bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetic anisotropy and geometrical frustration in the Ising spin-chain system Sr5Rh4O12
Authors: Ge M. , Korneta O. B. , Qi T. F. , Parkin S. , Schlottmann P. , Cao G.
Published: April 2011

A structural and thermodynamic study of the newly synthesized single crystal Sr5Rh4O12 is reported. Sr5Rh4O12 consists of a triangular lattice of spin-chains running along the c-axis. It is antiferromagnetically ordered below 23 K with the intrachain and interchain coupling being ferromagnetic (FM) and antiferromagnetic (AFM), respectively. There is strong evidence for an Ising character in the interaction and geometrical frustration that causes incomplete long-range AFM order. The isothermal magnetization exhibits two steplike transitions leading to a ferrimagnetic state at 2.4 T and a FM state at 4.8 T, respectively. Sr5Rh4O12 is a unique frustrated spin-chain system ever found in 4d and 5d-based materials without a presence of an incomplete 3d-electron shell.
Effect of laser beam parameters on magnetic properties of Nd–Fe–B thick-film magnets fabricated by pulsed laser deposition
Authors: Fukunaga H. , Kamikawatoko T. , Nakano M. , Yanai T. , Yamashita F.
Published: April 2011

The effects of varying the laser power and the spot diameter of a laser beam on the magnetic properties, morphology, and deposition rate of Nd–Fe–B thick-film magnets fabricated by pulsed laser deposition (PLD) were investigated. Reducing the laser fluence on the target reduces the remanence and increases the Nd content and consequently the coercivity of the prepared films. The spot size of the laser beam was found to affect the film surface morphology, the deposition rate, and the reproducibility of the magnetic properties of the prepared films. Reducing the spot size reduces the number of droplets and the reproducibility of the magnetic properties and increases the droplet size. Controlling the spot size of the laser beam enabled us to maximize the deposition rate. Consequently, a coercivity of 1210 kA/m and a remanence of 0.51 T were obtained at a deposition rate of 11.8 μm/(h·W). This deposition rate is 30% greater than the highest previously reported deposition rate by PLD.
Ultrahigh coercivity in ternary Tb-Fe-B melt-spun ribbons
Authors: Liu R. M. , Yue M. , Na R. , Deng Y. W. , Zhang D. T. , Liu W. Q. , Zhang J. X.
Published: April 2011

The structure and magnetic properties were studied for ternary Tb-Fe-B melt-spun ribbons with nominal composition of Tb14Fe86–xBx (x = 5.2–6.8). Effect of boron content and melt-spun wheel speed on the coercivity of the ribbons was investigated. With the increase of boron content, the coercivity of the Tb-Fe-B ribbons increases first, and then decreases. XRD results show that the impurities of TbFe2 phase and FeB phase exist in low boron content and high boron content ribbons, respectively, resulting in the coercivity degradation of the ribbons. For the Tb14Fe79.6B6.4 ribbons, the wheel speed plays an important role in their magnetic properties. As the wheel speed increases from 5 to 25 m/s, the saturation magnetization and the remanence of the ribbons drop monotonically, while the coercivity increases first, peaks at 77.4 kOe, and then decreases. Further SEM observation indicates that the microstructure of the optimal ribbons was composed of fine and uniform crystal grains, which was responsible for the ultrahigh intrinsic coercivity of the ribbons.
Influence of magnetostatic interactions on the magnetization reversal of patterned magnetic elements
Authors: Yin Xioalu , Liou S. H. , Adeyeye A. O. , Jain S. , Han Baoshan
Published: April 2011

The magnetization reversal in patterned thin-film arrays of elliptical submicron permalloy elements has been investigated by magnetic-force microscopy and micro-magneto-optic Kerr effect. Three different spatial arrangements of chains are considered, namely chains aligned parallel to the long axis of the ellipse, chains aligned parallel to the short axis of the ellipse, and arrays with roughly equal element-to-element spacings in both directions. Comparison of the hysteresis loops in an in-plane field perpendicular to the ellipses’ long axes shows that the magnetization reversibility is highest for chains along the long axis. This is due to the nearly coherent magnetization rotation in the applied magnetic field and to the formation of a head-to-tail domain arrangement. Other arrangements, such as chains of ellipses aligned parallel to short axis, yield flux-closure domains as the applied magnetic field is changed.
On the magnetization reversal of the oxide-based exchange spring magnet
Authors: Roy Debangsu , Shivakumara C , Anil Kumar P. S.
Published: April 2011

The role of the soft phase (Ni0.8Zn0.2Fe2O4) on the magnetization reversal and coercivity mechanism of the Ni0.8Zn0.2Fe2O4/BaFe12O19 nanocomposite has been investigated. The presence of the interacting field and the disorder in the nanocomposite has been confirmed by the variation of Jr/Jr(∞) vs Jd/Jr(∞) and the irreversible magnetization. To understand the relative strength of the pinning and the nucleation, the magnetic viscosity measurement has been done and the thermal activation volume has been estimated. From the Barbier plot and the activation volume measurement, the dominant mechanism governing the magnetization reversal process has been proposed.
Non-equilibrium transient thermal grating relaxation in metal
Authors: Maznev A. A. , Johnson Jeremy A. , Nelson Keith A.
Published: April 2011

