Which effective viscosity?

Magmas undergoing shear are prime examples of flows that involve the transport of solids and gases by a separate (silicate melt) carrier phase. Such flows are called multiphase, and have attracted much attention due to their important range of engineering applications. Where the volume fraction of the dispersed phase (crystals) is large, the influence of particles on the fluid motion becomes significant and must be taken into account in any explanation of the bulk behaviour of the mixture. For congested magma deforming well in excess of the dilute limit (particle concentrations >40% by volume), sudden changes in the effective or relative viscosity can be expected. The picture is complicated further by the fact that the melt phase is temperature- and shear-rate-dependent. In the absence of a constitutive law for the flow of congested magma under an applied force, it is far from clear which of the many hundreds of empirical formulae devised to predict the rheology of suspensions as the particle fraction increases with time are best suited. Some of the more commonly used expressions in geology and engineering are reviewed with an aim to home in on those variables key to an improved understanding of magma rheology. These include a temperature, compositional and shear-rate dependency of viscosity of the melt phase with the shear-rate dependency of the crystal (particle) packing arrangement. Building on previous formulations, a new expression for the effective (relative) viscosity of magma is proposed that gives users the option to define a packing fraction range as a function of shear stress. Comparison is drawn between processes (segregation, clustering, jamming), common in industrial slurries, and structures seen preserved in igneous rocks. An equivalence is made such that congested magma, viewed in purely mechanical terms as a high-temperature slurry, is an inherently non-equilibrium material where flow at large Péclet numbers may result in shear thinning and spontaneous development of layering

Activation of the heat shock transcription factor Hsf1 is essential for the full virulence of the fungal pathogen Candida albicans

Peer reviewedPublisher PD

Reporters for the analysis of N-glycosylation in Candida albicans

Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.Peer reviewedPublisher PD

Balancing end-to-end budgets of the Georges Bank ecosystem

Author Posting. © Elsevier, 2007. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution. The definitive version was published in Progress In Oceanography 74 (2007): 423-448, doi:10.1016/j.pocean.2007.05.003.Oceanographic regimes on the continental shelf display a great range in the time scales of physical exchange, biochemical processes and trophic transfers. The close surface-to-seabed physical coupling at intermediate scales of weeks to months means that the open ocean simplification to a purely pelagic food web is inadequate. Top-down trophic depictions, starting from the fish populations, are insufficient to constrain a system involving extensive nutrient recycling at lower trophic levels and subject to physical forcing as well as fishing. These pelagic-benthic interactions are found on all continental shelves but are particularly important on the relatively shallow Georges Bank in the northwest Atlantic. We have generated budgets for the lower food web for three physical regimes (well mixed, transitional and stratified) and for three seasons (spring, summer and fall/winter). The calculations show that vertical mixing and lateral exchange between the three regimes are important for zooplankton production as well as for nutrient input. Benthic suspension feeders are an additional critical pathway for transfers to higher trophic levels. Estimates of production by mesozooplankton, benthic suspension feeders and deposit feeders, derived primarily from data collected during the GLOBEC years of 1995-1999, provide input to an upper food web. Diets of commercial fish populations are used to calculate food requirements in three fish categories, planktivores, benthivores and piscivores, for four decades, 1963-2002, between which there were major changes in the fish communities. Comparisons of inputs from the lower web with fish energetic requirements for plankton and benthos indicate that we obtained reasonable agreement for the last three decades, 1973 to 2002. However, for the first decade, the fish food requirements were significantly less than the inputs. This decade, 1963-1972, corresponds to a period characterized by a strong Labrador Current and lower nitrate levels at the shelf edge, demonstrating how strong bottom-up physical forcing may determine overall fish yields.The research was done under the aegis of the U.S.-GLOBEC Northwest Atlantic Georges Bank Study, a program sponsored jointly by the U.S. National Science Foundation and the U.S. National Oceanic and Atmospheric Administration. We acknowledge NOAA-CICOR award NA17RJ1233 (J.H. Steele), NSF awards OCE0217399 (D.J. Gifford), OCE0217122 (J.J. Bisagni) and OCE0217257 (M.E. Sieracki). W.T. Stockhausen was supported by the NOAA Sponsored Coastal Ocean Research Program

