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  • December 18, 2012
  • 06:07 PM

How to Build a Neuron: step 4

by TheCellularScale in The Cellular Scale

And now, the next step in neuron building! You can see all the previous steps and shortcuts here. Step 4 is adding intrinsic channels to your neuron.Potassium Channel (source)Pretty much all neurons need sodium and potassium channels so they can fire action potentials, but other channels such as calcium channels are also commonly seen in computational models. To add these channels you have to extract the parameters from known data. This means extracting Boltzmann curves and time constant informa........ Read more »

Kispersky TJ, Caplan JS, & Marder E. (2012) Increase in sodium conductance decreases firing rate and gain in model neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience, 32(32), 10995-1004. PMID: 22875933  

  • December 18, 2012
  • 12:02 PM

Brain-Computer Interface Allows Woman To Feed Herself Using Robotic Arm

by Zach Urbina in United Academics

A neurobiology team at the University of Pittsburgh has given a Jan Scheuermann the power to do something that a degenerative disease had taken away. Thanks to a brain-computer interface and a robotic arm she affectionately calls “Hector,” Jan is now able to feed herself, despite her paralysis.... Read more »

Collinger, J., Wodlinger, B., Downey, J., Wang, W., Tyler-Kabara, E., Weber, D., McMorland, A., Velliste, M., Boninger, M., & Schwartz, A. (2012) High-performance neuroprosthetic control by an individual with tetraplegia. The Lancet. DOI: 10.1016/S0140-6736(12)61816-9  

  • December 16, 2012
  • 10:37 PM

Using light to detect the internal damage of materials

by Cath in Basal Science (BS) Clarified

You can usually tell when a material is about to fail, you might see sagging, cracks, dents, holes, etc. But sometimes materials can fail suddenly—without warning— this known as catastrophic [...]... Read more »

  • December 10, 2012
  • 05:45 PM

Biofuel that’s better than carbon neutral

by Perikis Livas in Chilon

The race is on to create a biofuel that sucks carbon out of the sky and locks it away where it can’t warm the planet

THE green sludge burbles away quietly in its tangle of tubes in the Spanish desert. Soaking up sunshine and carbon dioxide from a nearby factory, it grows quickly. Every day, workers skim off some sludge and take it away to be transformed into oil. People do in a single day what it took geology 400 million years to accomplish.

Indeed, this is no ordinary oil. It belong........ Read more »

Bob Holmes. (2012) Biofuel that's better than carbon neutral. New Scientist. info:/

  • December 10, 2012
  • 11:41 AM

Are Physicians Using Medical Smartphones Apps?

by William Yates, M.D. in Brain Posts

The number and types of medical apps for physicians and other medical providers is rapidly increasing.  Smart phone apps (i.e. iPhone and Android apps) have the potential to allow physicians real time access to medical records, treatment guidelines and medical reference information. As these apps increase in number and type, it will be important to understand the facilitators and barriers to implementation in the medical setting.  Additionally, research will be needed to document ........ Read more »

  • December 9, 2012
  • 08:32 AM

Earliest stars were formed when the age of the Universe was…

by Usman Paracha in SayPeople

Recently, scientists from MIT published a research paper in the journal Nature in which they showed their work of “Extremely metal-poor gas at a redshift of 7”. They utilized infrared spectrometer, which they placed onto the Magellan Telescope, a massive ground-based telescope in Chile. They calculated the elements and based on the observations about the heavy elements they believe that the earliest stars might have been formed 750 million years after the formation of Universe.

&l........ Read more »

Pletsch, H., Guillemot, L., Fehrmann, H., Allen, B., Kramer, M., Aulbert, C., Ackermann, M., Ajello, M., de Angelis, A., Atwood, W.... (2012) Binary Millisecond Pulsar Discovery via Gamma-Ray Pulsations. Science, 338(6112), 1314-1317. DOI: 10.1126/science.1229054  

Ackermann, M., Ajello, M., Allafort, A., Schady, P., Baldini, L., Ballet, J., Barbiellini, G., Bastieri, D., Bellazzini, R., Blandford, R.... (2012) The Imprint of the Extragalactic Background Light in the Gamma-Ray Spectra of Blazars. Science, 338(6111), 1190-1192. DOI: 10.1126/science.1227160  

