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  • September 22, 2012
  • 11:02 AM
  • 880 views

OMG! An Open Molecule Generator!

by egonw in Chem-bla-ics

Earlier this week an important cheminformatics paper appeared in the Journal of Cheminformatics. It is about the Open Molecule Generator (see below for the paper). This was one important piece of functionality still missing from Open Source cheminformatics. This works uses the Chemistry Development Kit, and was written by Julio Peironcely.

The Analytical Biosciences' group of Prof. Hankemeier (and many others, including also Theo Reijmers) and funded by the Netherlands Metab........ Read more »

Julio E Peironcely, Miguel Rojas-Chertó, Davide Fichera, Theo Reijmers, Leon Coulier, Jean-Loup Faulon, & Thomas Hankemeier. (2012) OMG: open molecule generator. Journal of Cheminformatics, 21. DOI: 10.1186/1758-2946-4-21  

  • September 22, 2012
  • 08:00 AM
  • 611 views

New Caledonian crows reason about hidden causal agents

by Rogue Medic in Rogue Medic

We have generally believed that animals are not capable of very complex thought, even though many species use tools and engage in other complex behaviors.

Even a bird brain appears to be capable of understanding things that are not visible may be affecting their environment.

This study looks at whether New Caledonian crows, that were caught just for this experiment, are capable of attributing actions to a hidden cause, when they see that possible cause come and go.... Read more »

  • September 17, 2012
  • 10:30 PM
  • 816 views

How to Build a Neuron: Shortcuts

by TheCellularScale in The Cellular Scale

So you want to build a neuron, but don't have the time to fill and stain it, digitally reconstruct it, or even to knit one. Knitting Neuroscience from Knit a Neuron Well you are in luck because a lot of scientists have collected a lot of data already and some of them are even willing to openly share their work.  While it is great that people are willing to share their data, that willingness alone is not enough to actually make the data widely accessible (or searchable for that mat........ Read more »

  • September 13, 2012
  • 08:59 PM
  • 380 views

This is your brain on implants (spoiler: it’s better)

by aimee in misc.ience

Today, the Journal of Neural Engineering published rather an interesting paper. In it, they showed that they had been able to restore (and in some cases, improve) decision-making ability in primates through the use of an implanted prosthetic. Sounds like something out of science fiction, doesn’t it?     The region of the brain responsible [...]

[Click on the hyperlinked headline for more of the goodness]... Read more »

  • September 11, 2012
  • 05:28 PM
  • 461 views

A tougher and more stretchable hydrogel

by Cath in Basal Science (BS) Clarified

Why settle for good enough, when there can be improvements?  “Conventional hydrogels are very weak and brittle—imagine a spoon breaking through jelly,” says lead author Jeong-Yun Sun, a postdoctoral fellow [...]... Read more »

S. Khetan, C. Chung, & JA. Burdick. (2009) Tuning hydrogel properties for applications in tissue engineering. Conference proceedings : .. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference, 2094-6. PMID: 19963530  

O. Wichterle, & D. Lim. (1960) Hydrophilic Gels for Biological Use. Nature, 117. DOI: 10.1038/185117a0  

Jeong-Yun Sun, Xuanhe Zhao, Widusha R. K. Illeperuma Ovijit Chaudhuri, Kyu Hwan Oh, David J. Mooney, Joost J. Vlassak, & Zhigang Suo. (2012) Highly stretchable and tough hydrogels. Nature, 133. DOI: 10.1038/nature11409  

  • September 10, 2012
  • 06:33 AM
  • 476 views

Coming Soon: New Species of Metals

by Andrew Porterfield in United Academics

Most metallic things around us—bridges, microchip wires, buildings—are made of arrays of tiny crystals that owe their strength to an orderly, repeating pattern of grains. However, these mixtures, or alloys, of different metals are unstable; under heat or stress they tend to meld together and become larger and weaker. But the right mix can produce a metal that’s stronger, more heat-resistant and capable of creating structures never thought possible.... Read more »

Tongjai Chookajorn, Heather A. Murdoch, Christopher A. Schuh. (2012) Design of Stable Nanocrystalline Alloys. Science. DOI: 10.1126/science.1224737  

  • September 6, 2012
  • 11:00 AM
  • 469 views

L-systems and algorithmic sound experiments

by Alejandro Mosquera in amsqr

New user-generated content music genres such as the "Bytebeat", that is a new genre of electronic music where a piece of rhythmic and/or somewhat melodic music is generated in real-time using just a relatively short formula. In this experiment I combine both approaches, generative L-systems and executable formulae.... Read more »

