bluuebunny/crossref_metadata_2025 huggingface dataset:
Expansion Mechanisms and Functional Annotations of Hypothetical Genes in the Rice Genome
Authors: Jiang Shu-Ye , Christoffels Alan , Ramamoorthy Rengasamy , Ramachandran Srinivasan
Published: June 2009

In each completely sequenced genome, 30% to 50% of genes are annotated as uncharacterized hypothetical genes. In the rice (Oryza sativa) genome, 10,918 hypothetical genes were annotated in the latest version (release 6) of the Michigan State University rice genome annotation. We have implemented an integrative approach to analyze their duplication/expansion and function. The analyses show that tandem/segmental duplication and transposition/retrotransposition have significantly contributed to the expansion of hypothetical genes despite their different contribution rates. A total of 3,769 hypothetical genes have been detected from retrogene, tandem, segmental, Pack-MULE, or long terminated direct repeat-related duplication/expansion. The nonsynonymous substitutions per site and synonymous substitutions per site analyses showed that 21.65% of them were still functional, accounting for 7.47% of total hypothetical genes. Global expression analyses have identified 1,672 expressed hypothetical genes. Among them, 415 genes might function in a developmental stage-specific manner. Antisense strand expression and small RNA analyses have demonstrated that a high percentage of these hypothetical genes might play important roles in negatively regulating gene expression. Homologous searches against Arabidopsis (Arabidopsis thaliana), maize (Zea mays), sorghum (Sorghum bicolor), and indica rice genomes suggest that most of the hypothetical genes could be annotated from recently evolved genomic sequences. These data advance the understanding of rice hypothetical genes as being involved in lineage-specific expansion and that they function in a specific developmental stage. Our analyses also provide a valuable means to facilitate the characterization and functional annotation of hypothetical genes in other organisms.
The Magnesium-Chelatase H Subunit Binds Abscisic Acid and Functions in Abscisic Acid Signaling: New Evidence in Arabidopsis
Authors: Wu Fu-Qing , Xin Qi , Cao Zheng , Liu Zhi-Qiang , Du Shu-Yuan , Mei Chao , Zhao Chen-Xi , Wang Xiao-Fang , Shang Yi , Jiang Tao , Zhang Xiao-Feng , Yan Lu , Zhao Rui , Cui Zi-Ning , Liu Rui , Sun Hai-Li , Yang Xin-Ling , Su Zhen , Zhang Da-Peng
Published: June 2009

Using a newly developed abscisic acid (ABA)-affinity chromatography technique, we showed that the magnesium-chelatase H subunit ABAR/CHLH (for putative abscisic acid receptor/chelatase H subunit) specifically binds ABA through the C-terminal half but not the N-terminal half. A set of potential agonists/antagonists to ABA, including 2-trans,4-trans-ABA, gibberellin, cytokinin-like regulator 6-benzylaminopurine, auxin indole-3-acetic acid, auxin-like substance naphthalene acetic acid, and jasmonic acid methyl ester, did not bind ABAR/CHLH. A C-terminal C370 truncated ABAR with 369 amino acid residues (631–999) was shown to bind ABA, which may be a core of the ABA-binding domain in the C-terminal half. Consistently, expression of the ABAR/CHLH C-terminal half truncated proteins fused with green fluorescent protein (GFP) in wild-type plants conferred ABA hypersensitivity in all major ABA responses, including seed germination, postgermination growth, and stomatal movement, and the expression of the same truncated proteins fused with GFP in an ABA-insensitive cch mutant of the ABAR/CHLH gene restored the ABA sensitivity of the mutant in all of the ABA responses. However, the effect of expression of the ABAR N-terminal half fused with GFP in the wild-type plants was limited to seedling growth, and the restoring effect of the ABA sensitivity of the cch mutant was limited to seed germination. In addition, we identified two new mutant alleles of ABAR/CHLH from the mutant pool in the Arabidopsis Biological Resource Center via Arabidopsis (Arabidopsis thaliana) Targeting-Induced Local Lesions in Genomes. The abar-2 mutant has a point mutation resulting in the N-terminal Leu-348→Phe, and the abar-3 mutant has a point mutation resulting in the N-terminal Ser-183→Phe. The two mutants show altered ABA-related phenotypes in seed germination and postgermination growth but not in stomatal movement. These findings support the idea that ABAR/CHLH is an ABA receptor and reveal that the C-terminal half of ABAR/CHLH plays a central role in ABA signaling, which is consistent with its ABA-binding ability, but the N-terminal half is also functionally required, likely through a regulatory action on the C-terminal half.
Truffles Regulate Plant Root Morphogenesis via the Production of Auxin and Ethylene
Authors: Splivallo Richard , Fischer Urs , Göbel Cornelia , Feussner Ivo , Karlovsky Petr
Published: June 2009

