Sensitivity analysis and parameter estimation for distributed hydrological modeling: potential of variational methods

Variational methods are widely used for the analysis and control of computationally intensive spatially distributed systems. In particular, the adjoint state method enables a very efficient calculation of the derivatives of an objective function (response function to be analysed or cost function to be optimised) with respect to model inputs. In this contribution, it is shown that the potential of variational methods for distributed catchment scale hydrology should be considered. A distributed flash flood model, coupling kinematic wave overland flow and Green Ampt infiltration, is applied to a small catchment of the Thoré basin and used as a relatively simple (synthetic observations) but didactic application case. It is shown that forward and adjoint sensitivity analysis provide a local but extensive insight on the relation between the assigned model parameters and the simulated hydrological response. Spatially distributed parameter sensitivities can be obtained for a very modest calculation effort (~6 times the computing time of a single model run) and the singular value decomposition (SVD) of the Jacobian matrix provides an interesting perspective for the analysis of the rainfall-runoff relation. For the estimation of model parameters, adjoint-based derivatives were found exceedingly efficient in driving a bound-constrained quasi-Newton algorithm. The reference parameter set is retrieved independently from the optimization initial condition when the very common dimension reduction strategy (i.e. scalar multipliers) is adopted. Furthermore, the sensitivity analysis results suggest that most of the variability in this high-dimensional parameter space can be captured with a few orthogonal directions. A parametrization based on the SVD leading singular vectors was found very promising but should be combined with another regularization strategy in order to prevent overfitting

System Synchronizes Recordings from Separated Video Cameras

A system of electronic hardware and software for synchronizing recordings from multiple, physically separated video cameras is being developed, primarily for use in multiple-look-angle video production. The system, the time code used in the system, and the underlying method of synchronization upon which the design of the system is based are denoted generally by the term "Geo-TimeCode(TradeMark)." The system is embodied mostly in compact, lightweight, portable units (see figure) denoted video time-code units (VTUs) - one VTU for each video camera. The system is scalable in that any number of camera recordings can be synchronized. The estimated retail price per unit would be about $350 (in 2006 dollars). The need for this or another synchronization system external to video cameras arises because most video cameras do not include internal means for maintaining synchronization with other video cameras. Unlike prior video-camera-synchronization systems, this system does not depend on continuous cable or radio links between cameras (however, it does depend on occasional cable links lasting a few seconds). Also, whereas the time codes used in prior video-camera-synchronization systems typically repeat after 24 hours, the time code used in this system does not repeat for slightly more than 136 years; hence, this system is much better suited for long-term deployment of multiple cameras

Sensitivity Analysis and Parameter Estimation for Distributed Hydrological Modeling: Potential of Variational Methods

Variational methods are widely used for the analysis and control of computationally intensive spatially distributed systems. In particular, the adjoint state method enables a very efficient calculation of the derivatives of an objective function (response function to be analysed or cost function to be optimised) with respect to model inputs. In this contribution, it is shown that the potential of variational methods for distributed catchment scale hydrology should be considered. A distributed flash flood model, coupling kinematic wave overland flow and Green Ampt infiltration, is applied to a small catchment of the Thor´e basin and used as a relatively simple (synthetic observations) but didactic application case. It is shown that forward and adjoint sensitivity analysis provide a local but extensive insight on the relation between the assigned model parameters and the simulated hydrological response. Spatially distributed parameter sensitivities can be obtained for a very modest calculation effort (6 times the computing time of a single model run) and the singular value decomposition (SVD) of the Jacobian matrix provides an interesting perspective for the analysis of the rainfall-runoff relation. For the estimation of model parameters, adjoint-based derivatives were found exceedingly efficient in driving a bound-constrained quasi-Newton algorithm. The reference parameter set is retrieved independently from the optimization initial condition when the very common dimension reduction strategy (i.e. scalar multipliers) is adopted. Furthermore, the sensitivity analysis results suggest that most of the variability in this high-dimensional parameter space can be captured with a few orthogonal directions. A parametrization based on the SVD leading singular vectors was found very promising but should be combined with another regularization strategy in order to prevent overfitting.JRC.G.9-Econometrics and applied statistic

Functional plasticity of antibacterial EndoU toxins.

