Multidimensional Longwave Forcing of Boundary Layer Cloud Systems

This is the publisher's version, also available electronically from http://journals.ametsoc.org/doi/abs/10.1175/2008JAS2733.1.The importance of multidimensional (MD) longwave radiative effects on cloud dynamics is evaluated in an eddy-resolving model (ERM)—the two-dimensional analog to large-eddy simulation (LES)—framework employing multidimensional radiative transfer [Spherical Harmonics Discrete Ordinate Method (SHDOM)]. Simulations are performed for a case of unbroken, marine boundary layer stratocumulus and a broken field of trade cumulus. “Snapshot” calculations of MD and independent pixel approximation (IPA; 1D) radiative transfer applied to simulated cloud fields show that the total radiative forcing changes only slightly, although the MD effects significantly modify the spatial structure of the radiative forcing. Simulations of each cloud type employing MD and IPA radiative transfer, however, differ little. For the solid cloud case, relative to using IPA, the MD simulation exhibits a slight reduction in entrainment rate and boundary layer total kinetic energy (TKE) relative to the IPA simulation. This reduction is consistent with both the slight decrease in net radiative forcing and a negative correlation between local vertical velocity and radiative forcing, which implies a damping of boundary layer eddies. Snapshot calculations of the broken cloud case suggest a slight increase in radiative cooling, although few systematic differences are noted in the interactive simulations. This result is attributed to the fact that radiative cooling is a relatively minor contribution to the total energetics. For the cloud systems in this study, the use of IPA longwave radiative transfer is sufficiently accurate to capture the dynamical behavior of boundary layer clouds. Further investigations are required to generalize this conclusion for other cloud types and longer time integrations

Substantiating a political public sphere in the Scottish press : a comparative analysis

This article uses content analysis to characterize the performance of the media in a national public sphere, by setting apart those qualities that typify internal press coverage of a political event. The article looks at the coverage of the 1999 devolved Scottish election from the day before the election until the day after. It uses a word count to measure the election material in Scottish newspapers the Herald, the Press and Journal and the Scotsman, and United Kingdom newspapers the Guardian, the Independent and The Times, and categorizes that material according to discourse type, day and page selection. The article finds a number of qualities that typify the Scottish sample in particular, and might be broadly indicative of a political public sphere in action. Firstly, and not unexpectedly, it finds that the Scottish newspapers carry significantly more election coverage. Just as tellingly, though, the article finds that the Scottish papers offer a greater proportion of advice and background information, in the form of opinion columns and feature articles. It also finds that the Scottish papers place a greater concentration of both informative and evaluative material in the period before the vote, consistent with their making a contribution to informed political action. Lastly, the article finds that the Scottish sample situates coverage nearer the front of the paper and places a greater proportion on recto pages. The article therefore argues that the Scottish papers display features that distinguish them from the UK papers, and are broadly consistent with their forming part of a deliberative public sphere, and suggests that these qualities might be explored as a means of judging future media performance

Arguably big biology: Sociology, spatiality and the knockout mouse project

© 2013 copyright Palgrave MacmillanThis is a post-peer-review, pre-copyedit version of an article published in BioSocieties. The definitive publisher-authenticated version BioSocieties, 2013, Vol. 8, pp. 417-431 is available online at: http://www.palgrave-journals.com/biosoc/journal/v8/n4/full/biosoc201325a.htmlFollowing the completion of the Human Genome Project (HGP), a critical challenge has been how to make biological sense of the amassed sequence data and translate this into clinical applications. A range of large biological research projects, as well as more distributed experimental collaborations, are seeking to realise this through translational research initiatives and postgenomic approaches. Drawing on interviews with key participants, this article explores the biological assumptions, sociological challenges and spatial imaginaries at play in arguments around one of these developments, which is using genetically altered mice to understand gene function. The knockout mouse project (KOMP) is a large-scale initiative in functional genomics, seeking to produce a ‘knockout mouse’ for each gene in the mouse’s genome, which can then be used to answer questions about gene function in mammals. KOMP is frequently framed as one successor to the HGP, emblematic of the ambitions of internationally coordinated biological research. However, the development of new technologies for generating and managing genetically altered mice, alongside the challenge of asking biologically meaningful questions of vast numbers of animals, is creating new frictions in this extension and intensification of biological research practices. This article introduces two separate approaches to the future of international research using mutant mice as stakeholders to negotiate the biological, sociological and spatial challenges of collaboration. The first centres on the directed research practices and sociological assumptions of KOMP, as individual researchers are reorganised around shared animals, databases and infrastructures. The second highlights an alternative vision of the future of biomedical research, using distributed management to enhance the sensitivities and efficiencies of existing experimental practices over space. These exemplify two different tactics in the organisation of an ‘arguably’ big biology. They also critically embody different sociological and spatial imaginaries for the collaborative practices of international translational research

The 3′–5′ proofreading exonuclease of archaeal family-B DNA polymerase hinders the copying of template strand deaminated bases