Truffles are symbiotic fungi that form ectomycorrhizas with plant roots. Here we present evidence that at an early stage of the interaction, i.e. prior to physical contact, mycelia of the white truffle Tuber borchii and the black truffle Tuber melanopsorum induce alterations in root morphology of the host Cistus incanus and the nonhost Arabidopsis (Arabidopsis thaliana; i.e. primary root shortening, lateral root formation, root hair stimulation). This was most likely due to the production of indole-3-acetic acid (IAA) and ethylene by the mycelium. Application of a mixture of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid and IAA fully mimicked the root morphology induced by the mycelium for both host and nonhost plants. Application of the single hormones only partially mimicked it. Furthermore, primary root growth was not inhibited in the Arabidopsis auxin transport mutant aux1-7 by truffle metabolites while root branching was less effected in the ethylene-insensitive mutant ein2-LH. The double mutant aux1-7;ein2-LH displayed reduced sensitivity to fungus-induced primary root shortening and branching. In agreement with the signaling nature of truffle metabolites, increased expression of the auxin response reporter DR5∷GFP in Arabidopsis root meristems subjected to the mycelium could be observed, confirming that truffles modify the endogenous hormonal balance of plants. Last, we demonstrate that truffles synthesize ethylene from l-methionine probably through the α-keto-γ-(methylthio)butyric acid pathway. Taken together, these results establish the central role of IAA and ethylene as signal molecules in truffle/plant interactions.
Level-raising for Saito–Kurokawa forms
Authors: Sorensen Claus M.
Published: June 2009

This paper provides congruences between unstable and stable automorphic forms for the symplectic similitude group GSp(4). More precisely, we raise the level of certain CAP representations Π arising from classical modular forms. We first transfer Π toπon a suitable inner formG; this is achieved byθ-lifting. Forπ, we prove a precise level-raising result that is inspired by the work of Bellaiche and Clozel and which relies on computations of Schmidt. We thus obtain a$\tilde {\pi }$congruent toπ, with a local component that is irreducibly induced from an unramified twist of the Steinberg representation of the Klingen parabolic. To transfer$\tilde {\pi }$back to GSp(4), we use Arthur’s stable trace formula. Since$\tilde {\pi }$has a local component of the above type, all endoscopic error terms vanish. Indeed, by results due to Weissauer, we only need to show that such a component does not participate in theθ-correspondence with any GO(4); this is an exercise in using Kudla’s filtration of the Jacquet modules of the Weil representation. We therefore obtain a cuspidal automorphic representation$\tilde {\Pi }$of GSp(4), congruent to Π, which is neither CAP nor endoscopic. It is crucial for our application that we can arrange for$\tilde {\Pi }$to have vectors fixed by the non-special maximal compact subgroups at all primes dividingN. SinceGis necessarily ramified at some primer, we have to show a non-special analogue of the fundamental lemma atr. Finally, we give an application of our main result to the Bloch–Kato conjecture, assuming a conjecture of Skinner and Urban on the rank of the monodromy operators at the primes dividingN.
The Crushing Characteristics of Square Tubes With Blast-Induced Imperfections—Part I: Experiments
Authors: Yuen S. Chung Kim , Nurick G. N.
Published: June 2009

This two-part article presents the results of experimental and numerical work on the crushing characteristics of square tubes, with blast-induced imperfections, subjected to axial load. In Part I, the experimental studies are presented. The approach in the studies involves creating imperfections on opposite sides at midlength of a square tube by means of localized blast loads to create three types of imperfections; nontouching domes, rebound domes, and capped domes. These imperfections change the geometry and the material properties in the midsection of the tubes and hence affect the crushing characteristics. While the blast-induced imperfections enhance the energy absorption characteristics of the tubes they also affect the lobe formation process. In Part II, the finite element package ABAQUS/EXPLICIT v6.5-6 is used to construct a 12 symmetry model by means of shell and continuum elements to simulate the tube response to the localized blast loads followed by dynamic axial loading in the form of a rigid mass impacting at a specified initial velocity. The hydrodynamic code AUTODYN is used to characterize the localized blast pressure time and spatial history. The predictions show satisfactory correlation with experiments for both crushed shapes and crushed distance.
The Crushing Characteristics of Square Tubes With Blast-Induced Imperfections—Part II: Numerical Simulations
Authors: Yuen S. Chung Kim , Nurick G. N.
Published: June 2009

This two-part paper presents the results of experimental and numerical work on the crushing characteristics of square tubes, with blast-induced imperfections, subjected to axial load. In Part I, the experimental studies are presented. The approach in the studies involves creating imperfections on opposite sides at midlength of a square tube by means of localized blast loads to create three types of imperfections: nontouching domes, rebound domes, and capped domes. These imperfections change the geometry and the material properties in the midsection of the tubes and hence affect the crushing characteristics. While the blast-induced imperfections enhance the energy absorption characteristics of the tubes they also affect the lobe formation process. In Part II, the finite element package ABAQUS/EXPLICIT v6.5–6 is used to construct a 12 symmetry model by means of shell and continuum elements to simulate the tube response to the localized blast loads followed by dynamic axial loading in the form of a rigid mass impacting at a specified initial velocity. The hydrodynamic code AUTODYN is used to characterize the localized blast pressure time and spatial history. The predictions show satisfactory correlation with experiments for both crushed shapes and crushed distance.
Fully Lagrangian Modeling of Dynamics of MEMS With Thin Beams—Part II: Damped Vibrations
Authors: Ghosh Ranajay , Mukherjee Subrata
Published: June 2009

