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Live adaptation of organ models in the OR

The non-deformed liver model (red) adapts to the deformed surface profile (blue). Credit: Graphics: Dr. Stefanie Speidel, KIT, in Medical Physics, 41
During minimally invasive operations, a surgeon has to trust the information displayed on the screen: A virtual 3D model of the respective organ shows where a tumor is located and where sensitive vessels can be found. Soft tissue, such as the tissue of the liver, however, deforms during breathing or when the scalpel is applied. Endoscopic cameras record in real time how the surface deforms, but do not show the deformation of deeper structures such as tumors. Young scientists of the Karlsruhe Institute of Technology (KIT) have now developed a real-time capable computation method to adapt the virtual organ to the deformed surface profile.

The principle appears to be simple: Based on computer tomography image data, the scientists construct a virtual 3D model of the respective organ, including the tumor, prior to operation. During the operation, cameras scan the surface of the organ and generate a stiff profile mask. To this virtual mold, the 3D model then is to fit snuggly, like jelly to a given form. The Young Investigator Group of Dr. Stefanie Speidel analyzed this geometrical problem of shape adaptation from the physical perspective. "We model the surface profile as electrically negative and the volume model of the organ as electrically positive charged," Speidel explains. "Now, both attract each other and the elastic volume model slides into the immovable profile mask." The adapted 3D model then reveals to the surgeon how the tumor has moved with the deformation of the organ.

Simulations and experiments using a close-to-reality phantom liver have demonstrated that the electrostatic-elastic method even works when only parts of the deformed surface profile are available. This is the usual situation at the hospital. The human liver is surrounded by other organs and, hence, only partly visible by endoscopic cameras. "Only those structures that are clearly identified as parts of the liver by our system are assigned an electric charge," says Dr. Stefan Suwelack who, as part of Speidel's group, wrote his Ph.D. thesis on this subject. Problems only arise, if far less than half of the deformed surface is visible. To stabilize computation in such cases, the KIT researchers can use clear reference points, such as crossing vessels. Their method, however, in contrary to others does not rely on such references from the outset.

In addition, the model of the KIT researchers is more precise than conventional methods, because it also considers biomechanical factors of the liver, such as the elasticity of the tissue. So for instance, the phantom liver used by the scientists consists of two different silicones: A harder material for the capsule, i.e. the outer shell of the liver, and a softer material for the inner liver tissue.

As a result of their physical approach, the young scientists also succeeded in accelerating the computation process. As shape adaptation was described by electrostatic and elastic energies, they found a single mathematical formula. Using this formula, even conventional computers equipped with a single processing unit only work so quickly that the method is competitive. Contrary to conventional computation methods, however, the new method is also suited for parallel computers. Using such a computer, the Young Investigator Group now plans to model organ deformations stably in real time.

Volunteers can now help scientists seek Ebola cure in their (computer's) spare time

The Scripps Research Institute’s Professor Erica Ollmann Saphire is leading the new effort against Ebola. Credit: Photo courtesy of The Scripps Research Institute.
Although some medical therapies show promise as treatments for Ebola, scientists are still looking urgently for a definitive cure.

For the first time, anyone with access to a computer or Android-based mobile device can help scientists perform this critical research -- no financial contribution, passport or PhD necessary. In fact, volunteers can be asleep, traveling or on a coffee break when they help researchers search for an Ebola cure.

Beginning today, anyone can download a safe and free app that will put their devices to work when the machines would otherwise be idle. With their collective processing power, the computers will form a virtual supercomputer to help The Scripps Research Institute (TSRI) screen millions of chemical compounds to identify new drug leads for treating Ebola. 
Meanwhile, the devices will remain fully available for normal use by their owners.

This citizen science effort is possible through a partnership with IBM's (NYSE: IBM) World Community Grid, which has been making similar data-driven health and sustainability initiatives possible for 10 years as a free, philanthropic service to the science community. 
The "Outsmart Ebola Together" volunteer computing project announced today is being run by the Ollmann Saphire laboratory at TSRI, which has mapped the structures and vulnerabilities of the proteins comprising the Ebola virus.

The best candidate compounds that emerge from this crowdsourced effort will be physically tested in the lab to pinpoint their effectiveness against real virus infection. The most promising compounds will then be modified to perform even better, at lower concentrations, and with fewer side effects. Subsequent drug trials could ultimately lead to an approved medicine.

Crowdsourcing this citizen science effort will dramatically accelerate the process of identifying a cure. The speed and scale of a drug search is essential, as this particularly lethal disease continues to spread and mutate. Once believed to be less of a widespread public health risk than other communicable diseases because of its existence in mainly isolated regions, Ebola now carries a higher risk of spreading farther because people are more mobile than ever before.

"Our molecular images of the Ebola virus are like enemy reconnaissance," said Dr. Erica Ollmann Saphire of TSRI, one of the largest private biomedical research institutes in the United States. "These images show us where the virus is vulnerable and the targets we need to hit. In the Outsmart Ebola Together project, we will be able to harness World Community 
Grid's virtual supercomputing power to find the drugs we need to aim at these targets."

