bluuebunny/crossref_metadata_2025 huggingface dataset:
Plant–microbial competition for nitrogen uncoupled from soil C:N ratios
Authors: Månsson Katarina , Bengtson Per , Falkengren‐Grerup Ursula , Bengtsson Göran
Published: September 2009

A green house experiment was designed to test the idea that competition for inorganic nitrogen (N) between plants and heterotrophic microorganisms occurs in soils with high C:N ratios, qualifying for N limited microbial activity, but not at low C:N ratios. The short‐term (24 h)15N uptake by the grassFestuca giganteaand microorganisms in planted and unplanted soils was determined, and the bacterial activity was measured by the3H‐thymidine incorporation technique. Two deciduous forest soils, with C:N‐ratios of 20 and 31, and the 20 soil amended with litter to a C:N ratio of 34, were used. A novel and important part of the experimental design was the preparation of the unplanted reference soil with plants present until the competition assay started by the addition of15N labelled ammonium () or nitrate). The results suggested that plants and soil microorganisms competed for mineral N but under influence of other factors than the soil C:N ratio. The plants reduced the microbial uptake ofandin the soil with low C:N ratio, which also had the lowest bacterial activity. The plants had a larger N uptake than microorganisms in the two natural soils but smaller in the litter‐amended, and their presence enhanced the bacterial activity, especially in the latter soil. The litter‐amended soil with its high C:N ratio and easily decomposable C was the soil that best fulfilled the criteria for competition, including a net consumption of mineral N during the assay, the lowest plant uptake of mineral N due to the high N immobilization by microorganisms, and a reduced microbial15N uptake‐to‐bacterial activity in the presence of plants. Thus, other factors, such as the decomposability of the soil C and the bacterial activity, were more important than the soil C:N ratio to the outcome of plant–microbial competition for N.
The origin of failed subhaloes and the common mass scale of the Milky Way satellite galaxies
Authors: Okamoto Takashi , Frenk Carlos S.
Published: September 2009

We study the formation histories and present-day structure of satellite galaxies formed in a high-resolution hydrodynamic simulation of a Milky Way like galaxy. The simulated satellites span nearly four orders of magnitude in luminosity but have a very similar mass within their inner 600 pc, ∼3 × 107M⊙, with very little scatter. This result is in agreement with the recent measurements for dwarf spheroidal galaxies (dSphs) in the Milky Way by Strigari et al. In our simulations, a preferred mass scale arises naturally from the effects of the early re-ionization of gas. These impose a sharp threshold of ∼12kms−1 on the circular velocity of haloes which can cool gas and make stars. At the present day, subhaloes that host satellites as luminous as the classical Milky Way dwarfs (LV≥ 2.6 × 105L⊙) have typically grown to have circular velocities of ≳20 km s−1. There are, however, subhaloes with similar circular velocities today which were, nevertheless, below threshold at re-ionization and thus remain dark. Star formation in above-threshold haloes is truncated when the halo is accreted into the main galaxy progenitor. Thus, many properties of today's dwarf satellites such as their luminosity and star formation rate are set by their accretion time.
Practical Postcalibration Uncertainty Analysis: Yucca Mountain, Nevada
Authors: James Scott C. , Doherty John E. , Eddebbarh Al‐Aziz
Published: September 2009

The values of parameters in a groundwater flow model govern the precision of predictions of future system behavior. Predictive precision, thus, typically depends on an ability to infer values of system properties from historical measurements through calibration. When such data are scarce, or when their information content with respect to parameters that are most relevant to predictions of interest is weak, predictive uncertainty may be high, even if the model is “calibrated.” Recent advances help recognize this condition, quantitatively evaluate predictive uncertainty, and suggest a path toward improved predictive accuracy by identifying sources of predictive uncertainty and by determining what observations will most effectively reduce this uncertainty. We demonstrate linear and nonlinear predictive error/uncertainty analyses as applied to a groundwater flow model of Yucca Mountain, Nevada, the United States' proposed site for disposal of high‐level radioactive waste. Linear and nonlinear uncertainty analyses are readily implemented as an adjunct to model calibration with medium to high parameterization density. Linear analysis yields contributions made by each parameter to a prediction's uncertainty and the worth of different observations, both existing and yet‐to‐be‐gathered, toward reducing this uncertainty. Nonlinear analysis provides more accurate characterization of the uncertainty of model predictions while yielding their (approximate) probability distribution functions. This article applies the above methods to a prediction of specific discharge and confirms the uncertainty bounds on specific discharge supplied in the Yucca Mountain Project License Application.
Epimedium jingzhouense sp. nov. (Berberidaceae) from Hunan, China
Authors: Xia Guo‐Hua , Li Gen‐You
Published: September 2009

Epimedium jingzhouense from the Hunan Province in central–southeastern China is described, illustrated and compared with its nearest allies, E. myrianthum, E. multiflorum and E. boreali‐guizhouense.
Impatiens nanlingensis sp. nov. (Balsaminaceae) from Guangdong, China
Authors: Dong An‐Qiang , Chen Lin , Xing Fu‐Wu
Published: September 2009