  • August 31, 2012
  • 08:28 AM
  • 546 views

Here Come The Cyborgs

by gunnardw in The Beast, the Bard and the Bot

Cyborgs, or cybernetic organisms, are creatures in which biological tissues and artificial additions are closely intertwined. Well-known recent examples include moths and beetles that can be controlled through the use of electronic steering mechanisms attached to their brains. But, the … Continue reading →... Read more »

Tian, B., Liu, J., Dvir, T., Jin, L., Tsui, J.H., Qing, Q., Suo, Z., Langer, R., Kohane, D.S., & Lieber, C.M. (2012) Macroporous nanowire nanoelectronic scaffolds for synthetic tissues. Nature Materials. DOI: 10.1038/nmat3404  

  • August 30, 2012
  • 09:00 PM
  • 741 views

How to Build a Neuron: Step 2

by TheCellularScale in The Cellular Scale

Recently we've discussed the first step in how to build a neuron. Today we will discuss step 2: reconstructing that stained cell.Hippocampus CA1 Pyramidal neuron (from Neuromorpho.org)There are a couple of ways that you turn an image (or image stack) of a neuron into a digital neuron file like the one pictured above.  Basically there is an easy way and a hard way.  The hard way is to reconstruct the neuron manually, where you literally trace the neuron by hand.  The easy way is to........ Read more »

  • August 29, 2012
  • 10:53 PM
  • 367 views

What are we really recycling?

by Cath in Basal Science (BS) Clarified

Having grown up with reduce, reuse, recycle campaigns (Tweety’s Global Patrol circa 1990), recycling is part of my daily routine. In fact, I’ve even spent time at a Japanese university lab [...]... Read more »

Reck BK, & Graedel TE. (2012) Challenges in metal recycling. Science (New York, N.Y.), 337(6095), 690-5. PMID: 22879508  

  • August 29, 2012
  • 05:30 PM
  • 606 views

how to weave machinery into biology

by Greg Fish in weird things

As we’re starting to test artificially grown organs, scientists are wondering how to make sure that their methods result in viable tissues. One of the first steps was to take organ growth into three dimensions, letting the cells grow on a scaffold and self-organize into the right muscles, valves, and other soft tissue. Usually these scaffolds are derived from existing organs purified of all their old cells and many are designed to break down into [...]... Read more »

Bozhi Tian,, Jia Liu,, Tal Dvir,, Lihua Jin,, Jonathan H. Tsui,, Quan Qing,, Zhigang Suo,, Robert Langer,, Daniel S. Kohane,, & Charles M. Lieber. (2012) Macroporous nanowire nanoelectronic scaffolds for synthetic tissues. Nature Materials. DOI: 10.1038/nmat3404  

  • August 29, 2012
  • 09:08 AM
  • 1,059 views

Video Tip of the Week: GenoCAD for Synthetic Biology

by Mary in OpenHelix

The field of synthetic biology has been simmering for quite a while. It occasionally takes a big leap, such as when Venter’s team published about their work on M. genitalium, and it took a big leap recently with the paper about modeling a lot of the cellular processes in a simple cell that I talked [...]... Read more »

  • August 28, 2012
  • 02:20 PM
  • 1,154 views

How does an ant colony coordinate its behaviour?

by sedeer in Inspiring Science

A recent study looking at how colonies of ants regulate their foraging behaviour has caused a bit of a buzz online. A …Continue reading »... Read more »

  • August 27, 2012
  • 02:24 PM
  • 824 views

Developing New Astro Surgery Tools for NASA Deep Space Missions

by Perikis Livas in Tracing Knowledge

A team of biomedical engineering researchers from Carnegie Mellon University and the University of Louisville are developing surgical tools that could be used for future expeditionary spaceflights to the moon, an asteroid or Mars.

