bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of carbon monoxide (CO) delivery by a CO donor or hemoglobin on vascular hypoxia inducible factor 1α and mitochondrial respiration
Authors: Reiter Chad E.N. , Alayash Abdu I.
Published: May 2012

We examined carbon monoxide (CO) delivery by carbon monoxide‐releasing molecule 2 (CORM‐2) or hemoglobin (Hb) on cellular oxygen sensing and mitochondrial respiration in bovine aortic endothelial cells (BAECs). CORM‐2 reduced hypoxia‐inducible factor‐1α (HIF‐1α) and endothelin‐1 (ET‐1) expression in normoxic and hypoxic cells, but while Hb alone significantly reduced HIF‐1α stabilization in hypoxic cells, CO delivered by Hb (Hb‐CO) had no effect on HIF‐1α stabilization. CO dose‐dependently increased basal oxygen consumption and reduced overall mitochondrial respiratory capacity. Hb‐CO increased basal oxygen consumption but did not alter respiratory capacity. Together, CO reduced ET‐1, and, at low doses, had no effect on endothelial mitochondria oxygen consumption. CO ligation to Hb may be developed further as non‐vasoactive oxygen therapeutic without compromising mitochondrial function.
Hybrid knowledge: the transnational co-production of the gas centrifuge for uranium enrichment in the 1960s
Authors: KRIGE JOHN
Published: May 2012

The ‘how’ and the ‘why’ of knowledge circulation is explored in a study of the encounter between American and British nuclear scientists and engineers who together developed a gas centrifuge to enrich uranium in the 1960s. A fine-grained analysis of the transnational encounter reveals that the ‘how’ engages a wide variety of sometimes mundane modes of exchange in a series of face-to-face interactions over several years. The ‘why’ is driven by the reciprocal wish to improve the performance of the centrifuge, though this motive is embedded in the asymmetric field of the ‘special relationship’ in nuclear matters between the United Kingdom and the United States. The result of the encounter is co-produced, hybrid knowledge in which the national provenance of the contributions from each side of the Atlantic is at once diluted and a contested site for the affirmation of national power.
Three-way assessment of long-chain n-3 PUFA nutrition: by questionnaire and matched blood and skin samples
Authors: Wallingford Sarah C. , Pilkington Suzanne M. , Massey Karen A. , Al-Aasswad Naser M. I. , Ibiebele Torukiri I. , Celia Hughes Maria , Bennett Susan , Nicolaou Anna , Rhodes Lesley E. , Green Adèle C.
Published: May 2012

The long-chain n-3 PUFA, EPA, is believed to be important for skin health, including roles in the modulation of inflammation and protection from photodamage. FFQ and blood levels are used as non-invasive proxies for assessing skin PUFA levels, but studies examining how well these proxies reflect target organ content are lacking. In seventy-eight healthy women (mean age 42·8, range 21–60 years) residing in Greater Manchester, we performed a quantitative analysis of long-chain n-3 PUFA nutrition estimated from a self-reported FFQ (n 75) and correlated this with n-3 PUFA concentrations in erythrocytes (n 72) and dermis (n 39). Linear associations between the three n-3 PUFA measurements were assessed by Spearman correlation coefficients and agreement between these measurements was estimated. Average total dietary content of the principal long-chain n-3 PUFA EPA and DHA was 171 (sd 168) and 236 (sd 248) mg/d, respectively. EPA showed significant correlations between FFQ assessments and both erythrocyte (r 0·57, P< 0·0001) and dermal (r 0·33, P= 0·05) levels, as well as between erythrocytes and dermis (r 0·45, P= 0·008). FFQ intake of DHA and the sum of n-3 PUFA also correlated well with erythrocyte concentrations (r 0·50, P< 0·0001; r 0·27, P= 0·03). Agreement between ranked thirds of dietary intake, blood and dermis approached 50 % for EPA and DHA, though gross misclassification was lower for EPA. Thus, FFQ estimates and circulating levels of the dietary long-chain n-3 PUFA, EPA, may be utilised as well-correlated measures of its dermal bioavailability.
Salvage: Macrina and the Christian Project of Cultural Reclamation
Authors: Muehlberger Ellen
Published: May 2012

While many have seen the equation between Macrina and Socrates drawn in the Treatise on the Soul and the Resurrection as Gregory of Nyssa's attempt to honor his sister, a closer look at Gregory's attitude about the relative power of Christianity at the end of the fourth century suggests the opposite: that the character of Macrina lends validity to Socrates and, by extension, to non-Christian intellectual traditions. In this article, I argue that the Treatise is part of a larger project of cultural reclamation enacted by some Christians near the end of the fourth century. The educational reforms of the emperor Julian had instituted a public discourse of evaluation by which one's reading material indicated one's religious identity; after Julian, some Christians adopted this idea, yet in reverse, arguing that reading traditional literature was out of the question for Christians, as it would signal a non-Christian religious commitment. Gregory's Treatise on the Soul and the Resurrection was an effort to walk back the effects of that discourse and to return Christian pedagogy, philosophy, and cultural evaluation to a stance of ambivalence regarding Greek literature.
The Spread of Antislavery Sentiment through Proslavery Tracts in the Transatlantic Evangelical Community, 1740s–1770s
Authors: Yoon Young Hwi
Published: May 2012

