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  • November 19, 2012
  • 01:27 AM

Airbag Saved My Life: the Carolina Review’s Clinical Derpitude Continues

by csoeder in Topologic Oceans

I had thought that once I graduated college, annoying student publications would quit being so… annoying. Alas, this isn’t the case. A previous article examined the quality of analysis at the Carolina Review, UNC’s ‘journal of conservative thought and opinion’; let’s see if things have approved any in the handful of years that I’ve been [...]... Read more »

Wenzel, T., & Ross, M. (2008) Safer Vehicles for People and the Planet. American Scientist, 96(2), 122. DOI: 10.1511/2008.70.3638  

  • November 18, 2012
  • 03:39 PM

DHSs and histone modifications: methylation, acetylation, citrullination, and phosphorylation

by egonw in Chem-bla-ics

One day on, and still struggling with the chemistry behind gene regulation. Let no biologist ever tell me again not to use acronyms (yes, I am looking at you!). But it is interesting. I learned a lot about ChIP, histone modifications, etc, etc. This is an amazing world, where specific histone complex protein residues get methylated, acetylated, citrullinated, and phosphorylated. Of course, all this is in the context of the ENCODE meeting we have tomorrow at BiGCaT, where I will try to cover a paper by Thurman et al.
In that paper, Thurman studies the links between DNase I hypersensitive sites (DHSs) and markers of regulation. These DHSs are areas between histones where the DNA is free of histone proteins. There are remarkable images around showing histones as beads on a string, and the distances in nucleotides between histones is in fact not that large. In fact, a histone, despite a large complex, sterically hindering 50% of the DNA access does not stop translation; the transcription complexes apparently have no trouble passing the histones, as described by Felsenfeld et al. Quite amazing!

Now, those histones are chemically modified with acetyl, methyl, phosphates, and other groups. At well-describes residues, and each easily regulates modification of other steps. And everything regulates gene expression. Oh, and as we say yesterday, all that is regulated by metabolites, which in turn... Lovely. Try modeling that mathematically :) Here's what Abcam has to say about it:

Acetylation is generally linked to gene activation. Acetylation on Lys-10 (H3K9ac) impairs methylation at Arg-9 (H3R8me2s). Acetylation on Lys-19 (H3K18ac) and Lys-24 (H3K24ac) favors methylation at Arg-18 (H3R17me). Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription. Asymmetric dimethylation at Arg-18 (H3R17me2a) by CARM1 is linked to gene activation. Symmetric dimethylation at Arg-9 (H3R8me2s) by PRMT5 is linked to gene repression. Asymmetric dimethylation at Arg-3 (H3R2me2a) by PRMT6 is linked to gene repression and is mutually exclusive with H3 Lys-5 methylation (H3K4me2 and H3K4me3). H3R2me2a is present at the 3' of genes regardless of their transcription state and is enriched on inactive promoters, while it is absent on active promoters. Methylation at Lys-5 (H3K4me), Lys-37 (H3K36me) and Lys-80 (H3K79me) are linked to gene activation. Methylation at Lys-5 (H3K4me) facilitates subsequent acetylation of H3 and H4. ... ...

And that goes on for a while. Ambitiously, I started converting things I read into a WikiPathways:

I think that will keep me busy for a while. I won't even attempt to complete it further tonight. I have given up on that about an hour ago. In fact, I returned to the paper by Thurman, as I still have to figure out how their experimental methods work. In fact, how does one even detect the chemical modification of a histone, and to which DNA sequence on any of the chromosomes it belongs?? I mean, that's not AFM or STM, I say...

No, it's ChiP. ChIP on a chip, in fact. They have antibodies are stick particularly to a histones with one particular modification. That is how I actually ended up on that Abcam web page in the first place. Check out this nice western blot. With a huge antibody detecting whether there is an acetyl modification. Wicked!

Well, earlier I learned that proteins detecting methylated CpG bases not because of the methyl group (which amazed me already), but by a distorted hydration in the major groove due to MeCP2 binding. Seriously! Eat that, organic chemist friends!

So, Thurman and friends find distal DHSs and relate these to cis-regulatory elements. To some extend, puzzling, because the above tells us that a lot of regulatory work is happening outside those DHSs. But then again, I did read today about DNA methylation triggering histone modifications. It seems there is so much interactions going on, that it resembles a melting pot. Oh wait, that makes sense; it's one big one pot synthesis anyway.