Thermal grating relaxation in a metal with predominantly electronic heat transport is analyzed within the framework of the two-temperature model. Analytical solutions are obtained in the one-dimensional case, whereas the two-dimensional model simulating laser-induced transient grating experiment requires a numerical step to obtain time-domain solutions. When the grating period becomes comparable to (λ/G)1/2, where λ is the thermal conductivity and G the electron-phonon coupling constant, local thermal equilibrium between electrons and the lattice is not established even on a time scale much longer than the electron-phonon relaxation time. As a result, the thermal grating relaxation time is longer than predicted by the classical thermal diffusion model. For metals with high electron mobility such as gold, the effect is significant for thermal grating periods on the order of or under a micron and needs to be taken into account in the analysis of the laser-induced transient grating measurements.
Identification of parameters of the Jiles–Atherton model by neural networks
Authors: Trapanese Marco
Published: April 2011

In this paper a procedure for the identification of the parameters of the Jiles–Atherton (JA) model is presented. The parameters of the JA model of a material are found by using a neural network trained by a collection of hysteresis curves, whose parameters are known. After a presentation of the Jiles–Atherton model, the neural network and the training procedure are described and the method is validated by using some numerical, as well as experimental, data.
Effect of carbon concentration on shear modulus of (W1/2Al1/2)CZ
Authors: Wang L. L. , Lian J. S. , Jiang Q.
Published: April 2011

Using density functional theory (DFT), we have studied the effect of carbon concentration Z on the shear modulus G, elastic constant cij, and Poisson ratio ν of carbides (W1/2Al1/2)CZ while the most stable structures are determined by calculating the lowest formation energy. It is found that the maximal G value and the lowest Poisson ratio ν value are reached at Z = 3/4 due to atomic configuration changes, additionally, G values of (W1/2Al1/2)CZ should be lower than that of WC due to lower cij values. The results of electronic analysis show that the increased covalent bonding of C-2p and W-5d contributes to anisotropic cij and G positively and results in a lower ν value because the excess negative charge induced by the substitution of Al3+ for W4+ is balanced by decreasing C atoms.
Projective synchronization of two coupled excitable spiral waves
Authors: Nie Haichun , Xie Lingling , Gao Jihua , Zhan Meng
Published: April 2011

Interaction of two identical excitable spiral waves in a bilayer system is studied. We find that the two spiral waves can be completely synchronized if the coupling strength is sufficiently large. Prior to the complete synchronization, we find a new type of weak synchronization between the two coupled systems, i.e., the spiral wave of the driven system has the same geometric shape as the spiral wave of the driving system but with a much lower amplitude. This general behavior, called projective synchronization of two spiral waves, is similar to projective synchronization of two coupled nonlinear oscillators, which has been extensively studied before. The underlying mechanism is uncovered by the study of pulse collision in one-dimensional systems.
Note: Creep character of piezoelectric actuator under switched capacitor charge pump control
Authors: Ma Yu Ting , Huang Liang , Liu Yong Bin , Feng Zhi Hua
Published: April 2011

A major deficiency in piezoelectric actuator performance is caused by hysteresis and creep effects. Switched capacitor charge pump control was previously proved to be an effective way to reduce hysteresis. In this work, creep character of a piezoelectric stack under charge pump control is investigated and modeled. Experiments show that the creep can be reduced by about 77% compared with the one under voltage control. The creep factor denoting the degree of creep shows hysteresis loops similar to displacement outputs under voltage control.
Dependence of selectivity on plasma conditions in selective etching in submicrometer pitch grating on InP surface by CH4/H2 reactive ion etching
Authors: Yamamoto Norio
Published: April 2011

We studied selective etching and polymer deposition in submicrometer pitch gratings on the surface of InP using reactive ion etching with methane and hydrogen and investigated the plasma condition dependence of the selectivity. Using a mask structure consisting of regions with and without a thick layer on a grating-patterned thin layer, we achieved selective etching in submicrometer pitch gratings. In experiments conducted on the same surface at the same time, the InP is selectively etched in the window of the grating in the region with the thick layer, but it is not etched, and polymer is deposited, in the window of the grating in the region without the thick layer. We found that the selectivity depends on the plasma conditions, such as the hydrogen flow rate, pressure, and plasma power in reactive ion etching. This dependence might result from the variation in the ionic atoms of hydrogen or hydrocarbon/hydrogen, which are attracted to the charged mask and supplied to the window of the grating.
Selective epitaxial growth of Ge/Si0.15Ge0.85 quantum wells on Si substrate using reduced pressure chemical vapor deposition
Authors: Ren Shen , Rong Yiwen , Kamins Theodore I. , Harris James S. , Miller David A. B.
Published: April 2011

We investigate the selective epitaxial growth of Ge/Si0.15Ge0.85 quantum wells on prepatterned silicon substrates by reduced pressure chemical vapor deposition. A vertical p-i-n Si0.1Ge0.9 diode with Ge/Si0.15Ge0.85 quantum wells in the intrinsic region is selectively grown in holes in a SiO2 mask. We find perfect growth selectivity and very low dependence on size or arrangement of the mask holes. The fabricated p-i-n diode shows very low reverse leakage current and high breakdown voltage, suggesting good epitaxy quality. The quantum-confined Stark effect in this quantum-well system is observed for wavelengths >1.5 μm at room temperature.
Composite polarizability and the construction of an invariant function of refraction and mass density for solutions
Authors: Szymański Krzysztof , Petrache Horia I.
Published: April 2011

