bluuebunny/crossref_metadata_2025 huggingface dataset:
The detectability of cracks using sonic IR
Authors: Morbidini Marco , Cawley Peter
Published: May 2009

This paper proposes a methodology to study the detectability of fatigue cracks in metals using sonic IR (also known as thermosonics). The method relies on the validation of simple finite-element thermal models of the cracks and specimens in which the thermal loads have been defined by means of a priori measurement of the additional damping introduced in the specimens by each crack. This estimate of crack damping is used in conjunction with a local measurement of the vibration strain during ultrasonic excitation to retrieve the power released at the crack; these functions are then input to the thermal model of the specimens to find the resulting temperature rises (sonic IR signals). The method was validated on mild steel beams with two-dimensional cracks obtained in the low-cycle fatigue regime as well as nickel-based superalloy beams with three-dimensional “thumbnail” cracks generated in the high-cycle fatigue regime. The equivalent 40kHz strain necessary to obtain a desired temperature rise was calculated for cracks in the nickel superalloy set, and the detectability of cracks as a function of length in the range of 1–5mm was discussed.
Methanol synthesis on ZnO(0001¯). I. Hydrogen coverage, charge state of oxygen vacancies, and chemical reactivity
Authors: Kiss Janos , Witt Alexander , Meyer Bernd , Marx Dominik
Published: May 2009

Oxygen vacancies on ZnO(0001¯) have been proposed to be the catalytically active sites for methanol synthesis on pure ZnO. The charge state and thus the chemical reactivity of such vacancies on this polar O-terminated basal plane of ZnO is expected to be intimately connected to the degree of its hydroxylation in view of its Tasker type(3) unstable character. Here, the interplay between hydrogen adsorption and the thermodynamic stability of O vacancies in various charge states, corresponding formally to F++, F+, F0, F−, and F−− centers, is investigated using electronic structure calculations. Assuming thermodynamic equilibrium of the defective surface with a hydrogen containing gas phase the thermodynamically most stable O vacancy type is determined as a function of temperature and pressure. For the adsorption of H2 molecules at O vacancy sites it is found that the homolytic process leads to energetically more favorable structures than heterolytic adsorption and hydride formation. By homolytic adsorption and desorption one can switch between F++, F0, and F−− or between F+ and F−, a process which is believed to occur during methanol synthesis. However, the barrier for heterolytic dissociation of H2 at O vacancies is significantly lower compared to homolytic cleavage. Furthermore, the barrier for transforming hydridic hydrogen, i.e., ZnH species, to protonic hydrogen, i.e., OH species together with a reduction of ZnO itself, is quite high. This implies that hydridic H− species created as a result of heterolytic dissociation might have a long enough lifetime at O vacancies that they will be available for methanol synthesis. ZnH and OH vibrational frequencies have been computed in order to assist future experimental assignments.
An accurate density functional theory calculation for electronic excitation energies: The least-squares support vector machine
Authors: Gao Ting , Sun Shi-Ling , Shi Li-Li , Li Hui , Li Hong-Zhi , Su Zhong-Min , Lu Ying-Hua
Published: May 2009

Support vector machines (SVMs), as a novel type of learning machine, has been very successful in pattern recognition and function estimation problems. In this paper we introduce least-squares (LS) SVMs to improve the calculation accuracy of density functional theory. As a demonstration, this combined quantum mechanical calculation with LS-SVM correction approach has been applied to evaluate the electronic excitation energies of 160 organic molecules. The newly introduced LS-SVM approach reduces the root-mean-square deviation of the calculated electronic excitation energies of 160 organic molecules from 0.32 to 0.11 eV for the B3LYP/6-31G(d) calculation. Thus, the LS-SVM correction on top of B3LYP/6-31G(d) is a better method to correct electronic excitation energies and can be used as the approximation of experimental results which are impossible to obtain experimentally.
H
3
+
as a trap for noble gases-3: Multiple trapping of neon, argon, and krypton in XnH3+ (n=1–3)
Authors: Pauzat F. , Ellinger Y. , Pilmé J. , Mousis O.
Published: May 2009

Recent studies on the formation of XH3+ noble gas complexes have shown strategic implications for the composition of the atmospheres of the giant planets as well as for the composition of comets. One crucial factor in the astrophysical process is the relative abundances of the noble gases versus H3+. It is the context in which the possibility for clustering with more than one noble gas (XnH3+ up to n=3) has been investigated for noble gases X ranging from neon to krypton. In order to assert our results, a variety of methods have been used including ab initio coupled cluster CCSD and CCSD(T), MP2, and density functional BH&HLYP levels of theory. All complexes with one, two, and three noble gases are found to be stable in the Ne, Ar, and Kr families. These stable structures are planar with the noble gases attached to the apices of the H3+ triangle. The binding energy of the nth atom, defined as the XnH3+→Xn−1H3++X reaction energy, increases slightly with n varying from 1 to 3 in the neon series, while it decreases in the argon series and shows a minimum for n=2 in the krypton series. The origin of this phenomenon is to be found in the variations in the respective vibrational energies. A topological analysis of the electron localization function shows the importance of the charge transfer from the noble gases toward H3+ as a driving force in the bonding along the series. It is also consistent with the increase in the atomic polarizabilities from neon to krypton. Rotational constants and harmonic frequencies are reported in order to provide a body of data to be used for the detection in laboratory prior to space observations. This study strongly suggests that the noble gases could be sequestered even in an environment where the H3+ abundance is small.
A comparative study of the centroid and ring-polymer molecular dynamics methods for approximating quantum time correlation functions from path integrals
Authors: Pérez Alejandro , Tuckerman Mark E. , Müser Martin H.
Published: May 2009