In the history of the Atlantic antislavery movement, two events were of great importance: the Great Awakening and the American Revolution. In the 1730s and 1740s, many evangelicals stimulated by the religious revival, travelled to the opposite side of the Atlantic, preached the gospel, and published a number of books that contained their evangelical faith and ideals. Through these activities many evangelicals in Anglo-American communities shared common interests, faith, and ideology, and some found a channel of transatlantic communication in which they were able to debate the slavery issue. The American Revolution also contributed to creating an atmosphere of tension in the 1770s, in which antislavery sentiment became transformed into moral conviction. The development of this ideology can be explained by the spread of antipathy toward slavery in the Atlantic world before the Revolution. This essay focuses on the change in the evangelical mindset between these two religio-political events, asking: how did the antislavery sentiment spread through the transatlantic evangelical network from the 1740s into the 1770s?
Genetic-basis analysis of heterotic loci in Dongxiang common wild rice (Oryza rufipogonGriff.)
Authors: LUO XIAO-JIN , XIN XIAO-YUN , YANG JIN-SHUI
Published: May 2012

Heterosis is widely used in genetic crop improvement; however, the genetic basis of heterosis is incompletely understood. The use of whole-genome segregating populations poses a problem for establishing the genetic basis of heterosis, in that interactions often mask the effects of individual loci. However, introgression line (IL) populations permit the partitioning of heterosis into defined genomic regions, eliminating a major part of the genome-wide epistasis. In our previous study, based on mid-parental heterosis (HMP) value with single-point analysis, 42 heterotic loci (HLs) associated with six yield-related traits were detected in wild and cultivated rice using a set of 265 ILs of Dongxiang common wild rice (Oryza rufipogonGriff.). In this study, the genetic effects of HLs were determined as the combined effects of both additive and dominant gene actions, estimated from the performance values of testcross F1s and the dominance effects estimated from theHMPvalues of testcross F1s. We characterized the gene action type at each HL. Thirty-eight of the 42 HLs were over-dominant, and in the absence of epistasis, four HLs were dominant. Therefore, we favour that over-dominance is a major genetic basis of ‘wild-cultivar’ crosses at the single functional Mendelian locus level.
Genome-wide association mapping including phenotypes from relatives without genotypes
Authors: WANG H. , MISZTAL I. , AGUILAR I. , LEGARRA A. , MUIR W. M.
Published: May 2012

A common problem for genome-wide association analysis (GWAS) is lack of power for detection of quantitative trait loci (QTLs) and precision for fine mapping. Here, we present a statistical method, termed single-step GBLUP (ssGBLUP), which increases both power and precision without increasing genotyping costs by taking advantage of phenotypes from other related and unrelated subjects. The procedure achieves these goals by blending traditional pedigree relationships with those derived from genetic markers, and by conversion of estimated breeding values (EBVs) to marker effects and weights. Additionally, the application of mixed model approaches allow for both simple and complex analyses that involve multiple traits and confounding factors, such as environmental, epigenetic or maternal environmental effects. Efficiency of the method was examined using simulations with 15 800 subjects, of which 1500 were genotyped. Thirty QTLs were simulated across genome and assumed heritability was 0·5. Comparisons included ssGBLUP applied directly to phenotypes, BayesB and classical GWAS (CGWAS) with deregressed proofs. An average accuracy of prediction 0·89 was obtained by ssGBLUP after one iteration, which was 0·01 higher than by BayesB. Power and precision for GWAS applications were evaluated by the correlation between true QTL effects and the sum ofmadjacent single nucleotide polymorphism (SNP) effects. The highest correlations were 0·82 and 0·74 for ssGBLUP and CGWAS withm=8, and 0·83 for BayesB withm=16. Standard deviations of the correlations across replicates were several times higher in BayesB than in ssGBLUP. The ssGBLUP method with marker weights is faster, more accurate and easier to implement for GWAS applications without computing pseudo-data.
Phylogeography of Lyme borreliosis-group spirochetes and methicillin-resistantStaphylococcus aureus
Authors: MARGOS GABRIELE , CASTILLO-RAMÍREZ SANTIAGO , HOEN ANNE GATEWOOD
Published: May 2012

Multilocus sequence typing (MLST) and multilocus sequence analysis (MLSA) have revolutionized understanding the global epidemiology of many medically relevant bacteria utilizing a number, mostly seven, of housekeeping genes. A more recent introduction, single nucleotide polymorphisms (SNPs), constitutes an even more powerful tool for bacterial typing, population genetic studies and phylogeography. The introduction of massive parallel sequencing has made genome re-sequencing and SNP discovery more economical for investigations of microbial organisms. In this paper we review phylogeographic studies on Lyme borreliosis (LB)-group spirochetes and methicillin-resistantStaphylococcus aureus(MRSA). Members of the LB-group spirochetes are tick-transmitted zoonotic bacteria that have many hosts and differ in their degree of host specialism, constituting a highly complex system. MRSA is a directly transmitted pathogen that may be acquired by contact with infected people, animals or MRSA-contaminated objects. For the LB-group spirochetes, MLSA has proved a powerful tool for species assignment and phylogeographic investigations while forS. aureus, genome-wide SNP data have been used to study the very short-term evolution of two important MRSA lineages, ST239 and ST225. These data are detailed in this review.
Cognitive ability in early adulthood is associated with later suicide and suicide attempt: the role of risk factors over the life course
Authors: Sörberg A. , Allebeck P. , Melin B. , Gunnell D. , Hemmingsson T.
Published: May 2012

Background

Cognitive ability/intelligence quotient (IQ) in youth has previously been associated with subsequent completed and attempted suicide, but little is known about the mechanisms underlying the associations. This study aims to assess the roles of various risk factors over the life course in explaining the observed relationships.