Re-examination of dynamical ionic polarizabilities in water solutions leads to the formulation of a solution function r(c), which combines the indices of refraction and mass densities of solutions. We show that this function should be independent of ionic concentration if the composite polarizabilities of hydrated solute clusters are constant. Using existing experimental data for a number of aqueous salt and organic solutions, we find that the r(c) function is either constant or varies linearly with concentration, in most cases with negligible slope. We use this function to compare ionic polarizabilities of crystals and aqueous solutions and to highlight how solute polarizabilities at infinite dilution scale with the electronic valence shell of cations and anions. The proposed r(c) function can be used generally to verify the consistency of experimental measurements and of simulation results, and it provides a test of assumptions in current theories of ionic polarizabilities.
Response to “Comment on ‘Heat capacity, enthalpy fluctuations, and configurational entropy in broken ergodic systems’” [J. Chem. Phys. 134, 147101 (2011)]
Authors: Mauro John C. , Loucks Roger J. , Sen Sabyasachi
Published: April 2011

We show that Johari's critique of our work is based on a misunderstanding of ergodic theory and a disregard for the broken ergodic nature of glass. His analysis is in contradiction with well established experimental results in specific heat spectroscopy, shear-mechanical spectroscopy, and the vanishing of heat capacity in the limit of zero temperature. Based on these misinterpretations, Johari arrives at the erroneous conclusion that the residual entropy of glass is real. However, we show that Johari's result is an artifact in direct contradiction with both rigorous theory and experimental measurements.
Higher order two- and three-body dispersion coefficients for alkali isoelectronic sequences by a variationally stable procedure
Authors: Huang Shi-Zhong , Sun Qiu-Feng
Published: April 2011

Using the variationally stable method of Gao and Starace, and the simple ground state wave function of the valence electron previously suggested by Patil and Tang, the multipolar polarizabilities of Li, Na, K, Rb, Cs, Be+, Mg+, Ca+, Sr+, Ba+, the two-body dispersion coefficients of homonuclear and heteronuclear interactions from C6 to C40, as well as the three-body dispersion coefficients Z(L1, L2, L3) (up to Li = 5), are investigated. Higher order van der Waals dispersion coefficients Cn (n > 24) and Z(L1, L2, L3) (Li > 3) are reported for the first time. Comparisons with previous calculations found in the literature show that this approach is capable of yielding precise and fast convergent values for higher order dispersion coefficients for alkali-metal atoms.
Deep levels in tungsten doped n-type 3C–SiC
Authors: Beyer F. C. , Hemmingsson C. G. , Gällström A. , Leone S. , Pedersen H. , Henry A. , Janzén E.
Published: April 2011

Tungsten was incorporated in SiC and W related defects were investigated using deep level transient spectroscopy. In agreement with literature, two levels related to W were detected in 4H–SiC, whereas only the deeper level was observed in 6H–SiC. The predicted energy level for W in 3C–SiC was observed (EC−0.47 eV). Tungsten serves as a common reference level in SiC. The detected intrinsic levels align as well: E1 (EC−0.57 eV) in 3C–SiC is proposed to have the same origin, likely VC, as EH6/7 in 4H–SiC and E7 in 6H–SiC, respectively.
Magnetic interaction in perpendicular recording media with synthetic nucleation layers
Authors: Piramanayagam S. N. , Tan H. K. , Ranjbar M. , Wong S. K. , Sbiaa R. , Chong T. C.
Published: April 2011

Perpendicular recording media, where the CoCrPt-oxide recording layer is deposited on carbon based synthetic nucleation (SN) layers, have been proposed for recording applications and studied using first-order reversal curves for their magnetic interaction behavior. The magnetic properties of media with SN layer show better intergranular segregation whereas the media without SN layer shows otherwise. It is proposed that a dual SN layer structure, where an SN layer deposited above and below the high pressure sputtered Ru layer is suitable for achieving smaller grain size as well as better intergranular segregation.
Micromagnetic study of spin wave propagation in bicomponent magnonic crystal waveguides
Authors: Ma F. S. , Lim H. S. , Wang Z. K. , Piramanayagam S. N. , Ng S. C. , Kuok M. H.
Published: April 2011

The propagation of spin waves in bicomponent magnonic crystal waveguides has been investigated by micromagnetic simulations. The nanostructured waveguides studied are regular square lattice arrays of circular Fe dots embedded in an yttrium iron garnet matrix. Our simulations show that the waveguides exhibit wide magnonic band gaps of the order of 10 GHz. Band gap tunability, arising from variations in the filling fraction, lattice constant, and applied magnetic field has been demonstrated. Our findings would be of value to the efficient transmission and processing of microwave signals on the nanoscale by means of spin waves.
Observation of spermidine-induced attractive forces in self-assembled monolayers of single stranded DNA using a microcantilever sensor
Authors: Mertens J. , Tamayo J. , Kosaka P. , Calleja M.
Published: April 2011