The problems of ergodicity and internal consistency in the centroid and ring-polymer molecular dynamics methods are addressed in the context of a comparative study of the two methods. Enhanced sampling in ring-polymer molecular dynamics (RPMD) is achieved by first performing an equilibrium path integral calculation and then launching RPMD trajectories from selected, stochastically independent equilibrium configurations. It is shown that this approach converges more rapidly than periodic resampling of velocities from a single long RPMD run. Dynamical quantities obtained from RPMD and centroid molecular dynamics (CMD) are compared to exact results for a variety of model systems. Fully converged results for correlations functions are presented for several one dimensional systems and para-hydrogen near its triple point using an improved sampling technique. Our results indicate that CMD shows very similar performance to RPMD. The quality of each method is further assessed via a new χ2 descriptor constructed by transforming approximate real-time correlation functions from CMD and RPMD trajectories to imaginary time and comparing these to numerically exact imaginary time correlation functions. For para-hydrogen near its triple point, it is found that adiabatic CMD and RPMD both have similar χ2 error.
Phase-contrast imaging and tomography at 60 keV using a conventional x-ray tube source
Authors: Donath Tilman , Pfeiffer Franz , Bunk Oliver , Groot Waldemar , Bednarzik Martin , Grünzweig Christian , Hempel Eckhard , Popescu Stefan , Hoheisel Martin , David Christian
Published: May 2009

Phase-contrast imaging at laboratory-based x-ray sources using grating interferometers has been developed over the last few years for x-ray energies of up to 28 keV. Here, we show first phase-contrast projection and tomographic images recorded at significantly higher x-ray energies, produced by an x-ray tube source operated at 100 kV acceleration voltage. We find our measured tomographic phase images in good agreement with tabulated data. The extension of phase-contrast imaging to this significantly higher x-ray energy opens up many applications of the technique in medicine and industrial nondestructive testing.
Comment on “High efficiency electron spin polarization analyzer based on exchange scattering at Fe/W(001)” [Rev. Sci. Instrum. 79, 083303 (2008)]
Authors: Ocaña Roberto
Published: May 2009

A recent article [Winkelmann et al., Rev. Sci. Instrum. 79, 083303 (2008)] reports on a compact detector to analyze the electron spin based on exchange scattering at Fe(001) thin film grown on W(001) with chemisorbed oxygen in the p(1×1) structure. The results obtained with the same detector without oxygen coverage show, however, a better performance in terms of both asymmetry and figure of merit. It is also argued that the characterization performed only allows to make qualitative comparisons with other existing detectors based on the same exchange scattering since the polarization of the incident beam has not been measured in situ.
Inertia dominated drop collisions. I. On the universal flow in the lamella
Authors: Roisman Ilia V. , Berberović Edin , Tropea Cam
Published: May 2009

This study is devoted to the analysis of inertia dominated axisymmetric drop collisions with a dry substrate or with another liquid drop. All the previous theoretical and semiempirical models of drop collisions are based on the assumption that the flow in the lamella and its thickness are determined by the impact conditions, mainly by the Reynolds and Weber numbers. In this study the existing experimental data are compared to existing and new numerical simulations for the shape of the lamella generated at the early times of drop impact for various impact conditions. The results show that if the Reynolds and Weber numbers are high enough, the evolution of the lamella thickness almost does not depend on the viscosity and surface tension. Therefore these results completely change our understanding of the flow generated by drop collisions. Moreover, we demonstrate that the theoretical models based on the approximation of the shape of the deforming drop by a disk and the models based on the energy balance approach are not correct. Finally, universal dimensionless distributions for the lamella thickness, velocity, and pressure are obtained from the numerical simulations of drop impact onto a symmetry plane (associated with the binary drop collisions). These universal distributions are valid for high impact Weber and Reynolds numbers.
Development of a dielectric-barrier discharge enhanced microplasma jet
Authors: Kiriu Shinya , Miyazoe Hiroyuki , Takamine Fumitoshi , Sai Masaki , Choi Jai Hyuk , Tomai Takaaki , Terashima Kazuo
Published: May 2009

A low-power ultrahigh-frequency-driven inductively coupled microplasma (ICMP) source equipped with dielectric-barrier discharge (DBD) was developed to realize a low-temperature and high-density plasma in fine quartz capillaries with inner diameters of less than 1.0 mm. A stable plasma was generated and its sustainability was independent of the gas flow rate. This plasma jet had a longer plume than that of a thermoelectron-enhanced microplasma jet, and time-resolved characterization suggested interactions between ICMP and DBD jets. By optical emission spectroscopy characterization, the gas temperature and electron density inside a capillary were estimated to be 400–1000 K and 1013–1014 cm−3, respectively.
Response to “Comment on ‘Quantum correction to Landau damping of electron plasma waves’ ” [Phys. Plasmas 16, 054703 (2009)]
Authors: Zhu Jun , Ji Peiyong , Lu Nan
Published: May 2009

