Global analysis of gene expression reveals mRNA superinduction is required for the inducible immune response to a bacterial pathogen.

The inducible innate immune response to infection requires a concerted process of gene expression that is regulated at multiple levels. Most global analyses of the innate immune response have focused on transcription induced by defined immunostimulatory ligands, such as lipopolysaccharide. However, the response to pathogens involves additional complexity, as pathogens interfere with virtually every step of gene expression. How cells respond to pathogen-mediated disruption of gene expression to nevertheless initiate protective responses remains unclear. We previously discovered that a pathogen-mediated blockade of host protein synthesis provokes the production of specific pro-inflammatory cytokines. It remains unclear how these cytokines are produced despite the global pathogen-induced block of translation. We addressed this question by using parallel RNAseq and ribosome profiling to characterize the response of macrophages to infection with the intracellular bacterial pathogen Legionella pneumophila. Our results reveal that mRNA superinduction is required for the inducible immune response to a bacterial pathogen

Numerical renormalization-group study of the Bose-Fermi Kondo model

We extend the numerical renormalization-group method to Bose-Fermi Kondo models (BFKMs), describing a local moment coupled to a conduction band and a dissipative bosonic bath. We apply the method to the Ising-symmetry BFKM with a bosonic bath spectral function $\eta(\omega)\propto \omega^s$, of interest in connection with heavy-fermion criticality. For $0<s<1$, an interacting critical point, characterized by hyperscaling of exponents and $\omega/T$-scaling, describes a quantum phase transition between Kondo-screened and localized phases. Connection is made to other results for the BFKM and the spin-boson model.Comment: 4 pages, 4 figure

CALENDAR VS. WEEKS TO EXPIRATION LIVESTOCK BASIS FORECASTS: WHICH IS BETTER?

The ability to accurately forecast basis is crucial to risk management strategies employed by many agribusiness firms. Previous research has examined how to effectively use basis forecasts and what factors affect basis, but literature focusing on forecasting basis is sparse. This research evaluates the impact of adopting a time-to-expiration approach, as compared to the more common calendar approach, when forecasting feeder cattle, live cattle, and hog basis. Furthermore, the optimal number of past year's basis levels to include in making basis predictions is evaluated in an out-of-sample framework. Absolute basis forecasts errors are generated for all three commodities and evaluated to determine the signifcance of the two issues mentioned above. Results indicate that basis forecasters should consider using three-year historical averages for feeder cattle and four-year historical averages for live cattle and lean hogs when making basis forecasts. Furthermore, the use of a time-to-expiration method of calculating historical average basis results in very little improvement in basis prediction accuracy compared to the calendar approach.livestock prices, basis, hedging, basis forecasts, Livestock Production/Industries, Marketing,

Monitoring of nitrogen leaching on a dairy farm during four drainage seasons

peer-reviewedThe authors acknowledge funding from the Environmental Protection Agency and Teagasc under the 2000–2006 RTDI programme.The effect of four commonly used dairy farm management systems (treatments), on nitrogen leaching to 1 m was studied over a 4-year period from October 2001 to April 2005. The treatments were (i) grazed plots receiving dirty water, (ii) 2-cut silage plots receiving slurry, (iii) grazed plots and (iv) 1-cut silage plots receiving slurry. All plots had fertiliser N applied; the soil was free-draining overlying fissured limestone. Mean 4-year N input (kg/ha) was 319 and mean annual stocking density was ~2.38 LU/ha. The annual average and weekly NO3-N and NH4-N concentrations in drainage water were analysed for all years, using a repeated measures analysis. For the annual NO3-N data, there was an interaction between treatment and year (P < 0.001). There were significant differences (P < 0.05) in NO3-N concentrations between the treatments in all years except the third. For the NH4-N data there was no interaction between treatment and year or main effect of treatment but there were differences between years (P < 0.01). Mean weekly concentrations were analysed separately for each year. For NO3-N, in all years but the third, there was an interaction between treatment and week (P < 0.001); this occurred with NH4-N, in all 4 years. Dirty water was significantly higher than grazed-fertiliser only and 1-cut silage in NO3-N concentrations in 2001–02; in 2002–03, dirty water and 2-cut silage were significantly higher than the other treatments; while in 2004–05, dirty water and grazed-fertiliser only were significantly higher than the other two treatments. The overall 4-year mean NO3-N and NH4-N concentrations were 8.2 and 0.297 mg/L, respectively.Environmental Protection Agenc

Improving Cattle Basis Forecasting

Successful risk management strategies for agribusiness firms based on futures and options contracts are contingent on their ability to accurately forecast basis. This research addresses three primary questions as they relate to basis forecasting accuracy: (a) What is the impact of adopting a time-to-expiration approach, as compared to the more common calendar-date approach? (b) What is the optimal number of years to include in calculations when forecasting livestock basis using historical averages? and (c) What is the effect of incorporating current basis information into a historical-average-based forecast? Results indicate that use of the time-to-expiration approach has little impact on forecast accuracy compared to using a simple calendar approach, but forecast accuracy is improved by incorporating at least a portion of current basis information into basis forecasts.basis, basis forecasts, cattle prices, current information, hedging, Livestock Production/Industries,

LIVESTOCK BASIS FORECASTS: HOW BENEFICIAL IS THE INCLUSION OF CURRENT INFORMATION?

Successful risk management strategies for agribusiness firms are contingent on the ability to accurately forecast basis. There has been substantial research on the actual use of basis forecasts, yet little research has been conducted on actually forecasting basis. This study evaluates the effect incorporating current basis information into a historical-average-based-forecast has on forecasting accuracy when forecasting live cattle and feeder cattle basis. Furthermore, the optimal weight to place on this current information is evaluated in an out-of-sample framework. Root mean squared errors are generated for both commodities and evaluated to determine the significance of these issues. Results suggest that livestock basis forecasters should consider incorporating a proportion of the difference in current basis and the historical average of the current week when making their projections. The optimal amount of current information to include declines as the time interval between the week the forecast is being made and the week being forecasted increases.livestock prices, hedging, basis forecasts, current information, Livestock Production/Industries, Marketing,

On the Hamiltonian Constraint of Loop Quantum Cosmology

In this paper we construct the Hamiltonian constraint operator of loop quantum cosmology using holonomies defined for arbitrary irreducible SU(2) representations labeled by spin J. We show that modifications to the effective semi-classical equations of motion arise both in the gravitational part of the constraint as well as matter terms. The modifications are important for phenomenological investigations of the cosmological imprints of loop quantum cosmology. We discuss the implications for the early universe evolution

Semi-classical States, Effective Dynamics and Classical Emergence in Loop Quantum Cosmology

We construct physical semi-classical states annihilated by the Hamiltonian constraint operator in the framework of loop quantum cosmology as a method of systematically determining the regime and validity of the semi-classical limit of the quantum theory. Our results indicate that the evolution can be effectively described using continuous classical equations of motion with non-perturbative corrections down to near the Planck scale below which the universe can only be described by the discrete quantum constraint. These results, for the first time, provide concrete evidence of the emergence of classicality in loop quantum cosmology and also clearly demarcate the domain of validity of different effective theories. We prove the validity of modified Friedmann dynamics incorporating discrete quanum geometry effects which can lead to various new phenomenological applications. Furthermore the understanding of semi-classical states allows for a framework for interpreting the quantum wavefunctions and understanding questions of a semi-classical nature within the quantum theory of loop quantum cosmology.Comment: Accepted for publication in Phys Rev D. Updated version to matc