Transposon and deletion mutagenesis of genes involved in perchlorate reduction in Azospira suillum PS.

UnlabelledAlthough much work on the biochemistry of the key enzymes of bacterial perchlorate reduction, chlorite dismutase, and perchlorate reductase has been published, understanding of the molecular mechanisms of this metabolism has been somewhat hampered by the lack of a clear model system amenable to genetic manipulation. Using transposon mutagenesis and clean deletions, genes important for perchlorate reduction in Azospira suillum PS have been identified both inside and outside the previously described perchlorate reduction genomic island (PRI). Transposon mutagenesis identified 18 insertions in 11 genes that completely abrogate growth via reduction of perchlorate but have no phenotype during denitrification. Of the mutants deficient in perchlorate reduction, 14 had insertions that were mapped to eight different genes within the PRI, highlighting its importance in this metabolism. To further explore the role of these genes, we also developed systems for constructing unmarked deletions and for complementing these deletions. Using these tools, every core gene in the PRI was systematically deleted; 8 of the 17 genes conserved in the PRI are essential for perchlorate respiration, including 3 genes that comprise a unique histidine kinase system. Interestingly, the other 9 genes in the PRI are not essential for perchlorate reduction and may thus have unknown functions during this metabolism. We present a model detailing our current understanding of perchlorate reduction that incorporates new concepts about this metabolism.ImportanceAlthough perchlorate is generated naturally in the environment, groundwater contamination is largely a result of industrial activity. Bacteria capable of respiring perchlorate and remediating contaminated water have been isolated, but relatively little is known about the biochemistry and genetics of this process. Here we used two complementary approaches to identify genes involved in perchlorate reduction. Most of these genes are located on a genomic island, which is potentially capable of moving between organisms. Some of the genes identified are known to be directly involved in the metabolism of perchlorate, but other new genes likely regulate the metabolism in response to environmental signals. This work has uncovered new questions about the regulation, energetics, and evolution of perchlorate reduction but also presents the tools to address them

Learning to Generate Images with Perceptual Similarity Metrics

Deep networks are increasingly being applied to problems involving image synthesis, e.g., generating images from textual descriptions and reconstructing an input image from a compact representation. Supervised training of image-synthesis networks typically uses a pixel-wise loss (PL) to indicate the mismatch between a generated image and its corresponding target image. We propose instead to use a loss function that is better calibrated to human perceptual judgments of image quality: the multiscale structural-similarity score (MS-SSIM). Because MS-SSIM is differentiable, it is easily incorporated into gradient-descent learning. We compare the consequences of using MS-SSIM versus PL loss on training deterministic and stochastic autoencoders. For three different architectures, we collected human judgments of the quality of image reconstructions. Observers reliably prefer images synthesized by MS-SSIM-optimized models over those synthesized by PL-optimized models, for two distinct PL measures ($\ell_1$ and $\ell_2$ distances). We also explore the effect of training objective on image encoding and analyze conditions under which perceptually-optimized representations yield better performance on image classification. Finally, we demonstrate the superiority of perceptually-optimized networks for super-resolution imaging. Just as computer vision has advanced through the use of convolutional architectures that mimic the structure of the mammalian visual system, we argue that significant additional advances can be made in modeling images through the use of training objectives that are well aligned to characteristics of human perception

A Case for Redundant Arrays of Hybrid Disks (RAHD)

Hybrid Hard Disk Drive was originally concepted by Samsung, which incorporates a Flash memory in a magnetic disk. The combined ultra-high-density benefits of magnetic storage and the low-power and fast read access of NAND technology inspires us to construct Redundant Arrays of Hybrid Disks (RAHD) to offer a possible alternative to today’s Redundant Arrays of Independent Disks (RAIDs) and/or Massive Arrays of Idle Disks (MAIDs). We first design an internal management system (including Energy-Efficient Control) for hybrid disks. Three traces collected from real systems as well as a synthetic trace are then used to evaluate the RAHD arrays. The trace-driven experimental results show: in the high speed mode, a RAHD outplays the purely-magnetic-disk-based RAIDs by a factor of 2.4–4; in the energy-efficient mode, a RAHD4/5 can save up to 89% of energy at little performance degradationPeer reviewe

¿El tamaño y la orientación del grupo intruso afecta a la distancia de iniciación al vuelo en aves?

