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  • May 12, 2012
  • 10:27 AM
  • 647 views

'Danger and Evolution in the Twilight Zone': Guest post by Randen Patterson and Gaurav Bhardwaj

by Jonathan Eisen in The Tree of Life




Figure 1. PHYRN concept and work flow.

'Danger and Evolution in the twilight zone'

I have been communicating with Randen Patterson on and off over the last five years or so about his efforts to try and study the evolution of gene families when the sequence similarity in the gene family is so low that making multiple sequence alignments are very difficult.  Recently, Randen moved to UC Davis so I have been talking / emailing with jim more and more about this issue.  Of note, Randen has a new paper in PLoS One about this topic: Bhardwaj G, Ko KD, Hong Y, Zhang Z, Ho NL, et al. (2012) PHYRN: A Robust Method for Phylogenetic Analysis of Highly Divergent Sequences. PLoS ONE 7(4): e34261. doi:10.1371/journal.pone.0034261.




Figure 8. Model for the Evolution of the DANGER Superfamily.


I invited Randen and the first author Gaurav Bhardwaj to do a guest post here providing some of the story behind their paper for my ongoing series on this topic.  I note - if you have published an open access paper on some topic related to this blog I would love to have a guest post from you too.   I note - I personally love the fact that they used the "DANGER" family as an example to test their method.


Here is their guest post:


A fundamental problem to phylogenetic inference in the “twilight zone” (<25% pairwise identity), let alone the “midnight zone” (<12% pairwise identity), is the inability to accurately assign evolutionary relationships at these levels of divergence with statistical confidence. This lack of resolution arises from difficulties in separating the phylogenetic signal from the random noise at these levels of divergence. This obviously and ultimately stymies all attempts to truly resolve the Tree of Life. Since most attempts at phylogenetic inferences in twilight/midnight zone have relied on MSA, and with no clear answer on the best phylogenetic methods to resolve protein families in twilight/midnight zone, we have presented rest of this blog post as two questions representative of these problems.  

Question1: Is MSA required for accurate phylogenetic inference? 

Our Opinion: MSA is an excellent tool for the inference from conserved data sets, but it has been shown by others and us, that the quality of MSA degrades rapidly in the twilight zone. Further, the quest for an optimal MSA becomes increasingly difficult with increased number of taxa under study. Although, quality of MSA methods has improved in last two decades, we have not made significant improvements towards overcoming these problems. Multiple groups have also designed alignment-free methods (see Hohl and Ragan, Syst. Biol. 2007), but so far none of these methods has been able to provide better phylogenetic accuracy than MSA+ML methods. We recently published a manuscript in PLoS One entitled “PHYRN: A Robust Method for Phylogenetic Analysis of Highly Divergent Sequences” introducing a hybrid profile-based method. Our approach focuses on measuring phylogenetic signal from homologous biological patterns (functional domains, structural folds, etc), and their subsequent amplification and encoding as phylogenetic profile. Further, we adopt a distance estimation algorithm that is alignment-free, and thus bypasses the need for an optimal MSA. Our benchmarking studies with synthetic (from ROSE and Seqgen) and biological datasets show that PHYRN outperforms other traditional methods (distance, parsimony and Maximum Liklihood), and provides significantly accurate phylogenies even in data sets exhibiting ~8% average pairwise identity. While this still needs to be evaluated in other simulations (varying tree shapes, rates, models), we are convinced that these types of methods do work and deserve further exploration. 

Question 2: How can we as a field critically and fairly evaluate phylogenetic methods? 

Our Opinion: A similar problem plagued the field of structural biology whereby there were multiple methods for structural predictions, but no clear way of standardizing or evaluating their performance.  An additional problem that applies to phylogenetic inference is that, unlike crystal structures of proteins, phylogenies do not have a corresponding “answer” that can be obtained.  Synthetic data sets have tried to answer this question to a certain extent by simulating protein evolution and providing true evolutionary histories that can be used for benchmarking.  However, these simulations cannot truly replicate biological evolution (e.g. indel distribution, translocations, biologically relevant birth-death models, etc). In our opinion, we need a CASP-like model (solution adopted by our friends in computational structural biology), where same data sets (with true evolutionary history known only to organizers) are inferred by all the research groups, and then submitted for a critical evaluation to the organizers. To convert this thought to reality, we hereby announce CAPE (Critical Assessment of Protein Evolution) for Summer 2012. We are still in pre-production stages, and we welcome any suggestions, comments and inputs about data sets, scoring and evaluating methods.   




