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  • November 3, 2014
  • 05:55 PM
  • 473 views

Reshaping the Limits of Synthetic Biology

by Dr. Jekyll in Lunatic Laboratories

Ever think you could have built something better if you had a hand in the design? Sometimes people just have a desire to make, after all the maker movement is huge for a reason. Well geneticists have a new toy tool to play with —dubbed “the telomerator”—that could redefine the limits of synthetic biology and advance how successfully living things can be engineered or constructed in the laboratory based on an organism’s genetic, chemical base-pair structure. How cool is that?!... Read more »

J. Boeke et al. (2014) Circular permutation of a synthetic eukaryotic chromosome with the telomerator. Proceedings of the National Academy of Sciences. info:/10.1073/pnas.1414399111

  • October 24, 2014
  • 04:27 AM
  • 504 views

Collective Structures in Software Projects

by Jörg Friedrich in Software Engineering Economics

To understand the social dynamics of complex software development processes, it is necessary to analyze in which structures the persons involved and how this involvement affected their work. Damian Tamburri has in recent years identified the relevant social structures in a number of publications, analyzed and graded on their effect. He first distinguishes four basic […]... Read more »

Tamburri, D., Lago, P., & Vliet, H. (2013) Organizational social structures for software engineering. ACM Computing Surveys, 46(1), 1-35. DOI: 10.1145/2522968.2522971  

  • October 21, 2014
  • 04:51 PM
  • 562 views

Dude, wheres my Hover Car? Oh wait…

by Dr. Jekyll in Lunatic Laboratories

We all (of a certain age) remember the Jetsons, a futuristic family with hi-tech gadgets and gizmos. However, nothing said, “the future is here” quite like things hovering. Even in the movie Back to the future, they have hover boards and flying cars. Unfortunately we don’t, which is a shame because according to the 1950’s we are the future, we should have hover-cars and hover boards… well the wait is over. Yep, introducing the first real hover board!... Read more »

Hendo Hover. (2014) Hendo Hoverboards - World's first REAL hoverboard. Kickstarter. info:other/Here

  • October 20, 2014
  • 04:50 PM
  • 749 views

A Venusian Mystery Explored Once More

by Dr. Jekyll in Lunatic Laboratories

Venus, the place where women are from... supposedly. To say Venus has a harsh climate would be an understatement, this is one of many reasons why we will never (or maybe not soon) see a "long lasting" Venus rover counterpart to our Mars rover missions. Still, the planet (much like all the other plants) can teach us a lot about not just our own origins, but the origins of the universe. Also like all our neighbor planets Venus is hiding something beneath its brilliant shroud of clouds, a mystery that might be soon solved, all thanks to a new re-analysis of twenty-year-old spacecraft data.... Read more »

Harrington, E. et. Al. (2014) The puzzle of radar-bright highlands on venus: a high-spatial resolution study in Ovda regio. Geological Society of America. info:other/136-4

  • October 20, 2014
  • 12:12 PM
  • 921 views

How a camera and quantum physics could improve phone security

by This Science is Crazy! in This Science Is Crazy!

New study uses mobile phone camera to detect light, using shot noise to generate true random numbers which researchers hope could be used for encryption in the future.... Read more »

Sanguinetti, B., Martin, A., Zbinden, H., & Gisin, N. (2014) Quantum Random Number Generation on a Mobile Phone. Physical Review X, 4(3). DOI: 10.1103/PhysRevX.4.031056  

  • October 19, 2014
  • 07:24 AM
  • 332 views

Power Makes People Deliberate Less Over Emails

by Neuroskeptic in Neuroskeptic_Discover

When it comes to emails, power makes people spend less time thinking and more time typing. So say German cyber-psychologists Annika Scholl and Kai Sassenberg in a new paper just published: Experienced Social Power Reduces Deliberation During E-Mail Communication In their study, they recruited 49 undergraduate students. Each participant was first randomly assigned to play […]The post Power Makes People Deliberate Less Over Emails appeared first on Neuroskeptic.... Read more »

  • October 14, 2014
  • 04:58 PM
  • 569 views

Carbon’s Place in a Silicon World

by Dr. Jekyll in Lunatic Laboratories

Everything is silicon based, well mainly your computer, your TV, your ipad, and pretty much every piece of electronics in existence. Still the world turns and so does technology; at a similarly fast pace no less. Even as the 2014 Nobel Prize in Physics has enshrined light emitting diodes (LEDs) as the single most significant and disruptive energy-efficient lighting solution of today, scientists around the world continue unabated to search for the even-better-bulbs of tomorrow. In this search we are now ditching silicon for new carbon-based electronics.... Read more »