We present three arguments to demonstrate that the comment on our paper [J. Zhu, P. Ji, and N. Lu, Phys. Plasmas 16, 032105 (2009)] by Zheng is incorrect, and the validity and feasibility of our start point are confirmed in this response.
Investigation of spatiotemporal behavior of the plasma density during the development of the thermocurrent instability
Authors: Hatami M. M. , Shokri B. , Niknam A. R. , Aliakbari A.
Published: May 2009

Considering a weakly ionized, collisional, quasineutral plasma placed in an electric field under the condition of nonresonant Cerenkov radiation and using the hydrodynamic model, a nonlinear diffusionlike equation with negative diffusion coefficient is obtained, which describes the dynamics of plasma density during the development of the thermocurrent instability. This equation is solved by the Adomian decomposition method. According to this solution, the spatiotemporal behavior of the plasma density during the growth of the thermocurrent instability is investigated. It is shown that the development of the thermocurrent instability causes the initial perturbations in the plasma density to grow. Also, it is shown that the increment in these perturbations continues until the growth of the thermocurrent instability ceases due to the breakdown of the quasineutrality condition. In this case, it is seen that the profile of the plasma density does not change any more and gets to a constant limit.
Photodissociation of dibromoethanes at 248 nm: An ignored channel of Br2 elimination
Authors: Lee Hsin-Lung , Lee Ping-Chen , Tsai Po-Yu , Lin King-Chuen , Kuo H. H. , Chen P. H. , Chang A. H. H.
Published: May 2009

Br 2 molecular elimination is probed in the photodissociation of 1,1- and 1,2-C2H4Br2 isomeric forms at 248 nm by using cavity ring-down absorption spectroscopy. Their photodissociation processes differ markedly from each other. The quantum yield of the Br2 fragment in 1,2-dibromoethane is 0.36±0.18, in contrast to a value of 0.05±0.03 in 1,1-dibromoethane. The vibrational population ratios of Br2(v=1)/Br2(v=0) are 0.8±0.1 and 0.5±0.2 for 1,2- and 1,1-dibromoethanes, respectively. The Br2 yield densities are found to increase by a factor of 35% and 190% for 1,2- and 1,1-dibromoethanes within the same temperature increment. In the ab initio potential energy calculations, the transition state (TS) along the adiabatic ground state surface may correlate to the Br2 products. The TS energy for 1,2-dibromoethane is well below the excitation energy at 483 kJ/mol, whereas that for 1,1-dibromoethane is slightly above. Such a small TS energy barrier impedes the photodissociation of the ground state 1,1-dibromoethane such that the production yield of Br2 may become relatively low, but rise rapidly with the temperature. The TS structure shows a larger bond distance of Br–Br in 1,2-dibromoethane than that in 1,1-dibromoethane. That explains why the former isomer may result in hotter vibrational population of the Br2 fragments.
Characterizing the detection system nonlinearity, internal inelastic background, and transmission function of an electron spectrometer for use in x-ray photoelectron spectroscopy
Authors: Wicks R. C. , Ingle N. J. C.
Published: May 2009

We present a method for removing spectrometer specific contributions to x-ray photoelectron spectroscopy data. We consider the degree of linearity of the detection system, the strength of the internal analyzer inelastic background, and finally determine the spectrometer’s transmission function. The procedures presented here are performed on a SPECS Phoibos 150 hemispherical analyzer with a two-dimensional detection system, but are applicable to a wide variety of different electron spectrometers. The spectrometer’s detection system is found to deviate from linear behavior by a few percent over the whole intensity range studied. The size of the analyzer internal inelastic scattering has been measured, and we find that it can normally be neglected at large pass energies or high kinetic energies for most types of analysis (contributing less than 1% at 100 eV pass energy). Finally, we measure the transmission function of the analyzer and lens system for a variety of different settings with the preceding corrections applied, and find that the form of the transmission function is dependent on small changes in the system’s settings.
An electro-optic modulator-assisted wavevector-resolving Brillouin light scattering setup
Authors: Neumann T. , Schneider T. , Serga A. A. , Hillebrands B.
Published: May 2009

Brillouin light scattering spectroscopy is a powerful technique which incorporates several extensions such as space-, time-, phase-, and wavevector-resolution. Here, we report on the improvement of the wavevector-resolving setup by including an electro-optic modulator. This provides a reference to calibrate the position of the diaphragm hole which is used for wavevector selection. The accuracy of this calibration is only limited by the accuracy of the wavevector measurement itself. To demonstrate the validity of the approach the wavevectors of dipole-dominated spin waves excited by a microstrip antenna were measured.
A cluster algorithm for Monte Carlo simulation at constant pressure
Authors: Almarza N. G.
Published: May 2009

