Computer Science / Engineering posts
- October 25, 2010
- 07:38 PM
- 619 views
Finding Parameters for Cancer Progression and other Complex Biological Models
by Michael Long in Phased
Diego Fernandez Slezak (Buenos Aires University, Argentina), Gustavo Stolovitzky (IBM), and coworkers show that a mathematical "best fit" to a complex biological model may be biologically implausible.... Read more »
Fernández Slezak, D., Suárez, C., Cecchi, G. A., Marshall, G., & Stolovitzky, G. (2010) When the Optimal Is Not the Best: Parameter Estimation in Complex Biological Models. PLoS ONE, 5(10). DOI: 10.1371/journal.pone.0013283
- October 22, 2010
- 05:54 PM
- 740 views
Yes, diversity matters
by David Basanta in Cancerevo: Cancer evolution
Diversity matters and I am not talking about the workplace. It does in cancer (I am writing this from an NCI organised meeting in the context of the ICBP, where one one the main themes is the role of...... Read more »
Palmer TM, Doak DF, Stanton ML, Bronstein JL, Kiers ET, Young TP, Goheen JR, & Pringle RM. (2010) Synergy of multiple partners, including freeloaders, increases host fitness in a multispecies mutualism. Proceedings of the National Academy of Sciences of the United States of America, 107(40), 17234-9. PMID: 20855614
- October 21, 2010
- 10:00 AM
- 1,233 views
Open source software pays its way
by David Bradley in Sciencetext
Open source computing was once described as an “anarchistic, caffeinated, hirsute world of hackers”. But, this cliché of beardy nerds fueling themselves on coffee and slaving over a hot desktop till the wee small hours is thoroughly outmoded, if it were ever true. Open source software products are developed and licensed under terms that allow [...]Post from: David Bradley's Sciencetext Tech TalkOpen source software pays its way
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Jon Perr, Melissa M. Appleyard, & Patrick Sullivan. (2010) Open for business: emerging business models in open source software. Int. J. Technology Management, 52(3/4), 432-456. info:/
- October 19, 2010
- 02:20 AM
- 1,542 views
Patients Group Communication on Facebook a Good Idea?
by Dr Shock in Dr Shock MD PhD
Social networking sites such as Facebook are used for several disease specific information changes. They have become sources of knowledge, support and engagement especially for patients with chronic diseases such as diabetes.
One recent survey indicates patients search the Internet more frequently than they communicate with their doctors about health care questions
Recent research evaluated the [...]
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Greene, J., Choudhry, N., Kilabuk, E., & Shrank, W. (2010) Online Social Networking by Patients with Diabetes: A Qualitative Evaluation of Communication with Facebook. Journal of General Internal Medicine. DOI: 10.1007/s11606-010-1526-3
- October 18, 2010
- 12:23 PM
- 539 views
Internal coarse-graining of molecular systems
Feret J, Danos V, Krivine J, Harmer R, & Fontana W (2009). Internal coarse-graining of molecular systems. Proceedings of the National Academy of Sciences of the United States of America, 106 (16), 6453-8 PMID: 19346467, PNAS page, Supporting Information. Models of molecular dynamics suffer from combinatorial explosion: the phenomenon of an exponential number of [...]... Read more »
Feret J, Danos V, Krivine J, Harmer R, & Fontana W. (2009) Internal coarse-graining of molecular systems. Proceedings of the National Academy of Sciences of the United States of America, 106(16), 6453-8. PMID: 19346467
- October 14, 2010
- 03:44 PM
- 966 views
Thursday Threads: Disruption in Library Acquisitions, Publishing, and Remedial Education plus Checking Assumptions of Cloud Computing and a National Digital Library
by Peter Murray in Disruptive Library Technology Jester
If it is Thursday it must mean it is time for another in this series of Thursday Threads posts. This week there are an abundance of things that could fall into the category of “disruptive innovation” in libraries and higher education. If you find these interesting, you might want to subscribe to my FriendFeed stream [...]Post from: Disruptive Library Technology JesterThursday Threads: Disruption in Library Acquisitions, Publishing, and Remedial Education plus Checking Assumptions of Cloud Computing and a National Digital Library
