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  • December 4, 2012
  • 09:00 AM
  • 394 views

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
  • 715 views

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
  • 822 views

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
  • 443 views

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
  • 451 views

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
  • 215 views

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
  • 914 views

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
  • 564 views

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
  • 559 views

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
  • 653 views

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
  • 576 views

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
  • 584 views

Scientists print out ‘walking’ biological machines

by Flora Malein in floramalein.com

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  

  • November 16, 2012
  • 08:56 AM
  • 415 views

Airships: The Future of Air Travel?

by Jason Carr in Wired Cosmos

Considering the fact that airships have been around for a while now, it’s hard to believe that they are thought of as emerging technologies today. But that’s exactly the case given recent advances in this arena. Hydrogen airships have a troubled history due to several significant historical disasters. However, new technologies could help reduce this [...]... Read more »

Michele Trancossi, Antonio Dumas, Mauro Madonia, Jose Pascoa, & Dean Vucinic. (2012) Fire-safe Airship System Design. SAE Int. J. Aerosp. , 11-21. info:/10.4271/2012-01-1512

  • November 12, 2012
  • 06:54 AM
  • 531 views

CERN collider could be world’s fastest stopwatch

by Flora Malein in floramalein.com

The clock would keep time based on extremely short light pulses given out when ‘heavy ions’, nuclei that belong to heavy atoms such as lead, are smashed together at speed within the collider. To read more click here. Sources:  Ipp, A., & Somkuti, P. (2012). Yoctosecond Metrology Through Hanbury Brown–Twiss Correlations from a Quark-Gluon Plasma [...]... Read more »

  • November 11, 2012
  • 08:51 PM
  • 722 views

Cut your brain some SLACK

by TheCellularScale in The Cellular Scale

Action potentials are the main means of communication between neurons, and their exact timing can be really important. But the specific timing of action potentials is really important in the auditory system, because the auditory system encodes (among other things) information about sound wave frequency. Sound waves (source)I've previously written about auditory processing with regards to the wonder that is the chicken brain, but today we will focus on timing-specificity in the mammalian br........ Read more »

Yang B, Desai R, & Kaczmarek LK. (2007) Slack and Slick K(Na) channels regulate the accuracy of timing of auditory neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience, 27(10), 2617-27. PMID: 17344399  

  • November 7, 2012
  • 10:10 AM
  • 890 views

Political Animals

by Miss Behavior in The Scorpion and the Frog

Now that we are finally on the other side of one of the longest, most expensive political campaign seasons of United States history, we find ourselves with a new mixed-bag of leaders. Our nation’s decision-makers include career politicians and new freshman politicians; they include lawyers, military members, doctors, businessmen, farmers, ministers, educators, scientists, pilots, and entertainers; they include Protestants, Catholics, Jews, Quakers, Mormons, Buddhists and Muslims; they include ........ Read more »

  • October 29, 2012
  • 11:00 AM
  • 723 views

Can the domains of Music Cognition and Music Information Retrieval inform each other?

by Henkjan Honing in Music Matters

In about a weeks time the 13th ISMIR (International Society for Music Information Retrieval) conference will be held. This is a conference on the processing, searching, organizing and accessing music-related data. It attracts a research community that is intrigued by the revolution in music distribution and storage brought about by digital technology which generated quite some research activity and interest in academia as well as in industry.... Read more »

Aucouturier, J., & Bigand, E. (2012) Mel Cepstrum . Proc. of the 13th International Society for Music Information Retrieval Conference, 397-402. info:/

Volk. A., & Honingh, A. (eds). (2012) Mathematical and Computational Approaches to Music: Three Methodological Reflections . Journal of Mathematics and Music, 6(2). info:/10.1080/17459737.2012.704154

  • October 28, 2012
  • 03:56 AM
  • 1,198 views

Jumping Dynamics of a Simple Robot

by Ajinkya Kamat in Brilliance Ardent



Robots fascinate all of us. While few robots are just fun toys many other robots can perform many complex tasks for us. In past decade the field of robotics has advanced by leaps and bounces making robots smarter and smarter. We have created robots, which can explore terrains- terrestrial as well as extra-terrestrial-, where even humans haven't reached. To traverse a terrain with obstacles ... Read more »

Aguilar, J., Lesov, A., Wiesenfeld, K., & Goldman, D. (2012) Lift-Off Dynamics in a Simple Jumping Robot. Physical Review Letters, 109(17). DOI: 10.1103/PhysRevLett.109.174301  

  • October 27, 2012
  • 04:49 AM
  • 509 views

Is fMRI About To Get Fifty Times Faster?

by Neuroskeptic in Neuroskeptic

According to a paper just published, a new technique of functional MRI scanning (fMRI) could soon allow neuroscientists to measure brain activity far faster: Generalized iNverse imaging (GIN): Ultrafast fMRI with physiological noise correctionAuthors Boyacioglu and Barth claim remarkable things for the technique:We find that the spatial localization of activation for GIN is comparable to an EPI protocol and that maximum z-scores increase significantly... with a high temporal resolution of 50 mil........ Read more »

Boyacioglu R, & Barth M. (2012) Generalized iNverse imaging (GIN): Ultrafast fMRI with physiological noise correction. Magnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine. PMID: 23097342  

  • October 25, 2012
  • 10:15 PM
  • 610 views

Ohtsuki-Nowak transform for replicator dynamics on random graphs

by Artem Kaznatcheev in Evolutionary Games Group

We have seen that the replicator equation can be a useful tool in understanding evolutionary games. We’ve already used it for a first look at perception and deception, and the cognitive cost of agency. However, the replicator equation comes with a number of inherent assumptions and limitations. The limitation Hisashi Ohtsuki and Martin Nowak wanted [...]... Read more »

Ohtsuki H, & Nowak MA. (2006) The replicator equation on graphs. Journal of Theoretical Biology, 243(1), 86-97. PMID: 16860343  

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