Micro-electro-mechanical systems (MEMS) often use beam or plate shaped conductors that are very thin with h/L≈O(10−2–10−3) (in terms of the thickness h and length L of a beam or side of a square plate). A companion paper (Ghosh and Mukherjee, 2009, “Fully Lagrangian Modeling of Dynamics of MEMS With Thin Beams—Part I: Undamped Vibrations,” ASME J. Appl. Mech., 76, p. 051007) addresses the coupled electromechanical problem of MEMS devices composed of thin beams. A new boundary element method (BEM) is coupled with the finite element method (FEM) by Ghosh and Mukherjee, and undamped vibrations are addressed there. The effect of damping due to the surrounding fluid modeled as Stokes flow is included in the present paper. Here, the elastic field modeled by the FEM is coupled with the applied electric field and the fluid field, both modeled by the BEM. As for the electric field, the BEM is adapted to efficiently handle narrow gaps between thin beams for the Stokes flow problem. The coupling of the various fields is carried out using a Newton scheme based on a Lagrangian description of the various domains. Numerical results are presented for damped vibrations of MEMS beams.
The Effects of Strong Cubic Nonlinearity on the Existence of Periodic Solutions of the Mathieu–Duffing Equation
Authors: Kovacic Ivana , Cveticanin Livija
Published: June 2009

This paper deals with systems governed by the Mathieu–Duffing equation, with a time-dependent coefficient of the linear term and a constant, not necessarily small coefficient of the cubic term. This coefficient can be positive or negative. The method of strained parameters applied to a linear system governed by the Mathieu equation is extended to a strongly nonlinear system. As a result, the curves corresponding to the parameter values at which periodic solutions exist are obtained. It is shown that they strongly depend on the value of the coefficient of nonlinearity and the initial conditions. The corresponding parameter planes are plotted. Numerical integrations are carried out to confirm the analytical results.
Comparison and Validation of Two Models of Netting Deformation
Authors: O’Neill F. G. , Priour D.
Published: June 2009

The predictions of two numerical models of the deformation of fishing netting are compared. Analytical solutions are found to the differential equations that govern one of these models, and these solutions are used to evaluate the accuracy of both. There is very good agreement between the numerical solutions and the corresponding analytical values. The models are also applied to the deformation of networks where there is an in-plane shear resistance. Although there are no analytical solutions available, the similarity of the numerical solutions gives confidence in both methods.
Validation of Nonlinear Viscoelastic Contact Force Models for Low Speed Impact
Authors: Zhang Yuning , Sharf Inna
Published: June 2009

Compliant contact force modeling has become a popular approach for contact and impact dynamics simulation of multibody systems. In this area, the nonlinear viscoelastic contact force model developed by Hunt and Crossley (1975, “Coefficient of Restitution Interpreted as Damping in Vibroimpact,” ASME J. Appl. Mech., 42, pp. 440–445) over 2 decades ago has become a trademark with applications of the model ranging from intermittent dynamics of mechanisms to engagement dynamics of helicopter rotors and implementations in commercial multibody dynamics simulators. The distinguishing feature of this model is that it employs a nonlinear damping term to model the energy dissipation during contact, where the damping coefficient is related to the coefficient of restitution. Since its conception, the model prompted several investigations on how to evaluate the damping coefficient, in turn resulting in several variations on the original Hunt–Crossley model. In this paper, the authors aim to experimentally validate the Hunt–Crossley type of contact force models and furthermore to compare the experimental results to the model predictions obtained with different values of the damping coefficient. This paper reports our findings from the sphere to flat impact experiments, conducted for a range of initial impacting velocities using a pendulum test rig. The unique features of this investigation are that the impact forces are deduced from the acceleration measurements of the impacting body, and the experiments are conducted with specimens of different yield strengths. The experimental forces are compared with those predicted from the contact dynamics simulation of the experimental scenario. The experiments, in addition to generating novel impact measurements, provide a number of insights into both the study of impact and the impact response.
Rotating Beams and Nonrotating Beams With Shared Eigenpair
Authors: Kumar Ananth , Ganguli Ranjan
Published: June 2009

In this paper, we look for rotating beams whose eigenpair (frequency and mode-shape) is the same as that of uniform nonrotating beams for a particular mode. It is found that, for any given mode, there exist flexural stiffness functions (FSFs) for which the jth mode eigenpair of a rotating beam, with uniform mass distribution, is identical to that of a corresponding nonrotating uniform beam with the same length and mass distribution. By putting the derived FSF in the finite element analysis of a rotating cantilever beam, the frequencies and mode-shapes of a nonrotating cantilever beam are obtained. For the first mode, a physically feasible equivalent rotating beam exists, but for higher modes, the flexural stiffness has internal singularities. Strategies for addressing the singularities in the FSF for finite element analysis are provided. The proposed functions can be used as test-functions for rotating beam codes and for targeted destiffening of rotating beams.
Local Damage Evolution of Double Cantilever Beam Specimens During Crack Initiation Process: A Natural Boundary Condition Based Method
Authors: Ouyang Zhenyu , Li Guoqiang
Published: June 2009