Impatiens nanlingensis A. Q. Dong & F. W. Xing, a new species of Impatiens (Balsaminaceae) from Guangdong, China, is described and illustrated. It is morphologically similar to I. jinggangensis Y. L. Chen, but differs mainly by its lateral united petals; basal lobes suborbicular, marked with yellow stripes; distal lobes narrowly caudate, apex tailed. It also resembles I. bicornuta, but I. bicornuta differs mainly in its longer peduncles, up to 25 cm, pale blue–purple flowers and broadly sigmoid‐curved–saccate lower sepal.
Egocentric Spatial Representation in Action and Perception*
Authors: BRISCOE ROBERT
Published: September 2009

Neuropsychological findings used to motivate the “two visual systems” hypothesis have been taken to endanger a pair of widely accepted claims about spatial representation in conscious visual experience. The first is the claim that visual experience represents 3‐D space around the perceiver using an egocentric frame of reference. The second is the claim that there is a constitutive link between the spatial contents of visual experience and the perceiver’s bodily actions. In this paper, I review and assess three main sources of evidence for the two visual systems hypothesis. I argue that the best interpretation of the evidence is in fact consistent with both claims. I conclude with some brief remarks on the relation between visual consciousness and rational agency.
Undermining State Capacity: Vertical and Horizontal Diffusions of Fiscal Power in China
Authors: Zhan Jing Vivian
Published: September 2009

Since the late 1970s, China's fiscal system has facilitated the initiation and implementation of economic reforms and greatly contributed to China's remarkable economic achievements. However, weaknesses of the fiscal system have been exposed that have aroused concerns about the weakening of state capacity. While many have discussed the loss of central fiscal control over localities under decentralization and its negative consequences, not enough attention has been paid to another major problem: the diffusion of fiscal power to nonfiscal government departments. In this article, I argue that the existence of the extra‐budgetary system has granted ad hoc taxation power to nonfiscal departments and led to the mismanagement of fiscal revenue. Compared with the vertical diffusion of fiscal power, i.e., the devolution of fiscal authority from central to lower‐level governments, the horizontal diffusion of fiscal power is more difficult to control and more detrimental to the institutionalization of China's fiscal system.
Vietnam and East Asian Monetary Cooperation: Efforts and Policies
Authors: Thuy Van Le Thi
Published: September 2009

The article focuses on Vietnam's participation in East Asian monetary cooperation. It argues that monetary cooperation is necessary for the regional countries, including Vietnam. Perspectives on regional monetary cooperation are considered with the Chiang Mai Initiative in the short term, and an Asian monetary system, Asian monetary fund, and Asian monetary union in the medium and long terms. More important, the author emphasizes Vietnam's efforts and policies in this cooperation. Vietnam has done a great deal to support East Asian monetary cooperation by joining many working groups within the context of ASEAN+3. However, more economic reforms should be undertaken to further upgrade Vietnam's participation in regional monetary cooperation. The author finally makes some recommendations that will help Vietnam's policy makers strengthen the country's participation in East Asian monetary cooperation.
The Red Flag and the Ring: The Dances Surrounding Sino‐Vatican Ties
Authors: Luehrmann Laura M.
Published: September 2009

This article examines the possibilities of re‐established diplomatic relations between the People's Republic of China and the Vatican, or the Holy See. It presents this diplomatic dance in historical context and discusses the potential benefits and trade‐offs as seen from both sides. The complex relations between multiple Catholic communities within China, especially the “registered” and the “unregistered” church communities, as well as the contentious positions of clerical leadership in China, Hong Kong, and Taiwan, are discussed. Special attention is given to recent events during the pontificate of Benedict XVI, including the Papal Letter to Chinese Catholics of 2007. Both major actors, the Roman Catholic Church and the People's Republic of China, are treated as dominantly political players attempting to strengthen their hand in a rapidly changing political, social, and economic climate.
Heat Treatment Selection and Forming Strategies for 6082 Aluminum Alloy
Authors: Aginagalde Andrea , Gomez Xabier , Galdos Lander , García Carlos
Published: September 2009

Aluminum 6XXX alloys show high strength to weight ratios and are thus promising materials for today’s transport industry lightweight construction efforts. When considering both deformation and final mechanical properties, high ductility is interesting from the conformability point of view. On the other hand, high resistance is necessary in the automotive structural parts (which can be obtained through T6 precipitation heat treatment) but leads to reduced ductility. In order to increase aluminum alloys’ formability, warm forming is commonly applied. In contradiction to this, this article shows how the tensile deformation behavior of the 6082 T6 alloy is not affected by the temperature. In this work, the necessary formability values to obtain the parts are achieved, deforming the material under O annealed condition. But this strategy is focused on the formability perspective; therefore, the final mechanical properties do not achieve the necessary strength requirements. As a solution, the possibility of applying the T6 heat treatment after forming the parts (in annealed condition) is studied. A tensile characterization of the post-heat-treated specimens obtained from the deformed experimental part results in high flow stress levels, and thus, the strategy is validated. Nevertheless, the heat treatment leads to geometrical distortions in the final part, and thus, a last calibration step should be added to the forming process in order to obtain the desired shape.
Inverse Calculation of Uniaxial Stress-Strain Curves From Bending Test Data
Authors: Schajer G. S. , An Y.
Published: September 2009