Method

The present investigation is a cohort study based on data on IQ test performance and covariates, recorded on 49 321 Swedish men conscripted in 1969–1970, at ages 18–20 years. Information on suicides and hospital admissions for suicide attempt up to the age of 57 years, childhood and adult socio-economic position, and adult family formation, was obtained from linkage to national registers.

Results

Lower IQ was associated with increased risks of both suicide and suicide attempt during the 36 years of follow-up. The associations followed a dose–response pattern. They were attenuated by approximately 45% in models controlling for social background, mental ill-health, aspects of personality and behavior, adult socio-economic position and family formation. Based on one-unit decreases in IQ test performance on a nine-point scale, the hazard ratios between ages 35 and 57 years were: for suicide 1.19 [95% confidence interval (CI) 1.13–1.25], fully adjusted 1.10 (95% CI 1.04–1.18); and for suicide attempt 1.25 (95% CI 1.20–1.31), fully adjusted 1.14 (95% CI 1.09–1.20).

Conclusions

Cognitive ability was found to be associated with subsequent completed and attempted suicide. The associations were attenuated by 45% after controlling for risk factors measured over the life course. Psychiatric diagnosis, maladjustment and aspects of personality in young adulthood, and social circumstances in later adulthood, contributed in attenuating the associations.
Social Policy Digest Online
Authors: Bennett Fran , Jones Ken
Published: May 2012

The Social Policy Digest is a major online resource providing up-to-date listings of developments across the whole range of social policy issues - including links to source materials and related commentaries. The Digest is published by Cambridge University Press on behalf of the Social Policy Association.
The equine intestinal microbiome
Authors: Costa Marcio C. , Weese J. Scott
Published: May 2012

The equine intestinal tract contains a complex microbial population (microbiota) that plays an important role in health and disease. Despite the undeniable importance of a ‘normal’ microbiota, understanding of the composition and function of this population is currently limited. As methods to characterize the microbiota and its genetic makeup (the microbiome) have evolved, the composition and complexity of this population are starting to be revealed. As is befitting a hindgut fermenter, members of the Firmicutes phylum appear to predominate, yet there are significant populations of numerous other phyla. The microbiome appears to be profoundly altered in certain disease states, and better understanding of these alterations may offer hope for novel preventive and therapeutic measures. The development and increasing availability of next generation sequencing and bioinformatics methods offer a revolution in microbiome evaluation and it is likely that significant advances will be made in the near future. Yet, proper use of these methods requires further study of basic aspects such as optimal testing protocols, the relationship of the fecal microbiome to more proximal locations where disease occurs, normal intra- and inter-horse variation, seasonal variation, and similar factors.
Skeletons in the Closet: Transitional Justice in Post-Communist Europe. By Monika Nalepa
Authors: Gibson James L.
Published: May 2012

Skeletons in the Closet: Transitional Justice in Post-Communist Europe. By Monika Nalepa. New York: Cambridge University Press, 2010. 328p. $88.00 cloth, $27.00 paper.

In the not-too-distant past, systematic transitional justice research was a rarity. Normative treatises on various aspects of the justice of transitions have long been a staple of the human rights literature, but empirical and analytical inquiries into the causes and consequences of efforts to deal with the past have not.
Terrorism and Civil War: A Spatial and Temporal Approach to a Conceptual Problem
Authors: Findley Michael G. , Young Joseph K.
Published: May 2012

What is the relationship between civil war and terrorism? Most current research on these topics either explicitly or implicitly separates the two, in spite of compelling reasons to consider them together. In this paper, we examine the extent to which terrorism and civil war overlap and then unpack various temporal and spatial patterns. To accomplish this, we use newly geo-referenced terror event data to offer a global overview of where and when terrorist events happen and whether they occur inside or outside of civil war zones. Furthermore, we conduct an exploratory analysis of six separate cases that have elements of comparability but also occur in unique contexts, which illustrate some of the patterns in terrorism and civil war. The data show a high degree of overlap between terrorism and ongoing civil war and, further, indicate that a substantial amount of terrorism occurs prior to civil wars in Latin America, but yet follows civil war in other regions of the world. While the study of terrorism and of civil war mostly occurs in separate scholarly communities, we argue for more work that incorporates insights from each research program and we offer a possibility for future research by considering how geo-referenced terror and civil war data may be utilized together. More generally, we expect these results to apply to a wide variety of attitudes and behaviors in contentious politics.
Retreating from the Brink: Theorizing Mass Violence and the Dynamics of Restraint
Authors: Straus Scott
Published: May 2012