The paper discusses an enormous amount of experimental work, and I cannot seem to be able to make sense of it all. There are striking aspects to it, which I will touch upon momentarily. But I cannot help but mentioning that I am not sure they could either. Their Discussion section leaves something to be desired, like an actual discussion. Instead, they just summarize the paper.

They used ChIP with Cell Signaling's 9751 antibody recognizing H3K4me3, with formaldehyde-induced crosslinking. It actually turns out, that the peaks for this modification are right on top of the DNA part from which the transcript is made, in line with Felsenfeld's observation. Upstream of that, where the promotors are expected, that is where DNase I signals are found. That is, I think this means that the DHS upstream of the histone where transcription starts is where the promotor regulation happens. With transcription factors (TFs), of course. And in those DHS regions, that is where DNA methylation happens, and Thurman finds DNA methylation in those regions, inhibiting TFs binding, because the already mentioned MeCP2 already takes that place.

Now, then they make a jump from this low level chemistry, to a genome wide landscape. Well, they actually start with that, but as a chemist, I am more of a bottom-up guy (that is an IT method). They report that most DHSs are found in introns and at distal locations. The first is striking: the ratio between intron/exon is >99. Does that imply that exons basically are always DNA wrapped around histones?? Does that actually then tell me that transcription actually sort of requires steric hindrance of the histone?? Ha, those diagrams biologists would be even more misleading that they have been to me (don't ask me how long it took me to learn that there are some 10-40 mitochondria per cell! and I still do not know if all copies in the cell have the same DNA, or if they are more like a population like your microbiome).

Now, distal DHSs are the second largest group, and capture some 40-45% of all DHSs. Distal means typically more than 2.5 kb away from the TSS (transcriptional start sites). Most of them are somewhere between 10 and 50 kb away. Now, isn't that something? That is distant indeed!

What? Still with me? Let's do some math. It's hard, and I hope to get it right. A human has about 3 billion base pairs (I'll take the WikiPedia count). The paper finds almost 3 million DHSs. That means that the average distance between DHSs is about 1 kb. Compare that to their diagram 1b, outline in the previous paragraph. That means that the DHSs must be very densely placed around the transcribed genes. Indeed, they report ratios of up to and above a 100 fold increase. It must be like that, because otherwise, you cannot get those distances for distal DHSs.

Now, another interesting aspect of the paper, is that they find different DHSs for different cell types. That, in fact, increases the average distance between DHSs: those 3 million they find is for 125 cell lines, and more DHSs are found in less then 20 cell lines. Only promotor-related DHSs seem to be more persistent between cell lines. This implies that different cell lines, have different genes unfolded in nucleosome/DHS rich areas (defining the chromatin accessibility), triggering different gene expression. That all makes sense, and rather existing too. As such, it seems to me that this map effectively gives a predictive model, indicating which genes are expressed in which cell types.

A further question they ask is if DNA (not histone) methylation is the cause of the result of DHSs. The confirm earlier found correlation between DNA methylation and gene silencing. They basically question if the things like MeCP2 binding happen because no transcription factor is in the way, or that TF cannot bind because MeCP2 is there. Chemically, these are perhaps equivalent: they have competing binding affinities. Except that the methylation must happen at some point too. The suggest that that may be due DNA getting randomly methylated, perhaps not unlike passive demethylation. Chemically, that does not make sense to. I would guess there are many chemical species in the cell that would get more easily methylated... They believe to have found evidence for passive deposition, but also find positive correlation between methylation and gene expression. I would say, the answer is still out there.