Simcoe, R., Sullivan, P., Cooksey, K., Kao, M., Matejek, M., & Burgasser, A. (2012) Extremely metal-poor gas at a redshift of 7. Nature, 492(7427), 79-82. DOI: 10.1038/nature11612  

  • December 7, 2012
  • 01:20 PM

Synthetic fuels could eliminate entire U.S. need for crude oil, create 'new economy'

by Perikis Livas in Chilon

The United States could eliminate the need for crude oil by using a combination of coal, natural gas and non-food crops to make synthetic fuel, a team of Princeton researchers has found.

Besides economic and national security benefits, the plan has potential environmental advantages. Because plants absorb carbon dioxide to grow, the United States could cut vehicle greenhouse emissions by as much as 50 percent in the next several decades using non-food crops to create liquid fuels, the researc........ Read more »

John Sullivan. (2012) Synthetic fuels could eliminate entire U.S. need for crude oil, create 'new economy'. Princeton University Office of Engineering Communications. info:/

  • December 4, 2012
  • 05:25 PM

MIT's Milli-Motein: Things Just Got a Lot More Interesting

by Perikis Livas in Chilon

If the idea that matter can be organized in a way that’s similar to binary code seems implausible, get ready for a shock: It can. An MIT team has created a milli-motein — a tiny device made of millimeter-sized components with a motorized design inspired by proteins. Milli-moteins can naturally fold themselves into almost any shape imaginable.... Read more »

Peter Suciu. (2012) MIT's Milli-Motein: Things Just Got a Lot More Interesting. TechNewsWorld. info:/

  • December 4, 2012
  • 09:00 AM

Evaluating CTC isolation device performance

by pratt_ed in CTC Engineer

I’ve previously discussed how to sort CTCs, and the standards used to characterize device performance. Today, I’ll explain what some of the most common evaluation metrics are, and place them in context of eventual clinical/industrial application.... Read more »

Marrinucci Dena, Bethel Kelly, Lazar Daniel, Fisher Jennifer, Huynh Edward, Clark Peter, Bruce Richard, Nieva Jorge, & Kuhn Peter. (2010) Cytomorphology of circulating colorectal tumor cells:a small case series. Journal of oncology. PMID: 20111743  

Kirby Brian J, Jodari Mona, Loftus Matthew S, Gakhar Gunjan, Pratt Erica D, Chanel-Vos Chantal, Gleghorn Jason P, Santana Steven M, Liu He, & Smith James P. (2012) Functional characterization of circulating tumor cells with a prostate-cancer-specific microfluidic device. PloS one. PMID: 22558290  

  • November 30, 2012
  • 09:22 AM

Cancer Cell Lines & CTCs: Benchmarking versus Application

by pratt_ed in CTC Engineer

In my “How to Sort CTCs” series, I covered a variety of sorting methodologies used for patient prognosis. However, before clinical implementation, it is important characterize device performance with a series of standards. This is impossible to do with a patient blood sample, because there is an unknown number of CTCs floating around with other blood cells, which can be effected by the cancer treatment process (e.g. radiation patients often have anemia)1. Furthermore, this is all changing d........ Read more »

Kirby Brian J, Jodari Mona, Loftus Matthew S, Gakhar Gunjan, Pratt Erica D, Chanel-Vos Chantal, Gleghorn Jason P, Santana Steven M, Liu He, & Smith James P. (2012) Functional characterization of circulating tumor cells with a prostate-cancer-specific microfluidic device. PloS one. PMID: 22558290  

Powell Ashley A, Talasaz Amirali H, Zhang Haiyu, Coram Marc A, Reddy Anupama, Deng Glenn, Telli Melinda L, Advani Ranjana H, Carlson Robert W, & Mollick Joseph A. (2012) Single cell profiling of circulating tumor cells: transcriptional heterogeneity and diversity from breast cancer cell lines. PloS one. PMID: 22586443  

