The first half of the 20th century is famous for revolutionary changes — paradigm shifts as Kuhn would say — across the sciences and other systems of thought. Disheartened by the scars of the First World War, European thinkers sought refuge by shifting their worldviews away from those of their fathers. In fields like biology, […]... Read more »
Kaznatcheev, Artem. (2013) Complexity of evolutionary equilibria in static fitness landscapes. ArXiv. arXiv: 1308.5094v1
From Siri answering our questions and Watson advising nurses to smart apps that aggregate information to help us out (or spy on us), artificial intelligence is transforming our world. Despite incredible advances, somehow these amazingly “intelligent” systems sometimes seem profoundly stupid. Hector Levesque, a professor of computer science at the University of Toronto, likens them to savants. He was recently awarded the Research Excellence Award at the International Joint Conference on Artificial Intelligence in Beijing; he used his acceptance speech to highlight important questions about our approach to artificial intelligence and what it can tell us about ourselves.... Read more »
Rahman, Altaf and Ng, Vincent. (2013) Resolving Complex Cases of Definite Pronouns: The Winograd Schema Challenge. Proceedings of the 2012 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning. info:/
Computer models are used to inform policy decisions about energy, but existing models are generally “black boxes” that don’t show how they work, making it impossible for anyone to replicate their findings. Researchers from North Carolina State University have developed a new open-source model and are sharing the data they put into it, to allow anyone to check their work—an important advance given the environmental and economic impact of energy policy decisions.... Read more »
Huntera K., Sreepathib S., DeCarolisa J.F. (2013) Modeling for Insight Using Tools for Energy Model Optimization and Analysis. Energy Economics, 339-349. DOI: 10.1016/j.eneco.2013.07.014
A ring of protein and pigments, half synthetic and half natural, can be used to quickly prototype light-harvesting antennas that absorb more sunlight than fully natural ones.... Read more »
Kunche Aravindu, Olga Mass, Pothiappan Vairaprakash, Joseph W. Springer, Eunkyung Yang, Dariusz M. Niedzwiedzki, Christine Kirmaier,b David F. Bocian, Dewey Holten, Jonathan S. Lindsey. (2013) Amphiphilic chlorins and bacteriochlorins in micellar environments. Molecular design, de novo synthesis, and photophysical properties. Chemical Science, 4(9), 3459-3477. DOI: 10.1039/c3sc51335a
On February 12, 2001, the human genome project released its first formal report. It was a great day for biology, and a wonderful birthday present for Darwin. However, it was also a humbling confrontation with complexity and prompted Steven Jay Gould to write in the New York Times: [The Human Genome project revealed that] Home […]... Read more »
Kauffman S, & Levin S. (1987) Towards a general theory of adaptive walks on rugged landscapes. Journal of Theoretical Biology, 128(1), 11-45. PMID: 3431131
If we look at image processing from the mathematical perspective, all digital images are just arrays of numbers. Across different fields of study, image processing applications (although initially developed for very specific needs) often use similar image processing routines based on common algorithms. Why I am writing all this?... Read more »
Jennifer L. West, & Ian D. Cameron. (2006) Using the medical image processing package, ImageJ, for astronomy. J.Roy.Astron.Soc.Canada100:242-248,2006. arXiv: astro-ph/0611686v1
Michelle Borkin (Initiative in Innovative Computing, Harvard University), Alyssa Goodman (Initiative in Innovative Computing/Harvard-Smithsonian Center for Astrophysics), Michael Halle (Initiative in Innovative Computing/Harvard Medical School), Douglas A. (2006) Application of Medical Imaging Software to 3D Visualization of Astronomical Data. arXiv.org. info:/
Covington K, McCreedy ES, Chen M, Carass A, Aucoin N, & Landman BA. (2010) Interfaces and Integration of Medical Image Analysis Frameworks: Challenges and Opportunities. Annual ORNL Biomedical Science and Engineering Center Conference ORNL Biomedical Science and Engineering Center Conference, 1-4. PMID: 21151892
A fungus and E. coli bacteria have joined forces to turn tough, waste plant material into isobutanol, a biofuel that matches gasoline’s properties better than ethanol. University of Michigan research team members said the principle also could be used to produce other valuable chemicals such as plastics.... Read more »
Jeremy J. Mintya, Marc E. Singera, Scott A. Scholzb, Chang-Hoon Baea, Jung-Ho Ahna, Clifton E. Fosterc, James C. Liaod, Xiaoxia Nina Lin. (2013) Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. http://www.pnas.org/content/early/2013/08/13/1218447110. DOI: 10.1073/pnas.1218447110
Large glass windows provide better natural lighting conditions, but also let in more heat, therefore bringing higher air-conditioning bills. The Harvard researchers recently proposed to solve the problem by fitting the windows with a bioinspired microfluidic circulatory system. Now, researchers at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have designed a new material—a thin coating of nanocrystals embedded in glass—that can dynamically modify sunlight as it passes through a window.... Read more »
Anna Llordés, Guillermo Garcia, Jaume Gazquez, Delia J. Milliron. (2013) Tunable near-infrared and visible light transmittance in nanocrystal-in-glass composites. Nature, 323-326. DOI: 10.1038/nature12398
