Computer Science / Engineering posts
- February 11, 2013
- 11:36 AM
- 144 views
Cell Circuits Remember Their History
by Jason Carr in Wired Cosmos
MIT engineers have created genetic circuits in bacterial cells that not only perform logic functions, but also remember the results, which are encoded in the cell’s DNA and passed on for dozens of generations. The circuits, described in the Feb. 10 online edition of Nature Biotechnology (citation below), could be used as long-term environmental sensors, efficient controls [...]... Read more »
Siuti, P., Yazbek, J., & Lu, T. (2013) Synthetic circuits integrating logic and memory in living cells. Nature Biotechnology. DOI: 10.1038/nbt.2510
- February 7, 2013
- 06:07 PM
- 85 views
The difference between the RF and the NNI distance
by Leonardo Martins in bioMCMC
Just to complement my answer to a blog post, where I maintain that the Nearest-Neighbor Interchange (NNI) distance is not equivalent to the Robinson-Foulds (RF) distance, a simple example:Where we can see that trees T1 and T2 differ only in the location of nodes A and B -- on these trees, we can naturally think of the nodes A, B, 1,..., 6 as representing leaves, but they might also be large subtrees.The RF distance is the number of edges (=branches) that are unique to each tree (that's why it's ........ Read more »
Bryant David. (2004) The Splits in the Neighborhood of a Tree. Annals of Combinatorics, 8(1), 1-11. DOI: 10.1007/s00026-004-0200-z
- January 29, 2013
- 07:31 PM
- 44 views
Microstructure of Film Coated Tablets
by Axel Zeitler in Pharmaceutical Solid State Research Cluster (PSSRC)
Since 2007 when terahertz pulsed imaging (TPI) was first developed to non-destructively measure the coating thickness of pharmaceutical tablets there has been intense research in the PSSRC into how this technique can help improve the quality of pharmaceutical coatings and thus make controlled release technology based on coatings of single dosage forms attractive to industry.... Read more »
Zeitler, J., Shen, Y., Baker, C., Taday, P., Pepper, M., & Rades, T. (2007) Analysis of coating structures and interfaces in solid oral dosage forms by three dimensional terahertz pulsed imaging. Journal of Pharmaceutical Sciences, 96(2), 330-340. DOI: 10.1002/jps.20789
Brock, D., Zeitler, J., Funke, A., Knop, K., & Kleinebudde, P. (2012) A comparison of quality control methods for active coating processes. International Journal of Pharmaceutics, 439(1-2), 289-295. DOI: 10.1016/j.ijpharm.2012.09.021
- January 24, 2013
- 04:45 AM
- 206 views
Storage and successful retrieval of a huge amount of data utilizing DNA strands
by Usman Paracha in SayPeople
Researchers have converted the dream of a huge amount of DNA storage and its accurate retrieval into reality.
This research has been published online in the journal Nature.
