bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct numerical simulation of a high-Froude-number turbulent open-channel flow
Authors: Yamamoto Yoshinobu , Kunugi Tomoaki
Published: December 2011

In this study, we successfully conducted a direct numerical simulation of a high-Fr turbulent open-channel flow at a Froude number of 1.8 and a Reynolds number of 2325 based on bulk velocity, gravitational acceleration, water depth, and kinetic viscosity, using the multi-interface advection and reconstruction solver (MARS). We confirmed that typical wall-bounded turbulent structures were observed in this high-Fr open-channel flow. On the other hand, near free-surface, surface deformations are constituted of large-scale gentle bumpy waves with the maximum wave height corresponding to approximately 4% of the water depth and small-scale isotropic waves on the large-scale waves. The large-scale waves would generate the high-speed streaky structures near the free-surface and the scale of the small waves would be equivalent to the near free-surface turbulent kinetic energy. Near the free-surface, wall-normal turbulent intensity and energy-dissipation rates increase toward the free-surface, and the tendencies of turbulent statistical quantities near the free-surface are in good agreement with the experimental measurements obtained using a laser Doppler anemometer (LDA) (Nakayama and Nezu, “Bursts near the free-surface in open-channel flows and their relationships with turbulence structures,” J. Hydraulic, Coastal and Environmental Eng. JSCE 635/II, 31 1999). As well as the rigid-lid turbulent open-channel flow, turbulent intensity distribution from the vertical component to the streamwise one is predominant beneath the free-surface.
Towards a more accurate reference interaction site model integral equation theory for molecular liquids
Authors: Kežić Bernarda , Perera Aurélien
Published: December 2011

A systematic approach for increasing the accuracy of the reference interaction site model (RISM) theory is introduced that uses input from simulation results to produce very accurate site-site pair correlation functions for single component molecular liquids. The methodology allows the computation of the “RISM bridge function.” Realistic molecular liquids such as water, alcohols, amides, and others are investigated, and the merits and limitations of the method for each of these liquids are examined in relation to the known deficiencies of the RISM theory.
Demonstration of 505 nm laser diodes using wavelength-stable semipolar (2021¯) InGaN/GaN quantum wells
Authors: Huang Chia-Yen , Hardy Matthew T. , Fujito Kenji , Feezell Daniel F. , Speck James S. , DenBaars Steven P. , Nakamura Shuji
Published: December 2011

We demonstrate GaN-based semipolar (2021¯) laser diodes (LD) in the green region of the spectrum. 505 nm lasing was observed under pulsed operation, with a threshold current density (Jth) of 27.5 kA/cm2 and a threshold voltage (Vth) of 15.5 V. The blueshift of spontaneous emission was less than 5 nm when varying the injection current level from 125 A/cm2 to threshold. Simulations show that the reduced blueshift can be attributed to the minimal dependence of the energy potential profile in the active region on the applied bias and current injection level.
Molecular binding energies from partition density functional theory
Authors: Nafziger Jonathan , Wu Qin , Wasserman Adam
Published: December 2011

Approximate molecular calculations via standard Kohn-Sham density functional theory are exactly reproduced by performing self-consistent calculations on isolated fragments via partition density functional theory [P. Elliott, K. Burke, M. H. Cohen, and A. Wasserman, Phys. Rev. A 82, 024501 (2010)]. We illustrate this with the binding curves of small diatomic molecules. We find that partition energies are in all cases qualitatively similar and numerically close to actual binding energies. We discuss qualitative features of the associated partition potentials.
Gravity-driven flow over heated, porous, wavy surfaces
Authors: Ogden K. A. , D’Alessio S. J. D. , Pascal J. P.
Published: December 2011

The method of weighted residuals for thin film flow down an inclined plane is extended to include the effects of bottom waviness, heating, and permeability in this study. A bottom slip condition is used to account for permeability and a constant temperature bottom boundary condition is applied. A weighted residual model (WRM) is derived and used to predict the combined effects of bottom waviness, heating, and permeability on the stability of the flow. In the absence of bottom topography, the results are compared to theoretical predictions from the corresponding Benney equation and also to existing Orr-Sommerfeld predictions. The excellent agreement found indicates that the model does faithfully predict the theoretical critical Reynolds number, which accounts for heating and permeability, and these effects are found to destabilize the flow. Floquet theory is used to investigate how bottom waviness influences the stability of the flow. Finally, numerical simulations of the model equations are also conducted and compared with numerical solutions of the full Navier-Stokes equations for the case with bottom permeability. These results are also found to agree well, which suggests that the WRM remains valid even when permeability is included.
Invariant x-ray elastic constants and their use in determining hydrostatic stress
Authors: Murray Conal E.
Published: December 2011

