Archives: 8/2009
Complicated pediatric cardiac surgeries, such as staged Fontan reconstruction in children born with an univentricular heart, present great challenges when planning for each procedure. Unique anatomies bring unknowns into the physiologic (hemodynamics) equation, often requiring surgeons to make difficult decisions when predicting the outcome of a specific approach. Now scientists at Georgia Tech and clinicians at Children’s Hospital of Philadelphia have developed a software tool that analyzes patients’ own MRI scans to simulate various possible surgical options and their outcomes.
Georgia Tech reports:
The patient described in this paper, Amanda Mayer, age four, of Staten Island, N.Y., had previously undergone all three stages of the Fontan procedure at The Children’s Hospital of Philadelphia, but developed severe complications. Her oxygen saturation was very low—only 72 percent, compared to normal levels of at least 95 percent—which indicated the possibility of abnormal connections between the veins and arteries in one of her lungs. Normally, the liver releases hormonal factors that prevent these abnormal connections, so the presence of the malformations indicated a low supply of hepatic blood to the lung.
The image-based surgical planning consisted of five major steps: acquiring magnetic resonance images of the child’s heart at different times in the cardiac cycle, modeling the preoperative heart anatomy and blood flow, performing virtual surgeries, using computational fluid dynamics to model the proposed postoperative flow, and measuring the distribution of liver-derived hormonal factors and other clinically relevant parameters as feedback to the surgeon.
For this particular patient, the team saw a highly uneven flow distribution—the left lung was receiving about 70 percent of the blood pumped out by the heart, but only five percent of the hepatic blood. Both observations suggested left lung malformations, but closer examination of the flow structures in that particular patient revealed that the competition between different vessels at the center of the original Fontan connection effectively forced all hepatic factors into the right lung even though a vast majority of total cardiac output went to the left lung.
To facilitate the design of the surgical options that would correct this problem, Jarek Rossignac, Ph.D., a professor in Georgia Tech’s School of Interactive Computing, developed Surgem, an interactive geometric modeling environment that allowed the surgeon to use both hands and natural gestures in three-dimensions to grab, pull, twist and bend a three-dimensional computer representation of the patient’s anatomy. After analyzing the three-dimensional reconstruction of the failing cardiovascular geometry, the team considered three surgical options.
The research team then performed computational fluid dynamics simulations on all three options to investigate for each how well blood would flow to the lungs and the amount of energy required to drive blood through each connection design. These measures of clinical performance allowed the cardiologists and surgeons to conduct a risk/benefit analysis, which also included factors such as difficulty of completion and potential complications.
Of the three choices, Spray favored the option that showed a slightly higher energy cost but exhibited the best performance with regards to hepatic factor distribution to the left and right lungs. Five months after the surgery, Mayer showed a dramatic improvement in her overall clinical condition and oxygen saturation levels, which increased from 72 to 94 percent. Mayer is breathing easier and is now able to play actively like other children, according to her cardiologist, Donald Putman, M.D., of Staten Island, N.Y.
Here’s a short demo of the interactive surgical planner:
Image: (Top) 3D model of hepatic flow distribution pre-surgery. (Bottom) Post-surgery hepatic flow distribution options. The surgeon ultimately selected the third option. (Image courtesy of Ajit Yoganathan)
Full story: MRI Simulation of Blood Flow Helps Plan Child’s Delicate Heart Surgery…
Abstract in JACC Cardiovascular Imaging: Correction of Pulmonary Arteriovenous Malformation Using Image-Based Surgical Planning
As we’ve reported in the last few years, Helicos BioSciences out of Cambridge, MA has been working on a revolutionary new method of sequencing DNA molecules. The technique does not require any cloning, amplification or ligation to be performed, but uses a novel combination of physics, chemistry, and computer vision to identify base pairs at an unprecedented speed. This week researchers from Stanford University and Howard Hughes Medical Institute are reporting the sequencing of an entire human genome using a Helicos machine within four weeks at a cheap cost of only $50,000.
The basics of the technology from Helicos BioSciences:
Within two flow cells, billions of single molecules of sample DNA are captured on an application-specific proprietary surface. These captured strands serve as templates for the sequencing-by-synthesis process:
Polymerase and one fluorescently labeled nucleotide (C, G, A or T) are added.
* The polymerase catalyzes the sequence-specific incorporation of fluorescent nucleotides into nascent complementary strands on all the templates.
* After a wash step, which removes all free nucleotides, the incorporated nucleotides are imaged and their positions recorded.
* The fluorescent group is removed in a highly efficient cleavage process, leaving behind the incorporated nucleotide.
* The process continues through each of the other three bases.