The research problem driving this paper is the absence of a strong theory that accounts for variation among cases that have similar probabilities of escalating to genocide and similar forms of organized (usually state-led) mass violence against civilians. Much of the existing theory on genocide focuses on explaining under what conditions and by what processes regimes commit large-scale violence against civilians. I argue that a critical missing dimension to studies of genocide, but also more generally to the study of political violence, is a methodological recognition of negative cases and a theoretical recognition of the dynamics of restraint that helps to explain such negative cases. That is, in addition to asking what causes leaders to choose to escalate violence, I argue that scholars should emphasize conditions that prompt moderation, de-escalation, or non-escalation. I propose an alternative framework for how to conceptualize the process of political violence and review the literature to identify key restraint mechanisms at micro, meso, and macro levels of analysis. I further articulate a provisional theory of genocide using this new analytical framework. I illustrate my argument with an empirical analysis of mass violence cases in Sub-Saharan Africa since independence, and with a more in-depth analysis of comparable crises in Rwanda and Côte d'Ivoire, where the trajectories of violence differed significantly. While this paper draws on extensive empirical research, my primary purpose is not to advance a developed new theory or to test particular hypotheses, but rather to outline a research agenda that promises to draw from and contribute to recent work on the comparative politics of violence.
Too Much Information? Political Science, the University, and the Public Sphere
Authors: Anderson Lisa
Published: May 2012

This article argues that the technological structure of the modern world has reshaped drastically the role of political scientists as purveyors of information. Only a few decades ago, scholars were still central to the development, collection and dissemination of knowledge. But the transformation in the availability of data due to the proliferation of social media and research engines creates a new environment in which scholars can no longer claim to be the erudite carriers of hard-to-get facts. In order to play a constructive role in this quickly changing setting, political scientists need to invent a new identity for themselves as active practitioners engaged in a dynamic dialogue with students and policymakers.
The value of high‐frequency, high‐precision methane isotopologue measurements for source and sink estimation
Authors: Rigby M. , Manning A. J. , Prinn R. G.
Published: May 2012

We present an observing system simulation experiment examining the potential benefits of new methane isotopologues measurements for global‐ and national‐scale source and sink inversions. New measurements are expected in the coming years, using quantum cascade laser spectroscopy with sample preconcentration, that will allow observations ofδ13C ‐ CH4 and δD ‐ CH4at approximately hourly intervals and higher precision than previously possible. Using model‐generated ‘pseudo‐data’, we predict the variability that these new systems should encounter in the atmosphere, and estimate the additional uncertainty reduction that should result from their use in source and sink inversions. We find that much of theδ‐value variability from seasonal to daily timescales should be resolvable at the target precision of the new observations. For global source estimation, we find additional uncertainty reductions of between 3–9 Tg/year for four major source categories (microbial, biomass burning, landfill and fossil fuel), compared to mole fraction‐only inversions, if the higher end of the anticipated isotopologue‐measurement precisions can be achieved. On national scales, we obtain average uncertainty reductions of ∼10% of the source strength for countries close to high‐frequency monitoring sites, although the degree of uncertainty reduction on such small scales varies significantly (from close to 0% to almost 50%) for different sources and countries.
Net currents in the wave bottom boundary layer: On waveshape streaming and progressive wave streaming
Authors: Kranenburg Wouter M. , Ribberink Jan S. , Uittenbogaard Rob E. , Hulscher Suzanne J. M. H.
Published: May 2012

The net current (streaming) in a turbulent bottom boundary layer under waves above a flat bed, identified as potentially relevant for sediment transport, is mainly determined by two competing mechanisms: an onshore streaming resulting from the horizontal non‐uniformity of the velocity field under progressive free surface waves, and an offshore streaming related to the nonlinearity of the waveshape. The latter actually contains two contributions: oscillatory velocities under nonlinear waves are characterized in terms of velocity‐skewness and acceleration‐skewness (with pure velocity‐skewness under Stokes waves and acceleration‐skewness under steep sawtooth waves), and both separately induce offshore streaming. This paper describes a 1DV Reynolds‐averaged boundary layer model withk‐εturbulence closure that includes all these streaming processes. The model is validated against measured period‐averaged and time‐dependent velocities, from 4 different well‐documented laboratory experiments with these processes in isolation and in combination. Subsequently, the model is applied in a numerical study on the waveshape and free surface effects on streaming. The results show how the dimensionless parameterskh (relative water depth) and A/kN (relative bed roughness) influence the (dimensionless) streaming velocity and shear stress and the balance between the mechanisms. For decreasing kh, the relative importance of waveshape streaming over progressive wave streaming increases, qualitatively consistent with earlier analytical modeling. Unlike earlier results, simulations for increased roughness (smaller A/kN) show a shift of the streaming profile in onshore direction for all kh. Finally, the results are parameterized and the possible implications of the streaming processes on sediment transport are shortly discussed.
Continuous measurements of net CO2 exchange by vegetation and soils in a suburban landscape
Authors: Peters Emily B. , McFadden Joseph P.
Published: May 2012