The measurement of stress using x-ray diffraction requires knowledge of the constitutive equation linking strain and stress for the sample under investigation. With the exception of single-crystal materials, a unique constitutive relation does not exist requiring an average over the diffracting ensemble. Such averaging techniques provide bounds to the range of x-ray elastic constants, whose values depend on the elastic anisotropy of the material, the mechanical response of the crystallites and often the x-ray reflection chosen. In fact, for materials possessing cubic symmetry, the general x-ray stress equation can be reduced to a form that relates the measured strain to the hydrostatic stress and the bulk modulus, quantities that are invariant with respect to crystal orientation. These orientations do not correspond to stress-free values but rather to lattice parameters that are independent of the x-ray reflection used. Examples include the application of this technique to a test case of an isotropic, biaxially stressed film, and determining the triaxial stress states in capped features. The validity of these orientations, which are developed for specific stress states, relies on the assumption that the polycrystalline aggregate behaves as a quasi-isotropic ensemble.
Monte Carlo simulation methods for computing the wetting and drying properties of model systems
Authors: Rane Kaustubh S. , Kumar Vaibhaw , Errington Jeffrey R.
Published: December 2011

We introduce general Monte Carlo simulation methods for determining the wetting and drying properties of model systems. We employ an interface-potential-based approach in which the interfacial properties of a system are related to the surface excess free energy of a thin fluid film in contact with a surface. Two versions of this approach are explored: a “spreading” method focused on the growth of a thin liquid film from a surface in a mother vapor and a “drying” method focused on the growth of a thin vapor film from a surface in a mother liquid. The former provides a direct measure of the spreading coefficient while the latter provides an analogous drying coefficient. When coupled with an independent measure of the liquid–vapor surface tension, these coefficients enable one to compute the contact angle. We also show how one can combine information gathered from application of the spreading and drying methods at a common state point to obtain direct measures of the contact angle and liquid–vapor surface tension. The computational strategies introduced here are applied to two model systems. One includes a monatomic Lennard-Jones fluid that interacts with a structureless substrate via a long-ranged substrate potential. The second model contains a monatomic Lennard-Jones fluid that interacts with an atomistically detailed substrate via a short-ranged potential. Expanded ensemble techniques are coupled with the interface potential approach to compile the temperature- and substrate strength-dependence of various interfacial properties for these systems. Overall, we find that the approach pursued here provides an efficient and precise means to calculate the wetting and drying properties of model systems.
Multi-domain resonance in textured Z-type hexagonal ferrite
Authors: Kato Tomotsugu , Mikami Hideto , Noguchi Shin
Published: December 2011

The resonance frequency of a non-saturated Z-type hexagonal ferrite under a demagnetizing field effect was formulated. The permeabilities along the c-axis and the c-plane were measured by a specimen cut from the c-plane-textured Z-type ferrite, and the resonance frequency was measured as a μ″ peak. The resonance frequency measured from the permeability in the c-plane increases dramatically as the specimen’s thickness increases. On the other hand, the resonance frequency measured from the permeability along the c-axis remains fairly constant. We tried to analyze the reason for the large difference in the resonance frequency depending on the crystal orientation using multi-domain resonance theory. As a result, the resonance frequency of a textured Z-type ferrite has been expressed when the high frequency magnetic field is parallel and normal to the c-plane. Therefore, it is confirmed that a demagnetizing field increases the resonance frequency, especially when the high frequency magnetic field is parallel to the c-plane. This result would contribute to the development a high performance inductance element.
Stress-controlled Pb(Zr0.52Ti0.48)O3 thick films by thermal expansion mismatch between substrate and Pb(Zr0.52Ti0.48)O3 film
Authors: Han Guifang , Ryu Jungho , Yoon Woon-Ha , Choi Jong-Jin , Hahn Byung-Dong , Kim Jong-Woo , Park Dong-Soo , Ahn Cheol-Woo , Priya Shashank , Jeong Dae-Yong
Published: December 2011

Polycrystalline Pb(Zr0.52Ti0.48)O3 (PZT) thick films (thickness ∼10 μm) were successfully fabricated by using a novel aerosol deposition technique on Si wafer, sapphire, and single crystal yitria stabilized zirconia (YSZ) wafer substrates with Pt electrodes and their dielectric, ferroelectric, and piezoelectric properties, and in-plane stresses were investigated. The films with different stress conditions were simply controlled by the coefficient of thermal expansion (CTE) misfit of PZT films and substrates. The results showed that the films bearing in-plane compressive stress deposited on the YSZ and sapphire substrates have superior dielectric, ferroelectric (∼90%), and piezoelectric (>200%) properties over that of the Si wafer. Among these three substrates, YSZ shows superior properties of the PZT films. However, films on Si wafer with tensile stress present lower properties. We believed that in-plane compressive stresses within the films are benefited, the formation of c-domain parallel to the thickness direction resulting in the higher piezoelectric properties. These results suggest that the properties of polycrystalline PZT thick films can be adjusted by simply choosing the substrates with different CTEs.
Deep levels in iron doped n- and p-type 4H-SiC
Authors: Beyer F. C. , Hemmingsson C. G , Leone S. , Lin Y.-C. , Gällström A. , Henry A. , Janzén E.
Published: December 2011

Deep levels were detected in Fe-doped n- and p-type 4H-SiC using deep level transient spectroscopy (DLTS). One defect level (EC–0.39 eV) was detected in n-type material. DLTS spectra of p-type 4H-SiC show two dominant peaks (EV + 0.97 eV and EV + 1.46 eV). Secondary ion mass spectrometry measurements confirm the presence of Fe in both n- and p-type 4H-SiC epitaxial layers. The majority of the capture process for Fe1, Fe2, and Fe3 is multi-phonon emission assisted. These three detected peaks are suggested to be related to Fe.
Chirality control of magnetic vortex in a square Py dot using current-induced Oersted field
Authors: Yakata S. , Miyata M. , Honda S. , Itoh H. , Wada H. , Kimura T.
Published: December 2011