Uniaxial tension and compression stress-strain curves are simultaneously evaluated from load and surface strain data measured during a bending test. The required calculations for the uniaxial results are expressed as integral equations and solved in that form using inverse methods. This approach is taken to reduce the extreme numerical sensitivity of calculations based on equations expressed in differential form. The inverse solution method presented addresses the numerical sensitivity issue by using Tikhonov regularization. The use of a priori information is explored as a means of further stabilizing the stress-strain curve evaluation. The characteristics of the inverse solution are investigated using experimental data from bending and uniaxial tests.
Yield and Deformation in Biaxially Stressed Multilayer Metallic Thin Films
Authors: Overman N. R. , Overman C. T. , Zbib H. M. , Bahr D. F.
Published: September 2009

Multilayer thin films of CuNb, CuNi, and CuNbNi with 20 nm individual layer thicknesses were fabricated by magnetron sputtering on oxide coated silicon wafers. The mechanical properties of the films were measured using bulge testing and nanoindentation. Elastic and plastic properties were determined for freestanding films in both square and rectangular window geometries. A finite element model of the window was used to determine the yielding behavior to account for stress concentrations in the membranes. The initial yield in a pressurized membrane, on the order of 400–500 MPa, is approximately one-half of the flow stress inferred from nanoindentation hardness results between 1.9 GPa and 3.4 GPa, and is a result of microscale yielding prior to uniform deformation in these high strength systems.
Atomistic Modeling of Grain Boundaries and Dislocation Processes in Metallic Polycrystalline Materials
Authors: Spearot Douglas E. , McDowell David L.
Published: September 2009

The objective of this review article is to provide a concise discussion of atomistic modeling efforts aimed at understanding the nanoscale behavior and the role of grain boundaries in plasticity of metallic polycrystalline materials. Atomistic simulations of grain boundary behavior during plastic deformation have focused mainly on three distinct configurations: (i) bicrystal models, (ii) columnar nanocrystalline models, and (iii) 3D nanocrystalline models. Bicrystal models facilitate the isolation of specific mechanisms that occur at the grain boundary during plastic deformation, whereas columnar and 3D nanocrystalline models allow for an evaluation of triple junctions and complex stress states characteristic of polycrystalline microstructures. Ultimately, both sets of calculations have merits and are necessary to determine the role of grain boundary structure on material properties. Future directions in grain boundary modeling are discussed, including studies focused on the role of grain boundary impurities and issues related to linking grain boundary mechanisms observed via atomistic simulation with continuum models of grain boundary plasticity.
Influence of Manufacturing Processes and Microstructures on the Performance and Manufacturability of Advanced High Strength Steels
Authors: Choi K. S. , Liu W. N. , Sun X. , Khaleel M. A. , Fekete J. R.
Published: September 2009

Advanced high strength steels (AHSS) are performance-based steel grades and their global material properties can be achieved with various steel chemistries and manufacturing processes, leading to various microstructures. In this paper, we investigate the influence of the manufacturing process and the resulting microstructure difference on the overall mechanical properties, as well as the local formability behaviors of AHSS. For this purpose, we first examined the basic material properties and the transformation kinetics of three different commercial transformation induced plasticity (TRIP) 800 steels under different testing temperatures. The experimental results show that the mechanical and microstructural properties of the TRIP 800 steels significantly depend on the thermomechanical processing parameters employed in making these steels. Next, we examined the local formability of two commercial dual phase (DP) 980 steels which exhibit noticeably different formability during the stamping process. Microstructure-based finite element analyses are carried out to simulate the localized deformation process with the two DP 980 microstructures, and the results suggest that the possible reason for the difference in formability lies in the morphology of the hard martensite phase in the DP microstructure. The results of this study suggest that a set of updated material acceptance and screening criteria is needed to better quantify and ensure the manufacturability of AHSS.
Review of Hierarchical Multiscale Modeling to Describe the Mechanical Behavior of Amorphous Polymers
Authors: Bouvard J. L. , Ward D. K. , Hossain D. , Nouranian S. , Marin E. B. , Horstemeyer M. F.
Published: September 2009

Modern computational methods have proved invaluable for the design and analysis of structural components using lightweight materials. The challenge of optimizing lightweight materials in the design of industrial components relates to incorporating structure-property relationships within the computational strategy to incur robust designs. One effective methodology of incorporating structure-property relationships within a simulation-based design framework is to employ a hierarchical multiscale modeling strategy. This paper reviews techniques of multiscale modeling to predict the mechanical behavior of amorphous polymers. Hierarchical multiscale methods bridge nanoscale mechanisms to the macroscale/continuum by introducing a set of structure-property relationships. This review discusses the current state of the art and challenges for three distinct scales: quantum, atomistic/coarse graining, and continuum mechanics. For each scale, we review the modeling techniques and tools, as well as discuss important recent contributions. To help focus the review, we have mainly considered research devoted to amorphous polymers.
Modeling of Lath Martensitic Microstructures and Failure Evolution in Steel Alloys
Authors: Hatem T. M. , Zikry M. A.
Published: September 2009

A multiple-slip dislocation-density-based crystalline formulation, specialized finite-element formulations, and Voronoi tessellations adapted to martensitic orientations were used to investigate dislocation-density activities and crack tip blunting in high strength martensitic steels. The formulation is based on accounting for variant morphologies and orientations, retained austenite, and initial dislocations densities that are uniquely inherent to martensitic microstructures. The effects of variant distributions and arrangements are investigated for different crack and void interaction distributions and arrangements. The analysis indicates that for certain orientations related to specific variant block arrangements, which correspond to random low angle orientations, cracks can be blunted by dislocation-density activities along transgranular planes. For other variant block arrangements, which correspond to random high angle orientations, sharp crack growth can occur due to dislocation activities along intergranular planes.
Advances in Discrete Dislocations Dynamics and Multiscale Modeling
Authors: Groh S. , Zbib H. M.
Published: September 2009