Bhardwaj, G., Ko, K., Hong, Y., Zhang, Z., Ho, N., Chintapalli, S., Kline, L., Gotlin, M., Hartranft, D., Patterson, M., Dave, F., Smith, E., Holmes, E., Patterson, R., & van Rossum, D. (2012). PHYRN: A Robust Method for Phylogenetic Analysis of Highly Divergent Sequences PLoS ONE, 7 (4) DOI: 10.1371/journal.pone.0034261
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This is from the "Tree of Life Blog"
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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... Read more »

Bhardwaj, G., Ko, K., Hong, Y., Zhang, Z., Ho, N., Chintapalli, S., Kline, L., Gotlin, M., Hartranft, D., Patterson, M.... (2012) PHYRN: A Robust Method for Phylogenetic Analysis of Highly Divergent Sequences. PLoS ONE, 7(4). DOI: 10.1371/journal.pone.0034261  

  • May 11, 2012
  • 09:58 AM
  • 629 views

Journal Fire: Bonfire of the Vanity Journals?

by Duncan Hull in O'Really?

When I first heard about Journal Fire, I thought, Great! someone is going to take all the closed-access scientific journals and make a big bonfire of them! At the top of this bonfire is the burning effigy of a wicker man, representing the very worst of the vanity journals.... Read more »

Deans Andrew R., Yoder Matthew J., & Balhoff James P. (2012) Time to change how we describe biodiversity. Trends in Ecology , 27(2), 84. DOI: 10.1016/j.tree.2011.11.007  

  • May 10, 2012
  • 01:58 PM
  • 508 views

Neighbourhood Watch for cloud computing

by David Bradley in Sciencetext

Hey, you! Get off of that cloud! Cloud computing is on the rise, as we have discussed her on many an occasion. It’s useful for fast and robust web hosting, it’s great for anywhere email access, for remote file storage and backup (DropBox Wuala GoogleDrive etc), for sharing large media files, whether movies, music files, [...]Post from: David Bradley's Sciencetext Tech TalkNeighbourhood Watch for cloud computing
... Read more »

Sudhir N. Dhage, & B.B. Meshram. (2012) Intrusion detection system in cloud computing environment. International Journal of Cloud Computing, 1(2/3), 261-282. info:/

  • May 7, 2012
  • 09:28 PM
  • 704 views

Science in superheroes

by Cath in Basal Science (BS) Clarified

The magic of the movies mean almost anything can happen. You can time travel, control objects with your mind, or even heal yourself no matter how serious your injuries are. But did you know that filmmakers often consult scientists and engineers for their input in movies? Dr. Jim Kakalios, a professor at the University of [...]... Read more »

  • May 3, 2012
  • 04:30 PM
  • 550 views

Putting the Squeeze on Microfluidics

by Hector Munoz in Microfluidic Future

Microfluidic devices are able to process small volumes of liquid and are comprised of microscale components, but the devices themselves are not often small themselves. These labs-on-chips are often limited to lives in labs instead of the remote areas that could really benefit from their use. The limitation comes in the form of support equipment used to process or analyze assays that are expensive, bulky, energy consuming and/or require trained professional operators. Syringe pumps are often used in labs to drive liquids used in assays at specific flow rates and to ensure that the right volume is used. The need for complicated, external flow equipment was recently addressed by a group from Peking University. The group’s paper, “Squeeze-chip: a finger-controlled microfluidic flow network device and its application to biochemical assays” was recently featured on the cover of Lab on a Chip.... Read more »

  • May 3, 2012
  • 10:00 AM
  • 760 views

Need to re-invent the Web (badly)? There’s an App for that!

by Duncan Hull in O'Really?