We have proposed a method for controlling the vortex chirality in a squared permalloy dot by using the circular Oersted field locally induced by flowing a DC current across a small Py/Cu junctions. The reliability of the chirality control has been evaluated by measuring the nonlocal spin valve signal. The desired vortex chirality has been obtained when the injecting DC current has a moderate magnitude. However, the large DC current is found to reduce the control reliability. Another possibility for controlling the vortex structure using the large DC current injection was also discussed.
Guided ion beam and theoretical study of the reactions of Os+ with H2, D2, and HD
Authors: Hinton Christopher S. , Citir Murat , Armentrout P. B.
Published: December 2011

Reactions of the third-row transition metal cation Os+ with H2, D2, and HD to form OsH+ (OsD+) were studied using a guided ion beam tandem mass spectrometer. A flow tube ion source produces Os+ in its 6D (6s15d6) electronic ground state level. Corresponding state-specific reaction cross sections are obtained. The kinetic energy dependences of the cross sections for the endothermic formation of OsH+ and OsD+ are analyzed to give a 0 K bond dissociation energy of D0(Os+–H) = 2.45 ± 0.10 eV. Quantum chemical calculations are performed here at several levels of theory, with B3LYP approaches generally overestimating the experimental bond energy whereas results obtained using BHLYP and CCSD(T), coupled-cluster with single, double, and perturbative triple excitations, levels show good agreement. Theory also provides the electronic structures of these species and the potential energy surfaces for reaction. Results from the reactions with HD provide insight into the reaction mechanism and indicate that Os+ reacts via a direct reaction. We also compare this third-row transition metal system with the first-row and second-row congeners, Fe+ and Ru+, and find that Os+ reacts more efficiently with dihydrogen, forming a stronger M+–H bond. These differences can be attributed to the lanthanide contraction and relativistic effects.
Pulsed laser noise analysis and pump-probe signal detection with a data acquisition card
Authors: Werley Christopher A. , Teo Stephanie M. , Nelson Keith A.
Published: December 2011

A photodiode and data acquisition card whose sampling clock is synchronized to the repetition rate of a laser are used to measure the energy of each laser pulse. Simple analysis of the data yields the noise spectrum from very low frequencies up to half the repetition rate and quantifies the pulse energy distribution. When two photodiodes for balanced detection are used in combination with an optical modulator, the technique is capable of detecting very weak pump-probe signals (ΔI/I0 ∼ 10−5 at 1 kHz), with a sensitivity that is competitive with a lock-in amplifier. Detection with the data acquisition card is versatile and offers many advantages including full quantification of noise during each stage of signal processing, arbitrary digital filtering in silico after data collection is complete, direct readout of percent signal modulation, and easy adaptation for fast scanning of delay between pump and probe.
Time-resolved soft x-ray absorption setup using multi-bunch operation modes at synchrotrons
Authors: Stebel L. , Malvestuto M. , Capogrosso V. , Sigalotti P. , Ressel B. , Bondino F. , Magnano E. , Cautero G. , Parmigiani F.
Published: December 2011

Here, we report on a novel experimental apparatus for performing time-resolved soft x-ray absorption spectroscopy in the sub-ns time scale using non-hybrid multi-bunch mode synchrotron radiation. The present setup is based on a variable repetition rate Ti:sapphire laser (pump pulse) synchronized with the ∼500 MHz x-ray synchrotron radiation bunches and on a detection system that discriminates and singles out the significant x-ray photon pulses by means of a custom made photon counting unit. The whole setup has been validated by measuring the time evolution of the L3 absorption edge during the melting and the solidification of a Ge single crystal irradiated by an intense ultrafast laser pulse. These results pave the way for performing synchrotron time-resolved experiments in the sub-ns time domain with variable repetition rate exploiting the full flux of the synchrotron radiation.
Sustained inertial-capillary oscillations and jet formation in displacement flow in a tube
Authors: Sui Yi , Spelt Peter D. M.
Published: December 2011

We study inertial effects in the displacement of a fluid in a capillary by a more viscous fluid, using a numerical method. A level-set approach is employed to track the meniscus, and a Navier slip boundary condition is imposed in order to alleviate a stress singularity at the moving contact line. Various flow regimes are identified with a Reynolds number and a capillary number as the main parameters. At relatively low Reynolds number, the meniscus forms a steady shape, and the interfacial curvature at the tube centre can change from being concave to convex upon increasing the Reynolds number if the displacing fluid is wetting to the tube surface. For wetting displacing fluids, beyond a critical Reynolds number, a quasi-steady solution is no longer found: instead, the interface undergoes non-dampened periodic oscillations and, at even larger values of the Reynolds number, quasi-periodically, and the interface evolves from simple wavy shapes to complex shapes with multiple wavy units. This oscillating state is observed for sufficiently small contact angle values defined from the displacing fluid (<80°). Beyond a second critical Reynolds number, the displacing fluid forms a jet and the meniscus advances with a nearly constant speed which decreases with Re. This is also observed at large contact angle values. In a developing jet, however, the interface shape remains partially quasi-steady, near the contact line region and the tube centre. The flow behaviour is shown to be robust over a range of other governing parameters, including the capillary number and the slip length. The potential implications of the work on network models of two-phase flow through porous media are discussed.
Evaluating daylighting potential and energy efficiency in a classroom building
Authors: Krüger E. L. , Fonseca S. D.
Published: December 2011