OK, that's about how far I got now. The last two pages I have to read again, and see what papers I need to read to make sense of that. And I will try ... Read more »

Thurman, R., Rynes, E., Humbert, R., Vierstra, J., Maurano, M., Haugen, E., Sheffield, N., Stergachis, A., Wang, H., Vernot, B.... (2012) The accessible chromatin landscape of the human genome. Nature, 489(7414), 75-82. DOI: 10.1038/nature11232  

Felsenfeld G, Boyes J, Chung J, Clark D, & Studitsky V. (1996) Chromatin structure and gene expression. Proceedings of the National Academy of Sciences of the United States of America, 93(18), 9384-8. PMID: 8790338  

  • November 16, 2012
  • 03:42 PM

How to Build a Neuron: step 3

by TheCellularScale in The Cellular Scale

Steps 1 and 2 of neuron-building, as well as an important set of shortcuts can be found in the How to Build a Neuron index. Step 3 is deciding which simulation software or programming language you want to use. Simulated Neuron in Genesis (source)The big two are Genesis and Neuron. They are pretty similar in a lot of ways, but Genesis runs in Linux and Neuron runs in windows. However, you can run Genesis in windows if you install the Linux environment Cygwin.Both programs can read in morphological data, but they use different syntax and coding procedures. There are other types of neural simulators as well, and an ongoing problem in the field of computational neuroscience is compatibility between programs. If someone has done the work to make a beautiful Purkinje cell in Genesis like the one above, it will take a lot of time and effort to translate that neuron into a different simulator such as Neuron. Gleeson et al., (2010) explains this problem and presents a possible solution in the form of the "Neuron Open Markup Language" or NeuroML. "Computer modeling is becoming an increasingly valuable tool in the study of the complex interactions underlying the behavior of the brain. Software applications have been developed which make it easier to create models of neural networks as well as detailed models which replicate the electrical activity of individual neurons. The code formats used by each of these applications are generally incompatible however, making it difficult to exchange models and ideas between researchers....Creating a common, accessible model description format will expose more of the model details to the wider neuroscience community, thus increasing their quality and reliability, as for other Open Source software. NeuroML will also allow a greater “ecosystem” of tools to be developed for building, simulating and analyzing these complex neuronal systems." -Gleeson et al (2010) Author SummaryNeuroML is basically a "simulator-independent" neuronal description language. A neuron built with or converted to NeuroML should be able to run on Neuron, Genesis, and plenty of other platforms. Gleeson et al. validated NeuroML by using a simulated pyramidal neuron converted to NeuroML format and run with several different simulators.Gleeson et al., (2010) Figure 7Zooming in:Neuron, Genesis, Moose, Psics comparisonAll the simulators overlay so tightly that you can barely tell that they are separate lines.So when building you neuron, take care to follow the NeuroML format and then you and others can use it with any simulator you want. © TheCellularScaleGleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US, Barnes SR, Dimitrova YD, & Silver RA (2010). NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS computational biology, 6 (6) PMID: 20585541... Read more »

Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US.... (2010) NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS computational biology, 6(6). PMID: 20585541  

  • November 16, 2012
  • 01:02 PM

The Disposable Dilemma

by Whitney Campbell in Green Screen

Expendable objects were not innovated recently. Although washi are now linked to origami, for instance, people have been using the small sheets as disposable facial tissues since at least the seventeenth century, when the litter of Hasekura Tsunenaga's retinue reportedly surprised French courtiers. Similarly, around 200,000 to 400,000 years earlier, hominins near present-day Tel Aviv temporarily used flint flakes to carve meat, later startling archeologists with the "short-lived usage" of their discarded "meat-cutting blades," perhaps "the world's oldest known disposable knives."... Read more »

  • November 16, 2012
  • 11:00 AM

Scientists print out ‘walking’ biological machines

by Flora Malein in

It sounds like something dreamt up by a science fiction writer, but scientists have created a walking ‘bio-bot’ made from rat heart cells and hydrogels, using a 3-D printer. The biological machines are 7 millimetres long, and resemble a miniature springboard with one long, thin leg that is supported by a stouter supporting leg. The [...]... Read more »

Chan, V., Park, K., Collens, M., Kong, H., Saif, T., & Bashir, R. (2012) Development of Miniaturized Walking Biological Machines. Scientific Reports. DOI: 10.1038/srep00857  

  • November 16, 2012
  • 08:56 AM

Airships: The Future of Air Travel?

by Jason Carr in Wired Cosmos

Considering the fact that airships have been around for a while now, it’s hard to believe that they are thought of as emerging technologies today. But that’s exactly the case given recent advances in this arena. Hydrogen airships have a troubled history due to several significant historical disasters. However, new technologies could help reduce this [...]... Read more »

Michele Trancossi, Antonio Dumas, Mauro Madonia, Jose Pascoa, & Dean Vucinic. (2012) Fire-safe Airship System Design. SAE Int. J. Aerosp. , 11-21. info:/10.4271/2012-01-1512

