bluuebunny/crossref_metadata_2025 huggingface dataset:
Remote vibration measurement: A wireless passive surface acoustic wave resonator fast probing strategy
Authors: Friedt J.-M. , Droit C. , Ballandras S. , Alzuaga S. , Martin G. , Sandoz P.
Published: May 2012

Surface acoustic wave (SAW) resonators can advantageously operate as passive sensors which can be interrogated through a wireless link. Amongst the practical applications of such devices, structural health monitoring through stress measurement and more generally vibration characteristics of mechanical structures benefit from the ability to bury such sensors within the considered structure (wireless and battery-less). However, measurement bandwidth becomes a significant challenge when measuring wideband vibration characteristics of mechanical structures. A fast SAW resonator measurement scheme is demonstrated here. The measurement bandwidth is limited by the physical settling time of the resonator (Q/π periods), requiring only two probe pulses through a monostatic RADAR-like electronic setup to identify the sensor resonance frequency and hence stress on a resonator acting as a strain gauge. A measurement update rate of 4800 Hz using a high quality factor SAW resonator operating in the 434 MHz Industrial, Scientific and Medical band is experimentally demonstrated.
Detection of nanosecond-scale, high power THz pulses with a field effect transistor
Authors: Preu S. , Lu H. , Sherwin M. S. , Gossard A. C.
Published: May 2012

We demonstrate detection and resolution of high power, 34 ns free electron laser pulses using a rectifying field effect transistor. The detector remains linear up to an input power of 11 ± 0.5 W at a pulse energy of 20 ± 1 μJ at 240 GHz. We compare its performance to a protected Schottky diode, finding a shorter intrinsic time constant. The damage threshold is estimated to be a few 100 W. The detector is, therefore, well-suited for characterizing high power THz pulses. We further demonstrate that the same detector can be used to detect low power continuous-wave THz signals with a post detection limited noise floor of 3.1 μW/\documentclass[12pt]{minimal}\begin{document}$\sqrt{Hz}$\end{document}Hz. Such ultrafast, high power detectors are important tools for high power and high energy THz facilities such as free electron lasers.
A theoretical investigation of the feasibility of Tannor-Rice type control: Application to selective bond breakage in gas-phase dihalomethanes
Authors: Shu Chuan-Cun , Rozgonyi Tamás , González Leticia , Henriksen Niels E.
Published: May 2012

Within the $\tilde {\rm B}$B̃ absorption band of CH2BrCl, we theoretically analyze the laser-induced control of the Br/Cl branching ratio, Br + CH2Cl ← CH2BrCl → CH2Br + Cl, with CH2BrCl initially in its vibrational ground state. For weak-field excitation, the Br/Cl branching ratio increases as a function of wavelength, however, for wavelengths below 180 nm the branching ratio cannot be made smaller than 0.4. Using optimal control theory, we show that the branching ratio can be made significantly less than 0.4, only when very strong fields are employed. Thus, the present work strongly suggests that a Tannor-Rice type laser control mechanism for selective bond breakage in CH2BrCl cannot take place without accompanying photoionization.
Enhanced spin figure of merit in a Rashba quantum dot ring connected to ferromagnetic leads
Authors: Zheng Jun , Chi Feng
Published: May 2012

Spin-dependent thermoelectric effect is studied in an Aharonov-Bohm ring with a quantum dot (QD) inserted in one of its arms. We consider that the ring is connected to external ferromagnetic electrodes and there exists Rashba spin-orbit (RSO) interaction in the QD. The spin thermopower Ss and the spin figure of merit ZsT are calculated in terms of the Keldysh Green’s function method. We found that the ZsT value can be significantly enhanced by the coaction of the ferromagnetism of the leads and the RSO interaction. By optimizing the structure parameters, the value of ZsT can be up to 1 at room temperature. In addition, pure spin-up (spin-down) thermopower (or Seebeck coefficient) can be generated with high ZsT values. Our results indicate that such a single dot ring may be used as a high efficiency spin thermoelectric generator.
On the completely integrable case of the Rössler system
Authors: Tudoran Răzvan M. , Gîrban Anania
Published: May 2012

In this paper, we present some relevant dynamical properties of the Rössler system from the Poisson dynamics point of view.
Reversible high-pressure phase transition in LaN
Authors: Schneider Sebastian B. , Baumann Dominik , Salamat Ashkan , Schnick Wolfgang
Published: May 2012