* Multiple four-base cycles result in complementary strands greater than 25 bases in length synthesized on billions of templates—providing a greater than 25-base read from each of those individual templates.
More about the announcement from Ars Technica…
Stanford press release: Professor sequences his entire genome at low cost, with small team…
Article in Nature Biotechnology: Single-molecule sequencing of an individual human genome
Product page: HeliScope™ Single Molecule Sequencer
Flashbacks: Helicos BioSciences Sequences Entire Genome from a Single Molecule of DNA; High Speed Sequencing of Single DNA
Zogby International recently conducted a poll of American adults asking how likely they are to be interested in having assistive microchips implanted in their brains. Would people be interested in having the Internet wired straight to their brains, or perhaps a chip that programs the immune system to ward off all disease? Turns out that up to a quarter of the population seems willing to do it, given enough practical benefit from the implantation.
John Zogby analyzes the findings at Forbes.com:
A quick analysis reveals a hierarchy of needs. One in four would be open to allowing an artificial intelligence into his or her body to ward off disease (and possibly mortality itself). Slightly fewer are so sure knowledge is power that they too would want the chip implant. But only 6% would want a computer chip just to be entertained. Being wired to the Internet can satisfy a lot of needs, both practical and prurient. So the fact that we found 13% who might want to turn themselves into Me.com makes some sense in this needs hierarchy.
We don’t know how many would-be cyberheads might actually go through with this when the hypothetical physician enters the room with surgical lasers and nano-sized computer chips in hand. But we can certainly draw conclusions from our polls about which demographic groups are most open to being hooked up to the Internet and computer technology. This is especially true in the survey of 41,175, where sub-group sizes are in the thousands.
If your first guess is that younger people are the most likely, you are correct, but only to a degree. On being wired to the Internet, the First Global generation of 18- to 29-year-olds is the leader at 24%. The percentages decline with age to only 8% of people 65 and older. First Globals are also more likely than the other age groups to want the entertainment chip, but that number is still only 10%. First Globals are about 5% more likely to want the knowledge chip. However, there is no age difference on the immunity chip question.
We were pretty excited when Nintendo announced at the E3 Expo in June that they would be releasing a pulse oximetry attachment for the Wii. Now, a few more details are emerging.
Nintendo president Satoru Iwata mentioned in a Q & A that Nintendo “would like to deliver the actual product not too late in the year next year.” The software is said to consist of a relaxation or meditation theme, but Iwata did mention the possibility of “measuring how horrified a player is in a horror title.” We cannot wait to start giving patients stress tests by playing Resident Evil.
Nintendo : First Quarter Financial Results Briefing for Fiscal Year Ending March 2010 Q & A…
Flashback : Nintendo Wii Makes Pulse Oximetry Fun
(hat tip Joystiq via Engadget)
Physarum polycephalum, an amoeboid slide mold, is a single-celled organism that can form plasmodium (multinucleate masses of protoplasm, also called protoplasmic veins), that spreads through cytoplasmic streaming. The interesting thing about the mold is its logical way of distributing the veins. The organism hates light and spreads towards food.
Dr. Andrew Adamatzky from University of the West of England Bristol just published a paper in arXiv that outlines a general way of constructing a biological computer that can take advantage of this organism’s behavior.
The Physics arXiv Blog explains:
Physarum polycephalum has a complex lifestyle but in one phase of its existence it forms a single-celled creature called a plasmodium that is visible to the naked eye. When this creature forages for food, it physically surrounds whatever it has settled on for lunch, secretes a few enzymes and digests it. If it finds several food sources, it sends out numerous tubes that form a kind of digestive network. It is this network that can find its way efficiently through a maze (provided there is food in the middle).
Here’s how it works. You “program” this biocomputer by creating a pattern of lights and oak flakes that make a kind of obstacle course for the plasmodium to negotiate. You then “run” the program by allowing the creature to tackle this obstacle course and you read out the result by examining the shape of the network that the plasmodium forms.
More from the Physics arXiv Blog…
Image: Protoplasmic network shaped by light obstacles.
Full article from arXiv: Steering plasmodium with light: Dynamical programming of Physarum machine (.pdf)
One way to study biological structures is to dissect or visualize them. Another is to actually model the molecular structure of the material and run computer simulations to study how it functions. MIT researchers have now used the modeling technique called “materiomics” to study how collagen behaves in patients suffering from osteogenesis imperfecta. Here are the basics of the study findings from the MIT news room:
In what may be the first detailed molecular-based multi-scale analysis of the role of a materials’ failure in human disease, a paper in the Aug. 5 issue of Biophysical Journal describes exactly how the substituted amino acid repels other amino acids rather than forming chemical bonds with them, creating a radically altered structure at the nanoscale that results in severely compromised tissue at the macroscale. This approach to the study of disease, referred to as “materiomics” by the lead researcher on the project, Professor Markus Buehler of MIT’s Department of Civil and Environmental Engineering, could prove valuable in the study of other diseases – particularly collagen- and other protein-based diseases – where a material’s behavior and breakdown play a critical role.