In this paper, we analyze the possibility of using daylight as the main source of light for learning and teaching activities in a classroom building of the Universidade Tecnológica Federal do Paraná, in Curitiba, Brazil. Beginning with a survey on light bulb and luminaire types used in the building and on the potential of daylighting in such environments, six different classroom types with different solar orientations were selected for analysis. The research methods included the estimation of daylighting potential from obtained daylight coefficients (DCs) for periods of the year and sky conditions, other than those of the onsite measurements; the evaluation of conformity of the lighting system to the Brazilian RTQ Code (Regulamento Técnico de Qualidade), an energy consumption rating system, aimed at reducing electric energy consumption in office buildings; the estimation of electric energy demand for a combined use of daylighting and lighting system; the proposal of an efficient lighting system; and cost assessment using payback analysis. Results suggest energy savings of up to 94% when integrating daylight with the artificial lighting system, a payback within the range of 22–60 months for a complete substitution of the existing lighting system for a more efficient one.
Mechanical and thermal properties of methane clathrate hydrates as an alternative energy resource
Authors: Huo Hu , Liu Yuan , Zheng Zhaoyang , Zhao Jijun , Jin Changqing , Lv Tianquan
Published: December 2011

Mechanical, acoustic and thermal properties for three common hydrates structures sI, sII, and sH were investigated using first-principles methods. Elastic constants were estimated by fitting strain energy versus Lagrangian strain. Bulk modulus, shear modulus, Young’s modulus and Poisson’s ratio deduced from elastic constants are in reasonable agreement to experimental values. The longitude and transverse velocity compare reasonably with the experimental results with systematical overestimation. Using the quasi-harmonic approximation and Debye model, some thermal properties including heat capacity, linear thermal expansion, Grüneisen parameter, and Debye temperature for structure sI and sII were estimated and compared with available experiments.
Effects of aging on the mobility and lifetime of carriers in organic bulk heterojunction solar cells
Authors: Singh Vinamrita , Arora Swati , Bhatnagar P. K. , Arora Manoj , Tandon R. P.
Published: December 2011

Mobility and lifetime of the carriers are two very crucial parameters, which can account for the aging of a photovoltaic device, because changes in morphology, electrode/polymer interfaces, etc., will finally result in decrease of mobility and lifetime of carriers. In the present work, we have tried to explain our experimental data with the help of theoretical analysis based on our earlier model in which we have incorporated the activity at electrode interfaces in terms of density of surface states, thickness of interface layer, and tunneling probability. Calculations show that decrease in mobility for a cell under illumination is much faster than in a dark cell. Photoinduced oxidation plays a dominant role in fast degradation of the mobility. The lifetime is also seen to decrease because of modification of parameters such as interface thickness, density of interface states, and roughness.
Combinatorial reshaping of the
Candida antarctica
lipase A substrate pocket for enantioselectivity using an extremely condensed library
Authors: Sandström Anders G. , Wikmark Ylva , Engström Karin , Nyhlén Jonas , Bäckvall Jan-E.
Published: December 2011

A highly combinatorial structure-based protein engineering method for obtaining enantioselectivity is reported that results in a thorough modification of the substrate binding pocket of
Candida antarctica
lipase A (CALA). Nine amino acid residues surrounding the entire pocket were simultaneously mutated, contributing to a reshaping of the substrate pocket to give increased enantioselectivity and activity for a sterically demanding substrate. This approach seems to be powerful for developing enantioselectivity when a complete reshaping of the active site is required. Screening toward ibuprofen ester
1
, a substrate for which previously used methods had failed, gave variants with a significantly increased enantioselectivity and activity. Wild-type CALA has a moderate activity with an
E
value of only 3.4 toward this substrate. The best variant had an
E
value of 100 and it also displayed a high activity. The variation at each mutated position was highly reduced, comprising only the wild type and an alternative residue, preferably a smaller one with similar properties. These minimal binary variations allow for an extremely condensed protein library. With this highly combinatorial method synergistic effects are accounted for and the protein fitness landscape is explored efficiently.
Binary complex crystal structure of DNA polymerase β reveals multiple conformations of the templating 8-oxoguanine lesion
Authors: Batra Vinod K. , Shock David D. , Beard William A. , McKenna Charles E. , Wilson Samuel H.
Published: December 2011