In situ high-pressure X-ray powder diffraction experiments on LaN up to 60.1 GPa at ambient temperature in a diamond-anvil cell revealed a reversible, first-order structural phase transition starting at ∼22.8 GPa and completed at ∼26.5 GPa from the ambient cubic phase (Fm3¯m, no. 225) to a tetragonal high-pressure phase (P4/nmm, no. 19, a = 4.1060(6), c = 3.0446(6) Å, Z = 2, wRp = 0.011), which has not been claimed in theoretical predictions. HP-LaN is isotypic with a high-pressure polymorph of BaO, which crystallizes in a tetragonally distorted CsCl-type structure. The phase transition is accompanied by a volume collapse of about 11% which corresponds well with the reported data on HP-BaO. A linear extrapolation of the c/a ratio of the tetragonally distorted CsCl-type sub-cell reaches a value c/a = 1 of cubic CsCl-type HP-LaN at 91(12) GPa. In addition, the compressibility of LaN was investigated and resulted in a bulk modulus for the ambient pressure phase of B0 = 135(3) GPa and B′ = 5.0(5) after fitting a third-order Birch-Murnaghan equation of state to the experimental p–V data. The corresponding extrapolated bulk modulus of HP-LaN is found to be B0 = 278(6) GPa and its pressure derivative B′ = 1.2(2). Both as-calculated bulk moduli are compared to the respective values obtained from an Eulerian strain versus normalized stress plot to be 143(2) GPa for ambient LaN and 293(7) GPa for HP-LaN. Compared to other binary nitrides such as δ-ZrN or δ-HfN having bulk moduli of 285 GPa and 306 GPa, respectively, the extrapolated bulk moduli of HP-LaN are in the same order of magnitude, ranking HP-LaN as a highly incompressible material.
Electrical stabilities and memory mechanisms of organic bistable devices fabricated utilizing a poly(3,4-ethylene-dioxythiophene): Poly(styrenesulfonate) layer with a poly(methyl methacrylate) buffer layer
Authors: Min Son Jung , Seung Song Woo , Ho Yoo Chan , Yeol Yun Dong , Whan Kim Tae
Published: May 2012

Organic bistable devices (OBDs) based on a poly(3,4-ethylene-dioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) layer with a poly(methyl methacrylate) (PMMA) buffer layer were fabricated on indium-tin-oxide (ITO)-coated polyethylene terephthalate (PET) flexible substrates. Current-voltage curves for the Al/PEDOT:PSS/PMMA/ITO/PET device showed current bistabilities with an ON/OFF current ratio of 1 × 103, indicative of a significant enhancement of memory storage. The endurance number of the ON/OFF switchings for the OBDs was above 1 × 105 cycles showing high potential applications in read only memory devices. The memory mechanisms for the OBDs on the basis of oxidation and reduction operations were attributed to the filament processes.
Realization of autofocusing system for laser direct writing on non-planar surfaces
Authors: Luo Jianbo , Liang Yiyong , Yang Guoguang
Published: May 2012

This paper presents an autofocusing system for laser direct writing on non-planar surfaces, including focus error signal detection and focusing control. The focus error signal detection is based on modified confocal techniques, which features easy implementation, independence of the tilt angles of non-planar surfaces, and excellent suppression of common-mode noise or variable system factors. We also present a macro/micro dual-drive mechanism and its synchronous operation for focusing control on non-planar surfaces. Finally, a performance evaluation of the autofocusing system is presented. The uniform line width of 2.1 μm for a pattern on a convex spherical substrate with a curvature radius of 100 mm shows the autofocusing system performs well.
Performance enhancement of organic light-emitting diodes by chlorine plasma treatment of indium tin oxide
Authors: Cao X. A. , Zhang Y. Q.
Published: May 2012

The characteristics of green phosphorescent organic light-emitting diodes (OLEDs) fabricated on ITO/glass substrates pretreated with low-energy O2 and Cl2 plasma were compared. At 20 mA/cm2, the OLEDs with O2 and Cl2 plasma-treated indium tin oxide (ITO) had voltages of 9.6 and 7.6 eV, and brightness of 9580 and 12380 cd/m2, respectively. At ∼104 cd/m2, the latter had a 30% higher external quantum efficiency and a 74% higher power efficiency. Photoelectron spectroscopies revealed that Cl2 plasma treatment created stable In-Cl bonds and raised the work function of ITO by up to 0.9 eV. These results suggest that the better energy level alignment at the chlorinated ITO/organic interface enhances hole injection, leading to more efficient and more reliable operation of the OLEDs. The developed plasma chlorination process is very effective for surface modification of ITO and compatible with the fabrication of various organic electronics.
Nanowire arrays, surface anisotropy, magnetoelastic effects and spintronics
Authors: Tannous C. , Ghaddar A. , Gieraltowski J.
Published: May 2012

