bluuebunny/crossref_metadata_2025 huggingface dataset:
Indium out-diffusion in Al2O3/InGaAs stacks during anneal at different ambient conditions
Authors: Krylov Igor , Winter Roy , Ritter Dan , Eizenberg Moshe
Published: June 2014

Indium out-diffusion during anneal enhances leakage currents in metal/dielectric/InGaAs gate stacks. In this work, we study the influence of ambient conditions during anneal on indium out-diffusion in Al2O3/InGaAs structures, prior to the gate metal deposition. Using X-ray photoemission spectroscopy and time of flight secondary ions mass spectrometry, we observed much lower indium concentrations in the Al2O3 layer following vacuum and O2 anneals compared to forming gas or nitrogen anneals. The electrical characteristics of the Ni/Al2O3/InGaAs gate stack following these pre-metallization anneals as well as after subsequent post metallization anneals are presented. Possible explanations for the role of the annealing ambient conditions on indium out-diffusion are presented.
Crystal orientation dependence of current-perpendicular-to-plane giant magnetoresistance of pseudo spin-valves with epitaxial Co2Fe(Ge0.5Ga0.5) Heusler alloy layers
Authors: Chen Jiamin , Li Songtian , Furubayashi T. , Takahashi Y. K. , Hono K.
Published: June 2014

The magnetoresistive (MR) properties of Co2Fe(Ge0.5Ga0.5) (CFGG) Heusler alloy-based current-perpendicular-to-plane giant magnetoresistance pseudo-spin-valves (PSVs) are investigated. The PSV films are epitaxially grown on a sapphire (112¯0) substrate with an Ag or Cu spacer layer, and their magnetoresistive properties are compared with those of PSV grown on MgO(001) substrates. For substrates with an Ag spacer, the PSV with the (001)[110]CFGG//(001)[010]Ag interface grown on MgO(001) exhibits a higher MR output compared with the (110)[001]CFGG//(111)[11¯0]Ag interface grown on sapphire (112¯0). In contrast, a higher MR output is obtained using a Cu spacer with the (110)[001]CFGG//(111)[11¯0]Cu interface. These results demonstrate that the MR outputs depend upon the crystal orientation at the interface, and that interfaces with a small misfit tend to exhibit a larger MR output. This indicates the influence of crystal orientation as well as lattice mismatch upon the interfacial spin scattering asymmetry.
Thermodynamic of fluids from a general equation of state: The molecular discrete perturbation theory
Authors: Gámez Francisco
Published: June 2014

An extensive generalisation of the discrete perturbation theory for molecular multipolar non-spherical fluids is presented. An analytical expression for the Helmholtz free energy for an equivalent discrete potential is given as a function of density, temperature, and intermolecular parameters with implicit shape and multipolar dependence. By varying the intermolecular parameters through their geometrical and multipolar dependence, a set of molecular fluids are considered and their vapor–liquid phase diagrams are tested against available simulation data. Concretely, multipolar and non-polar Kihara and chainlike fluids are tested and it is found that this theoretical approach is able to reproduce qualitatively and quantitatively well the Monte Carlo data for the selected molecular potentials, except near the critical region.
Solute dynamics in block-copolymer reverse micelles: Do water content and copolymer concentration alter the microenvironment?
Authors: Prabhu Sugosh R. , Dutt G. B.
Published: June 2014

Solute dynamics has been explored in reverse micelles formed with the triblock copolymer (EO)13–(PO)30–(EO)13 (L64), where EO and PO represent ethylene oxide and propylene oxide units, respectively, with small amounts of water in p-xylene. To this effect, nonradiative rate constants (knr) and reorientation times (τr) of two carbocyanine derivatives, 3,3′-diethyloxadicarbocyanine iodide (DODCI) and merocyanine 540 (MC 540) have been measured at different mole ratios of water to copolymer (W) and also at three copolymer concentrations. By examining the nonradiative rate constants and the reorientation times of the two solutes, the microenvironment offered by L64/water/p-xylene reverse micellar system has been investigated. It has been observed that there is no variation in the nonradiative rate constants as well as in the reorientation times of both DODCI and MC 540 with an increase in W and [L64]. Since knr represents activated twist motion about the double bonds for these solutes, it is sensitive to the local friction and likewise, τr also provides information about the microenvironment. Thus, the results of this study indicate that DODCI and MC 540 are located in the cores of the L64 reverse micelles that are made up of hydrated ethylene oxide blocks and the hydration levels are not altered despite an increase in the water content and copolymer concentration. In other words, there is no variation in the microenvironment offered by L64/water/p-xylene reverse micellar system upon increasing W and [L64].
A field programmable gated array-based method for performing high-precise instantaneous burst carrier frequency measurement
Authors: Zhang Peng , Wang Houjun , Li Li , Guo Lianping , Wang Ping
Published: June 2014