Oxidation of genomic DNA forms the guanine lesion 7,8-dihydro-8-oxoguanine (8-oxoG). When in the template base position during DNA synthesis the 8-oxoG lesion has dual coding potential by virtue of its
anti
- and
syn
-conformations, base pairing with cytosine and adenine, respectively. This impacts mutagenesis, because insertion of adenine opposite template 8-oxoG can result in a G to T transversion. DNA polymerases vary by orders of magnitude in their preferences for mutagenic vs. error-free 8-oxoG lesion bypass. Yet, the structural basis for lesion bypass specificity is not well understood. The DNA base excision repair enzyme DNA polymerase (pol) β is presented with gap-filling synthesis opposite 8-oxoG during repair and has similar insertion efficiencies for dCTP and dATP. We report the structure of pol β in binary complex with template 8-oxoG in a base excision repair substrate. The structure reveals both the
syn
- and
anti
-conformations of template 8-oxoG in the confines of the polymerase active site, consistent with the dual coding observed kinetically for this enzyme. A ternary complex structure of pol β with the
syn
-8-oxoG:
anti
-A Hoogsteen base pair in the closed fully assembled preinsertion active site is also reported. The
syn
-conformation of 8-oxoG is stabilized by minor groove hydrogen bonding between the side chain of Arg283 and O8 of 8-oxoG. An adjustment in the position of the phosphodiester backbone 5′-phosphate enables 8-oxoG to adopt the
syn
-conformation.
The receptor tyrosine kinase ErbB3 maintains the balance between luminal and basal breast epithelium
Authors: Balko Justin M. , Miller Todd W. , Morrison Meghan M. , Hutchinson Katherine , Young Christian , Rinehart Cammie , Sánchez Violeta , Jee David , Polyak Kornelia , Prat Aleix , Perou Charles M. , Arteaga Carlos L. , Cook Rebecca S.
Published: December 2011

ErbB3 harbors weak kinase activity, but strongly activates downstream phosphatidylinositol 3-kinase/Akt signaling through heterodimerization with and activation by other ErbB receptor tyrosine kinases. We report here that ErbB3 loss in the luminal mammary epithelium of mice impaired Akt and MAPK signaling and reduced luminal cell proliferation and survival.
ERBB3
mRNA expression levels were highest in luminal mammary populations and lowest in basal cell/stem cell populations. ErbB3 loss in mammary epithelial cells shifted gene expression patterns toward a mammary basal cell/stem cell signature. ErbB3 depletion-induced gene expression changes were rescued upon activation of Akt and MAPK signaling. Interestingly, proliferation and expansion of the mammary basal epithelium (BE) occurred upon ErbB3 targeting in the luminal epithelium, but not upon its targeting in the BE. Multiple cytokines, including interleukin 6, were induced upon ErbB3 depletion in luminal epithelium cells, which increased growth of BE cells. Taken together, these results suggest that ErbB3 regulates the balance of differentiated breast epithelial cell types by regulating their growth and survival through autocrine- and paracrine-signaling mechanisms.
Capture and imaging of a prehairpin fusion intermediate of the paramyxovirus PIV5
Authors: Kim Yong Ho , Donald Jason E. , Grigoryan Gevorg , Leser George P. , Fadeev Alexander Y. , Lamb Robert A. , DeGrado William F.
Published: December 2011

During cell entry, enveloped viruses fuse their viral membrane with a cellular membrane in a process driven by energetically favorable, large-scale conformational rearrangements of their fusion proteins. Structures of the pre- and postfusion states of the fusion proteins including paramyxovirus PIV5 F and influenza virus hemagglutinin suggest that this occurs via two intermediates. Following formation of an initial complex, the proteins structurally elongate, driving a hydrophobic N-terminal “fusion peptide” away from the protein surface into the target membrane. Paradoxically, this first conformation change moves the viral and cellular bilayers further apart. Next, the fusion proteins form a hairpin that drives the two membranes into close opposition. While the pre- and postfusion hairpin forms have been characterized crystallographically, the transiently extended prehairpin intermediate has not been visualized. To provide evidence for this extended intermediate we measured the interbilayer spacing of a paramyxovirus trapped in the process of fusing with solid-supported bilayers. A gold-labeled peptide that binds the prehairpin intermediate was used to stabilize and specifically image F-proteins in the prehairpin intermediate. The interbilayer spacing is precisely that predicted from a computational model of the prehairpin, providing strong evidence for its structure and functional role. Moreover, the F-proteins in the prehairpin conformation preferentially localize to a patch between the target and viral membranes, consistent with the fact that the formation of the prehairpin is triggered by local contacts between F- and neighboring viral receptor-binding proteins (HN) only when HN binds lipids in its target membrane.
PopDrowser: the Population Drosophila Browser
Authors: Ràmia Miquel , Librado Pablo , Casillas Sònia , Rozas Julio , Barbadilla Antonio
Published: December 2011

Motivation: The completion of 168 genome sequences from a single population of Drosophila melanogaster provides a global view of genomic variation and an understanding of the evolutionary forces shaping the patterns of DNA polymorphism and divergence along the genome.

Results: We present the ‘Population Drosophila Browser’ (PopDrowser), a new genome browser specially designed for the automatic analysis and representation of genetic variation across the D. melanogaster genome sequence. PopDrowser allows estimating and visualizing the values of a number of DNA polymorphism and divergence summary statistics, linkage disequilibrium parameters and several neutrality tests. PopDrowser also allows performing custom analyses on-the-fly using user-selected parameters.

Availability: PopDrowser is freely available from http://PopDrowser.uab.cat.