  • November 12, 2012
  • 06:54 AM

CERN collider could be world’s fastest stopwatch

by Flora Malein in

The clock would keep time based on extremely short light pulses given out when ‘heavy ions’, nuclei that belong to heavy atoms such as lead, are smashed together at speed within the collider. To read more click here. Sources:  Ipp, A., & Somkuti, P. (2012). Yoctosecond Metrology Through Hanbury Brown–Twiss Correlations from a Quark-Gluon Plasma [...]... Read more »

  • November 11, 2012
  • 08:51 PM

Cut your brain some SLACK

by TheCellularScale in The Cellular Scale

Action potentials are the main means of communication between neurons, and their exact timing can be really important. But the specific timing of action potentials is really important in the auditory system, because the auditory system encodes (among other things) information about sound wave frequency. Sound waves (source)I've previously written about auditory processing with regards to the wonder that is the chicken brain, but today we will focus on timing-specificity in the mammalian brainstem. Specifically, some weird channels in the Medial Nucleus of the Trapezoid Body (the MNTB). Mammalian Auditory Brainstem (source)At the Society for Neuroscience meeting, I learned about the sodium-activated potassium channels which help the electric fish fire super-fast super-large action potentials. I was suprised to learn that sodium-activated potassium channels are located in many parts of the mammalian brain. A paper from the Kaczmarek lab at Yale explains that these sodium-activated potassium channel (SLICK and SLACK) are present in the mouse auditory brainstem and contribute to the 'temporal accuracy' of the MNTB neurons. Yang et al. (2007) record the action potentials from these neurons at a range of frequencies and show that the neuron can 'keep' up with the frequencies better when more sodium is present. Yang et al., 2007 Figure 9BIn the figure above, the 'flatter' the line, the better the 'temporal accuracy.' They also made a computational model of this neuron and ran simulations altering the sodium values and reversal potential. Yang et al., 2007 Figure 9DTheir model simulations are similar to their experimental recordings, in that more sodium results in more temporal accuary of the action potential. They confirmed that this was dues to a sodium-activated potassium channel by directly activating SLACK and seeing a similar improvement in temporal accuracy. The SLACK channel still blows my mind, but its role in helping the auditory system fire with the utmost precision actually makes a lot of sense. © TheCellularScaleYang B, Desai R, & Kaczmarek LK (2007). Slack and Slick K(Na) channels regulate the accuracy of timing of auditory neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience, 27 (10), 2617-27 PMID: 17344399... Read more »

Yang B, Desai R, & Kaczmarek LK. (2007) Slack and Slick K(Na) channels regulate the accuracy of timing of auditory neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience, 27(10), 2617-27. PMID: 17344399  