This paper proposes an instantaneous burst carrier frequency measurement scheme combined with timestamping counting method based on field programmable gated array. With the multiplication and phase shift of counting clock, multiple parallel counters run continuously, and the times of rising edge of measured frequency fx are counted simultaneously. The frequency of fx is calculated using the least squares line fitting method of regression analysis from the count values of fx and timestamping clock. Experiment results show that the proposed approach can effectively reduce the error introduced by the quantization error of ±1, improve measurement accuracy by about 2 to 3 digits, reduce measurement uncertainty by more than 20%, and diminish the processing time to 200 ns compared to traditional methods under the same measurement conditions.
Eckart−Sayvetz conditions revisited
Authors: Szalay Viktor
Published: June 2014

It is shown that vibrational displacements satisfying the Eckart−Sayvetz conditions can be constructed by projection of unconstrained displacements. This result has a number of interesting direct and indirect ramifications: (i) The normal coordinates corresponding to an electronic state or an isotopologue of a molecule are transformed to those of another state or isotopologue by a linear and, in general, non-orthogonal transformation. (ii) Novel interpretation of axis switching. (iii) One may enhance the separation of rotational-large-amplitude internal motions and the vibrational motions beyond that offered by the standard use of the Eckart−Sayvetz conditions. (iv) The rotational-vibrational Hamiltonian given in terms of curvilinear internal coordinates may be derived with elementary mathematical tools while taking into account the Eckart conditions with or without enhancement.
Current-driven domain wall mobility in polycrystalline Permalloy nanowires: A numerical study
Authors: Leliaert J. , Van de Wiele B. , Vansteenkiste A. , Laurson L. , Durin G. , Dupré L. , Van Waeyenberge B.
Published: June 2014

A complete understanding of domain wall motion in magnetic nanowires is required to enable future nanowire based spintronics devices to work reliably. The production process dictates that the samples are polycrystalline. In this contribution, we present a method to investigate the effects of material grains on domain wall motion using the GPU-based micromagnetic software package MuMax3. We use this method to study current-driven vortex domain wall motion in polycrystalline Permalloy nanowires and find that the influence of material grains is fourfold: an extrinsic pinning at low current densities, an increasing effective damping with disorder strength, shifts in the Walker breakdown current density, and the possibility of the vortex core to switch polarity at grain boundaries.
Adsorption-induced changes of the structure of the tethered chain layers in a simple fluid
Authors: Borówko M. , Sokołowski S. , Staszewski T.
Published: June 2014

We use density functional theory to study the influence of fluid adsorption on the structure of grafted chain layer. The chains are modeled as freely jointed spheres. The chain segments and spherical molecules of the fluid interact via the Lennard-Jones potential. The fluid molecules are attracted by the substrate. We calculate the excess adsorption isotherms, the average height of tethered chains, and the force acting on selected segments of the chains. The parameters that were varied include the length of grafted chains, the grafting density, the parameters characterizing fluid-chain and fluid-surface interactions, the bulk fluid density, and temperature. We show that depending on the density of the bulk fluid the height of the bonded layer increases, remains constant, or decreases with increasing temperature.
Communication: Direct measurements of nascent O(3P0,1,2) fine-structure distributions and branching ratios of correlated spin-orbit resolved product channels CO(ã3Π; v) + O(3P0,1,2) and CO($\tilde X{}^1\Sigma ^ + $X̃Σ+1; v) + O(3P0,1,2) in VUV photodissociation of CO2
Authors: Lu Zhou , Chang Yih Chung , Gao Hong , Benitez Yanice , Song Yu , Ng C. Y. , Jackson W. M.
Published: June 2014

We present a generally applicable experimental method for the direct measurement of nascent spin-orbit state distributions of atomic photofragments based on the detection of vacuum ultraviolet (VUV)-excited autoionizing-Rydberg (VUV-EAR) states. The incorporation of this VUV-EAR method in the application of the newly established VUV-VUV laser velocity-map-imaging-photoion (VMI-PI) apparatus has made possible the branching ratio measurement for correlated spin-orbit state resolved product channels, CO(ã3Π; v) + O(3P0,1,2) and CO($\tilde X{}^1\Sigma ^ + $X̃Σ+1; v) + O(3P0,1,2), formed by VUV photoexcitation of CO2 to the 4s(101) Rydberg state at 97,955.7 cm−1. The total kinetic energy release (TKER) spectra obtained from the O+ VMI-PI images of O(3P0,1,2) reveal the formation of correlated CO(ã3Π; v = 0–2) with well-resolved v = 0–2 vibrational bands. This observation shows that the dissociation of CO2 to form the spin-allowed CO(ã3Π; v = 0–2) + O(3P0,1,2) channel has no potential energy barrier. The TKER spectra for the spin-forbidden CO($\tilde X{}^1\Sigma ^ + $X̃Σ+1; v) + O(3P0,1,2) channel were found to exhibit broad profiles, indicative of the formation of a broad range of rovibrational states of CO($\tilde X{}^1\Sigma ^ + $X̃Σ+1) with significant vibrational populations for v = 18–26. While the VMI-PI images for the CO(ã3Π; v = 0–2) + O(3P0,1,2) channel are anisotropic, indicating that the predissociation of CO2 4s(101) occurs via a near linear configuration in a time scale shorter than the rotational period, the angular distributions for the CO($\tilde X{}^1\Sigma ^ + $X̃Σ+1; v) + O(3P0,1,2) channel are close to isotropic, revealing a slower predissociation process, which possibly occurs on a triplet surface via an intersystem crossing mechanism.
Micro-contacting of single and periodically arrayed columnar silicon structures by focused ion beam techniques
Authors: Friedrich F. , Herfurth N. , Teodoreanu A.-M. , Sontheimer T. , Preidel V. , Rech B. , Boit C.
Published: June 2014

