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"We describe a search for primitive trinomials of high degree and its interaction with the Great Internet Mersenne prime search (GIMPS). The search is complete for trinomials whose degree is the exponent of a Mersenne prime, for all 47 currently known Mersenne primes."
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"Investigating the relation between the structure and behavior of complex biological networks often involves posing the following two questions: Is a hypothesized structure of a regulatory network consistent with the observed behavior? And can a proposed structure generate a desired behavior? Answering these questions presupposes that we are able to test the compatibility of network structure and behavior. We cast these questions into a parameter search problem for qualitative models of regulatory networks…. We develop a method based on symbolic model checking that avoids enumerating all possible parametrizations, and show that this method performs well on real biological problems, using the IRMA synthetic network and benchmark experimental data sets. We test the consistency between the IRMA network structure and the time-series data, and search for parameter modifications that would improve the robustness of the external control of the system behavior."
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"All rolled into one big ball, the biggest thing to take away from this post is to find the job that will make you happy. These are all just things that I have that make me happy, so maybe they’ll help you find that great place to work. Because of all these reasons and probably some others I’ll think of after publishing this post, thoughtbot has my heart. Barring anything very unexpected, and until I’ve gotten sick of design, you’ll find me here at my desk inside thoughtbot HQ. I can only hope you have the same luxury or soon find a place that makes you just as happy."
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"Software projects are displayed by Gource as an animated tree with the root directory of the project at its centre. Directories appear as branches with files as leaves. Developers can be seen working on the tree at the times they contributed to the project."
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"As a web developer you really have no excuse for not knowing everything there is to know about URLs, there is just not that much to them. But, I have found that even experienced developers often have some glaring holes in their knowledge of URLs. So, I thought I would do a quick tour of everything that every developer should know about URLs. Strap yourself in – this won't take long

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"Our findings suggest that in ravens, bystanders may console victims with whom they share a valuable relationship, thus alleviating the victims' post-conflict distress. Conversely victims may affiliate with bystanders after a conflict in order to reduce the likelihood of renewed aggression. These results stress the importance of relationship quality in determining the occurrence and function of post-conflict interactions, and show that ravens may be sensitive to the emotions of others."
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"The occurrence of the nonzero leftmost digit, i.e., 1, 2, …, 9, of numbers from many real world sources is not uniformly distributed as one might naively expect, but instead, the nature favors smaller ones according to a logarithmic distribution, named Benford's law. We investigate three kinds of widely used physical statistics, i.e., the Boltzmann-Gibbs (BG) distribution, the Fermi-Dirac (FD) distribution, and the Bose-Einstein (BE) distribution, and find that the BG and FD distributions both fluctuate slightly in a periodic manner around the Benford distribution with respect to the temperature of the system, while the BE distribution conforms to it exactly whatever the temperature is. Thus the Benford's law seems to present a general pattern for physical statistics and might be even more fundamental and profound in nature. Furthermore, various elegant properties of Benford's law, especially the mantissa distribution of data sets, are discussed."
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"As the study of information processing in living cells moves from individual pathways to complex regulatory networks, mathematical models and simulation become indispensable tools for analyzing the complex behavior of such networks and can provide deep insights into the functioning of cells. The dynamics of gene expression, for example, can be modeled with Boolean networks (BNs). These are mathematical models of low complexity, but have the advantage of being able to capture essential properties of gene-regulatory networks. However, current implementations of BNs only focus on different sub-aspects of this model and do not allow for a seamless integration into existing preprocessing pipelines. RESULTS: BoolNet efficiently integrates methods for synchronous, asynchronous and probabilistic BNs. This includes reconstructing networks from time series, generating random networks, robustness analysis via perturbation, Markov chain simulations [&c]"
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"What is it that mathematicians accomplish?"
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"Computational Complexity studies the power and limitations of efficient computation. So is efficient computation purely an abstract mathematical object or is it trying to model a real world phenomenon? I would argue the latter. Efficient computation occurs not just in computers but in biological systems, physical systems, chemical systems, economic systems and much more. Physics focuses on the "what", computational complexity on the "how"."
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"The underlying reality of a succession of interbreeding populations is a vastly complicated network N. Since Darwin, species trees have been used as a simplified description of the relationships which summarize the overly complicated network N. Recent evidence of hybridization and lateral gene transfer, however, suggest that there are situations where trees are inadequate. Consequently it is important to determine properties that characterize networks closely related to N and possibly more complicated than trees but lacking the full complexity of N."
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"Pay attention to the path the steepest descent takes until finding the optimum at x = 1 and y = 1. It is said that an evolution strategy would follow a similar path if its population could be infinite. Since, so far, there are no real computers with infinite memory, such assumption cannot be verified in the real world."
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"This is a guide to the R programming language."
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"Microbial ecosystems have been widely used in industrial production, but the inter-relationships of organisms within them haven't been completely clarified due to complex composition and structure of natural microbial ecosystems. So it is challenging for ecologists to get deep insights on how ecosystems function and interplay with surrounding environments. But the recent progresses in synthetic biology show that construction of artificial ecosystems where relationships of species are comparatively clear could help us further uncover the meadow of those tiny societies. By using two quorum-sensing signal transduction circuits, this research designed, simulated and constructed a synthetic ecosystem where various population dynamics formed by changing environmental factors."
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"While some of the anti-fraud remedies of the securities laws still apply in 144A transactions, these have been watered down in recent years by Congressional action and judicial interpretation. In a series of opinions authored first by Justice Powell and then by Justice Kennedy, the Supreme Court has steadily scaled back the scope of the securities laws. Opinions by Justice Kennedy, in particular, limited the impact of anti-fraud protections as well as the ability of investors to sue gatekeepers who play a significant role in preparing offerings."
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"Now folks, it's pretty revealing when lobbyists have become so accustomed to their privileged access and backroom dealings with politicians –as went on in regards to Cheney's energy discussions, and each of the Bush tax cuts drawn up by a secretive group of GOP without any sunlight (or bipartisansip), for example, and too much with the health care bill as well–that they don't even bother to hide their scorn for the public's views and their hopes for getting that back room deal to go their way. No wonder Wall Street honchos have been so brazenly arrogant about their "entitlement" to bonuses, their rights to continue proprietary trading and hedge funds and derivatives desks–"doing God's work" says Goldman CEO Blankfein–when they are merely running a casino market to strip as much gold off suckers as possible with their "financial innovations" like synthetic CDOs that made the market many times more volatile than "real" securitizations…"
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"Since the microscope has no lenses, it does not magnify the images. Yet it is able to gain resolution just under two micrometers, and makes images that are about as clear as those made by a conventional 40X microscope. This is made possible by image-processing software. "We compensate for everything in the digital regime," says Ozcan. As light from the LED passes through a given type of cell, the light bends or diffracts in a characteristic way depending on the cell's size, shape, and refractive index. Data picked up by the light-sensing chip is carried to a cell phone for analysis. Ozcan has previously demonstrated running software on the phone that consults a library of diffraction signatures characteristic of particular cell types and bacteria to identify and count the cells in the sample."
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"A recent study by researchers in Yale and published in PNAS shows that there are significant differences between the network topologies of living systems like E. coli and complex pieces of software such as the Linux Operating System."