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  • February 21, 2014
  • 04:43 AM
  • 334 views

Slow publishing innovation

by egonw in Chem-bla-ics

Elsevier is not the only publisher with a large innovation inertia. In fact, I think many large organizations do, particularly if there are too many interdependencies, causing too long lines. Greg Laundrum made me aware that one American Chemical Society journal is now going to encourage (not require) machine readable forms of chemical structures to be included in their flagship. The reasoning by Gilson et al. is balanced. It is also 15 years too late. This question was relevant at the end of the last century. The technologies were already more advanced than what will now be adopted. 15 years!!! Seriously, that's close to the time it takes to bring a new drug on the market!Look at what they suggest and think about it. Include SMILES strings for structures in the paper. I very much welcome this, of course, despite I am not a big fan of SMILES at all. They could have said something about OpenSMILES too, which is more precise. They do say something about the InChI and InChIKey, but not that the SMILES string can more precisely reflect the drawing. I wonder why they don't go for a format that can actually capture the image, like CML or a MDL molfile. Then again, a SMILES copy/pastes so nicely. Talking about slow innovation. There is zero technical reason you could not copy/paste a MDL molfile into a spreadsheet (and you can with many tools, in fact...)Now, I still have tons of questions. What tool will be used to validate the correctness and absence of ambiguity before the publication? Will the SMILES strings be validated at all? And at what level? Will it have to be compatible with particular tools? Does it have to be compatible with OpenSMILES? Under what license will these SMILES be available (can we data mine DOI-SMILES links and openly share them)? What was the reasoning for finally adopting this? Will the journal also accept submission where both SMILES and other formats are provided? Will they accept or deny SMARTS strings (e.g. for Markush structures)?All in all, I second the others, and am happy to see this step. I do hope they do not stop here and wait again 15 years for another step. In fact, they ask for input on jmc@jmedchem.acs.org. That is double promising! Gilson MK, Georg G, & Wang S (2014). Digital Chemistry in the Journal of Medicinal Chemistry. Journal of medicinal chemistry PMID: 24521446... Read more »

Gilson MK, Georg G, & Wang S. (2014) Digital Chemistry in the Journal of Medicinal Chemistry. Journal of medicinal chemistry. PMID: 24521446  

  • February 19, 2014
  • 04:38 PM
  • 299 views

Pomegranate-Shaped Electrode Could Lead to More Powerful Batteries

by dailyfusion in The Daily Fusion

An electrode designed like a pomegranate — with silicon nanoparticles clustered like seeds in a tough carbon rind — overcomes several remaining obstacles to using silicon for a new generation of lithium-ion batteries, say its inventors at Stanford University and the Department of Energy’s SLAC National Accelerator Laboratory.... Read more »

  • February 15, 2014
  • 12:59 PM
  • 356 views

A Hop, Skip, and a pre-synaptic Patch

by TheCellularScale in The Cellular Scale

This new technique is just too cool not to blog about.  Novak et al. 2013 Figure 1A pre-synaptic patch clampThe synapse is the connection between two neurons. The pre-synaptic part is from the neuron sending a signal and the post-synaptic part is from the neuron receiving the signal. If you want to learn about the connection between the two neurons, you want to know what is happening on both sides of the synapse. It's relatively easy to record signals from the post-synaptic side using patch clamp or sharp electrode recording, but it is much much harder (basically impossible until now) to record from the pre-synaptic side.There is a gigantic synapse called the Calyx of Held where the pre-synaptic side is huge and envelops the post-synaptic side like a baseball glove holding a baseball.Calyx of Held (a schematic diagram) source The calyx of held is relatively easy to record from because it is so huge. So it is essentially where all the information about pre-synaptic terminals comes from. But Novak et al. have published a paper using this 'electrode hopping' technique to find and patch normal sized pre-synaptic terminals. A computer controlled nanopipette (which is essentially a micropipette) goes up comes back down across a layer of cells. It 'senses' cell membrane by an increase in resistance and stops before it hits the cell. Then it raises up again and moves over a little bit and comes back down. After a bazillion hops, the whole surface of an area of cell can be mapped. You can see a video of this in their very nice video abstract. After they have mapped an area, they find a pre-synaptic terminal (called a bouton) and they use the same pipette that was just used to map the area to patch the bouton (They have to make the opening of the pipette bigger first, so they just smash it into the glass near the tissue until it breaks...!!.. .but apparently that works). They patch the pre-synaptic bouton and record the calcium channels that help the pre-syanptic cell send its signal to the post-synaptic cell. © TheCellularScaleNovak P, Gorelik J, Vivekananda U, Shevchuk AI, Ermolyuk YS, Bailey RJ, Bushby AJ, Moss GW, Rusakov DA, Klenerman D, Kullmann DM, Volynski KE, & Korchev YE (2013). Nanoscale-targeted patch-clamp recordings of functional presynaptic ion channels. Neuron, 79 (6), 1067-77 PMID: 24050398... Read more »

