Uniform random generation of large acyclic digraphs

Directed acyclic graphs are the basic representation of the structure underlying Bayesian networks, which represent multivariate probability distributions. In many practical applications, such as the reverse engineering of gene regulatory networks, not only the estimation of model parameters but the reconstruction of the structure itself is of great interest. As well as for the assessment of different structure learning algorithms in simulation studies, a uniform sample from the space of directed acyclic graphs is required to evaluate the prevalence of certain structural features. Here we analyse how to sample acyclic digraphs uniformly at random through recursive enumeration, an approach previously thought too computationally involved. Based on complexity considerations, we discuss in particular how the enumeration directly provides an exact method, which avoids the convergence issues of the alternative Markov chain methods and is actually computationally much faster. The limiting behaviour of the distribution of acyclic digraphs then allows us to sample arbitrarily large graphs. Building on the ideas of recursive enumeration based sampling we also introduce a novel hybrid Markov chain with much faster convergence than current alternatives while still being easy to adapt to various restrictions. Finally we discuss how to include such restrictions in the combinatorial enumeration and the new hybrid Markov chain method for efficient uniform sampling of the corresponding graphs.Comment: 15 pages, 2 figures. To appear in Statistics and Computin

Management of Avena ludoviciana and Phalaris paradoxa with barley and less herbicide in subtropical Australia

The competitive advantage of barley compared with wheat was quantified for suppressing seed production of Avena ludoviciana Durieu. (wild oats) andPhalaris paradoxa L. (paradoxa grass), and for improving herbicide effectiveness on these major winter grass weeds of the subtropical grain region of Australia. Eight field experiments were broadcast with weed seed before sowing wheat or barley, in which the emerged weeds were then treated with 4 herbicide doses (0, 25, 50, 100% of recommended rates). Yield reduction from untreated weeds was on average 4 times greater in wheat than in barley, with greater losses from A. ludoviciana than P. paradoxa. Barley did not affect weed emergence, but suppressed weed tiller density and, to a lesser extent, the number of weed seeds per tiller. Seed production was, on average, 4340 and 5105 seeds/m2 for A. ludoviciana and P. paradoxa, respectively, in untreated wheat compared with 555 and 50 seeds/m2 in untreated barley. Weed seed production following treatment with 25% herbicide rate in barley was similar or less than that after treatment with 100% herbicide rate in wheat. Overall, 25% herbicide rate was optimal for both conserving yield and minimising weed seed production in barley. For wheat, maximum yield was achieved with 50% herbicide but weed seed production was lowest with 100% herbicide rate. This indicates that weeds can be effectively controlled in barley with considerably less herbicide than required in wheat, highlighting the importance of including barley as a part of weed management strategies that aim to reduce herbicide inputs

Present Effects of Past Wildfires on Leaf Litter Breakdown in Stream Ecosystems

We investigated the present effects from a 10-year-old wildfire on leaf litter breakdown rates in 3 headwater streams in central Idaho. These systems experienced a massive debris flow one year after the fire. Based on soil instability and burn patterns, we identified 3 stream conditions: unburned, burned only, and burned/scoured. We placed leaf bags containing willow leaves (Salix sp.) in each stream type and removed bags at various time intervals until all bags were collected 100 days after their introduction. Leaf material was dried and weighed, and decay rate coefficients were calculated. Macroinvertebrates colonizing the bags were enumerated and identified, and selected taxa were placed into trophic groups. We found that the unburned stream had the fastest leaf litter breakdown rate, the lowest level of incident light reaching the stream, and the largest amount of benthic organic matter. The burned/scoured stream was nearly opposite in all respects. Numbers of 2 detritivore invertebrate taxa, Serratella tibialis and Zapada oregonensis, were highest in the unburned stream but lowest in the burned/scoured stream. A third taxon, Baetis sp., showed the opposite relationship. Presence of predatory invertebrates did not affect detritivore abundance or leaf decay rate in the bags. Our research suggests that recovery response variables of some stream systems may not have returned to prefire levels even a decade after the initial wildfire. In this study, the recovery of our streams appears to be connected to the return of the riparian zone, though fire-induced debris flows may slow or alter final recovery of the stream system

A microsatellite marker for yellow rust resistance in wheat

Bulk segregant analysis (BSA) was used to identify molecular markers associated with yellow rust disease resistance in wheat (Triticum aestivum L.). DNAs isolated from the selected yellow rust tolerant and susceptible F-2 individuals derived from a cross between yellow rust resistant and susceptible wheat genotypes were used to established a "tolerant" and a "susceptible" DNA pool. The BSA was then performed on these DNA pools using 230 markers that were previously mapped onto the individual wheat chromosomes. One of the SSR markers (Xgwm382) located on chromosome group 2 (A, B, D genomes) was present in the resistant parent and the resistant bulk but not in the susceptible parent and the susceptible bulk, suggesting that this marker is linked to a yellow rust resistance gene. The presence of Xgwm382 was also tested in 108 additional wheat genotypes differing in yellow rust resistance. This analysis showed that 81% of the wheat genotypes known to be yellow rust resistant had the Xgwm382 marker, further suggesting that the presence of this marker correlates with yellow rust resistance in diverse wheat germplasm. Therefore, Xgwm382 could be useful for marker assisted selection of yellow rust resistances genotypes in wheat breeding programs

Atmospheric Heating and Wind Acceleration: Results for Cool Evolved Stars based on Proposed Processes