Micron-sized, periodic crystalline Silicon columns on glass substrate were electrically contacted with a transparent conductive oxide front contact and a focused ion beam processed local back contact. Individual column contacts as well as arrays of >100 contacted columns were processed. Current-voltage characteristics of the devices were determined. By comparison with characteristics obtained from adapted device simulation, the absorber defect density was reconstructed. The contacting scheme allows the fabrication of testing devices in order to evaluate the electronic potential of promising semiconductor microstructures.
General rotating quantum vortex filaments in the low-temperature Svistunov model of the local induction approximation
Authors: Van Gorder Robert A.
Published: June 2014

In his study of superfluid turbulence in the low-temperature limit, Svistunov [“Superfluid turbulence in the low-temperature limit,” Phys. Rev. B 52, 3647 (1995)] derived a Hamiltonian equation for the self-induced motion of a vortex filament. Under the local induction approximation (LIA), the Svistunov formulation is equivalent to a nonlinear dispersive partial differential equation. In this paper, we consider a family of rotating vortex filament solutions for the LIA reduction of the Svistunov formulation, which we refer to as the 2D LIA (since it permits a potential formulation in terms of two of the three Cartesian coordinates). This class of solutions holds the well-known Hasimoto-type planar vortex filament [H. Hasimoto, “Motion of a vortex filament and its relation to elastica,” J. Phys. Soc. Jpn. 31, 293 (1971)] as one reduction and helical solutions as another. More generally, we obtain solutions which are periodic in the space variable. A systematic analytical study of the behavior of such solutions is carried out. In the case where vortex filaments have small deviations from the axis of rotation, closed analytical forms of the filament solutions are given. A variety of numerical simulations are provided to demonstrate the wide range of rotating filament behaviors possible. Doing so, we are able to determine a number of vortex filament structures not previously studied. We find that the solution structure progresses from planar to helical, and then to more intricate and complex filament structures, possibly indicating the onset of superfluid turbulence.
Band split in multiband all-dielectric left-handed metamaterials
Authors: Du Bai , Wang Jun , Xu Zhuo , Xia Song , Wang Jiafu , Qu Shaobo
Published: June 2014

In this paper, we propose and fabricate multiband all-dielectric left-handed metamaterials (ADMs) in the X-band microwave regime. The ADMs are fabricated by a combination of dielectric resonators in shapes of cubes and rods. The ADMs can exhibit two left-handed pass bands while the rods contact the sidewalls of the waveguide. A band split phenomenon is observed when the boundary conditions of dielectric rods change. The two pass bands can diverge into three left-handed pass bands when the rods do not contact the waveguide. By using field analysis and dielectric resonator theory, we prove that the boundary conditions have a strong influence on the resonant modes of the rod resonator, which plays key roles in left-handedness. The boundary tuned resonant modes can broaden our ways of designing new types of metamaterials.
Trapping and aerogelation of nanoparticles in negative gravity hydrocarbon flames
Authors: Chakrabarty Rajan K. , Novosselov Igor V. , Beres Nicholas D. , Moosmüller Hans , Sorensen Christopher M. , Stipe Christopher B.
Published: June 2014

We report the experimental realization of continuous carbon aerogel production using a flame aerosol reactor by operating it in negative gravity (−g; up-side-down configuration). Buoyancy opposes the fuel and air flow forces in −g, which eliminates convectional outflow of nanoparticles from the flame and traps them in a distinctive non-tipping, flicker-free, cylindrical flame body, where they grow to millimeter-size aerogel particles and gravitationally fall out. Computational fluid dynamics simulations show that a closed-loop recirculation zone is set up in −g flames, which reduces the time to gel for nanoparticles by ≈106 s, compared to positive gravity (upward rising) flames. Our results open up new possibilities of one-step gas-phase synthesis of a wide variety of aerogels on an industrial scale.
Structural and dynamical fluctuations in off-stoichiometric NiMnGa shape-memory alloys
Authors: Barabash R. I. , Barabash O. M. , Karapetrova E. A. , Manley M. E.
Published: June 2014

Measurements and modeling of the 3D diffuse scattering from off-stoichiometric NiMnGa shape memory alloys reveal evidence of structural and dynamical precursors to the phase transition. A model of the diffuse scattering in the high temperature cubic L21 phase indicates that at temperatures tens of degrees higher than transition temperature, Tc, the lattice exhibits tetragonally distorted local regions that are clear precursors to the phase transition. The model also accounts for lattice deformation caused by precursor nanoregions of the martensite phase and thermal scattering from phonons and agrees well with the observed diffuse scattering maps in reciprocal space. A distinctive feature of the diffuse scattering is that it is highly anisotropic: Around (H0H) reflections, the diffuse scattering is strongly compressed along the [H0H] and enhanced along the [−H0H] direction. Additionally, localized intensity maxima associated with phasons are observed at temperatures 30–50 K above Tc. They clearly demonstrate that each phason corresponds to an individual point in reciprocal space, which is consistent with dynamical phase fluctuations of a well-formed charge density wave resulting from Peierls instability.
Scalable self-assembled reduced graphene oxide transistors on flexible substrate
Authors: Wang Zhenxing , Eigler Siegfried , Halik Marcus
Published: June 2014

