Difficulties in Testing for Covarion-Like Properties of Sequences under the Confounding Influence of Changing Proportions of Variable Sites

The covarion (COV)-like properties of sequences are poorly described and their impact on phylogenetic analyses poorly understood. We demonstrate using simulations that, under an evolutionary model where the proportion of variable sites changes in nonadjacent lineages, log likelihood values for rates across site (RAS) and COV models become similar, making models difficult to distinguish. Further, although COV and RAS models provide a great improvement in likelihood scores over a homogeneous model with these simulated data, reconstruction accuracy of tree building is low, suggesting caution when it is suspected that proportions of variable sites differ in different evolutionary lineages. We study the performance of a recently developed contingency test that detects the presence of COV-type evolution modified for protein data. We report that if proportions of variable sites (pvar) change in a lineage-specific manner such that their distributions in different lineages become sufficiently nonoverlapping, then the contingency test can incorrectly suggest a homogeneous model. Also of concern is the possibility of different proportions of variable sites between the groups being studied. In a study of chloroplast proteins, interpretation of the test is found to be susceptible to different partitioning of taxon groups, making the test very subjective in its implementation. Extreme intergroup differences in the extent of divergence and difference in proportions of variable sites could be contributing to this effect

Spectral and Spin Measurement of Two Small and Fast-Rotating Near-Earth Asteroids

In May 2012 two asteroids made near-miss "grazing" passes at distances of a few Earth-radii: 2012 KP24 passed at nine Earth-radii and 2012 KT42 at only three Earth-radii. The latter passed inside the orbital distance of geosynchronous satellites. From spectral and imaging measurements using NASA's 3-m Infrared Telescope Facility (IRTF), we deduce taxonomic, rotational, and physical properties. Their spectral characteristics are somewhat atypical among near-Earth asteroids: C-complex for 2012 KP24 and B-type for 2012 KT42, from which we interpret the albedos of both asteroids to be between 0.10 and 0.15 and effective diameters of 20+-2 and 6+-1 meters, respectively. Among B-type asteroids, the spectrum of 2012 KT42 is most similar to 3200 Phaethon and 4015 Wilson-Harrington. Not only are these among the smallest asteroids spectrally measured, we also find they are among the fastest-spinning: 2012 KP24 completes a rotation in 2.5008+-0.0006 minutes and 2012 KT42 rotates in 3.634+-0.001 minutes.Comment: 4 pages, 3 figures, accepted for publication in Icaru

Seasonal, Taxonomic, and Local Habitat Components of Bird-window Collisions on an Urban University Campus in Cleveland, OH

Author Institution: Department of Biological, Geological & Environmental Sciences, Cleveland State UniversityAuthor Institution: Department of Ornithology, Cleveland Museum of Natural HistoryMigrating birds congregate near the shores of Lake Erie during migration and may be funneled through small green spaces within the urban matrix of Great Lake coastal cities, where they are at risk of higher mortality from manmade structures. Bird deaths due to window collisions were assessed amongst a complex of low-rise buildings (<30 m) on a university campus in Cleveland, OH. A 1.8 km route was surveyed three times per week during a 12-month period. Deaths were tested against null hypotheses that season, taxonomy, and building attributes had no significant relationship with avian mortality. We recovered 271 dead birds of 50 species, all of which were consistent with regional bird lists and Neotropical-Nearctic and North American migrants through Ohio. Deaths occurred non-randomly by week, month, and migratory status with 90 percent of deaths occurring during spring and fall migrations. Consequently, migrants (warblers: 34 percent of species richness, 30 percent of deaths; sparrows: 14 percent of richness, 35 percent of deaths) were observed nine times more frequently than residents. Neotropical-Nearctic migrant species outnumbered North American migrant species. Although there was no statistical difference between the compass direction of a building facade and the number of deaths, deaths were not randomly distributed among campus buildings. Rather, significantly more deaths occurred at facades with higher percentages of glass. The presence of trees within 5 m of a window and the reflection of trees in windows were also associated with a greater risk of fatality. A better understanding of the factors associated with bird-window collisions is a pressing issue in the conservation of migratory birds

Liver function as an engineering system

Process Systems Engineering has tackled a wide range of problems including manufacturing, the environment, and advanced materials design. Here we discuss how tools can be deployed to tackle medical problems which involve complex chemical transformations and spatial phenomena looking in particular at the liver system, the body's chemical factory. We show how an existing model has been developed to model distributed behavior necessary to predict the behavior of drugs for treating liver disease. The model has been used to predict the effects of suppression of de novo lipogenesis, stimulation of β-oxidation and a combination of the two. A reduced model has also been used to explore the prediction of behavior of hormones in the blood stream controlling glucose levels to ensure that levels are kept within safe bounds using interval methods. The predictions are made resulting from uncertainty in two key parameters with oscillating input resulting from regular feeding