Despite the biological relevance, the physical origin of attraction between highly negatively charged DNA strands in condensation remains an open question. We have used microcantilever sensors to study the forces involved in DNA condensation by spermidine. The experiments were performed under flow conditions with gold-coated cantilevers sensitized with thiolated single stranded DNA. The experiments show that above a critical concentration of spermidine, the DNA strands abruptly experiences large attractive forces. The critical spermidine concentration for the transition increases with the monovalent salt concentration. The experiments provide a direct insight of the forces responsible of condensation.
Selection of phage-displayed peptides on live adherent cells in microfluidic channels
Authors: Wang Jinpeng , Liu Yanli , Teesalu Tambet , Sugahara Kazuki N. , Kotamrajua Venkata Ramana , Adams Jonathan D. , Ferguson Brian S. , Gong Qiang , Oh Seung Soo , Csordas Andrew T. , Cho Minseon , Ruoslahti Erkki , Xiao Yi , Soh H. Tom
Published: April 2011

Affinity reagents that bind to specific molecular targets are an essential tool for both diagnostics and targeted therapeutics. There is a particular need for advanced technologies for the generation of reagents that specifically target cell-surface markers, because transmembrane proteins are notoriously difficult to express in recombinant form. We have previously shown that microfluidics offers many advantages for generating affinity reagents against purified protein targets, and we have now significantly extended this approach to achieve successful in vitro selection of T7 phage-displayed peptides that recognize markers expressed on live, adherent cells within a microfluidic channel. As a model, we have targeted neuropilin-1 (NRP-1), a membrane-bound receptor expressed at the surface of human prostate carcinoma cells that plays central roles in angiogenesis, cell migration, and invasion. We show that, compared to conventional biopanning methods, microfluidic selection enables more efficient discovery of peptides with higher affinity and specificity by providing controllable and reproducible means for applying stringent selection conditions against minimal amounts of target cells without loss. Using our microfluidic system, we isolate peptide sequences with superior binding affinity and specificity relative to the well known NRP-1-binding RPARPAR peptide. As such microfluidic systems can be used with a wide range of biocombinatorial libraries and tissue types, we believe that our method represents an effective approach toward efficient biomarker discovery from patient samples.
Simplicity in melt densification in multicomponent magmatic reservoirs in Earth’s interior revealed by multinuclear magnetic resonance
Authors: Lee Sung Keun
Published: April 2011

Pressure-induced changes in properties of multicomponent silicate melts in magma oceans controlled chemical differentiation of the silicate earth and the composition of partial melts that might have formed hidden reservoirs. Although melt properties show complex pressure dependences, the melt structures at high pressure and the atomistic origins of these changes are largely unknown because of their complex pressure–composition dependence, intrinsic to multicomponent magmatic melts. Chemical constraints such as the nonbridging oxygen (NBO) content at 1 atm, rather than the structural parameters for melt polymerization, are commonly used to account for pressure-induced changes in the melt properties. Here, we show that the pressure-induced NBO fraction in diverse silicate melts show a simple and general trend where all the reported experimental NBO fractions at high pressure converge into a single decaying function. The pressure-induced changes in the NBO fraction account for and predict the silica content, nonlinear variations in entropy, and the transport properties of silicate melts in Earth’s mantle. The melt properties at high pressure are largely different from what can be predicted for silicate melts with a fixed NBO fraction at 1 atm. The current results with simplicity in melt polymerization at high pressure provide a molecular link to the chemical differentiation, possibly missing Si content in primary mantle through formation of hidden Si-rich mantle reservoirs.
Langlands reciprocity for the even-dimensional noncommutative tori
Authors: Nikolaev Igor
Published: April 2011

We conjecture an explicit formula for the higher-dimensional Dirichlet character; the formula is based on the

K
K

-theory of the so-called noncommutative tori. It is proved that our conjecture is true for the two-dimensional and one-dimensional (degenerate) noncommutative tori. In the second case, one gets a noncommutative analog of the Artin reciprocity law.
High-resolution imaging of the immunological synapse and T-cell receptor microclustering through microfabricated substrates
Authors: Biggs M. J. P. , Milone M. C. , Santos L. C. , Gondarenko A. , Wind S. J.
Published: April 2011

T-cell activation via antigen presentation is associated with the formation of a macromolecular membrane assembly termed the immunological synapse (IS). The genesis of the IS and the onset of juxtacrine signalling is characterized by the formation of cell membrane microclusters and the organization of such into segregated microdomains. A central zone rich in T-cell receptor (TCR)–major histocompatibility complex microclusters termed the central supramolecular activation cluster (cSMAC) forms the bullseye of this structure, while the cellular interface surrounding the cSMAC is characterized by regions enriched in adhesion and co-stimulatory molecules.In vitro, the study of dynamic TCR microcluster coalescence and IS genesis in T-cell populations is hampered by cell migration within the culture system and resolution constraints resulting from lateral cell–cell contact. Here, we detail a novel system describing the fabrication of micropit arrays designed to sequester single T-cell–antigen presenting cell (APC) conjugates and promote IS formation in the horizontal imaging plane for high-resolution studies of microcluster dynamics. We subsequently use this system to describe the formation of the cSMAC in T-cell populations and to investigate the morphology of the interfacial APC membrane.
On the formalization and reuse of scientific research
Authors: King Ross D. , Liakata Maria , Lu Chuan , Oliver Stephen G. , Soldatova Larisa N.
Published: April 2011