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Baliga, J., Ayre, R., Hinton, K., & Tucker, R. (2010) Green Cloud Computing: Balancing Energy in Processing, Storage and Transport. Proceedings of the IEEE. DOI: 10.1109/JPROC.2010.2060451
- October 12, 2010
- 10:45 PM
- 597 views
You are the Chosen One, at least by your bacteria
by Aurametrix team in Health Technologies
Host genomics is not the main decision-making factor for bacteria immigrating into human body, but it is an important factor. Two papers recently published in the Proceedings of the National Academy of Sciences help to understand why you are chosen and how the choosers make their decisions. ... Read more »
Ben-Jacob E, & Schultz D. (2010) Bacteria determine fate by playing dice with controlled odds. Proceedings of the National Academy of Sciences of the United States of America, 107(30), 13197-8. PMID: 20660309
Andrew K. Benson,, Scott A. Kelly,, Ryan Legge,, Fangrui Ma,, Soo Jen Low,, Jaehyoung Kim,, Min Zhang,, Phaik Lyn Oh,, Derrick Nehrenberg,, Kunjie Hu,.... (2010) Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors . PNAS. info:/
- October 12, 2010
- 10:00 PM
- 1,116 views
Figuring out figures in scientific papers: new search / ranking method outline in PLoS One paper
by Jonathan Eisen in The Tree of Life
Just a quick post here. A colleague just sent me a link to her fascinating new paper in PLoS One: PLoS ONE: Automatic Figure Ranking and User Interfacing for Intelligent Figure Search
In this paper Hong Yu from the University of Wisconsin in Milwaukee describes a system for better automated characterization of figures from scientific papers. The system is available through their webserver "Ask Hermes".
If you want to learn more about the system I suggest you read the paper. Or watch their video.
Basically the general idea is summarized in their background section of the abstract:
Figures are important experimental results that are typically reported in full-text bioscience articles. Bioscience researchers need to access figures to validate research facts and to formulate or to test novel research hypotheses. On the other hand, the sheer volume of bioscience literature has made it difficult to access figures. Therefore, we are developing an intelligent figure search engine (http://figuresearch.askhermes.org). Existing research in figure search treats each figure equally, but we introduce a novel concept of “figure ranking”: figures appearing in a full-text biomedical article can be ranked by their contribution to the knowledge discovery.I particularly like that they also allow searching just for open access figures, which may be of significant value to people who want to do things like make a slide presentation with no copyrighted/protected material in it. For example see the results of a search for open access figures using the keyword phylogenomics.
Anyway - definitely worth checking this out.
Yu, H., Liu, F., & Ramesh, B. (2010). Automatic Figure Ranking and User Interfacing for Intelligent Figure Search PLoS ONE, 5 (10) DOI: 10.1371/journal.pone.0012983
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This is from the "Tree of Life Blog"
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.
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... Read more »
Yu, H., Liu, F., & Ramesh, B. (2010) Automatic Figure Ranking and User Interfacing for Intelligent Figure Search. PLoS ONE, 5(10). DOI: 10.1371/journal.pone.0012983
- October 11, 2010
- 01:57 AM
- 618 views
Why do you Blog?
by Dr Shock in Dr Shock MD PhD
Why does someone write a personal blog and not simply use the Internet for taking in media content? Personal blogs are composed of shorter posts concerning the blogger’s life in contrast to filter blog. Filter blogs are devoted to external information, such as politics or news and are far better researched than personal blogs.
From recent [...]
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Hollenbaugh, E. (2010) Motives for Maintaining Personal Journal Blogs. Cyberpsychology, Behavior, and Social Networking, 2147483647. DOI: 10.1089/cyber.2009.0403
- October 5, 2010
- 10:41 PM
- 640 views
When is webometrics most useful?