In a suburban neighborhood of Minneapolis–Saint Paul, Minnesota, USA, we simultaneously measured net CO2 exchange of trees using sap flow and leaf gas exchange measurements, net CO2exchange of a turfgrass lawn using eddy covariance from a portable tower, and total surface‐atmosphere CO2 fluxes (FC) using an eddy covariance system on a tall tower. Two years of continuous measurements showed that net CO2exchange varied among vegetation types, with the largest growing‐season (Apr–Nov) net CO2 uptake on a per cover area basis from evergreen needleleaf trees (−603 g C m−2), followed by deciduous broadleaf trees (−216 g C m−2), irrigated turfgrass (−211 g C m−2), and non‐irrigated turfgrass (−115 g C m−2). Vegetation types showed seasonal patterns of CO2exchange similar to those observed in natural ecosystems. Scaled‐up net CO2 exchange from vegetation and soils (FC(VegSoil)) agreed closely with landscape FC measurements from the tall tower at times when fossil fuel emissions were at a minimum. Although FC(VegSoil) did not offset fossil fuel emissions on an annual basis, the temporal pattern of FC(VegSoil) did significantly alter the seasonality of FC. Total growing season FC(VegSoil)in recreational land‐use areas averaged −165 g C m−2 and was dominated by turfgrass CO2 exchange (representing 77% of the total), whereas FC(VegSoil) in residential areas averaged −124 g C m−2 and was dominated by trees (representing 78% of the total). Our results suggest urban vegetation types can capture much of the variability required to predict seasonal patterns and differences in FC(VegSoil) that could result from changes in land use or vegetation composition in temperate cities.
Are two elements better than one? Dual isotope‐ratio detrending of evaporative effects on lake carbonate paleoelevation proxies
Authors: Horton Travis W. , Oze Christopher
Published: May 2012

Stable isotope‐based proxy methods enhance our ability to interpret geodynamical histories for tectonic provinces via paleoelevational reconstructions. These methods require that the unmodified isotopic composition of meteoric water is recorded by authigenic minerals, a critical assumption that has not been tested across wide‐ranging environmental and topographical contexts. Here, we show that Quaternary lake carbonateδ18O values are not strongly, nor significantly, correlated with regional elevation due to the isotopic modification of in‐flow waters following entry into the lake environment. These modifications are largely caused by surface water evaporation, and can result in >3 km errors in paleoelevation estimates if not accounted for. However, our analysis suggests that positive shifts in surface waterδ18O are accompanied by similar magnitude shifts in δ13C‐DIC. This positive co‐variation inδ18O and δ13C may be used to detrend lake carbonate compositions for the effects of surface water evaporation using a parameter we define here as the ‘13C‐excess’. When Tibetan lakes are excluded from the data set,13C‐excess values are significantly correlated with mean up‐slope hypsometric altitude with an error of ±500 m. Application of the13C‐excess approach to Cenozoic lake carbonate records from the western U.S. Cordillera both challenges and reinforces previous paleoelevational interpretations based onδ18O alone.
Near‐synchronous and delayed initiation of long run‐out submarine sediment flows from a record‐breaking river flood, offshore Taiwan
Authors: Carter L. , Milliman J. D. , Talling P. J. , Gavey R. , Wynn R. B.
Published: May 2012

Subsea fiber‐optic telecommunication cables can break under fast sediment flows that travel 100s of kilometers through the deep ocean in response to earthquakes and submarine landslides. Similar flows are inferred to form from major river floods whose sediment‐laden waters plunge and travel along the seabed. However, the complex initiation of flood‐related flows and their hazard potential have not been observed until now. Here we use cable fault data from the Gaoping Canyon/Manila Trench off Taiwan to show that a major river flood, formed during Typhoon Morakot (2009), generated two, long run‐out, destructive sediment flows; one during peak flood and the other 3 days later. The latter flow was more damaging with speeds and run‐out similar to that of landslide‐triggered turbidity currents formed in the same catchment. If the second flow was due to remobilized canyon sediment, it occurred during low earthquake (>Mw 2.0) activity, suggesting other triggering mechanisms.
Projected changes to precipitation extremes for northeast Canadian watersheds using a multi‐RCM ensemble
Authors: Monette A. , Sushama L. , Khaliq M. N. , Laprise R. , Roy R.
Published: May 2012

This study focuses on projected changes to seasonal (May–October) single‐ and multiday (i.e., 1‐, 2‐, 3‐, 5‐, 7‐, and 10‐day) precipitation extremes for 21 Northeast Canadian watersheds using a multi‐Regional Climate Model (RCM) ensemble available through the North American Regional Climate Change Assessment Program (NARCCAP). The set of simulations considered in this study includes simulations performed by six RCMs for the 1980–2004 period driven by National Centre for Environmental Prediction reanalysis II and those driven by four Atmosphere‐Ocean General Circulation Models (AOGCMs) for the current 1971–2000 and future 2041–2070 periods. Regional frequency analysis approach is used to develop projected changes to selected 10‐, 30‐ and 50‐yr return levels of precipitation extremes. The performance errors due to internal dynamics and physics of the RCMs and those due to the lateral boundary data from driving AOGCMs are studied. The use of a multi‐RCM ensemble enabled a simple quantification of RCMs' structural and AOGCM related uncertainties in terms of the coefficient of variation. In general, the structural uncertainty appears to be larger than that associated with the choice of the driving AOGCM for majority of the precipitation characteristics and watersheds considered. Analyses of ensemble‐averaged projected changes to various return levels show an increase for most of the watersheds, with smaller changes and higher uncertainties over the southeasternmost watersheds compared to the rest. It is expected that increases in return levels of precipitation extremes will have important implications for water resources related activities such as hydropower generation in this region of Canada.
Linear interference and the initiation of extratropical stratosphere‐troposphere interactions
Authors: Smith Karen L. , Kushner Paul J.
Published: May 2012