The reuse of scientific knowledge obtained from one investigation in another investigation is basic to the advance of science. Scientific investigations should therefore be recorded in ways that promote the reuse of the knowledge they generate. The use of logical formalisms to describe scientific knowledge has potential advantages in facilitating such reuse. Here, we propose a formal framework for using logical formalisms to promote reuse. We demonstrate the utility of this framework by using it in a worked example from biology: demonstrating cycles of investigation formalization [
F
] and reuse [
R
] to generate new knowledge. We first used logic to formally describe a Robot scientist investigation into yeast (
Saccharomyces cerevisiae
) functional genomics [
f
1
]. With Robot scientists, unlike human scientists, the production of comprehensive metadata about their investigations is a natural by-product of the way they work. We then demonstrated how this formalism enabled the reuse of the research in investigating yeast phenotypes [
r
1
=
R
(
f
1
)]. This investigation found that the removal of non-essential enzymes generally resulted in enhanced growth. The phenotype investigation was then formally described using the same logical formalism as the functional genomics investigation [
f
2
=
F
(
r
1
)]. We then demonstrated how this formalism enabled the reuse of the phenotype investigation to investigate yeast systems-biology modelling [
r
2
=
R
(
f
2
)]. This investigation found that yeast flux-balance analysis models fail to predict the observed changes in growth. Finally, the systems biology investigation was formalized for reuse in future investigations [
f
3
=
F
(
r
2
)]. These cycles of reuse are a model for the general reuse of scientific knowledge.
Asymmetric interaction and indeterminate fitness correlation between cooperative partners in the fig–fig wasp mutualism
Authors: Wang Rui-Wu , Sun Bao-Fa , Zheng Qi , Shi Lei , Zhu Lixing
Published: April 2011

Empirical observations have shown that cooperative partners can compete for common resources, but what factors determine whether partners cooperate or compete remain unclear. Using the reciprocal fig–fig wasp mutualism, we show that nonlinear amplification of interference competition between fig wasps—which limits the fig wasps' ability to use a common resource (i.e. female flowers)—keeps the common resource unsaturated, making cooperation locally stable. When interference competition was manually prevented, the fitness correlation between figs and fig wasps went from positive to negative. This indicates that genetic relatedness or reciprocal exchange between cooperative players, which could create spatial heterogeneity or self-restraint, was not sufficient to maintain stable cooperation. Moreover, our analysis of field-collected data shows that the fitness correlation between cooperative partners varies stochastically, and that the mainly positive fitness correlation observed during the warm season shifts to a negative correlation during the cold season owing to an increase in the initial oviposition efficiency of each fig wasp. This implies that the discriminative sanction of less-cooperative wasps (i.e. by decreasing the egg deposition efficiency per fig wasp) but reward to cooperative wasps by fig, a control of the initial value, will facilitate a stable mutualism. Our finding that asymmetric interaction leading to an indeterminate fitness interaction between symbiont (i.e. cooperative actors) and host (i.e. recipient) has the potential to explain why conflict has been empirically observed in both well-documented intraspecific and interspecific cooperation systems.
Binding of glycosaminoglycan saccharides to hydroxyapatite surfaces: a density functional theory study
Authors: Streeter Ian , de Leeuw Nora H.
Published: April 2011

Density functional theory calculations implemented by the SIESTA code are used to study the interactions of the saccharidesN-acetylgalactosamine (GalNAc) and glucuronic acid (GlcA) with the (0001) and () surfaces of the mineral hydroxyapatite (HAP). GalNAc and GlcA are the constituent monosaccharides of chondroitin, which is a glycosaminoglycan found in bone and cartilage, and whose interactions with HAP have been implicated as a controlling factor in the process of biomineralization. Geometry optimization calculations are used to identify low-energy adsorption structures of the monosaccharides on the HAP surfaces, and to calculate the corresponding adsorption energies. The calculations show that GalNAc interacts with HAP principally through its hydroxy and acetyl amine functional groups, and deprotonated GlcA interacts principally through its hydroxy and carboxylate functional groups. The mode and the strength of adsorption depend on the orientation of the saccharide with respect to the HAP surface, which has implications for the structural conformation of chondroitin chains in the presence of HAP. Both monosaccharides bind more strongly to the () surface than to the (0001) surface.
Binding constraints on the evolution of enzymes and signalling proteins: the important role of negative pleiotropy
Authors: Liberles David A. , Tisdell Makayla D. M. , Grahnen Johan A.
Published: April 2011