Archaeal family B polymerases bind tightly to the deaminated bases uracil and hypoxanthine in single-stranded DNA, stalling replication on encountering these pro-mutagenic deoxynucleosides four steps ahead of the primer–template junction. When uracil is specifically bound, the polymerase–DNA complex exists in the editing rather than the polymerization conformation, despite the duplex region of the primer-template being perfectly base-paired. In this article, the interplay between the 3′–5′ proofreading exonuclease activity and binding of uracil/hypoxanthine is addressed, using the family-B DNA polymerase from Pyrococcus furiosus. When uracil/hypoxanthine is bound four bases ahead of the primer–template junction (+4 position), both the polymerase and the exonuclease are inhibited, profoundly for the polymerase activity. However, if the polymerase approaches closer to the deaminated bases, locating it at +3, +2, +1 or even 0 (paired with the extreme 3′ base in the primer), the exonuclease activity is strongly stimulated. In these situations, the exonuclease activity is actually stronger than that seen with mismatched primer-templates, even though the deaminated base-containing primer-templates are correctly base-paired. The resulting exonucleolytic degradation of the primer serves to move the uracil/hypoxanthine away from the primer–template junction, restoring the stalling position to +4. Thus the 3′–5′ proofreading exonuclease contributes to the inability of the polymerase to replicate beyond deaminated bases

Surface electrons at plasma walls

In this chapter we introduce a microscopic modelling of the surplus electrons on the plasma wall which complements the classical description of the plasma sheath. First we introduce a model for the electron surface layer to study the quasistationary electron distribution and the potential at an unbiased plasma wall. Then we calculate sticking coefficients and desorption times for electron trapping in the image states. Finally we study how surplus electrons affect light scattering and how charge signatures offer the possibility of a novel charge measurement for dust grains.Comment: To appear in Complex Plasmas: Scientific Challenges and Technological Opportunities, Editors: M. Bonitz, K. Becker, J. Lopez and H. Thomse

SNPs and Other Features as They Predispose to Complex Disease: Genome-Wide Predictive Analysis of a Quantitative Phenotype for Hypertension

Though recently they have fallen into some disrepute, genome-wide association studies (GWAS) have been formulated and applied to understanding essential hypertension. The principal goal here is to use data gathered in a GWAS to gauge the extent to which SNPs and their interactions with other features can be combined to predict mean arterial blood pressure (MAP) in 3138 pre-menopausal and naturally post-menopausal white women. More precisely, we quantify the extent to which data as described permit prediction of MAP beyond what is possible from traditional risk factors such as blood cholesterol levels and glucose levels. Of course, these traditional risk factors are genetic, though typically not explicitly so. In all, there were 44 such risk factors/clinical variables measured and 377,790 single nucleotide polymorphisms (SNPs) genotyped. Data for women we studied are from first visit measurements taken as part of the Atherosclerotic Risk in Communities (ARIC) study. We begin by assessing non-SNP features in their abilities to predict MAP, employing a novel regression technique with two stages, first the discovery of main effects and next discovery of their interactions. The long list of SNPs genotyped is reduced to a manageable list for combining with non-SNP features in prediction. We adapted Efron's local false discovery rate to produce this reduced list. Selected non-SNP and SNP features and their interactions are used to predict MAP using adaptive linear regression. We quantify quality of prediction by an estimated coefficient of determination (R2). We compare the accuracy of prediction with and without information from SNPs

From silence to primary definer: The rise of the Intelligence lobby in the public sphere

Until the end of the Cold War the UK intelligence services were not officially acknowledged, and their personnel were banned from entering the public sphere. From 1989 the UK government began to put the intelligence services on a legal footing and to release the identity of the heads of the intelligence agencies. Since then, public engagement by the intelligence agencies has gathered pace. What this article hypothesises is that there is now, in the UK, an effective intelligence lobby of former insiders who engage in the public sphere – using on the record briefings – to counter criticism of the intelligence community and to promote a narrative and vision of what UK intelligence should do, how it is supported and how oversight is conducted. Content analysis and framing models of non-broadcast coverage of intelligence debates, focusing on the 36 months after the Snowden revelations, confirm an active and rolling lobby of current and former intelligence officials. The paper concludes that the extent of the lobby’s interventions in the public sphere is a matter for debate and possible concern

Measurement of χ c1 and χ c2 production with s√ = 7 TeV pp collisions at ATLAS

The prompt and non-prompt production cross-sections for the χ c1 and χ c2 charmonium states are measured in pp collisions at s√ = 7 TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χ c states are reconstructed through the radiative decay χ c → J/ψγ (with J/ψ → μ + μ −) where photons are reconstructed from γ → e + e − conversions. The production rate of the χ c2 state relative to the χ c1 state is measured for prompt and non-prompt χ c as a function of J/ψ transverse momentum. The prompt χ c cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χ c decays. The fractions of χ c1 and χ c2 produced in b-hadron decays are also measured

Single hadron response measurement and calorimeter jet energy scale uncertainty with the ATLAS detector at the LHC

The uncertainty on the calorimeter energy response to jets of particles is derived for the ATLAS experiment at the Large Hadron Collider (LHC). First, the calorimeter response to single isolated charged hadrons is measured and compared to the Monte Carlo simulation using proton-proton collisions at centre-of-mass energies of sqrt(s) = 900 GeV and 7 TeV collected during 2009 and 2010. Then, using the decay of K_s and Lambda particles, the calorimeter response to specific types of particles (positively and negatively charged pions, protons, and anti-protons) is measured and compared to the Monte Carlo predictions. Finally, the jet energy scale uncertainty is determined by propagating the response uncertainty for single charged and neutral particles to jets. The response uncertainty is 2-5% for central isolated hadrons and 1-3% for the final calorimeter jet energy scale.Comment: 24 pages plus author list (36 pages total), 23 figures, 1 table, submitted to European Physical Journal

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011