Discrete dislocation dynamics is a numerical tool developed to model the plasticity of crystalline materials at an intermediate length scale, between the atomistic modeling and the crystal plasticity theory. In this review we show, using examples from the literature, how a discrete dislocation model can be used either in a hierarchical or a concurrent multiscale framework. In the last section of this review, we show through the uniaxial compression of microcrystal application, how a concurrent multiscale model involving a discrete dislocation framework can be used for predictive purposes.
Human Foot Placement and Balance in the Sagittal Plane
Authors: Millard Matthew , Wight Derek , McPhee John , Kubica Eric , Wang David
Published: September 2009

Foot placement has long been recognized as the primary mechanism that humans use to restore balance. Many biomechanists have examined where humans place their feet during gait, perturbations, and athletic events. Roboticists have also used foot placement as a means of control but with limited success. Recently, Wight et al. (2008, “Introduction of the Foot Placement Estimator: A Dynamic Measure of Balance for Bipedal Robotics,” ASME J. Comput. Nonlinear Dyn., 3, p. 011009) introduced a planar foot placement estimator (FPE) algorithm that will restore balance to a simplified biped that is falling. This study tested the FPE as a candidate function for sagittal plane human-foot-placement (HFP) by recording the kinematics of 14 healthy subjects while they performed ten walking trials at three speeds. The FPE was highly correlated with HFP (ρ≥0.997) and its accuracy varied linearly from 2.6 cm to −8.3 cm as walking speed increased. A sensitivity analysis revealed that assumption violations of the FPE cannot account for the velocity-dependent changes in FPE-HFP error suggesting that this behavior is volitional.
Rheological, morphological and structural properties of PE/PA/nanoclay ternary blends: Effect of clay weight fraction
Authors: Huitric Jacques , Ville Julien , Médéric Pascal , Moan Michel , Aubry Thierry
Published: September 2009

The effect of an organically modified layered silicate on the rheological, morphological, and structural properties of immiscible polyethylene/polyamide (PE/PA) blends was investigated. The blends have been prepared for PA weight fractions ranging from 10 to 90% and at clay weight fractions from 1 to 6%. Scanning electron microscopy and transmission electron microscopy have been used to study the morphology and the structure of the blends. The dispersed phase size was shown to decrease with increasing clay content up to 2% and tends to stabilize at higher fractions. For PE matrix blends, clay particles were shown to be essentially located at the interface of the two polymers, forming an interphase whose thickness grows with clay fraction. For PA matrix blends with 2% of clay, the interphase thickness is stabilized at 11 nm; further clay addition leads to dispersion of clay within PA. Oscillatory and steady shear measurements have shown that PE matrix ternary blends behaved like polymer blends and underlined the contribution of an interphase at high clay fractions. For sufficiently filled PA matrix blends, a yield behavior was observed. The behavior of PA matrix ternary blends, dominated by the organoclay dispersed in PA, is similar to that of nanocomposites.
Concentration dependence of the longest relaxation times of dilute and semi-dilute polymer solutions
Authors: Liu Yonggang , Jun Yonggun , Steinberg Victor
Published: September 2009

The longest relaxation times of polymer solutions of semi-flexible T4 DNA and flexible 18 M molar mass polyacrylamide (PAAm) in dilute and semi-dilute concentration range are studied by the polymer extension relaxation of stretched single DNA molecules and by the stress relaxation of PAAm solutions measurements. For both polymer solutions, the longest relaxation time normalized by the value at infinite dilution with the same solvent viscosity τ/τ0 increases with increasing concentration. In the dilute regime, the longest relaxation time increases just slightly with increasing concentration as τ/τ0=[1+cA−2(cA)1.5+2(cA)2] as well as the empirical relation of τ/τ0=exp(cA) up to c∼3c∗ with A≈0.5[η], where c∗ is the overlap concentration, in accord with the theory and previous experiments. For the semi-dilute solutions, the scaling of τ/τ0 with concentration shows two different exponents in two concentration regions, corresponding to the unentangled and entangled regimes. The exponents are consistent with those expected by the theory of dynamical scaling for semi-dilute polymer solutions. The crossover concentration from the unentangled to entangled regime ce is found to be ∼9c∗ in a good solvent, in accord with other experiments based on the relaxation of a single molecule, the diffusion coefficient, and the solution viscosity measurements. We also test the universality of the concentration dependence of the longest relaxation time for both flexible and semi-flexible polymers in both good and Θ solvents in the dilute and semi-dilute regimes by analyzing literature data sets.
Viscoelastic properties and gelation of an elastin-like polypeptide
Authors: Cirulis Judith T. , Keeley Fred W. , James David F.
Published: September 2009