I love the convenience of mobile applications but hate the way they re-invent the wheel and are killing the Web. What can be done about it?... Read more »

Zittrain J. (2007) Saving the internet. Harvard business review, 85(6), 49. PMID: 17580647  

  • May 3, 2012
  • 05:00 AM
  • 496 views

User-generated content Informality

by Alejandro Mosquera in amsqr

The relevance of informality analysis in social media texts... Read more »

Alejandro Mosquera, & Paloma Moreda. (2011) Enhancing the discovery of informality levels in Web 2.0 texts. Proceedings of the 3rd Language Technology Conference (LTC 2011), Poland. info:/

  • May 1, 2012
  • 12:50 PM
  • 957 views

Virtual Reality for Worms

by TheCellularScale in The Cellular Scale

How do you build a virtual environment for a worm? The Nematode C. Elegans with glowing neurons (source)Using a little optogenetic trickery, you can directly activate specific worm neurons with light.  If you know your worm neurons, you can stimulate ones that make it think it has suddenly touched something with its nose or that the environment is suddenly very salty.  Before we dive into worm VR, let's back up and discuss this specific worm.The Magnificent C. ElegansC. Elegans is a surprisingly popular subject of study in neuroscience. It has a simple and well defined nervous system that contains only 302 neurons (in the hermaphrodite, the rare males have a few extra neurons).  All the neurons and even all the connections between the neurons have been pretty well characterized.  They are small (hundreds can fit on a standard sized petri dish) and they reproduce quickly.  And it that wasn't enough to make C. elegans a desirable subject for study, they can be genetically altered with relative ease, and exhibit rudimentary learning skills.  A recent technological development has made clever use of genetic tools that allow calcium influx (an indicator of neural activity) to be visualized in neurons and allow neurons to be activated by light. Faumont et al., (2011) have created a worm tracking system that uses the fluorescence from a genetically altered neuron to locate the worm and recenter the microscope on the worm in real time. This allows for completely non-invasive visualization of neuronal calcium/activity in the awake behaving animal.  The recent paper in PLoS One, describes exactly how they got the microscope to track the worm in real time without blurring of the signal or messing up the calcium imaging. The paper is open access, so you can go read the details for free.To see this larger and more clearly, you can download this video and their 4 other supplementary videos here.  In this video, you can see the animal moving around in the top left, the path it follows in the top right, the calcium fluorescence signal in the bottom left (notice the calcium neuron is always in the field of view), and the activity of this particular neuron when the worm is traveling either forward (blue) or backward (red).  The "Dedicated Circuit" HypothesisThe neuron imaged in this video is called AVB, and it is a 'command neuron'.  Faumont et al. show that it increases in activity when the worm is moving forward and decreases when the worm moves backwards.  A similar command neuron, AVA, does just the opposite, increasing when the worm moves backward and decreasing when it moves forward.  These data support what is called the "dedicated circuit hypothesis" which says that the worm uses one set of neurons to go forward and a completely different set of neurons to move backwards.While Faumont et al. shows that the dedicated circuit hypothesis is supported for command neurons, they find that the activity of the actual motor neurons (the neurons on the body wall that control contraction of the muscles) does not support this hypothesis.  If the dedicated circuit hypothesis was true, the A-type motor neurons should only be active and oscillating during backward movement, and the B-type motor neurons should only be active during forward movement.  They found that this wasn't true, that both were active and oscillating during both forward and backward motion.  Virtual Reality for WormsNow back to virtual reality.  This Faumont et al. paper is a showcase of new tools that can be used to study C. Elegans in a simultaneously macroscopic and microscopic way.  One of the new techniques the introduce is the optogenetic stimulation of specific neurons in specific places to create and 'environment' for the worm.  Faumont et al., 2011 Figure 2When they genetically express channel rhodopsin, the channel which activates neurons when exposed to blue light in the ASH neuron (a neuron sensitive to osmolarity, or saltiness, changes), they can activate that neuron whenever they want by turning on the blue light.  They create a virtual environment by tracking the worm as it travels in a field, and activating the blue light when it reaches a certain xy coordinate.  In the figure above they activate the neuron when the worm's nose is within the outer ring (traces turn blue).  This makes the worm 'think' that the ring is full of saltier liquid than the rest of the area.  This virtual environment takes away all the technical difficulties of actually creating a ring of salty water in a pool of less salty water, and the VR environment can be quickly and easily changed into any shape or size, when desired.  This new tracking method, in combination with calcium imaging and optogenetics, represents a leap forward in cellular scale neuroscience, to non-invasively visualize neuronal activity, activate neurons, and record the coinciding behavior is a combination mammalian neuroscientists can only dream about.Note: there are ways to image calcium in the neurons of moving mice, but even this requires installing a 'window' into the skull and mounting a mini-microscope on the mouse's head. In addition, the neurons visualized are limited to the ones closest to the surface of the brain.© TheCellularScale... Read more »

