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Posted: Sep 02, 2016

'Materials that compute' advances as engineers demonstrate pattern recognition

(Nanowerk News) The potential to develop "materials that compute" has taken another leap at the University of Pittsburgh's Swanson School of Engineering, where researchers for the first time have demonstrated that the material can be designed to recognize simple patterns. This responsive, hybrid material, powered by its own chemical reactions, could one day be integrated into clothing and used to monitor the human body, or developed as a skin for "squishy" robots.
"Pattern recognition for materials that compute", published today in the AAAS journal Science Advances, continues the research of Anna C. Balazs, Distinguished Professor of Chemical and Petroleum Engineering, and Steven P. Levitan, the John A. Jurenko Professor of Electrical and Computer Engineering. Co-investigators are Yan Fang, lead author and graduate student researcher in the Department of Electrical and Computer Engineering; and Victor V. Yashin, Research Assistant Professor of Chemical and Petroleum Engineering.
How Materials that Compute Recognize a Number Pattern
This is a conceptual illustration of pattern recognition process performed by hybrid gel oscillator system. (Image: Yan Fang)
The computations were modeled utilizing Belousov-Zhabotinsky (BZ) gels, a substance that oscillates in the absence of external stimuli, with an overlaying piezoelectric (PZ) cantilever. These so-called BZ-PZ units combine Dr. Balazs' research in BZ gels and Dr. Levitan's expertise in computational modeling and oscillator-based computing systems.
"BZ-PZ computations are not digital, like most people are familiar with, and so to recognize something like a blurred pattern within an image requires nonconventional computing," Dr. Balazs explained. "For the first time, we have been able to show how these materials would perform the computations for pattern recognition."
Dr. Levitan and Mr. Fang first stored a pattern of numbers as a set of polarities in the BZ-PZ units, and the input patterns are coded through the initial phase of the oscillations imposed on these units. The computational modeling revealed that the input pattern closest to the stored pattern exhibits the fastest convergence time to the stable synchronization behavior, and is the most effective at recognizing patterns. In this study, the materials were programmed to recognize black-and-white pixels in the shape of numbers that had been distorted.
Compared to a traditional computer, these computations are slow and take minutes. However, Dr. Yashin notes that the results are similar to nature, which moves at a "snail's pace."
"Individual events are slow because the period of the BZ oscillations is slow," Dr. Yashin said. "However, there are some tasks that need a longer analysis, and are more natural in function. That's why this type of system is perfect to monitor environments like the human body."
For example, Dr. Yashin said that patients recovering from a hand injury could wear a glove that monitors movement, and can inform doctors whether the hand is healing properly or if the patient has improved mobility. Another use would be to monitor individuals at risk for early onset Alzheimer's, by wearing footwear that would analyze gait and compare results against normal movements, or a garment that monitors cardiovascular activity for people at risk of heart disease or stroke.
Since the devices convert chemical reactions to electrical energy, there would be no need for external electrical power. This would also be ideal for a robot or other device that could utilize the material as a sensory skin.
"Our next goal is to expand from analyzing black-and-white pixels to grayscale and more complicated images and shapes, as well as to enhance the devices storage capability," Mr. Fang said. "This was an exciting step for us and reveals that the concept of "materials that compute" is viable."
The research is funded by a five-year National Science Foundation Integrated NSF Support Promoting Interdisciplinary Research and Education (INSPIRE) grant, which focuses on complex and pressing scientific problems that lie at the intersection of traditional disciplines.
Source: University of Pittsburgh
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piantadosi et al figure 1 pic

Is ambiguity dysfunctional for communicatively efficient systems?

Based on yesterday’s post, where I argued degeneracy emerges as a design solution for ambiguity pressures, a Reddit commentator pointed me to a cool paper by Piantadosi et al (2012) that contained the following quote:

The natural approach has always been: Is [language] well designed for use, understood typically as use for communication? I think that’s the wrong question. The use of language for communication might turn out to be a kind of epiphenomenon… If you want to make sure that we never misunderstand one another, for that purpose language is not well designed, because you have such properties as ambiguity. If we want to have the property that the things that we usually would like to say come out short and simple, well, it probably doesn’t have that property (Chomsky, 2002: 107).

The paper itself argues against Chomsky's position by claiming ambiguity allows for more efficient communication systems. First of all, looking at ambiguity from the perspective of coding theory, Piantadosi et al argue that any good communication system will leave out information already in the context (assuming the context is informative about the intended meaning). Their other point, and one which they test through a corpus analysis of English, Dutch and German, suggests that as long as there are some ambiguities the context can resolve, then ambiguity will be used to make communication easier. In short, ambiguity emerges as a result of tradeoffs between ease of production and ease of comprehension, with communication systems favouring hearer inference over speaker effort:

The essential asymmetry is: inference is cheap, articulation expensive, and thus the design requirements are for a system that maximizes inference. (Hence … linguistic coding is to be thought of less like definitive content and more like interpretive clue.) (Levinson, 2000: 29).

If this asymmetry exists, and hearers are good at disambiguating in context, then a direct result of such a tradeoff should be that linguistic units which require less effort should be more ambiguous. This is what they found in results from their corpus analysis of word length, word frequency and phonotactic probability:

We tested predictions of this theory, showing that words and syllables which are more efficient are preferentially re-used in language through ambiguity, allowing for greater ease overall. Our regression on homophones, polysemous words, and syllables – though similar – are theoretically and statistically independent. We therefore interpret positive results in each as strong evidence for the view that ambiguity exists for reasons of communicative efficiency (Piantadosi et al., 2012: 288).

At some point, I’d like to offer a more comprehensive overview of this paper, but this will have to wait until I’ve read more of the literature. Until then, here’s some graphs of the results from their paper:

ResearchBlogging.org Piantadosi, S., Tily, H., & Gibson, E. (2012). The communicative function of ambiguity in language Cognition, 122 (3), 280-291 DOI: 10.1016/j.cognition.2011.10.004


Knights Templar

Knights Templar

The Knights TemplarThe Knights Templar were known as the original Christian warriors and were considered to be the special forces of the Crusades. They were armed with swords and armor, as well as Europe's wealth. Their original mission was to ensure the safety of Christian's who made their pilgrimage to Jerusalem.

The organization was founded in the aftermath of the First Crusade of 1096, was endorsed by the Roman Catholic Church around 1129 and existed for approximately two centuries. The Order became a favored charity throughout Christendom and grew rapidly in membership and power.