To enable graphene oxide (GO) flakes for application based on solution processable technology, we show that they can be self-assembled from solution on flexible substrate driven by a Coulomb interaction with the self-assembled monolayer (SAM). Field-effect transistors exhibit a high hole mobility around 14 cm2/V·s after a reduction process from GO to reduced GO (rGO), and meanwhile the device resistance shows a linear scaling behavior with the channel length. Due to the flexibility of the SAM, the device parameters maintain stable, while different strains are applied to the substrate. This approach makes the combination of rGO and SAM suitable for low-cost flexible applications.
The interband optical absorption in silicon quantum wells: Application of the 30-band k ⋅ p model
Authors: Čukarić Nemanja A. , Tadić Milan Ž. , Partoens Bart , Peeters F. M.
Published: June 2014

The interband optical absorption in Si/SiO2 quantum wells is calculated as function of the well width (W) and the evolution from an indirect to a direct gap material as function of the well width is investigated. In order to compute the electron states in the conduction band, the 30-band k ⋅ p model is employed, whereas the 6-band Luttinger-Kohn model is used for the hole states. We found that the effective direct band gap in the quantum well agrees very well with the W–2 scaling result of the single-band model. The interband matrix elements for linear polarized light oscillate with the quantum well width, which agrees qualitatively with a single band calculation. Our theoretical results indicate that the absorption can be maximized by a proper choice of the well width. However, the obtained absorption coefficients are at least an order of magnitude smaller than for a typical direct semiconductor even for a well width of 2 nm.
Transitions to improved confinement regimes induced by changes in heating in zero-dimensional models for tokamak plasmas
Authors: Zhu H. , Chapman S. C. , Dendy R. O. , Itoh K.
Published: June 2014

It is shown that rapid substantial changes in heating rate can induce transitions to improved energy confinement regimes in zero-dimensional models for tokamak plasma phenomenology. We examine for the first time the effect of step changes in heating rate in the models of Kim and Diamond [Phys. Rev. Lett. 90, 185006 (2003)] and Malkov and Diamond [Phys. Plasmas 16, 012504 (2009)], which nonlinearly couple the evolving temperature gradient, micro-turbulence, and a mesoscale flow; and in the extension of Zhu et al. [Phys. Plasmas 20, 042302 (2013)], which couples to a second mesoscale flow component. The temperature gradient rises, as does the confinement time defined by analogy with the fusion context, while micro-turbulence is suppressed. This outcome is robust against variation of heating rise time and against introduction of an additional variable into the model. It is also demonstrated that oscillating changes in heating rate can drive the level of micro-turbulence through a period-doubling path to chaos, where the amplitude of the oscillatory component of the heating rate is the control parameter.
LptE binds to and alters the physical state of LPS to catalyze its assembly at the cell surface
Authors: Malojčić Goran , Andres Dorothee , Grabowicz Marcin , George Alexander H. , Ruiz Natividad , Silhavy Thomas J. , Kahne Daniel
Published: June 2014

Significance

The outermost membrane of Gram-negative bacteria contains lipopolysaccharide (LPS), and its proper placement on the cell surface is required to establish an effective permeability barrier. The presence of LPS prevents small hydrophobic molecules from entering the cell making it difficult to develop antibiotics. LPS is synthesized inside the cell and must move across three compartments to the cell surface. The final step of LPS transport (Lpt), translocation of LPS across the outer membrane, is accomplished by a two-protein complex (LptDE) that must insert LPS into its outer leaflet. We have identified a binding site within LptE critical for the proper function of the translocon. LptE binds LPS and changes its physical state to facilitate its translocation through the outer membrane.
Normal levels of the antiprion proteins Btn2 and Cur1 cure most newly formed [URE3] prion variants
Authors: Wickner Reed B. , Bezsonov Evgeny , Bateman David A.
Published: June 2014

Significance

The [URE3] prion (infectious protein) is an amyloid (filamentous polymer) of Ure2p. Overproduction of Btn2p or Cur1p cure this prion, and Btn2p colocalizes with Ure2p aggregates in the curing process. We show that most [URE3] variants arising in the absence of Btn2p and Cur1p are cured by restoring the normal levels of these two proteins. The variants cured by normal levels of Btn2p and Cur1p are those with low seed number, a low number of heritable particles, consistent with seed aggregation, and sequestration as the curing mechanism. These Btn2p and Cur1p antiprion proteins are members of the Hook protein family, metazoan members of which have roles in microtubule-dependent movement of organelles and aggregates in the cell.
Measurement of endo-α-mannosidase activity using a fluorescently labeled oligosaccharide derivative
Authors: Iwamoto Shogo , Kasahara Yuta , Kamei Ken-ichi , Seko Akira , Takeda Yoichi , Ito Yukishige , Matsuo Ichiro
Published: June 2014