Strawberry fruit resistance to simulated handling

Harvest operations are currently the main source of mechanical injury of strawberry (Fragaria x ananassa Duch.). Experiments were designed to simulate conditions encountered during commercial handling. Individual fruits were subjected to impact or compression forces with similar energy to determine the sensitivity to mechanical injury. Bruise volume was used as the measurement of injury. Bruise severity increased as a function of impact energy for both impact types. However, dropped fruits had larger bruise volume than fruits submitted to pendulum impactor at the same energy level. Doubling the impact energy (0.040 to 0.083 J) increased bruise volume by 7 times (13 to 91 mm³). Fruits dropped from 380 mm (0.075 J) showed 71% greater bruise volume than those dropped from either 130 mm (0.025 J) or 200 mm (0.040 J). Compressed fruits showed higher bruise volume than other tests. Some cultivars are more susceptible to compression forces than others. 'Sweet Charlie' berries showed bruise volume 40% higher than the others cultivars when subjected to compression. Fruits subjected to impact showed bruise volume lower than the compressed fruits, indicating the possibility to be handled and graded in a packing line.A etapa de colheita é a principal fonte de danos físicos ao morango (Fragaria x ananassa Duch.). Experimentos foram realizados para simular condições encontradas durante manuseio. Frutos foram submetidos individualmente às forças de impacto e compressão em energias similares para determinar sensibilidade dos frutos a danos físicos. Volume da injúria física foi utilizado para mensurar a incidência do dano físico ocorrido. Severidade da lesão aumenta, com incremento da energia, tanto para força de impacto como para compressão. Todavia, frutos submetidos à queda livre demonstraram maiores volumes de danos físicos do que frutos submetidos a danos ocasionados por pendulo no mesmo nível de energia. Dobrando a energia de impacto (0,040 para 0,083 J) ocorreu aumento no volume da injúria em sete vezes (13 para 91 mm³). Frutos submetidos à queda de 380 mm (0,075 J) demonstraram volumes de danos físicos 71% superiores do que aqueles ocasionados em queda de 130 mm (0,025 J) ou 200 mm (0,040 J). Frutos em teste de compressão mostraram maiores volumes de injúrias físicas do que outros testes. Alguns cultivares são mais sensíveis à força de compressão do que outros. Frutos cultivar 'Sweet Charlie' apresentaram volume de injúria 40% superiores do que outros quando submetidos à força de compressão. Morangos submetidos à força de impacto demonstraram volume de injúria inferior do que aqueles comprimidos, indicando a possibilidade dos morangos serem classificados e manuseados em uma linha de beneficiamento

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

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

Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC

Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the anti-kt algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. Rcp varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables, submitted to Physics Letters B. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02

Measurement of the polarisation of W bosons produced with large transverse momentum in pp collisions at sqrt(s) = 7 TeV with the ATLAS experiment

This paper describes an analysis of the angular distribution of W->enu and W->munu decays, using data from pp collisions at sqrt(s) = 7 TeV recorded with the ATLAS detector at the LHC in 2010, corresponding to an integrated luminosity of about 35 pb^-1. Using the decay lepton transverse momentum and the missing transverse energy, the W decay angular distribution projected onto the transverse plane is obtained and analysed in terms of helicity fractions f0, fL and fR over two ranges of W transverse momentum (ptw): 35 < ptw < 50 GeV and ptw > 50 GeV. Good agreement is found with theoretical predictions. For ptw > 50 GeV, the values of f0 and fL-fR, averaged over charge and lepton flavour, are measured to be : f0 = 0.127 +/- 0.030 +/- 0.108 and fL-fR = 0.252 +/- 0.017 +/- 0.030, where the first uncertainties are statistical, and the second include all systematic effects.Comment: 19 pages plus author list (34 pages total), 9 figures, 11 tables, revised author list, matches European Journal of Physics C versio