ALBERT

Description: Hydrologic processes during extreme rainfall events are poorly characterized because of the rarity of measurements. Improved understanding of hydrologic controls on natural hazards is needed because of the potential for substantial risk during extreme precipitation events. We present field measurements of the degree of soil saturation and estimates of available soil-water storage during the September 2013 Colorado extreme rainfall event at burned (wildfire in 2010) and unburned hillslopes with north- and south-facing slope aspects. Soil saturation was more strongly correlated with slope aspect than with recent fire history; south-facing hillslopes became fully saturated while north-facing hillslopes did not. Our results suggest multiple explanations for why aspect-dependent hydrologic controls favor saturation development on south-facing slopes, causing reductions in effective stress and triggering of slope failures during extreme rainfall. Aspect-dependent hydrologic behavior may result from (1) a larger gravel and stone fraction, and hence lower soil-water storage capacity, on south-facing slopes, and (2) lower weathered-bedrock permeability on south-facing slopes, because of lower tree density and associated deep roots penetrating bedrock as well as less intense weathering, inhibiting soil drainage.

Description: As one of the few known species in an active phase of intron proliferation, the microcrustacean Daphnia pulex is an especially attractive system for interrogating the gain and loss of introns in natural populations. In this study, we used a comparative population-genomic approach to identify and characterize 90 recently gained introns in this species. Molecular clock analyses indicate that these introns arose between 3.9 x 10 5 and 1.45 x 10 4 years ago, with a spike in intron proliferation approximately 5.2 x 10 4 to 1.22 x 10 5 years ago. Parallel gains at homologous positions contribute to 47.8% (43/90) of discovered new introns. A disproportionally large number of new introns were found in historically isolated populations in Oregon. Nonetheless, derived, intron-bearing alleles were also identified in a wide range of geographic locations, suggesting intron gain and, to a lesser degree, intron loss are important sources of genetic variation in natural populations of Daphnia . A majority (55/90 or 61.1%) of the identified neointrons have associated internal direct repeats with lengths and compositions that are unlikely to occur by chance, suggesting repeated bouts of staggered double-strand breaks (DSBs) during their evolution. Accordingly, internal, staggered DSBs may contribute to a passive trend toward increased length and sequence diversity in nascent introns.

Description: We present ultraviolet, optical and near-infrared observations of the interacting transient SN 2009ip, covering the period from the start of the outburst in 2012 October until the end of the 2012 observing season. The transient reached a peak magnitude of M V  = –17.7 mag, with a total integrated luminosity of 1.9  x 10 49 erg over the period of 2012 August–December. The light curve fades rapidly, dropping by 4.5 mag from the V -band peak in 100 d. The optical and near-infrared spectra are dominated by narrow emission lines with broad electron scattering wings, signalling a dense circumstellar environment, together with multiple components of broad emission and absorption in H and He at velocities in the range 0.5–1.2  x 10 4 km s –1 . We see no evidence for nucleosynthesized material in SN 2009ip, even in late-time pseudo-nebular spectra. We set a limit of 〈0.02 M on the mass of any possible synthesized 56 Ni from the late-time light curve. A simple model for the narrow Balmer lines is presented and used to derive number densities for the circumstellar medium in the range ~10 9 –10 10 cm –3 . Our near-infrared data do not show any excess at longer wavelengths, and we see no other signs of dust formation. Our last data, taken in 2012 December, show that SN 2009ip has spectroscopically evolved to something quite similar to its appearance in late 2009, albeit with higher velocities. It is possible that neither of the eruptive and high-luminosity events of SN 2009ip were induced by a core collapse. We show that the peak and total integrated luminosity can be due to the efficient conversion of kinetic energy from colliding ejecta, and that around 0.05–0.1 M of material moving at 0.5–1  x 10 4 km s –1 could comfortably produce the observed luminosity. We discuss the possibility that these shells were ejected by the pulsational pair instability mechanism, in which case the progenitor star may still exist, and will be observed after the current outburst fades. The long-term monitoring of SN 2009ip, due to its proximity, has given the most extensive data set yet gathered of a high-luminosity interacting transient and its progenitor. It is possible that some purported Type IIn supernovae are in fact analogues of the 2012b event and that pre-explosion outbursts have gone undetected.

Description: Let K be a number field, let ( x ) K ( x ) be a rational function of degree d 〉1, and let α K be a wandering point such that n (α)!=0 for all n 〉0. We prove that if the abc -conjecture holds for K , then for all but finitely many positive integers n , there is a prime p of K such that v p ( n (α))〉0 and v p ( m (α))≤0 for all positive integers m 〈 n . Under appropriate ramification hypotheses, we can replace the condition v p ( n (α))〉0 with the stronger condition v p ( n (α))=1. We prove the same result unconditionally for function fields of characteristic 0 when is not isotrivial.

Description: Cell signaling pathways and metabolic networks are often modeled using ordinary differential equations (ODEs) to represent the production/consumption of molecular species over time. Regardless whether a model is built de novo or adapted from previous models, there is a need to estimate kinetic rate constants based on time-series experimental measurements of molecular abundance. For data-rich cases such as proteomic measurements of all species, spline-based parameter estimation algorithms have been developed to avoid solving all the ODEs explicitly. We report the development of a web server for a spline-based method. Systematic Parameter Estimation for Data-Rich Environments (SPEDRE) estimates reaction rates for biochemical networks. As input, it takes the connectivity of the network and the concentrations of the molecular species at discrete time points. SPEDRE is intended for large sparse networks, such as signaling cascades with many proteins but few reactions per protein. If data are available for all species in the network, it provides global coverage of the parameter space, at low resolution and with approximate accuracy. The output is an optimized value for each reaction rate parameter, accompanied by a range and bin plot. SPEDRE uses tools from COPASI for pre-processing and post-processing. SPEDRE is a free service at http://LTKLab.org/SPEDRE .

Description: Motivation : Computational models of biological signalling networks, based on ordinary differential equations (ODEs), have generated many insights into cellular dynamics, but the model-building process typically requires estimating rate parameters based on experimentally observed concentrations. New proteomic methods can measure concentrations for all molecular species in a pathway; this creates a new opportunity to decompose the optimization of rate parameters. Results : In contrast with conventional parameter estimation methods that minimize the disagreement between simulated and observed concentrations, the SPEDRE method fits spline curves through observed concentration points, estimates derivatives and then matches the derivatives to the production and consumption of each species. This reformulation of the problem permits an extreme decomposition of the high-dimensional optimization into a product of low-dimensional factors, each factor enforcing the equality of one ODE at one time slice. Coarsely discretized solutions to the factors can be computed systematically. Then the discrete solutions are combined using loopy belief propagation, and refined using local optimization. SPEDRE has unique asymptotic behaviour with runtime polynomial in the number of molecules and timepoints, but exponential in the degree of the biochemical network. SPEDRE performance is comparatively evaluated on a novel model of Akt activation dynamics including redox-mediated inactivation of PTEN (phosphatase and tensin homologue). Availability and implementation : Web service, software and supplementary information are available at www.LtkLab.org/SPEDRE Supplementary information: Supplementary data are available at Bioinformatics online. Contact : LisaTK@nus.edu.sg

Description: We show that the reduction to positive characteristic of the multiplier ideal in the sense of de Fernex and Hacon agrees with the test ideal for infinitely many primes, assuming that the variety is numerically ${{\mathbb Q}}$ -Gorenstein. It follows, in particular, that this reduction property holds in dimension 2 for all normal surfaces.