IBM's World Community Grid has successfully run other projects that search for drug candidates for both high- and low-profile diseases -- such as AIDS, cancer, malaria, Dengue fever, and influenza. It has enabled multiple breakthroughs, such as helping the Chiba Cancer Center in Japan discover seven new drug candidates to fight childhood neuroblastoma. The IBM-managed program also hosts projects that have led to important scientific advances in renewable energy and water purification technology.

"It is a privilege to partner with The Scripps Research Institute to advance the process of identifying an Ebola cure," said Stanley S. Litow, IBM's vice president of Corporate Citizenship and president of the IBM International Foundation. "It is only fitting that IBM's World Community Grid 10-year anniversary of accomplishments coincide with the launch of perhaps one of the most critical scientific and humanitarian efforts."

Conceived and managed by IBM, and powered by IBM's reliable and secure SoftLayer cloud technology, World Community Grid provides computing power to scientists by harnessing the unused, surplus cycle time of volunteers' computers and mobile devices. The software receives, completes, and returns small computational assignments to scientists. The combined power contributed by hundreds of thousands of volunteers has created one of the fastest virtual supercomputers on the planet, advancing scientific work by hundreds of years.

Nearly three million computers and mobile devices used by more than 680,000 people and 460 institutions from 80 countries have contributed virtual supercomputing power for vitally important projects on World Community Grid over the last 10 years. Since the program's inception, World Community Grid volunteers have powered more than 20 research projects, donating more than one million years of computing time to scientific research, and enabled important scientific advances in health and sustainability. IBM invites researchers to submit research project proposals to receive this free resource, and invites members of the public to donate their unused computing power to these efforts at worldcommunitygrid.org.

TSRI also invites members of the public to support Dr. Saphire's crowdfunding campaign at www.crowdrise.com/CUREEBOLA to secure resources needed to analyze the enormous volume of data generated by Outsmart Ebola Together.

The software used for screenings in the Outsmart Ebola Together project is called AutoDock and AutoDock VINA, developed by the Olson laboratory at TSRI.

World Community Grid is enabled by software developed in 2002 by Berkeley Open Infrastructure for Network Computing (BOINC) at the University of California, Berkeley and with support from the National Science Foundation. The BOINC project choreographs the technical aspects of volunteer computing.

How does the brain react to virtual reality? Completely different pattern of activity in brain

Illusions (stock image). UCLA neurophysicists have found that space-mapping neurons in the brain react differently to virtual reality than they do to real-world environments. Credit: © agsandrew / Fotolia
UCLA neurophysicists have found that space-mapping neurons in the brain react differently to virtual reality than they do to real-world environments. Their findings could be significant for people who use virtual reality for gaming, military, commercial, scientific or other purposes.

"The pattern of activity in a brain region involved in spatial learning in the virtual world is completely different than when it processes activity in the real world," said Mayank Mehta, a UCLA professor of physics, neurology and neurobiology in the UCLA College and the study's senior author. "Since so many people are using virtual reality, it is important to understand why there are such big differences."

The study was published today in the journal Nature Neuroscience.

The scientists were studying the hippocampus, a region of the brain involved in diseases such as Alzheimer's, stroke, depression, schizophrenia, epilepsy and post-traumatic stress disorder. The hippocampus also plays an important role in forming new memories and creating mental maps of space. For example, when a person explores a room, hippocampal neurons become selectively active, providing a "cognitive map" of the environment.

The mechanisms by which the brain makes those cognitive maps remains a mystery, but neuroscientists have surmised that the hippocampus computes distances between the subject and surrounding landmarks, such as buildings and mountains. But in a real maze, other cues, such as smells and sounds, can also help the brain determine spaces and distances.

To test whether the hippocampus could actually form spatial maps using only visual landmarks, Mehta's team devised a noninvasive virtual reality environment and studied how the hippocampal neurons in the brains of rats reacted in the virtual world without the ability to use smells and sounds as cues.

Researchers placed a small harness around rats and put them on a treadmill surrounded by a "virtual world" on large video screens -- a virtual environment they describe as even more immersive than IMAX -- in an otherwise dark, quiet room. The scientists measured the rats' behavior and the activity of hundreds of neurons in their hippocampi, said UCLA graduate student Lavanya Acharya, a lead author on the research.

The researchers also measured the rats' behavior and neural activity when they walked in a real room designed to look exactly like the virtual reality room.

The scientists were surprised to find that the results from the virtual and real environments were entirely different. In the virtual world, the rats' hippocampal neurons seemed to fire completely randomly, as if the neurons had no idea where the rat was -- even though the rats seemed to behave perfectly normally in the real and virtual worlds.

"The 'map' disappeared completely," said Mehta, director of a W.M. Keck Foundation Neurophysics center and a member of UCLA's Brain Research Institute. "Nobody expected this. The neuron activity was a random function of the rat's position in the virtual world."

