bluuebunny/crossref_metadata_2025 huggingface dataset:
Energy fluxes and evaporation mechanisms in an Atlantic blanket bog in southwestern Ireland
Authors: Sottocornola Matteo , Kiely Gerard
Published: November 2010

Water and energy fluxes control the development of northern peatlands and influence their carbon budget. Blanket bogs are peatlands that occur in temperate maritime regions where precipitation is much greater than evapotranspiration (ET). In this paper, five years (October 2002–September 2007) of ET and energy fluxes derived from eddy‐covariance measurements were analyzed in the context of the predicted climate change for Ireland. Monthly ET at the Glencar Atlantic blanket bog varied little, ranging between a minimum of 12 mm month−1 and a maximum of 56 mm month−1 over the five years, resulting in an annual ET average of 394 mm, with typical highest daily values of 2.5–3.0 mm. Compared to other peatland types, Glencar had lower summer ET and a lower ET/potential ET ratio, despite having higher precipitation and water table. The ET was limited not only by the low vapor pressure deficit and cool summer temperatures but also by the low cover of vascular plants and mosses (essential for transpiration). The energy budget was similar to other peatland types in terms of net radiation and sensible heat fluxes, but had lower latent and higher ground heat fluxes. A comparison among the five years suggests that the predicted climate change (greater winter precipitation, lower summer precipitation, and higher all year round temperatures) will probably increase winter ET, while the summer energy flux patterns will not be profoundly affected. However, if the frequency of summer rain events should diminish, the moss component of these ecosystems may become water stressed, ultimately leading to lower evapotranspiration.
RNA channelling by the eukaryotic exosome
Authors: Malet Hélène , Topf Maya , Clare Daniel K , Ebert Judith , Bonneau Fabien , Basquin Jerome , Drazkowska Karolina , Tomecki Rafal , Dziembowski Andrzej , Conti Elena , Saibil Helen R , Lorentzen Esben
Published: November 2010

The eukaryotic exosome is a key nuclease for the degradation, processing and quality control of a wide variety of RNAs. Here, we report electron microscopic reconstructions and pseudo‐atomic models of the ten‐subunit Saccharomyces cerevisiae exosome in the unbound and RNA‐bound states. In the RNA‐bound structures, extra density that is visible at the entry and exit sites of the exosome channel indicates that a substrate‐threading mechanism is used by the eukaryotic exosome. This channelling mechanism seems to be conserved in exosome‐like complexes from all domains of life, and might have been present in the most recent common ancestor.
Receptor for activated C kinase 1 stimulates nascent polypeptide‐dependent translation arrest
Authors: Kuroha Kazushige , Akamatsu Mayuko , Dimitrova Lyudmila , Ito Takehiko , Kato Yuki , Shirahige Katsuhiko , Inada Toshifumi
Published: November 2010

Nascent peptide‐dependent translation arrest is crucial for the quality control of eukaryotic gene expression. Here we show that the receptor for activated C kinase 1 (RACK1) participates in nascent peptide‐dependent translation arrest, and that its binding to the 40S subunit is crucial for this. Translation arrest by a nascent peptide results in Dom34/Hbs1‐independent endonucleolytic cleavage of mRNA, and this is stimulated by RACK1. We propose that RACK1 stimulates the translation arrest that is induced by basic amino‐acid sequences that leads to endonucleolytic cleavage of the mRNA, as well as to co‐translational protein degradation.
Adapting natural resource management to climate change on the Olympic Peninsula
Authors: Halofsky Jessica , Peterson David
Published: November 2010

Climate change presents a major challenge to natural resource managers both because of the magnitude of potential effects of climate change on ecosystem structure, process, and function, and because of the uncertainty associated with those potential ecological effects. Concrete ways to adapt to climate change are needed to help natural resource managers take the first steps to incorporate climate change into management and take advantage of opportunities to balance the negative effects of climate change. We initiated a climate change adaptation case study at Olympic National Forest and Olympic National Park to determine how to adapt management of federal lands on the Olympic Peninsula to climate change. As a part of the case study process, we conducted a vulnerability assessment that involved a review of available climate model projections to determine likely levels of exposure to climate change on the Olympic Peninsula, and a review of relevant literature and available effects model projections to identify likely climate change sensitivities in each of four focus areas on the Olympic Peninsula, including hydrology and roads, fish, vegetation, and wildlife. We also identified management constraints at the forest and park to evaluate some aspects of institutional capacity to implement adaptive actions. The vulnerability assessment process set the stage for development of adaptation options through scientist-manager workshops.The case study process produced concrete adaptation options for Olympic National Forest and Park and illustrated the utility of place-based vulnerability assessments and scientist-manager workshops in adapting to climate change. A key finding of the assessment was that the current general management at the forest and park, with restoration as a primary goal, is consistent with managing for resilience to prepare ecosystems for a changing climate. However, the effort highlighted some potential issues related to climate change that challenge current precepts and management guidelines, and helped to identify new potential actions, and actions that could be increased and re-prioritized. For example, the case study process identified numerous ways to maintain ecosystem function and biodiversity, and increase resilience to climate change. However, the looming questions of when to consider assisted migration or when and how to redefine exotic species remain for discussion. Although questions remain, the case study process was an essential first step for Olympic National Forest and Olympic National Park in preparing for climate change. The process used and ideas produced can be used to help other natural resource managers in adapting to climate change.
Variable consumer responses to invasion by Microstegium vimineum: The role of indirect effects
Authors: DeVore Jayna , Maerz John
Published: November 2010