We propose an efficient algorithm to sample the volume in Monte Carlo simulations in the isobaric-isothermal ensemble. The method is designed to be applied in the simulation of hard-core models at high density. The algorithm is based in the generation of clusters of particles. At the volume change step, the distances between pairs of particles belonging to the same cluster do not change. This is done by rescaling the positions of the center of mass of each cluster instead of the position of each individual particle. We have tested the performance of the algorithm by simulating fluid and solid phases of hard spheres, finding that in both cases the algorithm is much more efficient than the standard procedure. Moreover, the efficiency of the method measured in terms of correlation ”time” does not depend on the system size in contrast with the standard method, in which the sampling becomes rapidly inefficient as the system size increases. We have used the procedure to compute with high precision the equation of state of the face-centered-cubic phase of the hard sphere system for different system sizes. Using these results we have estimated the equation of state at the thermodynamic limit. The results are compared to different equations of state proposed in literature.
Oxygen electromigration induced nonvolatile resistance switching at Ag/La2CuO4+x interface
Authors: Shi J. P. , Zhao Y. G. , Zhang H. J. , Tian H. F. , Zhang X. P.
Published: May 2009

The authors report on the temperature dependence of electronic transport property of Ag/La2CuO4+x (LCO) heterostructures with different oxygen contents. Bipolar resistance switching was observed in the sample with larger oxygen content and disappears below 200 K, consistent with the characteristic temperature of oxygen migration in LCO. The resistance relaxation of the low resistance state shows similar behavior as that of oxygen diffusion in LCO and vanishes below 200 K. Analysis of the results strongly indicates that the resistance switching results from the modulation of Schottky barrier by oxygen electromigration at the interface.
Thermoelectric properties of bismuth nanowires in a quartz template
Authors: Murata Masayuki , Nakamura Daiki , Hasegawa Yasuhiro , Komine Takashi , Taguchi Takashi , Nakamura Shinichiro , Jovovic Vladimir , Heremans Joseph P.
Published: May 2009

Bismuth nanowires with lengths of over 1 mm length and diameters of the order of nanometers have been fabricated by high-pressure injection into a quartz template. The temperature dependences of the Seebeck coefficient and resistivity were simultaneously measured over the temperature range of 77–300 K. The Seebeck coefficient and resistivity at 300 K were estimated to be approximately −57 μV/K and 1.31 μΩ m, respectively. We also estimated the mobilities of electrons and holes to determine their temperature dependences. We found that the temperature dependence of the resistivity can be accounted for by the reduction in the mobility.
Gigantic enhancement in response and reset time of ZnO UV nanosensor by utilizing Schottky contact and surface functionalization
Authors: Zhou Jun , Gu Yudong , Hu Youfan , Mai Wenjie , Yeh Ping-Hung , Bao Gang , Sood Ashok K. , Polla Dennis L. , Wang Zhong Lin
Published: May 2009

UV response of ZnO nanowire nanosensor has been studied under ambient condition. By utilizing Schottky contact instead of Ohmic contact in device fabrication, the UV sensitivity of the nanosensor has been improved by four orders of magnitude, and the reset time has been drastically reduced from ∼417 to ∼0.8 s. By further surface functionalization with function polymers, the reset time has been reduced to ∼20 ms even without correcting the electronic response of the measurement system. These results demonstrate an effective approach for building high response and fast reset UV detectors.
Polarization sensitive silicon photodiodes using nanostructured metallic grids
Authors: Guillaumée M. , Dunbar L. A. , Santschi Ch. , Grenet E. , Eckert R. , Martin O. J. F. , Stanley R. P.
Published: May 2009

In this paper, we present the design, fabrication, and characterization of wire grid polarizers. These polarizers show high extinction ratios and high transmission with structure dimensions that are compatible with current complementary metal-oxide-semiconductor (CMOS) technology. To design these wire grids, we first analyze the transmission properties of single apertures. From the understanding of a single aperture, we apply a modal expansion method to model wire grids. The most promising grids are fabricated on both a glass substrate and CMOS photodiode. An extinction ratio higher than 200 is measured.
The grain boundary related p-type conductivity in ZnO films prepared by ultrasonic spray pyrolysis
Authors: Wang Bin , Min Jiahua , Zhao Yue , Sang Wenbin , Wang Changjun
Published: May 2009

Intrinsic p-type ZnO thin film was fabricated on sapphire substrate by ultrasonic spray pyrolysis, the p-type ZnO film is achieved using O2 as the carrier gas, with a resistivity of 2.18 Ω cm−1, a carrier concentration of 1.10×1016 cm−3, and a high Hall mobility of 261 cm2/V s. The scanning capacitance microscopy images and annealing the p-type ZnO indicate that the absorbed oxygen in the grain boundary (GB) aroused the p-type conductivity, and the high Hall mobility of the p-type ZnO film own to the quasi-two-dimensional hole gas, which was induced by the negatively charged interface states in the GBs.
All-polymer solar cells based on a blend of poly[3-(10-n-octyl-3-phenothiazine-vinylene)thiophene-co-2,5-thiophene] and poly[1,4-dioctyloxyl-p-2,5-dicyanophenylenevinylene]
Authors: Sang Guangyi , Zou Yingping , Huang Yu , Zhao Guangjin , Yang Yi , Li Yongfang
Published: May 2009

We report all-polymer solar cells (PSCs) based on a polymer blend of poly[3-(10-n-octyl-3-phenothiazine-vinylene)thiophene-co-2,5-thiophene] as donor and poly[1,4-dioctyloxyl-p-2,5-dicyanophenylenevinylene] as acceptor. Strong photoluminescence quenching is observed in the polymer blend indicating the photoinduced charge transfer occurs between the two polymers. The power conversion efficiency of the PSC was improved from 0.41% to 0.8% after 120 °C postannealing, under the illumination of AM 1.5, 100 mW/cm2. We attribute the improved efficiency to better morphological features of the photoactive layer after thermal annealing.
Ian Gordon Ross 1926 - 2006
Authors: Fischer Gad , Gilbert Robert G.
Published: May 2009