by Hadas Shema in Information Culture
Like many terms in Information Science (including 'Information Science' itself) the term 'webometrics' is pretty vague. Björneborn and Ingwersen (2004) defined webometrics as "the study of the quantitative aspects of the construction and use of information resources, structures and technologies on the Web drawing on bibliometric and informetric approaches." I guess this definition will have to do for the time being. Thelwall*, Klitkou, Verbeek, Stuart and Vincent (2010) set out to find in which fields webometrics is most effective. The result is quite a long paper, that I'm going to be very general about its conclusions. As expected, webometrics doesn't have the same effectiveness in every field. It is at its best with emerging and/or "hot" fields. That is because web publication is easier and faster than publication in traditional scientific outlets, and researchers can publish ongoing results with little delay.In some disciplines plenty of their products aren't regularly published in journals (social sciences, humanities, applied fields, etc.) and therefore aren't as well-covered by bibliometrical databases as disciplines with a journal-publishing culture. Bibliometrics is also bound to have a poor coverage of multidisciplinary fields, because their outputs are published in various outlets and are often cited in different manners. In general, webometrics analysis gives better results in fields with standards and/or norms for web publishing, but the results might not be reliable in fields where a small number of research groups and their projects (databases, web portals and so on) have an disproportional web presence. Collaborations are often better caught in webometric analysis, since not all collaborative works have "official" outputs. Webometrics works better for smaller fields. It's harder to get a complete picture of large fields with current methods. Last but not least: webometric analysis is usually faster and cheaper than bibliometric one.Thelwall and his colleagues concluded that "whilst webometrics is still inferior to bibliometrics for most purposes it seems that it has advantages for some types of field, particularly new, small fields, and can deliver policy-relevant (process) indicators to promote effective collaboration and communication," (in short: use with caution). Appropriate disclosure: Prof. Thelwall is one of my dissertation advisors . My favorite from his long list of achievements is that he managed to publish a serious research paper including a YouTube cat video. Thelwall, M., Klitkou, A., Verbeek, A., Stuart, D., & Vincent, C. (2010). Policy-relevant Webometrics for individual scientific fields Journal of the American Society for Information Science and Technology, 61 (7), 1464-1475 DOI: 10.1002/asi.21345... Read more »
Thelwall, M., Klitkou, A., Verbeek, A., Stuart, D., & Vincent, C. (2010) Policy-relevant Webometrics for individual scientific fields. Journal of the American Society for Information Science and Technology, 61(7), 1464-1475. DOI: 10.1002/asi.21345
- October 3, 2010
- 08:10 PM
- 464 views
Authorities and hubs in Twitter conference feeds
by Hadas Shema in Information Culture
"Understanding how Twitter is used to spread scientific messages" is another conference paper studying the scientific uses of Twitter. Letierce, Passant, Breslin and Decker (2010) analysed Twitter feeds from the International Semantic Web Conference (#iswc2009), the Online Information Conference 2009 (#online09) and the European Semantic Technology Conference (#estc2009). First, they checked the distribution of tweets per user, then the distribution of tweets that were directed to individuals (@user messages). They found that both were Power Law distributions.After that, they used the HITS (Hyperlink-Induced Topic Search) algorithm to determine the hubs and authorities of the conference feeds. Users who addressed many @user messages were considered hubs, while the users who received many @user tweets were considered authorities. Letierce et al.'s not-very-surprising conclusion was that users with both high hub and authorities scores were often the organizers of the events studied in the research. Also, users with real-world authority (their example was @timberners_lee) also had t-authority. Of course, Letierce and her colleagues couldn't determine if there are more real-world authorities that don't use Twitter (perhaps a content analysis of the tweets can determine if there are talks about people who aren't Twitter users, but that's very time-consuming and not the point of the research here). The paper includes a small survey (61 participants) done by the authors, but I chose not to discuss it here, because of the small sample. Letierce, J., Passant, A., Breslin, J., & Decker, S. (2010). Understanding how Twitter is used to spread scientific messages Proceedings of the WebSci10: Extending the Frontiers of Society On-Line, April 26-27th, Raleigh, NC: US.... Read more »
Letierce, J., Passant, A., Breslin, J., & Decker, S. (2010) Understanding how Twitter is used to spread scientific messages. Proceedings of the WebSci10: Extending the Frontiers of Society On-Line, April 26-27th, Raleigh, NC: US. info:/
- September 29, 2010
- 08:00 AM
- 1,149 views
Finding a private place on the wireless net
by David Bradley in Sciencetext
Increasingly, we live in a wireless world, hundreds of millions of people connect to the internet through Wi-Fi networks, use mobile phones, or wireless broadband and devices connect to computer systems through wireless sensors and other gadgets. Wireless – the next generation Many observers suggest that the next generation wireless networks (NGWNs) will see the [...]Post from: David Bradley's Sciencetext Tech TalkFinding a private place on the wireless net
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Chakchai So-In, Raj Jain, Subharthi Paul, & Jianli Pan. (2010) Virtual ID: ID/locator split in a mobile IP environment for mobility, multihoming and location privacy for the next generation wireless networks. Int. J. Internet Protocol Technology, 5(3), 142-153. info:/
- September 28, 2010
- 05:37 PM
- 873 views
K: Japan's Next-Generation Supercomputer
by Olexandr Isayev in olexandrisayev.com
Fujitsu announced that today it began shipping the computing units for Japan's Next-Generation Supercomputer, nicknamed the "K" computer.... Read more »
Ajima, Y., Sumimoto, S., & Shimizu, T. (2009) Tofu: A 6D Mesh/Torus Interconnect for Exascale Computers. Computer, 42(11), 36-40. DOI: 10.1109/MC.2009.370
- September 15, 2010
- 03:31 PM
- 970 views
Through a (Brain) Scanner, Darkly
by Lindsay in Autist's Corner
Explains Ecker et al. (2010)'s statistical analysis of the geometry of MRI-derived computer models of 20 autistic men's brains, compared with normal and abnormal (ADHD) controls... Read more »
Ecker C, Marquand A, Mourão-Miranda J, Johnston P, Daly EM, Brammer MJ, Maltezos S, Murphy CM, Robertson D, Williams SC.... (2010) Describing the brain in autism in five dimensions--magnetic resonance imaging-assisted diagnosis of autism spectrum disorder using a multiparameter classification approach. The Journal of neuroscience : the official journal of the Society for Neuroscience, 30(32), 10612-23. PMID: 20702694
- September 14, 2010
- 08:00 AM
- 1,422 views
7 rules for social networking
by David Bradley in Sciencetext
Technology is transforming the way we many of us communicate. From those queuing up to join the “privacy aware” social network Diaspora and the half a billion Facebook users to Africans bartering call-time on mobile phones through cellular banking and the countless Brazilian users of Google Orkut. We are all becoming connected. The Internet began [...]Post from: David Bradley's Sciencetext Tech Talk7 rules for social networking
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Tanuja Singh, & Joe Cullinane. (2010) Social networks and marketing: potential and pitfalls. Int. J. Electronic Marketing and Retailing, 3(3), 202-220. info:/
- September 11, 2010
- 02:36 PM
- 1,587 views
when bad quantum physics invade military news
by Greg Fish in weird things
As said by Futurama’s mad scientist at large, Professor Farnsworth, quantum mechanics mean that anything can happen for any reason or without one. Of course this was really a swipe at how so many of us tend to see the complex physics of quantum objects, and it’s a very valid one since there’s a seemingly [...]... Read more »
Jin, X., Ren, J., Yang, B., Yi, Z., Zhou, F., Xu, X., Wang, S., Yang, D., Hu, Y., Jiang, S.... (2010) Experimental free-space quantum teleportation. Nature Photonics, 4(6), 376-381. DOI: 10.1038/nphoton.2010.87
Lydersen, L., Wiechers, C., Wittmann, C., Elser, D., Skaar, J., & Makarov, V. (2010) Hacking commercial quantum cryptography systems by tailored bright illumination. Nature Photonics. DOI: 10.1038/nphoton.2010.214
- September 10, 2010
- 05:16 PM
- 692 views
fMRI, BOLD and the Beautiful
by amiya in Physiology physics woven fine
When we want to examine the brain of a person noninvasively by Computed Tomography (CT) or MRI, we get a ‘snapshot’ of the anatomy (or pathology, if any) of the subject’s brain. We are however clueless as to its functional aspect. fMRI or Functional Magnetic Resonant Imaging allows us to do just that. The difference is not unlike a ‘still picture’ versus a ‘video of a moving train’. PET scans, previously described, also can asses the functional state of the brain.Whenever we do a task, think, dream, memorize, speak or see things, the brain is not activated as a whole; but only certain portions of it are activated. Activation, here, means increased metabolic activity of neurons in certain areas of the brain. Naturally, these ‘metabolically active’ neurons would demand more energy which would power them. The blood supply to these areas increases as a result of this metabolically driven vasodilation. The arteries then bring in glucose and oxygen with them, with Oxygen being transported in the form of Oxyhemoglobin (oxygenated hemoglobin or HbO2). Neurons on the other hand use up the oxygen contained in the blood, thereby reducing it to de-oxyhemoglobin or simply Hb. However, the alteration in tissue perfusion exceeds the extraction of