You might think that a smartphone is a smartphone the world over or that perceptions of tablet PCs are the same from nation to nation. Internationally, speaking, isn’t a laptop still a laptop regardless of location? A new study by researchers in the US and India suggests otherwise. The authors of the study suggest that [...]Post from: David Bradley's Sciencetext Tech TalkTechnology with attitude
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Kallol Bagchi, Purnendu Mandal, & Arunabha Mukhopadhyay. (2011) Attitude towards technology development: a cross-cultural study of India and the USA. Int. J. Information Systems and Change Management, 5(1), 3-21. info:/
do_sud_thumb("http://neurobonkers.com/wp-content/uploads/2011/03/computer-doctor.jpg","One Nanostep for Technology, One... Read more »
Khodayari-Rostamabad A, Reilly JP, Hasey G, Debruin H, & Maccrimmon D. (2010) Diagnosis of psychiatric disorders using EEG data and employing a statistical decision model. Conference proceedings : .. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference, 4006-9. PMID: 21097280
Khodayari-Rostamabad, A., Hasey, G., MacCrimmon, D., Reilly, J., & Bruin, H. (2010) A pilot study to determine whether machine learning methodologies using pre-treatment electroencephalography can predict the symptomatic response to clozapine therapy. Clinical Neurophysiology, 121(12), 1998-2006. DOI: 10.1016/j.clinph.2010.05.009
Charles DeBattista, Gustavo Kinrys, Daniel Hoffman, Corey Goldstein, John Zajecka, James Kocsis, Martin Teicher, Steven Potkin, Adrian Preda, Gurmeet Multani, Len Brandt, Mark Schiller, Dan Iosifescu, Maurizio Fava. (2011) The use of referenced-EEG (rEEG) in assisting medication selection for the treatment of depression . Psychiatric Research, 15(12), 64-75. DOI: The use of referenced-EEG (rEEG) in assisting medication selection for the treatment of depression
Too often we look for a single perfect answer to our problems. In the energy crisis people are often disappointed when hybrid batteries are found to be so environmentally unfriendly or that wind power is often incredibly harmful to local bird life or that solar cell arrays often use a lot of water in areas that are pretty arid to begin with.Researchers looking into the future of space flight looked at combining a rocket propellant with an electric sail. An electric sail has some similarities to a solar sail in that they are both low mass propulsion systems however a solar sail uses the acceleration of photons to create slight accelerations to the apparatus while an electric sail uses an array of long, thin positively charged tethers that repel solar wind protons while attracting solar wind electrons. These arrays have all been proposed as a method of space flight that would require no additional propellant as accelerating and decelerating more mass requires more wasted energy. However an electric sail would only function in space and the gains to acceleration can sometimes be minute.The researchers used the Hohmann transfer numbers as a starting point for interplanetary travel between Earth and its neighbors. Typical planet to planet rendezvous would include a period of time where the spacecraft was accelerating to give it a necessary velocity delta to escape Earth's orbit, then a period where it would coast to reach the orbit of the planet it's attempting to reach. Minimum flight times were calculated for this basic transfer orbit as between 0.289 years to reach Mercury and 30.613 years to reach Neptune.The authors looked an ideal thrust-on time in comparison to minimum flight time because while shortest flight would generally be ideal you would also want to reduce your thrust time in case of your propulsion system failure. So it was better to look at a ratio between the two. They looked initially at having a secondary thrust phase after an initial coasting phase but found using the total time and thrust time ratio meant it was always optimal to have only one thrust phase followed by a coasting phase.Their initial starting point was an object in circular orbit around the earth to which they then simulated times it might take that object to reach planets in the solar system using either a typical rocket propulsion system or the hybrid rocket and electric sail option. In the first option the rocket propellant and inertia allow it to reach the escape velocity. But in the case of the electric sail, the sail's acceleration can contribute during the thrust time towards achieving the delta velocity which of course reduces the amount of propellant the spacecraft would have to carry. I summed up their results in a slightly more clear graph.Perhaps not surprisingly flights to Mercury and Venus were worse with the hybrid system. Though, an electric sail only system would save considerable fuel and mass and could be considered to Mercury and Venus. The major time savings were seen the farther out into the solar system. The hybrid system doesn't solve long term space flight concerns but it does add another weapon to our arsenal that perhaps future spaceflights will employ multiple methods of propulsion.Quarta, A., Mengali, G., & Janhunen, P. (2011). Optimal interplanetary rendezvous combining electric sail and high thrust propulsion system Acta Astronautica, 68 (5-6), 603-621 DOI: 10.1016/j.actaastro.2010.01.024... Read more »
Quarta, A., Mengali, G., & Janhunen, P. (2011) Optimal interplanetary rendezvous combining electric sail and high thrust propulsion system. Acta Astronautica, 68(5-6), 603-621. DOI: 10.1016/j.actaastro.2010.01.024
If players succeed at a game (play well), they only enjoy the game if they feel they were responsible for that success.
