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  • October 24, 2012
  • 07:03 AM
  • 438 views

Scientists Find New Method to Test Bridges’ Health: Listening to Them “Singing in the Rain”

by Jaime Menchén in United Academics

It might become the most efficient and cost-effective method to check if a bridge needs repairing: Just spray the bridge’s deck with water and record the sound. That way, according to researchers at the Brigham Young University, in the US, may be possible to detect delamination (separation of structural layers) in bridges.... Read more »

  • October 22, 2012
  • 06:24 AM
  • 601 views

Large-N gauge theories on the lattice

by Marco Frasca in The Gauge Connection

Today I have found on arXiv a very nice review about large-N gauge theories on the lattice (see here). The authors, Biagio Lucini and Marco Panero, are well-known experts on lattice gauge theories being this their main area of investigation. This review, to appear on Physics Report, gives a nice introduction to this approach to [...]... Read more »

Biagio Lucini, & Marco Panero. (2012) SU(N) gauge theories at large N. arXiv. arXiv: 1210.4997v1

Marco Frasca. (2008) Yang-Mills Propagators and QCD. Nuclear Physics B (Proc. Suppl.) 186 (2009) 260-263. arXiv: 0807.4299v2

D. Gomez Dumm, & N. N. Scoccola. (2004) Characteristics of the chiral phase transition in nonlocal quark models. Phys.Rev. C72 (2005) 014909. arXiv: hep-ph/0410262v2

Marco Frasca. (2011) Chiral symmetry in the low-energy limit of QCD at finite temperature. Phys. Rev. C 84, 055208 (2011). arXiv: 1105.5274v4

  • October 18, 2012
  • 10:42 AM
  • 925 views

Searching for Extraterrestrial Microbes

by Jason Carr in Wired Cosmos

Locating thermophiles in other parts of the universe could very well aid in the search for extraterrestrial life. Most people have agreed that if life is found among the stars, it will be microbial (at least in the near-term future). Many individuals have also suggested that intelligent life forms might very well be extinct in [...]... Read more »

  • October 18, 2012
  • 07:15 AM
  • 579 views

OneZoom: Zooming in on the tree of life

by gunnardw in The Beast, the Bard and the Bot

The evolution of life is often depicted in a tree-like fashion (although, at some places, it might be more like a web). This tree analog for life’s evolution is evident in a new project to visualize the evolutionary relationships of … Continue reading →... Read more »

  • October 15, 2012
  • 10:55 AM
  • 751 views

Using METI Satellites to Find E.T.

by Jason Carr in Wired Cosmos

Cellular networks are all the rage these days. A lot of people believe that mobile technologies will eventually replace desktops/laptops entirely. Regardless, they only work with terrestrial communications networks here on Earth. What if a similar network could be built beyond our planet? Considering that all electromagnetic radiation travels at the speed of light, the [...]... Read more »

  • October 14, 2012
  • 05:55 AM
  • 769 views

Citizen science and digital platforms: folding it all the way to outer space

by Cobb & Hecht in Do You Believe In Dog?

ScienceRewired is a philanthropic initiative that aims to promote public engagement in science through digital and social technologies. Their mission is to aid non-technical science practitioners and the digital domain in working together, to look at science from new perspectives while helping educate and empower individuals to create significant positive change in the world. Their focus spreads across science education, science communication and citizen science initiatives – what’s not to love about that?!(source)I was fortunate to be awarded a scholarship to attend the day in Adelaide (730km / 450 miles away from home) by the Australian Science Communicators. The event was themed ‘Connect, Collaborate and Communicate for Change’ and intended to bring together science communicators, academics, media professionals and digital visionaries for a one day conference of debate, insight and education as a springboard for ongoing communication and action. We heard from a wide range of wonderful speakers about different digital/social media initiatives (most session content has been reported here), but what I wanted to share with you today were two really exciting and different projects that are underway using citizen science.(source)(source)What is Citizen Science anyway?Citizen science has been gaining momentum since the mid-1990’s, but just in case you haven’t heard the term before, relax. You already know what it is even if you haven’t heard the label. Simply put, it’s when amateur scientists or non-professionally-scientific people (i.e. general public) collaborate and help contribute to science. The internet has made this super easy.... Read more »