Three years ago, Buehler used atomistic-based multi-scale modeling to describe in detail the hierarchical structure of collagen, the tissue comprising most structural material in mammalian bodies. His model incorporates a bottom-up description of collagen, accounting for the hierarchical assembly of molecules, each of which consists of three helical threads of amino acids. The molecules are arranged in packets called fibrils that collectively make up whole tissue.
In new research, Buehler and Sebastien Uzel, a graduate student at MIT, and Alfonso Gautieri, Alberto Redaelli and Simone Vesentini of Politecnico di Milano modeled type I collagen’s behavior at the atomistic level all the way up to the scale of the fibrils that make up whole tissue.
The different forms of severity in brittle bone disease correlate with a particular genetic mutation; some amino acid substitutions for glycine create more severe forms of osteogenesis imperfecta.
Using atomistic modeling, the researchers demonstrate exactly how the substitution of eight different amino acids in place of glycine changes the electrochemical behavior of the collagen molecules and affects the mechanical properties of the collagen tissue. They learned that the mutations creating the most severe form of the disease also correlate with the greatest magnitude of adverse effects in creating more pronounced rifts in the tissue, which lead to the deterioration and failure of the tissue.
Image: The image at top depicts a healthy collagen fibril. The image below it depicts a fibril with brittle bone disease displaying the small rifts (in orange) that form in collagen tissue at the sites where an incorrect amino acid has been substituted for glycine.
Press release: Tiny rifts create fragility of brittle bone disease
Abstract in Biophysical Journal: Molecular and Mesoscale Mechanisms of Osteogenesis Imperfecta Disease in Collagen Fibrils
Students Design Guide Symbols for Patients; Our Editors Can’t Recognise Own Profession
by on Aug 10, 2009 • 1:27 am
University of Cincinnati design students have been working on a new set of logos to guide people in clinical facilities from one place to another. Although this must be the millionth time that new medical signage has been designed, the aesthetic of these ones is definitely of a contemporary nature. As a side note to the students, we would like to point out that the first symbol is a useless one: no patient ever wonders from radiology dept or lab looking for “anesthesiology”. Plus one of our editors, an anesthesiologist, couldn’t even recognize the symbol.
The project challenge for students is straightforward but substantial: Develop symbols that could serve to guide any population – speaking any language and representing any reading or education level – to specific points in a hospital or other health-care setting. So, for instance, develop a symbol that would communicate and guide users to specific service areas: hospital admission, dental care, genetics counseling, mental health services, ophthalmology, nutrition counseling, pathology, radiology and more.
A first round of testing on the student-created symbols will begin in September 2009. That’s when students’ final symbol designs will be reviewed in a series of recognition and comprehension tests.
The symbols judged to be the best performers in terms of comprehension and recognition will then be integrated into surveys administered in pockets of language groups (both English and non-English speakers) in Cincinnati, Ohio; Kent, Ohio; and Ames, Iowa.
Finally, the symbols that “make the grade” in terms of this community user survey/testing will be made available to actual health-care settings, pilot sites already working to implement health symbols as signage.
Press release with slideshow of other logos: UC Project Goal: You Won’t Get Lost at the Hospital…
Current methods of preventing embolisms when inflating angioplasty balloons require a separate filter to be placed down the stream to catch any loose particles. An Israeli company called Angioslide has developed a new balloon catheter by the same name that features the filter, and an aspiration technology, within the balloon itself. Since only one device is inserted, the procedure can be done safer with probably fewer potential complications.
Some details about the device from Globes:
After the balloon is inflated within the blood vessel, a hook on the guidewire is gently pulled backwards, pulling after it the far end of the balloon, so that it folds back within the balloon, forming a hollow cone. This creates negative pressure in the space vacated by the end of the balloon that draws into it the problematic debris. Then, when the balloon is deflated, the debris at the bottom of the cone is trapped inside and can easily be pulled out.
The company’s first product is designed for use in opening blocked blood vessels in limbs, where there is currently no competition from the filter method, so that there is no need for comparative trials.
Device info page: Angioslide…
More from Globes: Medical device co Angioslide raises $8.3m…
Below the fold is a video loop demonstrating the mechanics of the Angioslide:
