Bench Press

Here at Bench Press we’re fans of PLoS because they strive to expand access to the world’s scientific and medical literature with their open access stance as well as other experimental endeavors such as PLoS Currents: Influenza. That’s why when I checked in on PLoS Biology I was intrigued by a new collection titled Genomics of Emerging Infectious Diseases.

The collection is a series of essays, perspectives, and reviews discussing the potential genomics research holds in understanding emerging infectious diseases. While I haven’t had a chance to read through very much of the collection yet, one perspective written by Rajesh Gupta, Mark H. Michalski, and Frank R. Rijsberman suggests an interesting plan for infectious disease research. They suggest beginning an Infectious Disease Genomics Project (IDGP), much like the Human Genome Project.

The IDGP would be:

a coordinated, large-scale, international effort focused on the genomes of pathogens, vectors, hosts, and reservoirs and linked to end-point surveillance and response systems. Such a project could coordinate activities in four specific areas: generating data, linking data, analyzing data, and applying data.

The figure above illustrates some of the specific things the authors envision the IDGP being able to coordinate. Ideally the IDGP provides:

• A “roadmap” for researchers to follow in sequencing and monitoring emerging pathogens that allow researchers worldwide to aid in global efforts while continuing critical research on local diseases.
• Advanced data management in an easy to use, open-source, real-time interface. With an emphasis on linking as much data with relevant details (e.g. literature references).
• A centralized analytical toolbox with dynamic databases allowing for collaboration worldwide in addition to improved access for researchers in resource-limited settings.
• Ability to incorporate emerging technologies and provide access (e.g. new assay methods, next generation sequencers).

Personally I find the IDGP very intriguing simply from the standpoint of developing a framework for worldwide scientific collaboration. If this were successful it could provide a model for future projects. On a practical level, providing a network of this sort for scientists to rely on could at least increase the speed at which emerging diseases are detected. Increasing the speed of detection is always a good thing when dealing with novel pathogens with pandemic potential. It’ll be interesting to see what the scientific community thinks about beginning an IDGP.

Readers any thoughts?

(Source – PLoS Biology: Can an Infectious Disease Genomics Project Predict and Prevent the Next Pandemic?)

Previously, Ben wrote a post about innovative use of the virtual world Second Life for simulating N-body problems. One of the groups behind the impressive OpenSim mod, the Meta Institute of Computational Astrophysics (MICA), is incredibly unique in that the organization itself is an exploration into the utility of emerging virtual world (VW) technologies (e.g. SecondLife) for scientific and academic work.

A group of scientists from the California Institute of Technology, Princeton, Drexel University, and the Massachusetts Institute of Technology founded MICA in the spring of 2008 in order to explore and take advantage of what they saw as a new frontier in collaboration and information dissemination. MICA’s goals are¹:

• Exploration, development and promotion of VWs and VR technologies for professional research in astronomy and related fields.
• To provide and develop novel social networking venues and mechanisms for scientific collaboration and communications, including professional meetings, effective telepresence, etc.
• Use of VWs and VR technologies for education and public outreach.
• To act as a forum for exchange of ideas and joint efforts with other scientific disciplines in promoting these goals for science and scholarship in general.

In addition to the collaborative research we’ve written about before MICA also “conducts weekly professional seminars, bi-weekly popular lectures, and many other regularly scheduled and occasional professional discussions and public outreach events, all of them in [SecondLife].” A screenshot of one of their astrophysics seminars can been seen below. MICA has also begun experimenting with various teaching formats for undergraduate and graduate level courses.

MICA members attending a weekly astrophysics seminar by Dr. M. Trenti, given in the StellaNova sim in SecondLife.

What really impresses me about MICA however is their belief in the platform.

[W]e wish to lead by example, and demonstrate the utility of VWs and immersive VR environments generally for scientific research in fields other than humanities and social sciences (where we believe the case is already strong). In that process, we hope to define the “best practices” and optimal use of VR tools in research and education, including scholarly communications. This is the kind of activity that we expect will engage a much broader segment of the academic community in exploration and use of VR technologies. Second, we hope to develop new research tools and techniques, and help lay the foundations of the informational environments for the next generation of VR-enabled Web.

Hopefully MICA’s innovative use of SecondLife will prompt other scientists to follow. I definitely want to check out one of the lectures one of these days.

(Exploring Use of Virtual Worlds as a Scientific Research Platform: The Meta-Institute for Computational Astrophysics)

A few weeks ago I wrote a post about the development of the Standoff Patient Triage Tool, an impressive use of lasers in order to make health critical readings of patients from a distance. Well one of the best things about science is that many people can utilize the same tools to come up with unique methods and solutions for any given problem. In this case, researchers have used lasers to develop a technology that could someday revolutionize imaging procedures in medicine.

Photoacoustic imaging of melanoma in vivo.

Photoacoustic tomography is the basis behind a new imaging technology being developed in hopes of providing more flexible and cost effective devices for physicians. The technique takes advantage of ultrasonic emissions produced when a non-ionizing laser pulse is directed towards a tissue. The emissions, resulting from transient thermoelastic expansion of the target tissue due to absorption of the laser energy, are detected and analyzed with various algorithms to construct an image (2D or 3D) of the targeted area. This differs from the reliance on the doppler shift produced by the reflected laser beam in the SPTT.

Images of vasculature like the one seen on the right can be produced by using photoacoustic tomography without the injection of contrast as differences between the molecular composition of the target can be used instead. In the example to the right, the difference between oxygenated and deoxygenated blood is an effective natural contrast. Photoacoustic tomography also presents other benefits over traditional imaging techniques as explained by The Economist:

CT scans also involve potentially harmful ionising radiation. And MRI and CT scans are very expensive, using machines that cost millions of dollars and require dedicated staff to operate them. Photoacoustic tomography, by contrast, could eventually be performed using portable hand-held devices, similar to those used for ultrasound scanning. This would allow doctors to diagnose and monitor patients in clinics, and reduce the need to refer them to consultants.

The adaptability of this nascent technology is also impressive as researchers are already looking at using it to detect specific ailments such as brain lesions and cancer. In the case of cancer, the ability to accurately image vasculature could allow doctors to monitor patients for the development of new blood vessels (angiogenesis) a hallmark of cancer development.

While there are some issues to work out with this new technique, such as the lack of imaging depth (ultrasound signal emitted is reduced the deeper the tissue lies) and ultrasound distortion from varying tissue types within the human body (e.g. bone vs muscle), photoacoustic imaging is a very promising new technology.

(Source)

During the past month’s global swine flu emergency providing health care professionals around the world with accurate information was critical to understanding and potentially containing the outbreak. The time sensitive nature of dealing with an emerging disease highlighted the importance of developing an effective communication channel that is quick, accurate, and accessible by numerous individuals. Traditional paper distribution channels, mailing notifications to primary care physicians, can delay the receipt of time sensitive materials by 72-96 hours. Thus, the question becomes how do you design a system that can be accessed quickly and easily by a maximum number of health care professionals, while still providing quality information.

A new web application developed by the Indiana Health Information Exchange (IHIE) interfacing with a service called Docs4Docs®, provided by the Regenstrief Institute, appears to have answered that question. The IHIE’s web portal allows electronic communication of public health messages to any registered health care provider. Registered users can also send messages back through the portal to be disseminated across the network. The web portal’s simplicity allows it to bridge the gap between paper-based and electronic-based medical offices thereby ensuring that even doctors in rural areas without advanced IT infrastructure can receive and contribute critical information.

Docs4Docs® also leverages the Indiana Network for Patient Care (INPC) which is a secure community health records system, providing patient data whenever needed. Dr. Shaun Grannis, a Regenstrief researcher, explains “[b]y working with our public health partners to seamlessly deliver public health alerts in precisely the same manner that physicians receive time-sensitive clinical information for patient care, we ensure that physicians have the right information at the time they need to see it”. This was exemplified by the first electronic health alert sent out across the Docs4Docs® network with regards to the emerging H1N1 crisis on April 29, 2009.

Last year Regenstrief scientists received a $10 million, 5 year contract from the Centers for Disease Control in order to continue working on developing electronic records and notification systems like those that make up the backbone of the Docs4Docs® service in Indiana. I for one believe that money is going to good use and look forward to seeing other states follow Indiana’s lead with regards to developing new electronic records and notification systems.

In order to deal with the global outbreak of swine flu effectively, tracking the number of swine flu cases is imperative. Having as much accurate data as possible regarding the epidemic is essential for evaluating what moves the global community ought to start taking to make it through this outbreak. Thus, using quick and accurate tools to evaluate the countless samples  being collected around the world is an absolute necessity. Luckily scientists at the University of Colorado and InDevR, a small biotech in Colorado, may have exactly what the world needs in a microarray chip dubbed the FluChip.

In 2005 Dr. Kathy Rowlen, CEO of InDevR, led a team at the University of Colorado working with the Centers for Disease Control and Prevention (CDC) in developing the FluChip in order to allow labs across the world to quickly distinguish samples between 72 different influenza strains. Her group’s work produced a viable testing platform that produced results in less than 12 hours with impressive accuracy.

Now Dr. Kathy Rowlen and InDevR have licensed the FluChip technology from the University of Colorado. InDevR has arranged to begin testing samples of the swine flu on a M-gene variant of the FluChip while also working on improving the initial design by incorporating new technologies, hopefully making a new assay basic enough that any lab with PCR capabilities will be able to utilize it. Here’s to hoping the FluChip will help us get a better picture of the current state of the swine flu epidemic.

InDevR Press Release:

InDevR, a small biotech company in Boulder, CO, announced today that they have licensed the FluChip technology from the University of Colorado.  The FluChip was invented by a joint team of scientists at the University of Colorado and the Centers for Disease Control and Prevention in an NIH sponsored effort led by Professor Kathy Rowlen.  Rowlen, now the CEO of InDevR, said that InDevR has arranged to test genetic material from the recent swine H1N1 virus on the MChip as well as other versions of the FluChip which are under development.  According to Rowlen “Based on work we conducted a couple of years ago, it appears that the M-gene version of the FluChip will be able to distinguish human H1N1 viruses from the new swine H1N1 virus.  If that proves to be the case, the FluChip will be a much needed and powerful new tool for surveillance since all of the current influenza diagnostics on the market are unable to subtype this virus.” The most popular diagnostic tests for influenza include rapid immunoassays, which are only able to identify the type (A or B) of influenza virus, and reverse-transcriptase polymerase chain reaction assays, which were designed for human-adapted influenza viruses and are not able to identify the swine H1N1 subtype.  State Public Health Laboratories must now send any influenza A viruses that cannot be subtyped using existing diagnostics to the CDC for analysis by genome sequencing or viral isolation.  The CDC must select viruses to analyze since it is not possible to run every sample collected from a large number of Public Health Labs.

The M-gene based FluChip has been demonstrated to delineate human-adapted viruses from non-human viruses, such as the H1N1 virus that caused the 1918 “Spanish Flu”.  “Since the FluChip assay can be conducted within a single day it could be employed in State Public Health Laboratories to greatly enhance influenza surveillance and our ability to track the virus,” Rowlen said.  InDevR will combine the FluChip technology with an innovative detection technology (NESATM), which InDevR also licensed from the University of Colorado and further developed with NIH sponsorship, to make the FluChip assay inexpensive and easy to use in any lab that has basic PCR capabilities.  “Kathy and her team have been engaged with this and similar diagnostic technology for many years,” said Mary Tapolsky, Senior Licensing Manager at the University of Colorado Technology Transfer Office. “CU TTO is excited about this experienced and motivated group developing and commercializing this promising technology.

Thanks to the internet the enterprise of playing practical jokes on the world has become incredibly easy and every year now I look forward to seeing what hilarious items pop up throughout the internet. So here’s a quick list of some of my favorite tech/science April Fools jokes for 2009:

Google masters artificial intelligence. The brilliant people over at Google continue to amaze by creating the world’s first “artificial intelligence tasked-array system” which they’ve dubbed the Cognitive Autoheuristic Distributed-Intelligence Entity (CADIE). Apparently it’s already cranking out changes at Google: “Earlier today, for instance, CADIE deduced from a quick scan of the visual segment of the social web a set of online design principles from which she derived this intriguing homepage.”

Gmail Autopilot. Thanks to CADIE e-mail’s even easier than before. By using the Gmail Autopilot one can set simple sliders to manage all your e-mail without going through the hassle of reading and writing. E-mail will never be the same again. Nigeria may become more wealthy though…

Let Gmail Autopilot handle all your e-mail conversations.

Tiny black hole on Earth created by Large Hadron Collider. CERN admits that the real reason they shut down the LHC was due to the creation of a “tiny black hole” that they have “kept under quarantine” and are monitoring as we speak.

Qualcomm, on the cutting edge of Bioengineering. Qualcomm best known for it’s CDMA technology for wireless networks has delved into cutting edge research to improve wireless network coverage around the world. The video below takes an exclusive look behind the scenes of Qualcomm’s latest work.

Happy April Fools!

CO₂ + 2 H₂O + light –> (CH₂O)_n + H₂O + O₂

The equation above was the first thing I ever learned about photosynthesis. A simple equation that stated that the input of water, carbon dioxide, and light would allow a plant to produce sugar, water, and oxygen. The equation is just a simple overview of the impressive chain of events that take place within each cell of a plant undergoing photosynthesis. While scientists have studied and admired photosynthesis in great detail; producing a cost-effective artificial system for harnessing light for energy has proven to be a difficult proposition.

Today, much of the research being done focuses on finding ways to improve efficiency of solar cells thereby making them more cost effective. Some research is even being done to produce artificial “trees” that contain solar cells in the leaves as well as piezoelectric elements to harness kinetic energy from the wind and rain. While all these different approaches are promising and are obviously photosynthesis inspired none of them truly imitate the basic chemical reaction that is the crux of photosynthesis. That’s why I was really impressed when I read about researchers, at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory, who’ve discovered nanocrystals of cobalt oxide are capable of splitting water with only the application of visible light.

An excerpt from Physorg.com’s article:

Green plants perform the photooxidation of water molecules within a complex of proteins called Photosystem II, in which manganese-containing enzymes serve as the catalyst. Manganese-based organometallic complexes modeled off Photosystem II have shown some promise as photocatalysts for water oxidation but some suffer from being water insoluble and none are very robust. In looking for purely inorganic catalysts that would dissolve in water and would be far more robust than biomimetic materials, Frei and Jiao turned to cobalt oxide, a highly abundant material that is an an important industrial catalyst. When Frei and Jiao tested micron-sized particles of cobalt oxide, they found the particles were inefficient and not nearly fast enough to serve as photocatalysts. However, when they nano-sized the particles it was another story.

“The yield for clusters of cobalt oxide (Co₃O₄) nano-sized crystals was about 1,600 times higher than for micron-sized particles,” said Frei, “and the turnover frequency (speed) was about 1,140 oxygen molecules per second per cluster, which is commensurate with solar flux at ground level (approximately 1,000 Watts per square meter).”

Frei and Jiao hope to tie this breakthrough into a liquid fuel producing system that’s renewable and scrubs the atmosphere of CO₂ in the process. With their work on cobalt oxide they’ve made an important first step in producing a viable artificial photosynthetic system. I sure hope nature’s ok with us taking a page from her playbook.

(Image Credit – Simple Photosynthesis , Image Credit – Aritifical photosynthesis concept , Complete Physorg.com article)

*edited the photosynthesis formula meant to use the general one, but instead I used some wack combination of the two.

Having read and watched a fair amount of science fiction during my formative years, I’ve always been enamored with the concept of nanobots being used within the human body to help maintain our health. While the reality of microscopic machines moving to normally inaccessible areas of the human body and performing life saving tasks is still decades away, researchers led by Professor James Friend at Australia’s Monash University have demonstrated a proof of concept piezoelectric ultrasonic motor that could be a crucial step in providing locomotion for the nanosurgical robots of tomorrow.

In the abstract of their paper they describe their concept as:

A motor for in vivo microbot propulsion is presented with a stator diameter of 250 µm, demonstrating the potential to directly drive a flagellum for swimming at up to 1295 rpm with a torque of 13 nN m. The motor uses coupled axial-torsional vibration at 652–682 kHz in a helically cut structure excited by a thickness-polarized piezoelectric element.

Piezoelectric ultrasonic motors like the one designed by the team are built to harness special materials that exhibit the piezoelectric effect. Materials like lead zirconate titanate, thanks to the piezoelectric effect, are capable of producing electricity when stress is applied as well as the converse, producing stress when an electrical field is applied. This effect is already used in a variety of everyday applications, such as electric guitar pickups as well as auto-focus in reflex cameras. The motor (seen below), called the Proteus, designed by Friend’s team is made up of three main components: the piezoelectric element, the stator, and the rotor.

The team began to design the Proteus by utilizing computer models (seen below) to produce a novel robust stator design. They determined a helically cut stator would serve best in transferring stress and turning the rotor. The group hopes to improve their model in future work by incorporating further criteria and motor components.

After utilizing computer models to design the stator a prototype was fabricated for physical tests. Various tests were run to ascertain the potential of the Proteus. The group’s tests are promising as they found the “output power [is] on the order of what is necessary to navigate small human arteries.” In addition to the promising power output, the stator design is currently “70% smaller than the smallest design produced so far”.

While the design of a small motor is still just a small first step towards in vivo swimming surgical nanobot I can’t help but think about the possibilities this innovation will lead to. Maybe Professor Friend can contact Dr. Gracias at John Hopkins about working on a swimming microgripper next.

All graphics and quotes from:

B Watson, J Friend and L Yeo 2009. Piezoelectric ultrasonic resonant motor with stator diameter less than 250 µm: the Proteus motor. Journal of Micromechanics and Microengineering.

Some scary news if you’re an IT guy (although promising if, like us, you believe in the power of alternative processors), but basically it shows that the Playstation 3′s super-powered Cell processor really is useful for more than just Metal Gear Solid. 

Brilliant visual depiction of research described below

By using the computational power of a cluster of 200 PS3s, researchers were able to create a fake certificate allowing them to usurp certification authority from Verisign’s RapidSSL public encryption method. What that means is that the researcher’s were able to create their own certificates, meaning that they could fool any browser into believing whatever identity the researchers threw at them. Translated into real-world terms, it means that the researchers could have, had they wanted to, convinced your browser that they were your bank, your ISP, eBay, or potentially a legitimate Microsoft/Apple software update. 

Image of the "Playstation Lab" cluster which executed the hack.

The source of the hack comes from a weakness in using MD5, a popular hash-generating function which is supposed to turn large files into short 128-bit “passwords”. A 128-bit password may not seem like much (imagine converting a 200 page book into a short 200-letter sentence, you can’t recreate the book from that sentence), but the magic is that, like other cryptography methods, it is supposed to be incredibly difficult to create two files with the same MD5 “password” — a so-called “collision”. 

However, MD5 is not perfect, as a computationally intensive means of finding collisions was demonstrated in 2007, and while many certificate authorities had switched away from MD5, there were few who genuinely believed that the computational power was readily available to break it. And, while 200 Playstation 3′s is not super-easy to come by, given the profitability of such a scam, this recent exploit demonstrates that it no longer requires a massive multi-million dollar supercomputer to do the number-crunching needed (the researchers estimated that only $20,000 worth of computing power on Amazon’s Elastic Compute Cloud was needed to generate the fake certificate).

Thankfully, Verisign has confirmed that they are committed to phasing out MD5, and Microsoft and Mozilla have been fully briefed on the risk. Let us hope that is more than just empty promises.

(Image source: Playstation Lab cluster)

Having spent the past couple weeks helping pack up and move the lab. I noticed my lab had an abundance of ancient data storage devices. Various floppy/zip disks and future museum pieces (Macintosh LC anybody?) were found hiding in all manner of locations. While I’m certain that we have paper copies of any data that could be found in those disks and computers archiving or even simply accessing the data on many of them might be impossible today.

An article from Physorg.com discusses the potential of a “digital dark age” resulting from an unintended consequence of continued technological innovation. Much like the inaccessible data that I found during my lab’s move, society’s rapid digital advancement has rendered it vulnerable to what Jerome P. McDonough, assistant professor in the Graduate School of Library and Information Science at the University of Illinois at Urbana-Champaign terms a “digital dark age”. The whole article is fascinating as it details several potential data black holes. A few interesting examples:

Magnetic tape, which stores most of the world’s computer backups, can degrade within a decade. According to the National Archives Web site by the mid-1970s, only two machines could read the data from the 1960 U.S. Census: One was in Japan, the other in the Smithsonian Institution. Some of the data collected from NASA’s 1976 Viking landing on Mars is unreadable and lost forever.

It’s a shame that valuable data from, not only a historic event, but also one of such exploratory significance is now lost forever. McDonough goes on to talk about the potential loss of political and popular culture due to data obsolescence and closed platforms.

McDonough also cited Obama’s political advertising inside the latest editions of the popular videogames “Burnout Paradise” and “NBA Live” as an example of something that ought to be preserved for future generations but could possibly be lost because of the proprietary nature of videogames and videogame platforms.

“It’s not a matter of just preserving the game itself. There are whole parts of popular and political culture that we won’t be able to preserve if we can’t preserve what’s going on inside the gaming world.”

McDonough’s discussion of videogames is only the tip of the iceberg. The enormous amount of user generated content that currently provides so much amusement (youtube, failblog, etc…) is a large part of modern culture and it’d be a shame if measures aren’t taken to ensure that future generations have access to it. Hopefully we’ll heed the warnings of information scientists like McDonough and begin making progress towards protecting our digital information by attempting to future proof as best as possible.

Personally after sorting through and moving the “digital archives” of my lab I’m ready to start taking some steps to future proof my digital existence.

Steps that I plan on taking:

• Reducing my reliance on proprietary file formats (bye bye Word).
• Duplicating my backups onto various media periodically.
• Migrating to new storage technologies, such as “the cloud” (Google engineers can figure out how to keep my data safe, right?)
• Make sure this blog’s future proof =).

Any suggestions on other steps I could take?