“In deep space, surgical procedures will be severely complicated by absence of gravity, where it becomes difficult to prevent cabin contamination from blood and body fluids,” said James Antaki, a professor of biomedical engineering at CMU.... Read more »

Carnegie Mellon University. (2012) Press Release: Carnegie Mellon University Biomedical Engineers Lead Collaborative Team Developing New Astro Surgery Tools for NASA Deep Space Missions. Press Release: Carnegie Mellon University. info:/

  • August 26, 2012
  • 02:44 PM
  • 653 views

The Logistics of Scientific Growth in the 21st Century

by caseybergman in I wish you'd made me angry earlier

Over the last few months, I’ve noticed an growing number of reports about declining opportunities and increasing pressure for early stage academic researchers (Ph.D. students, post-docs and junior faculty). For example, the Washington Post published an article in early July about trends in the U.S. scientific job market entitled “U.S. pushes for more scientists, but [...]... Read more »

  • August 22, 2012
  • 06:45 PM
  • 819 views

Sensor detects glucose in saliva and tears for diabetes testing

by Perikis Livas in Tracing Knowledge

Researchers have created a new type of biosensor that can detect minute concentrations of glucose in saliva, tears and urine and might be manufactured at low cost because it does not require many processing steps to produce.... Read more »

Emil Venere. (2012) Sensor detects glucose in saliva and tears for diabetes testing. Purdue University News. info:/

  • August 22, 2012
  • 10:43 AM
  • 569 views

Video Tip of the Week: G-nome Surfer for table-top genome browsing

by Mary in OpenHelix

The other day a tweet came over my “genome” search column that intrigued me: RT @oshaer: Our paper on a tabletop interface for collaborative exploration of genomic data is finally available online: http://t.co/VQMD67wi Tabletop interface? Wha? Ok–I had to check this out. And, in fact, this group has software that will let you explore eukaryotic [...]... Read more »

Shaer O., Strait M., Valdes C., Wang H., Feng T., Lintz M., Ferreirae M., Grote C., Tempel K., & Liu S. (2012) The design, development, and deployment of a tabletop interface for collaborative exploration of genomic data. International Journal of Human-Computer Studies, 70(10), 764. DOI: 10.1016/j.ijhcs.2012.05.003  

  • August 19, 2012
  • 12:29 PM
  • 1,078 views

How to Build a Neuron: Step 1

by TheCellularScale in The Cellular Scale

There are many reasons to try to build a neuron, but fully building a model neuron is an extensive process with many steps.  Today we will discuss the very first step in the neuron-building process: determining the activity and  shape of the neuron. Biocytin filled cortical neurons (source)To determine the shape of neuron, you have to stain it somehow.  There are several ways to do this, but we will focus on the biocytin filling method. To determine the activity of a neuron, ........ Read more »

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  

  • August 17, 2012
  • 06:20 AM
  • 749 views

What is the collective noun for a group of Systems Biologists?

by Duncan Hull in O'Really?

What happened was, I was looking for a Creatively Commons licensed picture of Pedro Mendes to upload to commons.wikimedia.org. That’s not the footballing Pedro Mendes who played for Rangers, Spurs, Pompey and Porto but the systems biologist Pedro Mendes who plays for Virginia Tech and Manchester. Thankfully, another systems biologist, Michael Hucka kindly pointed to his impressive collection of pictures, taken at various events over the years which include some shots of Pedro. Looking at t........ Read more »

Lander Arthur D. (2010) The edges of understanding. BMC Biology, 8(1). DOI: 10.1186/1741-7007-8-40  

Kitano Hiroaki. (2002) Systems Biology: A Brief Overview. Science, 295(5560), 1664. DOI: 10.1126/science.1069492  

Ideker Trey, Galitski Timothy, & Hood Leroy. (2001) Systems Biology: A new approach to decoding life . Annual Review of Genomics and Human Genetics, 2(1), 372. DOI: 10.1146/annurev.genom.2.1.343  

  • August 16, 2012
  • 03:30 PM
  • 442 views

Studying the Effects of Confinement on Cell Division

by Hector Munoz in Microfluidic Future

On Microfluidic Future I like reviewing advancements in therapeutic or diagnostic devices because I’m really drawn to those areas of research. Every once in a while, however, I take interest in research for the sake for knowledge, like the Root Chip. I recently came across an article from Dino Di Carlo of UCLA that describes a microfluidic device used to study cancer cells. The article, “Increased Asymmetric and Multi-Daughter Cell Division in Mechanically Confined Microenvironments&........ Read more »

Henry Tat Kwong Tse, Westbrook McConnell Weaver, & Dino Di Carlo. (2012) Increased Asymmetric and Multi-Daughter Cell Division in Mechanically Confined Microenvironments. PLoS ONE, 7(6). info:/

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