Predicting Secondary Structures, Contact Numbers, and Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence by Critical Random Networks

Prediction of one-dimensional protein structures such as secondary structures and contact numbers is useful for the three-dimensional structure prediction and important for the understanding of sequence-structure relationship. Here we present a new machine-learning method, critical random networks (CRNs), for predicting one-dimensional structures, and apply it, with position-specific scoring matrices, to the prediction of secondary structures (SS), contact numbers (CN), and residue-wise contact orders (RWCO). The present method achieves, on average, $Q_3$ accuracy of 77.8% for SS, correlation coefficients of 0.726 and 0.601 for CN and RWCO, respectively. The accuracy of the SS prediction is comparable to other state-of-the-art methods, and that of the CN prediction is a significant improvement over previous methods. We give a detailed formulation of critical random networks-based prediction scheme, and examine the context-dependence of prediction accuracies. In order to study the nonlinear and multi-body effects, we compare the CRNs-based method with a purely linear method based on position-specific scoring matrices. Although not superior to the CRNs-based method, the surprisingly good accuracy achieved by the linear method highlights the difficulty in extracting structural features of higher order from amino acid sequence beyond that provided by the position-specific scoring matrices.Comment: 20 pages, 1 figure, 5 tables; minor revision; accepted for publication in BIOPHYSIC

Characterization of on-road vehicle emissions in the Mexico City Metropolitan Area using a mobile laboratory in chase and fleet average measurement modes during the MCMA-2003 field campaign

A mobile laboratory was used to measure on-road vehicle emission ratios during the MCMA-2003 field campaign held during the spring of 2003 in the Mexico City Metropolitan Area (MCMA). The measured emission ratios represent a sample of emissions of in-use vehicles under real world driving conditions for the MCMA. From the relative amounts of NO_x and selected VOC's sampled, the results indicate that the technique is capable of differentiating among vehicle categories and fuel type in real world driving conditions. Emission ratios for NO_x, NO_y, NH₃, H₂CO, CH₃CHO, and other selected volatile organic compounds (VOCs) are presented for chase sampled vehicles in the form of frequency distributions as well as estimates for the fleet averaged emissions. Our measurements of emission ratios for both CNG and gasoline powered "colectivos" (public transportation buses that are intensively used in the MCMA) indicate that – in a mole per mole basis – have significantly larger NO_x and aldehydes emissions ratios as compared to other sampled vehicles in the MCMA. Similarly, ratios of selected VOCs and NO_y showed a strong dependence on traffic mode. These results are compared with the vehicle emissions inventory for the MCMA, other vehicle emissions measurements in the MCMA, and measurements of on-road emissions in U.S. cities. We estimate NO_x emissions as 100 600±29 200 metric tons per year for light duty gasoline vehicles in the MCMA for 2003. According to these results, annual NO_x emissions estimated in the emissions inventory for this category are within the range of our estimated NO_x annual emissions. Our estimates for motor vehicle emissions of benzene, toluene, formaldehyde, and acetaldehyde in the MCMA indicate these species are present in concentrations higher than previously reported. The high motor vehicle aldehyde emissions may have an impact on the photochemistry of urban areas

Chaos in cosmological Hamiltonians

This paper summarises a numerical investigation which aimed to identify and characterise regular and chaotic behaviour in time-dependent Hamiltonians H(r,p,t) = p^2/2 + U(r,t), with U=R(t)V(r) or U=V[R(t)r], where V(r) is a polynomial in x, y, and/or z, and R = const * t^p is a time-dependent scale factor. When p is not too negative, one can distinguish between regular and chaotic behaviour by determining whether an orbit segment exhibits a sensitive dependence on initial conditions. However, chaotic segments in these potentials differ from chaotic segments in time-independent potentials in that a small initial perturbation will usually exhibit a sub- or super-exponential growth in time. Although not periodic, regular segments typically exhibit simpler shapes, topologies, and Fourier spectra than do chaotic segments. This distinction between regular and chaotic behaviour is not absolute since a single orbit segment can seemingly change from regular to chaotic and visa versa. All these observed phenomena can be understood in terms of a simple theoretical model.Comment: 16 pages LaTeX, including 5 figures, no macros require

Competing for Refugees: A Market-Based Solution to a Humanitarian Crisis

The current refugee crisis demands novel legal solutions, and new ways of summoning the political will to implement them. As a matter of national incentives, the goal must be to design mechanisms that discourage countries of origin from creating refugees, and encourage host countries to welcome them. One way to achieve this would be to recognize that persecuted refugee groups have a financial claim against their countries of origin, and that this claim can be traded to host nations in exchange for acceptance. Modifications to the international apparatus would be necessary, but the basic legal elements of this proposal already exist. In short, international law can and should give refugees a legal asset, give host nations incentives to accept them, and give oppressive countries of origin the bill

Salt intrusion in multi-channel estuaries: a case study in the Mekong Delta, Vietnam

There is a well-tested theory for the computation of salt intrusion in alluvial estuaries that is fully analytical and predictive. The theory uses analytical equations to predict the mixing behaviour of the estuary based on measurable quantities, such as channel topography, river discharge and tidal characteristics. It applies to single-channel topographies and estuaries that demonstrate moderate tidal damping. The Mekong delta is a multi-channel estuary where the tide is damped due to a relatively strong river discharge (in the order of 2000 m³/s), even during the dry season. As a result the Mekong is a strongly riverine estuary. This paper aims to test if the theory can be applied to such a riverine multi-channel estuary, and to see if possible adjustments or generalisations need to be made. The paper presents salt intrusion measurements that were done by moving boat in 2005, to which the salt intrusion model was calibrated. The theory has been expanded to cater for tidal damping. Subsequently the model has been validated with observations made at fixed locations over the years 1998 and 1999. Finally it has been tested whether the Mekong calibration fits the overall predictive equations derived in other estuaries. The test has been successful and led to a slight adjustment of the predictive equation to cater for estuaries that experience a sloping bottom