As Jacob Scott pointed out, everybody — theorist or experimentalist — “has a logical construct (a model) in his or her head” when studying anything. This model might be mathematically explicit or implicit in the mind, but it is there and if the world is mechanistic (or if we only want to consider mechanistic theories […]... Read more »
Wright, S. (1932) The roles of mutation, inbreeding, crossbreeding, and selection in evolution. Proceedings of the Sixth International Congress of Genetics, 356-366. info:/
A research team led by Professor Tobin J. Marks of Northwestern University reports the design and synthesis of new polymer semiconductors and the realization of polymer solar cells with fill factors of 80 percent a first. This number is close to that of silicon solar cells.... Read more »
Xugang Guo, Nanjia Zhou, Sylvia J. Lou, Jeremy Smith, Daniel B. Tice, Jonathan W. Hennek, Rocío Ponce Ortiz, Juan T. López Navarrete, Shuyou Li, Joseph Strzalka, Lin X. Chen, Robert P. H. Chang, Antonio Facchetti, Tobin J. Marks. (2013) Polymer solar cells with enhanced fill factors. Nature Photonics. DOI: 10.1038/nphoton.2013.207
Scientists at the University of Washington have developed a new wireless communication system that allows devices to interact with each other without relying on batteries or wires for power. The devices are using existing radio signals scattered around both as a power source and as a signal carrier.... Read more »
Liu V., Parks A., Talla V., Gollakota S., Wetherall D., Smith J. (2013) Ambient Backscatter: Wireless Communication Out of Thin Air. Proceedings of the ACM SIGCOMM 2013 conference, 39-50. DOI: 10.1145/2486001.2486015
As demand rises for more fuel-efficient vehicles, knowledge compiled over several years about diesel engines and a new strategy known as “low-temperature combustion” (LTC) might soon lead auto manufacturers and consumers to broader use of cleaner diesel engines in the United States.... Read more »
Mark P.B. Musculus, Paul C. Miles, Lyle M. Pickett. (2013) Conceptual models for partially premixed low-temperature diesel combustion. Progress in Energy and Combustion Science, 39(2-3), 246-283. DOI: 10.1016/j.pecs.2012.09.001
Pioneering research in neuroengineering is bringing us closer to creating neural prostheses that replicate the function damaged brain tissue.... Read more »
Berger TW, Hampson RE, Song D, Goonawardena A, Marmarelis VZ, & Deadwyler SA. (2011) A cortical neural prosthesis for restoring and enhancing memory. Journal of neural engineering, 8(4), 46017. PMID: 21677369
Hampson RE, Song D, Chan RH, Sweatt AJ, Riley MR, Gerhardt GA, Shin DC, Marmarelis VZ, Berger TW, & Deadwyler SA. (2012) A nonlinear model for hippocampal cognitive prosthesis: memory facilitation by hippocampal ensemble stimulation. IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society, 20(2), 184-97. PMID: 22438334
A neat paper from Schoenmakers et al of the Dutch Donders Institute reports on Linear reconstruction of perceived images from human brain activity It introduces a new mathematical approach for decoding (or ‘brain reading’) the image that someone is looking at, pixel-by-pixel, based on the pattern of neural activity in their visual cortex. The results [...]The post Brain Reading Reads “Brains” From A Reading Brain appeared first on Neuroskeptic.... Read more »
Schoenmakers S, Barth M, Heskes T, & van Gerven MA. (2013) Linear reconstruction of perceived images from human brain activity. NeuroImage. PMID: 23886984
Physics in Medicine and Biology is one of my favorite journals and recently they have awarded the best paper published in 2012: Defrise M, Rezaei A, & Nuyts J (2012). Time-of-flight PET data determine the attenuation sinogram up to a constant. Physics in medicine and biology, 57 (4), 885-99 PMID: 22290428 I have scan through this paper before, since it is actually a topic close to my work. Time-Of-Flight Positron Emission Tomography is one of the great trends of PET imaging and attenuation correction can be a struggle, specially for the new PET-MRI scanners, so the use of new information for attenuation correction will be important.I have met the authors in conferences, two seniors Prof. Nuyts (researcher best known for Maximum a Posteriori reconstruction) and Prof. Defrise (researcher best known for Fourier Rebinning) and A. Rezaei is a young researcher with a promising career. Congratulations!Image from here... Read more »
Defrise M, Rezaei A, & Nuyts J. (2012) Time-of-flight PET data determine the attenuation sinogram up to a constant. Physics in medicine and biology, 57(4), 885-99. PMID: 22290428
Researchers at North Carolina State University have created a new flexible nano-scaffold for rechargeable lithium ion batteries that could help make cell phone and electric car batteries last longer.... Read more »
Fu, K., Yildiz, O., Bhanushali, H., Wang, Y., Stano, K., Xue, L., Zhang, X., Bradford, P.D. (2013) Aligned Carbon Nanotube-Silicon Sheets: A Novel Nano-architecture for Flexible Lithium Ion Battery Electrodes. Advanced Materials. DOI: 10.1002/adma.201301920
You Tube: This week’s tip of the week is on Gemini which is the acronym for “GENome MINing.” Unlike most of the tips we give every week, this one is a software package. But, it is does use and integrate with many internet databases such as dbSNP, ENCODE, UCSC, ClinVar and KEGG. It’s also a […]... Read more »
Paila U, Chapman BA, Kirchner R, & Quinlan AR. (2013) GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations. PLoS computational biology, 9(7). PMID: 23874191
Scientists swear they had a really good reason for building a robotic fish, getting some other fish drunk, and then chasing them around with it.