In this research, scientists have successfully stored an audio file of 26 seconds from the Martin Luther King's 1963 "I have a dream" speech on the adenine, thymine, cytosine and guanine components of synthesized DNA. Not only had this but they also stored all 154 of Shakespeare's sonnets, a digital ........ Read more »
Goldman, N., Bertone, P., Chen, S., Dessimoz, C., LeProust, E., Sipos, B., & Birney, E. (2013) Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature. DOI: 10.1038/nature11875
- January 23, 2013
- 07:38 AM
- 175 views
Sending Odors and Tastes as an Email Attachment
by Jason Carr in Wired Cosmos
Research into cybernetic organs has been largely focused on replacements for disabled individuals who have lost a limb. Electronic noses and tongues are designed for a radically different purpose. Humans perceive different chemicals as various tastes and odors. Many types of additives are industrially manufactured to replicate certain flavors or scents. Electronic noses and tongues [...]... Read more »
Fujioka K, Arakawa E, Kita J, Aoyama Y, Manome Y, Ikeda K, & Yamamoto K. (2013) Detection of Aeromonas hydrophila in Liquid Media by Volatile Production Similarity Patterns, Using a FF-2A Electronic Nose. Sensors (Basel, Switzerland), 13(1), 736-45. PMID: 23296330
Schneider, J. (2006) Detection of fruit odors using an electronic nose. SPIE Newsroom. DOI: 10.1117/2.1200602.0137
Ciosek, P., & Wróblewski, W. (2007) Sensor arrays for liquid sensing – electronic tongue systems. The Analyst, 132(10), 963. DOI: 10.1039/b705107g
Zakaria A, Shakaff AY, Masnan MJ, Ahmad MN, Adom AH, Jaafar MN, Ghani SA, Abdullah AH, Aziz AH, Kamarudin LM.... (2011) A biomimetic sensor for the classification of honeys of different floral origin and the detection of adulteration. Sensors (Basel, Switzerland), 11(8), 7799-822. PMID: 22164046
- January 22, 2013
- 03:54 PM
- 142 views
These dudes figured out how to identify supposedly anonymous people whose genomes are publically available
by Sick Papes in Sick Papes
Super nasty genome hacking I CANT BELIEVE IT!!... Read more »
Gymrek M, McGuire AL, Golan D, Halperin E, & Erlich Y. (2013) Identifying personal genomes by surname inference. Science (New York, N.Y.), 339(6117), 321-4. PMID: 23329047
- January 22, 2013
- 04:09 AM
- 202 views
ToxBank: the next generation toxicology
by egonw in Chem-bla-ics
Before I moved to my current position in Maastricht, I had the great pleasure to work with Prof. Roland Grafström (check his pathway bioinformatics done with his then PhD Rebecca) and Prof. Bengt Fadeel at the Karolinska Institutet. During this year I part-time worked on ToxBank and part-time on nano-QSAR, and worked on semantics, predictive toxicology, and Open Data. This blog post is about the ToxBank work.
I promised firework, and the first rockets are heading upw........ Read more »
Kohonen, P., Benfenati, E., Bower, D., Ceder, R., Crump, M., Cross, K., Grafström, R., Healy, L., Helma, C., Jeliazkova, N.... (2013) The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing. Molecular Informatics. DOI: 10.1002/minf.201200114
- January 20, 2013
- 12:00 PM
- 263 views
New nanotech fiber: Robust handling, shocking performance
by Perikis Livas in Tracing Knowledge
Rice University’s latest nanotechnology breakthrough was more than 10 years in the making, but it still came with a shock. Scientists from Rice, the Dutch firm Teijin Aramid, the U.S. Air Force and Israel’s Technion Institute this week unveiled a new carbon nanotube (CNT) fiber that looks and acts like textile thread and conducts electricity and heat like a metal wire. In this week’s issue of Science, the researchers describe an industrially scalable process for making the thre........ Read more »
Jade Boyd. (2013) New nanotech fiber: Robust handling, shocking performance. Rice University News. info:/
- January 18, 2013
- 09:47 AM
- 154 views
On "Join Papester Collective 1.0: How to reply to #icanhazpdf in 3 seconds"
by Eugenio Maria Battaglia in Science to Grok
I'm totally supporting this potential system theorized some days ago by Micah Allen and his friend Hauke on Allen's Neuroconscience blog . They discuss a quick and reliable strategy to share papers behind a paywall.
The proposed system is really easy and accessible by everyone, since it uses particular twitter's #hashtags for query and response.
I strongly believe that what started after Aaron Swartz's dead with #pdftribute, and continued with #sharecredentials (unfortunate........ Read more »
Cook, J., & Attari, S. (2012) Paying for What Was Free: Lessons from the Paywall . Cyberpsychology, Behavior, and Social Networking, 15(12), 682-687. DOI: 10.1089/cyber.2012.0251
- January 17, 2013
- 01:54 PM
- 171 views
How to export, delete and replace your Mendeley account and library
by Duncan Hull in O'Really?