Background/Question/Methods

As both basal resources and autogenic ecosystem engineers, plants play an important role in structuring consumer communities. Plant invasion can alter important ecosystem properties such as habitat complexity, nutrient availability, and abiotic properties, and the hyper-productive, high-nutrient nature of many invaders may make the influence of these plants especially pronounced. While direct influences of these processes on competitors and predators may be relatively foreseeable, the consequences of indirect effects on consumers living within these invaded habitats are more difficult to predict. In order to determine the response of various forest floor consumers to invasion by the exotic grass _Microstegium vimineum_ we stocked large enclosures spanning eight independent invasion fronts with metamorphic individuals of three amphibian species; Anaxyrus [Bufo] americanus (American toads), Lithobates [Rana] sphenocephalus (southern leopard frogs), and Notophthalmus viridescens (eastern newts). Using robust capture periods we tracked the survival and growth of these individuals. We also investigated the mechanisms behind these responses by tracking invertebrate abundance and abiotic factors on either side of each of these invasion fronts and performing additional manipulations, such as predator manipulations and analyses of foraging success, designed to investigate the effects of both bottom-up and top-down influences on these consumers.

Results/Conclusions

We found that invasion by M. vimineum could have significant effects on consumer performance (for example, the survival of metamorphic A. americanus was significantly lower in invaded areas) but that the nature and strength of these influences varied between species as well as ontogenetically, as L. sphenocephalus was not similarly affected and the influences on A. americanus dissipated over time. It appears that the negative influences of invasion on metamorphic toad survival were largely driven by top-down processes associated with the accumulation of invertebrate predators in invaded areas, while abiotic and bottom-up influences were more important factors for individuals large or fast enough to escape capture by invertebrate predators. We conclude that the influences of plant invasion on consumer communities can be varied, complicated, and far-reaching.
Plant species diversity and genetic diversity interactively influence community properties and ecosystem processes
Authors: Crawford Kerri , Rudgers Jennifer
Published: November 2010

Background/Questions/Methods:

Biodiversity is a critical element of community properties and ecosystem processes. Both plant species richness and genetic diversity positively affect processes ranging from primary production, ecosystem stability, and the maintenance of diversity. In nature, it is likely that species diversity and genetic diversity interactively affect how communities are structured and ecosystems function. However, the relative contribution of species diversity and genetic diversity to ecological processes has been rarely documented, and potential interactions between the two levels of diversity have not been investigated. Here, I report results from a common garden experiment conducted in a coastal freshwater dune habitat at Sleeping Bear Dunes National Lakeshore in Empire, MI. I manipulated plant species diversity (0, 1, 3, or 6 species) and genetic diversity (0, 1, 3, or 6 populations) within a dominant, dune-building species (Ammophila breviligulata) to address how both levels of diversity simultaneously influence ecological properties and processes.

Results/Conclusions:

In 2008, plant diversity influenced a wide range of ecological responses. Plant species diversity and genetic diversity within the dominant species synergistically increased above-ground biomass production, with biomass increasing the most with genetic diversity when there were 6 plant species present. A similar pattern was found for arthropod morphospecies richness and abundance. Separately, neither species diversity nor genetic diversity affected either biomass production or the arthropod community. Plant diversity also influenced below-ground properties and processes. For example, nematode abundance doubled with both increasing species diversity and genetic diversity, but there was no interaction between the two levels of diversity. These results suggest that interactions between levels of diversity are an important, but often overlooked, aspect of how diversity structures communities and mediates ecosystem processes and suggests that increasing awareness of these interactions may inform conservation and restoration strategies.
UniRule - Automatic Annotation In UniProtKB
Authors: Bridge Alan , Poggioli Diego , O'Donovan Claire
Published: November 2010

The UniProt KnowledgeBase (UniProtKB) provides a stable, comprehensive, freely accessible, centralized resource on protein sequences and functional annotation. UniProtKB consists of two sections: UniProtKB/SwissProt, a section containing records that are manually annotated with information extracted from the literature and curator-evaluated computational analysis, and UniProtKB/TrEMBL, a section containing computationally analysed records enriched with automatic annotation and classification.Automatic annotation is an essential complement to manual annotation, which cannot keep pace with either current or projected rates of growth of UniProtKB. To this end UniProt is developing an integrated annotation system termed UniRule, which is based on both manually curated and automatically generated annotation rules and signatures. UniRule provides a variety of annotation types including protein names, general functional annotation in the form of free text and controlled vocabularies, sequence annotation including domains and residues of functional importance, and inferred family relationships.At the time of writing (UniProtKB release 2010_08), UniRule provides annotations for around 30% of more than 11 million UniProtKB/TrEMBL entries. The UniRule system and plans for its future development will be presented.
Ab initio calculations and synthesis of the off-stoichiometric half-Heusler phase Ni1−xMn1+xSb
Authors: Ekholm M. , Larsson P. , Alling B. , Helmersson U. , Abrikosov I. A.
Published: November 2010