Tropoelastin, the native monomeric form of elastin, and elastin-like polypeptides undergo a process of temperature-induced phase separation (coacervation) resulting in self-organization of a polymeric network that can subsequently be cross-linked into an elastomeric polymer. In this study, the rheological properties of a recombinantly produced polypeptide mimicking the sequences and domain arrangements of tropoelastin were investigated to understand post-coacervation changes in structure and assembly. This polypeptide, designated EP20-24-24, consisted of three hydrophobic domains of native human tropoelastin flanking two cross-linking domains. Temperature-induced formation of coacervate droplets resulted in a small increase in viscosity. A higher temperature produced a second temperature-dependent transition (Tv) to a gel state characterized by a much higher viscosity, strong shear thinning, and a high ratio of storage to loss moduli. This gel state was fully reversible if the temperature was immediately lowered. However, incubation above Tv for 60 min resulted in a further transformation of the network, limiting thermal reversibility of the gelation process. These results demonstrate that for elastin-like polypeptides mimicking the sequence and domain arrangements of tropoelastin, temperature-induced coacervation and transition of the coacervate to a gel-like state are distinguishable events with separate transition temperatures. Moreover, gels formed by these elastin-like polypeptides undergo a process of maturation, reducing the reversibility of the gel state.
Obtaining reliable transient rheological data on concentrated short fiber suspensions using a rotational rheometer
Authors: Eberle Aaron P. R. , Baird Donald G. , Wapperom Peter , Vélez-García Gregorio M.
Published: September 2009

The conventional method for obtaining transient rheological data on short glass fiber-filled polymeric fluids is to use the parallel disk (PP) geometry in a rotational rheometer. Using the PP geometry large transient stress overshoot behavior was observed during the startup of flow measurements on a 30 wt % short glass fiber-filled polybutylene terephthalate. A contributing factor to this behavior is believed to be induced fiber collisions caused by the inhomogeneous velocity field (radial varying velocity gradient). A novel approach was taken in which a “donut” shaped sample was used in a cone-and-plate device (CP-D) to maintain a sufficient gap to fiber length ratio. The magnitude of the first normal stress difference was reduced by 70%, and the time to reach steady state was reduced by 100 strain units. The Lipscomb model coupled with the Folgar–Tucker model for the evolution of fiber orientation was fit to the stress growth behavior measured using both the PP geometry and CP-D resulting in different parameters. In addition, the fitted model parameters were found to depend on the initial fiber orientation. It is believed that the CP-D allows for an accurate determination of the stress growth behavior and eventually will allow one to obtain unambiguous model parameters.
Structural analysis of non-aqueous layered silicate suspensions subjected to shear flow
Authors: Mobuchon Christophe , Carreau Pierre J. , Heuzey Marie-Claude
Published: September 2009

Non-aqueous layered silicate suspensions exhibit a complex rheological behavior due to a multiple length scale structure, which is sensitive to flow and flow history. In the present work, the nature of flow-induced non-equilibrium and metastable structures in non-aqueous layered silicate suspensions based on natural and organo-modified sodium montmorillonites was examined using rheometry and confocal laser scanning microscopy (CLSM). The scaling behavior of their linear and non-linear viscoelastic properties was investigated. Based on fractal scaling theories, the scaling laws of the solid-like properties were ascribed to the presence of space-filling percolating networks consisting of clusters with a mass-fractal dimensionality, Df∼2. CLSM allowed us to detect the formation of aggregates under flow and to characterize their microscopic length scale. The shear-rate dependency of the microstructure characteristic length scale was attributed to a reversible shear-induced aggregation process. Upon cessation of flow, the observed thixotropic behavior of these suspensions was inferred from the CLSM observations to stem from local rearrangements at the nano-scale.
Interface slippage study between polyamide 12 and ethylene butene copolymer melt in capillary extrusion
Authors: Yang Jinhai , White James L.
Published: September 2009

Extrusion of a polyamide 12 (PA12) material through a capillary die coated with an ethylene butene copolymer (EBM) was studied. The EBM coated die significantly increased the flow rates of the PA12 melt compared to a clean die at the same extrusion pressure. Introducing a maleic anhydride grafted ethylene-octene copolymer (EOM-g-MAH) into the EBM suppressed the effect. This behavior seems only explained by significant interface slippage between PA12 and EBM melts, which could be eliminated by introducing covalent chemical bonds across the interface. A mathematical analysis was carried out to calculate the interface slippage. The shear stress where slippage began to occur was around 0.045 MPa and the slippage velocity was around 15 mm/s at 0.1 MPa. Adding EOM-g-MAH could largely decrease the interfacial tension between EBM and PA12, thus largely decrease the interface slippage.
Dynamic Processes Governing Lower-Tropospheric HDO/H
2
O Ratios as Observed from Space and Ground
Authors: Frankenberg Christian , Yoshimura Kei , Warneke Thorsten , Aben Ilse , Butz André , Deutscher Nicholas , Griffith David , Hase Frank , Notholt Justus , Schneider Matthias , Schrijver Hans , Röckmann Thomas
Published: September 2009

Cycling Around

Water vapor is the most important greenhouse gas, and clouds are one of the most important components of climate, but the global hydrological cycle is still poorly-enough understood that the atmospheric cycling of water and cloud formation are inadequately represented in global climate models. As the transformation from liquid into vapor tends to deplete water of the isotope deuterium,

Frankenburg
et al.

(p.
1374
) were able to use satellite measurements of global “heavy” water abundances to provide a deeper understanding of atmospheric water dynamics.
Folding DNA into Twisted and Curved Nanoscale Shapes
Authors: Dietz Hendrik , Douglas Shawn M. , Shih William M.
Published: September 2009

Stressful Self-Assembly

One way to control shape during the assembly of an object is to design in stresses that cause a planned amount of deformation.