Vertical fluxes of wave activity from the troposphere to the stratosphere correlate negatively with the Northern Annular Mode (NAM) index in the stratosphere and subsequently in the troposphere. Recent studies have shown that stratospheric NAM variability is also negatively correlated with the amplitude of the wave pattern coherent with the large‐scale climatological stationary wavefield; when the climatological stationary wavefield is amplified or attenuated, the stratospheric jet correspondingly weakens or strengthens. Here we quantify the importance of this linear interference effect in initiating stratosphere‐troposphere interactions by performing a decomposition of the vertical wave activity flux using reanalysis data. The interannual variability in vertical wave activity flux in both the Northern and Southern Hemisphere extratropics is dominated by linear interference of quasi‐stationary waves during the season of strongest stratosphere‐troposphere coupling. Composite analysis of anomalous vertical wave activity flux events reveals the significant role of linear interference and shows that “linear” and “nonlinear” events are essentially independent. Linear interference is the dominant contribution to the vertical wave activity flux anomalies preceding displacement stratospheric sudden warmings (SSWs) while split SSWs are preceded by nonlinear wave activity flux anomalies. Wave activity variability controls the timing of stratospheric final warmings, and this variability is shown to be dominated by linear interference, particularly in the Southern Hemisphere. The persistence of the linear interference component of the vertical wave activity flux, corresponding to persistent constructive or destructive interference between the wave‐1 component of climatological stationary wave and the wave anomaly, may help improve wintertime extratropical predictability.
On the angular effect of residual clouds and aerosols in clear‐sky infrared window radiance observations: Sensitivity analyses
Authors: Nalli Nicholas R. , Barnet Christopher D. , Maddy Eric S. , Gambacorta Antonia
Published: May 2012

Accurate environmental satellite observations and calculations of top‐of‐atmosphere infrared (IR) spectral radiances are required for the accurate retrieval of environmental data records (EDRs), including atmospheric vertical temperature and moisture profiles. For this reason it is important that systematic differences between observations and calculations under well‐characterized conditions be minimal, and because most sensors must scan the earth surface to facilitate global coverage, this should include unbiased agreement over the range of zenith angles encountered. This paper investigates the “clear‐sky observations” commonly used in such analyses, which include “cloud‐masked” data (as is typical from imagers), as well as “cloud‐cleared radiances” (as is typical from hyper/ultraspectral sounders). Here we derive simple physical conceptual models to examine quantitatively the longwave IR brightness temperature sensitivity arising from the increasing probability of cloudy fields‐of‐view with zenith angle, or alternatively from increased slant‐path through an aerosol layer. To model the angular effect of clouds, we apply previously derived probability of clear line‐of‐sight (PCLoS) models for single‐layer broken opaque clouds. We then generalize this approach to account for the impact of high, semitransparent (non‐opaque) cold clouds, by deriving analytical expressions for the mean slant‐paths through each of the idealized shapes under consideration. Our sensitivity analyses suggest that contamination by residual clouds and/or aerosols within clear‐sky observations can have a measurable concave‐up impact (i.e., an increasing positive bias symmetric over the scanning range) on the angular agreement of hypothetical “observations” with “calculations.” The magnitudes are typically on the order of couple tenths of a Kelvin or more depending on the residual absolute cloud fraction and optical depth (i.e., the degree of cloud contamination), the residual aerosol optical depth (i.e., the degree of aerosol contamination), the temperature difference between the surface and the residual cloud/aerosol layers, and the shape and vertical aspect ratio of the clouds.
A 300‐year Vietnam hydroclimate and ENSO variability record reconstructed from tree ringδ18O
Authors: Sano Masaki , Xu Chenxi , Nakatsuka Takeshi
Published: May 2012

A tree ring δ18O chronology is developed for the past 300 years (1705–2004) using 6 cypress trees from northern Vietnam to reconstruct long‐term hydroclimatic variations in the summer monsoon season. To the best of our knowledge, this is the first well‐replicated tree ringδ18O chronology from Southeast Asia, as well as the longest yet produced. Response analyses reveal that tree ring δ18O is significantly correlated with temperature, precipitation, and the Palmer Drought Severity Index (PDSI) during the period May–October, with highest correlation to the PDSI. Our δ18O chronology accounts for 44% of the PDSI variance, and is in good agreement with a 52‐year tree ringδ18O chronology from northern Laos (r = 0.77), indicating that regional hydroclimatic signals are well recorded in the δ18O data. Spatial correlation analyses with global sea surface temperatures suggest that the tropical Pacific plays an important role in modulating hydroclimate over the study region. Further, the δ18O chronology correlates significantly with El Niño–Southern Oscillation (ENSO)‐related indices, and is therefore used to reconstruct the annual Multivariate ENSO Index. Because previously published ENSO reconstructions are based mainly on proxy records originating from North America and/or the tropical Pacific, the future development of a tree ringδ18O network from mainland Southeast Asia could lead to an independent and more robust reconstruction of ENSO variability.
An early Lutetian carbon‐cycle perturbation: Insights from the Gorrondatxe section (western Pyrenees, Bay of Biscay)
Authors: Payros Aitor , Ortiz Silvia , Alegret Laia , Orue‐Etxebarria Xabier , Apellaniz Estibaliz , Molina Eustoquio
Published: May 2012