  • May 1, 2012
  • 08:24 AM
  • 616 views

Cybernetics – Left Ventricular Assist Device

by Jason Carr in Wired Cosmos

Left ventricular assist device technology isn’t necessarily new, but it is one of the biggest harbingers of cybernetic technology. People with weak hearts that are waiting for a donor can use these sorts of heart pumps to bridge patients over until they can receive a full transplant. However, such LVAD machines are usually located in [...]... Read more »

Rizzieri, A., Verheijde, J., Rady, M., & McGregor, J. (2008) Ethical challenges with the left ventricular assist device as a destination therapy. Philosophy, Ethics, and Humanities in Medicine, 3(1), 20. DOI: 10.1186/1747-5341-3-20  

  • April 30, 2012
  • 03:03 PM
  • 1,003 views

Math Shows Today's Writers Are Less Influenced by the Past

by Elizabeth Preston in Inkfish




When Charles Dickens wrote It was the of, it was the of, the immortal first words in A Tale of Two Cities, he can't have imagined that 21st-century computer scientists would parse his prepositions and pronouns as part of vast literary data sets. But today's researchers are studying the unimportant words in books to find important literary trends. With the meaty words taken out, language becomes a numbers game.

To see how literary styles evolve over time--a science dubbed "stylometry"--researchers led by James Hughes at Dartmouth College turned to Project Gutenberg. The site contains the full text of more than 38,000 out-of-copyright books. Researchers began their mining expedition by digging out every author who wrote after 1550, had a known date of birth and (when relevant) death, and had at least 5 English-language books digitized.

These criteria gave the researchers a set of 537 authors with 7,733 published works. But they weren't interested in every word of those books. Nouns and adjectives were out: No Kareninas or Lolitas, nothing nice or bad or beautiful, no roads or homes or people. Most verbs were out, except for forms of the utilitarian to be. No one could speak or walk or Fly, good Fleance!

It may seem that the researchers were stripping all the information-containing words out of the sentences, and in fact that was their goal: "Content-free" words were all they wanted. The 307-word vocabulary that remained from the books was mostly prepositions, conjunctions, and articles.

This linguistic filler, the little stitches that hold together the good stuff, is known to contain a kind of authorial fingerprint. We may not think much about these words when we're writing or speaking, but scientists can use them to define our style.

Hughes and his team used computer analysis to score each author's similarity to every other author. They found that before the late 18th century, authors's stylistic similarity didn't depend on how close to each other they lived. (Each author was represented by a single year, the midpoint between his or her birth and death.) During this time period, authors who lived in the same generation didn't influence each other's styles much more than authors who lived hundreds of years away.

But from the late 18th century to today, it was a different story. Stylistically, authors were more similar to their contemporaries than to other writers. By the late 19th century, writers closely matched the style of other writers who lived at the same time (at least according to the computers tallying up their non-content words). This influence dropped off outside of 30 years. In other words, authors who lived more than three decades away each other may as well have lived centuries away, for all the similarity between their writing.

Looking at more recent books, that window of influence seems to become even tighter. Among authors from the first half of the 20th century, the similarity of style drops off beyond just 23 years.

Over time, authors have become more and more influenced by the other authors writing at the same time. The researchers say this may simply be due to the number of books published. In the early part of their dataset, there were few enough books around that a studious person could read, well, most of them. But as more and more books were published, contemporary books made up a larger share of what was available to read. Authors have filled more and more shelves in their libraries with books by their peers--and this has made them more likely to echo each other's styles.

Because Project Gutenberg relies on public-domain material, there weren't very many authors after the mid-20th century included in this study. Looking forward, "You would expect a continued diminishing of influence," says Daniel Rockmore, the paper's senior author. Contemporary books take up an ever greater portion of what's available to read. In addition to the huge number of books published each year (more than 288,000 in the United States in 2009), there are now e-books and e-readers and Japanese Twitter novels.

A century from now, we may be able to look back and see that today's authors had an ever-condensing frame of influence. Of course, by then literary styles might only last a week. Most books will be forgotten, but every author will be a revolutionary.