Dietz
et al.

(p.
725
; see the Perspective by

Liu and Yan

) designed DNA helix bundles, arranged in honeycomb lattices, in which some of the helices have insertions or deletions relative to the other helices in the bundles. The stresses help the bundles assemble into objects on the scale of tens of nanometers. Both the direction and degree of bending could be controlled, and curvatures as tight as 6 nanometers achieved. Complex shapes, such as square-toothed gears, could be created by combining multiple curved elements.
Looming Global-Scale Failures and Missing Institutions
Authors: Walker Brian , Barrett Scott , Polasky Stephen , Galaz Victor , Folke Carl , Engström Gustav , Ackerman Frank , Arrow Ken , Carpenter Stephen , Chopra Kanchan , Daily Gretchen , Ehrlich Paul , Hughes Terry , Kautsky Nils , Levin Simon , Mäler Karl-Göran , Shogren Jason , Vincent Jeff , Xepapadeas Tasos , de Zeeuw Aart
Published: September 2009

Navigating global changes requires a coevolving set of collaborative, global institutions.
30,000-Year-Old Wild Flax Fibers
Authors: Kvavadze Eliso , Bar-Yosef Ofer , Belfer-Cohen Anna , Boaretto Elisabetta , Jakeli Nino , Matskevich Zinovi , Meshveliani Tengiz
Published: September 2009

Dyed flax fibers from 30,000 years ago show that humans in the Caucasus were making colored twine at that time.
Endogenous Nitric Oxide Protects Bacteria Against a Wide Spectrum of Antibiotics
Authors: Gusarov Ivan , Shatalin Konstantin , Starodubtseva Marina , Nudler Evgeny
Published: September 2009

It's a Gas

Many antibiotics, including beta-lactams, aminoglycosides, and quinolones, kill bacteria (at least in part) by oxidative stress.Gusarovet al.(p.1380) show that nitric oxide (NO) produced by bacterial NO synthases (bNOS) protects bacteria, includingStaphylococcus aureusandBacillus anthracis, against toxic agents they may encounter in the soil or in host organisms. Thus, bNOS activity is specifically induced in response to antibiotics and, in turn, activates the expression of another key antioxidant enzyme: superoxide dismutase. Hence, NO-mediated antibiotic resistance not only operates by direct chemical modification of toxic molecules, but also alleviates oxidative stress caused by naturally occurring antibiotics.
Tuned for Transposition: Molecular Determinants Underlying the Hyperactivity of a
Stowaway
MITE
Authors: Yang Guojun , Nagel Dawn Holligan , Feschotte Cédric , Hancock C. Nathan , Wessler Susan R.
Published: September 2009

MITE-y Jumps

Tranposable elements are genetic elements ubiquitous to most genomes, and their expansion, loss, and potential movement are major components of genome evolution. A type of noncoding transposable element in plants, known as a MITE (minature inverted repeat transposable element), shows evidence of recent expansion within specific rice genomes. However, these elements lack the necessary transposase to help them move.

Yang
et al.

(p.
1391
; see the Perspective by

González and Petrov

) found that the expansion of MITEs occurs because they exploit the activity of other, unrelated, transposons and consequently identified the molecular determinants that allowed mobilization. Surprisingly, the element coding for the transposase repressed its own movement unless the MITE was present. These findings may explain why some genetic elements can replicate within the genome and reach high copy numbers while others do not.
Extremely Efficient Multiple Electron-Hole Pair Generation in Carbon Nanotube Photodiodes
Authors: Gabor Nathaniel M. , Zhong Zhaohui , Bosnick Ken , Park Jiwoong , McEuen Paul L.
Published: September 2009

Efficient Carbon Nanotube Photodiodes

A single photon absorbed in a single-walled carbon nanotube device can generate multiple unbound particles carrying an electric charge.

Gabor
et al.

(p.
1367
) report that in such a device at low temperatures, excitation with light of increasing energy leads to well-defined stepwise increases in current. Interestingly, because of the unique band structure of carbon nanotubes, this behavior is analogous to particle-antiparticle creation commonly observed in high-energy particle physics. These observations point to the promise of investigations in other nanoscale carbon systems, such as graphene, and could lead to numerous applications, including highly sensitive photon detection and ultra-efficient photovoltaics.
A Critical Course Change

Ecosystem-Based Management for the Oceans
Karen McLeod and Heather Leslie, Eds.

Island Press, Washington, DC, 2009. 391 pp. $90. ISBN 9781597261548. Paper, $45. ISBN 9781597261555.
Authors: Chan Kai M. A. , Gregr Edward J. , Klain Sarah
Published: September 2009

The contributors describe and discuss the application of ecosystem-based management to coastal and ocean systems.
Addressing the Graduation Gap
Crossing the Finish Line
Completing College at America's Public Universities

by William G. Bowen, Matthew M. Chingos, and Michael S. McPherson

Princeton University Press, Princeton, NJ, 2009. 413 pp. $27.95, £19.95. ISBN 9780691137483.
Authors: Atkinson Richard C. , Geiser Saul
Published: September 2009

The authors consider why more than 40% of the students who enter U.S. four-year colleges fail to graduate and what can be done to reduce that number.
Went Fishing, Caught a Snake
Authors: Meijer Dies
Published: September 2009