The Templar knights wore distinctive white mantles with a red cross. They were the most skilled fighters of the Crusades. The non-combatant members of the Order managed the economic infrastructure throughout Christendom, introducing financial techniques that became an early form of banking.

King Philip IV of France was deeply indebted to the Knights Templar Order, but lost trust in the Order upon hearing rumors of their secret initiations. When the Holy Land was lost, support for the Order began to lose effectiveness and King Philip IV of France began to pressure Pope Clement V to take action against the Knights Order.

In 1307, many of the Order's members in France were arrested, tortured into giving false confessions and then burned at the stake. In 1312, Pope Clement, under continuing pressure from King Philip, disbanded the Order. The abrupt disappearance of a major part of the European infrastructure gave rise to speculation and legends, which have kept the 'Templar' name alive today.

On March 19, 1314, Jacques de Molay who was the Grand Master of the Knights Templar was said to have cursed King Philip and the Pope Clement while being burned at the stake. The tale goes that the curse asked both Philip and Clement to join Jacques within a year. Oddly enough, Clement died one month later and Philip IV died seven months after that.

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The Community for Technology Leaders
Green Image
Issue No. 10 - October (2008 vol. 30)
ISSN: 0162-8828
pp: 1683-1698
Luc Van Gool , ETH Zurich KU Leuven, Zurich Leuven
Bastian Leibe , ETH Zurich, Zurich
Konrad Schindler , ETH Zurich, Zurich
Nico Cornelis , KU Leuven, Leuven
We present a novel approach for multi-object tracking which considers object detection and spacetime trajectory estimation as a coupled optimization problem. Our approach is formulated in an MDL hypothesis selection framework, which allows it to recover from mismatches and temporarily lost tracks. Building upon a multi-view/multi-category object detector, it localizes cars and pedestrians in the input images. The 2D object detections are converted to 3D observations, which are accumulated in a world coordinate frame. Trajectory analysis in a spacetime window yields physically plausible trajectory candidates. Tracking is achieved by performing model selection after every frame. At each time instant, our approach searches for the globally optimal set of spacetime trajectories which provides the best explanation for the current image and all evidence collected so far, while satisfying the constraints that no two objects may occupy the same physical space, nor explain the same image pixels at any time. Successful trajectory hypotheses are then fed back to guide object detection in future frames. The resulting approach can initialize automatically and track a large and varying number of objects from both static and moving cameras. We evaluate our approach on several challenging video sequences with both a surveillance-type scenario and a scenario where the input videos are taken from a moving vehicle.
Vision and Scene Understanding, Video analysis, Scene Analysis, Object recognition, Tracking
Luc Van Gool, Bastian Leibe, Konrad Schindler, Nico Cornelis, "Coupled Object Detection and Tracking from Static Cameras and Moving Vehicles", IEEE Transactions on Pattern Analysis & Machine Intelligence, vol. 30, no. , pp. 1683-1698, October 2008, doi:10.1109/TPAMI.2008.170
114 ms
(Ver )


flickr-free-ic3d pan white

Coneflower and Hummingbird Moth; at Eternity's Gate

I dream of painting and then I paint my dream.

~ Vincent van Gogh.

Vincent van Gogh, the master dutch painter, is known world-wide for his numerous paintings of outstanding quality. In addition to being intrigued by his art, I am also fascinated by the unchartered depths of his amazing mind. His mind was clinically depressed and depression, if you ask me, is the worst mental state to be in where life ceases to be meaningful. Additionally, van Gogh also suffered from bipolar disorder, a disease where the mind is torn between opposite extremes. Vincent was described as ‘two persons: one, marvelously gifted, tender and refined, the other, egotistic and hard hearted’ by his brother Theo who was also his best friend. Such a turbulent mind is predestined to sink the person it dictates and ruin one or more nearby lives. As a result of possessing such unruly minds, many lesser men among us die little deaths every day until the thread snaps for good. Despite dragging himself through several such diminutive deaths Vincent dared to dream of painting and painted his dreams. He decidedly knew his mind well and wanted to master it like the paint on his easel. It takes character of the extreme kind to stand up to utter nonsense of one’s own mind which in van Gogh’s case forgot things at whim, reasoned for the unreasonable, hallucinated vividly, grew furious for no obvious cause, and hurt incessantly. Have you seen his ‘at eternity’s gate’? The pain of his mind shines though in this masterpiece. For a man so forlorn and wasted, he painted his redemption on canvas and religiously believed his work to be the anecdote of his troubled mind. He feared that his mind will ruin his talent and worked relentlessly until a bout of suicidal depression made him sink a bullet in his lower chest which killed him slowly over the next two days. He eventually lost to his tormented mind but not before putting up a gallant fight that is still celebrated in our best art galleries.

Vincent van Gogh stood there at eternity’s gate as two men; the first who was destroyed and was depicted on the canvas by the second who believed he could still make those bold brush strokes speak on behalf of his soul. On days when I scatter myself, van Gogh looms large on my mind. He reminds me that I will always have a second choice during my humble turn at eternity’s gate where I can either clench my head in despair or walk right through the portal. And I fear, I will do both.

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Field of Science

post doc job opportunity on ribosome biochemistry!

It's been sooooo long since I blogged, I'm actually ashamed to come back and post anything now! There is probably some proper term for that like "bloggers' guilt." Aha, yes, a quick google suggests this is a real term!

Anyway, with one thing and another, life has been busy. And while I'd love to say I'm here to write about some exciting topic that's caught my interest (and there are many!), I'm actually back on Blogger to advertise a job opportunity to work with Vasili and I. This one:

Project description:
The focus of the project is biochemical analysis of Bacillus subtilis ribosome-associated stress factors. The project addresses questions generated through bioinformatic analysis of ribosomal factors, and will comprise of a biochemical research programme backed up by a complementary set of microbiological and structural investigations. The position is co-financed by funds from Ragnar Söderberg and Carl Tryggers foundations.
Our laboratory uses a combination of experimental (in vitro biochemistry in a reconstituted translational system, NGS-based techniques for in vivo biochemistry, as well as microbiological techniques) and in silico (molecular evolution) approaches. We are currently supported by the Swedish Research Council, Ragnar Söderberg foundation, Kempe foundation, Carl Tryggers foundation, as well as Umeå University funds.
For further information please contact Dr. Vasili Hauryliuk, or Dr. Gemma C. Atkinson, See also our web page:
A successful candidate should meet the following criteria:
- Documented proficiency in biochemical assays
- Strong skills in experimental design and interpretation
- A high level of proficiency in written and spoken English, as well as scientific writing
- A strong publication record in international, peer reviewed journals
- An ability to work effectively independently and as a group
- A willingness to learn new techniques
Highly desired:
- Experience in ribosomal biochemistry / RNA biochemistry
- Experience in bacterial genetics, particularly Bacillus subtilis
Applications should be written in English, comprise of a cover letter, CV with a publication list and contact information of at least two referees. Documents should be in MS Word or PDF format and submitted electronically to Dr. Vasili Hauryliuk,, or Dr. Gemma Atkinson, The position is available starting spring 2015 (negotiable).
Please share with anyone who might be interested!