Ian Gordon Ross (1926?2006) was educated at the University of Sydney (BSc 1943?1946, MSc 1947?1949) and University College London (PhD 1949?1952), did postdoctoral research at Florida State University (1953?1954), and was a staff member at the University of Sydney, 1954?1967. In 1968, he moved to the Australian National University (ANU) as Professor of Chemistry, where he also became Dean of Science (1973), Deputy Vice-Chancellor (1977) and Pro-Vice-Chancellor (Special Projects) (1989?1990). He was instrumental in setting up Anutech, the commercial arm of the University. He was a driving force behind the establishment of undergraduate and postgraduate engineering at the ANU. His research centred on electronic spectroscopy of pi systems.
Interactions between zebrafish pigment cells responsible for the generation of Turing patterns
Authors: Nakamasu Akiko , Takahashi Go , Kanbe Akio , Kondo Shigeru
Published: May 2009

The reaction–diffusion system is one of the most studied nonlinear mechanisms that generate spatially periodic structures autonomous. On the basis of many mathematical studies using computer simulations, it is assumed that animal skin patterns are the most typical examples of the Turing pattern (stationary periodic pattern produced by the reaction–diffusion system). However, the mechanism underlying pattern formation remains unknown because the molecular or cellular basis of the phenomenon has yet to be identified. In this study, we identified the interaction network between the pigment cells of zebrafish, and showed that this interaction network possesses the properties necessary to form the Turing pattern. When the pigment cells in a restricted region were killed with laser treatment, new pigment cells developed to regenerate the striped pattern. We also found that the development and survival of the cells were influenced by the positioning of the surrounding cells. When melanophores and xanthophores were located at adjacent positions, these cells excluded one another. However, melanophores required a mass of xanthophores distributed in a more distant region for both differentiation and survival. Interestingly, the local effect of these cells is opposite to that of their effects long range. This relationship satisfies the necessary conditions required for stable pattern formation in the reaction–diffusion model. Simulation calculations for the deduced network generated wild-type pigment patterns as well as other mutant patterns. Our findings here allow further investigation of Turing pattern formation within the context of cell biology.
High antigen levels are the cause of T cell exhaustion during chronic viral infection
Authors: Mueller Scott N. , Ahmed Rafi
Published: May 2009

Many persistent viral infections induce dysfunctional T cell responses. Although a negative correlation exists between viral load and T cell responses during chronic infection, it is not known whether high antigen levels are the cause or just the consequence of T cell exhaustion. Furthermore, it is unclear what role antigen presentation by bone-marrow (BM) derived versus infected parenchymal cells has on T cell exhaustion. To address these issues, we examined the influence of antigen presentation by different cell types on CD8
+
T cell responses during persistent infection of mice with lymphocytic choriomeningitis virus (LCMV) clone 13. We generated BM chimeric mice, in which non-BM derived cells were MHC class I deficient. Virus-specific CD8
+
T cells in lymphoid and nonlymphoid tissues were increased in both number and ability to produce cytokines in these mice soon after infection. However, viral clearance from infected MHC I
−/−
parenchyma was significantly impaired, despite increased populations of cytokine producing CTL. The CD8
+
T cell response was overwhelmed by sustained antigen persistence, becoming increasingly exhausted within 4–6 weeks. Thus, we find that (
i
) sustained antigen presentation directly drives T cell exhaustion during a chronic viral infection, (
ii
) CTL require direct antigen-MHC interactions to clear virus-infected cells, and (
iii
) persistent interactions with antigen presented on both hematopoietic and nonhematopoietic cells negatively impacts virus-specific T cell responses during chronic infection.
A distinct role for secreted fibroblast growth factor-binding proteins in development
Authors: Gibby Krissa A. , McDonnell Kevin , Schmidt Marcel O. , Wellstein Anton
Published: May 2009

FGFs modulate diverse biological processes including embryonic development. Secreted FGF-binding proteins (BPs) can release FGFs from their local extracellular matrix storage, chaperone them to their cognate receptors, and thus modulate FGF signaling. Here we describe 2 chicken BP homologs (chBP) that show distinct expression peaks at embryonic days E7.5 (
chBP2
) and E11.5 (
chBP1
), although their tissue distribution is similar (skin = intestine>lung>heart, liver). Embryos were grown ex ovo to monitor the phenotypic impact of a timed in vivo knockdown of expression peaks by microinjection of specific siRNAs targeted to either of the chBPs. Knockdown of peak expression of
chBP2
caused embryonic lethality within <5 days. Surviving embryos showed defective ventral wall closure indicative of altered dorsoventral patterning. This defect coincided with reduced expression of
HoxB7
but not
HoxB8
that are involved in the control of thoracic/abdominal segment morphology. Also, MAPK phosphatase 3, a negative regulator of FGF signaling, and
sonic hedgehog
that can participate in feedback control of the FGF pathway were reduced, reflecting altered FGF signaling. Knockdown of the
chBP1
expression peak caused embryonic lethality within <3 days although no distinct morphologic phenotype or pathways alterations were apparent. We conclude that BPs play a significant role in fine-tuning the complex FGF signaling network during distinct phases of embryonic development.
Measurement of filling factor 5/2 quasiparticle interference with observation of charge e/4 and e/2 period oscillations
Authors: Willett R. L. , Pfeiffer L. N. , West K. W.
Published: May 2009