Cohesive zone models are being increasingly used to simulate fracture and debonding processes in metallic, polymeric, and ceramic materials and their composites. The crack initiation process as well as its actual stress and damage distribution beyond crack tip are important for understanding fracture of materials and debonding of adhesively bonded joints. In the current model, a natural boundary condition based method is proposed, and thus the concept of extended crack length (characteristic length l) is no longer required and more realistic and natural local deformation beyond crack tip can be obtained. The new analytical approach, which can consider both crack initiation and propagation as well as local deformation and interfacial stress distribution, can be explicitly obtained as a function of the remote peel load P with the given bilinear cohesive laws. An intrinsic geometric constraint condition is then used to solve the remote peel load P. The nonlinear response in both the ascending and descending stages of loading is accurately predicted by the current model, as evidenced by a comparison with both experimental results and finite element analysis results. It is found that the local deformation and interfacial stress beyond crack tip are relatively stable during crack propagation. It is also found that, when the cohesive strength is low, it has a significant effect on the critical peel load and loadline deflection. In principle, the approach developed in the current study can be extended to multilinear cohesive laws, although only bilinear cohesive law is presented in this work as an example.
On a Screw Dislocation Interacting With Two Viscous Interfaces
Authors: Wang X. , Pan E.
Published: June 2009

We investigate a screw dislocation interacting with two concentric circular linear viscous interfaces. The inner viscous interface is formed by the circular inhomogeneity and the interphase layer, and the outer viscous interface by the interphase layer and the unbounded matrix. The time-dependent stresses in the inhomogeneity, interphase layer, and unbounded matrix induced by the screw dislocation located within the interphase layer are derived. Also obtained is the time-dependent image force on the screw dislocation due to its interaction with the two viscous interfaces. It is found that when the interphase layer is more compliant than both the inhomogeneity and the matrix, three transient equilibrium positions (two are unstable and one is stable) for the dislocation can coexist at a certain early time moment. If the inhomogeneity and matrix possess the same shear modulus, and the characteristic times for the two viscous interfaces are also the same, a fixed equilibrium position always exists for the dislocation. In addition, when the interphase layer is stiffer than the inhomogeneity and matrix, the fixed equilibrium position is always an unstable one; on the other hand, when the interface layer is more compliant than the inhomogeneity and matrix, the nature of the fixed equilibrium position depends on the time: the fixed equilibrium position is a stable one if the time is below a critical value, and it is an unstable one if the time is above the critical value. In addition, a saddle point transient equilibrium position for the dislocation can also be observed under certain conditions.
Confined Thin Film
Delamination in the Presence of Intersurface Forces With Finite Range and
Magnitude
Authors: Wan Kai-tak , Julien Scott
E.
Published: June 2009

A circular membrane clamped at the periphery is allowed to adhere to or to delaminate from a planar surface of a cylindrical punch in the presence of intersurface forces with finite range and magnitude. Assuming a uniform disjoining pressure within the cohesive zone at the delamination front, the adhesion-delamination mechanics is obtained by a thermodynamic energy balance. Interrelations between the instantaneous applied load, punch displacement, and contact circle, and the resulting critical thresholds of “pinch-off,” “pull-off,” and “pull-in” are derived from the first principles. Two limiting cases are obtained: (i) intersurface force with long range and small magnitude in reminiscence of the classical Derjaguin–Muller–Toporov (DMT) model and (ii) short range and large magnitude alluding to the Johnson–Kendall–Roberts (JKR) model. The DMT-JKR transitional behavior has significant impacts on adhesion measurements, micro-electromechanical systems, and life-sciences.
Computational Modeling of Damage Development in Composite Laminates Subjected to Transverse Dynamic Loading
Authors: Forghani Alireza , Vaziri Reza
Published: June 2009

This paper presents a robust computational model for the response of composite laminates to high intensity transverse dynamic loading emanating from local impact by a projectile and distributed pressure pulse due to a blast. Delaminations are modeled using a cohesive type tie-break interface introduced between sublaminates while intralaminar damage mechanisms within the sublaminates are captured in a smeared manner using a strain-softening plastic-damage model. In the latter case, a nonlocal regularization scheme is used to address the spurious mesh dependency and mesh-orientation problems that occur with all local strain-softening type constitutive models. The results for the predicted damage patterns using the nonlocal approach are encouraging and qualitatively agree with the experimental observations. The predictive performance of the proposed numerical model is assessed through comparisons with available instrumented impact test results on a class of carbon-fiber reinforced polymer (CFRP) composite laminates. Force-time histories and other derived cross-plots such as the force versus projectile displacement and progression of projectile energy loss as a function of time are compared with available experimental results to demonstrate the efficacy of the model in capturing the details of the dynamic response. Another case study involving the blast loading of CFRP composite laminates is used to further highlight the capability of the proposed model in simulating the global structural response of composite laminates subjected to distributed pressure pulses.
Fluid-Structure and Shock-Bubble Interaction Effects During Underwater Explosions Near Composite Structures
Authors: Young Yin L. , Liu Zhanke , Xie Wenfeng
Published: June 2009