Resonance field Hres variation obtained from ferromagnetic resonance measurements performed versus field angle on ferromagnetic nickel nanowire arrays with different diameters (15 nm to 100 nm) and with temperature varying from liquid helium (4.2 K) to room value indicate presence of large surface anisotropy for small diameter (<50 nm) and strong magnetoelastic effects for all diameters. Extracting this information from temperature variation of anisotropy terms allows us to infer that magnetoelastic behavior versus temperature and nanowire diameter might have important implications for the design of nanowire based spintronic devices such as magnetic racetrack memory, logic and storage media, and devices.
Development of a continuous testing apparatus for temperature reduction performance of cool coatings
Authors: Song Zhongnan , Shi Yunxing , Zhang Weidong , Song Jianrong , Qu Jian , Li Yanwen , Wang Zhongde
Published: May 2012

The working principle of a continuous testing apparatus for the temperature reduction performance of cool coatings is presented in this work. The apparatus consists of infrared reflector type lamps, an adiabatic box, and a data acquisition system. It was calibrated with the different conventional reference panels. The tests for dynamic and steady state temperature reduction performances were illustrated with two cool coatings. Results obtained directly from the simultaneous measurement are in good agreement with those calculated from separate measurements, thus confirming this apparatus as a valuable experimental tool for research and development of cool coatings.
Spin-transfer switching in full-Heusler Co2FeAl-based magnetic tunnel junctions
Authors: Sukegawa Hiroaki , Wen Zhenchao , Kondou Kouta , Kasai Shinya , Mitani Seiji , Inomata Koichiro
Published: May 2012

We demonstrated spin-transfer magnetization switching using magnetic tunnel junctions (MTJs) with a full-Heusler alloy Co2FeAl (CFA). We prepared CFA (1.5 nm)/MgO/CoFe (4 nm) (“CFA-free”) and CFA (30 nm)/MgO/CoFeB (2 nm) (“CFA-reference”) MTJs on a Cr(001) layer. The intrinsic critical current density (Jc0) of the CFA-free (CFA-reference) MTJ was 29 MA/cm2 (7.1 MA/cm2). The larger Jc0 of the CFA-free MTJ is attributed to the significant enhancement of the Gilbert damping factor (∼0.04) of the CFA due to the Cr layer. The Jc0 of the CFA-reference is as small as that reported for typical CoFeB/MgO/CoFeB MTJs.
A normal incident quantum cascade detector enhanced by surface plasmons
Authors: Zhai Shen-Qiang , Liu Jun-Qi , Liu Feng-Qi , Wang Zhan-Guo
Published: May 2012

We demonstrate a normal incident quantum cascade detector excited by surface plasmons resonance using an Au two-dimensional hole array integrated on top of the detector absorption region. With normal incidence, the device has a maximal responsivity value of 8.4 mA/W at 160 K and can work up to room temperature with a responsivity of 1.02 mA/W. Compared with the 45° polished edge coupling device, the two-dimensional hole array can lead to quantum efficiency enhancement at most measured temperatures, and at 140 K the quantum efficiency is enhanced most strongly by 69%.
Phase matching for surface plasmon enhanced second harmonic generation in a gold grating slab
Authors: Luong Ngoc , Cheng Cheng-Wen , Shih Min-Hsiung , Kuang Wan
Published: May 2012

Surface plasmon enhanced second harmonic generation in gold grating slabs was investigated. The efficiency is analyzed with respect to the phase matching at the fundamental and the second harmonic frequencies. A classical electromagnetic model was developed under the weak nonlinearity approximation and solved by the finite element method. The measured zeroth order transmitted second harmonic intensity was found to be in quantitative agreement with numerical results. It is shown experimentally and numerically that proper phase matching at both frequencies improves the second harmonic efficiency.
Broadband Purcell effect: Radiative decay engineering with metamaterials
Authors: Jacob Zubin , Smolyaninov Igor I. , Narimanov Evgenii E.
Published: May 2012