Contact:  miquel.ramia@uab.cat
Pulmonary hypertension predicts all‐cause mortality in patients with heart failure: a retrospective cohort study
Authors: Szwejkowski Benjamin R. , Elder Douglas H.J. , Shearer Fiona , Jack David , Choy Anna Maria J. , Pringle Stuart D. , Struthers Allan D. , George Jacob , Lang Chim C.
Published: December 2011

Aims

The presence of pulmonary hypertension (PH) in left ventricular systolic dysfunction (LVSD) and symptomatic heart failure is an ominous sign. There are insufficient data regarding the risk conferred by increasing severity of PH in patients with heart failure.

Methods and results

We performed a record linkage study in Tayside, Scotland (population ∼400 000) utilizing the Tayside echocardiogram database (>50 000 echocardiograms) maintained by the Health Informatics Centre (HIC). Data sets from the HIC include mortality data, cardiovascular medications, and other healthcare activities linked anonymously by the community health index (CHI) number. Patients were included in the analysis if they had LVSD, had a valid right ventricular systolic pressure (RVSP) measurement, and had a loop diuretic prescription (provided not more than 1 year prior to echocardiogram). A Cox proportional hazard model was used to examine the effects of RVSP on all‐cause mortality. A total of 1612 patients [mean age, 75.2 ± 10.9 (SD) years; 57.4% male] met the entry criteria. Mean RVSP for the cohort was 44.9 ± 13.1 mmHg and mean follow‐up was 2.8 ± 2.5 years. For each 5 mmHg stepwise increase in RVSP, after adjustment for confounding factors including the degree of LVSD and the presence of chronic obstructive pulmonary disease, the hazard ratio (HR) for all‐cause mortality was 1.06 (1.03–1.08, P < 0.001).

Conclusions

Pulmonary hypertension predicted all‐cause mortality in a heterogeneous group of patients with heart failure. Each 5 mmHg rise in RVSP was associated with a 6% increased risk of death.
Personality predicts individual responsiveness to the risks of starvation and predation
Authors: Quinn J. L. , Cole E. F. , Bates J. , Payne R. W. , Cresswell W.
Published: December 2011

Theory suggests that individual personality is tightly linked to individual life histories and to environmental variation. The reactive–proactive axis, for example, is thought to reflect whether individuals prioritize productivity or survival, mutually exclusive options that can be caused by conflicts between foraging and anti-predation behaviour. Evidence for this trade-off hypothesis, however, is limited. Here, we tested experimentally whether exploration behaviour (EB), an assay of proactivity, could explain how great tits (Parus major) respond to changes in starvation and predation risk. Individuals were presented with two feeders, holding good or poor quality food, which interchanged between safe and dangerous positions 10 m apart, across two 24 h treatments. Starvation risk was assumed to be highest in the morning and lowest in the afternoon. The proportion of time spent feeding on good quality food (PTG) rather than poor quality food was repeatable within treatments, but individuals varied in how PTG changed with respect to predation- and starvation-risk across treatments. This individual plasticity variation in foraging behaviour was linked to EB, as predicted by the reactive–proactive axis, but only among individuals in dominant social classes. Our results support the trade-off hypothesis at the level of individuals in a wild population, and suggest that fine-scale temporal and spatial variation may play important roles in the evolution of personality.
Simultaneous brightness contrast of foragingPapiliobutterflies
Authors: Kinoshita Michiyo , Takahashi Yuki , Arikawa Kentaro
Published: December 2011

This study focuses on the sense of brightness in the foraging Japanese yellow swallowtail butterfly,Papilio xuthus. We presented two red discs of different intensity on a grey background to butterflies, and trained them to select one of the discs. They were successfully trained to select either a high intensity or a low intensity disc. The trained butterflies were tested on their ability to perceive brightness in two different protocols: (i) two orange discs of different intensity presented on the same intensity grey background and (ii) two orange discs of the same intensity separately presented on a grey background that was either higher or lower in intensity than the training background. The butterflies trained to high intensity red selected the orange disc of high intensity in protocol 1, and the disc on the background of low intensity grey in protocol 2. We obtained similar results in another set of experiments with purple discs instead of orange discs. The choices of the butterflies trained to low intensity red were opposite to those just described. Taken together, we conclude thatPapiliohas the ability to learn brightness and darkness of targets independent of colour, and that they have the so-called simultaneous brightness contrast.
Sphingobacterium kyonggiense sp. nov., isolated from chloroethene-contaminated soil, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium mizutaii
Authors: Choi Hyun-Ah , Lee Sang-Seob
Published: December 2011

A Gram-reaction-negative, strictly aerobic, rod-shaped, non-motile strain, designated 2-1-2T, was isolated from perchloroethylene/trichloroethene-contaminated soil in Suwon, South Korea. A polyphasic approach was used to study the taxonomic position of strain 2-1-2T. Strain 2-1-2Tshowed highest 16S rRNA gene sequence similarities toSphingobacterium daejeonenseTR6-04T(97.9 %) andSphingobacterium mizutaiiATCC 33299T(97.1 %); sequence similarities to otherSphingobacteriumspecies were less than 93.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 2-1-2Tbelonged to the clade formed by members of the genusSphingobacteriumin the familySphingobacteriaceae. The G+C content of the genomic DNA was 36.6 mol%. Strain 2-1-2Tshowed the typical chemotaxonomic features of the genusSphingobacterium, with the presence of a ceramide phosphorylethanolamine (CerPE-2) as the major ceramide, menaquinone 7 (MK-7) as the predominant respiratory quinone and iso-C15 : 0, iso-C17 : 03-OH and summed feature 3 (comprising iso-C15 : 02-OH and/or C16 : 1ω7c) as the major fatty acids. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, and DNA–DNA relatedness, strain 2-1-2Trepresents a novel species of the genusSphingobacterium, for which the nameSphingobacterium kyonggiensesp. nov. is proposed; the type strain is 2-1-2T( = KEMC 2241-005T = JCM 16704T). Emended descriptions ofSphingobacterium daejeonenseandSphingobacterium mizutaiiare also proposed.
Actinoplanes atraurantiacus sp. nov., isolated from soil
Authors: Zhang Yabo , Zhang Jianli , Fan Lei , Pang Huancheng , Xin Yuhua , Zhang Xuefang
Published: December 2011