There is an increasing interest in the use of composites for marine/naval structures to reduce weight and maintenance cost, and to improve hydrodynamic and/or structural performance. In particular, recent works suggest that the use of a lightweight, soft core layer can significantly reduce the load transfer to the back layer of a sandwich structure when subjected to shock or impulse loads. The objective of this work is to investigate the role of fluid-structure interaction (FSI) and shock-bubble interaction in the transient response of composite structures during underwater explosions (UNDEX). The spatial distribution of UNDEX loads is different from uniform planar shocks due to the spherically propagating pressure front, and the temporal characteristics are also different due to the importance of shock-bubble interactions. Both effects influence the FSI response of the composite structure. A previously validated 2D Eulerian–Lagrangian numerical method is used to investigate fluid-structure and shock-bubble interaction effects during UNDEX near composite structures. Via a series of numerical experiments, the relative importance of different effects, namely, the Taylor’s FSI effect (1963, “The Pressure and Impulse of Submarine Explosion Waves on Plates” Scientific Papers of G. I. Taylor, 3, pp. 287–303), the bending/stretching effect, the core compression effect, and the boundary effect, are quantitatively and qualitatively evaluated. Insights for practical modeling, analysis, and design of blast-resistant sandwich structures are also drawn from the analysis.
Finite Element
Analysis of Plugging Failure in Steel Plates Struck by Blunt
Projectiles
Authors: Kane A. , Børvik T. , Hopperstad O.
S. , Langseth M.
Published: June 2009

In this paper, the influence of mesh sensitivity on the fracture predictions during penetration and perforation of hardened blunt-nose cylindrical steel projectiles in plates of Weldox 460E, Weldox 700E, and Weldox 900E steel has been studied. The main objective is to try to describe the experimentally obtained trend of a decrease in ballistic limit velocity with increased target strength when the plates are impacted by blunt projectiles. This behavior is due to the occurrence of highly localized shear bands as the target strength increases. The impact tests are analyzed using the explicit solver of a nonlinear finite element code. A thermoelastic-thermoviscoplastic constitutive model with coupled or uncoupled ductile damage was used in the simulations. It was found that the residual velocity continuously increases when the element size is decreased from 125 μm to 15 μm in the shear zone, and that this increase is significantly stronger for impact velocities close to the ballistic limit. The ballistic limit decreases by up to 25% when the size of the element is decreased from 125 μm to 30 μm; the decrease being somewhat greater for the two steels with the highest strength. Even with the finest mesh, the experimental trend of a decreasing ballistic limit with increasing target strength was not predicted in the simulations, neither with coupled nor uncoupled damage. Nonlocal simulations based on smoothing of the damage and temperature fields, which are the two variables causing the softening, were carried out for the Weldox steels and a mesh size of 30 μm. These simulations indicate a reduction in the mesh sensitivity for both the coupled and uncoupled damage approaches when nonlocal averaging is employed.
The Influence of
Material Properties and Confinement on the Dynamic Penetration of Alumina by Hard
Spheres
Authors: Wei Z. , Evans A.
G. , Deshpande V. S.
Published: June 2009

The ability of a ceramic to resist penetration by projectiles depends, in a coupled manner, on its confinement and its mechanical properties. In order to explore the fundamental inter-relationships, a simulation protocol is required that permits the microstructure and normative properties (hardness and toughness) to be used as input parameters. Potential for attaining this goal has been provided by a recent constitutive model, devised by Deshpande and Evans (DE) [2008, “Inelastic Deformation and Energy Dissipation in Ceramics: A Mechanics-Based Dynamic Constitutive Model,” J. Mech. Phys. Solids, 56, pp. 3077–3100] that incorporates the contributions to the inelastic strain from both plasticity and microcracking. Before implementing the DE model, various comparisons with experimental measurements are required. Previously, the model has been successfully used to predict the quasistatic penetration of alumina by hard spheres. In the present assessment, simulations of the dynamic penetration of confined alumina cylinders are presented as a function of microstructure and properties and compared with literature measurements of the ballistic mass efficiency. It is shown that the model replicates the measured trends with hardness and grain size. Motivated by this comparison, further simulations are used to gain a basic understanding of the respective roles of plasticity and microcracking on penetration and to elucidate the phenomena governing projectile defeat.
Energy and Momentum Transfer in Air Shocks
Authors: Hutchinson John W.
Published: June 2009

A series of one-dimensional studies is presented to reveal basic aspects of momentum and energy transfer to plates in air blasts. Intense air waves are initiated as either an isolated propagating wave or by the sudden release of a highly compressed air layer. Wave momentum is determined in terms of the energy characterizing the compressed layer. The interaction of intense waves with freestanding plates is computed with emphasis on the momentum and/or energy transferred to the plate. A simple conjecture, backed by numerical simulations, is put forward related to the momentum transmitted to massive plates. The role of the standoff distance between the compressed air layer and the plate is elucidated. Throughout, dimensionless parameters are selected to highlight the most important groups of parameters and to reduce parametric dependencies to the extent possible.
Graphene: Status and Prospects
Authors: Geim A. K.
Published: June 2009

Expanding Flatland

Since its discovery and isolation some 5 years ago, research on graphene has exploded. The sheets of carbon atoms, just one atom thick, exhibit a vast array of properties—mechanical, optical, and electrical—that make it an ideal test bed to probe fundamental problems in physics, as well as lending itself to a wide portfolio of applications.
Geim
(p.
1530
), the discoverer of this remarkable material, reviews recent advances and discusses what other developments may be in store for this material.
Comment on “Experimental Test of Self-Shielding in Vacuum Ultraviolet Photodissociation of CO”
Authors: Lyons James R. , Lewis Roy S. , Clayton Robert N.
Published: June 2009

