Bench Press

You won't want to buy a new Lambhorgini until it comes packaged with the DySCAS architecture.

No, I don’t mean buying a new BMW or Ferrari (although, for the environmentally inclined, I do suggest investing in a hybrid). Thanks to the EU-funded DySCAS Project and its researchers, “upgrading your car” might refer to upgrading the car’s software rather than its engine. Developed for over two and a half years, this new technology could revolutionize the automotive industry. The motivation of this project was to allow cars to keep up with the times. Because an owner generally uses a car for about ten years, the DySCAS Project will allow cars to update software through the internet and avoid becoming digitally obsolete. With technology advancing at such a rapid pace, even a car’s onboard software can be left in the dust without proper updates. Old media formats for the entertainment system and outdated maps for the navigation system are just two examples of this.

“Cars take many years to develop and most are designed to be on the road for perhaps a decade. In that time, technology can change a lot, but currently there is no efficient way to update the software in these vehicles”

In addition to keeping up to date files on hand, there are other plans to allow communication and syncing of different media devices, such as PDAs and cell phones, to the car’s system.

While the first step in this project is to update non-critical systems only, eventually, the plan is to release patches which might influence safety mechanisms such as automatic braking and engine timing. It wouldn’t be hard to envision changes to the braking system’s software in order to maximize fuel economy or backup safety protocols for the driver in case one set malfunctions. These are all parts of a plan to deploy a dynamically reconfiguration system which assesses real-time data and makes proper adjustments to the car itself. However, implementing these new features is still a far way off. For now, the researchers have created a static architecture called AUTOSAR, which will hopefully be the prototype for a more dynamic, upgradable architecture in the future.

For me, this new innovation demonstates another example on how technology can help save lives. Obviously, any technology influencing the performance of a car must be thoroughly tested (virtual test dummies anyone?), but iterative testing and releases of progressively safer software can curb automotive related deaths significantly. I adamantly believe the more we incorporate technology into our everyday lives, the more good will come from it.

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Today modern medicine provides patients with numerous drugs for an enormous number of health issues. For example, getting relief from a headache can be as simple as popping open a bottle of aspirin and swallowing a couple pills. While to the patient the delivery of the drug begins and ends with swallowing those two pills with a glass of water, to the scientists working on the drug that’s simply the beginning of numerous steps that hopefully result in a drug surviving the trip through the body to it’s intended target and doing it’s job.

Drugs are therefore designed not just to solve a problem but to survive the human body’s natural mechanisms. The gauntlet of obstacles that a drug faces upon entry into the body is a major reason why many researchers continue to look into innovative techniques for delivering pharmaceuticals.

That’s where research being conducted by Drs. Stefan Franzen and Steve Lommel comes in. Working with the red clover necrotic mosaic virus (RCNMV), Drs. Franzen and Lommel have developed a potential revolutionary drug delivery platform.

Figure 1. Production of Drug Vector

Drs. Franzen and Lommel take advantage of a 17 nanometer space within the 38 nanometer icosahedral capsid of RCNMV in order to store therapeutics. The RCNMV infused with the drugs could then be used to deliver the drugs in a cell specific manner with the addition of targeting peptides.

The preparation of the drug carrying virus is elegant in it’s simplicity and produces a robust delivery mechanism (See Fig 1). First RCNMV is treated with EDTA to open pores in the capsid. Next therapeutics are infused through these open pores. The pores are then sealed with Ca²⁺ which is key in releasing the drug later upon viral entry to the cell. The prepared virus can then be purified via dialysis followed by adding target specific peptides.

The elegance of using Ca²⁺ to seal the pores lies in the fact that the human bloodstream is abundant in calcium. Inside cells, calcium levels are much lower, allowing the pores to open up thereby delivering the infused therapeutics only when the target cell has been entered.

In vitro work with Doxorubicin, a cancer drug, infused RCNMV shows promising results (see Fig 2.) promoting apoptosis only when provided with targeting peptides allowing the drug to be delivered to the interior of cells.

Figure 2. Delivery of Doxorubicin RCNMV to HeLa cells

A potential application of this research is in cancer treatment. Current chemotherapy treatments often result in dramatic side effects as the drugs do not distinguish between diseased and healthy cells. While these results are probably still years from resulting in a commercial therapy it provides hope that in the near future doctors will be able to prescribe chemotherapy treatments with dramatically reduced side effects thanks to target specific delivery of the drugs.

(Sources: NCSU – results. , NCSU News , Franzen Presentation – Plant Virus Nanotechnology)

We’ve written before about the ability of scientists to use distributed computing to pool the computing power of millions of users over the internet to solve sophisticated mathematical problems. But imagine if we could actually pool the brainpower of volunteers — but in a way which doesn’t involve jacking our brains into the Matrix.

