Silva E.,Karolinska Institutet |
Silva E.,Karolinska University Hospital |
O'Gorman M.,Nonlinear Dynamics |
Becker S.,Karolinska University Hospital |
And 5 more authors.
Journal of Proteome Research | Year: 2010
Historically, the use of two-dimensional electrophoresis (2-DE) in quantitative proteomics has been hampered by significant technical variance. Over the past decade, a range of technological leaps have reduced the overall variance of 2-DE, thus turning the technology into a robust platform for quantitative intact proteomics. However, as the confounding gel-to-gel variation improves, the variance arising from the subsequent image analysis becomes more prominent. Limitations in image alignment and spot detection of previous generations of 2-DE analysis software have demanded considerable user-intervention and manual editing, resulting in introduction of a large degree of subjectivity and softwareinduced variance. We evaluated the performance of SameSpots, representing a new generation of 2-DE image analysis software, using both DIGE and traditional single-stain 2-DE approaches. Evaluations of the software-induced variance in relation to other sources of variance, as well as the subjectivity through comparison of analyses performed by an expert user and a novice lab-user, were performed, In terms of statistical power, the less-experienced user achieved the better results, but no discernible difference was detected in multivariate comparisons between the users. In conclusion, we found that SameSpots represents improvements both in reproducibility and objectivity in relation to previous generations of 2-DE analysis software. © 2010 American Chemical Society.
Creating anything new requires testing the limits of what already exists and delving into uncertainty. This is what Themistoklis Sapsis does regularly. “My work is on systems for which we understand as much as we don’t understand,” the assistant professor of mechanical engineering and director of the Stochastic Analysis and Nonlinear Dynamics Lab says. By using analytical and computational methods, Sapsis tries to predict and optimize behavior, particularly when the dynamics and excitations are uncertain and occasionally extreme. This places much of his work in the ocean environment, and whether it’s an energy-harvesting configuration or an ocean structure, his goal is to create designs that maintain operational robustness and safety regardless of the constantly varying conditions. A typical example of Sapsis’ work is analyzing the behavior of a ship in extreme weather. It’s a system and environment that combines nonlinear dynamics and uncertainty. The latter is caused by the broad range of possible conditions that a ship can encounter and results in the greatest range of possible outcomes that run from benign to catastrophic, he says. The former is an element that’s often overlooked but essential for the realistic description of the ship’s behavior. By studying them together, the potential increases for being able to produce a better structure. However, the computational cost of such analysis is often prohibitive even with modern capabilities, Sapsis says. In ship design, there are certain known factors, such as dimensions and hull geometry. There are also less predictable elements, such as the intensity of water crashing into the front and sides. Add to that the possibility of extreme weather. It’s not a regular occurrence, but it will happen, and when it does, a ship needs to be able to perform reliably. What’s needed, Sapsis says, is the development of new mathematical methods that will be able to define the envelope of safe operations, taking into account even rare events. In order to achieve such a goal, one has to focus on the statistics of the response, which indirectly describe all possible scenarios, rather than the isolated analysis of every possible outcome, which would be prohibitively expensive, he says. Along with the advantage of taking into account even rare events, Sapsis’ approach brings other advantages. He focuses on developing algorithms inexpensive enough so they can run off of a laptop, rather than a cluster of computers, keeping costs to a minimum. That freedom and flexibility lead to a more efficient and safe design. “It means less cost, higher speed and higher reliability,” Sapsis says. Sapsis also works on energy harvesting, particularly as it relates to powering small electronic devices. The same challenges apply as with a ship in the ocean: He looks at an excitation that varies in its occurrence and intensity. Using nonlinear configurations in this realm allows him to not rely on the energy content of a specific frequency, giving a broader range of resonances, he says. Through a “carefully designed oscillator,” Sapsis says that his group is looking to capture energy from walking, walking quickly, and running. These three motions have completely different characteristics, and a traditional approach relying on linear oscillators would require a separate set of design parameters for each case. Using nonlinear mechanical oscillators capable of adaptively resonating with the different paces, kinetic energy would be absorbed and transformed into electromagnetic energy with a robust level of efficiency, ultimately extending the cell battery’s life, he says. The challenge, much like with dealing with ocean waves, is in the characteristics of the excitation. Kinetic energy doesn’t always efficiently covert into usable energy. Because different people produce different accelerations when they move, Sapsis says that his design goal is fairly simple: to create consistency and maintain robustness. To do that, he needs a model, and he’s chosen a ubiquitous one. “We are inspired by what nature does,” Sapsis says, noting that turbulence, found in atmospheric and oceanic flows, is an example of robust energy transfer from scale-to-scale that he’s trying to mimic in mechanical settings. The need for some pushing Like many of his MIT colleagues, Sapsis work applies to a range of industries: design of ships and offshore structures, reliability of communication and power networks, energy harvesting, and vibration mitigation. The one consistent element is the need for collaboration. Sapsis says that while academia and industry are inclined to have an initial mutual reticence, there are benefits from both sides moving closer to each other. Academia can explore issues that aren’t merely theoretical or niche-based but address a larger market need, and industry gets to train the next generation of engineers. Sapsis adds that more than merely co-existing, there’s a greater opportunity to be taken. The two realms need to brainstorm common-interest problems and push themselves to explore issues that aren’t usually touched upon, especially ones that incorporate the uncertainty factor into design principles. Doing that will both produce stronger results for a given project and ingrain a mentality and higher expectations for future work. “We have to go beyond the low hanging fruit,” Sapsis says.