Sharon Bahena-Garrido, Norihiro Shimoi, Daisuke Abe, Toshimasa Hojo, Yasumitsu Tanaka, & Kazuyuki Tohji. (2014) Plannar light source using a phosphor screen with single-walled carbon nanotubes as field emitters. Review of Scientific Instruments. info:/http://dx.doi.org/10.1063/1.4895913

  • October 9, 2014
  • 04:10 PM
  • 809 views

Solar Panel Hybrid is Cheap and Super Efficient

by Dr. Jekyll in Lunatic Laboratories

Solar cells are inefficient, it’s a sad fact. With todays technology they boast about a 10-15% efficiency, compare that to todays gas engine at roughly 20-25% and you can see it’s not quite up to par. Well that could all change very soon thanks to a new method for transferring energy from organic to inorganic semiconductors. This could boost the efficiency of widely used inorganic solar cells to as close as 100% efficiency as they can get.... Read more »

Tabachnyk M, Ehrler B, Gélinas S, Böhm ML, Walker BJ, Musselman KP, Greenham NC, Friend RH, & Rao A. (2014) Resonant energy transfer of triplet excitons from pentacene to PbSe nanocrystals. Nature materials. PMID: 25282509  

  • October 7, 2014
  • 05:17 AM
  • 655 views

Story behind our paper on speeding-up all-against-all comparisons for homology inference

by Christophe Dessimoz in Open Reading Frame

This post accompanies a recent publication and is part of our
series story behind the paper,
inspired by Jonathan Eisen’s series of the same
name.

One fundamental step in sequence analysis is the identification of homologous
sequences, sequences related through common ancestry. There are many different
ways of identifying homolog but they broadly fall into two categories:
all-against-all comparisons and clustering.

The all-against-all approach aligns every sequence with every other one. This
is straighforward to implement, relatively sensitive, and robust to variations
in sequence lengths. The main downside of all-against-all comparisons is the
quadratic computational cost with respect to the number of sequences.

In contrast, clustering works by using one representative sequence or profile
per homologous family of genes (clusters), thus limiting the number of
required comparisons to one per cluster. Assuming a fixed (or nearly fixed)
number of clusters, the computational cost is (nearly) linear in the number of
input sequences. Clustering methods however tend to miss more homologous
relationships than the all-against-all.

Can the sensitivity of the all-against-all be achieved at the speed of clustering?

The OMA database—developed in our lab—currently
relies upon an all-against-all. With 8,798,758 protein sequences from 1706
genomes in the latest release, this represents 38.7 trillion alignments. We
could probably cope with a few thousands genomes more, but will struggle to
get to the next order of magnitude with the current pipeline.

Furthermore, it is difficult to accept that as we increasingly sample the protein
sequence universe, even though we know more and more about its diversity, the
marginal computational cost of adding sequences goes higher, not lower.

In this project, we thus set out to try to achieve the sensitivity of the
all-against-all at the speed of clustering.

Transitivity of homology

In principle, homology is a transitive relationship: if gene A is homologous
to gene B, and gene B is homologous to gene C, this implies that gene A is
homologous to gene C. Transitive relationships are typically a good fit for
clustering.

In practice, however, things are more complicated. Homology can be difficult
to ascertain for very divergent sequences. Furthermore, homology is not always
transitive due to insertions, deletions, fusion, fissions, and other events
that may cause inconsistencies in terms of matching residues across multiple
homologs. This figure illustrates these problems and outlines the ideas
we implemented to address them:




Encouraging results

Putting together the ideas outlined in the figure above, we were pleasantly
surprised to see that clustering can indeed be both sensitive and fast. We
obtained 4-5x speed-ups across various datasets while recovering ~99.9% of all
homologous relationships identified through all-against-all.

In comparison, general purpose clustering approaches such as
kClust or
UCLUST—which admittedly have not been
designed to identify distant homologs
effectively—only recover
~10% of all homologous relationships. They are, however, several orders of
magnitude faster.

Only the beginning

The results of our proof-of-concept implementation are thus very
encouraging. We have plans to follow up with a long list of refinement ideas,
many of which we discuss in the manuscript. One essential
refinement will be to parallelise the new approach. This is not as
straightforward as with all-against-all compraisons, but we think it can be
done.