Novak P, Gorelik J, Vivekananda U, Shevchuk AI, Ermolyuk YS, Bailey RJ, Bushby AJ, Moss GW, Rusakov DA, Klenerman D.... (2013) Nanoscale-targeted patch-clamp recordings of functional presynaptic ion channels. Neuron, 79(6), 1067-77. PMID: 24050398  

  • February 14, 2014
  • 11:45 PM
  • 459 views

Evolution is a special kind of (machine) learning

by Artem Kaznatcheev in Evolutionary Games Group

Theoretical computer science has a long history of peering through the algorithmic lens at the brain, mind, and learning. In fact, I would argue that the field was born from the epistemological questions of what can our minds learn of mathematical truth through formal proofs. The perspective became more scientific with McCullock & Pitts’ (1943) […]... Read more »

Valiant, L.G. (2009) Evolvability. Journal of the ACM, 56(1), 3. DOI: 10.1145/1462153.1462156  

  • February 13, 2014
  • 06:11 PM
  • 288 views

Study Suggests Using Industrial Waste for Fracking

by dailyfusion in The Daily Fusion

Industrial and domestic waste materials are viable alternative sources of raw materials for engineering proppants for use in shale gas and oil recovery, according to Penn State material scientists John Hellmann and Barry Scheetz.... Read more »

John R. Hellmann, Barry E. Scheetz, Walter G. Luscher, David G. Hartwich, and Ryan P. Koseki. (2014) Proppants for shale gas and oil recovery—Engineering ceramics for stimulation of unconventional energy resources. American Ceramic Society Bulletin, 93(1). info:other/AI96050

  • February 13, 2014
  • 09:35 AM
  • 236 views

Technology Prevents Spontaneous Combustion in Li-Ion Batteries

by dailyfusion in The Daily Fusion

In studying a material that prevents marine life from sticking to the bottom of ships, researchers led by chemist Joseph DeSimone at UNC-Chapel Hill have identified a surprising replacement for the only inherently flammable component of today’s lithium-ion batteries: the electrolyte.... Read more »

Dominica H. C. Wong, Jacob L. Thelen, Yanbao Fu, Didier Devaux, Ashish A. Pandya, Vincent S. Battaglia, Nitash P. Balsara, and Joseph M. DeSimone. (2014) Nonflammable perfluoropolyether-based electrolytes for lithium batteries. Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1314615111  

  • February 13, 2014
  • 06:46 AM
  • 274 views

Microbial Biomarker Discovery and How to Properly Format Your Data (Lefse)

by Geoffrey Hannigan in Prophage

Biomarker discovery is a big part of medical research. A biomarker is a clinical signal, like the presence of a gene in your genome or colonization of your lungs with a certain bacterial species, whose presence or absence indicates a disease state or predicts an increased risk for developing a disease state. These play important roles in medicine because they can allow for disease diagnosis (ie. the physician can test for the disease biomarker) or provide a prediction of whether the patient is at a higher risk for developing a condition (ie. a gene that puts a patient at higher risk for developing diabetes). There are some good programs out there for biomarker discovery, but one I particularly like is Lefse.... Read more »

Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S Garrett, & Curtis Huttenhower. (2011) Metagenomic biomarker discovery and explanation. Genome Biol. DOI: 10.1186/gb-2011-12-6-r60  

  • February 11, 2014
  • 03:12 PM
  • 399 views

Enduring Sharedom

by Jalees Rehman in Fragments of Truth

The recent study "Silent Listeners: The Evolution of Privacy and Disclosure on Facebook" conducted by researchers at Carnegie Mellon University monitored the public disclosure (information visible to all) and private disclosure (information visible to Facebook friends) of personal data by more than 5,000 Facebook users during the time period 2005-2011. ... Read more »

Fred Stutzman, Ralph Grossy, & Alessandro Acquistiz. (2012) Silent Listeners: The Evolution of Privacy and Disclosure on Facebook. Journal of Privacy and Confidentiality. info:/