Some related articles on Neo-Academic:How Do Video Games Motivate People? (VG Series Part 9/10)
Setting the Difficulty of Serious Training Games
College Courses as Live Games
... Read more »
Trepte, S., & Reinecke, L. (2011) The pleasures of success: Game-related efficacy experiences as a mediator between player performance and game enjoyment. Cyberpsychology, Behavior, and Social Networking, 2147483647. DOI: 10.1089/cyber.2010.0358
Well, here goes.
This is a post about a paper that has been a long long time coming. Today, a paper of mine is being published in PLoS One. The paper is titled "Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees" and is available at http://dx.plos.org/10.1371/journal.pone.0018011. (or if that link does not work you can get a copy here). This paper represents something I started a long time ago and I am going to try to describe the story behind the paper here.
I note - we are not doing a press release for the paper, for a few reasons. But one of them is that, well, I am starting to hate press releases. So I guess this is kind of my press release. But this will be a bit longer than most press releases. I note - my key fear here is that somehow in my communications with the press or in our text in the paper or in this post I will overstate our findings. Here is the punchline - we found some very phylogenetically novel forms of phylogenetic marker genes in metagenomic data. We do not have a conclusive explanation for the origin of these sequences. They may be from novel viruses. The may be ancient paralogs of the marker genes. Or they may be from a new branch of cellular organisms in the tree of life, distinct from bacteria, archaea or eukaryotes. I think most likely they are from novel viruses. But we just don't know.
First - a summary of what we did.
In the paper, we searched through metagenomic data (sequences from environmental samples) for phylogenetically novel sequences for three standard phylogenetic marker genes (ss-rRNA, recA, rpoB). We focused on sequences from the Venter Global Ocean Sampling data set because, well, we started this analysis many years ago when that was the best data set available (more on this below). What we were looking for were evolutionary lineages of these genes that were separate from the branches that corresponded to the three known "Domains" of life (bacteria, archaea and eukaryotes).
To search for such novel lineages in the metagenomic data, we built evolutionary trees using these genes where we included sequences from known organisms (and viruses) as well as sequences from metagenomic data. We then looked through the trees for groups that were both phylogenetically novel and included only environmental data (i.e., they were new compared to known organisms or viruses). This method did not work very well for rRNA sequences (largely because making high quality alignments of short phylogenetically novel rRNA sequences was difficult - more on this below). But with RecA and RpoB homologs we were able to generate what we believe to be robust phylogenetic trees. And in these trees we found evidence for phylogenetically very novel sequences in environmental data.
We then propose and discuss four potential mechanisms that could lead to the existence of such evolutionarily novel sequences. The two we consider most likely are the following(1) The sequences could be from novel viruses(2) The sequences could be from a fourth major branch on the tree of life
Unfortunately, we do not actually know what is the source of these sequences. So we cannot determine which of the theories is correct. Obviously if there is a novel lineages of cellular organisms out there, well, that would be cool. But we have no evidence right now if that is what is going on. Personally, I think it is most likely that these novel sequences are from weird viruses. But as far as we can tell, they truly could be from a fourth major branch of cellular organisms and thus even though we did not have the story completely pinned down, we decided to finally write up the paper to get other people to think about this issue.
