Metabolite essentiality elucidates robustness of Escherichia coli metabolism

Complex biological systems are very robust to genetic and environmental changes at all levels of organization. Many biological functions of Escherichia coli metabolism can be sustained against single-gene or even multiple-gene mutations by using redundant or alternative pathways. Thus, only a limited number of genes have been identified to be lethal to the cell. In this regard, the reaction-centric gene deletion study has a limitation in understanding the metabolic robustness. Here, we report the use of flux-sum, which is the summation of all incoming or outgoing fluxes around a particular metabolite under pseudo-steady state conditions, as a good conserved property for elucidating such robustness of E. coli from the metabolite point of view. The functional behavior, as well as the structural and evolutionary properties of metabolites essential to the cell survival, was investigated by means of a constraints-based flux analysis under perturbed conditions. The essential metabolites are capable of maintaining a steady flux-sum even against severe perturbation by actively redistributing the relevant fluxes. Disrupting the flux-sum maintenance was found to suppress cell growth. This approach of analyzing metabolite essentiality provides insight into cellular robustness and concomitant fragility, which can be used for several applications, including the development of new drugs for treating pathogens.Comment: Supplements available at http://stat.kaist.ac.kr/publication/2007/PJKim_pnas_supplement.pd

Far-ultraviolet Emission-line Morphologies of the Supernova Remnant G65.3+5.7

We present the first far-ultraviolet (FUV) emission-line morphologies of the whole region of the supernova remnant (SNR) G65.3+5.7 using the FIMS/SPEAR data. The morphologies of the C IV {\lambda}{\lambda}1548, 1551, He II {\lambda}1640, and O III] {\lambda}{\lambda}1661, 1666 lines appear to be closely related to the optical and/or soft X-ray images obtained in previous studies. Dramatic differences between the C IV morphology and the optical [O III] {\lambda}5007 image provide clues to a large resonant-scattering region and a foreground dust cloud. The FUV morphologies also reveal the overall distribution of various shocks in different evolutionary phases and an evolutionary asymmetry between the east and the southwest sides in terms of Galactic coordinates, possibly due to a Galactic density gradient in the global scale. The relative X-ray luminosity of G65.3+5.7 to C IV luminosity is considerably lower than those of the Cygnus Loop and the Vela SNRs. This implies that G65.3+5.7 has almost evolved into the radiative stage in the global sense and supports the previous proposal that G65.3+5.7 has lost its bright X-ray shell and become a member of mixed-morphology SNRs as it has evolved beyond the adiabatic stage.Comment: 6 pages, 3 figures, accepted for publication in The Ap

Fast, Interactive Worst-Case Execution Time Analysis With Back-Annotation

Abstract—For hard real-time systems, static code analysis is needed to derive a safe bound on the worst-case execution time (WCET). Virtually all prior work has focused on the accuracy of WCET analysis without regard to the speed of analysis. The resulting algorithms are often too slow to be integrated into the development cycle, requiring WCET analysis to be postponed until a final verification phase. In this paper we propose interactive WCET analysis as a new method to provide near-instantaneous WCET feedback to the developer during software programming. We show that interactive WCET analysis is feasible using tree-based WCET calculation. The feedback is realized with a plugin for the Java editor jEdit, where the WCET values are back-annotated to the Java source at the statement level. Comparison of this treebased approach with the implicit path enumeration technique (IPET) shows that tree-based analysis scales better with respect to program size and gives similar WCET values. Index Terms—Real time systems, performance analysis, software performance, software reliability, software algorithms, safety I

Systematic effects of carbon doping on the superconducting properties of Mg(B1−x_{1-x}Cx_x)2_2

The upper critical field, $H_{c2}$, of Mg(B$_{1-x}$C$_x$)$_2$ has been measured in order to probe the maximum magnetic field range for superconductivity that can be attained by C doping. Carbon doped boron filaments are prepared by CVD techniques, and then these fibers are then exposed to Mg vapor to form the superconducting compound. The transition temperatures are depressed about $1 K/$ C and $H_{c2}(T=0)$ rises at about $5 T/$ C. This means that 3.5% C will depress $T_c$ from $39.2 K$ to $36.2 K$ and raise $H_{c2}(T=0)$ from $16.0 T$ to $32.5 T$. Higher fields are probably attainable in the region of 5% C to 7% C. These rises in $H_{c2}$ are accompanied by a rise in resistivity at $40 K$ from about $0.5 \mu \Omega cm$ to about $10 \mu \Omega cm$. Given that the samples are polycrystalline wire segments, the experimentally determined $H_{c2}(T)$ curves represent the upper $H_{c2}(T)$ manifold associated with $H\perp c$