News that Reed Elsevier is in talks to buy Mendeley.com will have many scientists reaching for their “delete account” button. Mendeley has built an impressive user-base of scientists and other academics since they started, but the possibility of an Elsevier takeover has worried some of its users. Elsevier has a strained relationship with some groups in the scientific community [1], so it will be interesting to see how this plays out.
If you’ve built a personal library of sci........ Read more »
Whitfield, J. (2012) Elsevier boycott gathers pace. Nature. DOI: 10.1038/nature.2012.10010
Hull, D., Pettifer, S., & Kell, D. (2008) Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web. PLoS Computational Biology, 4(10). DOI: 10.1371/journal.pcbi.1000204
Attwood, T., Kell, D., McDermott, P., Marsh, J., Pettifer, S., & Thorne, D. (2010) Utopia documents: linking scholarly literature with research data. Bioinformatics, 26(18). DOI: 10.1093/bioinformatics/btq383
- January 17, 2013
- 10:15 AM
- 217 views
Soft Lego Built in the Computer
by Jason Carr in Wired Cosmos
Barbara Capone of the Computational Physics Group of the University of Vienna has developed a new method for the construction of building blocks at the nanoscale. The researcher in Soft Matter Physics, who works at the group of Christos Likos, Professor for Multiscale Computational Physics, is specialized on topics of self-assembly of materials at the [...]... Read more »
Capone, B., Coluzza, I., LoVerso, F., Likos, C., & Blaak, R. (2012) Telechelic Star Polymers as Self-Assembling Units from the Molecular to the Macroscopic Scale. Physical Review Letters, 109(23). DOI: 10.1103/PhysRevLett.109.238301
- January 16, 2013
- 04:11 PM
- 248 views
Oscar-worthy smoke signals
by Perikis Livas in Tracing Knowledge
Top honour for ETH-Zurich professor and Disney director Markus Gross: he is to receive a “Tech Oscar” from the Academy of Motion and Picture Arts and Sciences (AMPAS) along with three other computer scientists for a procedure they developed which leading special effects studios now use to simulate smoke and explosions in Hollywood films.... Read more »
Peter Rüegg. (2013) Oscar-worthy smoke signals. ETH Life. info:/
- January 16, 2013
- 02:24 AM
- 184 views
Show Some Love for the Data Glove
by Jason Carr in Wired Cosmos
Data Gloves (or wired gloves or cybergloves), as the name implies, are computer input devices that are worn on the hand like a glove. They utilize motion trackers to translate finger manipulations into electrical signals. In the near future, this technology might revolutionize the way that disabled people are able to access computer resources. For [...]... Read more »
Fahn, C., & Sun, H. (2010) Development of a Fingertip Glove Equipped with Magnetic Tracking Sensors. Sensors, 10(2), 1119-1140. DOI: 10.3390/s100201119
Yamaura H, Matsushita K, Kato R, & Yokoi H. (2009) Development of hand rehabilitation system for paralysis patient - universal design using wire-driven mechanism. Conference proceedings : .. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference, 7122-5. PMID: 19963950
HOSHINO, K. (2006) Dexterous Robot Hand Control with Data Glove by Human Imitation. IEICE Transactions on Information and Systems, E89-D(6), 1820-1825. DOI: 10.1093/ietisy/e89-d.6.1820
Dalley, S., Varol, H., & Goldfarb, M. (2012) A Method for the Control of Multigrasp Myoelectric Prosthetic Hands. IEEE Transactions on Neural Systems and Rehabilitation Engineering, 20(1), 58-67. DOI: 10.1109/TNSRE.2011.2175488
- January 14, 2013
- 10:52 PM
- 134 views
Brighter LEDs bioinspired from fireflies
by Cath in Basal Science (BS) Clarified
A team of researchers from Belgium, Canada, and France have developed a more efficient gallium nitride (GaN)-based LED using a design inspired by the firefly. The design, fabrication, and characterization of this [...]... Read more »
Bay, A., André, N., Sarrazin, M., Belarouci, A., Aimez, V., Francis, L., & Vigneron, J. (2013) Optimal overlayer inspired by Photuris firefly improves light-extraction efficiency of existing light-emitting diodes. Optics Express, 21(S1). DOI: 10.1364/OE.21.00A179
Bay, A., Cloetens, P., Suhonen, H., & Vigneron, J. (2013) Improved light extraction in the bioluminescent lantern of a Photuris firefly (Lampyridae). Optics Express, 21(1), 764. DOI: 10.1364/OE.21.000764
- January 11, 2013
- 11:59 AM
- 166 views
A joke about teaching and learning via Jason Bangbala
by Duncan Hull in O'Really?