A distinctive low‐carbonate interval interrupts the continuous limestone‐marl alternation of the deep‐marine Gorrondatxe section at the early Lutetian (middle Eocene) C21r/C21n Chron transition. The interval is characterized by increased abundance of turbidites and kaolinite, a 3‰ decline in the bulk δ13C record, a >1‰ decline in benthic foraminiferal δ13C followed by a gradual recovery, a distinct deterioration in foraminiferal preservation, high proportions of warm‐water planktic foraminifera and opportunistic benthic foraminifera, and reduced trace fossil and benthic foraminiferal diversity, thus recording a significant environmental perturbation. The onset of the perturbation correlates with the C21r‐H6 event recently defined in the Atlantic and Pacific oceans, which caused a 2°C warming of the seafloor and increased carbonate dissolution. The perturbation was likely caused by the input of 13C‐depleted carbon into the ocean‐atmosphere system, thus presenting many of the hallmarks of Paleogene hyperthermal deposits. However, from the available data it is not possible to conclusively state that the event was associated with extreme global warming. Based on our analysis, the perturbation lasted 226 kyr, from 47.44 to 47.214 Ma, and although this duration suggests that the triggering mechanism may have been similar to that of the Paleocene‐Eocene Thermal Maximum (PETM), the magnitude of the carbon input and the subsequent environmental perturbation during the early Lutetian event were not as severe as in the PETM.
Neurotoxicity Biomarkers in Experimental Acute and Chronic Brain Injury
Authors: Danilenko ULIANA I. , Khunteev GERMAN A. , Bagumyan ARTHUR , Izykenova GALINA A.
Published: May 2012

Mild traumatic brain injury (TBI) is believed to induce glutamate-mediated neurotoxicity, causing alterations in ionotropic glutamate receptors with subsequent brain injury sequelae. In this chapter, the possibility of peptide fragments of ionotropic glutamate receptors detected in the blood of rodents to serve as autoantigens and autoantibodies is explored using experimental models of mild brain injury. Effects of potential endogenous peptide inhibition of ionotropic glutamate receptors for preventive treatment of brain injury are also explored.
Fashioning NAMD, a History of Risk and Reward: Klaus Schulten Reminisces
Authors: Pollack Lisa
Published: May 2012

The freely available software code NAMD focuses on molecular dynamics simulations and is tailored for parallel computers. Although its emergence on the scene was circa 1995, its roots go back to 1987, when Klaus Schulten wagered all his grant money on two young physics students who promised to build him his own parallel supercomputer. This episode educated Schulten in the possibilities of using parallel computers in his own work, and he amassed a team of colleagues and students who created what NAMD is today. This is the backstory of NAMD and a scientist's turn to parallel computing, as recalled by Klaus Schulten. It is a history that encompasses instincts, hurdles and ultimately, personal risks.
Coarse-grain Protein Models
Authors: Ceres N. , Lavery R.
Published: May 2012

Coarse-graining is a powerful approach for modeling biomolecules that, over the last few decades, has been extensively applied to proteins. Coarse-grain models offer access to large systems and to slow processes without becoming computationally unmanageable. In addition, they are very versatile, enabling both the protein representation and the energy function to be adapted to the biological problem in hand. This review concentrates on modeling soluble proteins and their assemblies. It presents an overview of the coarse-grain representations, of the associated interaction potentials, and of the optimization procedures used to define them. It then shows how coarse-grain models have been used to understand processes involving proteins, from their initial folding to their functional properties, their binary interactions, and the assembly of large complexes.
Molecular Dynamics and Force Field Based Methods for Studying Quadruplex Nucleic Acids
Authors: Haider Shozeb M , Neidle Stephen
Published: May 2012

This chapter firstly introduces the concept of quadruplex nucleic acids, summarizing their major features. Molecular dynamics simulations on these systems are described, outlining the force-fields that have been used and the particular challenges posed by quadruplexes. The treatment of quadruplex electrostatics is uniquely complicated by the presence of an ion channel in these structures. The simulations and theoretical studies of quadruplex folding/unfolding that have been reported in the literature are critically summarized, as are various approaches to studying the energetics of quadruplex ligand complexes.
The Structure and Folding of Helical Junctions in RNA
Authors: Lilley David M. J.
Published: May 2012

