Transient dynamics of a superconducting nonlinear oscillator

We investigate the transient dynamics of a lumped-element oscillator based on a dc superconducting quantum interference device (SQUID). The SQUID is shunted with a capacitor forming a nonlinear oscillator with resonance frequency in the range of several GHz. The resonance frequency is varied by tuning the Josephson inductance of the SQUID with on-chip flux lines. We report measurements of decaying oscillations in the time domain following a brief excitation with a microwave pulse. The nonlinearity of the SQUID oscillator is probed by observing the ringdown response for different excitation amplitudes while the SQUID potential is varied by adjusting the flux bias. Simulations are performed on a model circuit by numerically solving the corresponding Langevin equations incorporating the SQUID potential at the experimental temperature and using parameters obtained from separate measurements characterizing the SQUID oscillator. Simulations are in good agreement with the experimental observations of the ringdowns as a function of applied magnetic flux and pulse amplitude. We observe a crossover between the occurrence of ringdowns close to resonance and adiabatic following at larger detuning from the resonance. We also discuss the occurrence of phase jumps at large amplitude drive. Finally, we briefly outline prospects for a readout scheme for superconducting flux qubits based on the discrimination between ringdown signals for different levels of magnetic flux coupled to the SQUID.Comment: 15 pages, 9 figure

Lymphotoxins and cytomegalovirus cooperatively induce interferon-beta, establishing host-virus détente

Tumor necrosis factor (TNF)-related cytokines regulate cell death and survival and provide strong selective pressures for viruses, such as cytomegalovirus (CMV), to evolve counterstrategies in order to persist in immune-competent hosts. Signaling by the lymphotoxin (LT)-β receptor or TNF receptor-1, but not Fas or TRAIL receptors, inhibits the cytopathicity and replication of human CMV by a nonapoptotic, reversible process that requires nuclear factor κB (NF-κB)-dependent induction of interferon-β (IFN-β). Efficient induction of IFN-β requires virus infection and LT signaling, demonstrating the need for both host and viral factors in the curtailment of viral replication without cellular elimination. LTα-deficient mice and LTβR-Fc transgenic mice were profoundly susceptible to murine CMV infection. Together, these results reveal an essential and conserved role for LTs in establishing host defense to CMV

Study of several factors affecting crew escape trajectories from the Space Shuttle Orbiter at low-subsonic speeds

Factors affecting the bailout characteristics from the space shuttle orbiter at low-subsonic speeds were investigated. In the 12-foot low-speed tunnel and the 4 by 7-meter tunnel with 0.03-scale models. The effect of crew-model exit velocity, body position, and body weight were studied with egress from the main side hatch with the orbiter upright and from the upper cabin hatch with the orbiter inverted. Crew model drag and flow field measurements around the orbiter were estimated. The high-angle-of-attack trim characteristics of the orbiter was determined by force tests in an attempt to improve bailout conditions. A computer simulation was made to evaluate the maneuver necessary to attain the high-angle-of-attack trim

Polarization sensitive spectroscopy of charged Quantum Dots

We present an experimental and theoretical study of the polarized photoluminescence spectrum of single semiconductor quantum dots in various charge states. We compare our high resolution polarization sensitive spectral measurements with a new many-carrier theoretical model, which was developed for this purpose. The model considers both the isotropic and anisotropic exchange interactions between all participating electron-hole pairs. With this addition, we calculate both the energies and polarizations of all optical transitions between collective, quantum dot confined charge carrier states. We succeed in identifying most of the measured spectral lines. In particular, the lines resulting from singly-, doubly- and triply- negatively charged excitons and biexcitons. We demonstrate that lines emanating from evenly charged states are linearly polarized. Their polarization direction does not necessarily coincide with the traditional crystallographic direction. It depends on the shells of the single carriers, which participate in the recombination process.Comment: 11 pages, 9 figures. Revised versio