What is the difference between primary, secondary and higher education?... Read more »
Vardi, M. (2012) Will MOOCs destroy academia?. Communications of the ACM, 55(11), 5-5. DOI: 10.1145/2366316.2366317
Khan, S. (2013) What college could be like. Communications of the ACM, 56(1), 41. DOI: 10.1145/2398356.2398370
Martin, F. (2012) Will massive open online courses change how we teach?. Communications of the ACM, 55(8), 26. DOI: 10.1145/2240236.2240246
- January 9, 2013
- 04:00 PM
- 81 views
Controlling variability - Likelihood calculus paper series review part 1
by Travis DeWolf in studywolf
Dr. Terry Sanger has a series of papers that have come out in the last few years describing what he has named ‘likelihood calculus’. The goal of these papers is to develop a ‘a theory of optimal control for variable, uncertain, and noisy systems that nevertheless accomplish real-world tasks reliably.’ The idea being that successful performance can be thought of as modulating variance of movement, allocating resources to tightly control motions when required and allowing variability in ta........ Read more »
Sanger TD. (2010) Controlling variability. Journal of motor behavior, 42(6), 401-7. PMID: 21184358
- January 7, 2013
- 09:24 PM
- 176 views
QR Codes to be used to prevent drug counterfeiting
by Cath in Basal Science (BS) Clarified
Think Quick Response (QR) codes are just for advertising products or transferring addresses and contact information between smartphones? Well, it turns out they can also be used to prevent drug [...]... Read more »
Han, S., Bae, H., Kim, J., Shin, S., Choi, S., Lee, S., Kwon, S., & Park, W. (2012) Lithographically Encoded Polymer Microtaggant Using High-Capacity and Error-Correctable QR Code for Anti-Counterfeiting of Drugs. Advanced Materials, 24(44), 5924-5929. DOI: 10.1002/adma.201201486
- January 7, 2013
- 02:27 PM
- 218 views
New Path to More Efficient Organic Solar Cells
by Jason Carr in Wired Cosmos
Why are efficient and affordable solar cells so highly coveted? Volume. The amount of solar energy lighting up Earth’s land mass every year is nearly 3,000 times the total amount of annual human energy use. But to compete with energy from fossil fuels, photovoltaic devices must convert sunlight to electricity with a certain measure of [...]... Read more »
Collins, B., Li, Z., Tumbleston, J., Gann, E., McNeill, C., & Ade, H. (2012) Absolute Measurement of Domain Composition and Nanoscale Size Distribution Explains Performance in PTB7:PC BM Solar Cells . Advanced Energy Materials. DOI: 10.1002/aenm.201200377
- January 4, 2013
- 11:43 AM
- 221 views
The Science of Choosing Space Pioneers
by Jason Carr in Wired Cosmos
I often ask others if they would live in space or on another planet if given the opportunity. More often than not, the answer is in the affirmative. But what if you were given the chance and actually wanted to go, but were declined because you weren’t selected by a computer algorithm as one of [...]... Read more »
Yusof, N., & van Loon, J. (2012) Engineering a Global City: The Case of Cyberjaya. Space and Culture, 15(4), 298-316. DOI: 10.1177/1206331212453676
Saaty, T., & Sagir, M. (2012) Global awareness, future city design and decision making. Journal of Systems Science and Systems Engineering, 21(3), 337-355. DOI: 10.1007/s11518-012-5196-z
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- January 4, 2013
- 10:44 AM
- 286 views
Cellular Recap of 2012 #2: favorites
by TheCellularScale in The Cellular Scale