A chromosphere is a universal attribute of stars of spectral type later than ~F5. Evolved (K and M) giants and supergiants (including the zeta Aurigae binaries) show extended and highly turbulent chromospheres, which develop into slow massive winds. The associated continuous mass loss has a significant impact on stellar evolution, and thence on the chemical evolution of galaxies. Yet despite the fundamental importance of those winds in astrophysics, the question of their origin(s) remains unsolved. What sources heat a chromosphere? What is the role of the chromosphere in the formation of stellar winds? This chapter provides a review of the observational requirements and theoretical approaches for modeling chromospheric heating and the acceleration of winds in single cool, evolved stars and in eclipsing binary stars, including physical models that have recently been proposed. It describes the successes that have been achieved so far by invoking acoustic and MHD waves to provide a physical description of plasma heating and wind acceleration, and discusses the challenges that still remain.Comment: 46 pages, 9 figures, 1 table; modified and unedited manuscript; accepted version to appear in: Giants of Eclipse, eds. E. Griffin and T. Ake (Berlin: Springer

Measurement of the ttbar Production Cross Section in ppbar Collisions at sqrt(s)=1.96 TeV using Lepton + Jets Events with Lifetime b-tagging

We present a measurement of the top quark pair ($t\bar{t}$) production cross section ($\sigma_{t\bar{t}}$) in $p\bar{p}$ collisions at $\sqrt{s}=1.96$ TeV using 230 pb$^{-1}$ of data collected by the D0 experiment at the Fermilab Tevatron Collider. We select events with one charged lepton (electron or muon), missing transverse energy, and jets in the final state. We employ lifetime-based b-jet identification techniques to further enhance the $t\bar{t}$ purity of the selected sample. For a top quark mass of 175 GeV, we measure $\sigma_{t\bar{t}}=8.6^{+1.6}_{-1.5}(stat.+syst.)\pm 0.6(lumi.)$ pb, in agreement with the standard model expectation.Comment: 7 pages, 2 figures, 3 tables Submitted to Phys.Rev.Let

Search for the standard model Higgs boson in tau final states

We present a search for the standard model Higgs boson using hadronically decaying tau leptons, in 1 inverse femtobarn of data collected with the D0 detector at the Fermilab Tevatron ppbar collider. We select two final states: tau plus missing transverse energy and b jets, and tau+ tau- plus jets. These final states are sensitive to a combination of associated W/Z boson plus Higgs boson, vector boson fusion and gluon-gluon fusion production processes. The observed ratio of the combined limit on the Higgs production cross section at the 95% C.L. to the standard model expectation is 29 for a Higgs boson mass of 115 GeV.Comment: publication versio

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Measurement of D*+/- meson production in jets from pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

This paper reports a measurement of D*+/- meson production in jets from proton-proton collisions at a center-of-mass energy of sqrt(s) = 7 TeV at the CERN Large Hadron Collider. The measurement is based on a data sample recorded with the ATLAS detector with an integrated luminosity of 0.30 pb^-1 for jets with transverse momentum between 25 and 70 GeV in the pseudorapidity range |eta| < 2.5. D*+/- mesons found in jets are fully reconstructed in the decay chain: D*+ -> D0pi+, D0 -> K-pi+, and its charge conjugate. The production rate is found to be N(D*+/-)/N(jet) = 0.025 +/- 0.001(stat.) +/- 0.004(syst.) for D*+/- mesons that carry a fraction z of the jet momentum in the range 0.3 < z < 1. Monte Carlo predictions fail to describe the data at small values of z, and this is most marked at low jet transverse momentum.Comment: 10 pages plus author list (22 pages total), 5 figures, 1 table, matches published version in Physical Review

Evolution of Heat Flow, Hydrothermal Circulation and Permeability on the Young Southern Flank of the Costa Rica Rift

We analyze 67 new conductive heat flow measurements on the southern flank of the Costa Rica Rift (CRR). Heat flow measurements cover five sites ranging in oceanic crustal age between approximately 1.6 and 5.7 Ma, and are co-located with a high-resolution multi-channel seismic line that extends from slightly north of the first heat flow site (1.6 Ma) to beyond ODP Hole 504B in 6.9 Ma crust. For the five heat flow sites, the mean observed conductive heat flow is ≈ 85 mWm−2. This value is approximately 30 per cent of the mean lithospheric heat flux expected from a half-space conductive cooling model, indicating that hydrothermal processes account for about 70 per cent of the heat loss. The advective heat loss fraction varies from site to site and is explained by a combination of outcrop to outcrop circulation through exposed basement outcrops and discharge through faults. Super-critical convection in Layer 2A extrusives occurs between 1.6 and 3.5 Ma, and flow through a thinly-sedimented basement high occurs at 4.6 Ma. Advective heat loss diminishes rapidly between ≈ 4.5 and ≈ 5.7 Ma, which contrasts with plate cooling reference models that predict a significant deficit in conductive heat flow up to ages ≈ 65 ± 10 Ma. At ≈ 5.7 Ma the CRR topography is buried under sediment with an average thickness ≈ 150 m, and hydrothermal circulation in the basement becomes sub-critical or perhaps marginally critical. The absence of significant advective heat loss at ≈ 5.7 Ma at the CRR is thus a function of both burial of basement exposure under the sediment load and a reduction in basement permeability that possibly occurs as result of mineral precipitation and original permeability at the time of formation. Permeability is a non-monotonic function of age along the southern flank of the CRR, in general agreement with seismic velocity tomography interpretations that reflect variations in the degree of ridge-axis magma supply and tectonic extension. Hydrothermal circulation in the young oceanic crust at southern flank of CRR is affected by the interplay and complex interconnectedness of variations in permeability, sediment thickness, topographical structure, and tectonic and magmatic activities with age