Below I give all sorts of other details about the project in the following areas
The history of the project
More detail on what is in the ... Read more »
Dongying Wu, Martin Wu, Aaron Halpern, Douglas B. Rusch, Shibu Yooseph, Marvin Frazier,, & J. Craig Venter, Jonathan A. Eisen. (2011) Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees. PLoS One, 6(3). info:/10.1371/journal.pone.0018011
Electronic health records are a hot topic in the world of medicine, as hospitals implement new computerized systems to meet federal incentives. Proponents of replacing paper records with electronic health records (EHR) in hospitals and other health care settings argue that the update will improve the efficiency of health care, cutting costs and making life [...]... Read more »
Robicsek A, Beaumont JL, Wright MO, Thomson RB Jr, Kaul KL, & Peterson LR. (2011) Electronic prediction rules for methicillin-resistant Staphylococcus aureus colonization. Infection control and hospital epidemiology : the official journal of the Society of Hospital Epidemiologists of America, 32(1), 9-19. PMID: 21121818
Receive DLTJ Thursday Threads:by E-mailby RSSDelivered by FeedBurner We’re taking a break this week from the HarperCollins e-book story; although the commentary continues from librarians (and a few authors), there hasn’t been anything new (that I’ve seen) from HarperCollins itself. There is still plenty more to look at, though. First up is a report from [...]... Read more »
Reynolds, Carl J., & Wyatt, Jeremy C. (2011) Open Source, Open Standards, and Health Care Information Systems. Journal of Medical Internet Research, 13(1). DOI: 10.2196/jmir.1521
For a company to be as successful as it possibly can be, one aspect of its ethos must be to acknowledge, nurture, and utilize the vast pool of knowledge held by its individual employees and its teams. One company that is apparently exemplary in this regard is South Korean electronics giant, Samsung Electronics, famed for [...]Post from: David Bradley's Sciencetext Tech TalkSamsung CoPS a load of knowledge
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Gyewan Moon. (2011) Effective implementation of Communities of Practices (CoPs) in a knowledge habitat: a case study of Samsung Electronics. Int. J. Services and Operations Management, 8(3), 335-346. info:/
As my readers know, I have built up a CUDA machine on my desktop for few bucks to have lattice QCD at my home. There are a couple of reasons to write this post and the most important of this is that Pedro Bicudo and Nuno Cardoso have got their paper published on an archival [...]... Read more »
Nuno Cardoso, & Pedro Bicudo. (2011) SU(2) Lattice Gauge Theory Simulations on Fermi GPUs. Journal of Computational Physics. info:/10.1016/j.jcp.2011.02.023
Rafael B. Frigori. (2009) Screening masses in quenched (2 1)d Yang-Mills theory: universality from dynamics?. Nuclear Physics B, Volume 833, Issues 1-2, 1 July 2010, Pages 17-27. arXiv: 0912.2871v2
Marco Frasca. (2010) Mapping theorem and Green functions in Yang-Mills theory. PoS(FacesQCD)039, 2011. arXiv: 1011.3643v3
my thoughts about a presentation Jeannette Wing gave, based on articles she has written about Computational Thinking... Read more »
Wing, J. (2008) Computational thinking and thinking about computing. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 366(1881), 3717-3725. DOI: 10.1098/rsta.2008.0118
Here is an experiment to investigate dependence on your “digital dummy”. A digital dummy is any computer, smart phone or other digital device on which you suckle data like a baby. Delete all your so-called “social networks” on LinkedIn, Facebook etc. Being sat in front of a computer is distinctly unsociable. Give your twitter account [...]... Read more »
Flisher, C. (2010) Getting plugged in: An overview of Internet addiction. Journal of Paediatrics and Child Health, 46(10), 557-559. DOI: 10.1111/j.1440-1754.2010.01879.x
Sometimes I envy philosophers. In what other discipline can one write extensive papers based on a random idea, just running with it for pages on end to see how far it will go? Whenever I have to describe an algorithm, there’s always some the nagging about showing time complexity, in Θ(g(x)) if possible, with a [...]... Read more »
Nick Bostrom. (2003) Are you living in a computer simulation?. Philosophical Quarterly, 53(211), 243-255. info:/
I encountered Bickel et al.'s article Remember the Future: Working Memory Training Decreases Delay Discounting Among Stimulant Addicts through another research blogger. It's way outside my area of expertise, but as someone who struggles with excessive delay discounting myself, I found it extremely interesting, so I hope any psychology experts reading this will forgive me for posting my musings on the article.Delay discounting is essentially the degree to which we consider rewards less valuable (or penalties less threatening) if they come later rather than now. It's something we all do to some degree or another, and it's not in principle completely illogical. After all, a delayed reward may never actually come, or may come after we no longer need it, while a delayed penalty may be avoided or may come after we have put ourselves in a position to better withstand it. The problem occurs when we discount future rewards and penalties to the point of being unable to maintain effective long-term resolve to address important life challenges.Read more »... Read more »
Bickel, W., Yi, R., Landes, R., Hill, P., & Baxter, C. (2011) Remember the Future: Working Memory Training Decreases Delay Discounting Among Stimulant Addicts. Biological Psychiatry, 69(3), 260-265. DOI: 10.1016/j.biopsych.2010.08.017
Potential applicants may never apply to work in your organization if your website does nothing to combat stereotypes about industry culture.