We show that metamaterials with hyperbolic dispersion support a large number of electromagnetic states that can couple to quantum emitters leading to a broadband Purcell effect. The proposed approach of radiative decay engineering, useful for applications such as single photon sources, fluorescence imaging, biosensing, and single molecule detection, also opens up the possibility of using hyperbolic metamaterials to probe the spontaneous emission properties of atoms and artificial atoms such as quantum dots.
A microfluidics approach towards high-throughput pathogen removal from blood using margination
Authors: Wei Hou Han , Gan Hiong Yap , Bhagat Ali Asgar S. , Li Leon D. , Lim Chwee Teck , Han Jongyoon
Published: May 2012

Sepsis is an adverse systemic inflammatory response caused by microbial infection in blood. This paper reports a simple microfluidic approach for intrinsic, non-specific removal of both microbes and inflammatory cellular components (platelets and leukocytes) from whole blood, inspired by the invivo phenomenon of leukocyte margination. As blood flows through a narrow microchannel (20 × 20 µm), deformable red blood cells (RBCs) migrate axially to the channel centre, resulting in margination of other cell types (bacteria, platelets, and leukocytes) towards the channel sides. By using a simple cascaded channel design, the blood samples undergo a 2-stage bacteria removal in a single pass through the device, thereby allowing higher bacterial removal efficiency. As an application for sepsis treatment, we demonstrated separation of Escherichia coli and Saccharomyces cerevisiae spiked into whole blood, achieving high removal efficiencies of ∼80% and ∼90%, respectively. Inflammatory cellular components were also depleted by >80% in the filtered blood samples which could help to modulate the host inflammatory response and potentially serve as a blood cleansing method for sepsis treatment. The developed technique offers significant advantages including high throughput (∼1 ml/h per channel) and label-free separation which allows non-specific removal of any blood-borne pathogens (bacteria and fungi). The continuous processing and collection mode could potentially enable the return of filtered blood back to the patient directly, similar to a simple and complete dialysis circuit setup. Lastly, we designed and tested a larger filtration device consisting of 6 channels in parallel (∼6 ml/h) and obtained similar filtration performances. Further multiplexing is possible by increasing channel parallelization or device stacking to achieve higher throughput comparable to convectional blood dialysis systems used in clinical settings.
Manipulating single annealed polyelectrolyte under alternating current electric fields: Collapse versus accumulation
Authors: Wang Shengqin , Zhu Yingxi
Published: May 2012

Effective manipulation and understanding of the structural and dynamic behaviors of a single polyelectrolyte (PE) under alternating current (AC) electric fields are of great scientific and technological importance because of its intimate relevance to emerging bionanotechnology. In this work, we employ fluorescence correlation spectroscopy (FCS) to study the conformational and AC-electrokinetic behaviors of a model annealed PE, poly(2-vinyl pyridine) (P2VP) under both spatially uniform and non-uniform AC fields at a single molecule level. Under spatially uniform AC-fields, we observe a gradual and continuous coil-to-globule conformational transition (CGT) of single P2VP at varied AC-frequency when a critical AC-field strength is exceeded, in contrast to the pH-induced abrupt CGT in the absence of AC-fields. On the contrary, under spatially non-uniform AC-fields, we observe field-driven net flow and accumulation of P2VP near high AC-field regions due to combined AC electro-osmosis and dielectrophoresis but surprisingly no conformational change. Thus, distinct AC-electric polarization effect on single annealed PE subject to AC-field homogeneity is suggested.
The influence of silicon nanoclusters on the optical properties of a-SiNx samples: A theoretical study
Authors: Guerra Roberto , Ippolito Mariella , Meloni Simone , Ossicini Stefano
Published: May 2012

By means of ab-initio calculations, we investigate the optical properties of pure a-SiNx samples, with x∈[0.4,1.8], and samples embedding silicon nanoclusters (NCs) of diameter 0.5≤d≤1.0 nm. In the pure samples, the optical absorption gap and the radiative recombination rate vary according to the concentration of Si-N bonds. In the presence of NCs, the radiative rate of the samples is barely affected, indicating that the intense photoluminescence of experimental samples is mostly due to the matrix itself rather than to the NCs. Besides, we evidence an important role of Si-N-Si bonds at the NC/matrix interface in the observed photoluminescence trend.
Enhancement in light emission efficiency of Si nanocrystal light-emitting diodes by a surface plasmon coupling
Authors: Huh Chul , Choi Chel-Jong , Kim Wanjoong , Kyu Kim Bong , Park Byoung-Jun , Jang Eun-Hye , Kim Sang-Hyeob , Yong Sung Gun
Published: May 2012