News Article | June 7, 2008
Many of today's underwater robots need to periodically come up to the surface to communicate with their human supervisors. But researchers at the University of Washington (UW) have developed a new kind of underwater vehicle. The Robofish can work cooperatively with each other. 'The Robofish, which are roughly the size of a 10-pound salmon, look a bit like fish because they use fins rather than propellers.' According to the researchers, such robots 'could cooperatively track moving targets underwater, such as groups of whales or spreading plumes of pollution, or explore caves, underneath ice-covered waters, or in dangerous environments where surfacing might not be possible.' But read more... You can see above a team of UW autonomous fin-actuated underwater vehicles. (Credit: UW Nonlinear Dynamics and Control Lab) "Currently, the robots are communicating with full-wave and half-wave wire antennas mounted externally to eliminate any radio loss incurred as a result of an air-water interface. The communication protocol currently implements a straight serial pass-through with Manchester (bi-phase) coding. A software state machine is used to continuously decode the output of the receiver, capturing any valid data and outputting it to the serial port." And above is a side view of the RoboFish 2.0. (Credit: UW Nonlinear Dynamics and Control Lab) Please note the red acoustic modem on the top of the robot. Here is a link to a larger version of this photograph. Finally, you can see above an inside view of the RoboFish. (Credit: UW Nonlinear Dynamics and Control Lab) as you can notice, the side panels are removable for easy access to electronics. Here is a link to a larger version of this photograph. This research project has been led by Kristi Morgansen, a UW assistant professor of aeronautics and astronautics in charge of the Nonlinear Dynamics and Control Lab (NDCL). She worked with UW doctoral students Daniel Klein and Benjamin Triplett who are members of her lab. She also collaborated with UW graduate student Patrick Bettale in electrical engineering and Julia Parrish, an associate professor in the UW's School of Aquatic and Fishery Sciences. So how did all the researchers found a way to coordinate the movements of the robots? According to the UW article, they faced "major challenges in having robots transmit information through dense water. [...] The energy required to send the information over long distances is prohibitive because the robots have limited battery power. What's more, signals can become garbled when they reflect off the surface or off of any obstacles. Messages were sent between the robots using low-frequency sonar pulses, or pressure waves. The new results showed that only about half the information was received successfully, yet because of the way the Robofish were programmed they were still able to accomplish their tasks. Robots that can independently carry out two simple sets of instructions -- swimming in the same direction or swimming in different directions -- will allow them to carry out more complicated missions." You'll find more details about the Robofish by looking at the NDCL research projects. Here is an excerpt about the "Fin Actuated Autonomous Underwater Vehicles" project. "Inspired by nature, our intent is to generate novel bio-inspired systems that can out-perform existing engineered systems in speed, agility and efficiency. We focus on bioinspired actuators (based on fish-fin type structures) to control fluid dynamic artifacts (both in and away from the boundary layer) that will ultimately affect speed, agility, and stealth of air and underwater autonomous vehicles. Many underwater vehicles use propellers: propellers provide high thrust, high drag, and low maneuverability. Vehicles using a fish-tail type system are more maneuverable, have the potential to turn in much shorter and more constrained spaces, to have lower drag, to be quieter, and to be more efficient." For your viewing pleasure, this specific page about Fin Actuated Autonomous Underwater Vehicle carries additional details including videos and photos which I've picked for this post. But for more technical information, you can browse the impressive NDCL list of publications. Here is my selection of two papers worth reading. The first one has been published in IEEE Transactions on Robotics under the name "Geometric methods for modeling and control of free-swimming