A standing problem in low-dimensional electron systems is the nature of the 5/2 fractional quantum Hall (FQH) state: Its elementary excitations are a focus for both elucidating the state's properties and as candidates in methods to perform topological quantum computation. Interferometric devices may be used to manipulate and measure quantum Hall edge excitations. Here we use a small-area edge state interferometer designed to observe quasiparticle interference effects. Oscillations consistent in detail with the Aharonov–Bohm effect are observed for integer quantum Hall and FQH states (filling factors ν = 2, 5/3, and 7/3) with periods corresponding to their respective charges and magnetic field positions. With these factors as charge calibrations, periodic transmission through the device consistent with quasiparticle charge e/4 is observed at ν = 5/2 and at lowest temperatures. The principal finding of this work is that, in addition to these e/4 oscillations, periodic structures corresponding to e/2 are also observed at 5/2 ν and at lowest temperatures. Properties of the e/4 and e/2 oscillations are examined with the device sensitivity sufficient to observe temperature evolution of the 5/2 quasiparticle interference. In the model of quasiparticle interference, this presence of an effective e/2 period may empirically reflect an e/2 quasiparticle charge or may reflect multiple passes of the e/4 quasiparticle around the interferometer. These results are discussed within a picture of e/4 quasiparticle excitations potentially possessing non-Abelian statistics. These studies demonstrate the capacity to perform interferometry on 5/2 excitations and reveal properties important for understanding this state and its excitations.
Life histories, blood revenge, and reproductive success among the Waorani of Ecuador
Authors: Beckerman Stephen , Erickson Pamela I. , Yost James , Regalado Jhanira , Jaramillo Lilia , Sparks Corey , Iromenga Moises , Long Kathryn
Published: May 2009

The Waorani may have the highest rate of homicide of any society known to anthropology. We interviewed 121 Waorani elders of both sexes to obtain genealogical information and recollections of raids in which they and their relatives participated. We also obtained complete raiding histories of 95 warriors. An analysis of the raiding histories, marital trajectories, and reproductive histories of these men reveals that more aggressive warriors have lower indices of reproductive success than their milder brethren. This result contrasts the findings of Chagnon [Chagnon N (1988)
Science
239:985–992] for the Yanomamo. We suggest that the spacing of revenge raids may be involved in the explanation of why the consequences of aggressiveness differ between these 2 warlike lowland South American peoples.
Evolutionary dynamics in set structured populations
Authors: Tarnita Corina E. , Antal Tibor , Ohtsuki Hisashi , Nowak Martin A.
Published: May 2009

Evolutionary dynamics are strongly affected by population structure. The outcome of an evolutionary process in a well-mixed population can be very different from that in a structured population. We introduce a powerful method to study dynamical population structure: evolutionary set theory. The individuals of a population are distributed over sets. Individuals interact with others who are in the same set. Any 2 individuals can have several sets in common. Some sets can be empty, whereas others have many members. Interactions occur in terms of an evolutionary game. The payoff of the game is interpreted as fitness. Both the strategy and the set memberships change under evolutionary updating. Therefore, the population structure itself is a consequence of evolutionary dynamics. We construct a general mathematical approach for studying any evolutionary game in set structured populations. As a particular example, we study the evolution of cooperation and derive precise conditions for cooperators to be selected over defectors.
Antioxidants prevent health-promoting effects of physical exercise in humans
Authors: Ristow Michael , Zarse Kim , Oberbach Andreas , Klöting Nora , Birringer Marc , Kiehntopf Michael , Stumvoll Michael , Kahn C. Ronald , Blüher Matthias
Published: May 2009

Exercise promotes longevity and ameliorates type 2 diabetes mellitus and insulin resistance. However, exercise also increases mitochondrial formation of presumably harmful reactive oxygen species (ROS). Antioxidants are widely used as supplements but whether they affect the health-promoting effects of exercise is unknown. We evaluated the effects of a combination of vitamin C (1000 mg/day) and vitamin E (400 IU/day) on insulin sensitivity as measured by glucose infusion rates (GIR) during a hyperinsulinemic, euglycemic clamp in previously untrained (
n
= 19) and pretrained (
n
= 20) healthy young men. Before and after a 4 week intervention of physical exercise, GIR was determined, and muscle biopsies for gene expression analyses as well as plasma samples were obtained to compare changes over baseline and potential influences of vitamins on exercise effects. Exercise increased parameters of insulin sensitivity (GIR and plasma adiponectin) only in the absence of antioxidants in both previously untrained (
P
< 0.001) and pretrained (
P
< 0.001) individuals. This was paralleled by increased expression of ROS-sensitive transcriptional regulators of insulin sensitivity and ROS defense capacity, peroxisome-proliferator-activated receptor gamma (PPARγ), and PPARγ coactivators PGC1α and PGC1β only in the absence of antioxidants (
P
< 0.001 for all). Molecular mediators of endogenous ROS defense (superoxide dismutases 1 and 2; glutathione peroxidase) were also induced by exercise, and this effect too was blocked by antioxidant supplementation. Consistent with the concept of mitohormesis, exercise-induced oxidative stress ameliorates insulin resistance and causes an adaptive response promoting endogenous antioxidant defense capacity. Supplementation with antioxidants may preclude these health-promoting effects of exercise in humans.
Decorin is a novel antagonistic ligand of the Met receptor
Authors: Goldoni Silvia , Humphries Ashley , Nyström Alexander , Sattar Sampurna , Owens Rick T. , McQuillan David J. , Ireton Keith , Iozzo Renato V.
Published: May 2009