We report an enhancement in light emission efficiency form Si nanocrystal (NC) light-emitting diodes (LEDs) via surface plasmons (SPs) by employing Au nanoparticles (NPs). Photoluminescence intensity of Si NCs with Au NPs was enhanced by 2 factors of magnitude due to the strong coupling of Si NCs and SP resonance modes of Au NPs. The electrical characteristics of Si NC LED were significantly improved, which was attributed to an increase in an electron injection into the Si NCs due to the formation of inhomogeneous Schottky barrier at the SiC-indium tin oxide interface. Moreover, light output power from the Si NC LED was enhanced by 50% due to both SP coupling and improved electrical properties. The results presented here can provide a very promising way to significantly enhance the performance of Si NC LED.
Resonant microwave-to-spin-wave transducer
Authors: Au Y. , Ahmad E. , Dmytriiev O. , Dvornik M. , Davison T. , Kruglyak V. V.
Published: May 2012

We use time resolved scanning Kerr microscopy and analytical and numerical calculations to demonstrate coupling of uniform global microwave field to propagating spin waves for emerging magnonic architectures. The coupling is mediated by the local dynamic dipolar field produced by the magnetization of a resonantly driven all-metallic magnetic microwave-to-spin-wave transducer. The local dipolar field can exceed that of the incident microwave field by one order of magnitude. Our numerical simulations demonstrate the ability of the transducer to unidirectionally emit coherent exchange spin waves of nanoscale wavelengths with the emission direction programmed by the magnetic state of the transducer.
Viable thermionic emission from graphene-covered metals
Authors: Starodub E. , Bartelt N. C. , McCarty K. F.
Published: May 2012

Thermionic emission from monolayer graphene grown on representative transition metals, Ir and Ru, is characterized by low-energy electron microscopy. Work functions were determined from the temperature dependence of the emission current and from the electron energy spectrum of emitted electrons. The high-temperature work function of the strongly interacting system graphene/Ru(0001) is sufficiently low, 3.3 ± 0.1 eV, to have technological potential for large-area emitters that are spatially uniform, efficient, and chemically inert. The thermionic work functions of the less strongly interacting system graphene/Ir(111) are over 1 eV larger and vary substantially (0.4 eV) between graphene orientations rotated by 30°.
Communication: Spectroscopic measurement of the binding energy of a carboxylic acid-water dimer
Authors: Gu Quanli , Knee J. L.
Published: May 2012

Infrared-ultraviolet two color pump-probe spectroscopy is used to measure the binding energy, D0, of a carboxylic acid-water dimer where the acid is 9-hydroxy-9-fluorenecarboxylic acid. The acid-water configuration presents a standard structure for the general acid-water interaction where the water bonds to the carboxylic acid group through two intermolecular hydrogen bonds. Photodissociation studies with product vibrational state resolution have enabled an accurate determination of the binding energy for this acid-water system to be D0 = 2975 ± 30 cm−1. Quantum chemical calculations are performed to compare with the experimental observations and a recent measurement on the water dimer (D0 = 1105 ± 10 cm−1).
High temperature operation of short wavelength InAs-based quantum cascade lasers
Authors: Laffaille P. , Moreno J. C. , Teissier R. , Bahriz M. , Baranov A. N.
Published: May 2012

InAs/AlSb quantum cascade lasers emitting at 3.06 and 3.22 μm at room temperature has been studied. The lasers with high reflection coating on back facets operated in pulse mode up to 400 and 423 K, respectively. The obtained results showed no dramatic performance degradation of the InAs-based QCLs with decreasing emission wavelength down to 3 μm.
Puzzling phonon dispersion curves and vibrational mode instability in superconducting MgCNi3
Authors: Jha Prafulla K. , Gupta Sanjay D. , Gupta Sanjeev K.
Published: May 2012