Feasibility study of the solar scientific instruments for Spacelab/Orbiter

The feasibility and economics of mounting and operating a set of solar scientific instruments in the backup Skylab Apollo Telescope Mount (ATM) hardware was evaluated. The instruments used as the study test payload and integrated into the ATM were: the Solar EUV Telescope/Spectrometer; the Solar Active Region Observing Telescope; and the Lyman Alpha White Light Coronagraph. The backup ATM hardware consists of a central cruciform structure, called the "SPAR', a "Sun End Canister' and a "Multiple Docking Adapter End Canister'. Basically, the ATM hardware and software provides a structural interface for the instruments; a closely controlled thermal environment; and a very accurate attitude and pointing control capability. The hardware is an identical set to the hardware that flow on Skylab

Electrostatic Patch Effect in Cylindrical Geometry. I. Potential and Energy between Slightly Non-Coaxial Cylinders

We study the effect of any uneven voltage distribution on two close cylindrical conductors with parallel axes that are slightly shifted in the radial and by any length in the axial direction. The investigation is especially motivated by certain precision measurements, such as the Satellite Test of the Equivalence Principle (STEP). By energy conservation, the force can be found as the energy gradient in the vector of the shift, which requires determining potential distribution and energy in the gap. The boundary value problem for the potential is solved, and energy is thus found to the second order in the small transverse shift, and to lowest order in the gap to cylinder radius ratio. The energy consists of three parts: the usual capacitor part due to the uniform potential difference, the one coming from the interaction between the voltage patches and the uniform voltage difference, and the energy of patch interaction, entirely independent of the uniform voltage. Patch effect forces and torques in the cylindrical configuration are derived and analyzed in the next two parts of this work.Comment: 26 pages, 1 Figure. Submitted to Classical and Quantum Gravit

Preserving entanglement under decoherence and sandwiching all separable states

Every entangled state can be perturbed, for instance by decoherence, and stay entangled. For a large class of pure entangled states, we show how large the perturbation can be. Our class includes all pure bipartite and all maximally entangled states. For an entangled state, E, the constucted neighborhood of entangled states is the region outside two parallel hyperplanes, which sandwich the set of all separable states. The states for which these neighborhoods are largest are the maximally entangled ones. As the number of particles, or the dimensions of the Hilbert spaces for two of the particles increases, the distance between two of the hyperplanes which sandwich the separable states goes to zero. It is easy to decide if a state Q is in the neighborhood of entangled states we construct for an entangled state E. One merely has to check if the trace of EQ is greater than a constant which depends upon E and which we determine.Comment: Corrected first author's e-mail address. All the rest remains unchange

On the Numerical Study of the Complexity and Fractal Dimension of CMB Anisotropies

We consider the problem of numerical computation of the Kolmogorov complexity and the fractal dimension of the anisotropy spots of Cosmic Microwave Background (CMB) radiation. Namely, we describe an algorithm of estimation of the complexity of spots given by certain pixel configuration on a grid and represent the results of computations for a series of structures of different complexity. Thus, we demonstrate the calculability of such an abstract descriptor as the Kolmogorov complexity for CMB digitized maps. The correlation of complexity of the anisotropy spots with their fractal dimension is revealed as well. This technique can be especially important while analyzing the data of the forthcoming space experiments.Comment: LATEX, 3 figure

Nonlinear software sensor for monitoring genetic regulation processes with noise and modeling errors

Nonlinear control techniques by means of a software sensor that are commonly used in chemical engineering could be also applied to genetic regulation processes. We provide here a realistic formulation of this procedure by introducing an additive white Gaussian noise, which is usually found in experimental data. Besides, we include model errors, meaning that we assume we do not know the nonlinear regulation function of the process. In order to illustrate this procedure, we employ the Goodwin dynamics of the concentrations [B.C. Goodwin, Temporal Oscillations in Cells, (Academic Press, New York, 1963)] in the simple form recently applied to single gene systems and some operon cases [H. De Jong, J. Comp. Biol. 9, 67 (2002)], which involves the dynamics of the mRNA, given protein, and metabolite concentrations. Further, we present results for a three gene case in co-regulated sets of transcription units as they occur in prokaryotes. However, instead of considering their full dynamics, we use only the data of the metabolites and a designed software sensor. We also show, more generally, that it is possible to rebuild the complete set of nonmeasured concentrations despite the uncertainties in the regulation function or, even more, in the case of not knowing the mRNA dynamics. In addition, the rebuilding of concentrations is not affected by the perturbation due to the additive white Gaussian noise and also we managed to filter the noisy output of the biological systemComment: 21 pages, 7 figures; also selected in vjbio of August 2005; this version corrects a misorder in the last three references of the published versio