Decorin, a member of the small leucine-rich proteoglycan gene family, impedes tumor cell growth by down-regulating the epidermal growth factor receptor. Decorin has a complex binding repertoire, thus, we predicted that decorin would modulate the bioactivity of other tyrosine kinase receptors. We discovered that decorin binds directly and with high affinity (Kd = ∼1.5 nM) to Met, the receptor for hepatocyte growth factor (HGF). Binding of decorin to Met is efficiently displaced by HGF and less efficiently by internalin B, a bacterial Met ligand. Interaction of decorin with Met induces transient receptor activation, recruitment of the E3 ubiquitin ligase c-Cbl, and rapid intracellular degradation of Met (half-life = ∼6 min). Decorin suppresses intracellular levels of β-catenin, a known downstream Met effector, and inhibits Met-mediated cell migration and growth. Thus, by antagonistically targeting multiple tyrosine kinase receptors, decorin contributes to reduction in primary tumor growth and metastastic spreading.
Immunoglobulin switch μ sequence causes RNA polymerase II accumulation and reduces dA hypermutation
Authors: Rajagopal Deepa , Maul Robert W. , Ghosh Amalendu , Chakraborty Tirtha , Khamlichi Ahmed Amine , Sen Ranjan , Gearhart Patricia J.
Published: May 2009

Repetitive DNA sequences in the immunoglobulin switch μ region form RNA-containing secondary structures and undergo hypermutation by activation-induced deaminase (AID). To examine how DNA structure affects transcription and hypermutation, we mapped the position of RNA polymerase II molecules and mutations across a 5-kb region spanning the intronic enhancer to the constant μ gene. For RNA polymerase II, the distribution was determined by nuclear run-on and chromatin immunoprecipitation assays in B cells from uracil-DNA glycosylase (UNG)–deficient mice stimulated ex vivo. RNA polymerases were found at a high density in DNA flanking both sides of a 1-kb repetitive sequence that forms the core of the switch region. The pileup of polymerases was similar in unstimulated and stimulated cells from Ung−/− and Aid−/−Ung−/− mice but was absent in cells from mice with a deletion of the switch region. For mutations, DNA was sequenced from Ung−/− B cells stimulated in vivo. Surprisingly, mutations of A nucleotides, which are incorporated by DNA polymerase η, decreased 10-fold before the repetitive sequence, suggesting that the polymerase was less active in this region. We propose that altered DNA structure in the switch region pauses RNA polymerase II and limits access of DNA polymerase η during hypermutation.
Effects of a sheared toroidal rotation on the stability boundary of the MHD modes in the tokamak edge pedestal
Authors: Aiba N. , Tokuda S. , Furukawa M. , Oyama N. , Ozeki T.
Published: May 2009

Effects of a sheared toroidal rotation are investigated numerically on the stability of the MHD modes in the tokamak edge pedestal, which relate to the type-I edge-localized mode. A linear MHD stability code MINERVA is newly developed for solving the Frieman–Rotenberg equation that is the linear ideal MHD equation with flow. Numerical stability analyses with this code reveal that the sheared toroidal rotation destabilizes edge localized MHD modes for rotation frequencies which are experimentally achievable, though the ballooning mode stability changes little by rotation. This rotation effect on the edge MHD stability becomes stronger as the toroidal mode number of the unstable MHD mode increases when the stability analysis was performed for MHD modes with toroidal mode numbers smaller than 40. The toroidal mode number of the unstable MHD mode depends on the stabilization of the current-driven mode and the ballooning mode by increasing the safety factor. This dependence of the toroidal mode number of the unstable mode on the safety factor is considered to be the reason that the destabilization by toroidal rotation is stronger for smaller edge safety factors.
Statistical analysis of fluctuation characteristics at high- and low-field sides in L-mode SOL plasmas of JT-60U
Authors: Tanaka H. , Ohno N. , Asakura N. , Tsuji Y. , Kawashima H. , Takamura S. , Uesugi Y.
Published: May 2009

For the first time, fluctuation characteristics at the high-field side (HFS) and low-field side (LFS) scrape-off-layers (SOLs) in L-mode plasmas of the JT-60U tokamak are compared in detail; the plasma transport is studied using reciprocating Langmuir probes. A statistical analysis based on probability density functions (PDFs) is employed to describe intermittent (nondiffusive) transport in SOL plasma fluctuations. It is found that positive bursty events associated with blobby plasma transport appear frequently at the LFS midplane. Further, the PDF at the LFS midplane is strongly positively skewed, while the PDF at the HFS SOL is close to a Gaussian distribution. The conventional conditional averaging method is improved by using the variable-interval time-averaging method along with it, which enables the precise reconstruction of the burst profile exhibiting a rapid increase and a slow decay. The radial evolution of plasma blobs is analysed by using an autocorrelation function, the short-time Fourier transform and wavelet analysis.
Estimating the posterior probability that genome-wide association findings are true or false
Authors: Bukszár József , McClay Joseph L. , van den Oord Edwin J. C. G.
Published: May 2009

Motivation: A limitation of current methods used to declare significance in genome-wide association studies (GWAS) is that they do not provide clear information about the probability that GWAS findings are true of false. This lack of information increases the chance of false discoveries and may result in real effects being missed.