A sinuous receptor links cAMP signaling to myelin formation by Schwann cells in the vertebrate nervous system.
VA Pulls the Plug on Disputed Study of Gulf War Illness
Authors: Marshall Eliot
Published: September 2009

A lavishly funded health study of veterans from the first Gulf War—favored by the U.S. Congress but viewed with skepticism by many scientists—hit a wall in August when its funder, the U.S. Department of Veterans Affairs, pulled out.
Melding Mammals and Molecules to Track Evolution
Authors: Pennisi Elizabeth
Published: September 2009

Harvard University evolutionary biologist Hopi Hoekstra's first college summer job—as a tick target for researchers assessing where and when hikers were most susceptible to attacks by Lyme disease–transmitting ticks—made her itch for more fieldwork and, eventually, a life as a biologist.
As China's Rare Earth R&D Becomes Ever More Rarefied, Others Tremble
Authors: Stone Richard
Published: September 2009

China owns a virtual monopoly on production of rare earth elements used in a wide range of high-tech devices, and it is catching up fast on applications.
Differentiation of Larva Migrans Caused byBaylisascaris procyonisandToxocaraSpecies by Western Blotting
Authors: Dangoudoubiyam Sriveny , Kazacos Kevin R.
Published: September 2009

Baylisascaris procyonisandToxocaraspecies are two important causes of larva migrans in humans. Larva migrans caused byToxocaraspp. is well known and is diagnosed serologically by enzyme immunoassay. Over a dozen cases of larva migrans and associated eosinophilic encephalitis caused byB. procyonishave also been reported, and at least a dozen additional cases are known. An enzyme-linked immunosorbent assay (ELISA) using the excretory-secretory (ES) antigen ofB. procyonislarvae is currently being used in our laboratory as an aid in the diagnosis of this infection in humans. Clinically affected individuals show very high reactivity (measured as the optical density) on this ELISA; however, a one-way cross-reactivity withToxocaraspp. has been observed. As an approach to differentiate these two infections based on serology, we performed Western blots, wherein theB. procyonisES antigen was reacted with serum samples from individuals known to be positive for eitherToxocaraspp. orB. procyonislarva migrans. Western blot results showed thatB. procyonisantigens of between 30 and 45 kDa were specifically identified only by the sera from individuals withBaylisascarislarva migrans, thus allowing for differentiation between the two infections. This included human patient serum samples submitted for serologic testing, as well as sera from rabbits experimentally infected withB. procyonis. When used in conjunction with the ELISA, Western blotting could be an efficient tool for diagnosis of this infection in humans.
Salmonella enterica
Serotype 4,5,12:i:−, an Emerging
Salmonella
Serotype That Represents Multiple Distinct Clones
Authors: Soyer Y. , Moreno Switt A. , Davis M. A. , Maurer J. , McDonough P. L. , Schoonmaker-Bopp D. J. , Dumas N. B. , Root T. , Warnick L. D. , Gröhn Y. T. , Wiedmann M.
Published: September 2009

The prevalence, among human clinical cases, of
Salmonella enterica
serotype 4,5,12:i:−, a serotype antigenically similar to
Salmonella enterica
serotype Typhimurium but lacking second-phase flagellar antigens, has increased considerably over the last 10 years. To probe the evolution and ecology of this emerging serotype, we characterized 190
Salmonella
isolates initially classified as
Salmonella
serotypes 4,5,12:i:− (
n
= 90) and Typhimurium (
n
= 100) and obtained from various sources in the United States and Spain. These isolates were characterized into six sequence types (determined by multilocus sequence typing [MLST]) and 79 pulsed-field gel electrophoresis types. The majority of
Salmonella
serotype 4,5,12:i:− and Typhimurium isolates (85 and 84 isolates, respectively) represented a single MLST type. Existing genome information revealed different genome deletions (which included genes responsible for phase 2 flagellum expression) in four Spanish
Salmonella
serotype 4,5,12:i:− isolates and one U.S.
Salmonella
serotype 4,5,12:i:− isolate. Fifty-nine isolates of both serotypes, representing different sources and geographical locations as well as different molecular subtypes, were thus screened for the presence of six genes and one specific region, all of which were previously found to show variable presence among
Salmonella
serotype 4,5,12:i:− and Typhimurium strains. All
Salmonella
serotype 4,5,12:i:− isolates lacked the phase 2 flagella genes
fljA
and
fljB
, which were present in all
Salmonella
serotype Typhimurium isolates. While all Spanish
Salmonella
serotype 4,5,12:i:− isolates carried the same deletion surrounding
fljAB
, all but two U.S. isolates showed a different genomic deletion; the two atypical U.S. isolates represented the “Spanish” deletion genotype and a unique deletion genotype.
Salmonella
serotype 4,5,12:i:− thus appears to represent at least two common clones, which cannot easily be differentiated with standard diagnostic procedures.
Development and Validation of a Multiplex Real-Time PCR Assay for Simultaneous Genotyping and Human T-Lymphotropic Virus Type 1, 2, and 3 Proviral Load Determination
Authors: Moens Britta , López Giovanni , Adaui Vanessa , González Elsa , Kerremans Lien , Clark Daniel , Verdonck Kristien , Gotuzzo Eduardo , Vanham Guido , Cassar Olivier , Gessain Antoine , Vandamme Anne-Mieke , Van Dooren Sonia
Published: September 2009