  • November 7, 2012
  • 10:10 AM

Political Animals

by Miss Behavior in The Scorpion and the Frog

Now that we are finally on the other side of one of the longest, most expensive political campaign seasons of United States history, we find ourselves with a new mixed-bag of leaders. Our nation’s decision-makers include career politicians and new freshman politicians; they include lawyers, military members, doctors, businessmen, farmers, ministers, educators, scientists, pilots, and entertainers; they include Protestants, Catholics, Jews, Quakers, Mormons, Buddhists and Muslims; they include white Americans, African Americans, Asian Americans, and Hispanic and Latino Americans; they include men and women; they include straight and gay people; and oh yeah, they include Republicans and Democrats. With so many differences that generate so many viewpoints, how will they ever find common ground to make the kind of decisions that will move our nation in a positive direction? Hey, Look guys! We make a peace sign! Image from Wikimedia. Research into group decision-making in social animals has shown that ants, fish, birds, and bees have all discovered strategies to make intelligent group decisions. If they can do it, we can do it, right? What can we learn from these critters about harnessing the knowledge in all of us to move our whole group in the best possible direction? We will explore these insights in this post, which is a mash-up of two previous posts. To see the originals, check out Can a Horde of Idiots Be a Genius? and Why This Horde of Idiots Is No Genius.Jean-Louis Deneubourg, a professor at the Free University of Brussels, and his colleagues tested the abilities of Argentine ants (a common dark-brown ant species) to collectively solve foraging problems. In one of these studies, the ants were provided with a bridge that connected the nest to a food source. This bridge split and fused in two places (like eyeglass frames), but at each split one branch was shorter than the other, resulting in a single shortest-path and multiple longer paths. After a few minutes, explorers crossed the bridge (by a meandering path) and discovered the food. This recruited foragers, each of which chose randomly between the short and the long branch at each split. Then suddenly, the foragers all started to prefer the shortest route. How did they do that?This figure from the Goss et al 1989 paper in Naturwissemschaften shows (a) the design of a single module, (b) ants scattered on the bridge after 4 minutes (I promise they’re there), and (c) ants mostly on the shortest path after 8 minutesYou can think of it this way: a single individual often tries to make decisions based on the uncertain information available to it. But if you have a group of individuals, they will likely each have information that differs somewhat from the information of others in the group. If they each make a decision based on their own information alone, they will likely result in a number of poor decisions and a few good ones. But if they can each base their decisions on the accumulation of all of the information of the group, they stand a much better chance of making a good decision. The more information accumulated, the more likely they are to make the best possible decision.In the case of the Argentine ant, the accumulated information takes the form of pheromone trails. Argentine ants lay pheromone trails both when leaving the nest and when returning to the nest. Ants that are lucky enough to take a shorter foraging route return to the nest sooner, increasing the pheromone concentration of the route each way. In this way, shorter routes develop more concentrated pheromone trails faster, which attract more ants, which further increase pheromone concentration of the shortest routes. In this way, an ant colony can make an intelligent decision (take the shortest foraging route) without any individual doing anything more intelligent than following a simple rule (follow the strongest pheromone signal).Home is where the heart is. Photo of a bee swarm by Tom SeeleyHoneybee colonies also solve complicated tasks with the use of communication. Tom Seeley at Cornell University and his colleagues have investigated the honeybee group decision-making process of finding a new home. When a colony outgrows their hive, hundreds of scouts will go in search of a suitable new home, preferably one that is high off the ground with a south-facing entrance and room to grow. During this time, the house-hunters will coalesce on a nearby branch while they search out and decide among new home options. This process can take anywhere from hours to days during which the colony is vulnerable and exposed. But they can’t be too hasty: choosing a new home that is too small or too exposed could be equally deadly. Although each swarm has a queen, she plays no role in making this life-or-death decision. Rather, this decision is made by a consensus among 300-500 scout bees that results after an intense “dance-debate”. If a scout finds a good candidate home, she returns to the colony and performs a waggle dance, a dance in which her body position and movements encode the directions to her site and her dancing vigor relates to how awesome she thinks the site is. Some scouts that see her dance may be persuaded to follow her directions and check out the site for themselves, and if impressed, may return to the hive and perform waggle dances too. Or they may follow another scout’s directions to a different site or even strike out on their own. Over time, scouts that are less enthusiastic about their discovered site stop dancing, in part discouraged by dancers for other sites that bump heads with them and beep at them in disagreement. Eventually, the majority of the dancing scouts are all dancing the same vigorous dance. But interestingly, few scouts ever visit more than one site. Better sites simply receive more vigorous “dance-votes” and then attract more scouts to do the same. Like ants in search of a foraging path, the intensity of the collective signal drives the group towards the best decision. Once a quorum is reached, the honeybees leave their branch as a single united swarm and move into their new home, which is almost always the best site. ... Read more »

  • October 29, 2012
  • 11:00 AM

Can the domains of Music Cognition and Music Information Retrieval inform each other?

by Henkjan Honing in Music Matters

In about a weeks time the 13th ISMIR (International Society for Music Information Retrieval) conference will be held. This is a conference on the processing, searching, organizing and accessing music-related data. It attracts a research community that is intrigued by the revolution in music distribution and storage brought about by digital technology which generated quite some research activity and interest in academia as well as in industry.... Read more »

Aucouturier, J., & Bigand, E. (2012) Mel Cepstrum . Proc. of the 13th International Society for Music Information Retrieval Conference, 397-402. info:/

Volk. A., & Honingh, A. (eds). (2012) Mathematical and Computational Approaches to Music: Three Methodological Reflections . Journal of Mathematics and Music, 6(2). info:/10.1080/17459737.2012.704154