A number of biophysical and population-genetic processes influence amino acid substitution rates. It is commonly recognized that proteins must fold into a native structure with preference over an unfolded state, and must bind to functional interacting partners favourably to function properly. What is less clear is how important folding and binding specificity are to amino acid substitution rates. A hypothesis of the importance of binding specificity in constraining sequence and functional evolution is presented. Examples include an evolutionary simulation of a population of SH2 sequences evolved by threading through the structure and binding to a native ligand, as well as SH3 domain signalling in yeast and selection for specificity in enzymatic reactions. An example in vampire bats where negative pleiotropy appears to have been adaptive is presented. Finally, considerations of compartmentalization and macromolecular crowding on negative pleiotropy are discussed.
Natural visual cues eliciting predator avoidance in fiddler crabs
Authors: Smolka Jochen , Zeil Jochen , Hemmi Jan M.
Published: April 2011

To efficiently provide an animal with relevant information, the design of its visual system should reflect the distribution of natural signals and the animal's tasks. In many behavioural contexts, however, we know comparatively little about the moment-to-moment information-processing challenges animals face in their daily lives. In predator avoidance, for instance, we lack an accurate description of the natural signal stream and its value for risk assessment throughout the prey's defensive behaviour. We characterized the visual signals generated by real, potentially predatory events by video-recording bird approaches towards anUca vomeriscolony. Using four synchronized cameras allowed us to simultaneously monitor predator avoidance responses of crabs. We reconstructed the signals generated by dangerous and non-dangerous flying animals, identified the cues that triggered escape responses and compared them with those triggering responses to dummy predators. Fiddler crabs responded to a combination of multiple visual cues (including retinal speed, elevation and visual flicker) that reflect the visual signatures of distinct bird and insect behaviours. This allowed crabs to discriminate between dangerous and non-dangerous events. The results demonstrate the importance of measuring natural sensory signatures of biologically relevant events in order to understand biological information processing and its effects on behavioural organization.
Three-dimensional displays and stereo vision
Authors: Westheimer Gerald
Published: April 2011

Procedures for three-dimensional image reconstruction that are based on the optical and neural apparatus of human stereoscopic vision have to be designed to work in conjunction with it. The principal methods of implementing stereo displays are described. Properties of the human visual system are outlined as they relate to depth discrimination capabilities and achieving optimal performance in stereo tasks. The concept of depth rendition is introduced to define the change in the parameters of three-dimensional configurations for cases in which the physical disposition of the stereo camera with respect to the viewed object differs from that of the observer's eyes.
Balancing sampling and specialization: an adaptationist model of incremental development
Authors: Frankenhuis Willem E. , Panchanathan Karthik
Published: April 2011

Development is typically a constructive process, in which phenotypes incrementally adapt to local ecologies. Here, we present a novel model in which natural selection shapes developmental systems based on the evolutionary ecology, and these systems adaptively guide phenotypic development. We assume that phenotypic construction is incremental and trades off with sampling cues to the environmental state. We computed the optimal developmental programmes across a range of evolutionary ecological conditions. Using these programmes, we simulated distributions of mature phenotypes. Our results show that organisms sample the environment most extensively when cues are moderately, not highly, informative. When the developmental programme relies heavily on sampling, individuals transition from sampling to specialization at different times in ontogeny, depending on the consistency of their sampled cue set; this finding suggests that stochastic sampling may result in individual differences in plasticity itself. In addition, we find that different selection pressures may favour similar developmental mechanisms, and that organisms may incorrectly calibrate development despite stable ontogenetic environments. We hope our model will stimulate adaptationist research on the constructive processes guiding development.
Evolution of olfaction in non-avian theropod dinosaurs and birds
Authors: Zelenitsky Darla K. , Therrien François , Ridgely Ryan C. , McGee Amanda R. , Witmer Lawrence M.
Published: April 2011

Little is known about the olfactory capabilities of extinct basal (non-neornithine) birds or the evolutionary changes in olfaction that occurred from non-avian theropods through modern birds. Although modern birds are known to have diverse olfactory capabilities, olfaction is generally considered to have declined during avian evolution as visual and vestibular sensory enhancements occurred in association with flight. To test the hypothesis that olfaction diminished through avian evolution, we assessed relative olfactory bulb size, here used as a neuroanatomical proxy for olfactory capabilities, in 157 species of non-avian theropods, fossil birds and living birds. We show that relative olfactory bulb size increased during non-avian maniraptoriform evolution, remained stable across the non-avian theropod/bird transition, and increased during basal bird and early neornithine evolution. From early neornithines through a major part of neornithine evolution, the relative size of the olfactory bulbs remained stable before decreasing in derived neoavian clades. Our results show that, rather than decreasing, the importance of olfaction actually increased during early bird evolution, representing a previously unrecognized sensory enhancement. The relatively larger olfactory bulbs of earliest neornithines, compared with those of basal birds, may have endowed neornithines with improved olfaction for more effective foraging or navigation skills, which in turn may have been a factor allowing them to survive the end-Cretaceous mass extinction.
Why do leafcutter bees cut leaves? New insights into the early evolution of bees
Authors: Litman Jessica R. , Danforth Bryan N. , Eardley Connal D. , Praz Christophe J.
Published: April 2011