  • February 7, 2014
  • 11:45 PM
  • 434 views

Misleading models: “How learning can guide evolution”

by Artem Kaznatcheev in Evolutionary Games Group

I often see examples of mathematicians, physicists, or computer scientists transitioning into other scientific disciplines and going on to great success. However, the converse is rare, and the only two examples I know is Edward Witten’s transition from an undergad in history and linguistics to a ground-breaking career in theoretical physicist, and Geoffrey Hinton‘s transition […]... Read more »

Hinton, G. E., & Nowlan, S. J. (1987) How learning can guide evolution. Complex Systems, 1(3), 495-502. info:/

  • February 5, 2014
  • 11:53 AM
  • 324 views

Piezoelectric Devices Harvest Energy From Heart, Lungs, Diaphragm

by dailyfusion in The Daily Fusion

Researchers at the University of Arizona and the University of Illinois have developed tiny piezoelectric power generators that can convert the motion of a beating heart into electrical energy.... Read more »

Canan Dagdeviren, Byung Duk Yang, Yewang Su, Phat L. Tran, Pauline Joe, Eric Anderson, Jing Xia, Vijay Doraiswamy, Behrooz Dehdashti, Xue Feng, Bingwei Lu, Robert Poston, Zain Khalpey, Roozbeh Ghaffari, Yonggang Huang, Marvin J. Slepian, and John A. Roger. (2014) Conformal piezoelectric energy harvesting and storage from motions of the heart, lung, and diaphragm. PNAS, 111(5), 1927-1932. DOI: 10.1073/pnas.1317233111  

  • February 3, 2014
  • 11:21 PM
  • 339 views

Digestive Diagnostics: Portable, Wearable, Insideable

by Aurametrix team in Irritable Bowel Blog

Next sensors will be in you, said a recent popular article. And some of them will monitor your digestive system.Accurate monitoring of digestion is hard. There are apps and high tech gadgets for that - like a fork that monitors eating speed or a watch that counts bites, but neither of them can provide a continuous and objective measures of what exactly is eaten and how it affects the digestive system.Thanks to wonders of modern technology, cows now have a device that can monitor the effects of food on their digestive system. Well Cow bovine health monitor, an inch thick capsule almost as long human hand, can be swallowed by a cow and measure the rumen pH and temperature within the digestive system every 15 minutes. It then transmits the data to a Bluetooth collar around the cow’s neck. This data can help to monitor the healthiness of cow's food intake, to predict its gas-forming potential in the short term, make sure it will lead to a high quality milk or prevent the development of health issues such as acidosis or infertility in the long term. The device can last between 80 to 100 days inside the cows.A smaller vitamin-sized device (1mm x 26mm with weigh less than 4 grams) was recently approved for use in humans. This ingestible pill camera - PillCamSB -  can monitor pressure, pH and temperature, gastrointestinal motility, lesions, ulcers, early signs of tumors and bleeding within the small bowel. FDA approved it for patients who have experienced an incomplete colonoscopy, as it lower-resolution-imaging can't completely replace the procedure.Food we eat and drugs we take can communicate from our insides too - Ingestible Event Maker sensor - size of a grain of sand - can be attached to any pill or a food item.Perhaps in the future we could rely on "insideables" to monitor our diet and automatically generate recommendations on what to eat and what to avoid? According to a song, The Future's So Bright Gotta Wear Shades.REFERENCES Kiourti, Asimina. (2014). Implantable and ingestible medical devices with wireless telemetry functionalities: A review of current status and challenges. Bioelectromagnetics, 35 (1), 1-15 DOI: 10.1002/bem.21813Hoskins, S.; Sobering, T.; Andresen, D.; Warren, S. (2009). Near-field wireless magnetic link for an ingestible cattle health monitoring pill Engineering in Medicine and Biology Society, 2009. EMBC 2009. Annual International Conference of the IEEE DOI: 10.1109/IEMBS.2009.5332812Wong WM, Bautista J, Dekel R, et al. Feasibility and tolerability of transnasal / per-oral placement of the wireless pH capsule vs. traditional 24-h oesophageal pH monitoring – a randomized trial. Aliment Pharmacol Ther. 2005; 21(2): 155-163.Hirono I, Richter JE. Practice Parameters Committee of the American College of Gastroenterology. ACG practice guidelines: esophageal reflux testing. Am J Gastroenterol. 2007; 102(3): 668-685.Teunissen LP, de Haan A, de Koning JJ, Daanen HA. Telemetry pill versus rectal and esophageal temperature during extreme rates of exercise-induced core temperature change. Physiol Meas. 2012 Jun;33(6):915-24. doi: 10.1088/0967-3334/33/6/915. Epub 2012 May 3. ... Read more »