Finding a new translation factor, and verifying it with help from my experimental friends

Joy of joys my most recent paper has just been published in Nucleic Acids Research!

Evolutionary and genetic analyses of mitochondrial translation initiation factors identify the missing mitochondrial IF3 in S. cerevisiae.

I'll give a little bit of background to the paper. I actually alluded to it last year when we were in the early stages of writing up.

It started with these papers by Gaur et al and Yassin et al, which claim that an insertion in mitochondrial initiation factor mIF2 evolved to compensate for a total lack of IF1 in mitochondria, which is universal in bacteria. This idea is really cute, and in fact they found that bovine mIF2 compensates for a lack of IF2+IF1 in E. coli. In addition, cryo-EM structures suggest the insertion occupies an overlapping site of the ribosome as IF1 does. However, I made an alignment of mIF2 from a broad distribution of eukaryotes and found there's a significant flaw with this hypothesis: mIF1 is absent in all eukaryotes, but the conserved insertion is only present in vertebrates. So somehow most eukaryotes through most of their evolutionary history have managed just fine without IF1 or the mIF2 insertion. This is a really nice example of how you really should do the comparative genomics of you want to make such sweeping claims as X evolved to replace Y. Here's the pic I made for my older blog post:

Just replace "protein 1" with IF2 and "protein 2" with IF1. Simple! The point is, if you only look at humans and bacteria, you may jump to a conclusion that isn't supported when you sample broadly across taxa.

My partner in life and crime, Vasili and I were thinking of writing up a teeny tiny paper about this, but then I started checking out more mitochondrial initiation factors...

Most eukaryotes carry have an orthologue of mitochondrial mIF3, but a homologue had never been found in Saccharomyces cerevisiae. Considering how important IF3 is for bacterial translation, and also how human mIF3 is associated with Parkinson's disease, it was a real bummer that this wasn't present in the yeast mitochondrial system. Well, actually, people just weren't looking hard enough. mIF3 is a small protein with a very biased amino acid content, so if just searching with BlastP, you only pick up a few of the most closely related sequences. I tried the more sensitive PSI-Blast and found an S. cerevisiae homolog called Aim23p. Aim23p was known to be a mitochondrial protein, but its function had not been predicted. Phylogenetic analysis confirmed Aim23p is the orthologue of mIF3. Cool! So our teeny tiny paper suddenly got more substantial.

The two domains of mIF3. The yellow sites are those that are strongly conserved between mIF3 and Aim23p. They are mainly internal, probably important for stabilising the structure. The outer faces are more variable, possibly reflecting lineage-specific evolution of inter-molecular interactions.

But the really cool stuff happened when we got our friends and collaborators from the lab of Piotr Kamenski in Moscow on board. Piotr's group showed that a knock-out of Aim23p can be complemented by Schizosaccharomyces pombe mIF3, strongly suggesting that Aim23 is the functional equivalent of mIF3 as well as the evolutionary orthologue.

I'm really happy about the results of this paper. It's a great feeling to predict something in silico that gets verified in vivo. Our next collaborative project with Piotr's group is a longer shot, but also bloody exciting, so fingers crossed!

Atkinson, G., Kuzmenko, A., Kamenski, P., Vysokikh, M., Lakunina, V., Tankov, S., Smirnova, E., Soosaar, A., Tenson, T., & Hauryliuk, V. (2012). Evolutionary and genetic analyses of mitochondrial translation initiation factors identify the missing mitochondrial IF3 in S. cerevisiae Nucleic Acids Research DOI: 10.1093/nar/gks272

Switches and latches on the ribosome

This post was chosen as an Editor's Selection for
Call me a geek, but I'm a big fan of translational GTPases (trGTPases). They're essential factors for translation by the ribosome, highly conserved in all life and they're ancient. Really ancient. There were at least three (EF-Tu, IF2 and EF-G) in the ancestor of all life on earth. These have subsequently diversified through gene duplication and subfunctionalisation into the multiple trGTPase subfamilies that are known today.

Since a lot of my research is on trGTPase evolution,  I was really interested to see this paper today in Nature Structural and Molecular Biology: A conserved proline switch on the ribosome facilitates the recruitment and binding of trGTPases.

In this paper, Wang et al have identified a universally conserved residue, Pro22 of ribosomal protein L11 that switches conformation upon trGTPase EF-G binding, controlling the L11 and L12 protein interactions required for each peptide elongation cycle. They find that EF-G carries peptidyl-prolyl cis-trans isomerase (PPIase) activity, driving conformational switching of two adjacent prolines (PS22) from a trans to cis orientation.

Most exciting for me is their claim that all known universal trGTPases contain an active PPIase center,  and therefore that the cis-trans isomerization of PS22 is a universal event required for efficient turnover of trGTPases throughout the translation process. This is pretty cool. Hang on though... structures show that the potential PPIase motif is located in the cleft between domains G and V of EF-G, but the other trGTPases they mention in the paper (IF2, EF-Tu, EF-G, EF4 (LepA) and RF3) don't carry a domain homologous to EF-G's C-terminal domain V, so how does that work? Their structural figures of RF3, EF-Tu and LepA show their predictions of where the PPIase centre might be in these proteins. In each case, the centre is formed by residues of the GTPase (G) domain that correspond to the EF-G PPIase sites, plus nearby residues in the non-homologous C-terminal domains of these various trGTPases. So we would predict that if this is a universal mechanism, at least those residues of the G domain that are involved should be universally conserved. Unfortunately, an alignment of this region isn't presented in the paper, but fortunately I have one up my sleeve:

The region of the G domain containing sites proposed to be acting as a PPIase (yellow highlighting). These are just upstream of the G4 nucleotide binding motif (highlighted in turquoise). These are consensus sequences: the residue shown for each trGTPase in each position is the most common amino acid found there across all sequences of the subfamily. In essence, each sequence is an average of hundreds of sequences.
The G domain is generally very well conserved across its length, with patches of universal conservation. However, the potential PPIase sites (yellow) are not universally conserved. The variability of these sites contrasts sharply with the nearby conserved G4 motif (one of the five motifs of the trGTPases - and in fact all GTPases - that coordinate the GTP/GDP nucleotides). It's disappointing, but this pattern of conservation doesn't really bear the hallmark of a universal mechanism. Indeed, Wang et al find that mutating the PPIase motif of EF-G has only a modest effect: a single turn of GTP hydrolysis was unaffected, but the multiple- turnover rates were inhibited by 15–40%. Similarly, mutation of PS22 did not completely abolish translation.