Some related articles on Neo-Academic:Desperation Can Cost You a Job
Don’t Use Foursquare To Improve Your Workplace
... Read more »
De Goede, M., Van Vianen, A., & Klehe, U. (2011) Attracting Applicants on the Web: PO fit, industry culture stereotypes, and website design. International Journal of Selection and Assessment, 19(1), 51-61. DOI: 10.1111/j.1468-2389.2010.00534.x
Search engines are big business so it’s perhaps no surprise that the companies running them expend so much energy trying to make their search engine results pages (SERPs) as good as possible. Superficially, this is done for their users, but given that the business models rely on good results generating good advertising revenues it’s also [...]Post from: David Bradley's Sciencetext Tech TalkBuilding a better Google
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Qu, G., & Wu, H. (2011) A weighted-graph-based approach for diversifying search results. International Journal of Knowledge and Web Intelligence, 2(1), 15. DOI: 10.1504/IJKWI.2011.038626
Planners looking to imbue their development with a little old school appeal have a best friend in alleys. The petite thoroughfares tuck bland garage doors behind friendlier looking houses, shrink lots to squeeze in more housing, and leave sidewalks and streets that are free of driveways and curb cuts. Alleys have their charm, I admit. [...]... Read more »
Alexander Garvin. (2002) Residential Suburbs. The American City: What Works, What Doesn't, 305-343. info:other/0071373675
The title of this blog post is the same as that of a seminal paper in computational geometry and VLSI design by Lingas, Pinter, Rivest and Shamir from 1982. The authors present an O(n^4) algorithm to produce a minimum-length rectangular partitioning of a rectilinear polygon without holes.... Read more »
Andrzej Lingas, Ron Y. Pinter, Ronald R. Rivest, & Adi Shamir. (1982) Minimum edge length partitioning of rectilinear polygons. Proceedings of the 20th Allerton Conference on Communication, 53-63. info:/
Want to build an artificial brain? – try building an embodied robot. It makes sense that to embody an AI system implies giving it a body to embody in. A guide to the advantages, challenges and problems of artificial embodied cognition are examined in a recent Frontiers in Psychology article (citation below).
We are given useful [...]... Read more »
Pezzulo, G., Barsalou, L., Cangelosi, A., Fischer, M., McRae, K., & Spivey, M. (2011) The Mechanics of Embodiment: A Dialog on Embodiment and Computational Modeling. Frontiers in Psychology. DOI: 10.3389/fpsyg.2011.00005
In Blink, Malcolm Gladwell discusses how experts do expert things. Essentially they develop granular languages to describe the characteristics of items, or experiences. Food tasters, for example, use a large and rich vocabulary with scores to...
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Sherry ST, Ward M, & Sirotkin K. (1999) dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome research, 9(8), 677-9. PMID: 10447503
1000 Genomes Project Consortium, Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, & McVean GA. (2010) A map of human genome variation from population-scale sequencing. Nature, 467(7319), 1061-73. PMID: 20981092
Let us discuss white roofing our homes, to reduce the urban heat island effect. This in turn could also help reduce global warming. A material can reflect, transmit, absorb and emit visible, infra-red and ultraviolet radiation coming from the Sun. Most materials do all of this in varying degrees so we express these properties as [...]... Read more »
Menon, S., Akbari, H., Mahanama, S., Sednev, I., & Levinson, R. (2010) Radiative forcing and temperature response to changes in urban albedos and associated CO2 offsets . Environmental Research Letters, 5(1), 14005. DOI: 10.1088/1748-9326/5/1/014005
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