As promised, here are my favorite posts from each month.January: The Human Neuron" not so special after all?Butti C, Santos M, Uppal N, & Hof PR (2011). Von Economo neurons: Clinical and evolutionary perspectives. Cortex; a journal devoted to the study of the nervous system and behavior PMID: 22130090February: If you give a mouse a placebo...Wise RA, Wang B, & You ZB (2008). Cocaine serves as a peripheral interoceptive conditioned stimulus for central glutamate and dopamine release. P........ Read more »
Butti C, Santos M, Uppal N, & Hof PR. (2011) Von Economo neurons: Clinical and evolutionary perspectives. Cortex; a journal devoted to the study of the nervous system and behavior. PMID: 22130090
Benolken RM, & Jacobson SL. (1970) Response properties of a sensory hair excised from Venus's flytrap. The Journal of general physiology, 56(1), 64-82. PMID: 5514161
Volkov AG, Adesina T, & Jovanov E. (2007) Closing of venus flytrap by electrical stimulation of motor cells. Plant signaling , 2(3), 139-45. PMID: 19516982
Forterre Y, Skotheim JM, Dumais J, & Mahadevan L. (2005) How the Venus flytrap snaps. Nature, 433(7024), 421-5. PMID: 15674293
Kindt M, Soeter M, & Vervliet B. (2009) Beyond extinction: erasing human fear responses and preventing the return of fear. Nature neuroscience, 12(3), 256-8. PMID: 19219038
Kim IJ, Zhang Y, Yamagata M, Meister M, & Sanes JR. (2008) Molecular identification of a retinal cell type that responds to upward motion. Nature, 452(7186), 478-82. PMID: 18368118
Kay JN, De la Huerta I, Kim IJ, Zhang Y, Yamagata M, Chu MW, Meister M, & Sanes JR. (2011) Retinal ganglion cells with distinct directional preferences differ in molecular identity, structure, and central projections. The Journal of neuroscience : the official journal of the Society for Neuroscience, 31(21), 7753-62. PMID: 21613488
Kraskov A, Dancause N, Quallo MM, Shepherd S, & Lemon RN. (2009) Corticospinal neurons in macaque ventral premotor cortex with mirror properties: a potential mechanism for action suppression?. Neuron, 64(6), 922-30. PMID: 20064397
Casile A, Caggiano V, & Ferrari PF. (2011) The mirror neuron system: a fresh view. The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry, 17(5), 524-38. PMID: 21467305
Blackiston DJ, Silva Casey E, & Weiss MR. (2008) Retention of memory through metamorphosis: can a moth remember what it learned as a caterpillar?. PloS one, 3(3). PMID: 18320055
Marx M, Günter RH, Hucko W, Radnikow G, & Feldmeyer D. (2012) Improved biocytin labeling and neuronal 3D reconstruction. Nature protocols, 7(2), 394-407. PMID: 22301777
Finger TE, & Kinnamon SC. (2011) Taste isn't just for taste buds anymore. F1000 biology reports, 20. PMID: 21941599
Triana-Del Rio R, Montero-Domínguez F, Cibrian-Llanderal T, Tecamachaltzi-Silvaran MB, Garcia LI, Manzo J, Hernandez ME, & Coria-Avila GA. (2011) Same-sex cohabitation under the effects of quinpirole induces a conditioned socio-sexual partner preference in males, but not in female rats. Pharmacology, biochemistry, and behavior, 99(4), 604-13. PMID: 21704064
Labour MN, Banc A, Tourrette A, Cunin F, Verdier JM, Devoisselle JM, Marcilhac A, & Belamie E. (2012) Thick collagen-based 3D matrices including growth factors to induce neurite outgrowth. Acta biomaterialia, 8(9), 3302-12. PMID: 22617741
Fu M, Yu X, Lu J, & Zuo Y. (2012) Repetitive motor learning induces coordinated formation of clustered dendritic spines in vivo. Nature, 483(7387), 92-5. PMID: 22343892
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