We perform a combined theoretical and experimental study of the phase stability and magnetism of the off-stoichiometric Ni1−xMn1+xSb in the half-Heusler crystal phase. Our work is motivated by the need for strategies to engineer the magnetism of potentially half-metallic materials, such as NiMnSb, for improved performance at elevated temperatures. By means of ab initio calculations we investigate Ni1−xMn1+xSb over the whole composition range 0≤x≤1 of Ni replacing Mn and show that at relevant temperatures, the half-Heusler phase should be thermodynamically stable up to at least x=0.20 with respect to the competing C38 structure of Mn2Sb. Furthermore we find that half-Heusler Ni1−xMn1+xSb retains half-metallic band structure over the whole concentration range and that the magnetic moments of substitutional MnNi atoms display magnetic exchange interactions an order of magnitude larger than the Ni–Mn interaction in NiMnSb. We also demonstrate experimentally that the alloys indeed can be created by synthesizing off-stoichiometric Ni1−xMn1+xSb films on MgO substrates by means of magnetron sputtering.
Dynamics of two identical vortices in linear shear
Authors: Trieling R. R. , Dam C. E. C. , van Heijst G. J. F.
Published: November 2010

The dynamics of two identical vortices in linear shear was studied both numerically and experimentally. Numerical simulations based on the technique of contour dynamics reveal that the vortex evolution in adverse shear is significantly different from that in cooperative shear. Vortices in adverse shear predominantly separate, whereas vortices in cooperative shear predominantly merge. In addition, adverse shear may destruct the vortices much in the same way as a single vortex in adverse shear, whereas cooperative shear stabilizes the vortices and thus enhances the possibility of vortex merger. The critical distance for vortex merger depends strongly on both the sign and the strength of the linear shear and, to a lesser extent, on the initial vorticity distribution. A simple vortex merger criterion is derived based on the interaction of two point vortices in linear shear. The different behavior of vortices in adverse and cooperative shear was confirmed by rotating-tank experiments.
Instantaneous nano-order fragmentation in mullite ceramics triggered by a shock-induced phase transition
Authors: Atou Toshiyuki , Kawai Nobuaki , Ito Shun , Yubuta Kunio , Kikuchi Masae
Published: November 2010

Mullite, a conventional refractory material, was observed to exhibit a peculiar nano-order fragmentation accompanying a phase transition induced by a shock wave. We propose a mechanism for this nanofragmentation, based on a comparative study of mullite-related materials. The microtextures of the mullite-related materials were affected by their initial crystal structure and chemical composition, indicating that oxygen vacancies in the crystal structure play an important role in the nanofragmentation. The results of the present study will help enable the deliberate control of the physical and mechanical properties of materials during high-velocity impact.
Diffuse reflectance spectroscopic mapping imaging applied to art objects materials determination from 200 up to 5000 nm
Authors: Karagiannis G. , Alexiadis D. , Damtsios A. , Sergiadis G. , Salpistis C.
Published: November 2010

The microsampling destructions caused by the sampling of analytical spectroscopic methods are generally not permitted to art objects. Consequently, the development of nondestructive analysis techniques is a necessity. In this work we present a set of signal processing and artificial intelligence techniques which support the operation of a novel device developed for the nondestructive identification of art objects. The proposed device combines ultraviolet, visible, near infrared, and midinfrared spectroscopy in diffuse reflectance mode to identify the materials that exist in each paint layer of an artwork.
Iterative linearized density matrix propagation for modeling coherent excitation energy transfer in photosynthetic light harvesting
Authors: Huo P. , Coker D. F.
Published: November 2010

Rather than incoherent hopping between chromophores, experimental evidence suggests that the excitation energy transfer in some biological light harvesting systems initially occurs coherently, and involves coherent superposition states in which excitation spreads over multiple chromophores separated by several nanometers. Treating such delocalized coherent superposition states in the presence of decoherence and dissipation arising from coupling to an environment is a significant challenge for conventional theoretical tools that either use a perturbative approach or make the Markovian approximation. In this paper, we extend the recently developed iterative linearized density matrix (ILDM) propagation scheme [E. R. Dunkel et al., J. Chem. Phys. 129, 114106 (2008)] to study coherent excitation energy transfer in a model of the Fenna–Matthews–Olsen light harvesting complex from green sulfur bacteria. This approach is nonperturbative and uses a discrete path integral description employing a short time approximation to the density matrix propagator that accounts for interference between forward and backward paths of the quantum excitonic system while linearizing the phase in the difference between the forward and backward paths of the environmental degrees of freedom resulting in a classical-like treatment of these variables. The approach avoids making the Markovian approximation and we demonstrate that it successfully describes the coherent beating of the site populations on different chromophores and gives good agreement with other methods that have been developed recently for going beyond the usual approximations, thus providing a new reliable theoretical tool to study coherent exciton transfer in light harvesting systems. We conclude with a discussion of decoherence in independent bilinearly coupled harmonic chromophore baths. The ILDM propagation approach in principle can be applied to more general descriptions of the environment.
Scaling of strength and ductility in bioinspired brick and mortar composites
Authors: Wilbrink David V. , Utz Marcel , Ritchie Robert O. , Begley Matthew R.
Published: November 2010