Meanwhile, the serial variant is available as part of the OMA
standalone package.

Reference



Wittwer, L., Piližota, I., Altenhoff, A., & Dessimoz, C. (2014). Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology PeerJ, 2:e607 DOI: 10.7717/peerj.607
... Read more »

  • September 25, 2014
  • 10:37 AM
  • 694 views

A New Discovery in the Treatment of Autoimmunity and Chronic Inflammation

by Dr. Jekyll in Lunatic Laboratories

Lupus, Type 1 diabetes, and multiple sclerosis are all diseases brought on by autoimmunity — the bodies inability to tell itself apart from foreign invaders. Finding a cure, or even a suitable treatment has been to put it gently a long, painful road, with little to show for it. On the forefront of the war against the body betrayal is immunosuppressants, which with them carry their own set of side effects and in most cases only off mild to moderate relief of symptoms. But that is all changing and new research on something called immunoproteasomes offer that new hope.... Read more »

Dubiella C, Cui H, Gersch M, Brouwer AJ, Sieber SA, Krüger A, Liskamp RM, & Groll M. (2014) Selective Inhibition of the Immunoproteasome by Ligand-Induced Crosslinking of the Active Site. Angewandte Chemie (International ed. in English). PMID: 25244435  

  • September 23, 2014
  • 01:55 PM
  • 693 views

Lie Detection using Brain Waves: It’s just as creepy as it sounds…

by Dr. Jekyll in Lunatic Laboratories

Currently lie detectors (polygraphs) are not admissible in court, this is because (despite what you may read) there is little proof to show that they are much better than a guess — coming in at roughly 50% accuracy. They aren’t really based in science, making them more of a toy. There might just be a new contender in the lie detection department coming soon however, researchers have found that brain activity can be used to tell whether someone recognizes details they encountered in normal, daily life.... Read more »

  • September 21, 2014
  • 02:33 PM
  • 620 views

Move over Carbon nanotubes introducing Diamond nanothreads

by Dr. Jekyll in Lunatic Laboratories

Carbon nanotubes, the wave of the future. Our hopes and dreams for the future have been firmly placed in using the unique material for everything from electronics to engineering. Unfortunately the production of carbon nanotubes has been hampered by setbacks, which as it turns out might not be a bad thing. This is because for the first time, scientists have discovered how to produce ultra-thin “diamond nanothreads” that promise extraordinary properties, including strength and stiffness greater than that of today’s strongest nanotubes and polymers.... Read more »

Fitzgibbons, T., Guthrie, M., Xu, E., Crespi, V., Davidowski, S., Cody, G., Alem, N., & Badding, J. (2014) Benzene-derived carbon nanothreads. Nature Materials. DOI: 10.1038/nmat4088  

  • September 19, 2014
  • 07:28 PM
  • 543 views

Nanosponges Clean up Antibody-mediated Autoimmune Disease

by Dr. Jekyll in Lunatic Laboratories

What does lupus, rheumatoid arthritis, type I diabetes, multiple sclerosis, and rheumatic heart disease have in common? All of these (and many other) apparently unrelated disorders are caused by autoimmunity, in which the immune system produces antibodies that attack normal, healthy cells and tissues. Currently considered incurable, these autoimmune diseases can be managed, but to varying degrees and not without serious side effects. Moreover, autoimmune diseases include a wide range of dysfunctional immune responses known as type II, type III, and type IV immune hypersensitivity reactions.... Read more »

Copp JA, Fang RH, Luk BT, Hu CM, Gao W, Zhang K, & Zhang L. (2014) Clearance of pathological antibodies using biomimetic nanoparticles. Proceedings of the National Academy of Sciences of the United States of America, 111(37), 13481-6. PMID: 25197051  

  • September 19, 2014
  • 06:25 PM
  • 669 views

Estimating how much we don't know

by Iddo Friedberg in Byte Size Biology

Most of our understanding of what genes do comes from computational predictions, rather than actual experiments. For almost any given gene that is sequenced, its function is determined by putting its sequence through one or more function annotation algorithms. Computational annotation is cheaper and more feasible than cloning, translating, and assaying the gene product (typically a protein) to find out exactly what it does. Experiments can be long, expensive and, in many cases, impossible to perform. But, by resorting to computational annotation of the function of proteins, we need to know how well can these algorithms actually perform.... Read more »