James M. Hughes, Nicholas J. Foti, David C. Krakauer, & Daniel N. Rockmore (2012). Quantitative patterns of stylistic influence in the evolution of literature PNAS : 10.1073/pnas.1115407109


Image: Library of Congress from ep_jhu/Flickr

... Read more »

James M. Hughes, Nicholas J. Foti, David C. Krakauer, & Daniel N. Rockmore. (2012) Quantitative patterns of stylistic influence in the evolution of literature. PNAS. info:/10.1073/pnas.1115407109

  • April 26, 2012
  • 10:43 PM
  • 843 views

Phthalates–why you should care about these plastic additives

by Cath in Basal Science (BS) Clarified

Aside from cost, aesthetics, and functionality, materials selection is now a topic priority for many consumers when they make a purchase. Consumers are becoming more aware of their choices for sustainable and reusable materials—even the potential health risks/toxicity associated with materials. This is especially true for products containing plastics, particularly the additives used to make [...]... Read more »

  • April 25, 2012
  • 11:54 AM
  • 895 views

Can a Horde of Idiots be a Genius?

by Miss Behavior in The Scorpion and the Frog

Let’s face it: The typical individual is not that bright. Just check out these human specimens: Yet somehow, if you get enough numbskulls together, the group can make some pretty intelligent decisions. We’ve seen this in a wide variety of organisms facing a number of different challenges.In a brilliant series of studies, 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. If a scout finds such a place, 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. Eventually, the majority of the 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 fly off together to their new home.But groups can develop better solutions than individuals even without communication. Gaia Dell’Ariccia at the University of Zurich in Switzerland and her colleagues explored homing pigeon navigation by placing GPS trackers on the backs of pigeons and releasing them from a familiar location either alone or in a group of six. Because they were all trained to fly home from this site, they all found their way home regardless of whether they were alone or in a group. But as a flock, the pigeons left sooner, rested less, flew faster, and took a more direct route than did the same birds when making the trip alone. By averaging the directional tendencies of everyone in the group, they were able to mutually correct the errors of each individual and follow the straightest path. In each of these examples, each individual has limited and uncertain information, but each individual has information that may be slightly different than their neighbors’. By combining this diverse information and making a collective decision, hordes of idiots can make genius decisions.Want to know more? Check these out:1. Couzin, I. (2009). Collective cognition in animal groups Trends in Cognitive Sciences, 13 (1), 36-43 DOI: 10.1016/j.tics.2008.10.002 2. ... Read more »

Couzin, I. (2009) Collective cognition in animal groups. Trends in Cognitive Sciences, 13(1), 36-43. DOI: 10.1016/j.tics.2008.10.002  

Goss, S., Aron, S., Deneubourg, J., & Pasteels, J. (1989) Self-organized shortcuts in the Argentine ant. Naturwissenschaften, 76(12), 579-581. DOI: 10.1007/BF00462870  

Dussutour, A., Nicolis, S., Deneubourg, J., & Fourcassié, V. (2006) Collective decisions in ants when foraging under crowded conditions. Behavioral Ecology and Sociobiology, 61(1), 17-30. DOI: 10.1007/s00265-006-0233-x  

  • April 24, 2012
  • 09:46 AM
  • 525 views

A hybrid social blogging platform

by David Bradley in Sciencetext

A while back I mentioned FriendLens as a tool for getting a different view of your friends’ Facebook photos. But, there is another Friend Lens being developed by John Gibbons and Arvin Agah of The University of Kansas, in Lawrence, using open source resources. (I suspect they will have to find a different name for [...]Post from: David Bradley's Sciencetext Tech TalkA hybrid social blogging platform
... Read more »

John W. Gibbons, & Arvin Agah. (2012) Friend Lens: novel web content sharing through strategic manipulation of cached html. Int. J. Web Based Communities, 8(2), 242-265. info:/

  • April 24, 2012
  • 05:38 AM
  • 620 views

Let’s Explore Surface Electromyography

by Jason Carr in Wired Cosmos

Surface electromyography is apparently now able to recognize and even synthesize speech based on a certain pattern. An acoustic signal is corrupted by high environmental noise. Astronauts that perform operations in spacesuits fall victim to this phenomenon. Earthbound firefighters are … Continue reading →... Read more »