In fact, L11 is actually one of the few ribosomal proteins that is not essential for life, which makes L11 knock out strains useful molecular biological tools (for example this paper). Therefore, the mechanistic details of this protein's role in translation, although very interesting of course, do not translate to an understanding of the core principles of how trGTPase work on the ribosome.

Are we really looking at something as concrete as a conserved "switch-and-latch" mechanism, or is PS22 just a trGTPase binding site with integral flexibility? Anyway, it's all interesting additional details of how trGTPases interact with the ribosome, and another plus: it got me blogging again after a long hiatus!

Wang L, Yang F, Zhang D, Chen Z, Xu RM, Nierhaus KH, Gong W, & Qin Y (2012). A conserved proline switch on the ribosome facilitates the recruitment and binding of trGTPases. Nature Structural & Molecular Biology PMID: 22407015

PhD position available in Molecular Evolution!

**** EDIT The position has now been filled and I'm no longer taking applications ****

Having got my Estonian Science Foundation grant funded recently, I have an open PhD position available! See below.

We are seeking a highly motivated PhD candidate to be supervised by Dr Gemma Atkinson within the group of Prof Tanel Tenson in the Institute of Technology, University of Tartu, Estonia.

Dr Atkinson’s research addresses protein functional evolution, using bioinformatic approaches and primarily focusing on the ancient families of proteins involved in translation of mRNA to protein. Members of these families are often essential for life and predate the last common ancestor of all life on earth. Thus by studying these proteins we can gain understanding of the fundamental processes of life, and how these processes have evolved over billions of years.

The PhD project will take advantage of the thousands of whole genome sequences now available for the study of evolution of protein families from the origin of life to the present day. Work will involve sensitive sequence searching to identify the presence and absence of particular proteins across genomes, phylogenetic analyses to reconstruct their emergence and evolution, and sequence analyses to link domain- and site-specific patterns of amino acid substitution with molecular function. Specifically, the proposed PhD project will target the ABC superfamily of ATP-binding enzymes found in all domains of life.  This superfamily comprises enigmatic proteins of diverse, and often unknown functions. Several ABC enzymes have recently been found to have important roles in regulation of translation such as ribosome recycling protein Rli1/ABCE1, yeast-specific elongation factor eEF3 and starvation response enzymes Gcn1 and Gcn20.

From the results of the PhD, it is expected that enzymes with novel roles in protein synthesis will come to light as interesting targets for subsequent experimental study. Dr Atkinson collaborates with the lab Dr Vasili Hauryliuk, also in Prof Tenson’s group, for biochemical and genetic validation of in silico results. If the candidate so wishes, there is an opportunity to gain practical lab experience in Dr Hauryliuk’s lab.

The candidate should have:
  • a Masters degree in a biological or computational discipline
  • a strong interest in, and enthusiasm for molecular evolution
  • familiarity with basic sequence and phylogenetic analyses
  • experience in using a programming language such as Python, Perl, Java etc
  • fluency in spoken and written English

Estonia has a rich culture and beautiful natural environment, with unspoiled forests, meadows and coastlines. Enjoying warm summers and cold winters, the historical city of Tartu is the intellectual capital of Estonia, and its university is the leading research and development institution in the country. The Institute of Technology is a lively, modern centre for biological and technological research.

The PhD will be funded by a monthly stipend, with additional monies available for regular attendance at international conferences and workshops, and for visiting labs abroad. Information on funding is available by request.

Applications should contain:
  • a full CV with detailed description of previous relevant experience
  • a statement of academic interests
  • an electronic version of the Masters thesis
  • the names and contact details of at least 2 referees

The candidate is expected to start at the latest September 2012. Please send applications and informal enquiries to

Gemma Atkinson
University of Tartu,
Institute of Technology
Nooruse  1, 50411 Tartu, Estonia

More information about the research of Dr Atkinson can be found here:

My creative contributions to the Festive Tree of Life

Happy holidays!

Bacterial genes in eukaryotes - function and phylogeny

Giant, glowing mitochondria in the Deutsches Museum, Munich

The first paper, published in GBE, considers humans alone:

David Alvarez-Ponce and James O. McInerney

Rooting the eukaryotic tree with mitochondrial and bacterial proteins
Romain Derelle and B. Franz Lang

Coevolution, from hummingbirds to proteins

Coevolution (two or more biological objects evolving together) is a common feature of the evolutionary process on all levels from the molecular to the organismal. One of the most beautiful examples is that of hummingbirds and ornithophilous flowers. Hummingbirds feed on the nectar from the flowers, pollinating them in the process. In this mutually beneficial relationship, the plants have evolved flowers that attract the birds with colours that are conspicuous to the bird, and are shaped to perfectly accommodate the bird's beak. This coevolution has happened in a number of hummingbird/plant pairs.

Pic from Wikipedia article on humming birds

For more information on hummingbird/plant coevolution, I direct you to the publications of Ethan Temeles. As usual though, this post will be about proteins, and not whole organisms... and it will include my own crude drawings as usual...

Fig 1. Ta-da! Hummingbird/plant coevolution is a nice analogy for protein receptor/ligand coevolution. Circles show residues directly involved in the interaction.
At the molecular level, an example of coevolution is in the establishment of receptor-ligand interactions  (Fig 1). The receptor protein binding site has evolved in concert with the binding site of the ligand. In Fig 1, variation of the yelow residues in the receptor is correlated with that of the green residues in the ligand. The yellow sites are close together in the structure, but not necessarily neighboring in the sequence. For example, the amino acid sequence backbone of these imaginary proteins might be arranged like this:
Fig 2. Black lines show the amino acid sequence of the protein, within its structural density.