oxygen by the neurons, so the concentration of deoxyhemoglobin within ‘the areas’ decreases. This causes molecular inhomogeneities in the magnetic field.Oxyhemoglobin is diamagnetic, meaning that they align perpendicularly to magnetic field lines. On the other hand, deoxyhemoglobin is paramagnetic, i.e. it aligns parallely and proportinately with the intensity of the magnetic field. This causes the inhomogeneity within the magnetic field (magnetic susceptibility) in the tissue sampled. This inhomogeneity is exploited in fMRI in terms of decay of transverse magnetization, T2*, with longer T2* values in HbO2 blood and shorter values in Hb (paramagnetic) blood.Since this stems from the oxygen content in blood, fMRI is also known as the BOLD ((blood oxygenation level dependent) effect.The machine is essentially the same as the MRI machine with echo planar imaging technology that permits faster imaging due to faster gradient switching, improved algorithm and faster CPU processing power. The patient/subject is placed inside the magnetic chamber and MRI signals are acquired, Fourier transformed and corrected for artifacts. Finally the computer reconstructs a 3D fMRI image out of this.As is obvious, we can learn about the motor areas of a patient by asking him to grasp an object or giving him any motor task and noticing which area(s) of the brain lights up. A neurosurgeon can then be cautious about not hurting these areas. Similarly, the mapping will help spare motor and other vital areas like auditory, visual and language areas from damage in radiotherapy procedures, in addition to neurosurgery. It can also detect occult Alzheimer’s disease and cognitive deficits including those of the autism spectrum and dyslexia (reading disorder).fMRI can also be employed to ‘read peoples’ minds’, thoughts and intentions. Watch the video below. Thus the legal and forensic implications are obvious. Whatever it may be, it seems that fMRI is very much here to stay, both in the clinics as well as in cognitive neuroscience research. It may also be combined with tractography, MRI or other diagnostic radiologic modalities.Hardenbergh et al combined Tractography techniques with fMRI, using a technique capable of rendering multiple color-coded functional activation volumes and fiber tract bundles. Many pharmacologically active drugs have effect on memory impairment, which can be seen in ‘telltale’ fMRI scans. Sperling et al studied the effects of lorazepam (a benzodiazepine) and scopolamine (an anticholinergic drug once used as ‘truth serum’ by the CIA) on healthy volunteers and found that they did impair memory and their functional coordinates could be reproducively mapped on fMRI scans (see figure on the left). I still shudder at the thought of what happened during my PG exam when I took a benzodiazepine.Last modified: neverReference: Integrated 3D Visualization of fMRI and DTI tractographyGore, J. (2003). Principles and practice of functional MRI of the human brain Journal of Clinical Investigation, 112 (1), 4-9 DOI: 10.1172/JCI200319010... Read more »
Gore, J. (2003) Principles and practice of functional MRI of the human brain. Journal of Clinical Investigation, 112(1), 4-9. DOI: 10.1172/JCI200319010
- September 7, 2010
- 11:47 PM
- 623 views
The World of Tractography Where The White Matter Tracts Appear Colored
by Amiya Kumar Sarkar in Physiology physics woven fine
White matter tractography, a relatively new MRI based technique, can delineate fiber tracts and assist in surgical planning and research.... Read more »
P. Mukherjee,, J.I. Berman,, S.W. Chung,, C.P. Hess, & R.G. Henry. (2008) Diffusion Tensor MR Imaging and Fiber Tractography: Theoretic Underpinnings. AM J Neuroradiol . DOI: 10.3174/ajnr.A1051
- September 7, 2010
- 01:54 AM
- 828 views
Gaming for good: human thought beats computer algorithms at solving protein structures
by Anna Goldstein in Berkeley Science Review Blog
Considering my fascination of late with unusual author lists in science papers, you can guess how excited I was to see an article in Nature that credited online gamers. I was especially amused to see that citation services like PubMed … Continue reading →... Read more »
Cooper S, Khatib F, Treuille A, Barbero J, Lee J, Beenen M, Leaver-Fay A, Baker D, Popović Z, & Players F. (2010) Predicting protein structures with a multiplayer online game. Nature, 466(7307), 756-60. PMID: 20686574
- September 6, 2010
- 01:58 AM
- 1,172 views
Web 2.0 Strategy for Medical Journals
by Dr Shock in Dr Shock MD PhD
I’m having a problem. I’m an editor for the Dutch/Flemish Journal of Psychiatry. Since I’m a blogger and on twitter and using many more web 2.0 tools I’m supposed to be the expert on web 2.0 and our journal. We’ve revamped our website and the journal is even on twitter. We’re planning presence on Facebook [...]
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Senoaji Wijaya, Marco Spruit, Wim Scheper, & Johan Versendaal. (2010) Web 2.0-based webstrategies for three different types of organizations. Computers in Human Behavior. info:/10.1016/j.chb.2010.07.041
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