Endo-α-mannosidase, a GH99-family glycoside hydrolase, cleaves α-mannoside linkages with glucose residues. This enzyme is proposed to play a critical role in N-glycan processing for deglucosylation. To measure endo-α-mannosidase activity, we synthesized a fluorescently labeled tetrasaccharide derivative (Glcα1-3Manα1-2Manα1-2Manα1-O–C3H6–NH-Dansyl) in a stereocontrolled manner. The tetrasaccharide skeleton was prepared by step-wise coupling using mannose donors 4 and 7. The 1,2-cis α-glycosidic linkage on the non-reducing end of the glucose residue was constructed by inversion of the stereochemistry of the C-2 hydroxyl group in the α-mannose residue. Finally, the dansyl group was introduced at the reducing end via an aminopropyl linker. This probe successfully measured endo-α-mannosidase activity.
Crystal structure of α-amylase from Oryza sativa: molecular insights into enzyme activity and thermostability
Authors: Ochiai Akihito , Sugai Hiroshi , Harada Kazuki , Tanaka Seiya , Ishiyama Yohei , Ito Kosuke , Tanaka Takaaki , Uchiumi Toshio , Taniguchi Masayuki , Mitsui Toshiaki
Published: June 2014

AmyI-1 is an α-amylase from Oryza sativa (rice) and plays a crucial role in degrading starch in various tissues and at various growth stages. This enzyme is a glycoprotein with an N-glycosylated carbohydrate chain, a unique characteristic among plant α-amylases. In this study, we report the first crystal structure of AmyI-1 at 2.2-Å resolution. The structure consists of a typical (β/α)8-barrel, which is well-conserved among most α-amylases in the glycoside hydrolase family-13. Structural superimposition indicated small variations in the catalytic domain and carbohydrate-binding sites between AmyI-1 and barley α-amylases. By contrast, regions around the N-linked glycosylation sites displayed lower conservation of amino acid residues, including Asn-263, Asn-265, Thr-307, Asn-342, Pro-373, and Ala-374 in AmyI-1, which are not conserved in barley α-amylases, suggesting that these residues may contribute to the construction of the structure of glycosylated AmyI-1. These results increase the depths of our understanding of the biological functions of AmyI-1.
Adaptive regularization, linearization, and discretization and a posteriori error control for the two-phase Stefan problem
Authors: Di Pietro Daniele , Vohralík Martin , Yousef Soleiman
Published: June 2014

We consider in this paper the time-dependent two-phase Stefan problem and derive a posteriori error estimates and adaptive strategies for its conforming spatial and backward Euler temporal discretizations. Regularization of the enthalpy-temperature function and iterative linearization of the arising systems of nonlinear algebraic equations are considered. Our estimators yield a guaranteed and fully computable upper bound on the dual norm of the residual, as well as on the

L
2

(

L
2

)

L^2(L^2)

error of the temperature and the

L
2

(

H

−
1

)

L^2(H^{-1})

error of the enthalpy. Moreover, they allow us to distinguish the space, time, regularization, and linearization error components. An adaptive algorithm is proposed, which ensures computational savings through the online choice of a sufficient regularization parameter, a stopping criterion for the linearization iterations, local space mesh refinement, time step adjustment, and equilibration of the spatial and temporal errors. We also prove the efficiency of our estimate. Our analysis is quite general and is not focused on a specific choice of the space discretization and of the linearization. As an example, we apply it to the vertex-centered finite volume (finite element with mass lumping and quadrature) and Newton methods. Numerical results illustrate the effectiveness of our estimates and the performance of the adaptive algorithm.
Optimal Directions for Directional Distance Functions: An Exploration of Potential Reductions of Greenhouse Gases
Authors: Hampf Benjamin , Krüger Jens J.
Published: June 2014

This article explores the reduction potential of greenhouse gases for major pollution‐emitting countries of the world using nonparametric productivity measurement methods and directional distance functions. In contrast to the existing literature, we apply optimization methods to endogenously determine optimal directions for the efficiency analysis. These directions represent the compromise of output enhancement and emissions reduction. The results show that for reasonable directions the adoption of best practices would lead to sizable emission reductions in a range of approximately 20% compared with current levels.
DAFGA: diversity analysis of functional gene amplicons
Authors: Kim Yongkyu , Liesack Werner
Published: June 2014

Summary: Diversity analysis of functional marker genes provides physiological insights into microbial guilds that perform an ecologically relevant process. However, it is challenging to group functional gene sequences to valid taxonomic units, primarily because of differences in the evolutionary rates of individual genes and possible horizontal gene transfer events. We developed a python script package named DAFGA, which estimates the evolutionary rate of a particular functional gene in a standardized manner by relating its sequence divergence to that of the 16S rRNA gene. As a result, DAFGA provides gene-specific parameter sets for operational taxonomic unit clustering and taxonomic assignment at desired rank, and it can be implemented into the diversity measurements offered by QIIME.

Availability and implementation: DAFGA is freely available with a manual and test data from https://github.com/outbig/DAFGA .