Wildlife managers use flight initiation distance (FID), the distance animals flee an approaching predator, to determine set back distances to minimize human impacts on wildlife. FID is typically estimated by a single person; this study examined the effects of intruder number and orientation on FID. Three different group size treatments (solitary person, two people side–by–side, two people one–behind–the–other) were applied to Pied Currawongs (Strepera graculina) and to Crimson Rosellas (Platycerus elegans). Rosellas flushed at significantly greater distances when approached by two people compared to a single person. This effect was not seen in currawongs. Intruder orientation did not influence the FID of either species. Results suggest that intruder number should be better integrated into estimates of set back distance to manage human visitation around sensitive species.Los gestores de la fauna utilizan la distancia de iniciación al vuelo (FID), la distancia a la que los animales huyen cuando se les acerca un depredador, para determinar las distancias de respuesta a fin de minimizar el impacto humano en la fauna. La FID es estimada típicamente por una sola persona; este estudio examinó los efectos del número y de la orientación del intruso en la FID. Se aplicaron tres tratamientos distintos de tamaño del grupo (persona solitaria, dos personas una al lado de la otra, dos personas una detras de la otra) a currawongs cálidos (Strepera graculina) y a pericos elegantes (Platycerus elegans). Los pericos elegantes huían a distancias perceptiblemente mayores cuando se le acercaban dos personas que cuando se le acercaba una sola. Este efecto no fue observado en los currawongs pálidos. La orientación del intruso no influenció en la FID de ninguna especie. Los resultados sugieren que el número de intrusos debería ser considerado en las estimaciones de las distancias de respuesta, para poder gestionar las visitas de personas cerca de especies sensibles

First-Order Reorientation of the Flux-Line Lattice in CaAlSi

The flux line lattice in CaAlSi has been studied by small angle neutron scattering. A well defined hexagonal flux line lattice is seen just above Hc1 in an applied field of only 54 Oe. A 30 degree reorientation of this vortex lattice has been observed in a very low field of 200 Oe. This reorientation transition appears to be of first-order and could be explained by non-local effects. The magnetic field dependence of the form factor is well described by a single penetration depth of 1496(1) angstroms and a single coherence length of 307(1) angstroms at 2 K. At 1.5 K the penetration depth anisotropy is 2.7(1) with the field applied perpendicular to the c axis and agrees with the coherence length anisotropy determined from critical field measurements.Comment: 5 pages including 6 figures, to appear in Physical Review Letter

Contact Interactions and Resonance-Like Physics at Present and Future Colliders from Unparticles

High scale conformal physics can lead to unusual unparticle stuff at our low energies. In this paper we discuss how the exchange of unparticles between Standard Model fields can lead to new contact interaction physics as well as a pseudoresonance-like structure, an unresonance, that might be observable at the Tevatron or LHC in, e.g., the Drell-Yan channel. The specific signatures of this scenario are quite unique and can be used to easily identify this new physics given sufficient integrated luminosity.Comment: 20 pages, 10 figs; minor text changes, ref added; typos correcte

ASTROD, ASTROD I and their gravitational-wave sensitivities

ASTROD (Astrodynamical Space Test of Relativity using Optical Devices) is a mission concept with three spacecraft -- one near L1/L2 point, one with an inner solar orbit and one with an outer solar orbit, ranging coherently with one another using lasers to test relativistic gravity, to measure the solar system and to detect gravitational waves. ASTROD I with one spacecraft ranging optically with ground stations is the first step toward the ASTROD mission. In this paper, we present the ASTROD I payload and accelerometer requirements, discuss the gravitational-wave sensitivities for ASTROD and ASTROD I, and compare them with LISA and radio-wave PDoppler-tracking of spacecraft.Comment: presented to the 5th Edoardo Amaldi Conference (July 6-11, 2003) and submitted to Classical and Quantum Gravit

Electronic signature of the vacancy ordering in NbO (Nb3O3)

We investigated the electronic structure of the vacancy-ordered 4d-transition metal monoxide NbO (Nb3O3) using angle-integrated soft- and hard-x-ray photoelectron spectroscopy as well as ultra-violet angle-resolved photoelectron spectroscopy. We found that density-functional-based band structure calculations can describe the spectral features accurately provided that self-interaction effects are taken into account. In the angle-resolved spectra we were able to identify the so-called vacancy band that characterizes the ordering of the vacancies. This together with the band structure results indicates the important role of the very large inter-Nb-4d hybridization for the formation of the ordered vacancies and the high thermal stability of the ordered structure of niobium monoxide

Status of and performance estimates for QCDOC

QCDOC is a supercomputer designed for high scalability at a low cost per node. We discuss the status of the project and provide performance estimates for large machines obtained from cycle accurate simulation of the QCDOC ASIC.Comment: 3 pages 1 figure. Lattice2002(machines

On the Connection Between Momentum Cutoff and Operator Cutoff Regularizations

Operator cutoff regularization based on the original Schwinger's proper-time formalism is examined. By constructing a regulating smearing function for the proper-time integration, we show how this regularization scheme simulates the usual momentum cutoff prescription yet preserves gauge symmetry even in the presence of the cutoff scales. Similarity between the operator cutoff regularization and the method of higher (covariant) derivatives is also observed. The invariant nature of the operator cutoff regularization makes it a promising tool for exploring the renormalization group flow of gauge theories in the spirit of Wilson-Kadanoff blocking transformation.Comment: 28 pages in plain TeX, no figures. revised and expande