  • September 17, 2014
  • 01:24 PM
  • 591 views

Biofilms: Using Bacteria for new Designer Nanomaterials

by Dr. Jekyll in Lunatic Laboratories

For most people biofilms conjure up images of slippery stones in a streambed and dirty drains. While there are plenty of "bad" biofilms around – they are even the same stuff that causes pesky dental plaque and a host of other more serious medical problems – a team of researchers sees biofilms as a robust new platform for designer nanomaterials that could clean up polluted rivers, manufacture pharmaceutical products, fabricate new textiles, and more.... Read more »

Peter Q. Nguyen,, Zsofia Botyanszki,, Pei Kun R. Tay,, & Neel S. Joshi. (2014) Programmable biofilm-based materials from engineered curli nanofibres. Nature Communications. info:/10.1038/ncomms5945

  • September 14, 2014
  • 02:24 PM
  • 492 views

Biospleen Helps Clean Blood to Prevent Sepsis

by Dr. Jekyll in Lunatic Laboratories

When a patient has sepsis Things can go downhill fast. A life-threatening condition in which bacteria or fungi multiply in a patient's blood -- sepsis is often too fast for antibiotics to help. But that's all about to change with the introduction of a new device -- inspired by the human spleen -- that may radically transform the way doctors treat sepsis.... Read more »

Kang JH, Super M, Yung CW, Cooper RM, Domansky K, Graveline AR, Mammoto T, Berthet JB, Tobin H, Cartwright MJ.... (2014) An extracorporeal blood-cleansing device for sepsis therapy. Nature medicine. PMID: 25216635  

  • September 11, 2014
  • 11:00 PM
  • 774 views

Transcendental idealism and Post’s variant of the Church-Turing thesis

by Artem Kaznatcheev in Evolutionary Games Group

One of the exciting things in reading philosophy, its history in particular, is experiencing the tension between different schools of thought. This excitement turns to beauty if a clear synthesis emerges to reconcile the conflicting ideas. In the middle to late 18th century, as the Age of Enlightenment was giving way to the Romantic era, […]... Read more »

Post, E.L. (1936) Finite combinatory processes -- formulation 1. Journal of Symbolic Logic, 1(3), 103-105. info:/

  • September 10, 2014
  • 02:26 PM
  • 549 views

Multiple Sclerosis and Myelin loss

by Dr. Jekyll in Lunatic Laboratories

Multiple sclerosis (MS) is an unpredictable, often disabling disease of the central nervous system that disrupts the flow of information within the brain, and between the brain and body. The exact cause is unknown, however people with multiple sclerosis lose myelin in the gray matter of their brains and the loss is closely correlated with the severity of the disease, according to a new magnetic resonance imaging (MRI) study.... Read more »

Vasily L. Yarnykh, James D. Bowen, Alexey Samsonov, Pavle Repovic, Angeli Mayadev, Peiqing Qian, Beena Gangadharan, Bart P. Keogh, Kenneth R. Maravilla, & Lily K. Jung Henson. (2014) Fast Whole-Brain Three-dimensional Macromolecular Proton Fraction Mapping in Multiple Sclerosis. Radiological Society of North America . info:/10.1148/radiol.14140528

  • September 9, 2014
  • 06:03 AM
  • 737 views

Punning with the Pub in PubMed: Are there any decent NCBI puns left? #PubMedPuns

by Duncan Hull in O'Really?

Many people claim they get all their best ideas in the Pub, but for lots of scientists their best ideas probably come from PubMed.gov – the NCBI’s monster database of biomedical literature. Consequently, the database has spawned a whole slew of tools that riff off the PubMed name, many puns and portmanteaus (aka “PubManteaus”), the pub-based wordplays are very common. All of this might make you wonder, are there any decent PubMed puns left? Here’s an incomplete collection.... Read more »

Gibney Elizabeth. (2014) How to tame the flood of literature. Nature, 513(7516). PMID: 25186906  

Kumar Neeraj, Berg Alexander, Belhumeur Peter N, & Nayar Shree. (2011) Describable Visual Attributes for Face Verification and Image Search. IEEE transactions on pattern analysis and machine intelligence. PMID: 21383395  