The human T-lymphotropic virus (HTLV) proviral load remains the best surrogate marker for disease progression. Real-time PCR techniques have been developed for detection and quantification of cosmopolitan HTLV type 1a (HTLV-1a) and HTLV-2. Since a growing level of diversity in subtypes and genotypes is observed, we developed a multiplex quantitative PCR for simultaneous detection, genotyping, and quantification of proviral loads of HTLV-1, 2, and 3. Our assay uses
tax
type-specific primers and dually labeled probes and has a dynamic range of 10
5
to 10 HTLV copies. One hundred sixty-three samples were analyzed, among which all of the different subtypes within each HTLV genotype could be detected. The performance of proviral load determination of our multiplex assay was compared with that of a previously published HTLV-1 singleplex quantitative PCR based on SYBR green detection, developed at a different institute. Linear regression analysis showed a statistically significant (
P
< 0.0001) and strong (
r
2
= 0.87) correlation between proviral load values measured with the two distinct real-time PCR assays. In conclusion, our novel assay offers an accurate molecular diagnosis and genotyping, together with the determination of the proviral load of HTLV-infected individuals, in a single amplification reaction. Moreover, our molecular assay could offer an alternative when current available serological assays are insufficient.
Multicenter Evaluation of Bactec MGIT 960 System for Second-Line Drug Susceptibility Testing of
Mycobacterium tuberculosis
Complex
Authors: Lin S.-Y. Grace , Desmond Edward , Bonato Donald , Gross Wendy , Siddiqi Salman
Published: September 2009

The Bactec MGIT 960 system for testing susceptibility to second-line drugs was evaluated with 117 clinical strains in a multicenter study. The four drugs studied were levofloxacin, amikacin, capreomycin, and ethionamide. The critical concentration established for levofloxacin and amikacin was 1.5 μg/ml, that established for capreomycin was 3.0 μg/ml, and that established for ethionamide was 5.0 μg/ml. The overall level of agreement between the agar proportion method and the MGIT 960 system was 96.4%, and the levels of agreement for the individuals drugs were 99.1% for levofloxacin, 100% for amikacin, 97.4% for capreomycin, and 88.9% for ethionamide. The rate of reproducibility of the drug susceptibility testing results between the participating laboratories was 99.5%.
Direct 16S rRNA Gene Sequencing from Clinical Specimens, with Special Focus on Polybacterial Samples and Interpretation of Mixed DNA Chromatograms
Authors: Kommedal Øyvind , Kvello Kristine , Skjåstad Rune , Langeland Nina , Wiker Harald G.
Published: September 2009

RipSeq (iSentio, Bergen, Norway) is a web-based application for the analysis of mixed DNA chromatograms. It opens the possibility to analyze chromatograms obtained by direct 16S rRNA gene sequencing from polybacterial human clinical samples. In this study, we used direct 16S rRNA gene sequencing to investigate 264 samples from a wide range of suspected human bacterial infections. The sequence-based identification was compared with the results from routine culture-based identification. A total of 151 samples were positive by the first PCR, producing 85 pure and 66 mixed DNA chromatograms. All mixed chromatograms were analyzed by RipSeq, although seven were so complex that only the dominant bacterial sequences could be identified. In general, sequence-based identification detected a larger number of species than did culture for samples from patients who had received antibiotics prior to sample collection and for samples containing anaerobic bacteria. RipSeq made it possible to apply this supplementary diagnostic tool to typical polybacterial specimens, such as internal abscesses, pleural fluids, and bile.
Comparison of BD Phoenix to Vitek 2, MicroScan MICroSTREP, and Etest for Antimicrobial Susceptibility Testing of
Streptococcus pneumoniae
Authors: Mittman Scott A. , Huard Richard C. , Della-Latta Phyllis , Whittier Susan
Published: September 2009

The performance of the BD Phoenix Automated Microbiology System (BD Diagnostic Systems) was compared to those of the Vitek 2 (bioMérieux), the MicroScan MICroSTREP
plus
(Siemens), and Etest (bioMérieux) for antibiotic susceptibility tests (AST) of 311 clinical isolates of
Streptococcus pneumoniae
. The overall essential agreement (EA) between each test system and the reference microdilution broth reference method for
S. pneumoniae
AST results was >95%. For Phoenix, the EAs of individual antimicrobial agents ranged from 90.4% (clindamycin) to 100% (vancomycin and gatifloxacin). The categorical agreements (CA) of Phoenix, Vitek 2, MicroScan, and Etest for penicillin were 95.5%, 94.2%, 98.7%, and 97.7%, respectively. The overall CA for Phoenix was 99.3% (1 very major error [VME] and 29 minor errors [mEs]), that for Vitek 2 was 98.8% (7 VMEs and 28 mEs), and those for MicroScan and Etest were 99.5% each (19 and 13 mEs, respectively). The average times to results for Phoenix, Vitek 2, and the manual methods were 12.1 h, 9.8 h, and 24 h, respectively. From these data, the Phoenix AST results demonstrated a high degree of agreement with all systems evaluated, although fewer VMEs were observed with the Phoenix than with the Vitek 2. Overall, both automated systems provided reliable AST results for the
S. pneumoniae
-antibiotic combinations in half the time required for the manual methods, rendering them more suitable for the demands of expedited reporting in the clinical setting.