Stark contrasts in clade species diversity are reported across the tree of life and are especially conspicuous when observed in closely related lineages. The explanation for such disparity has often been attributed to the evolution of key innovations that facilitate colonization of new ecological niches. The factors underlying diversification in bees remain poorly explored. Bees are thought to have originated from apoid wasps during the Mid-Cretaceous, a period that coincides with the appearance of angiosperm eudicot pollen grains in the fossil record. The reliance of bees on angiosperm pollen and their fundamental role as angiosperm pollinators have contributed to the idea that both groups may have undergone simultaneous radiations. We demonstrate that one key innovation—the inclusion of foreign material in nest construction—underlies both a massive range expansion and a significant increase in the rate of diversification within the second largest bee family, Megachilidae. Basal clades within the family are restricted to deserts and exhibit plesiomorphic features rarely observed among modern bees, but prevalent among apoid wasps. Our results suggest that early bees inherited a suite of behavioural traits that acted as powerful evolutionary constraints. While the transition to pollen as a larval food source opened an enormous ecological niche for the early bees, the exploitation of this niche and the subsequent diversification of bees only became possible after bees had evolved adaptations to overcome these constraints.
Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis
Authors: Erlich Yaniv , Edvardson Simon , Hodges Emily , Zenvirt Shamir , Thekkat Pramod , Shaag Avraham , Dor Talya , Hannon Gregory J. , Elpeleg Orly
Published: April 2011

Whole exome sequencing has become a pivotal methodology for rapid and cost-effective detection of pathogenic variations in Mendelian disorders. A major challenge of this approach is determining the causative mutation from a substantial number of bystander variations that do not play any role in the disease etiology. Current strategies to analyze variations have mainly relied on genetic and functional arguments such as mode of inheritance, conservation, and loss of function prediction. Here, we demonstrate that disease-network analysis provides an additional layer of information to stratify variations even in the presence of incomplete sequencing coverage, a known limitation of exome sequencing. We studied a case of Hereditary Spastic Paraparesis (HSP) in a single inbred Palestinian family. HSP is a group of neuropathological disorders that are characterized by abnormal gait and spasticity of the lower limbs. Forty-five loci have been associated with HSP and lesions in 20 genes have been documented to induce the disorder. We used whole exome sequencing and homozygosity mapping to create a list of possible candidates. After exhausting the genetic and functional arguments, we stratified the remaining candidates according to their similarity to the previously known disease genes. Our analysis implicated the causative mutation in the motor domain of KIF1A, a gene that has not yet associated with HSP, which functions in anterograde axonal transportation. Our strategy can be useful for a large class of disorders that are characterized by locus heterogeneity, particularly when studying disorders in single families.
The Bphi008a Gene Interacts with the Ethylene Pathway and Transcriptionally Regulates MAPK Genes in the Response of Rice to Brown Planthopper Feeding
Authors: Hu Jing , Zhou Jiangbo , Peng Xinxin , Xu Henghao , Liu Caixiang , Du Bo , Yuan Hongyu , Zhu Lili , He Guangcun
Published: April 2011

We examined ways in which the Brown planthopper induced008a (Bphi008a; AY256682) gene of rice (Oryza sativa) enhances the plant’s resistance to a specialist herbivore, the brown planthopper (BPH; Nilaparvata lugens). Measurement of the expression levels of ethylene synthases and of ethylene emissions showed that BPH feeding rapidly initiated the ethylene signaling pathway and up-regulated Bphi008a transcript levels after 6 to 96 h of feeding. In contrast, blocking ethylene transduction (using 1-methylcyclopropene) reduced Bphi008a transcript levels in wild-type plants fed upon by BPH. In vitro kinase assays showed that Bphi008a can be phosphorylated by rice Mitogen-activated Protein Kinase5 (OsMPK5), and yeast two-hybrid assays demonstrated that the carboxyl-terminal proline-rich region of Bphi008a interacts directly with this kinase. Furthermore, bimolecular fluorescence complementation assays showed that this interaction occurs in the nucleus. Subsequently, we found that Bphi008a up-regulation and down-regulation were accompanied by different changes in transcription levels of OsMPK5, OsMPK12, OsMPK13, and OsMPK17 in transgenic plants. Immunoblot analysis also showed that the OsMPK5 protein level increased in overexpressing plants and decreased in RNA interference plants after BPH feeding. In transgenic lines, changes in the expression levels of several enzymes that are important components of the defenses against the BPH were also observed. Finally, yeast two-hybrid screening results showed that Bphi008a is able to interact with a b-ZIP transcription factor (OsbZIP60) and a RNA polymerase polypeptide (SDRP).
β-Amylase–Like Proteins Function as Transcription Factors in Arabidopsis, Controlling Shoot Growth and Development
Authors: Reinhold Heike , Soyk Sebastian , Šimková Klára , Hostettler Carmen , Marafino John , Mainiero Samantha , Vaughan Cara K. , Monroe Jonathan D. , Zeeman Samuel C.
Published: April 2011