A Gram-positive-staining bacterium, designated Y16T, was isolated from a soil sample from Yunnan Province, China. The isolate grew optimally at 25–30 °C, grew at pH 6.0–9.0 and could grow with 3 % NaCl. Strain Y16T had cell-wall peptidoglycan based on meso-diaminopimelic acid. The predominant menaquinones were MK-9(H4) and MK-9(H2). The major fatty acid methyl esters were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and C16 : 0. These chemotaxonomic characteristics suggested that the organism belonged to the genus

Actinoplanes

. Strain Y16T shared 98.7, 98.3 and 97.9 % 16S rRNA gene sequence similarity with

Actinoplanes deccanensis

IFO 13994T,

A. abujensis

A4029T and

A. brasiliensis

DSM 43805T, respectively. The DNA G+C content of the isolate was 70.8 mol%. DNA–DNA relatedness between the novel isolate and the type strains of

A. deccanensis

,

A. abujensis

and

A. brasiliensis

was 35.2, 32.0 and 22.3 %, respectively. In addition, the pattern of phenotypic properties distinguished strain Y16T from its closest phylogenetic neighbours. It is therefore concluded that strain Y16T ( = CGMCC 4.6857T = JCM 17700T) represents a novel species of the genus

Actinoplanes

, for which the name Actinoplanes atraurantiacus sp. nov. is proposed.
Rhodococcus nanhaiensis sp. nov., an actinobacterium isolated from marine sediment
Authors: Li Jie , Zhao Guo-Zhen , Long Li-Juan , Wang Fa-Zuo , Tian Xin-Peng , Zhang Si , Li Wen-Jun
Published: December 2011

In this study, two strains (SCSIO 10187Tand SCSIO 10197) were isolated from a sediment sample collected from the South China Sea and characterized by using a polyphasic approach. Growth was observed at 15–35 °C (optimum 28 °C) and pH 5.0–8.0 (optimum pH 6.0). Based on 16S rRNA gene sequence analysis, the strains were identified as members of the genusRhodococcus. Phylogenetic analysis showed that the two strains clustered together and the 16S rRNA gene sequence similarities between them and other members of the genusRhodococcuswere 93.2–97.7 %. The menaquinone type was MK-8(H2). Major cellular fatty acids were C16 : 0, C18 : 1ω9c, C17 : 0, 10-methyl C18 : 0, C18 : 0, C19 : 0and C17 : 1ω8c. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The DNA G+C contents of strains SCSIO 10187Tand SCSIO 10197 were 63.7 and 63.2 mol%, respectively. The combined genotypic and phenotypic data showed that the two strains represent a novel species of the genusRhodococcus, for which the nameRhodococcus nanhaiensisis proposed; the type strain is SCSIO 10187T( = DSM 45608T = CCTCC AB 2011024T), with SCSIO 10197 ( = DSM 45609 = CCTCC AB 2011025) as a reference strain.
Working memory, long-term memory, and medial temporal lobe function
Authors: Jeneson Annette , Squire Larry R.
Published: December 2011

Early studies of memory-impaired patients with medial temporal lobe (MTL) damage led to the view that the hippocampus and related MTL structures are involved in the formation of long-term memory and that immediate memory and working memory are independent of these structures. This traditional idea has recently been revisited. Impaired performance in patients with MTL lesions on tasks with short retention intervals, or no retention interval, and neuroimaging findings with similar tasks have been interpreted to mean that the MTL is sometimes needed for working memory and possibly even for visual perception itself. We present a reappraisal of this interpretation. Our main conclusion is that, if the material to be learned exceeds working memory capacity, if the material is difficult to rehearse, or if attention is diverted, performance depends on long-term memory even when the retention interval is brief. This fundamental notion is better captured by the terms subspan memory and supraspan memory than by the terms short-term memory and long-term memory. We propose methods for determining when performance on short-delay tasks must depend on long-term (supraspan) memory and suggest that MTL lesions impair performance only when immediate memory and working memory are insufficient to support performance. In neuroimaging studies, MTL activity during encoding is influenced by the memory load and correlates positively with long-term retention of the material that was presented. The most parsimonious and consistent interpretation of all the data is that subspan memoranda are supported by immediate memory and working memory and are independent of the MTL.
An Arabidopsis GluTR Binding Protein Mediates Spatial Separation of 5-Aminolevulinic Acid Synthesis in Chloroplasts
Authors: Czarnecki Olaf , Hedtke Boris , Melzer Michael , Rothbart Maxi , Richter Andreas , Schröter Yvonne , Pfannschmidt Thomas , Grimm Bernhard
Published: December 2011

