account for urban and rural population differences, geographic distance and the anticipated supply of and demand for donor livers.

They calculated that their rearrangement could result in up to 14 percent more transplants each year, a sizable increase considering that more than 6,000 transplants were performed in 2009 alone. Researcher Andrew Schaefer, a faculty member in industrial engineering, said that the team’s proposed regions do not change how livers are allocated — the most critical patients still receive an organ first — but rather put more potential donors and recipients within range of one another. Schaefer worked with his former doctoral student and lead author Nan Kong, a Pitt alumnus now at Purdue University; Brady Hunsaker, a former industrial engineering faculty member now at Google Pittsburgh, and Mark S. Roberts, professor and chair of health policy and management in the Graduate School of Public Health.

The project was supported by grants from the National Science Foundation and the Air Force Office of Scientific Research.

“We’re simply redesigning the hierarchy by geographic and demographic information to increase the likelihood that recipients will be found closer to the liver’s point of origin,” Schaefer said. “Under the current system, a liver harvested in New Jersey is more likely to go to a patient in Beckley, West Virginia, than one in New York City. Plus, it is well known that there are big geographic disparities in procurement and that there are some places where it is better to be on an organ waiting list than others.”

Roberts, whose research includes developing mathematical models for efficient treatment, explained that regions are used by local organ-procurement organizations (OPOs) to provide livers to recipients in other parts of the country if recipients are not available at the local level. But the national regions were not developed scientifically or with efficiency in mind.

In the end, livers are wasted, he said. In some cases, dense populations supply and draw from rural areas that have neither the requisite need for nor stock of donor livers. For instance, Seattle is the largest city in the region covering the entire Pacific Northwest, plus Hawaii and Alaska. Oklahoma is paired only with Texas, which has more than six times the population. At the same time, large population centers such as New York City and New Jersey, which could easily support each other, are in separate regions while a swath of countryside in the Great Plains states has no large city handy.

To determine the most efficient regional arrangements, the Pitt researchers plugged procurement data from OPOs nationwide into an optimization model they developed called an integer program that considered more than a trillion configurations before finally deciding on the two most efficient, Schaefer said.

Both Pitt models basically break the Eastern United States into four proportioned population clusters — New England, New York City-New Jersey, the Southeast and the Rust Belt — while the Western states form two expansive regions anchored by dense areas. The entire West Coast — including population giant California — is combined with the Mountain states, the Southwest and Alaska and Hawaii. The northern Midwest joins the Chicago area in one model and, in the other, is part of an area that sweeps from North Carolina to Arizona and from Texas to North Dakota. Although the Western regions are huge, Schaefer said, the data the team used showed that grueling journeys from, say, Houston to Minnesota are not common and that giving sparsely populated areas access to a larger supply of potential donors makes such long distances worthwhile.

Illustrations of the current regional breakdown and both Pitt rearrangements are available at www.news.pitt.edu/news/Schaefer-donor-liver-redesign.

The team’s next step is to maximize fairness within the regions so that even more people have access to donor livers, Roberts said. The team demonstrates a method for ensuring equality in a paper to be published at a future date in the INFORMS Journal of Computing.

“If we can find a structure that benefits everyone, that’s the best chance of pushing these kinds of changes through,” Roberts said. “Still, it’s important that through this rearrangement we waste fewer organs and get more people transplanted by what is a significant number when you consider that that number represents real people.”

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The University Times Research Notes column reports on funding awarded to Pitt researchers as well as findings arising from University research.

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