Chakraborty
et al
. (Reports, 5 September 2008, p. 1328) demonstrated very large, wavelength-dependent mass-independent isotopic effects during carbon monoxide (CO) photodissociation and argued that self-shielding in CO was not responsible. We suggest that variations in band oscillator strengths and linewidths among CO isotopologs are responsible for most of the wavelength dependence observed and that the reported experiments confirm the importance of self-shielding during CO photodissociation.
Response to Comments on “Experimental Test of Self-Shielding in Vacuum Ultraviolet Photodissociation of CO”
Authors: Chakraborty Subrata , Ahmed Musahid , Jackson Teresa L. , Thiemens Mark H.
Published: June 2009

We address the comments by Lyons
et al
., Federman and Young, and Yin
et al
. regarding the interpretation of our carbon monoxide photodissociation experiments and provide further experimental data analysis, including measured synchrotron beam profiles. The experimental data do not support existing self-shielding models that attempt to explain observed meteoritic oxygen isotopic compositions because they rely on previously untested theoretical assumptions.
Nutrient Imbalances in Agricultural Development
Authors: Vitousek P. M. , Naylor R. , Crews T. , David M. B. , Drinkwater L. E. , Holland E. , Johnes P. J. , Katzenberger J. , Martinelli L. A. , Matson P. A. , Nziguheba G. , Ojima D. , Palm C. A. , Robertson G. P. , Sanchez P. A. , Townsend A. R. , Zhang F. S.
Published: June 2009

Nutrient additions to intensive agricultural systems range from inadequate to excessive—and both extremes have substantial human and environmental costs.
Comment on “Experimental Test of Self-Shielding in Vacuum Ultraviolet Photodissociation of CO”
Authors: Yin Qing-Zhu , Shi Xiaoyu , Chang Chao , Ng Cheuk-Yiu
Published: June 2009

Chakraborty
et al
. (Reports, 5 September 2008, p. 1328) concluded that an anomalously enriched atomic oxygen reservoir can be generated through carbon monoxide photodissociation without self-shielding. We show that this conclusion is based on the incorrect assumption that the spectral shifts of the 97.03-nanometers and 107.61-nanometers vibrational bands for C
16
O, C
17
O, and C
18
O are negligible and point out shortcomings of the low-resolution light source used in their experiments.
Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees
Authors: Liu Kevin , Raghavan Sindhu , Nelesen Serita , Linder C. Randal , Warnow Tandy
Published: June 2009

Rapid Tree Building

Phylogenetic reconstruction is used to determine the relationships between organisms and requires an accurate alignment and analysis of multiple sequences. Iterative rounds of alignment and tree building are often necessary to prevent errors in the phylogeny estimate. One such way to address this problem is to assess alignment and trees in a single step. However, efficient algorithms to analyze data sets of reasonable size have been lacking.

Liu
et al.

(p.
1561
; see the Perspective by

Löytynoja and Goldman

) describe an iterative approach that simultaneously incorporates both alignment and phylogeny and applies a fast maximum likelihood algorithm to the tree-building part. By assembling the components of the methods in this way, accurate results were obtained for up to 1000 sequences. Thus, it is possible to produce coestimation of sequence alignment and phylogeny that is both rapid and accurate.
Solar-Like Oscillations in a Massive Star
Authors: Belkacem Kévin , Samadi Réza , Goupil Marie-Jo , Lefèvre Laure , Baudin Fréderic , Deheuvels Sébastien , Dupret Marc-Antoine , Appourchaux Thierry , Scuflaire Richard , Auvergne Michel , Catala Claude , Michel Eric , Miglio Andrea , Montalban Josefina , Thoul Anne , Talon Suzanne , Baglin Annie , Noels Arlette
Published: June 2009

Star Gazing

Seismology of stars provides a unique insight into physical mechanisms taking place in their interior. Like the Sun, some stars have low-amplitude pulsations that are excited by turbulent convection in their outer layers.

Belkacem
et al.

(p.
1540
), using data gathered by the CoRoT satellite, report on low-amplitude, solar-like oscillations in a massive star that undergoes radial pulsations as a result of expanding and contracting layers in its interior. The finding opens the possibility of probing the interiors of this type of massive star, which can be the progenitors of supernovae.
Merkel Cells Are Essential for Light-Touch Responses
Authors: Maricich Stephen M. , Wellnitz Scott A. , Nelson Aislyn M. , Lesniak Daine R. , Gerling Gregory J. , Lumpkin Ellen A. , Zoghbi Huda Y.
Published: June 2009

Mysterious Merkel cells

Anatomists have known about the existence of Merkel cells in our skin for over a century. However, the function of these cells has been unclear and controversial. To solve this mystery,

Maricich
et al.

(p.
1580
) created a genetic deletion of Merkel cells. When Atoh1, a transcription factor expressed by Merkel cells, was conditionally deleted in the skin, Merkel cells were completely absent from Atoh1CKO mice. Using ex vivo skin and nerve preparations from the animals showed that Merkel cells are needed to properly encode light touch sensation in the skin.
Thriving in Salt
Authors: Boetius Antje , Joye Samantha
Published: June 2009

Saline environments from polar glaciers to the deep sea floor contain a surprising variety of organisms.
No Place Too Cold
Authors: Laybourn-Parry Johanna
Published: June 2009

Simple microbial food webs are found even in the coldest and most remote polar lakes.
Colloidal Quantum-Dot Photodetectors Exploiting Multiexciton Generation
Authors: Sukhovatkin Vlad , Hinds Sean , Brzozowski Lukasz , Sargent Edward H.
Published: June 2009

Reaping Gain from Decay

In photovoltaic devices, absorbed light excites electrons into a conduction band and thereby initiates electric current flow. Unfortunately, if the energy of the incident photons exceeds the threshold for this excitation (the bandgap), the excess tends to be wasted. Initially, a photon bearing several multiples of the bandgap energy may correspondingly promote several electrons, but before these can begin to travel through a circuit, most of them drop back down to the immobile state, transferring their packet of energy to a lone remaining carrier in a process termed “Auger decay.”