Now, imagine if it could be fun for the volunteers.

Imagine no longer. Fold.It was created less than a year ago at the University of Washington to do just that. Instead of pooling the computational power of millions of machines, it seeks to pool the “human intuition” of volunteers to solve challenging protein folding problems.

The basic scientific concept behind Fold.It is that nature will “push” chains of amino acids to adopt a folded structure which minimizes free energy. But, while free energy calculations can be done relatively easily, finding the structure that minimizes free energy is not so easy to do and requires immense computational power (which is why Folding@Home uses distributed computing).

But, humans have a gift which computers do not: the gift of intuition. While we may not be able to compute the free energies in our head, we have the ability to make logical jumps and do complex reasoning. While we might not necessarily understand how to calculate the strength of a hydrophobic interaction, we know enough that we should place two hydrophobic (non-polar) leucine amino acids near one another. While we may not be able to write a mathematical equation to describe the arc of a polypeptide chain, we can conceptualize and visualize that a chain should be more “scrunched up” or “stretched out”.

And that type of “soft reasoning” is the processing power Fold.It seeks to capture. Fold.It created a game which literally depicts a “raw” protein chain in all its unfolded glory and asks human players to fold it. And, by deploying another unique characteristic of human beings, our competitiveness, the game encourages users to try to aim for the protein structure with the lowest free energy. The current aim is to see if the gift of human logic and competition is enough to solve complicated protein folding problems which currently require massive brute force calculations by supercomputers/distributed systems, and if so, if human 3D intuition can be “taught” to computers.

A quick overview of the game:

The novelty of this approach is striking. Interestingly, if Fold.It is successful, it will have done three very impressive (and very difficult) things:

• Successfully used crowdsourcing by pooling the wisdom of volunteers to solve problems which traditional brute-force computation finds nearly intractable
• Successfully use machine learning to copy the pooled wisdom of the volunteers to create smarter machines capable of solving the important protein folding questions which may underlie disease processes like cancer and Alzheimer’s
• Developed a new avenue with which to mobilize the public – by giving the public a tangible way to actively connect with and help an important scientific endeavor in a fun and easy-to-understand way

Check it out!

Berkeley researchers are on the heels of settling debates over taxonomy using innovative computing methods.

Apparently, whoever came up with the saying “nothing good ever comes from cheating” didn’t go to Berkeley. Recently, a team of researchers at the University of California, Berkeley took a little bit of inspiration from plagiarism-detecting software and created a program which can compare the entire genomes of two distinct organisms. Using what are known as feature frequency profiles (FFP), professor of chemistry Sung-Hou Kim and his team were able to successfully compare the genomes of several different organisms, and in a sense, “map” the organisms’ evolutionary family tree.

Traditionally, methods of determining how closely related two species are focus on a very specific subset of genes that the organisms have in common. The differences and similarities in the genetic code are then counted up and a computer program constructs the family tree. The more differences in the genes, the more distantly related the organisms are. However, the drawback of this technique is that it relies on organisms having these specific genes in common. What may end up happening is that an organism may not have a “homologous” gene to compare it with. Additionally, two genes that are used for comparison oftentimes conflict with each other; one gene says two organisms should be closely related while another one says they shouldn’t. With this innovative new approach of using FFP’s, the entire genome is sequenced and compared, as opposed to several different genes, allowing scientists to view differences in a larger scope.

Maybe even more surprising, this idea of using FFP’s as a means of comparison transcends the realm of genetics. When applied to literary works, this algorithm was able to better detect similarities between texts by the same author, of the same genre, and of the same historical era, than other conventional methods.

I was just stunned when I saw this,” Kim said. One of the reasons this method works better, he said, may be that, while word frequency analysis treats each word independently, feature frequency analysis picks up syntax.

Armed with this technique, these researchers have successfully segregated the proteomes of bacteria, Archaea, and eukaryotes with genomes of varying complexity into distinct groups and domains. Whenever disagreement occurred between their findings and common scientific belief, there was generally some kind of ongoing debate over that particular organism’s taxonomy. Professor Kim and the rest of his colleagues hope that they can use this algorithm to classify some enigmatic viral genomes and possibly utilize it in other fronts, such as literature and electronic encoding.

To me, this breakthrough in comparative genomics is a chance to reflect on how marvelous and miraculous life and evolution are. To think that the entire human civilization arose from single celled organisms, and that the building blocks and impulses which act upon bacteria and micro-organisms to keep them alive are the very same mechanisms that we live on.