5-Aminolevulinic acid (ALA) is the universal precursor for tetrapyrrole biosynthesis and is synthesized in plants in three enzymatic steps: ligation of glutamate (Glu) to tRNAGlu by glutamyl-tRNA synthetase, reduction of activated Glu to Glu-1-semialdehyde by glutamyl-tRNA reductase (GluTR), and transamination to ALA by Glu 1-semialdehyde aminotransferase. ALA formation controls the metabolic flow into the tetrapyrrole biosynthetic pathway. GluTR is proposed to be the key regulatory enzyme that is tightly controlled at transcriptional and posttranslational levels. We identified a GluTR binding protein (GluTRBP; previously called PROTON GRADIENT REGULATION7) that is localized in chloroplasts and part of a 300-kD protein complex in the thylakoid membrane. Although the protein does not modulate activity of ALA synthesis, the knockout of GluTRBP is lethal in Arabidopsis thaliana, whereas mutants expressing reduced levels of GluTRBP contain less heme. GluTRBP expression correlates with a function in heme biosynthesis. It is postulated that GluTRBP contributes to subcompartmentalized ALA biosynthesis by maintaining a portion of GluTR at the plastid membrane that funnels ALA into the heme biosynthetic pathway. These results regarding GluTRBP support a model of plant ALA synthesis that is organized in two separate ALA pools in the chloroplast to provide appropriate substrate amounts for balanced synthesis of heme and chlorophyll.
GLYCOALKALOID METABOLISM1 Is Required for Steroidal Alkaloid Glycosylation and Prevention of Phytotoxicity in Tomato
Authors: Itkin Maxim , Rogachev Ilana , Alkan Noam , Rosenberg Tally , Malitsky Sergey , Masini Laura , Meir Sagit , Iijima Yoko , Aoki Koh , de Vos Ric , Prusky Dov , Burdman Saul , Beekwilder Jules , Aharoni Asaph
Published: December 2011

Steroidal alkaloids (SAs) are triterpene-derived specialized metabolites found in members of the Solanaceae family that provide plants with a chemical barrier against a broad range of pathogens. Their biosynthesis involves the action of glycosyltransferases to form steroidal glycoalkaloids (SGAs). To elucidate the metabolism of SGAs in the Solanaceae family, we examined the tomato (Solanum lycopersicum) GLYCOALKALOID METABOLISM1 (GAME1) gene. Our findings imply that GAME1 is a galactosyltransferase, largely performing glycosylation of the aglycone tomatidine, resulting in SGA production in green tissues. Downregulation of GAME1 resulted in an almost 50% reduction in α-tomatine levels (the major SGA in tomato) and a large increase in its precursors (i.e., tomatidenol and tomatidine). Surprisingly, GAME1-silenced plants displayed growth retardation and severe morphological phenotypes that we suggest occur as a result of altered membrane sterol levels caused by the accumulation of the aglycone tomatidine. Together, these findings highlight the role of GAME1 in the glycosylation of SAs and in reducing the toxicity of SA metabolites to the plant cell.
Flexible working conditions and decreasing levels of trust
Authors: Svensson Sven
Published: December 2011

Purpose

The purpose of this study is to analyse levels of generalized trust among employees who have adapted to increasing demands for flexibility in their working lives (nonstandard work) compared with employees in traditional employment (standard work).

Design/methodology/approach

Data were collected using a self‐administered questionnaire distributed to randomly selected individuals in Sweden (2004,n=5,080) and a workplace survey study of temporary agency workers (2008,n=119). Data were analysed using chi‐square tests and logistic regression analysis.

Findings

The results reveal that people in nonstandard positions display significantly lower levels of generalized trust compared to standard employees, where age, gender, and socio‐economic position are constant.

Practical implications

Since trust has proved to be a prerequisite for innovativeness, and both flexibility and innovation are officially accepted solutions for the troubles of post‐industrial society, the findings point to a possible paradox in the “new economy”.

Originality/value

The results of this study are unique in that they provide valuable support for the theory that flexible working conditions lead to decreasing levels of trust in society.
Which firms use measures?
Authors: Rahbek Gjerdrum Pedersen Esben , Sudzina Frantisek
Published: December 2011

Purpose

The purpose of this paper is to outline the anatomy of firms which adopt comprehensive performance measurement (PM) systems in order to gain an understanding of how internal (organisational capabilities) and external (perceived environmental uncertainties) factors shape performance measurement practices.

Design/methodology/approach

This paper hypothesises that firms dominated by organic capabilities and operating in unpredictable markets are more likely to adopt comprehensive PM systems. The statistical test of these hypotheses is based on a 2008 survey of 299 Danish firms.

Findings

This paper concludes that a limited number of internal and external factors have a significant influence on the adoption of PM systems. There is no consistent pattern, however, between the different sub‐categories of organisational capabilities/perceived environmental uncertainties and PM adoption.

Originality/value

Much has been said about how changes in the environment and business structure require firms to develop new ways to measure performance. Less has been done to study whether firms adopting comprehensive PM systems actually match the characteristics of the “new economy”. The findings from this study indicate that the relationship between PM adoption and the organisational characteristics/external environment is more complicated than anticipated.