DJ-1 interacts with and regulates paraoxonase-2, an enzyme critical for neuronal survival in response to oxidative stress.

Loss-of-function mutations in DJ-1 (PARK7) gene account for about 1% of all familial Parkinson's disease (PD). While its physiological function(s) are not completely clear, DJ-1 protects neurons against oxidative stress in both in vitro and in vivo models of PD. The molecular mechanism(s) through which DJ-1 alleviates oxidative stress-mediated damage remains elusive. In this study, we identified Paraoxonase-2 (PON2) as an interacting target of DJ-1. PON2 activity is elevated in response to oxidative stress and DJ-1 is crucial for this response. Importantly, we showed that PON2 deficiency hypersensitizes neurons to oxidative stress induced by MPP+ (1-methyl-4-phenylpyridinium). Conversely, over-expression of PON2 protects neurons in this death paradigm. Interestingly, PON2 effectively rescues DJ-1 deficiency-mediated hypersensitivity to oxidative stress. Taken together, our data suggest a model by which DJ-1 exerts its antioxidant activities, at least partly through regulation of PON2

The Parallel Complexity of Growth Models

This paper investigates the parallel complexity of several non-equilibrium growth models. Invasion percolation, Eden growth, ballistic deposition and solid-on-solid growth are all seemingly highly sequential processes that yield self-similar or self-affine random clusters. Nonetheless, we present fast parallel randomized algorithms for generating these clusters. The running times of the algorithms scale as $O(\log^2 N)$, where $N$ is the system size, and the number of processors required scale as a polynomial in $N$. The algorithms are based on fast parallel procedures for finding minimum weight paths; they illuminate the close connection between growth models and self-avoiding paths in random environments. In addition to their potential practical value, our algorithms serve to classify these growth models as less complex than other growth models, such as diffusion-limited aggregation, for which fast parallel algorithms probably do not exist.Comment: 20 pages, latex, submitted to J. Stat. Phys., UNH-TR94-0

Radiation Performance of 1 Gbit DDR SDRAMs Fabricated in the 90 nm CMOS Technology Node

We present Single Event Effect (SEE) and Total Ionizing Dose (TID) data for 1 Gbit DDR SDRAMs (90 nm CMOS technology) as well as comparing this data with earlier technology nodes from the same manufacturer

Multi-Exciton Spectroscopy of a Single Self Assembled Quantum Dot

We apply low temperature confocal optical microscopy to spatially resolve, and spectroscopically study a single self assembled quantum dot. By comparing the emission spectra obtained at various excitation levels to a theoretical many body model, we show that: Single exciton radiative recombination is very weak. Sharp spectral lines are due to optical transitions between confined multiexcitonic states among which excitons thermalize within their lifetime. Once these few states are fully occupied, broad bands appear due to transitions between states which contain continuum electrons.Comment: 12 pages, 4 figures, submitted for publication on Jan,28 199

Antiferromagnetism and Superconductivity in CeRhIn5_5

We discuss recent results on the heavy fermion superconductor CeRhIn$_5$ which presents ideal conditions to study the strong coupling between the suppression of antiferromagnetic order and the appearance of unconventional superconductivity. The appearance of superconductivity as function of pressure is strongly connected to the suppression of the magnetic order. Under magnetic field, the re-entrance of magnetic order inside the superconducting state shows that antiferromagnetism nucleates in the vortex cores. The suppression of antiferromagnetism in CeRhIn$_5$ by Sn doping is compared to that under hydrostatic pressure.Comment: 6 pages, 8 figures, to be published in Proc. Int. Conf. Heavy Electrons (ICHE2010) J. Phys. Soc. Jpn. 80 (2011