This paper provides scaling relationships between constituent properties and the uniaxial tensile response of synthetic “brick and mortar” composite materials inspired by nacre. The macroscopic strength and ductility (work of fracture) are predicted in terms of the brick properties (size, strength, and layout) and interface cohesive properties (e.g., maximum shear and normal stresses and separations). The results illustrate the trade-off between increasing strength and decreasing ductility with the increasing aspect ratio of the bricks. The models can be used to identify optimum mortar properties that maximize toughness for a given brick strength.
Quenching mechanisms of the optical centers in Eu3+-doped nanophosphors under charge transfer excitation
Authors: Shang Chunyu , Shang Xiaohong , Qu Yuqiu , Li Meicheng
Published: November 2010

As the size of Eu3+-doped phosphors decreases in nanoscale, the top of the valance band is elevated and the zero-phonon charge transfer (CT) energy is decreased; the rigidity of the lattice environment is decreased and the CT state (CTS) coordinate offset is enlarged. The decrease in zero-phonon CT energy and the enlargement of CTS coordinate offset mean the displacement of CTS in the configurational coordinate diagram (CCD). The CTS displacement in CCD results in the decrease in CTS feeding to the emitting D5 states and the increase in transition probability from the CTS to the F7 states, the excitation of the optical centers tends to be relaxed by sending phonons to the host lattice. Based on the quenching mechanisms of the optical centers progressively clarified in this paper, a feasible coating method is proposed to improve the luminescence efficiency for Eu3+-doped nanophosphors under CT excitation.
Nanoparticle arrangement by DNA-programmed self-assembly for catalyst applications
Authors: Maeda Y. , Akita T. , Daté M. , Takagi A. , Matsumoto T. , Fujitani T. , Kohyama M.
Published: November 2010

To examine the applicability of DNA-programmed self-assembly to preparation of nanoparticle-supported catalysts, the authors performed the arrangement control of Au nanoparticles on powder supports (TiO2 and glass) with this scheme. Scanning electron microscopy and atomic force microscopy observations confirmed that designed arrangement of two kinds of Au nanoparticles is possible on powder and crystal supports. Although catalytic activity of Au-particle/TiO2 systems for CO oxidation was almost inhibited by the presence of DNA, it was successfully recovered by the oxygen plasma treatment. These results indicate that the DNA-programmed self-assembly can be used as a preparation method of novel catalysts with designed nanostructures.
Nonstoichiometric BiFe0.9Ti0.05O3 multiferroic ceramics with ultrahigh electrical resistivity
Authors: Gu Yan Hong , Wang Yu , Chen Feng , Chan Helen Lai Wah , Chen Wan Ping
Published: November 2010

BiFeO 3 , BiFe0.9Ti0.1O3, and BiFe0.9Ti0.05O3 ceramics of relatively high perovskite phase content were prepared for a comparison study. While both BiFe0.9Ti0.1O3 and BiFe0.9Ti0.05O3 exhibit similarly improved weak ferromagnetism over BiFeO3, there exists a major difference in the x-ray diffraction patterns of BiFe0.9Ti0.1O3 and BiFe0.9Ti0.05O3, and the leakage current of BiFe0.9Ti0.05O3 is decreased by five orders of magnitude from that of BiFe0.9Ti0.1O3. With an ultrahigh electrical resistivity, over 1×1014 Ω cm, BiFe0.9Ti0.05O3 ceramic displays an especially low dielectric loss, 0.015 at 100 Hz, a remanent polarization Pr of 0.23 μC/cm2 and a remanent magnetization Mr of 0.13 emu/g at room temperature. It is proposed that the Fe-deficiency in BiFe0.9Ti0.05O3 decreases the amount of Fe2+ and leads to the ultrahigh electrical resistivity. Nonstoichiometric compositions should receive more attention for developing high quality BiFeO3 multiferroic materials.
Is Auger recombination the ultimate performance limiter in concentrator solar cells?
Authors: Vossier Alexis , Hirsch Baruch , Gordon Jeffrey M.
Published: November 2010

In principle, Auger recombination should constitute the ultimate limiting mechanism for concentrator photovoltaic performance as optical concentration, and hence current densities, are raised to progressively higher values. In reality, however, the effect will be rate-limiting only in indirect-band-gap solar cells—a point well established for silicon but not yet explored for germanium which comprises the lowest-energy junction in today's ultraefficient commercial multijunction concentrator solar cells. Detailed calculations of when Auger recombination should play a substantial role are presented, and reinforced by existing data.
Measurements of colliding shock wave and supersonic gas flow
Authors: Kaganovich D. , Helle M. H. , Gordon D. F. , Ting A.
Published: November 2010

The collision between a laser generated shock wave and a supersonic flow from a gas jet was studied using pump-probe Schlieren shadowgraphy. The velocity of a gas escaping into vacuum from a high pressure gas jet nozzle was measured and verified in simulation. Time resolved tracking of the shock wave provided critical information about the gas jet vertical velocity and horizontal gas density profile. The measured velocity of the diatomic gas jet was found to be close to the theoretical maximum escape velocity of the gas released into vacuum. Modification of the hemispherical shock wave structure by the supersonic flow was minimal. However, the propagation of the shock wave was observed to be substantially effected by the gas flow.
Electrostatically tunable optomechanical “zipper” cavity laser
Authors: Perahia R. , Cohen J. D. , Meenehan S. , Alegre T. P. Mayer , Painter O.
Published: November 2010