Magbanua Mark Jesus M, Sosa Eduardo V, Roy Ritu, Eisenbud Lauren E, Scott Janet H, Olshen Adam, Pinkel Dan, Rugo Hope, & Park John W. (2012) Genomic profiling of isolated circulating tumor cells from metastatic breast cancer patients. Cancer research. PMID: 23135909  

Borrell Brendan. (2010) How accurate are cancer cell lines?. Nature, 463(7283), 858-858. DOI: 10.1038/463858a  

Hofman V. J., Ilie M. I., Bonnetaud C., Selva E., Long E., Molina T., Vignaud J. M., Flejou J. F., Lantuejoul S., & Piaton E. (2010) Cytopathologic Detection of Circulating Tumor Cells Using the Isolation by Size of Epithelial Tumor Cell Method: Promises and Pitfalls. American Journal of Clinical Pathology, 135(1), 146-156. DOI: 10.1309/AJCP9X8OZBEIQVVI  

Stott Shannon L, Hsu Chia-Hsien, Tsukrov Dina I, Yu Min, Miyamoto David T, Waltman Belinda A, Rothenberg S Michael, Shah Ajay M, Smas Malgorzata E, & Korir George K. (2010) Isolation of circulating tumor cells using a microvortex-generating herringbone-chip. Proceedings of the National Academy of Sciences of the United States of America. PMID: 20930119  

Cho Edward H, Wendel Marco, Luttgen Madelyn, Yoshioka Craig, Marrinucci Dena, Lazar Daniel, Schram Ethan, Nieva Jorge, Bazhenova Lyudmila, & Morgan Alison. (2012) Characterization of circulating tumor cell aggregates identified in patients with epithelial tumors. Physical biology. PMID: 22306705  

  • November 29, 2012
  • 06:36 PM

Growing 3D Cells

by TheCellularScale in The Cellular Scale

Neurons don't grow in a vacuum. They have white fibers, other neurons, blood vessels and all sorts of other obstacles to grow around.Some NeuroArt (source)A recent paper from France details the making of a 3D environment that can facilitate 'realistic' neural growth. Labour et al. (2012) created a collagen biomimetic matrix which contains neural growth factor (NGF).  Labour et al., (2012) Figure 3These scanning electron microscope images show the porous fibril texture of the collagen matrix........ Read more »

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  

  • November 26, 2012
  • 10:45 PM

Close your eyes and tap your heels

by Aurametrix team in Health Technologies

GPS shoes can point to where you're going, but how will they know where to go? By consulting the map uploaded via USB and its own GPS receivers, wirelessly communicating with each other. For future models, you could probably set up WiFi to let your shoes download more information, talk with other people's shoes and modify your route on the go. So your footware might need its own network access, like agent Maxwell Smart's left shoe with a mobile subscription plan. The "No place like home" shoes a........ Read more »

  • November 26, 2012
  • 10:25 AM

How to Sort Circulating Tumor Cells Part IV: Electrokinetic Separation

by pratt_ed in CTC Engineer

Most CTC sorting devices target some observed cancer cell phenotype that was determined from studying tumor tissue directly, or from using immortalized cancer cell lines. This means that active sorting techniques, like size-based selection and immunocapture, require some level of a priori knowledge about CTCs before you can engineer a device to capture them. Microscopic characterization is one CTC identification method that circumvents this problem, fixing (killing) the cells, and then using ima........ Read more »

Pratt Erica D., Huang Chao, Hawkins Benjamin G., Gleghorn Jason P., & Kirby Brian J. (2011) Rare cell capture in microfluidic devices. Chemical Engineering Science, 66(7), 1508-1522. DOI: 10.1016/j.ces.2010.09.012  

  • November 22, 2012
  • 02:01 PM

Curious Cosmos

by Emarkham in GeneticCuckoo

A discussion of the recent advances in space exploration, looking specifically at the Mars Rover landing as well as other space phenomena during 2012. ... Read more »

E Markham. (2012) Curious Cosmos. Blogspot. info:/

  • November 20, 2012
  • 05:34 AM

A first paper on square root of a Brownian motion and quantum mechanics gets published!