  • October 28, 2012
  • 03:56 AM

Jumping Dynamics of a Simple Robot

by Ajinkya Kamat in Brilliance Ardent

Robots fascinate all of us. While few robots are just fun toys many other robots can perform many complex tasks for us. In past decade the field of robotics has advanced by leaps and bounces making robots smarter and smarter. We have created robots, which can explore terrains- terrestrial as well as extra-terrestrial-, where even humans haven't reached. To traverse a terrain with obstacles ... Read more »

Aguilar, J., Lesov, A., Wiesenfeld, K., & Goldman, D. (2012) Lift-Off Dynamics in a Simple Jumping Robot. Physical Review Letters, 109(17). DOI: 10.1103/PhysRevLett.109.174301  

  • October 27, 2012
  • 04:49 AM

Is fMRI About To Get Fifty Times Faster?

by Neuroskeptic in Neuroskeptic

According to a paper just published, a new technique of functional MRI scanning (fMRI) could soon allow neuroscientists to measure brain activity far faster: Generalized iNverse imaging (GIN): Ultrafast fMRI with physiological noise correctionAuthors Boyacioglu and Barth claim remarkable things for the technique:We find that the spatial localization of activation for GIN is comparable to an EPI protocol and that maximum z-scores increase significantly... with a high temporal resolution of 50 milliseconds.EPI, the current standard fMRI sequence, would have a temporal resolution of 2000 or 3000 milliseconds, so it's about 50 times faster.Other super-fast fMRI methods already exist (e.g. this one I blogged about), but they've generally achieved speed only at a cost: they've had to either sacrifice spatial resolution to achieve that, or limited themselves to scanning only a small fraction of the brain, or have been more subject to random noise and hence less sensitive.GIN, however, is said to cover the whole brain, with decent spatial resolution and signal-to-noise ratio. The data can be analyzed in exactly the same way as any other kind. So that's up to fifty times faster with no real drawbacks.That would be truly revolutionary - as the major limitation of fMRI at the moment is that it's much slower than other methods of recording brain activity.Check it out: this shows brain activation in response to simple visual stimuli, imaged with bog-standard EPI and GIN:So this is a big deal... if it does work, I'm sure neuroscientists the world over will be lining up to buy Boyacioglu and Barth a GIN and tonic.How does it work, and is it all it's cracked up to be? Well, I can't really say: the math is beyond me.In essence, rather than scanning the brain in 3D, slice by slice (like this), GIN only scans one 2D slice, but then manages to reconstruct the rest of the brain in 3D from just that slice, using dark, forbidden magicks... I mean mathematics. The principle is called parallel imaging and it's been around for several years, but with image quality limitations that GIN claims to have overcome.Perhaps my more technically-inclined readers will have more insightful comments.Boyacioglu R, and Barth M (2012). Generalized iNverse imaging (GIN): Ultrafast fMRI with physiological noise correction. Magnetic Resonance in Medicine PMID: 23097342... Read more »

Boyacioglu R, & Barth M. (2012) Generalized iNverse imaging (GIN): Ultrafast fMRI with physiological noise correction. Magnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine. PMID: 23097342  

  • October 25, 2012
  • 10:15 PM

Ohtsuki-Nowak transform for replicator dynamics on random graphs

by Artem Kaznatcheev in Evolutionary Games Group

We have seen that the replicator equation can be a useful tool in understanding evolutionary games. We’ve already used it for a first look at perception and deception, and the cognitive cost of agency. However, the replicator equation comes with a number of inherent assumptions and limitations. The limitation Hisashi Ohtsuki and Martin Nowak wanted [...]... Read more »

Ohtsuki H, & Nowak MA. (2006) The replicator equation on graphs. Journal of Theoretical Biology, 243(1), 86-97. PMID: 16860343  

  • October 25, 2012
  • 02:53 PM

Why You Should Reject the “Rejection Improves Impact” Meme

by caseybergman in I wish you'd made me angry earlier

Over the last two weeks, a meme has been making the rounds in the scientific twittersphere that goes something like “Rejection of a scientific manuscript improves its eventual impact”.  This idea is based a recent analysis of patterns of manuscript submission reported in Science by Calcagno et al., which has been actively touted in the [...]... Read more »

  • October 24, 2012
  • 07:03 AM

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

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

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

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

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

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  

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