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Huhmer A.F.R.,Thermo Fisher Scientific | Paulus A.,Life Science Group | Martin L.B.,Waters Corporation | Millis K.,Cambridge Isotope Laboratories andover | And 6 more authors.
Journal of Proteome Research | Year: 2013

The grand vision of the human proteome project (HPP) is moving closer to reality with the recent announcement by HUPO of the creation of the HPP consortium in charge of the development of a two-part HPP, one focused on the description of proteomes of biological samples or related to diseases (B/D-HPP) and the other dedicated to a systematic description of proteins as gene products encoded in the human genome (the C-HPP). This new initiative of HUPO seeks to identify and characterize at least one representative protein from every gene, create a protein distribution atlas and a protein pathway or network map. This vision for proteomics can be the roadmap of biological and clinical research for years to come if it delivers on its promises. The Industrial Advisory Board (IAB) to HUPO shares the visions of C-HPP. The IAB will support and critically accompany the overall project goals and the definitions of the critical milestones. The member companies are in a unique position to develop hardware and software, reagents and standards, procedures, and workflows to ensure a reliable source of tools available to the proteomics community worldwide. In collaboration with academia, the IAB member companies can and must develop the tools to reach the ambitious project goals. We offer to partner with and challenge the academic groups leading the CHPP to define both ambitious and obtainable goals and milestones to make the C-HPP a real and trusted resource for future biology. © 2012 American Chemical Society.

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.

Collins B.C.,University College Dublin | Collins B.C.,ETH Zurich | Miller C.A.,Agilent Technologies | Sposny A.,Institute for Toxicology | And 4 more authors.
Molecular and Cellular Proteomics | Year: 2012

There is a pressing and continued need for improved predictive power in preclinical pharmaceutical toxicology assessment as substantial numbers of drugs are still removed from the market, or from late-stage development, because of unanticipated issues of toxicity. In recent years a number of consortia have been formed with a view to integrating -omics molecular profiling strategies to increase the sensitivity and predictive power of preclinical toxicology evaluation. In this study we report on the LC-MS based proteomic analysis of the effects of the hepatotoxic compound EMD 335823 on liver from rats using an integrated discovery to targeted proteomics approach. This compound was one of a larger panel studied by a variety of molecular profiling techniques as part of the InnoMed PredTox Consortium. Label-free LC-MS analysis of hepatotoxicant EMD 335823 treated animals revealed only moderate correlation of individual protein expression with changes in mRNA expression observed by transcriptomic analysis of the same liver samples. Significantly however, analysis of the protein and transcript changes at the pathway level revealed they were in good agreement. This higher level analysis was also consistent with the previously suspected PPARα activity of the compound. Subsequently, a panel of potential biomarkers of liver toxicity was assembled from the label-free LC-MS proteomics discovery data, the previously acquired transcriptomics data and selected candidates identified from the literature. We developed and then deployed optimized selected reaction monitoring assays to undertake multiplexed measurement of 48 putative toxicity biomarkers in liver tissue. The development of the selected reaction monitoring assays was facilitated by the construction of a peptide MS/MS spectral library from pooled control and treated rat liver lysate using peptide fractionation by strong cation exchange and off-gel electrophoresis coupled to LC-MS/MS. After iterative optimization and quality control of the selected reaction monitoring assay panel, quantitative measurements of 48 putative biomarkers in the liver of EMD 335823 treated rats were carried out and this revealed that the panel is highly enriched for proteins modulated significantly on drug treatment/hepatotoxic insult. This proof-of-principle study provides a roadmap for future large scale pre-clinical toxicology biomarker verification studies whereby putative toxicity biomarkers assembled from multiple disparate sources can be evaluated at medium-high throughput by targeted MS. © 2012 by The American Society for Biochemistry and Molecular Biology, Inc.

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.