Hand Eric. (2010) Citizen science: People power. Nature, 466(7307), 687. DOI: 10.1038/466685a  

Khatib F., Cooper S., Tyka M. D., Xu K., Makedon I., Popovic Z., Baker D., & Players F. (2011) From the Cover: Algorithm discovery by protein folding game players. Proceedings of the National Academy of Sciences, 108(47), 18953. DOI: 10.1073/pnas.1115898108  

Parsons Jeffrey, Lukyanenko Roman, & Wiersma Yolanda. (2011) Easier citizen science is better. Nature, 471(7336), 37. DOI: 10.1038/471037a  

  • October 12, 2012
  • 05:35 AM
  • 892 views

What's new in Music Cognition and the Cognitive Sciences?

by Henkjan Honing in Music Matters

Why should music be of interest to cognitive scientists, and what role does it play in human cognition? ... Read more »

Pearce, Marcus, & Rohrmeier, Martin. (2012) Music Cognition and the Cognitive Sciences. Topics in Cognitive Science, 4(4), 468-484. info:/10.1111/j.1756-8765.2012.01226.x

  • October 11, 2012
  • 10:14 PM
  • 508 views

Powering electronics with stretchable batteries

by Cath in Basal Science (BS) Clarified

Potential health monitors like this one made of interlocking nanofibres are great—it’s flexible and conforms to your body. But what you don’t usually see is how these monitors might be [...]... Read more »

Abhinav M. Gaikwad, Alla M. Zamarayeva, Jamesley Rousseau, Howie Chu, Irving Derin, & Daniel A Steingart. (2012) Highly Stretchable Alkaline Batteries Based on an Embedded Conductive Fabric. Advanced Materials. DOI: 10.1002/adma.201201329  

  • October 8, 2012
  • 01:30 PM
  • 651 views

What Types of Feedback Should Students Receive?

by Eric Horowitz in peer-reviewed by my neurons

Throughout the school day there are hundreds of small reactions, judgments, and decisions that are tossed around in a student’s head. The question is, when, where, and how can students be given additional information that nudges these thoughts in directions that will lead to better learning outcomes... Read more »

Taminiau, E.M.C., Kester, L., Corbalan, G., Alessi, S.M., Moxnes, E., Gijselaers, W.H., Kirschner, P.A., & Van Merrienboer, J.J.G. (2012) Why advice on task selection may hamper learning in on-demand education. Computer in Human Behavior. DOI: 10.1016/j.chb.2012.07.028  

  • October 5, 2012
  • 12:42 AM
  • 531 views

Technology Is Rapidly Lowering the Cost of Testing

by Eric Horowitz in peer-reviewed by my neurons

People may view this as something for the good news/bad news file, but technology has quietly made it significantly easier to grade tests electronically. For example, a new paper in the Journal of Science Education and Technology highlights a system called “Eyegrade” : While most current solutions are based on expensive scanners, Eyegrade offers a [...]... Read more »

  • October 4, 2012
  • 03:50 PM
  • 572 views

A Microsyringe to Take the Pain out of Shots

by Hector Munoz in Microfluidic Future

Back when I was in sixth grade, I remember reading a little blurb in some science magazine at school that in the future we could receive shots via a method that would feel as soft as a banana peel. Although I’m now a champ at taking shots, it’s still not a bad idea. We’ve had transdermal patches (think nicotine and birth control) for some time now, but those release their medicine over a period of time. A syringe is capable of delivering a dose at once, and can take a biological sample too. Researchers from the University of Pisa have developed this ‘syringe of the future’ within ‘A minimally invasive microchip for transdermal injection/sampling applications’ in Lab on a Chip.... Read more »

  • October 1, 2012
  • 01:11 PM
  • 891 views

Does playing Solo or Vs make a Difference in Kinect or Wii? (Study)

by Stephen Yang in ExerGame Lab

If you thought yes, "you are correct Sir!" According to the current study, playing Xbox Kinect™ Reflex Ridge resulted in a 1 MET higher rating than Wii Sports Boxing, and playing multiplayer...