A tunable nanoscale “zipper” laser cavity, formed from two doubly clamped photonic crystal nanobeams, is demonstrated. Pulsed, room temperature, optically pumped lasing action at λ=1.3 μm is observed for cavities formed in a thin membrane containing InAsP/GaInAsP quantum-wells. Metal electrodes are deposited on the ends of the nanobeams to allow for microelectromechanical actuation. Electrostatic tuning over a range of Δλ=20 nm for an applied voltage amplitude of 9 V and modulation at a frequency as high as νm=6.7 MHz of the laser wavelength is demonstrated.
Solution-processed cross-linkable hole selective layer for polymer solar cells in the inverted structure
Authors: Sun Yanming , Gong Xiong , Hsu Ben B. Y. , Yip Hin-Lap , Jen Alex K.-Y. , Heeger Alan J.
Published: November 2010

Solution-processed cross-linkable tetraphenyldiamine-containing material (TPD-BVB) as a highly efficient hole selective transport layer was demonstrated. Polymer solar cells (PSCs) with an inverted structure fabricated with a thin cross-linked TPD-BVB film show comparable efficiency and superior long-term air stability when compared to devices fabricated with poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS). Thus, solution-processed TPD-BVB is an attractive alternative to PEDOT:PSS as a hole extraction layer in inverted structure PSCs.
Anisotropy-axis orientation effect on the magnetization of γ-Fe2O3 frozen ferrofluid
Authors: Nakamae S , Crauste-Thibierge C , Komatsu K , L'Hôte D , Vincent E , Dubois E , Dupuis V , Perzynski R
Published: November 2010

The effect of magnetic anisotropy-axis alignment on the superparamagnetic (SPM) and superspin glass (SSG) states in a frozen ferrofluid has been investigated. The ferrofluid studied here consists of maghemite nanoparticles (γ-Fe2O3, mean diameter = 8.6 nm) dispersed in glycerine at a volume fraction of ∼15%. In the high temperature SPM state, the magnetization of aligned ferrofluid increased by a factor varying between 2 and 4 with respect to that in the randomly oriented state. The negative interaction energy obtained from the Curie–Weiss fit to the high temperature susceptibility in the SPM states as well as the SSG phase onset temperature determined from the linear magnetization curves were found to be rather insensitive to the anisotropy-axis alignment. The low temperature ageing behaviour, explored via ‘zero-field cooled magnetization’ relaxation measurements, however, shows a distinct difference in the ageing dynamics in the anisotropy-axis aligned and randomly oriented SSG states.
Probing single magnetic nanoparticles by polarization-dependent soft x-ray absorption spectromicroscopy
Authors: Rodríguez A Fraile , Kleibert A , Bansmann J , Nolting F
Published: November 2010

Using photoemission electron microscopy, we have measured x-ray absorption (XAS) and x-ray magnetic circular dichroism (XMCD) spectra of single, three-dimensional iron nanoparticles in the size range 6–25 nm. We discuss the feasibility and limits of single-particle XAS and XMCD spectroscopy, in particular the influence of the experimental conditions such as nanofocusing effects, and analytical methods on the resulting spectra. While care must be taken in interpreting peak intensities, the overall line shape is less affected, which allows relative comparisons between different single particles in the ensemble and with reference spectra. Our work reveals that the spectral shape of both the isotropic absorption and the XMCD of single particles is retained for particles down to 6 nm and is in reasonable agreement with that of metallic bulk iron.
X-ray absorption measurements on nanoparticle systems: self-assembled arrays and dispersions
Authors: Antoniak C , Warland A , Darbandi M , Spasova M , Trunova A , Fauth K , Aziz E F , Farle M , Wende H
Published: November 2010

X-ray absorption spectroscopy methods are presented as a useful tool to determine local structure, composition and magnetic moments as well as to estimate the effective anisotropy of substrate supported self-assembled arrays of wet-chemically synthesized FePt nanoparticles. A compositional inhomogeneity within the nanoparticles yields reduced magnetic moments with respect to the corresponding bulk material and may also hinder the formation of the chemically ordered L10 phase in FePt nanoparticles. The latter is indicated by a reduced effective anisotropy, which is one order of magnitude smaller than expected from the known value of the corresponding bulk material.

As a new approach, measurements of the x-ray absorption near-edge structure of Fe-oxide nanoparticles in dispersion are presented and ageing effects are discussed on the basis of multiplet calculations.
Chemical trends in structure and magnetism of bimetallic nanoparticles from atomistic calculations
Authors: Gruner M E
Published: November 2010