Bacteria use several different secretion systems to deliver toxic EndoU ribonucleases into neighboring cells. Here, we present the first structure of a prokaryotic EndoU toxin in complex with its cognate immunity protein. The contact-dependent growth inhibition toxin CdiA-CTSTECO31 from Escherichia coli STEC_O31 adopts the eukaryotic EndoU fold and shares greatest structural homology with the nuclease domain of coronavirus Nsp15. The toxin contains a canonical His-His-Lys catalytic triad in the same arrangement as eukaryotic EndoU domains, but lacks the uridylate-specific ribonuclease activity that characterizes the superfamily. Comparative sequence analysis indicates that bacterial EndoU domains segregate into at least three major clades based on structural variations in the N-terminal subdomain. Representative EndoU nucleases from clades I and II degrade tRNA molecules with little specificity. In contrast, CdiA-CTSTECO31 and other clade III toxins are specific anticodon nucleases that cleave tRNAGlu between nucleotides C37 and m2 A38. These findings suggest that the EndoU fold is a versatile scaffold for the evolution of novel substrate specificities. Such functional plasticity may account for the widespread use of EndoU effectors by diverse inter-bacterial toxin delivery systems

A General Formula for Black Hole Gravitational Wave Kicks

Although the gravitational wave kick velocity in the orbital plane of coalescing black holes has been understood for some time, apparently conflicting formulae have been proposed for the dominant out-of-plane kick, each a good fit to different data sets. This is important to resolve because it is only the out-of-plane kicks that can reach more than 500 km/s and can thus eject merged remnants from galaxies. Using a different ansatz for the out-of-plane kick, we show that we can fit almost all existing data to better than 5 %. This is good enough for any astrophysical calculation, and shows that the previous apparent conflict was only because the two data sets explored different aspects of the kick parameter space.Comment: 14 pages

Effects of Temperature on Emergence and Seasonality of West Nile Virus in California

Temperature has played a critical role in the spatiotemporal dynamics of West Nile virus transmission throughout California from its introduction in 2003 through establishment by 2009. We compared two novel mechanistic measures of transmission risk, the temperature-dependent ratio of virus extrinsic incubation period to the mosquito gonotrophic period (BT), and the fundamental reproductive ratio (R0) based on a mathematical model, to analyze spatiotemporal patterns of receptivity to viral amplification. Maps of BT and R0 were created at 20-km scale and compared throughout California to seroconversions in sentinel chicken flocks at half-month intervals. Overall, estimates of BT and R0 agreed with intensity of transmission measured by the frequency of sentinel chicken seroconversions. Mechanistic measures such as these are important for understanding how temperature affects the spatiotemporal dynamics of West Nile virus transmission and for delineating risk estimates useful to inform vector control agency intervention decisions and communicate outbreak potential

On the Perturbative Nature of Color Superconductivity

Color superconductivity is a possible phase of high density QCD. We present a systematic derivation of the transition temperature, T_C, from the QCD Lagrangian through study of the di-quark proper vertex. With this approach, we confirm the dependence of T_C on the coupling g, namely $T_C \sim \mu g^{-5} e^{-\kappa/g}$, previously obtained from the one-gluon exchange approximation in the superconducting phase. The diagrammatic approach we employ allows us to examine the perturbative expansion of the vertex and the propagators. We find an additional O(1) contribution to the prefactor of the exponential from the one-loop quark self energy and that the other one-loop radiative contributions and the two gluon exchange vertex contribution are subleading.Comment: 13 pages, 3 figures, revtex, details and discussion expande

Exploratory analysis of genomic segmentations with Segtools

<p>Abstract</p> <p>Background</p> <p>As genome-wide experiments and annotations become more prevalent, researchers increasingly require tools to help interpret data at this scale. Many functional genomics experiments involve partitioning the genome into labeled segments, such that segments sharing the same label exhibit one or more biochemical or functional traits. For example, a collection of ChlP-seq experiments yields a compendium of peaks, each labeled with one or more associated DNA-binding proteins. Similarly, manually or automatically generated annotations of functional genomic elements, including <it>cis</it>-regulatory modules and protein-coding or RNA genes, can also be summarized as genomic segmentations.</p> <p>Results</p> <p>We present a software toolkit called <it>Segtools </it>that simplifies and automates the exploration of genomic segmentations. The software operates as a series of interacting tools, each of which provides one mode of summarization. These various tools can be pipelined and summarized in a single HTML page. We describe the Segtools toolkit and demonstrate its use in interpreting a collection of human histone modification data sets and <it>Plasmodium falciparum </it>local chromatin structure data sets.</p> <p>Conclusions</p> <p>Segtools provides a convenient, powerful means of interpreting a genomic segmentation.</p