by Marco Frasca in The Gauge Connection

Following my series of posts on the link between the square root of a stochastic process and quantum mechanics (see here, here, here, here, here), that I proved to exist both theoretically and experimentally, I am pleased to let you know that the first paper of my collaboration with Alfonso Farina and Matteo Sedehi was [...]... Read more »

Farina, A., Giompapa, S., Graziano, A., Liburdi, A., Ravanelli, M., & Zirilli, F. (2011) Tartaglia-Pascal’s triangle: a historical perspective with applications. Signal, Image and Video Processing. DOI: 10.1007/s11760-011-0228-6  

  • November 19, 2012
  • 01:27 AM

Airbag Saved My Life: the Carolina Review’s Clinical Derpitude Continues

by csoeder in Topologic Oceans

I had thought that once I graduated college, annoying student publications would quit being so… annoying. Alas, this isn’t the case. A previous article examined the quality of analysis at the Carolina Review, UNC’s ‘journal of conservative thought and opinion’; let’s see if things have approved any in the handful of years that I’ve been [...]... Read more »

Wenzel, T., & Ross, M. (2008) Safer Vehicles for People and the Planet. American Scientist, 96(2), 122. DOI: 10.1511/2008.70.3638  

  • November 18, 2012
  • 03:39 PM

DHSs and histone modifications: methylation, acetylation, citrullination, and phosphorylation

by egonw in Chem-bla-ics

One day on, and still struggling with the chemistry behind gene regulation. Let no biologist ever tell me again not to use acronyms (yes, I am looking at you!). But it is interesting. I learned a lot about ChIP, histone modifications, etc, etc. This is an amazing world, where specific histone complex protein residues get methylated, acetylated, citrullinated, and phosphorylated. Of course, all this is in the context of the ENCODE meeting we have tomorrow at BiGCaT, where I will try to ........ Read more »

Thurman, R., Rynes, E., Humbert, R., Vierstra, J., Maurano, M., Haugen, E., Sheffield, N., Stergachis, A., Wang, H., Vernot, B.... (2012) The accessible chromatin landscape of the human genome. Nature, 489(7414), 75-82. DOI: 10.1038/nature11232  

Felsenfeld G, Boyes J, Chung J, Clark D, & Studitsky V. (1996) Chromatin structure and gene expression. Proceedings of the National Academy of Sciences of the United States of America, 93(18), 9384-8. PMID: 8790338  

  • November 16, 2012
  • 03:42 PM

How to Build a Neuron: step 3

by TheCellularScale in The Cellular Scale

Steps 1 and 2 of neuron-building, as well as an important set of shortcuts can be found in the How to Build a Neuron index. Step 3 is deciding which simulation software or programming language you want to use. Simulated Neuron in Genesis (source)The big two are Genesis and Neuron. They are pretty similar in a lot of ways, but Genesis runs in Linux and Neuron runs in windows. However, you can run Genesis in windows if you install the Linux environment Cygwin.Both programs can read in morphologica........ Read more »

Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US.... (2010) NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS computational biology, 6(6). PMID: 20585541  

  • November 16, 2012
  • 01:02 PM

The Disposable Dilemma

by Whitney Campbell in Green Screen

Expendable objects were not innovated recently. Although washi are now linked to origami, for instance, people have been using the small sheets as disposable facial tissues since at least the seventeenth century, when the litter of Hasekura Tsunenaga's retinue reportedly surprised French courtiers. Similarly, around 200,000 to 400,000 years earlier, hominins near present-day Tel Aviv temporarily used flint flakes to carve meat, later startling archeologists with the "short-lived usage&........ Read more »

  • November 16, 2012
  • 11:00 AM

Scientists print out ‘walking’ biological machines

by Flora Malein in

It sounds like something dreamt up by a science fiction writer, but scientists have created a walking ‘bio-bot’ made from rat heart cells and hydrogels, using a 3-D printer. The biological machines are 7 millimetres long, and resemble a miniature springboard with one long, thin leg that is supported by a stouter supporting leg. The [...]... Read more »

Chan, V., Park, K., Collens, M., Kong, H., Saif, T., & Bashir, R. (2012) Development of Miniaturized Walking Biological Machines. Scientific Reports. DOI: 10.1038/srep00857  

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