By means of large scale first-principles calculations in the framework of density functional theory, structure and magnetism of 561 atom nanoparticles are compared in order to obtain a systematic picture of the evolution with respect to a change in the constitutional elements. The investigation comprises ordered and disordered, cuboctahedral, icosahedral and decahedral morphologies of composition A
265
B
296, where A is one of Mn, Fe and Co and B is Pt and, additionally, with A = Fe and B = Ni, Pd, Pt, Ir and Au. Fe–Ir and Fe–Pd and Co–Pt exhibit in comparison with Fe–Pt an increased tendency to form multiply-twinned structures and prefer segregation of the heavier element to the surface. The latter trend also applies to Fe–Au, where, on the other hand, icosahedral and crystalline motifs are very close in energy. Only in Mn–Pt the formation of multiply-twinned structures is effectively suppressed. The combinations with reduced valence electron concentration, Mn–Pt and Fe–Ir, exhibit a strong preference for antiferromagnetic spin order. The structural and magnetic trends are tentatively related to the change in features in the element and site-resolved electronic density of states.
A pilot genetic study reveals the absence of spatial genetic structure in Norway lobster (Nephrops norvegicus) on fishing grounds in Icelandic waters
Authors: Pampoulie Christophe , Skirnisdottir Sigurlaug , Hauksdottir Sigurbjorg , Olafsson Kristinn , Eiríksson Hrafnkell , Chosson Valérie , Hreggvidsson Gudmundur O. , Gunnarsson Gudmundur H. , Hjorleifsdottir Sigridur
Published: November 2010

Pampoulie, C., Skirnisdottir, S., Hauksdottir, S., Olafsson, K., Eiríksson, H., Chosson, V., Hreggvidsson, G. O., Gunnarsson, G. H., and Hjorleifsdottir, S. 2011. A pilot genetic study reveals the absence of spatial genetic structure in Norway lobster (Nephrops norvegicus) on fishing grounds in Icelandic waters. – ICES Journal of Marine Science, 68: 20–25. Stock structure of Norway lobster off southern Iceland was investigated using 12 microsatellite loci. No genetic method detected significant genetic differentiation among the locations sampled, even among Icelandic samples and an out-group from Scotland. Testing the power of resolution of microsatellite loci, the loci and sample sizes used were sufficient to detect significant genetic differentiation with confidence. The lack of genetic structure is discussed in terms of the level of gene flow, recent isolation of populations, and the statistical power of the experimental design.
An Introduction to Bayesian Inference via Variational Approximations
Authors: Grimmer Justin
Published: November 2010

Markov chain Monte Carlo (MCMC) methods have facilitated an explosion of interest in Bayesian methods. MCMC is an incredibly useful and important tool but can face difficulties when used to estimate complex posteriors or models applied to large data sets. In this paper, we show how a recently developed tool in computer science for fitting Bayesian models, variational approximations, can be used to facilitate the application of Bayesian models to political science data. Variational approximations are often much faster than MCMC for fully Bayesian inference and in some instances facilitate the estimation of models that would be otherwise impossible to estimate. As a deterministic posterior approximation method, variational approximations are guaranteed to converge and convergence is easily assessed. But variational approximations do have some limitations, which we detail below. Therefore, variational approximations are best suited to problems when fully Bayesian inference would otherwise be impossible. Through a series of examples, we demonstrate how variational approximations are useful for a variety of political science research. This includes models to describe legislative voting blocs and statistical models for political texts. The code that implements the models in this paper is available in the supplementary material.
Guidance for Clinical Trials for Children and Adolescents With Chronic Hepatitis C
Authors: Wirth Stefan , Kelly Deirdre , Sokal Etienne , Socha Piotr , Mieli‐Vergani Giorgina , Dhawan Anil , Lacaille Florence , Raymond Agnès Saint , Olivier Sophie , Taminiau Jan
Published: November 2010

Most children with chronic hepatitis C are infected vertically, have a low natural seroconversion rate, and carry a lifetime risk of cirrhosis and cancer. Affected children are usually asymptomatic, and histological findings are mild with a low risk of progression, although 5% develop significant liver disease in childhood.

The use of combination treatment with pegylated interferon‐α and ribavirin has changed the outcome and prognosis for this disease, with approximately 60% of children achieving sustained viral clearance. Combination therapy is not ideal for children because pegylated interferon is administered subcutaneously, impairs growth velocity, and both interferon and ribavirin have significant adverse effects that affect compliance. In addition, approximately 50% of children infected with genotype 1 do not respond to therapy. Thus, additional treatment options are required including improvement in dosing, reduction in the length of treatment, and evaluation of new drugs, such as protease inhibitors, which could be more effective for patients infected with genotype 1.

The primary goal of treatment is to eradicate the infection. The future clinical trial design should ensure that any new drugs demonstrate noninferiority to the present standard regimen in both children and adults. The measure for documenting substantial improvement above present therapy should be increased viral clearance rate or the same clearance rate, with a shorter duration of treatment and/or fewer adverse effects. We do not believe there is any need for a placebo arm because approved therapy is available and new treatments can be compared with present therapy.

Safety measures should include the standard recommended laboratory investigations, growth parameters, quality‐of‐life or psychological measures, and a requirement for long‐term follow‐up for up to 5 years.
Differential gene expression analysis of Paracoccidioides brasiliensis during keratinocyte infection
Authors: Peres da Silva Roberta , Matsumoto Marcelo Teruyuki , Braz Jaqueline Derissi , Voltan Aline Raquel , de Oliveira Haroldo Cesar , Soares Christiane Pienna , Mendes Giannini Maria José Soares
Published: November 2010