Results: We propose a method to estimate the posterior probability that a marker has (no) effect given its test statistic value, also called the local false discovery rate (FDR), in the GWAS. A critical step involves the estimation the parameters of the distribution of the true alternative tests. For this, we derived and implemented the real maximum likelihood function, which turned out to provide us with significantly more accurate estimates than the widely used mixture model likelihood. Actual GWAS data are used to illustrate properties of the posterior probability estimates empirically. In addition to evaluating individual markers, a variety of applications are conceivable. For instance, posterior probability estimates can be used to control the FDR more precisely than Benjamini–Hochberg procedure.

Availability: The codes are freely downloadable from the web site http://www.people.vcu.edu/∼jbukszar.

Contact:  jbukszar@vcu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Abscisic Acid Negatively Regulates Elicitor-Induced Synthesis of Capsidiol in Wild Tobacco
Authors: Mialoundama Alexis Samba , Heintz Dimitri , Debayle Delphine , Rahier Alain , Camara Bilal , Bouvier Florence
Published: May 2009

In the Solanaceae, biotic and abiotic elicitors induce de novo synthesis of sesquiterpenoid stress metabolites known as phytoalexins. Because plant hormones play critical roles in the induction of defense-responsive genes, we have explored the effect of abscisic acid (ABA) on the synthesis of capsidiol, the major wild tobacco (Nicotiana plumbaginifolia) sesquiterpenoid phytoalexin, using wild-type plants versus nonallelic mutants Npaba2 and Npaba1 that are deficient in ABA synthesis. Npaba2 and Npaba1 mutants exhibited a 2-fold higher synthesis of capsidiol than wild-type plants when elicited with either cellulase or arachidonic acid or when infected by Botrytis cinerea. The same trend was observed for the expression of the capsidiol biosynthetic genes 5-epi-aristolochene synthase and 5-epi-aristolochene hydroxylase. Treatment of wild-type plants with fluridone, an inhibitor of the upstream ABA pathway, recapitulated the behavior of Npaba2 and Npaba1 mutants, while the application of exogenous ABA reversed the enhanced synthesis of capsidiol in Npaba2 and Npaba1 mutants. Concomitant with the production of capsidiol, we observed the induction of ABA 8′-hydroxylase in elicited plants. In wild-type plants, the induction of ABA 8′-hydroxylase coincided with a decrease in ABA content and with the accumulation of ABA catabolic products such as phaseic acid and dihydrophaseic acid, suggesting a negative regulation exerted by ABA on capsidiol synthesis. Collectively, our data indicate that ABA is not required per se for the induction of capsidiol synthesis but is essentially implicated in a stress-response checkpoint to fine-tune the amplification of capsidiol synthesis in challenged plants.
Effect of screening mammography on breast cancer survival in comparison to other detection methods: A retrospective cohort study
Authors: Kawai Masaaki , Kuriyama Shinichi , Suzuki Akihiko , Nishino Yoshikazu , Ishida Takanori , Ohnuki Koji , Amari Masakazu , Tsuji Ichiro , Ohuchi Noriaki
Published: May 2009

The effectiveness of screening mammography (SMG) on mortality has been established in randomized controlled trials in Western countries, but not in Japan. This study evaluated the effectiveness by comparing the survival based on detection methods. The survivals were estimated by the Kaplan–Meier method. Breast cancer patients diagnosed from 1 January 1989 to 31 December 2000 were determined using the Miyagi Prefectural Cancer Registry and follow‐up was performed from the date of the diagnosis until the date of death or the end of follow‐up, 31 December 2005. The hazard ratios (HR) and 95% confidence interval (CI) of breast cancer death based on the detection methods were estimated by the Cox proportional‐hazard regression model. The mean age of the 7513 patients was 55.7 years (range, 15.0–99.3). The 5‐year survival associated with the SMG group, the clinical breast examination (CBE) group, and the self‐detection group was 98.3%, 94.3%, and 84.8%, respectively. The HR (95% CI) of deaths from breast cancer was 2.50 (1.10–5.69) for patients in the CBE group and 6.57 (2.94–14.64) for the self‐detection group in comparison to the SMG group. In women aged 50–59, the HRs were 1.64 (0.58–4.62) among the CBE group and 3.74 (1.39–10.03) among the self‐detection group, and the HRs for the CBE and self‐detection groups in women aged 60–69 were 2.96 (0.68–12.83) and 9.51 (2.36–38.26), respectively. After adjusting for stage, the HRs dropped remarkably. Screening mammography may be more effective in the elderly group and be able to reduce the mortality of breast cancer in Japan. (Cancer Sci 2009)