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 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. Complete report on Bioinformatics Market by Sector (Molecular Medicine, Agriculture, Forensic, Animal, Research & Gene Therapy), Segment (Sequencing Platforms, Knowledge Management & Data Analysis) & Application (Genomics, Proteomics & Metabolomics) - Global Forecast to 2020 available at Developing Asian countries such as China and India are lucrative markets for bioinformatics, owing to an increasing number of contract research organizations (CROs), rise in public and private sector investment, and growing industry -academia partnerships. Medical biotechnology accounted the largest share of bioinformatics market, by sector. 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 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. The qualitative data covers various levels of industry analysis such as market dynamics (drivers, restraints, opportunities, and threats), winning imperatives, and burning issues. The report also offers market sizes and data on the growth of various segments in the industry. It focuses on emerging and high-growth segments, high-growth regions, and initiatives of governments. The competitive landscape covers growth strategies adopted by industry players in the last three years. The company profiles comprise basic views on key players in the bioinformatics market and the product portfolios, developments, and strategies adopted by market players to maintain and increase their market shares in the near future. 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 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. "Latin American Bioinformatics Market by Sector (Agriculture, Molecular Medicine, Research & Animal), Segment (Sequencing Platforms, Knowledge Management Tools & Data Analysis Services) & Application (Genomics, Proteomics & Drug Design) - Forecasts to 2017" research report is now available with Companies like Accelrys Inc, Active Motif Inc, Affymetrix Inc, Agilent Technologies Inc, CLC Bio, Geneva Bioinfromatics (Genebio) Sa, Illumina Inc, Life Technologies Corporation, Partek, Incorporated and Perkinelmer Inc are discussed in this research available at "Biological Seed Treatment Market by Type (Microbial & Botanicals), Crop Type (Cereals & Grains, Oilseeds, & Pulses, Fruit & Vegetables) & Region - Global Trends & Forecast to 2019" research report is now available with Companies like Bayer Cropscience AG, Syngenta AG, BASF SE, Novozymes A/S, Koppert B.V, Italpollina S.P.A, Valent Biosciences Corporation, Verdesian Life Sciences Europe Ltd, Precision Laboratories LLC and Plant Health Care PLC are discussed in this research available at is your single source for all market research needs. Our database includes 500,000+ market research reports from over 100+ leading global publishers & in-depth market research studies of over 5000 micro markets. With comprehensive information about the publishers and the industries for which they publish market research reports, we help you in your purchase decision by mapping your information needs with our huge collection of reports.

News Article | June 6, 2008

As you leave the beach and head out into the ocean, there are a few regions you'll go through before reaching the 'deep' ocean. Nearest the shore is a relatively flat region known as the continental shelf, which extends out hundreds of kilometers; beyond this is the continental rise, which drops much more sharply into the depth of the ocean below. Along the continental rise, complex flows generate turbidity currents that aid in material transport and the creation of particle rich areas just above the ocean floor. New research shows that, under certain conditions, these flows actually help shape the continental rise itself. Researchers from the Center for Nonlinear Dynamics at the University of Texas at Austin have added to the understanding of the complex ocean movements that couple the tides, internal fluid waves, variations in density, and the shaping of the continental slope. As the ocean extends out beyond the well-mixed regions near the shore, density varies as a function of depth, and this becomes an important contributor to the fluid dynamics. Under certain conditions, this variation of density can lead to the formation of what are termed internal waves, waves that exist entirely within the ocean itself. The oscillatory motion of the ocean as the tides flow against large-scale underwater features can lead to a large number of these internal waves. To study this system, the researchers used the fact that, if one looks at this problem from a reference frame that is moving with the tides, the continental slope acts as a simple oscillating wavemaker. While no one can build the ocean, a simple wavemaker tank is well within the realm of modern engineering. The results of the experiments carried out in this wavemaker tank are set to be published in an upcoming edition of Physical Review Letters. The experiments monitored small titania particles in the tank as the "continental shelf" moved slowly left and right, mimicking the tide. The particles allowed them to generate images of how the fluid was moving about; florescent dye was used to visualize how rapidly mixing occurred in the flow region, and conductivity probes measured the fluid density. The team found that, when the slope at which the internal waves moved was similar to the slope of the continental shelf, strong resonant internal waves were generated. It's thought that these waves are capable of shaping the topography of the ocean floor.

News Article | September 24, 2013

UK startups raising financing have a new route to funds in the shape of a government-backed fund which can super-charge an Angel round with extra cash. The Angel CoFund is a UK government-backed £100m fund able to make initial investments of between £100,000 to £1 million into businesses, alongside syndicates of business angels. Launched in November 2011, it was an early backer of Yplan, the events app which this year raised $12 million and PlayJam (a games maker for smart TVs). The fund started out investing in just some parts of the UK, but now it works nationwide. And it’s now had its first exit in its short, two year history. Nonlinear Dynamics, a Newcastle firm that develops specialist software for analysing proteins, has been acquired by Waters Inc, one of largest companies in the analytical instruments industry, listed on the New York Stock Exchange and with a market cap of $8.85bn. The Angel CoFund released information to the effect that it had acquired approximately 5% of the company, whilst also investing in a convertible loan. It had originally invested £383,000, but the exit means its return was £1.086 million, or a 2.84x for the fund and its co-invested Angels. The Angel CoFund usually offers about one third again in funding to the startup which can really super-charge an investment. To date the fund has supported 32 companies, providing £12 million in direct investment alongside £50 million from business angels. The committee that makes the decisions about the investments includes Alan MacKay, CEO of Hermes GPE and a BVCA member and Alistair Arkley Advisory Board member of Seraphim Capital and Hotspur Capital. Other members of the committee are active Angels so we are not talking about inexperienced government officials here. The fund typically works quite quickly with Angel networks around the country, so it is worth startup entrepreneurs making their angel investors aware of the the Angel CoFund if they are not already. Clearly they have the capability to raise the levels of investment in a startup to a more workable level than a smaller Angel round might allow.

News Article | October 23, 2015

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.

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