Fairness, Efficiency and Insider Trading: Deconstructing the Coin of the Realm in the Information Age

Whether and how the federal securities laws should restrict insider trading is one of the most hotly debated topics in the securities law literature. Paradoxically, both the theoretical analysis and the legal rules concerning insider trading remain extraordinarily vague and ill-formed. What is the special character of insider trading that leads to this apparently irresolvable puzzle? In this Article, I argue that there is, in fact, nothing special about insider trading that creates this dilemma, but rather there is something special about the nature of information itself. Accordingly, this theoretical dilemma is not limited to insider trading regulation, but rather pervades all areas of intellectual property law. In this Article, I situate insider trading regulation within the larger body of intellectual property law by discussing three potential allocations of the property right in valuable inside information. First, inside information could be treated as a public resource, meaning that a person in possession of inside information could not legally exploit that advantage for personal profit. Such a regime would forbid some or all insider trading by forcing the disclosure to the marketplace of inside information prior to trading. I argue that regulators should reject this alternative because, despite it\u27s proponents\u27 tendency to justify the rule in terms of fairness, this proposal is unlikely to foster fairness in any meaningful way. Alternatively, the property right in valuable inside information could belong to issuers, as the producers of such information. I argue that regulators should reject this alternative because, despite its proponents? tendency to frame their arguments in terms of promoting informational efficiency, a legal regime treating inside information as the property of the issuer is unlikely to further that goal. In fact, such proposals assume an affirmative answer to a question that is fiercely debated in other areas of intellectual property law: does creating a property right in information producers incentivize additional production to the extent necessary to offset the social costs of excluding others from use of the information? Finally, the property right in valuable inside information could reside with outsider traders (traders who possess inside information, but are neither insiders nor constructive insiders of the issuer). I argue that regulators should pursue this alternative because, although there is no need to encourage issuers to create valuable inside information, the need to encourage the dissemination of such information to the marketplace has been recognized for many years. Accordingly, I propose in this Article a system of federal securities regulation that would permit trading by corporate outsiders who did not receive their information in a tip from an insider or constructive insider. Such a system, I argue, provides the hope of filling in the gaps left by the current disclose or abstain system, by encouraging the reflection of material information in stock market price without disclosure of the actual inside information. At the same time, this proposal avoids the perverse incentives and negative impacts on market efficiency attendant in a system that permits insider trading by corporate employees

Stellar Oscillons

We study the weakly nonlinear evolution of acoustic instability of a plane- parallel polytrope with thermal dissipation in the form of Newton's law of cooling. The most unstable horizontal wavenumbers form a band around zero and this permits the development of a nonlinear pattern theory leading to a complex Ginzburg-Landau equation (CGLE). Numerical solutions for a subcritical, quintic CGLE produce vertically oscillating, localized structures that resemble the oscillons observed in recent experiments of vibrated granular material.Comment: 12 Latex pages using aasms4.sty, 2 postscript figures, submitted to the proceedings of the Florida Workshop in Nonlinear Astrophysics and Physic

Corporate governance compliance and disclosure in the banking sector: using data from Japan

Using regression model this study investigates which characteristics of a bank is associated with the extent of corporate governance disclosure in Japan. The findings suggest that on average 8 banks out of a sample of 46 disclose optimal corporate governance information. The regression model results reveal in general that non-executive directors, cross-ownership, capital adequacy ratio and type of auditors are associated with the extent of corporate governance disclosure. Of these four variables, non-executive directors have a more significant impact on the extent of disclosure contrary to total assets and audit firms of banks in the context of Japan. The findings of this paper are relevant for corporate regulators, professional associations and developers of corporate governance code when designing or updating corporate governance code

The relative importance of competing pathways for the formation of high-molecular-weight peroxides in the ozonolysis of organic aerosol particles

High-molecular-weight (HMW) organic compounds are an important component of atmospheric particles, although their origins, possibly including in situ formation pathways, remain incompletely understood. This study investigates the formation of HMW organic peroxides through reactions involving stabilized Criegee intermediates (SCI's). The model system is methyl oleate (MO) mixed with dioctyl adipate (DOA) and myristic acid (MA) in submicron aerosol particles, and Criegee intermediates are formed by the ozonolysis of the double bond in methyl oleate. An aerosol flow tube coupled to a quadrupole aerosol mass spectrometer (AMS) is employed to determine the relative importance of different HMW organic peroxides following the ozonolysis of different mixing mole fractions of MO in DOA and MA. Possible peroxide products include secondary ozonides (SOZ's), α-acyloxyalkyl hydroperoxides and α-acyloxyalkyl alkyl peroxides (αAAHP-type compounds), diperoxides, and monoperoxide oligomers. Of these, the AMS data identify two SOZ's as major HMW products in the ozonolysis of pure methyl oleate as well as in an inert matrix of DOA to as low as 0.04 mole fraction MO. In comparison, in mixed particles of MO and MA, αAAHP-type compounds form in high yields for MO mole fractions of 0.5 or less, suggesting that SCI's efficiently attack the carboxylic acid group of myristic acid. The reactions of SCI's with carboxylic acid groups to form αAAHP-type compounds therefore compete with those of SCI's with aldehydes to form SOZ's, provided that both types of functionalities are present at significant concentrations. The results therefore suggest that SCI's in atmospheric particles contribute to the transformation of carboxylic acids and other protic groups into HMW organic peroxides