Thus, if the structure of the binding interface is known, it's possible to predict candidate coevolving sites. However from the sequence alone, it's not so straightforward.

As discussed in a recent paper of Gloor et al in MBE (and references within), there are two explanations for how covarying positions come to be (and these are actually the extremes of the distribution of possible mutational effects):

1. Suppressor mutations. These arise when a mutation with a deleterious phenotype is suppressed by another mutation at a different position.
2. Covarions. These are cases when both the original residue and the mutated residue are functionally compatible, but mutation alters the spectrum of amino acids possible at another location.

Covarying sites may occur in the same protein or in different proteins (Figs 3-4).

Fig 3. Stars show between-protein correlated mutations at two interaction sites

In between-protein coevolution, green sites coevolve with yellow sites in our example. But there is also within-protein coevolution among yellow site residues and among green site residues. Imagine for instance a change of green residue that multiple yellow resides interact with at different times (Fig 4). Or perhaps the middle yellow starred residue in Fig 4 mutating and causing different constraints in what residues the neighboring yellow sites can mutate to. Either way, the three yellow sites will covary.  Remember that those sites are far away from each other in the sequence. So by showing that these sites co-vary, we can predict that they are functionally related, even if we don't have a structure

Fig 4. Correlated mutations can also occur within one protein

Prediction of co-evolving sites can be useful for understanding cases when binding site residues are unconserved in a multiple sequence alignment. It can also be useful for predicting intermolecular interaction sites, and allosteric sites (for example Chen et al., 2006). An allosteric site can remotely affect the evolutionary pressures on a distant site by affecting the structural orientation of the protein (Fig 5).

Fig 5. Correlated mutations among binding site residues and an allosteric site.

Prediction of covarying sites is challenging, not only because they may not always be clustered together in sequence and structure, but because covariation is a combined result of structural and functional constraints and background noise from shared phylogenetic ancestry and random processes.

There are two classes of methods for predicting covarying sites: tree-aware and tree-unaware. Tree aware methods search for sites whose covariation can not be explained by phylogenetic relationships, while tree-unaware methods ignore phylogenetic relationships, instead searching for covarying sites with the strongest signal.  The two classes of methods are discussed in Caporase et al (2008), in which it is concluded that tree-unaware methods perform as well as tree-unaware.

Using a tree-unaware method, Gloor et al. (2010) examine covariation in phosphoglyerate kinase evolution. They identify nonconserved sites that covary, and through mutagenesis show that the sites are important for function and epistatic to each other (mutation in one affects the function of the other). They find that covarying positions are just as as diverse within and between clades as are noncovarying positions, and suggest that most covarying positions arise from processes more like the covarion model, than the suppression mutation model.

The importance of covariation in sequence evolution is of interest to people like myself who use patterns of sequence variation to predict protein function. In studying molecular evolution of function, we largely rely on the assumption that the most functionally important positions are those that are conserved over time. Although this is generally the case, it seems that some important sites that are able to covary may slip through the net.
Recently, I've been experimenting with the tree-unaware code of Dunn et al., (2008) to find covarying sites Preliminary results, based on the RelA family are... confusing. Residues that would be predicted to be interacting from the structure are not flagged up as covarying, while there are many pairs of predicted covaring sites that are physically distant and don't seem likely to be allostric sites from the structure. It seems like as with many real-life case studies, real biology is a little bit more complicated than naive sketches like mine would have you believe! Oh well, time to delve a little deeper into the data set...

References and further reading:

Caporaso, J., Smit, S., Easton, B., Hunter, L., Huttley, G., & Knight, R. (2008). Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics BMC Evolutionary Biology, 8 (1) DOI: 10.1186/1471-2148-8-327

Codoñer FM, & Fares MA (2008). Why should we care about molecular coevolution? Evolutionary bioinformatics online, 4, 29-38 PMID: 19204805

Chen, Y. (2006). Evolutionarily Conserved Allosteric Network in the Cys Loop Family of Ligand-gated Ion Channels Revealed by Statistical Covariance Analyses Journal of Biological Chemistry, 281 (26), 18184-18192 DOI: 10.1074/jbc.M600349200

Dunn, S., Wahl, L., & Gloor, G. (2007). Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction Bioinformatics, 24 (3), 333-340 DOI: 10.1093/bioinformatics/btm604

Gloor, G., Tyagi, G., Abrassart, D., Kingston, A., Fernandes, A., Dunn, S., & Brandl, C. (2010). Functionally Compensating Coevolving Positions Are Neither Homoplasic Nor Conserved in Clades Molecular Biology and Evolution, 27 (5), 1181-1191 DOI: 10.1093/molbev/msq004


Lee Fullbright
Publisher: Two Sisters & Company, an imprint of Telemachus Press, LLC
Pages: 382

2012 DISCOVERY AWARD WINNER, FIRST PLACE, LITERARY FICTIONSAN DIEGO BOOK AWARD, "BEST MYSTERY"2012 GEISEL AWARD FOR "BEST OF THE BEST," SAN DIEGO BOOK AWARDS 2013 READERS' FAVORITE INTERNATIONAL BOOK AWARDS GOLD MEDAL, "HISTORICAL MYSTERY"KIRKUS CRITICS' PICKMore from Kirkus Reviews: "Raised in a crumbling New England mansion by four women with personalities as split as a cracked mirror, young Francis Grayson has an obsessive need to fix them all. There's his mother, distant and beautiful Magdalene; his disfigured, suffocating Aunt Stella; his odious grandmother; and the bane of his existence, his abusive and delusional Aunt Lothian. For years, Francis plays a tricky game of duck and cover with the women, turning to music to stay sane. He finds a friend and mentor in Aidan Madsen, schoolmaster, local Revolutionary War historian, musician and keeper of the Grayson women's darkest secret ...
Amazon Rating:
4 stars from 465 ratings
BookLending.com Rating:
3.5 stars from 6 ratings


Tuesday 27th September 2016

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Where does it belong?

The activities in the Science section focus on; scientific enquiry, life processes and living things, materials and their properties and physical processes. Complete the activity by printing it onto A4 paper. This Science activity focuses on putting the electrical goods into the correct sections!

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New Look: Maken Shao

Atlus shares some higher res shots. Does this game do apart its DC counterpart?

In case you were in a hole all last week (or if you just didn't care enough to read all our news stories), Maken X is making the way from the Dreamcast to the PS2. Atlus is porting the Dreamcast first person slasher to the PS2 system, adding a slew of new features, changing the perspective to third person, and calling it Maken Shao.