Paracoccidioides brasiliensisis the agent of paracoccidioidomycosis, one of the most important systemic fungal diseases in Latin America. This initiates in lung tissue and can subsequently disseminate to other tissues. Clinical manifestations range from localized forms to disseminated disease that can progress to lethality, probably depending on the relationships among the virulence of the fungus, the immune response and the ability to interact with the surface structures and invade epithelial cells and mononuclear cells of the host. It is generally regarded as a multifocal disease, with oral lesions as the prominent feature. The aim of this study was to evaluateP. brasiliensisyeast infection in normal oral keratinocytes (NOKs). The differential expression of mRNAs and proteins was also determined when the fungus was placed in contact with the cell in order to characterize differentially expressed genes and proteins duringP. brasiliensisinfection. After contact with NOKs, the fungus appeared to induce alterations in the cells, which showed cellular extensions and cavitations, probably resulting from changes in the actin cytoskeleton seen at 5 and 8 h after infection. Levels of protein expression were higher after reisolation of the fungus from infected NOK culture compared with culture of the fungus in medium. The analysis identified transcripts related to 19 proteins involved in different biological processes. Transcripts were found with multiple functions including induction of cytokines, protein metabolism, alternative carbon metabolism, zinc transport and the stress response during contact with NOKs. The proteins found suggested that the yeast was in a stress situation, as indicated by the presence of RDS1. Nevertheless, the yeast seemed to be proliferating and metabolically active, as shown by the presence of a proteasome, short-chain acetylator, glucosamine-6-phosphate isomerase and ADP/ATP carrier transcripts. Additionally, metabolic pathways may have been activated in order to eliminate toxic substances from the cell as a zinc transporter was detected, which is a potential target for the development of future drugs.
The interaction between a non-pathogenic and a pathogenic strain synergistically enhances extra-intestinal virulence in Escherichia coli
Authors: Tourret Jérôme , Aloulou Meryem , Garry Louis , Tenaillon Olivier , Dion Sara , Ryffel Bernard , Monteiro Renato C. , Denamur Erick
Published: November 2010

Finding two or more genotypes of a single species within an infected sample is a not infrequent event. In this work, three Escherichia coli strains of decreasing extra-intestinal virulence (pathogenic B2S and B1S strains, and the avirulent K-12 MG1655 strain) were tested in septicaemia and urinary tract infection (UTI) mouse models, either separately or in pairs. Survival was monitored and bacteria were counted in various organs. Serum interleukin (IL)-6, tumour necrosis factor alpha (TNFα) and IL-10 were measured. We show that a mix of high amounts of B1S or of MG1655 with low amounts of B2S killed more rapidly (B1S), or killed more mice (MG1655), than either high amounts of B1S, high amounts of MG1655 or low amounts of B2S separately in the mouse septicaemia model. This bacterial synergy persisted when high amounts of dead or abnormal-LPS K-12 cells were injected together with a low amount of B2S. In both septicaemia and UTI models, significantly more bacteria were recovered from the organs of mice injected with the MG1655/B2S mix than from those of mice injected with the inocula separately. Consistently, in the septicaemia model, more IL-6 was secreted before death by the mice that were injected with the mix of bacteria than by the mice that were injected with the inocula separately. The synergistically enhanced mortality in the case of co-infection in the septicaemia model persisted in RFcγ
−/−, Myd88
−/− and IL-6−/− knockout mice. This synergistically increased virulence resulting from the interaction between an avirulent and a pathogenic strain of the same bacterial species raises questions about the role of avirulent bacteria in the development of some extra-intestinal infections.
Metal patch test results from 1990–2009
Authors: NONAKA Hiromitsu , NAKADA Tokio , IIJIMA Masafumi , MAIBACH Howard I.
Published: November 2010

Although metals are common contact allergens, clinical findings of metal contact dermatitis have varied. Such patients have subsequently become rare in Japan as gold dermatitis caused by ear piercing or baboon syndrome by broken thermometers. To evaluate such clinical findings and to determine the frequency of metal allergy, we analyzed the results of patch testing with 18 metals from 1990–2009. Nine hundred and thirty‐one patients (189 men and 742 women, mean age 39.0 years [standard deviation ± 17.8]) were tested. Metals were applied on the back for 2 days, and the results read with the International Contact Dermatitis Research Group (ICDRG) scoring system 3 days after application. Reactions of + to +++ were regarded as positive. Differences of positive rates between men and women, and patients from 1990–1999 and those from 2000–2009 were analyzed with the χ2‐test. Differences were considered significant at P < 0.05. The metal to which the most patients reacted was 5% nickel sulfate (27.2%), irrespective of sex and phase. Significantly more women reacted to nickel sulfate (P < 0.01), mercuric chloride (P < 0.05) and gold chloride (P < 0.01) than men. Significantly more patients in the 1990s reacted to palladium chloride, mercuric chloride and gold chloride (all P < 0.01) than from 2000–2009. Nickel has been the most common metal allergen and mercury‐sensitivity has decreased over 19 years in Japan.
The effects of lactic acid bacteria on the fermentation, aerobic stability and nutritive value of maize silage
Authors: Filya I. , Sucu E.
Published: November 2010