  • April 23, 2012
  • 12:15 PM
  • 644 views

When Cellular Automata Come to Life

by Jason Carr in Wired Cosmos

Cellular automata are probably the closest things to machine life that most people have gotten an opportunity to experiment with in recent years. John Conway invented a piece of software titled the Game of Life in 1970. He carefully set up the rules to create a balanced world. While this might sound like old news, [...]... Read more »

Arima V, Iurlo M, Zoli L, Kumar S, Piacenza M, Della Sala F, Matino F, Maruccio G, Rinaldi R, Paolucci F.... (2012) Toward Quantum-dot Cellular Automata units: thiolated-carbazole linked bisferrocenes. Nanoscale, 4(3), 813-23. PMID: 22159165  

  • April 23, 2012
  • 07:27 AM
  • 1,030 views

Robotic Telesurgery in Space

by Jason Carr in Wired Cosmos

Telemedicine is a field that uses telecommunications technology to provide healthcare at a distance. Certain computer systems can be linked to a physician’s office for diagnostic purposes. Different clinics and hospitals can be linked together. In the future, telemedicine could be used to perform robotic surgeries in space. Some forms of telemedicine have been in [...]... Read more »

  • April 19, 2012
  • 11:02 PM
  • 730 views

Nanoparticle-treated wood minimizes biocide leaching

by Cath in Basal Science (BS) Clarified

Sitting on the deck to drink your morning cup of coffee is a great way to start the day—but not when your deck is rotting. Fortunately wood products are protected with wood preservatives, often with chromate copper arsenate (CCA) [3]. But growing concerns over the safety and health effects [...]... Read more »

  • April 19, 2012
  • 03:00 PM
  • 507 views

Diagnosing Similar Diseases in Low Resource Settings

by Hector Munoz in Microfluidic Future

A lot of excitement surrounding microfluidics has been about its promising use in diagnosis in low-resource settings. Many infectious diseases present in developing countries are manageable or treatable with available medications, but still account for 1/3 of deaths. In these areas, multiple diseases present similar symptoms, leading to misdiagnosis and thus incorrect treatment. Hundreds of blood-based microfluidic immunoassays are available for diagnostic purposes, but they’re not all created equally. They require varying levels of sample processing or analysis that prohibit their deployment in low-resource settings. Further, while some diseases may have similar symptoms, they might require different detection techniques, with varying sample volumes, reagents and processing time, making it difficult to detect multiple diseases within the same system. This is the focus of recent work from Paul Yager of University of Washington. In his Lab on a Chip paper, “Progress toward multiplexed sample-to-result detection in low resource settings using microfluidic immunoassay cards,” he and his colleagues develop a system to detect both Typhoid fever and malaria.... Read more »

Lafleur, L., Stevens, D., McKenzie, K., Ramachandran, S., Spicar-Mihalic, P., Singhal, M., Arjyal, A., Osborn, J., Kauffman, P., Yager, P.... (2012) Progress toward multiplexed sample-to-result detection in low resource settings using microfluidic immunoassay cards. Lab on a Chip, 12(6), 1119. DOI: 10.1039/C2LC20751F  

  • April 19, 2012
  • 12:10 PM
  • 836 views

The Merging of Biology and Electronics [Research]

by Jason Carr in Wired Cosmos

The boundary between electronics and biology is blurring with the first detection by researchers at Department of Energy’s Oak Ridge National Laboratory of ferroelectric properties in an amino acid called glycine. A multi-institutional research team led by Andrei Kholkin of the University of Aveiro, Portugal, used a combination of experiments and modeling to identify and [...]... Read more »

Heredia, A., Meunier, V., Bdikin, I., Gracio, J., Balke, N., Jesse, S., Tselev, A., Agarwal, P., Sumpter, B., Kalinin, S.... (2012) Nanoscale Ferroelectricity in Crystalline γ-Glycine. Advanced Functional Materials. DOI: 10.1002/adfm.201103011  

  • April 12, 2012
  • 12:24 PM
  • 1,259 views

Why the RMS Titanic fractured: clues from the ship’s hull

by Cath in Basal Science (BS) Clarified

This Sunday will be 100th anniversary of the sinking of the Royal Mail Ship (RMS) Titanic. Over the years this tragic accident has been the topic of numerous books, films, exhibits—even a memorial cruise. Not only has this shipwreck captured the attention of the public, but the scientific community as well. Ever since the wreckage [...]... Read more »

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