Posts Tagged ‘computation’

Computing the ravages of time

Sunday, November 18th, 2007

Using Algorithms To Tackle Alzheimer’s Disease

by Regina Nuzzo, PhD
Biomedical Computation Review

Fall 2007
Feature Story

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In 1906, at a small medical meeting in Tubingen, Germany, physician Alois Alzheimer gave a now-famous presentation about a puzzling patient. At age 51, Auguste D.’s memory was failing rapidly. Confused and helpless, she was growing inarticulate and fearful of her family, Alzheimer reported. Auguste died four years later.

During the autopsy Alzheimer found dramatic shrinkage in Auguste’s brain, with cells that were already dead and dying at the time of her death — plus two kinds of microscopic deposits that Alzheimer had never seen before. He summed it up in his presentation abstract: “All in all, we are faced obviously with a peculiar disease process.”

Parsing PubMed

Sunday, April 15th, 2007

by Regina Nuzzo, Ph.D.
Biomedical Computation Review

Winter/Spring 2007
News Bytes

iHOP

Text-mining tools such as iHOP (Information Hyperlinked Over Proteins) are doing for biological literature what hyperlinks and search engines do for the Internet: organizing interconnected information in a fast, intuitive, searchable manner. And in January 2007, the service started to provide daily updates–extending the information network by about 2,000 new papers every day.

With genes and proteins acting as hyperlinks between sentences and abstracts, a large part of the PubMed knowledge base becomes a giant, navigable information network, says Robert Hoffmann, PhD, a postdoctoral fellow at Sloan-Kettering Institute who started the iHOP project while a researcher at the Protein Design Group at the National Center for Biotechnology (CNB) in Madrid, Spain. “The new version provides current information on even more genes and chemical compounds, covering 1,500 organisms ranging from human and chimpanzee to yeast and HIV,” Hoffman says. He and his colleagues also extended iHOP’s results to include drug interactions, and they’ve provided new ways to interact with the data–such as displaying “breaking news” found in papers from the past two years.

Computational Biomechanics: Making Strides Toward Patient Care

Tuesday, February 6th, 2007

by Regina Nuzzo, PhD
Biomedical Computation Review

Winter 2006/07
Feature Story

Walking Skeletons

Walk, run, bend, reach.

The elements of human movement have fascinated research scientists for centuries. To understand how muscles contract and joints flex, researchers have dissected cadavers and experimented with animals. They can describe how bones, muscles, and tendons connect in a complicated geometry; how muscles exert forces on joints; and even how sparks in the brain can trigger a muscle’s contraction.

Meanwhile, and mostly independently, clinicians have been treating people for sports injuries, stroke, and movement diseases such as cerebral palsy and osteoarthritis. Using trial and error, they’ve assessed which rehabilitative strategies and surgical interventions work best.

Until recently, these two perspectives have not been well integrated. Clinical observations might miss the interplay of forces that lead to an injured knee, while static equations regarding the flexion of a dead man’s knee may by themselves be of little help in treating a torn ligament. Researchers were missing the cause-and-effect models that linked the physical forces with the clinical outcomes.

Neurocomputation of Music, Faces and Belly Laughs

Saturday, November 4th, 2006

by Regina Nuzzo, PhD
Biomedical Computation Review

Fall 2006
News Bytes

fMRI-brain Peek inside the skull of a couch potato watching reruns on TV and you’ll see non-stop patterns of blood flow throughout the brain. If you learn to pick out which activity patterns match up with, say, a good belly laugh, then you might be on your way to reading the viewer’s internal experiences. Recently, experts from a variety of fields competed to glean subjective perceptions like humor from functional MRIs of TV viewers. They were surprisingly successful.

“Our goal is to know how the brain represents information,” says Walter Schneider, PhD, professor of psychology at the University of Pittsburgh and principal investigator of the Experience Based Cognition group, which sponsored the competition. “In theory, if we can understand the information in the activity of somebody’s brain, then we can understand what they perceived.”