Plants contain β-amylase–like proteins (BAMs; enzymes usually associated with starch breakdown) present in the nucleus rather than targeted to the chloroplast. They possess BRASSINAZOLE RESISTANT1 (BZR1)-type DNA binding domains—also found in transcription factors mediating brassinosteroid (BR) responses. The two Arabidopsis thaliana BZR1-BAM proteins (BAM7 and BAM8) bind a cis-regulatory element that both contains a G box and resembles a BR-responsive element. In protoplast transactivation assays, these BZR1-BAMs activate gene expression. Structural modeling suggests that the BAM domain's glucan binding cleft is intact, but the recombinant proteins are at least 1000 times less active than chloroplastic β-amylases. Deregulation of BZR1-BAMs (the bam7bam8 double mutant and BAM8-overexpressing plants) causes altered leaf growth and development. Of the genes upregulated in plants overexpressing BAM8 and downregulated in bam7bam8 plants, many carry the cis-regulatory element in their promoters. Many genes that respond to BRs are inversely regulated by BZR1-BAMs. We propose a role for BZR1-BAMs in controlling plant growth and development through crosstalk with BR signaling. Furthermore, we speculate that BZR1-BAMs may transmit metabolic signals by binding a ligand in their BAM domain, although diurnal changes in the concentration of maltose, a candidate ligand produced by chloroplastic β-amylases, do not influence their transcription factor function.
Negative Regulation of Anthocyanin Biosynthesis in Arabidopsis by a miR156-Targeted SPL Transcription Factor
Authors: Gou Jin-Ying , Felippes Felipe F. , Liu Chang-Jun , Weigel Detlef , Wang Jia-Wei
Published: April 2011

Flavonoids are synthesized through an important metabolic pathway that leads to the production of diverse secondary metabolites, including anthocyanins, flavonols, flavones, and proanthocyanidins. Anthocyanins and flavonols are derived from Phe and share common precursors, dihydroflavonols, which are substrates for both flavonol synthase and dihydroflavonol 4-reductase. In the stems of Arabidopsis thaliana, anthocyanins accumulate in an acropetal manner, with the highest level at the junction between rosette and stem. We show here that this accumulation pattern is under the regulation of miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes, which are deeply conserved and known to have important roles in regulating phase change and flowering. Increased miR156 activity promotes accumulation of anthocyanins, whereas reduced miR156 activity results in high levels of flavonols. We further provide evidence that at least one of the miR156 targets, SPL9, negatively regulates anthocyanin accumulation by directly preventing expression of anthocyanin biosynthetic genes through destabilization of a MYB-bHLH-WD40 transcriptional activation complex. Our results reveal a direct link between the transition to flowering and secondary metabolism and provide a potential target for manipulation of anthocyanin and flavonol content in plants.
Nitrogen and winter cover crop effects on spring and summer nutrient uptake
Authors: Read J. J. , Brink G. E. , McLaughlin M. R. , Sistani K. R.
Published: April 2011

Overseeded winter annuals in bermudagrass [Cynodon dactylon (L.) Pers.] improve annual dry‐matter (DM) yield and capture nutrients in fields receiving manure application. This study determined the DM and nutrient uptake responses of annual ryegrass (Lolium multiflorum L.), cereal rye (Secale cereale), berseem clover (Trifolium alexandrinum L.) and bermudagrass‐winter fallow to 0, 50, 100 and 150 kg N ha−1 applied approximately 2 months before a single spring harvest, and in addition to swine‐effluent N (258 and 533 kg ha−1 in summer 2000 and 2001, respectively). Under drought conditions in 2000, DM yield at the spring harvest was highest in ryegrass, and summer DM yield of bermudagrass was greater at 100 and 150 kg N ha−1 than 50 kg N ha−1(P < 0·05). The concentration and uptake of N at the spring harvest increased linearly across N rates in both years (P < 0.05). Cover crops differed in N uptake in 2000 (P < 0.01) and values ranged from approximately 141 kg N ha−1 in berseem clover to 86 kg N ha−1 in rye. Per unit of N applied, uptake of N increased by approximately 0·409 kg ha−1 in 2000 and 0·267 kg ha−1 in 2001; uptake of P increased by 0·029 and 0·014 kg ha−1 respectively. In 2000, uptake of P was responsive to N rate and this relationship was significant (P < 0·01) in winter fallow (slope = 0·032) and ryegrass (slope = 0·057). Increased uptake of N and P at the single spring harvest was due mainly to higher concentrations in herbage and not higher DM yield.
Do Nest Light Conditions Affect Rejection of Parasitic Eggs? A Test of the Light Environment Hypothesis
Authors: Honza Marcel , Procházka Petr , Morongová Klára , Čapek Miroslav , Jelínek Václav
Published: April 2011

Discrimination of foreign eggs is one of the most studied aspects of host defences against avian brood parasites. Although many factors affecting host egg‐recognition processes have already been evaluated, only a few attempts have been made to test the importance of light conditions in microhabitats of host nests. Here, we examined whether the objectively measured nest light environment affects great reed warbler (Acrocephalus arundinaceus) responses towards real common cuckoo (Cuculus canorus) eggs. More specifically, we predicted that parasitic eggs will be rejected with a lower frequency from nests placed in darker conditions than those in lighter conditions. However, we found no effect of the ambient light on egg‐rejection behaviour alone, but the photosynthetically active radiation exhibited a positive interactive effect with chromatic contrast between cuckoo and host eggs. Most rejection events were accomplished when cuckoo eggs of poor mimicry were laid in well‐lit nests. Our study suggests that this phenomenon may have important implications for the evolution of egg mimicry and host egg discrimination. We encourage further testing of the light environment hypothesis in other host species breeding in variable nest microhabitats and light conditions.