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... Read more »

  • October 1, 2012
  • 01:10 AM
  • 885 views

Does playing Solo or Vs make a Difference in Kinect or Wii? (Study)

by Stephen P. Yang, Ph.D. in ExerGame Lab

According to the current study, playing Xbox Kinect™ Reflex Ridge resulted in a 1 MET higher rating than Wii Sports Boxing, and playing multiplayer yielded a 0.5 MET increase compared to solo play... Read more »

  • September 26, 2012
  • 08:50 AM
  • 381 views

Fellows of the Wiki Society? The Royal Society in London experiments with Wikipedia

by Duncan Hull in O'Really?

Venerable and learned society experiments with wikipedia... Read more »

Wodak Shoshana J., Mietchen Daniel, Collings Andrew M., Russell Robert B., & Bourne Philip E. (2012) Topic Pages: PLoS Computational Biology Meets Wikipedia. PLoS Computational Biology, 8(3). DOI: 10.1371/journal.pcbi.1002446  

  • September 26, 2012
  • 01:38 AM
  • 901 views

Mirror, Mirror on the wall, Am I healthy after all?

by Aurametrix team in Health Technologies

Health gadgets continue to evolve in many forms and shapes - from something that fits in your pocket to something that is wearable or walkable. Everyday objects are turning into "Smart objects", building the foundation for the next version of the Internet. And it's not all smoke and mirrors. So let's talk about mirrors. Fairy tales and science fiction stories often pave the way to real world technology. Magic mirrors have been used in Snow White and Harry Potter's world. Now you can get one, too - manufactured by a Hong Kong company James Law Cybertecture International. Cybertecture mirror can tell you about the weather or your last weight readings reported by the scales. It can show you a TV channel, let you browse Facebook or twitter and help you to exercise. Impressive, yet so much more is yet to come.Could a mirror tell us how healthy we are? For example, could it measure our heart rate at a distance? Sure, it could. And it has already been demonstrated as a concept prototype (Cardiocam, MIT media labs, Poh et al. 2010), although the designer is now focusing on mobile devices (check his company Cardiio).What other health metrics could be performed by the mirror during your regular morning hygiene routine? If a camera can measure minute changes in the color of your face to determine your heart rate, it could also measure your facial expressions and emotions or perform observational analysis  - the first of four methods of diagnosis performed by traditional Chinese medicine. Prototypes for computerized facial diagnostic systems already have been developed. One recent study, for example, (Li et al 2012) analyzes lips. The software segments lips from the rest of the face and extracts color, texture and shape features. Special supervised learning algorithms are then able to classify lips as deep-red, purple, red or pale and make inferences related to energy levels and circulation. Health management applications will not be limited to smartphones or smart homes. All objects in our lives will gradually become "smarter." Mobile phones can already manage vacuum cleaners and thermostats. Refrigerators can tweet, check Google calendars, download recipes, play tunes and alert us about food spoilage. Mirrors can monitor our weight and exercise. There is still more emphasis these days on technological wizardry than on actual benefits, but systems like Aurametrix are bringing it all together and generating valuable insights. And perhaps, one day, we won't regard the mirror on the wall nagging us about losing weight or commenting on the bags under eyes is an invasion of privacy. Let's build the future piece by piece - and they will come.REFERENCESPoh MZ, McDuff DJ, & Picard RW (2010). Non-contact, automated cardiac pulse measurements using video imaging and blind source separation. Optics express, 18 (10), 10762-74 PMID: 20588929Li F, Zhao C, Xia Z, Wang Y, Zhou X, & Li GZ (2012). Computer-assisted lip diagnosis on traditional Chinese medicine using multi-class support vector machines. BMC complementary and alternative medicine, 12 (1) PMID: 22898352Littlewort, G., Whitehill, J., Wu, T., Fasel, I.R., Frank, M., Movellan, J.R., Bartlett, M.S. (2011) The Computer Expression Recognition Toolbox (CERT). Proceedings of the 9th IEEE Conference on Automatic Face and Gesture Recognition. ... Read more »