Contact:  yongkyu.kim@mpi-marburg.mpg.de
Rapid morphological divergence of a stream fish in response to changes in water flow
Authors: Cureton James C. , Broughton Richard E.
Published: June 2014

Recent evidence indicates that evolution can occur on a contemporary time scale. However, the precise timing and patterns of phenotypic change are not well known. Reservoir construction severely alters selective regimes in aquatic habitats due to abrupt cessation of water flow. We examined the spatial and temporal patterns of evolution of a widespread North American stream fish (
Pimephales vigilax
) in response to stream impoundment. Gross morphological changes occurred in
P. vigilax
populations following dam construction in each of seven different rivers. Significant changes in body depth, head shape and fin placement were observed relative to fish populations that occupied the rivers prior to dam construction. These changes occurred over a very small number of generations and independent populations exhibited common responses to similar selective pressures. The magnitude of change was observed to be greatest in the first 15 generations post-impoundment, followed by continued but more gradual change thereafter. This pattern suggests early directional selection facilitated by phenotypic plasticity in the first 10–20 years, followed by potential stabilizing selection as populations reached a new adaptive peak (or variation became exhausted). This study provides evidence for rapid, apparently adaptive, phenotypic divergence of natural populations due to major environmental perturbations in a changing world.
Revisiting non-offspring nursing: allonursing evolves when the costs are low
Authors: MacLeod K. J. , Lukas D.
Published: June 2014

Allonursing, the nursing of another female's offspring, is commonly assumed to have evolved through the benefits of kin selection or reciprocity. The evolution of allonursing may also be influenced by variation in the possible costs to allonurses. The relative influence of costs and benefits on the incidence of allonursing in mammals remains unexplored. We show, using comparative analyses, that where females group with kin, the presence or the absence of allonursing is not associated with further variation in relatedness. Allonursing is most common where females produce litters; here the relative investment per offspring is low, and the costs of nursing additional young are likely to be reduced. Our results suggest that variation in the potential benefits is not associated with the distribution of allonursing, but that allonursing can quickly evolve when the costs to allonurses of nursing additional offspring are low.
Changing motivations during migration: linking movement speed to reproductive status in a migratory large mammal
Authors: Singh Navinder J. , Ericsson Göran
Published: June 2014

A challenge in animal ecology is to link animal movement to demography. In general, reproducing and non-reproducing animals may show different movement patterns. Dramatic changes in reproductive status, such as the loss of an offspring during the course of migration, might also affect movement. Studies linking movement speed to reproductive status require individual monitoring of life-history events and hence are rare. Here, we link movement data from 98 GPS-collared female moose (
Alces alces
) to field observations of reproductive status and calf survival. We show that reproductive females move more quickly during migration than non-reproductive females. Further, the loss of a calf over the course of migration triggered a decrease in speed of the female. This is in contrast to what might be expected for females no longer constrained by an accompanying offspring. The observed patterns demonstrate that females of different reproductive status may have distinct movement patterns, and that the underlying motivation to move may be altered by a change in reproductive status during migration.
Conformal relativity with hypercomplex variables
Authors: Ulrych S.
Published: June 2014

Majorana's arbitrary spin theory is considered in a hyperbolic complex representation. The underlying differential equation is embedded into the gauge field theories of Sachs and Carmeli. In particular, the approach of Sachs can serve as a unified theory of general relativity and electroweak interactions. The method is extended to conformal space with the intention to introduce the strong interaction. It is then possible to use the wave equation, operating on representation functions of the conformal group, to describe the dynamics of matter fields. The resulting gauge groups resemble closely the gauge symmetries of Glashow–Salam–Weinberg and the standard model.
Numerical solutions of the semiclassical Boltzmann ellipsoidal-statistical kinetic model equation
Authors: Yang Jaw-Yen , Yan Chin-Yuan , Huang Juan-Chen , Li Zhihui
Published: June 2014

Computations of rarefied gas dynamical flows governed by the semiclassical Boltzmann ellipsoidal-statistical (ES) kinetic model equation using an accurate numerical method are presented. The semiclassical ES model was derived through the maximum entropy principle and conserves not only the mass, momentum and energy, but also contains additional higher order moments that differ from the standard quantum distributions. A different decoding procedure to obtain the necessary parameters for determining the ES distribution is also devised. The numerical method in phase space combines the discrete-ordinate method in momentum space and the high-resolution shock capturing method in physical space. Numerical solutions of two-dimensional Riemann problems for two configurations covering various degrees of rarefaction are presented and various contours of the quantities unique to this new model are illustrated. When the relaxation time becomes very small, the main flow features a display similar to that of ideal quantum gas dynamics, and the present solutions are found to be consistent with existing calculations for classical gas. The effect of a parameter that permits an adjustable Prandtl number in the flow is also studied.
When is it socially acceptable to feel sick?
Authors: Lopes Patricia C.
Published: June 2014

Disease is a ubiquitous and powerful evolutionary force. Hosts have evolved behavioural and physiological responses to disease that are associated with increased survival. Behavioural modifications, known as ‘sickness behaviours’, frequently involve symptoms such as lethargy, somnolence and anorexia. Current research has demonstrated that the social environment is a potent modulator of these behaviours: when conflicting social opportunities arise, animals can decrease or entirely forgo experiencing sickness symptoms. Here, I review how different social contexts, such as the presence of mates, caring for offspring, competing for territories or maintaining social status, affect the expression of sickness behaviours. Exploiting the circumstances that promote this behavioural plasticity will provide new insights into the evolutionary ecology of social behaviours. A deeper understanding of when and how this modulation takes place may lead to better tools to treat symptoms of infection and be relevant for the development of more efficient disease control programmes.
Language evolution: syntax before phonology?
Authors: Collier Katie , Bickel Balthasar , van Schaik Carel P. , Manser Marta B. , Townsend Simon W.
Published: June 2014