Explained Zahra Aghajan, a UCLA graduate student and another of the study's lead authors: 

"In fact, careful mathematical analysis showed that neurons in the virtual world were calculating the amount of distance the rat had walked, regardless of where he was in the virtual space."

They also were shocked to find that although the rats' hippocampal neurons were highly active in the real-world environment, more than half of those neurons shut down in the virtual space.

The virtual world used in the study was very similar to virtual reality environments used by humans, and neurons in a rat's brain would be very hard to distinguish from neurons in the human brain, Mehta said.

His conclusion: "The neural pattern in virtual reality is substantially different from the activity pattern in the real world. We need to fully understand how virtual reality affects the brain."

Neurons Bach would appreciate

In addition to analyzing the activity of individual neurons, Mehta's team studied larger groups of the brain cells. Previous research, including studies by his group, have revealed that groups of neurons create a complex pattern using brain rhythms.

"These complex rhythms are crucial for learning and memory, but we can't hear or feel these rhythms in our brain. They are hidden under the hood from us," Mehta said. "The complex pattern they make defies human imagination. The neurons in this memory-making region talk to each other using two entirely different languages at the same time. One of those languages is based on rhythm; the other is based on intensity."

Every neuron in the hippocampus speaks the two languages simultaneously, Mehta said, comparing the phenomenon to the multiple concurrent melodies of a Bach fugue.

Mehta's group reports that in the virtual world, the language based on rhythm has a similar structure to that in the real world, even though it says something entirely different in the two worlds. The language based on intensity, however, is entirely disrupted.

When people walk or try to remember something, the activity in the hippocampus becomes very rhythmic and these complex, rhythmic patterns appear, Mehta said. Those rhythms facilitate the formation of memories and our ability to recall them. Mehta hypothesizes that in some people with learning and memory disorders, these rhythms are impaired.

"Neurons involved in memory interact with other parts of the hippocampus like an orchestra," Mehta said. "It's not enough for every violinist and every trumpet player to play their music flawlessly. They also have to be perfectly synchronized."

Mehta believes that by retuning and synchronizing these rhythms, doctors will be able to repair damaged memory, but said doing so remains a huge challenge.

"The need to repair memories is enormous," noted Mehta, who said neurons and synapses -- the connections between neurons -- are amazingly complex machines.

Previous research by Mehta showed that the hippocampal circuit rapidly evolves with learning and that brain rhythms are crucial for this process. Mehta conducts his research with rats because analyzing complex brain circuits and neural activity with high precision currently is not possible in humans.

Other co-authors of the study were Jason Moore, a UCLA graduate student; Cliff Vuong, a research assistant who conducted the research as a UCLA undergraduate; and UCLA postdoctoral scholar Jesse Cushman. The research was funded by the W.M. Keck Foundation and the National Institutes of Health.

Source: University of California - Los Angeles

New technology allows medical professionals to step into their patients' shoes

Transports is a piece of technology that uses a low cost Raspberry Pi computer system, and allows users to recreate symptoms including dizziness and speech problems, along with wearable technology which creates a 6Hz tremor in the participant’s right hand. Credit: Image courtesy of University of Royal Holloway London
A pioneering piece of technology will allow users to experience the world through the eyes of a person with Young-Onset Parkinson's disease -- which could revolutionise the way carers and medical staff treat people with the degenerative condition.

Analogue, a theatre company set up by alumni of Royal Holloway, University of London has designed Transports -- a piece of technology which uses a low cost Raspberry Pi computer system, and allows users to recreate symptoms including dizziness and speech problems, along with wearable technology which creates a 6Hz tremor in the participant's right hand.
Young-Onset Parkinson's is a form of the neurological condition which affects people aged under 50. Symptoms of the disease include tremors, slowed movement and falls, and with no cure currently available, how care and treatment are managed can make a significant difference to a patient's quality of life.

The revolutionary project has been designed in collaboration with neuroscience specialist, Professor Narender Ramnani from the Department of Psychology at Royal Holloway, along with carers, researchers and people with the disease, at Parkinson's UK to ensure it is as effective and realistic as possible.

Liam Jarvis, Co-director of Analogue and Drama PhD Student at Royal Holloway, said: "Our principal interest is to work out how we can improve and facilitate communication and empathy by using simple technologies to immerse participants in the remote embodied experiences of others. Using inexpensive Raspberry Pi technology, we hope to expand the project to place participants inside different virtual subjects as an aid to better understand the experience of others."

The technology will now be tested with BSc psychology students at Royal Holloway and carers at Parkinson's UK to see how it can help medical practitioners better understand their patients and in the long term improve the treatment of the disease.

Anna Farrer, User Involvement Advisor at Parkinson's UK, said:"We know that people with Parkinson's feel that better public awareness about the condition would mean that they face less discrimination and have a better quality of life. Projects such as Transports have an important role educating the public, raising awareness -- and we hope, changing attitudes."

Source: University of Royal Holloway London
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