  • September 22, 2012
  • 07:11 PM
  • 905 views

Quantum computers | Κβαντικοί υπολογιστές

by Perikis Livas in Chilon

A research team led by Australian engineers has created the first working quantum bit based on a single atom in silicon, opening the way to ultra-powerful quantum computers of the future.

In a landmark paper published today in the journal Nature, the team describes how it was able to both read and write information using the spin, or magnetic orientation, of an electron bound to a single phosphorus atom embedded in a silicon chip.... Read more »

UNSW News, NATURE, Physics4u, Physicsgg, & Γούσια Πολυξένη. (2012) Quantum computers | Κβαντικοί υπολογιστές . Tracing Knowledge. info:/

  • September 22, 2012
  • 01:26 PM
  • 714 views

Can Video Games Teach Kids “Grit”?

by Eric Horowitz in peer-reviewed by my neurons

KIPP’s character report card and Paul Tough’s new book have laudably placed an emphasis on how emotional skills and character traits (e.g. persistence, curiosity, optimism, etc.) influence a child’s academic trajectory. Yet the question remains, will our education system make a real effort to emphasize these new ideas, or will they join things like Carol [...]... Read more »

  • September 22, 2012
  • 11:02 AM
  • 1,035 views

OMG! An Open Molecule Generator!

by egonw in Chem-bla-ics

Earlier this week an important cheminformatics paper appeared in the Journal of Cheminformatics. It is about the Open Molecule Generator (see below for the paper). This was one important piece of functionality still missing from Open Source cheminformatics. This works uses the Chemistry Development Kit, and was written by Julio Peironcely.

The Analytical Biosciences' group of Prof. Hankemeier (and many others, including also Theo Reijmers) and funded by the Netherlands Metabolomics Centre has been using the CDK for metabolomics for a while now, with Miguel Rojas-Chertó as other principle user (and of course CDK developer!). I congratulate them all with this piece of work, and particularly with their choice of license!

Julio (with the other authors) have picked up a difficult algorithm, based in mathematics, but not the straightforward graph theory either. Others have tried to implement structure generation in the CDK, and I looked into this too, when working in Christoph Steinbeck's group back in Cologne. What the OMG team has achieved is significant.

The paper compares their results with MolGen, resulting in results like those in this table (from the CC-SA-BY paper):



It shows that the results are identical, when you consider the atom types it uses. And the use the CDK atom type framework I initiated, which is way cool! Julio found the tables I constructed from earlier CDK code incomplete (as did others) and extended them, to match their needs.

One "problem" with their current code base is that it is quite slow compared to OMG. This is easily compensated by the added functionality of OMG, such as restricting the structure generation with multiple fragments. Now, the CDK data classes are know to be somewhat sluggish, as compared to competition, but the community is increasingly improving this.

But I also think that the OMG use of Naughty via JNI is not helping performance either, and I hope someone will soon jump in and convert that C code into Java code, which should speed up performance too. Another side to this is that removing the dependency on C code will also make it easier to integrate into other tools, like Bioclipse, Taverna, and KNIME.

Julio E Peironcely, Miguel Rojas-Chertó, Davide Fichera, Theo Reijmers, Leon Coulier, Jean-Loup Faulon, & Thomas Hankemeier (2012). OMG: open molecule generator Journal of Cheminformatics, 4 DOI: 10.1186/1758-2946-4-21... Read more »

Julio E Peironcely, Miguel Rojas-Chertó, Davide Fichera, Theo Reijmers, Leon Coulier, Jean-Loup Faulon, & Thomas Hankemeier. (2012) OMG: open molecule generator. Journal of Cheminformatics, 21. DOI: 10.1186/1758-2946-4-21  

  • September 22, 2012
  • 08:00 AM
  • 690 views

New Caledonian crows reason about hidden causal agents

by Rogue Medic in Rogue Medic

We have generally believed that animals are not capable of very complex thought, even though many species use tools and engage in other complex behaviors.