Phonology and syntax represent two layers of sound combination central to language's expressive power. Comparative animal studies represent one approach to understand the origins of these combinatorial layers. Traditionally, phonology, where meaningless sounds form words, has been considered a simpler combination than syntax, and thus should be more common in animals. A linguistically informed review of animal call sequences demonstrates that phonology in animal vocal systems is rare, whereas syntax is more widespread. In the light of this and the absence of phonology in some languages, we hypothesize that syntax, present in all languages, evolved before phonology.
A population of sexual
Daphnia pulex
resists invasion by asexual clones
Authors: Innes David J. , Ginn Michael
Published: June 2014

Asexual reproduction avoids the costs associated with sex, predicting that invading asexual clones can quickly replace sexual populations.
Daphnia pulex
populations in the Great Lakes area are predominately asexual, but the elimination of sexual populations by invading clones is poorly understood. Asexual clones were detected at low frequency in one rare sexual population in 1995, with some increase in frequency during 2003 and 2004. However, these clones remained at low frequency during further yearly sampling (2005–2013) with no evidence that the resident sexual population was in danger of elimination. There was evidence for hybridization between rare males produced by asexual clones and sexual females with the potential to produce new asexual genotypes and spread the genetic factors for asexuality. In a short-term laboratory competition experiment, the two most common asexual clones did not increase in frequency relative to a genetically diverse sexual population due in part to a greater investment in diapausing eggs that trades-off current population growth for increased contribution to the egg bank. Our results suggest that a successful invasion can be prolonged, requiring a combination of clonal genotypes with high fitness, persistence of clones in the egg bank and negative factors affecting the sexual population such as inbreeding depression resulting from population bottlenecks.
Hydrodynamics of fossil fishes
Authors: Fletcher Thomas , Altringham John , Peakall Jeffrey , Wignall Paul , Dorrell Robert
Published: June 2014

From their earliest origins, fishes have developed a suite of adaptations for locomotion in water, which determine performance and ultimately fitness. Even without data from behaviour, soft tissue and extant relatives, it is possible to infer a wealth of palaeobiological and palaeoecological information. As in extant species, aspects of gross morphology such as streamlining, fin position and tail type are optimized even in the earliest fishes, indicating similar life strategies have been present throughout their evolutionary history. As hydrodynamical studies become more sophisticated, increasingly complex fluid movement can be modelled, including vortex formation and boundary layer control. Drag-reducing riblets ornamenting the scales of fast-moving sharks have been subjected to particularly intense research, but this has not been extended to extinct forms. Riblets are a convergent adaptation seen in many Palaeozoic fishes, and probably served a similar hydrodynamic purpose. Conversely, structures which appear to increase skin friction may act as turbulisors, reducing overall drag while serving a protective function. Here, we examine the diverse adaptions that contribute to drag reduction in modern fishes and review the few attempts to elucidate the hydrodynamics of extinct forms.
Consequences of plant invasions on compartmentalization and species’ roles in plant–pollinator networks
Authors: Albrecht Matthias , Padrón Benigno , Bartomeus Ignasi , Traveset Anna
Published: June 2014

Compartmentalization—the organization of ecological interaction networks into subsets of species that do not interact with other subsets (true compartments) or interact more frequently among themselves than with other species (modules)—has been identified as a key property for the functioning, stability and evolution of ecological communities. Invasions by entomophilous invasive plants may profoundly alter the way interaction networks are compartmentalized. We analysed a comprehensive dataset of 40 paired plant–pollinator networks (invaded versus uninvaded) to test this hypothesis. We show that invasive plants have higher generalization levels with respect to their pollinators than natives. The consequences for network topology are that—rather than displacing native species from the network—plant invaders attracting pollinators into invaded modules tend to play new important topological roles (i.e. network hubs, module hubs and connectors) and cause role shifts in native species, creating larger modules that are more connected among each other. While the number of true compartments was lower in invaded compared with uninvaded networks, the effect of invasion on modularity was contingent on the study system. Interestingly, the generalization level of the invasive plants partially explains this pattern, with more generalized invaders contributing to a lower modularity. Our findings indicate that the altered interaction structure of invaded networks makes them more robust against simulated random secondary species extinctions, but more vulnerable when the typically highly connected invasive plants go extinct first. The consequences and pathways by which biological invasions alter the interaction structure of plant–pollinator communities highlighted in this study may have important dynamical and functional implications, for example, by influencing multi-species reciprocal selection regimes and coevolutionary processes.
Elaborate visual and acoustic signals evolve independently in a large, phenotypically diverse radiation of songbirds
Authors: Mason Nicholas A. , Shultz Allison J. , Burns Kevin J.
Published: June 2014