fin-actuated underwater vehicles" (Volume 23, Issue 6, Pages 1184-1199, December 2007). Here are two links to the abstract and to the full paper (PDF format, 15 pages, 775 KB). The second paper is named "Autonomous Underwater Multivehicle Control with Limited Communication: Theory and Experiment" and was included in the Proceedings of the Second IFAC Workshop on Navigation, Guidance and Control of Underwater Vehicles (NGCUV 2008), which was held in Killaloe, Ireland, in March, 2008. Here is a link to this paper (PDF format, 6 pages, 294 KB), from which the top image in this post has been extracted. Sources: Hannah Hickey, University Week, Vol. 25, No. 30, University of Washington, June 5, 2008; and various websites You'll find related stories by following the links below.
News Article | July 17, 2012
With the recent release of The Amazing Spider-Man (here’s a discussion of some of the math and science in that movie), I thought it necessary to revisit one of the more exciting moments of my academic career: Steve was my PhD adviser. Well, you can imagine my surprise when one day back in grad school I went to visit his office only to see the screenshot below taped outside his door: Unremarkable, right? It’s a screenshot of Peter Parker (Tobey Maguire) doing his homework in Spider-Man 2. But look at the shelf. Now look at the second book from the top. If you’ve been steeped in the world of applied mathematics, this book will be immediately recognizable to you. It’s the textbook authored by Steve called Nonlinear Dynamics and Chaos. This moment of discovery was incredible. My grad school adviser wrote a textbook used by a superhero! Applied math meets comics! What’s not to love? Clearly nothing. I have explored this intersection multiple times but nothing must compare to actually having your book used by a superhero in college. And in case you’re wondering the specifics of this scene, it takes place after Peter Parker disavows his superheroics and concentrates on his studies. It is 1:04:50 into the film.
News Article | April 17, 2015
The global bioinformatics market is estimated to reach $4.2 billion by the end in 2014 and is poised to reach $13.3 billion by 2020 at a CAGR of 20.9% from 2015 to 2020 - New Research Available at RnRMarketResearch.com. The report segments the global bioinformatics market by sectors, products and services, application and geography. Knowledge management tools accounted for the largest share of the global bioinformatics market, by product and service sin 2014. However, Bioinformatics platforms are expected to grow at the highest CAGR during the forecast period. 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This large share is attributed to increasing use of bioinformatics in drug discovery and development process for the faster development of new safe and effective drugs at a reduced cost. Prominent players in global bioinformatics market, they are Affymetrix Inc, Agilent Technologies, Biomax Informatics AG, Geneva Bioinformatics (Genebio) SA, ID Business Solutions Ltd, Illumina Inc, Integromics S.L, Nonlinear Dynamics Ltd. (Acquired By Waters Corporation), Life Technologies, Qiagen, Perkinelmer Inc, Applied Biological Materials (ABM) and Dnanexus Inc Order a copy of this report at http://www.rnrmarketresearch.com/contacts/purchase?rname=102532 From an insight perspective, bioinformatics market research report focuses on qualitative data, market size, and growth of various segments and sub segments, competitive landscape, and company profiles. 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The above-mentioned market research data, current market size, and forecast of future trends will help key players and new entrants to make the necessary decisions regarding product offerings, geographical focus, change in approach, R&D investments for innovations in products and technologies, and levels of output in order to remain successful. Priced at $4650 for a single user PDF, a discount on this research report can be requested at http://www.rnrmarketresearch.com/contacts/discount?rname=102532 On the basis of applications, the bioinformatics market is segmented into genomics, chemo informatics & drug design, proteomics, transcriptomics, metabolomics and molecular phylogenetics. Genomics is expected to be the fastest growing segment in the bioinformatics application market in the next five years. 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