Today, thanks to the newly opened Maken Shao website, we have some higher-res shots of the game than those that have been shown before. Unfortunately (yes, there's always an "unfortunately" when dealing with screenshots that have originated from a Japanese site), the shots are heavily JPEG-compressed, but you can still get a feel for how the game compares, visually, with its DC counterpart.

As for how it plays, we'll find out in late April when Maken Shao arrives on DVD-ROM format to Japan. Check back then for impressions.


Tag Archives: web development

Software Unit Testing – What is it and why is it important?

Software development is composed of individual components.  As developers are building these units, they build tests to verify them for correctness.  These tests can verify the environment, they can verify data, they can verify edge cases and include test harnesses.  In essence they verify that the code meets the design specification.

There are a few key advantages to the unit testing approach:

  1. Self-Documenting – The tests themselves provide a type of documentation for the system as a whole.
  2. Advances Refactoring – At a later date you may need to repair, rewrite or refactor portions of code.  Previously built unit tests provide a tremendous help to make sure your changes still meet the previous design specification.
  3. Simplifies Functional Testing – With unit testing as an ongoing concern, the final components will likely perform more reliably, and if not the tests & self-documentation may point to how or why they fail to meet some specification.

Sean Hull Quora Discussion – What is software unit testing?

Agile – What is it and why is it important?

Agile software development seeks a more lightweight methodology of making changes and releases to software.  In the traditional, incremental approach, large pieces of software are written at once, and releases happen less frequently.  Once features are complete, the testing phase happens, and then deployment to production.  These releases can happen over many weeks in time, so turnaround for new features tends to be slow.   Advocates would argue that this forces discipline in the process, and prevents haphazard releases and buggy software.

Agile methodologies, seek to accelerate releases of much smaller pieces of code. These releases can happen daily or even many times a day, as developers themselves are given the levers to push code.  Agile tends to be more reactive to business needs, with less planning and requirements gathering up front.

While Agile remains the buzzword of the day, it may not work for every software development project.  Web development & applications where small failures can easily be tolerated and where small teams are at work on the effort, make most sense.

Sean Hull asks on Quora – What is Agile software development and why is it important?

Object Relational Mapper – What is it and why is it important?

Object Relational Mappers or ORMs are a layer of software that sits between web developers and the database backend.  For instance if you’re using Ruby as your web development language, you’ll interact with MySQL through an ORM layer called ActiveRecord.  If you’re using Java, you may be fond of the ORM called Hibernate.

ORMs have been controversial because they expose two very different perspectives to software development.  On the one hand we have developers who are tasked with building applications, fulfilling business requirements, and satisfying functional requirements in a finite amount of time.  On the other hand we have operations teams which are tasked with managing resources, supporting applications, and maintaining uptime and availability.

Often these goals are opposing.  As many in the devops movement have pointed out, these teams don’t always work together keeping common goals in mind.  How does this play into the discussion of ORMs?

Relational databases are a technology developed in the 70’s that use an arcane language called SQL to move data in and out of them.  Advocates of ORMs would argue rightly so, that SQL is cumbersome and difficult to write, and that having a layer of software which helps you in this task is a great benefit.  To be sure it definitely helps the development effort, as software designers, architects and coders can focus more of their efforts on functional requirements and less on arcane minutiae of SQL.

Problems come when you bump up against scalability challenges.  The operations team is often tasked with supporting performance requirements.  Although this can often mean providing sufficient servers, disk, memory & cpu resources to support an application, it also means tuning the application.  Adding hardware can bring you 2x or 5x improvement.  Tuning an application can bring 10x or 100x improvement.  Inevitably this involves query tuning.

That’s where ORMs become problematic, as they don’t promote tweaking of queries.  They are a layer or buffer to keep query writing out of sight.

In our experience as performance and scalability experts for the past fifteen years, query tuning is the single biggest thing you can do to improve your web application.  Furthermore some of the most challenging and troublesome applications we’ve been asked to tune have been built on top of ORMs like Hibernate.

Sean Hull asks on Quora – What is an ORM and why is it important?

Decoupling – What is it and why is it important?

Processes are said to be coupled when they are tightly wound together, and dependent on one another.

A loose analogy might be replacing a traffic light by a traffic circle.  You keep the traffic moving, reducing the overall wait time for any car entering the intersection.

Decoupling web applications might involve replacing a makeshift queue your application currently implements in a table, with a message queuing service such as RabbitMQ or Amazon’s SQS.

Ultimately decoupling promotes scalability, as you can scale the pieces of your infrastructure that your capacity planning identifies to be bottlenecks.  What’s more you can make those pieces redundant, increasing high availability at the same time.

Sean Hull discusses on Quora: What is decoupling and why is it important?


Common Word Usage Errors

Accept: to receive something (I accepted the gift he offered me.)
Except: excluding something (Everyone except Mark got on the boat.)

Advice: opinion or information offered; a noun (She offered her advice.)
Advise: to offer advice to someone; a verb (The council will advise the king.)

Affect: to influence; a verb (The pungent odor will affect the party.)
Effect: result; a noun (The presentation had a powerful effect on the country.)

All ready: used as an adjective to express complete preparedness (I was all ready to go.)
Already: an adverb expressing time (Unfortunately, everyone had already left.)

All right: correct use
Alright: incorrect use

Awhile: an adverb (Stay awhile.)
A while: an article and noun (Stay for a while.)

Can: denotes ability (I can touch my toes.)
May: denotes permission (May I sit here?)

Complement: complete, accentuate (His cummerbund complemented her dress color.)
Compliment:  to give praise (He complimented me on my penmanship.)

Conscious: awake or perceiving; an adjective (Despite a head injury, he was conscious.)
Conscience: the voice in the back of your head; a noun (Chris didn't cheat because his conscience wouldn't let him.)

Everyday: something ordinary or common; an adjective (Those are my everyday shoes.)
Every day: used when something happens every single day (I clean my room every day.)

Good: describes nouns (That cake was really good.)
Well: describes verbs (She swims really well.)

Lead: either a noun (pronounced "led"), as in "the lead in the pencil," or a verb (pronounced "leed"), as in "lead me to your ruler."
Led: the past tense form of lead (I led the horse to water.)

Lose: to misplace something, a verb (Don't give the money to her; she'll lose it.)
Loose: the opposite of tight, an adjective (My shoelaces are loose.)

Principal: the head of a school (The principal will hold an assembly tomorrow.)
Principle: a theory or belief (The professor explained Platonic principles to us.)