The robotic bird head, too.
Researchers at the Polytechnic Institute of New York University and the Istituto Superiore di Sanità in Rome were interested in zebrafish. These thumb-sized, striped fish are laboratory favorites because their genome is well understood, they reproduce quickly, and their embryos are totally transparent.
One area of research that employs zebrafish is the study of emotions, including anxiety and fear. Outside of a lab, people may not spend much time pondering fish anxiety. But study coauthor Simone Macrì of the Istituto Superiore di Sanità says zebrafish can help unravel complex environmental and genetic interactions, such as emotion, because their genetics are not a mystery. Their simple brains are useful for "clarifying some fundamental aspects [of] emotions," he says.
It's easy to spook a little fish; all you have to do is show it a predator. But wrangling live predatory animals such as birds or other fish is inconvenient. It also adds an unwanted variable to an experiment, since your predator may not behave consistently (or may have moods of its own). So Macrì and his colleagues wondered if they could build robotic predators good enough to be stand-ins in these experiments.
They carefully crafted robots that looked like a natural zebrafish enemy, the Indian leaf fish. ("The visual appearance of the robotic fish was obtained by spray-painting the robot with an ivory base color followed by the hand painting of brown color patterns typical for this species," the authors write—in case this is a project you want to try at home—"as well as the attachment of small plastic eyes.") A motor let the robot fish wave their tails at various speeds. There was also a robotic heron head that plunged toward the water as if hunting.
To find out whether their robots made the same impression on zebrafish as a real predator, the researchers let the animals meet each other. Sure enough, zebrafish swam to the far side of their tank when a robotic leaf fish was in the water. When a robotic heron struck from above, zebrafish darted under a shelter.
Then, to make sure the fish were responding to the robots out of fear or anxiety, the researchers gave the zebrafish a drug that reduces anxiety: alcohol. After letting their subjects swim around in ethanol-spiked water, the researchers gave them the same tests. Now they didn't flee the robot fish and were slow to seek shelter after the robotic heron attack.
As the researchers had hoped, sober fish feared robotic predators, and alcohol lessened those fears. The results are published in PLOS ONE.
Macrì thinks this technique could help researchers who study anxiety with zebrafish improve their methods. As long as scientists are looking at simple behaviors, he says, "the robots are ideally suited." And after being chased by a giant robotic predator, zebrafish might need a drink anyway.
Images: left by Azul, via Wikimedia Commons; right Cianca et al. (In reality, the robotic fish were several times larger than the zebrafish.)
Valentina Cianca, Tiziana Bartolini, Maurizio Porfiri, & Simone Macrì (2013). A Robotics-Based Behavioral Paradigm to Measure Anxiety-Related Responses in Zebrafish PLOS ONE DOI: 10.1371/journal.pone.0069661
... Read more »
Valentina Cianca, Tiziana Bartolini, Maurizio Porfiri, & Simone Macrì. (2013) A Robotics-Based Behavioral Paradigm to Measure Anxiety-Related Responses in Zebrafish. PLOS ONE. DOI: 10.1371/journal.pone.0069661
Monash University researchers have brought next generation energy storage closer with an engineering first—a graphene-based device that is compact, yet lasts as long as a conventional battery.... Read more »
Yang X, Cheng C, Wang Y, Qiu L, & Li D. (2013) Liquid-mediated dense integration of graphene materials for compact capacitive energy storage. Science (New York, N.Y.), 341(6145), 534-7. PMID: 23908233
In our more and more individualistic societies we eventually need robots to fight loneliness. That is at least what the team members of Kibo Robot Project expect. They therefore sent their little walking and talking robot on his first mission last sunday, to accompany astronaut Koichi Wakata in space.... Read more »
Marian R. Banks, Lisa M. Willoughby, and William A. Banks. (2008) Animal-Assisted Therapy and Loneliness in Nursing Homes: Use of Robotic versus Living Dogs. jamda. info:/
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