Sukhovatkin
et al.

(p.
1542
) show that a photoconductive device design can actually leverage the Auger decay process to improve sensitivity in ultraviolet detection. Their detector, a thin film assembled from lead sulfide quantum dots, improves its response by up to a factor of four when the incident light frequency rises to several multiples of the bandgap.
Sexual Intercourse Involving Giant Sperm in Cretaceous Ostracode
Authors: Matzke-Karasz R. , Smith R. J. , Symonova R. , Miller C. G. , Tafforeau P.
Published: June 2009

Giant ostracode sperm date back at least 100 million years ago.
Squeezing the Water Out of HCl(aq)
Authors: Zwier Timothy S.
Published: June 2009

The controlled formation of clusters confined to helium droplets shows that just four water molecules are sufficient to dissolve hydrochloric acid into its ions.
Can Civilization (at Least the U.K.) Run Sustainably?
Sustainable Energy
Without the Hot Air

by David J. C. MacKay

UIT Cambridge, Cambridge, 2009. 384 pp. £45. ISBN 9781906860011. Paper, £19.99. ISBN 9780954452933. ()
Authors: Hoffert Marty
Published: June 2009

MacKay offers an accessible, quantitative account of the changes that are needed to switch the United Kingdom to sustainable energy sources.
Arguments over Early Arrivals
First Peoples in a New World
Colonizing Ice Age America

by David J. Meltzer

University of California Press, Berkeley, 2009. 480 pp. $29.95, £20.95. ISBN 9780520250529.
Authors: Flannery Tim
Published: June 2009

Writing for a broad, nonspecialist audience, Meltzer discusses both what we know about the early history of humans in the Americas and the often controversial research that has led to our current understanding of that topic.
Extracting Potentials from Spectra
Authors: Bernath Peter F.
Published: June 2009

An analysis of the spectra of the elusive beryllium dimer, aided by ab initio calculations, characterizes the molecule near its dissociation limit.
Uniting Alignments and Trees
Authors: Löytynoja Ari , Goldman Nick
Published: June 2009

An iterative method that estimates both sequence alignments and phylogenies leads to improved phylogenetic trees for large data sets.
Bridging the Gap and Staying Local
Authors: Korte Martin
Published: June 2009

Imaging with fluorescence reporters reveals the molecular nature of long-term memory storage at stimulated synapses.
Science Journalism Goes Global
Authors: Russell Cristine
Published: June 2009

When swine flu struck swiftly in Mexico, it created a challenge not only for international public health officials but also for journalists around the world assigned to follow the unfolding story. They needed to explain, in the face of great uncertainty and a nonstop news cycle, what the novel influenza A (H1N1) virus was and the potential dangers it posed. It was a difficult story handled most capably by experienced health and science reporters.
After Delays, WHO Agrees: The 2009 Pandemic Has Begun
Authors: Cohen Jon , Enserink Martin
Published: June 2009

When World Health Organization (WHO) chief Margaret Chan declared last week that for the first time in more than 40 years the world is facing an influenza pandemic, she simply stated what everybody already knew.
Expanded U.S. Drug Agency to Control Tobacco
Authors: Couzin-Frankel Jennifer , Koenig Robert
Published: June 2009

The U.S. Food and Drug Administration is on the cusp of gaining power for the first time to regulate cigarettes and other tobacco products.
Verification Experts Puzzled Over North Korea's Nuclear Test
Authors: Clery Daniel
Published: June 2009

The Comprehensive Nuclear-Test-Ban Treaty Organization revealed last week that its global network of radionuclide detectors, which sniff out faint wind-borne traces of radioactive elements such as xenon, had not picked up anything it could pin on the 25 May North Korean test.
A Final Push to Divvy Up the Sea by All the Rules
Authors: Kerr Richard A.
Published: June 2009

Is this the year that the United States finally ratifies the United Nations Convention on the Law of the Sea, an international agreement to conserve and manage the wealth of the ocean?
Italy's MIT Grows, And So Does Controversy Over It
Authors: Margottini Laura
Published: June 2009

Everyone wants to emulate the Massachusetts Institute of Technology, but Italy is discovering that not everyone agrees on how to do it.
Dark-Matter Model Multiplies Mass of Galactic Black Holes
Authors: Bhattacharjee Yudhijit
Published: June 2009

According to new research presented at the American Astronomical Society meeting, astronomers may have been systematically underestimating nearby black hole masses by a factor of two to three.
Star Studies Yield Better Yardsticks
Authors: Bhattacharjee Yudhijit
Published: June 2009

At the American Astronomical Society meeting, researchers presented findings that could make it easier to measure cosmic distances and help refine estimates of the rate of expansion of the universe.
The Promise of a Cure: 20 Years and Counting
Authors: Couzin-Frankel Jennifer
Published: June 2009