Then: used for a sequence of events or the passage of time (I went home, vacuumed, and then slept.)
Than: used in comparison (I'm heavier than she is.)

To: a preposition (Take that book to her.)
Too: used when there's too much, too many, too little of something (I grabbed for her, but she fell too fast.)
Two: the number (My daughter is two.)

We're: contraction for "we are" (We're glad to help.)
Where: location (Where are you going?)

Were: a past tense form of the verb be (They were walking side by side.)


Statistics for occurrence #1 of “Babylon” in book 7, chapter 8, section 25 of Xenophon, Anabasis:

...versed were as follows: Artimas of Lydia, Artacamas of Phrygia, Mithradates of Lycaonia and Cappadocia, Syennesis of Cilicia, Dernes of Phoenicia and Arabia, Belesys of Syria and Assyria, Rhoparas of Babylon , Arbacas of Media, Tiribazus of the Phasians and Hesperites; then the Carduchians, Chalybians, Chaldaeans, Macronians, Colchians, Mossynoecians, Coetians, and Tibarenians, who were independent; and t...

Max. Freq. Min. Freq.
Entity Corpus Doc Corpus Doc
Babylon (Iraq) 302 16 0 0 0 user votes
Babylon (New York, United States) 1 0 1 0 0 user votes
Babylon (Illinois, United States) 0 0 0 0 0 user votes
Babylon (Nevada, United States) 0 0 0 0 0 user votes


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Persuasive Essay Writing: Six Vital Steps

In many ways one has been reduced to making decisions that is different from the original intentions? Or maybe it was an argument, and it resulted to adopting another view or choice. The subtle device used in successfully changing ones decision is what is called a persuasive essay, as so long as it is written.

ProfEssays is known to be among the best persuasive writers, they have successfully written many essays including scholarship, personal, argumentative essays, analytical essays, custom essays, custom thesis, etc for many individuals and Companies.

From the above we can easily deduce the meaning of persuasive essay, the act of using deductive reasoning, logic, instances, experience, to make a point thereby shifting a reader’s original point of view.

Persuasive or argumentative essays is a bit complicated to write, you will may need the assistance of professional writers like ProfEssays to effectively produce a good work, not everyone is cut out for the job of writing, you can contact them for training, custom research papers, dissertations, etc. They offer the best in the industry, even if its an emergency work, ProfEssays guaranty you 8 hours of delivery, in case of custom paper, orders are fulfilled and delivered on time.

1. The first step is to know what you want to write about, what issues do you wish to convince your readers about. It is imperative you get this from the onset.

2. Second, ask your self, ‘who are my readers’? What are there opinion concerning my essay topic? You should know. Some subject already have a general opinion, while some don’t, so knowing this will help you to structure your essays.

3. Next is how to arrange your essay, is it base on facts, or theories? What experience or knowledge do you have to support if it’s based on theories, likewise what evidence is there to show if it’s based on facts. Please note that in writing this type of essay, use points that are purely factual, avoid writing theories.

4. Facts must be a product of research, especially if your topic happens to be a sensitive one, detailed investigation must be carried to project your points.

5. Provide quotes from notable personalities to support your facts, and remember to include sources and references to your work, don’t forget the reliable tool of using Statistics, and examples, if it can be substantiated then your are 75% sure attaining your goal of persuasion.

6. Lastly go through the essays, if possible give to four to ten people to read and offer some creative criticism.

Persuasive skill is needed in diverse areas of human lives and endeavors, example writing resumes, quotations, attending interviews, etc. So it is therefore compulsory to get the knowledge, or go to ProfEssays for all your writing needs, and enjoy their reliable customer care service, in addition to this you will enjoy top professional services, original work delivery no plagiarism, top of the art writing skills.

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The Irish Airline Pilots’ Association has claimed that Ryanair's corporate culture was responsible for three pilots on three flights issuing mayday calls on the same day last month.

The IALPA said that Ryanair’s league tables on the use of fuel led to the three planes making low-fuel emergency landings at Valencia Airport.

However, Ryanair has denied its fuel policy was responsible for the mayday calls on 26 July, when bad weather caused the flights to be diverted from Madrid.

It said the mayday calls occurred in extraordinary circumstances after more than an hour of extra flight time.

It added that the planes were not in imminent danger and landed with the required 30 minutes’ worth of fuel on board.

The Spanish Consumer Association has accused Ryanair of jeopardising passenger safety.

The Irish Aviation Authority and its Spanish equivalent are investigating the mayday calls.

Speaking on RTÉ's News at One, IALPA’s Evan Cullen said that Ryanair's corporate culture is putting pressure on pilots to make decisions they are not comfortable with.

Mr Cullen said: "These pilots came under the legal definition, the very regulations, of imminent danger, that's why the mayday calls were issued.

"The reasons why these guys hadn't enough fuel is because of the Ryanair policy and corporate culture with regard to fuel and the fuel policy."

However, speaking on the same programme, Ryanair spokesperson Stephen McNamara denied the claims.

He said the airplanes were not in imminent danger, but were required to make the mayday calls so that they could land with the required amount of leftover fuel.


ADB Promotes Asian Risk Financing to Guard against Disasters

Losses from natural disasters such as hurricanes and floods have risen faster than Asia-Pacific’s economy has expanded, according to a report from the Asian Development Bank (ADB), which recommends regional governments find ways to offer disaster risk financing instruments such as calamity funds, tax credits and catastrophe (cat) bonds to strengthen disaster resilience.

“Asia’s economic gain is being eroded by disasters, often hitting the poorest hardest,” said Bindu Lohani, ADB’s vice president for knowledge management and sustainable development. “As the global region most vulnerable to climate change, we no longer have a choice but to focus on disaster risk management.” Natural hazards continue to cause significant loss of life in the region. Between 1970 and 2010, 1.7 million hazard-related deaths were recorded in Asia and Pacific, representing 51% of the global total.

According to the bank’s report, titled
‘Investing in Resilience – Ensuring a Disaster-Resistant Future’
, significant investments to strengthen disaster resilience can reverse the trend. The report suggests that a range of factors contribute to the increasing disaster losses of recent years, such as inadequate risk data, weak and misaligned incentives, poor legislative and regulatory frameworks and enforcement, disjointed government, limited funding and power disparities.