The concept of a macroevolutionary trade-off among sexual signals has a storied history in evolutionary biology. Theory predicts that if multiple sexual signals are costly for males to produce or maintain and females prefer a single, sexually selected trait, then an inverse correlation between sexual signal elaborations is expected among species. However, empirical evidence for what has been termed the ‘transfer hypothesis’ is mixed, which may reflect different selective pressures among lineages, evolutionary covariates or methodological differences among studies. Here, we examine interspecific correlations between song and plumage elaboration in a phenotypically diverse, widespread radiation of songbirds, the tanagers. The tanagers (Thraupidae) are the largest family of songbirds, representing nearly 10% of all songbirds. We assess variation in song and plumage elaboration across 301 species, representing the largest scale comparative study of multimodal sexual signalling to date. We consider whether evolutionary covariates, including habitat, structural and carotenoid-based coloration, and subfamily groupings influence the relationship between song and plumage elaboration. We find that song and plumage elaboration are uncorrelated when considering all tanagers, although the relationship between song and plumage complexity varies among subfamilies. Taken together, we find that elaborate visual and vocal sexual signals evolve independently among tanagers.
Pair bonding prevents reinforcing effects of testosterone in male California mice in an unfamiliar environment
Authors: Zhao Xin , Marler Catherine A.
Published: June 2014

Testosterone (T) can be released by stimuli such as social interactions, and thereby influence future social behaviours. Because the reinforcing effects of T can induce preferences for specific environmental locations, T has the potential to alter behaviour through space use. In a monogamous species, this T pulse may contribute differently to space use in sexually naive (SN) and pair-bonded (PB) males: SN males may be more likely to explore new areas to set up a territory than PB males, which are more likely to defend an existing, established territory. In this study, we test for variation in T-driven space use by examining variation in the formation of conditioned place preferences (CPPs) in SN and PB male California mice. In the three-chambered CPP apparatus, subcutaneous administrations of physiological levels of T were used to repeatedly condition SN and PB males to a side chamber, which is an unfamiliar/neutral environment. The final tests revealed that T-induced CPPs in the side chamber are developed in SN, but not PB males. This study fills a gap in our knowledge about plasticity in the rewarding nature of T pulses, based on past social experience.
Bacterial methionine biosynthesis
Authors: Ferla Matteo P. , Patrick Wayne M.
Published: June 2014

Methionine is essential in all organisms, as it is both a proteinogenic amino acid and a component of the cofactor,S-adenosyl methionine. The metabolic pathway for its biosynthesis has been extensively characterized inEscherichia coli; however, it is becoming apparent that most bacterial species do not use theE. colipathway. Instead, studies on other organisms and genome sequencing data are uncovering significant diversity in the enzymes and metabolic intermediates that are used for methionine biosynthesis. This review summarizes the different biochemical strategies that are employed in the three key steps for methionine biosynthesis from homoserine (i.e. acylation, sulfurylation and methylation). A survey is presented of the presence and absence of the various biosynthetic enzymes in 1593 representative bacterial species, shedding light on the non-canonical nature of theE. colipathway. This review also highlights ways in which knowledge of methionine biosynthesis can be utilized for biotechnological applications. Finally, gaps in the current understanding of bacterial methionine biosynthesis are noted. For example, the paper discusses the presence of one gene (metC) in a large number of species that appear to lack the gene encoding the enzyme for the preceding step in the pathway (metB), as it is understood inE. coli. Therefore, this review aims to move the focus away fromE. coli, to better reflect the true diversity of bacterial pathways for methionine biosynthesis.
Crystallization and preliminary X-ray diffraction analysis of Gos1p, a yeast SNARE protein
Authors: Cheng Baoyun , Zhang Yujie , Guo Gongrui , Gao Yongxiang
Published: June 2014

The Gos1 protein (Golgi SNAP receptor complex member 1) is involved in the SNARE complex, which is the core machinery that drives membrane fusion between cargo-carrying vesicles and their target membranes in the secretory and endocytic pathways in yeast. Truncated versions of the Gos1 protein fromSaccharomyces cerevisiaewere cloned, expressed, purified and crystallized. The crystal belonged to space groupP212121, with unit-cell parametersa= 39.67,b= 43.58,c= 81.94 Å, α = β = γ = 90°. An X-ray diffraction data set was collected at 100 K to 1.63 Å resolution. Matthews coefficient (VM) calculations suggest that one molecule is present in the asymmetric unit, corresponding to a solvent content of ∼55%.
Identifying international market opportunities: the case of Italian companies in Egypt
Authors: Caiazza Rosa
Published: June 2014

Purpose

– The purpose of this paper is to investigate the differences and relations between Italy and Egypt and to identify main risks and opportunities for Italian firms that aim to operate in Egypt.

Design/methodology/approach

– The paper presents a qualitative analysis realized through some semi-structured questionnaire and a case study.

Findings

– High cultural difference, legal uncertainty and administrative instability are main problems in internationalization process of Italian firms in Egypt. Despite these problems, Italian firms still invest in Egypt because of economic opportunities and possible interactions.

Originality/value

– While interest towards Southern Mediterranean countries is increasing, there is little written on this topic. This article aims to fill the gap in literature on internationalization in emerging markets.