Helical junctions are discontinuities in a double-stranded nucleic acid, where a number of helices are connected through the covalent continuity of their strands. RNA can be viewed as double-helical segments that are connected by junctions. Junctions are very common structural elements in natural RNA species, affecting the trajectory of helices, mediating long range tertiary interactions and stabilizing medium-sized RNA species. Most natural junctions have formally-single stranded regions that connect the helical segments. Perfect four-way junctions (4H) exist, but many four-way junctions have single-stranded connecting sections. Three-way junctions almost always have at least one single-stranded section between helices. Pairwise coaxial stacking is a major driving force for the folding of helical junctions, and occurs in the majority of cases. Most have at least one pair of stacked helices; in the case of four-way junctions there are usually two stacked pairs. Two or more stacking conformers are usually possible, but the lowest free energy form normally places the fewest connecting nucleotides onto continuous strands. Single molecule experiments reveal interconversion of conformers. Other interconversions are also observed, such as between antiparallel and parallel conformations of 4H RNA junctions. These processes may provide flexibility during the biogenesis and assembly of complex RNA-based cellular species.
Dispersion-free component of non-covalent interaction via mutual polarization of fragment densities
Authors: Modrzejewski Marcin , Rajchel Łukasz , Szczęśniak Małgorzata M. , Chałasiński Grzegorz
Published: May 2012

Comprehensive tests within a diverse set of noncovalently bonded systems are carried out to assess the performance of the recently-developed dispersion-free approach in the framework of density functional theory [Ł. Rajchel, P. Żuchowski, M. Szczęśniak, and G. Chałasiński, Phys. Rev. Lett. 104, 163001 (2010)]10.1103/PhysRevLett.104.163001. A numerical algorithm which cures the convergence problems of the previous implementation is presented.
Using an incremental mean first passage approach to explore the viscosity dependent dynamics of the unbiased translocation of a polymer through a nanopore
Authors: de Haan Hendrick W. , Slater Gary W.
Published: May 2012

Noting the limitations of the standard characterization of translocation dynamics, an incremental mean first passage process methodology is used to more completely map the unbiased translocation of a polymer through a nanopore. In this approach, the average time t0 required to reach successively increasing displacements for the first time is recorded – a measure shown to be more commensurate with the mean first passage nature of translocation. Applying this methodology to the results of Langevin dynamics simulations performed in three dimensions across a range of viscosities, a rich set of dynamics spanning regular diffusion at low viscosities to sub-diffusion at higher viscosities is revealed. Further, while the scaling of the net translocation time τ with polymer length N is shown to be viscosity-dependent, common regimes are found across all viscosities: super-diffusive behaviour at short times, an N-independent backbone consistent with τ ∼ N2.0 at low viscosities and τ ∼ N2.2 at higher viscosities for intermediate times, and N-dependent deviations from the backbone near the completion of translocation.
Vacuum nanoelectronics: Back to the future?—Gate insulated nanoscale vacuum channel transistor
Authors: Han Jin-Woo , Sub Oh Jae , Meyyappan M.
Published: May 2012

A gate-insulated vacuum channel transistor was fabricated using standard silicon semiconductor processing. Advantages of the vacuum tube and transistor are combined here by nanofabrication. A photoresist ashing technique enabled the nanogap separation of the emitter and the collector, thus allowing operation at less than 10 V. A cut-off frequency fT of 0.46 THz has been obtained. The nanoscale vacuum tubes can provide high frequency/power output while satisfying the metrics of lightness, cost, lifetime, and stability at harsh conditions, and the operation voltage can be decreased comparable to the modern semiconductor devices.
Density and birefringence of a highly stable α,α,β-trisnaphthylbenzene glass
Authors: Dalal Shakeel S. , Sepúlveda A. , Pribil Greg K. , Fakhraai Zahra , Ediger M. D.
Published: May 2012

Spectroscopic ellipsometry has been used to understand the properties of α,α,β-trisnaphthylbenzene (ααβ-TNB) glasses vapor-deposited at a substrate temperature of 295 K (0.85 Tg). In a single temperature ramping experiment, a range of properties of the as-deposited glass can be measured, including density, fictive temperature, onset temperature, thermal expansion coefficient, and birefringence. The vapor-deposited ααβ-TNB glass is 1.3% more dense than the ordinary glass prepared by cooling at 1 K/min, is found to be birefringent, has a fictive temperature 35 K below that of the ordinary glass, and an onset temperature 20 K above that of the ordinary glass. The thermal expansion coefficient of the vapor-deposited ααβ-TNB glass is 14% lower than that of the ordinary glass, indicating that lower portions of the potential energy landscape have more harmonic potential minima than the parts accessible to the ordinary glass.
Imaging ion-molecule reactions: Charge transfer and C-N bond formation in the C+ + NH3 system
Authors: Pei Linsen , Farrar James M.
Published: May 2012

The velocity mapping ion imaging method is applied to the ion-molecule reactions occurring between C+ and NH3. The velocity space images are collected over the relative collision energy range from 1.5 to 3.3 eV, allowing both product kinetic energy distributions and angular distributions to be obtained from the data. The charge transfer process appears to be direct, dominated by long-range electron transfer that results in minimal deflection of the products. The product kinetic energy distributions are consistent with a process dominated by energy resonance. The kinetic energy distributions for C-N bond formation appear to scale with the total available energy, providing strong evidence that energy in the [CNH3]+ precursor to products is distributed statistically. The angular distributions for C-N bond formation show pronounced forward-backward symmetry, as expected for a complex that resembles a prolate symmetric top decaying along its symmetry axis.