Even a bird brain appears to be capable of understanding things that are not visible may be affecting their environment.

This study looks at whether New Caledonian crows, that were caught just for this experiment, are capable of attributing actions to a hidden cause, when they see that possible cause come and go.... Read more »

  • September 17, 2012
  • 10:30 PM
  • 954 views

How to Build a Neuron: Shortcuts

by TheCellularScale in The Cellular Scale

So you want to build a neuron, but don't have the time to fill and stain it, digitally reconstruct it, or even to knit one. Knitting Neuroscience from Knit a Neuron Well you are in luck because a lot of scientists have collected a lot of data already and some of them are even willing to openly share their work.  While it is great that people are willing to share their data, that willingness alone is not enough to actually make the data widely accessible (or searchable for that matter). To bridge the chasm, other scientists have developed databases and repositories.  These databases and repositories store large datasets and organize them in a searchable way.  The first shortcut to building a neuron I will discuss is the Cell Centered Database (CCDB).Sounds a little like "self-centered" but represents just the opposite: scientists willing to share their data with everyoneIn 2003, Martone and colleagues created the CCDB as a repository for 2D, 3D, and 4D images of cells that could be downloaded and used by researchers around the globe. There is a ton of data here, protein stains, electron microscopy, and fluorescent confocal images just to name a few.  While you could do a lot with this kind of information, I am just going to give you one example of how it can be used as a major short cut in the process of building a neuron. So say you want to make a model of a cerebellum purkinje cell, but you don't have the time or lab facilities to fill and stain your own neuron.  You could go to CCDB, type in 'purkinje neuron' in the search box and download whichever 3D image stack suits your fancy.  example Purkinje neuron that I just got from CCDBWith this data you could go straight to step 2: reconstructing the neuron.  But what if you don't have the time to digitally reconstruct the neuron?  We have already discussed how much time reconstructing a neuron can take, so it's pretty easy to see why you would want to bypass that step too. And in fact, there is a database for that! Halavi et al (2008) developed Neuromorpho.org as a repository for neural reconstructions. Neuromorpho.org has almost 8,000 downloadable digital reconstructions of neurons, which as they say on the website represents over 200,000 hours of manual reconstruction time.  NeuroMorpho.org, for all your neural needs.Similar to CCDB, Neuromorpho offers much more than just a shortcut for lazy computational modelers. It has such detailed information about each neuron that a whole project could be done simply by comparing neural characteristics of different cell classes or different species.  But my job here is to tell you how you can use it as a shortcut to building a neuron.Say you want to build a computational model of a CA1 Hippocampal Pyramidal Cell, but you don't want to stain it and you don't want to reconstruct it.  Well, just go to Neuromorpho.org and click 'browse by brain region' and then on 'hippocampus'. Then look through the 1,000 hippocampal cells (organized by class) that have already been reconstructed for you...Pyramidal cell in the Hippocampus from Neuromorpho.org ...and pick your favorite.  Then you can jump right on through to step 3. (coming soon)Halavi M, Polavaram S, Donohue DE, Hamilton G, Hoyt J, Smith KP, & Ascoli GA (2008). NeuroMorpho.Org implementation of digital neuroscience: dense coverage and integration with the NIF. Neuroinformatics, 6 (3), 241-52 PMID: 18949582Martone ME, Tran J, Wong WW, Sargis J, Fong L, Larson S, Lamont SP, Gupta A, & Ellisman MH (2008). The cell centered database project: an update on building community resources for managing and sharing 3D imaging data. Journal of structural biology, 161 (3), 220-31 PMID: 18054501... Read more »

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