  • February 1, 2014
  • 07:37 AM
  • 349 views

Using Smartphones for Occupancy Sensing Can Save Energy

by dailyfusion in The Daily Fusion

Berkeley Lab researcher Bruce Nordman had an idea several years ago to take advantage of existing devices in office buildings by using them for energy efficiency purposes. In the United States buildings are responsible for 73 percent of electricity consumption and about 39 percent of carbon dioxide emissions.... Read more »

  • January 24, 2014
  • 04:47 AM
  • 279 views

Let’s Do Business:) How People Use Emoticons At Work

by Nura Rutten in United Academics

Researchers find three communicative functions of smileys... Read more »

Skovholt, K., Grønning, A., & Kankaanranta, A. (2014) The Communicative Functions of Emoticons in Workplace E-Mails: :). Journal of Computer-Mediated Communication. DOI: 10.1111/jcc4.12063  

  • January 22, 2014
  • 03:45 PM
  • 184 views

TDD Improves Quality

by Greger Wikstrand in Greger Wikstrand

TDD Improves QualityTDD improves quality! That might sound obvious, but evidently it isn’t. Test driven development (TDD) is often cited as a key agile practice (1,2). But still, the evidence has been equivocal until now. What is TDD? If you already know what TDD is you should probably skip this section. If not, here is a super-brief […]From Greger Wikstrand - #agile, #projectmanagement, #ehealth, #mhealth #phr, #professionalism, #SoftwareEngineering by Greger Wikstrand .
Related posts:
The evidence is in – TDD works!
Automated Bug Fixing, Innovation and the Small World of SE Research
Success Factors for Outsourcing Companies


... Read more »

  • January 22, 2014
  • 09:35 AM
  • 251 views

Video Tip of the Week: StratomeX

by Mary in OpenHelix

Last week I talked about some of the terrific visualization tools from the Caleydo team, the ones that are focused on looking at pathway data. There’s another tool that I learned about in their newsletter that offers another type of visualization, which you can also supplement with pathway data. StratomeX offers a look at comparisons […]... Read more »

Schroeder Michael P, Gonzalez-Perez Abel, & Lopez-Bigas Nuria. (2013) Visualizing multidimensional cancer genomics data. Genome Medicine, 5(1), 9. DOI: 10.1186/gm413  

  • January 15, 2014
  • 02:51 PM
  • 312 views

3-D Photonic Crystals Help Thin-Film Solar Cells Absorb More Light

by dailyfusion in The Daily Fusion

Researchers have shown how to increase the efficiency of thin-film solar cells, a technology that could bring low-cost solar energy.... Read more »

  • January 15, 2014
  • 08:05 AM
  • 240 views

Video Tip of the Week: Entourage and enRoute from the Caleydo team

by Mary in OpenHelix

Have you dreamed of looking at genomic pathway data, with experimental information aligned with known pathway details, and wandering easily from one pathway node to another as you consider the implication of increased/decreased gene expression, or potential copy number variations? Easily hopping to related pathways to keep looking? Yeah–me too, for years .  If this […]... Read more »

  • January 14, 2014
  • 02:32 PM
  • 334 views

Acid Mine Drainage Can Remove Radioactivity From Fracking Wastewater

by dailyfusion in The Daily Fusion

Much of the naturally occurring radioactivity in fracking wastewater might be removed by blending it with another wastewater from acid mine drainage, according to a Duke University-led study.... Read more »

  • January 13, 2014
  • 11:45 PM
  • 334 views

Cataloging a year of blogging: the algorithmic world

by Artem Kaznatcheev in Evolutionary Games Group

Today is the last day of the Julian year, and tomorrow is Old New Years, so it is a great time to finish our overview of the three themes of TheEGG articles in 2013. We already looked at established applications of evolutionary game theory, and extending from behavior to society and mind; now, we will […]... Read more »

  • January 13, 2014
  • 07:08 PM
  • 344 views

Study Finds Flaws in Some Tidal Energy Schemes

by dailyfusion in The Daily Fusion

Renewable energy can be generated by harnessing the power from the tides, which can be predicted hundreds of years in advance. But the predicted energy gains from certain tidal energy schemes have been overestimated, according to a team of researchers in Liverpool.... Read more »

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