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

Background Functional annotations of large plant genome projects mostly provide information on gene function and gene families based on the presence of protein domains and gene homology, but not necessarily in association with gene expression or metabolic and regulatory networks. These additional annotations are necessary to understand the physiology, development and adaptation of a plant and its interaction with the environment. Results RiceCyc is a metabolic pathway networks database for rice. It is a snapshot of the substrates, metabolites, enzymes, reactions and pathways of primary and intermediary metabolism in rice. RiceCyc version 3.3 features 316 pathways and 6,643 peptide-coding genes mapped to 2,103 enzyme-catalyzed and 87 protein-mediated transport reactions. The initial functional annotations of rice genes with InterPro, Gene Ontology, MetaCyc, and Enzyme Commission (EC) numbers were enriched with annotations provided by KEGG and Gramene databases. The pathway inferences and the network diagrams were first predicted based on MetaCyc reference networks and plant pathways from the Plant Metabolic Network, using the Pathologic module of Pathway Tools. This was enriched by manually adding metabolic pathways and gene functions specifically reported for rice. The RiceCyc database is hierarchically browsable from pathway diagrams to the associated genes, metabolites and chemical structures. Through the integrated tool OMICs Viewer, users can upload transcriptomic, proteomic and metabolomic data to visualize expression patterns in a virtual cell. RiceCyc, along with additional species-specific pathway databases hosted in the Gramene project, facilitates comparative pathway analysis. Conclusions Here we describe the RiceCyc network development and discuss its contribution to rice genome annotations. As a case study to demonstrate the use of RiceCyc network as a discovery environment we carried out an integrated bioinformatic analysis of rice metabolic genes that are differentially regulated under diurnal photoperiod and biotic stress treatments. The analysis of publicly available rice transcriptome datasets led to the hypothesis that the complete tryptophan biosynthesis and its dependent metabolic pathways including serotonin biosynthesis are induced by taxonomically diverse pathogens while also being under diurnal regulation. The RiceCyc database is available online for free access at http://www.gramene.org/pathway

Mothers of Soldiers in Wartime: A National News Narrative

National news media represent mothers of US combat soldiers in the Iraq War as archetypal good mothers, that is, mothers who continue their maternal work even after their children are deployed. However, not all mothers are depicted as the archetypal patriotic mother, i.e., a good mother who is also stoic and silent about the war and her child\u27s role in it. Mothers of soldiers are portrayed as good mothers who sometimes also voice their attitudes about the war effort. The maternal attitudes ranged from complete support for the war to opposition to the war but support for the soldiers. The findings suggest a picture of wartime motherhood that is more nuanced than the historical image of the patriotic mother suggests

Thermal age, cytosine deamination and the veracity of 8,000 year old wheat DNA from sediments

YesRecently, the finding of 8,000 year old wheat DNA from submerged marine sediments (1) was challenged on the basis of a lack of signal of cytosine deamination relative to three other data sets generated from young samples of herbarium and museum specimens, and a 7,000 year old human skeleton preserved in a cave environment (2). The study used a new approach for low coverage data sets to which tools such as mapDamage cannot be applied to infer chemical damage patterns. Here we show from the analysis of 148 palaeogenomic data sets that the rate of cytosine deamination is a thermally correlated process, and that organellar generally shows higher rates of deamination than nuclear DNA in comparable environments. We categorize four clusters of deamination rates (alpha,beta,gamma,epsilon) that are associated with cold stable environments, cool but thermally fluctuating environments, and progressively warmer environments. These correlations show that the expected level of deamination in the sedaDNA would be extremely low. The low coverage approach to detect DNA damage by Weiss et al. (2) fails to identify damage samples from the cold class of deamination rates. Finally, different enzymes used in library preparation processes exhibit varying capability in reporting cytosine deamination damage in the 5 prime region of fragments. The PCR enzyme used in the sedaDNA study would not have had the capability to report 5 prime cytosine deamination, as they do not read over uracil residues, and signatures of damage would have better been sought at the 3 prime end. The 8,000 year old sedaDNA matches both the thermal age prediction of fragmentation, and the expected level of cytosine deamination for the preservation environment. Given these facts and the use of rigorous controls these data meet the criteria of authentic ancient DNA to an extremely stringent level