The discovery of the cystic fibrosis gene brought big hopes for gene-based medicine; although a lot has been achieved over 2 decades, the payoff remains just around the corner.
Radio Astronomers Go for High Gain With Mammoth Telescope
Authors: Hvistendahl Mara
Published: June 2009

Construction is about to commence on the world's biggest single-dish radio telescope, which will take aim at exotic beasts such as pulsars and dark galaxies.
ISO … 3.5 Million U.S. Jobs
Authors: Holden Constance
Published: June 2009

Economists are shaking their heads at the Obama Administration's claim to be able to count the jobs that will flow from the stimulus package.
Is Quantum Mechanics Tried, True, Wildly Successful, and Wrong?
Authors: Folger Tim
Published: June 2009

A skeptical physicist charges that his field has been wandering in a philosophical wilderness for 80 years. The good news: He thinks he knows the way out.
Life Science Technologies: Gene Transfer: Taming Diversity
Authors: May Mike
Published: June 2009

Transferring specific nucleic acids into cells can modulate gene function, thereby revealing the mechanism of action and ultimate role of specific stretches of DNA. Nonetheless, getting the nucleic acids into the right cells efficiently and without damaging them creates challenges as diverse as the cells themselves.
Beneficial Effects of a Combination of Korean Red Ginseng and Highly Active Antiretroviral Therapy in Human Immunodeficiency Virus Type 1-Infected Patients
Authors: Sung Heungsup , Jung You-Sun , Cho Young-Keol
Published: June 2009

To determine whether Korean red ginseng (KRG) has beneficial effects on human immunodeficiency virus type 1 (HIV-1)-infected patients administered highly active antiretroviral therapy (HAART), we analyzed the CD4 T-cell count, viral load, and resistance mutations to HAART in 46 individuals. Thirteen patients harbored resistance mutations at baseline. The study population was divided into two groups: specifically, a group treated with a combination of HAART plus KRG (23 patients) and a group treated with HAART alone (23 patients). The annual increase in CD4 T-cell count in the combination group was significantly higher than that in the group treated with HAART alone (
P
< 0.05). Overall, 21 patients harbored resistance mutations after 3 years of therapy. Following exclusion of 13 patients displaying baseline resistance mutations, 7.1% of patients (1/14) in the combination group and 42.1% (8/19) in the HAART group were identified with resistance mutations. One patient with baseline resistance mutations in the combination group did not display resistance mutations 3 years after HAART therapy. High-level resistance mutations were significantly lower in the combination group than in the group treated with HAART alone. Five patients showed no improvement in viral copy number (26.3% [5/19]) in the combination group and 9 (45.0% [9/20]) showed no improvement in the HAART-only group. Our data support the clinical utility of KRG intake during HAART therapy.
Statistical Approach To Estimate Vaccinia-Specific Neutralizing Antibody Titers Using a High-Throughput Assay
Authors: Kennedy Richard , Pankratz V. Shane , Swanson Eric , Watson David , Golding Hana , Poland Gregory A.
Published: June 2009

Because of the bioterrorism threat posed by agents such as variola virus, considerable time, resources, and effort have been devoted to biodefense preparation. One avenue of this research has been the development of rapid, sensitive, high-throughput assays to validate immune responses to poxviruses. Here we describe the adaptation of a β-galactosidase reporter-based vaccinia virus neutralization assay to large-scale use in a study that included over 1,000 subjects. We also describe the statistical methods involved in analyzing the large quantity of data generated. The assay and its associated methods should prove useful tools in monitoring immune responses to next-generation smallpox vaccines, studying poxvirus immunity, and evaluating therapeutic agents such as vaccinia virus immune globulin.
Detection of Cryptic Genospecies Misidentified as
Haemophilus influenzae
in Routine Clinical Samples by Assessment of Marker Genes
fucK
,
hap
, and
sodC
Authors: Nørskov-Lauritsen Niels
Published: June 2009

Clinical isolates of
Haemophilus influenzae
were assessed for the presence of
fucK
,
hap
, and
sodC
by hybridization with gene-specific probes, and isolates diverging from the expected
H. influenzae
genotype were characterized by phenotype and 16S rRNA gene sequencing. Two of 480 isolates were finally classified as variant strains (“nonhemolytic
Haemophilus haemolyticus
”).
Assessment of the Ability of a Fourth-Generation Immunoassay for Human Immunodeficiency Virus (HIV) Antibody and p24 Antigen To Detect both Acute and Recent HIV Infections in a High-Risk Setting
Authors: Pandori Mark W. , Hackett John , Louie Brian , Vallari Ana , Dowling Teri , Liska Sally , Klausner Jeffrey D.
Published: June 2009

An immunoassay (IA) that simultaneously detects both antibody to human immunodeficiency virus (HIV) and HIV p24 antigen (Architect HIV Ag/Ab Combo) was evaluated for its ability to detect HIV infection by using a panel of specimens collected from individuals recently infected with HIV type 1 (HIV-1). This IA was found to be capable of detecting the majority (89%) of infections, including 80% of those considered acute infections based on the presence of HIV RNA and the lack of detectable antibody to HIV. Substantial improvements in detection of recent infections by the Architect HIV Ag/Ab Combo relative to previous generations of IAs as well as the capacity to detect acute infections have important implications for HIV prevention strategies.