McEntyre Johanna R, Ananiadou Sophia, Andrews Stephen, Black William J, Boulderstone Richard, Buttery Paula, Chaplin David, Chevuru Sandeepreddy, Cobley Norman, & Coleman Lee-Ann. (2010) UKPMC: a full text article resource for the life sciences. Nucleic acids research. PMID: 21062818  

  • September 6, 2014
  • 06:22 PM
  • 966 views

Is the Internet of Things the Real Thing?

by Aurametrix team in Health Technologies

The Internet of Things: an exciting new world with a digital nervous system or a nightmare where objects take decisions while we are unconscious?15 years ago, when the term was first coined, it was about assigning everything around us a unique identity with RFID tags, to enable all material things to talk to each other and save us time for gathering and using information. As RFID tags dropped below 1 cent cost, and sensors, modems and devices are getting smaller, smarter and cheaper, this vision is moving closer to reality.The latest Gartner's Hype Cycle (August 2014) places the Internet of Things at the peak of Inflated Expectations, while Big Data evolving in tandem with IoT has already started to fall into the through of disillusionment, getting ready to join mobile health and cloud computing right there on the bottom of the through. Consumers are not ready to embrace the flood of smart wearables and appliances - as they don't really know what to do with them, don't perceive their value and are concerned about privacy and prices.Clay Christensen's theory of "disruptive technology" emphasizes that technologies tend to get better at a faster rate than users' needs increase. Next Big Thing often starts as an expensive "toy". When the telephone was first introduced it could only be afforded by the rich and it could only carry a signal over a short distance. If Watson really had said in 1943 that "there is a world market for maybe five computers", as Gordon Bell pointed out much later, it would have held true for some ten years.The first generation of IoT devices fell short of user needs and was rather primitive. Over a third of people who bought a smart wearable abandoned it a few months later. Yet, the "new" has never been hotter. It seems a new wearable is launching every week and we are constantly waiting for something newer and better, hoping it will finally answer the question "what can we do now that we could not do before?"However, the current generation of "smart things" is focused mostly on better designed hardware and higher-end consumers. Fashionable elegant-looking devices are supposed to make wearables more appealing and "design thinking" is one of today's hottest buzzwords. Withings Activité, Fitbit pendants from Tory Burch,  Yves Béhar's designed Vessyl, Diane Von Furstenberg's Google glass, Rebecca Minkoff's tech-enabled jewelry, and the new bracelet from Intel - MICA  - highlighted by pearls and other precious stones - are getting ready to conquer attention of consumers and developers. Especially developers - as the size of the market will depend on the number of developer-entrepreneurs creating value in it.The app economy taught hardware manufacturers that when people experiment they find ways to create value, often in unexpected ways.  But it also taught developers that they need to invest considerable time to build a marketable app and the chances of that app to make money are about 1 in 25,000. As the average age of developers keeps decreasing getting into the middle and high school years, the main benefit of app development becomes education and learning by itself. But will this be sufficient for the Internet of Things or will inter-networked things remain a toy for the wealthy? ReferencesAshton K. (2009). That 'Internet of Things' Thing, in the real world things matter more than ideas RFID Journal (June 22)Gartner's "Hype Cycle for Emerging Technologies, 2014" at http://www.gartner.com/document/2809728Harvard's Clayton Christensen on the economics of 'disruption' (techflash.com)Schreier G (2014). The internet of things for personalized health. Studies in health technology and informatics, 200, 22-31 PMID: 24851958Perera, C., Zaslavsky, A., Christen, P., & Georgakopoulos, D. (2014). Sensing as a service model for smart cities supported by Internet of Things Transactions on Emerging Telecommunications Technologies, 25 (1), 81-93 DOI: 10.1002/ett.2704Anderson J. amd Rainie L. (2014) The Internet of Things Will Thrive by 2025. Pew researchMackinlay M. (2013). Phases of Accuracy Diagnosis: (In)visibility of System Intersect, Vol 6, No 2... Read more »

Ashton K. (2009) That 'Internet of Things' Thing, in the real world things matter more than ideas. RFID Journal. info:/

Schreier G. (2014) The internet of things for personalized health. Studies in health technology and informatics, 22-31. PMID: 24851958  

Perera, C., Zaslavsky, A., Christen, P., & Georgakopoulos, D. (2014) Sensing as a service model for smart cities supported by Internet of Things. Transactions on Emerging Telecommunications Technologies, 25(1), 81-93. DOI: 10.1002/ett.2704  

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