The report examines the instruments and mechanisms that currently exist in Asia to protect against disasters, and offers solutions for stronger disaster resilience, including how disaster risks can be financed through disaster risk insurance and reinsurance, cat bonds and other vehicles. A wider range of disaster risk financing instruments is needed for Asia and the Pacific, which lags behind other regions in developing innovative financial solutions for disaster resilience. Less than 5% of disaster losses in developing Asia are insured, against 40% in developed countries.

To overcome these challenges, the report identifies critical next steps to better assess, reduce and manage disaster risk. It recommends that national and sub-national governments develop and implement comprehensive disaster risk financing strategies to provide post-disaster support to strengthen financial resilience.

Most Asian countries have disaster handling capabilities, but few have adequate provisions for financing post-disaster losses and rehabilitation. Disaster losses are expanding at a faster pace in Asia due to environmental degradation, climate change, demographic pressures, and widespread failure to consider disaster risk in designing and locating many critical development investments.

Related reading


From NextGov:

The Homeland Security Department is exploring technology that would use facial and iris recognition to track the departure of foreign visitors, according to contracting documents. “At land border exit[s], currently there are no biometrics captured resulting in an inability to accurately verify that a departing traveler matches a specific entry record,” states a market research survey released on Wednesday.


Sample Assignment: Multigenre Project
L. Langstraat, Associate Professor of English
Colorado State University

A Multigenre Project presents multiple, even conflicting, perspectives on a topic or event, in order to provide a rich context and present an aesthetically appealing product for an audience. Your multigenre project should reflect the following:

A focus:  You should not only include documents that relate to a general topic or event, but you should ensure that the documents forward a point of significance, a rhetorical purpose.

A coherent organization:  Documents should be created and organized in order to lead readers through the project, to help them understand your focus and purpose.  A series of seemingly unconnected pieces, though they may share a similar topic, will not result in a strong multigenre project.  Instead, readers should experience a sense of cohesion, a sense of connection and transition between each generic document in the project.  You can create coherence through transitional pieces between genres, your table of contents, etc.

Begin with an informal proposal for research. In this proposal, you have an opportunity to think-in-writing about your plans for your multigenre research.  This is an informal piece of writing about your research interests, the questions guiding those interests, and the potential genre documents you’d like to produce.  We’ll then give you feedback and suggestions about your ideas and guide you in the right direction for research.  Your proposal should include: a list of 5 questions that might guide your research; an explanation of WHY you’re interested in this topic; ideas about primary and secondary sources that might be useful?  Ideas about genres are you thinking about producing for your project (see list of genres); and a projection of how you will ensure that those genres can are connected, so that the mgp becomes a coherent whole, a clear argument?

The Multigenre Project includes at least 8 documents (including an Introduction, Table of Contents, 5 documents of different genres, and a works cited page) that offer a sustained argument about your chosen issue.  By creating documents in different genres (e.g., the academic research essay, editorials, feature stories, brochures, short fiction, charts, scripts, etc.), you learn to write for multiple audiences, multiple purposes, and multiple forums.

Your entire MGP should be presented in a theme that best fits your purposes.  Past students have “packaged” their MGPs as a CD, a scrapbook, a photo album, a patient file, an employee handbook, a manual, a newspaper, a magazine—the options are endless!  Just be sure to offer us a table of contents (TOC) that provides an overview of and title for each document.

Your Introduction serves as a guide to readers, helping us understand the issue you’re addressing, offering us insight about why you chose the genres you chose, etc.  The intro is your chance to help us understand why this topic is important, how we should “read” your documents, etc.  The intro may be written as a letter to readers, a magazine article, an editorial, etc.

The bulk of your MGP will be the five documents, each representing a different genre, that helps persuade your audience(s) to your point of view.  Aim for a good balance of genres, and be sure that at least three of your documents directly use the sources you’ve gathered from your library research.  By writing a traditional researched essay, a brochure that utilizes your research sources, a chart or other visual, a story drawing from the information you’ve gathered, a quiz based on researched sources, etc.—by approaching your research findings in a creative way, your MGP helps an audience understand many different perspectives about your topic.  Some of the documents you’ll include may be more time-intensive than others.  But the 5 documents that make up the body of your MGP should show your knowledge, creativity, and ability to persuade your audience(s) toward your central claim.

The MGP should conclude with a Works Cited page.  As you cite sources for each document, your citation approach should be appropriate for each genre.  It’s a rare ghost story, for example, that includes parenthetical citation practices!  But there are creative ways to ensure that you a) give credit to the source from which you draw information (e.g., discussing that info in your introduction, using endnotes/acknowledgment pages, etc.), and b) establish your credibility as a writer who has conducted significant research to support your opinion.


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Complete information about Indian Film Industry, Comprehensive coverage of Bollywood gossip, individual awards, Indian and Bollywood dance, Costume ideas and Makeup techniques, Hot songs from Bollywood.

If a movie has been made then there has to be some reward for the people who excel in this industry and this is where come in the awards. The first and the oldest award to be given in India was the prestigious black Lady or the filmfare awards.


Anxiety Could Be The Reason You Made A Bad Decision

Anxiety doesn’t just affect the way we feel — it can also have a significant impact on our daily behaviors, including our ability to make sound decisions.

A new study from neuroscientists at the University of Pittsburgh finds that anxiety disengages the prefrontal cortex, a brain region that’s critical for flexible decision-making, as well as attention and higher-order thinking.

“Anxiety is a mental health issue that affects our day-to-day life, including our decision-making,” Dr. Bita Moghaddam, a neuroscientist at the university and the study’s lead author, told The Huffington Post in an email. “By understanding the biological processes that make this happen, we can hopefully come up with better ways of treating this aspect of anxiety.”

For the study, which was published last week in The Journal of Neuroscience, the researchers monitored the activity of neurons in the prefrontal cortex of rats to see how their brain activity affected their decision-making ability.

Half of the rats were given an injection of an anxiety-inducing drug while the other half received a placebo injection. The rats then completed two decision-making tasks in which they were challenged to make the most optimal choices that led to a reward.

When the rats completed the task, both groups performed similarly. However, when they completed it for a second time researchers included environmental distractions, which resulted in the anxious rats making poorer decisions.

Why does anxiety lead to bad decisions in the face of distractions? On a neurological level, the researchers found that anxiety had a numbing effect on neurons in the prefrontal cortex. In other words, anxiety has a selective effect on the type of neuron activity that supports decision-making.

“Behavior including making decisions is encoded by specific groups of neurons in the brain,” Moghaddam said. “Anxiety essentially weakens the encoding power of a group —> Read More