Maize was harvested at one‐third milk line (297 g kg−1 DM) stage. All inoculants were applied at 1 × 106 cfu g−1 of fresh forage. After treatment, the chopped forages were ensiled in 1·5‐L anaerobic jars. Three jars per treatment were sampled on days 2, 4, 7, 12 and 90 after ensiling, for chemical and microbiological analysis. Homofermentative LAB‐inoculated silages had lower pH and higher lactate:acetate ratio (except for Lactobacillus plantarum/Pediococcus cerevisiae and L. plantarum/Propionibacterium acidipropionici) than the control and both heterofermentative LAB‐inoculated silages. Both L. buchneri inhibited yeast growth and CO2 production during exposure of silage to air. The L. plantarum/P. cerevisiae, L. plantarum (Ecosyl) and L. plantarum/Enterococcus faecium‐inoculated silages had higher dry‐matter digestibility than the control and L. buchneri‐inoculated silages. Inoculants did not affect digestibility of neutral detergent fibre, except for L. buchneri (Biotal), organic matter nor ME content of silages. The LAB silage inoculants generally had a positive effect on maize silage characteristics in terms of lower pH and shifting fermentation toward lactate with homofermentative LAB or toward acetate with L. buchneri. The use of L. buchneri can improve the aerobic stability of maize silages by the inhibition of yeast activity.
Ultrasound detects joint damage and bleeding in haemophilic arthropathy: a proposal of a score
Authors: MELCHIORRE D. , LINARI S. , INNOCENTI M. , BISCOGLIO I. , TOIGO M. , CERINIC M. M. , MORFINI M.
Published: November 2010

Summary.  Haemarthrosis triggers haemophilic arthropathy (HA) because bleeding starts synovitis immediately, damages cartilage and leads to loss of function and disability. The aim of our study was to investigate the capacity of ultrasonography (US) in detecting bleeding and joint damage in HA. The joints of 62 patients (pts) with haemophilia A or haemophilia B were consecutively evaluated and scored (score ranging from 0 to 21) for effusion (E), bone remodelling (BR), cartilage damage (CD), synovial hypertrophy (SH), haemosiderin (H), osteophytes (O), haemarthrosis (Hae), erosion (Er) and fibrotic septa (FS) with US. X‐rays [Pettersson Score (PXS)] were performed in 61 patients and clinical evaluation [World Federation Haemophiliac orthopaedic score (WFHO)] was performed in all patients. A total of 20 healthy subjects and 20 patients affected by Rheumatoid Arthritis (RA) were used as controls. Power Doppler US (PDUS) was performed in all patients on the knee, ankle and elbow joints. A total of 83 joints were studied (50 knees; 12 elbows and 21 ankles). US showed effusion in 57 joint, bone remodelling in 62, cartilage damage in 64, synovial hypertrophy in 45, haemosiderin in 39, osteophytes in 30, haemarthrosis in 24, erosion in 5 and fibrotic septa in 3. The X‐rays score showed remodelling in 47 joints, narrowing joint space in 44, displacement/angulation in 39, osteoporosis in 42, subchondral irregularity in 44, subchondral cyst formation in 37, osteophytes in 36 and erosions in 25. The US score in healthy subjects was always ≤5 (range 0 to 4). In haemophiliacs, 34 of 83 joints showed US score ≤5, and 49 US score >5. Joints with US score ≤5 had a low PXS (SRCC = 0.375, P < 0.01) and joints with US score >5 showed a high PXS (SRCC = 0.440, P < 0.01). A significant correlation between US score and PXS for bone remodelling [Spearman’s rho Correlation Coefficient (SRCC) = 0.429, P < 0.01] and for osteophytes (SRCC = 0.308 P < 0.05) was found. The correlation between the US score and number of bleedings in 83 joints was very significant (SRCC = 0.375, P < 0.01). A total of 24 bleeding joints were identified and verified with aspiration of haematic fluid. US may detect bone and cartilage alterations and synovitis. Indeed, PDUS identified bleeding also in asymptomatic joints and was able to show different entity of haemarthrosis. US may be a feasible and reliable tool to evaluate joint modifications in HA.
Variation partitioning in canonical ordination reveals no effect of soil but an effect of co‐occurring species on translocation success in Iris atrofusca
Authors: Volis Sergei , Dorman Michael , Blecher Michael , Sapir Yuval , Burdeniy Lev
Published: November 2010

1. Despite being expensive, complicated and less successful than the conservation of primary habitat, translocation is rapidly gaining importance as a conservation approach due to accelerated loss of natural environment. Finding the optimal abiotic and biotic conditions needed for successful translocation of plants can be difficult for species with limited information on prior distribution. Unfortunately, this is often the case with endangered plant species, including those urgently needing action.

2. We present a method of evaluating the relative importance of multiple environmental parameters in translocation success. This method is based on the application of variation partitioning in canonical ordination and it allows usage of not only multiple independent biotic and abiotic variables, but also multiple dependent variables for fitness estimates.

3. In this study, six soil parameters together with the abundance of 61 plant species and their total biomass were used to explain the variation in translocation success of Iris atrofusca plants among 22 microsites. The relative importance of each of the three factors was estimated using ordination techniques.

4. Soil characteristics and total biomass of other plants did not significantly affect the performance of translocated irises, but the species composition of the surrounding vegetation did have a significant effect. The abundance of relatively rare species was closely correlated with iris performance. It is likely that these species do not affect the irises directly but instead represent environmental conditions not measured in this study, which are necessary for the survival of irises.

5. Synthesis and applications.Variation partitioning appears to be a highly promising method for planning the translocation of plants and evaluating success due to its ability to estimate the unique contribution of each of two or more sets of environmental factors. It can be used to monitor success, and to identify the key contributory factors, in experimental translocations preceding actual introduction of plants in conservation programmes.