A first principles calculation of the lattice dynamical properties of superconducting MgCNi3 has been performed using density functional perturbation theory (DFPT). The calculated phonon dispersion curves and phonon density of states have been compared with inelastic x-ray scattering (IXS) and inelastic neutron scattering (INS) measurements. We show for the first time that phonon dispersion curves for MgCNi3 in whole Brillouin zone are positive (stable phonon modes) and in good agreement with the experimental data. The phonon DOS shows absence of phonon density of states at zero energy unlike earlier calculations. There is a good agreement between calculated and experimental electron-phonon parameter and superconducting transition temperature. The Eliasberg function is quantitatively as well as qualitatively different from the phonon density of states. The lattice specific heat and Debye temperature do not show any anomalous behaviour.
Reactor experiment reveals neutrino oscillation’s third mixing angle
Authors: Schwarzschild Bertram M.
Published: May 2012

A nonzero value for this elusive parameter offers a possible explanation for the cosmic shortage of antimatter.
Shhhh. Listen to the data
Authors: Feder Toni
Published: May 2012

Sifting through large amounts of data, monitoring data streams, and communicating results are promising areas for sonification.
Fostering a research “ecosystem”
Authors: Kramer David
Published: May 2012

Universities and DOE labs are in solidarity about support for research.
Obama urges renewed efforts on arms control
Authors: Kramer David
Published: May 2012

Several nations are reported to have shed all their weapons-usable materials, but the president warns that the threat of nuclear terrorism remains.
Nuclear security agency and weapons labs at odds
Authors: Kramer David
Published: May 2012

Micromanagement by NNSA is blamed for adding hundreds of millions of dollars in labs’ extra costs.
Taking steps toward the next big particle collider
Authors: Feder Toni
Published: May 2012

Two candidate successors to the Large Hadron Collider are closing ranks, and a move is afoot for Japan to be the host.
White House seeks to get a handle on “big data”
Authors: Kramer David
Published: May 2012

Scientific enterprise is “drowning in data but starving for understanding.”
Molding the flow of light: Photonics in astronomy
Authors: Bland-Hawthorn Joss , Kern Pierre
Published: May 2012

Light gathered and focused by a telescope must often be refocused onto spectrographs and other complex instruments. To such ends, astronomers are coming to realize the benefits of photonics.
Distribution of living Cupressaceae reflects the breakup of Pangea
Authors: Mao Kangshan , Milne Richard I. , Zhang Libing , Peng Yanling , Liu Jianquan , Thomas Philip , Mill Robert R. , S. Renner Susanne
Published: May 2012

Most extant genus-level radiations in gymnosperms are of Oligocene age or younger, reflecting widespread extinction during climate cooling at the Oligocene/Miocene boundary [∼23 million years ago (Ma)]. Recent biogeographic studies have revealed many instances of long-distance dispersal in gymnosperms as well as in angiosperms. Acting together, extinction and long-distance dispersal are likely to erase historical biogeographic signals. Notwithstanding this problem, we show that phylogenetic relationships in the gymnosperm family Cupressaceae (162 species, 32 genera) exhibit patterns expected from the Jurassic/Cretaceous breakup of Pangea. A phylogeny was generated for 122 representatives covering all genera, using up to 10,000 nucleotides of plastid, mitochondrial, and nuclear sequence per species. Relying on 16 fossil calibration points and three molecular dating methods, we show that Cupressaceae originated during the Triassic, when Pangea was intact. Vicariance between the two subfamilies, the Laurasian Cupressoideae and the Gondwanan Callitroideae, occurred around 153 Ma (124–183 Ma), when Gondwana and Laurasia were separating. Three further intercontinental disjunctions involving the Northern and Southern Hemisphere are coincidental with or immediately followed the breakup of Pangea.
Structural basis of a protein partner switch that regulates the general stress response of α-proteobacteria
Authors: Herrou Julien , Rotskoff Grant , Luo Yun , Roux Benoît , Crosson Sean
Published: May 2012

α-Proteobacteria uniquely integrate features of two-component signal transduction (TCS) and alternative sigma factor (σ) regulation to control transcription in response to general stress. The core of this regulatory system is the PhyR protein, which contains a σ-like (SL) domain and a TCS receiver domain. Aspartyl phosphorylation of the PhyR receiver in response to stress signals promotes binding of the anti-σ factor, NepR, to PhyR-SL. This mechanism, whereby NepR switches binding between its cognate σ factor and phospho-PhyR (PhyR∼P), controls transcription of the general stress regulon. We have defined the structural basis of the PhyR∼P/NepR interaction in
Caulobacter crescentus
and characterized the effect of aspartyl phosphorylation on PhyR structure by molecular dynamics simulations. Our data support a model in which phosphorylation of the PhyR receiver domain promotes its dissociation from the PhyR-SL domain, which exposes the NepR binding site. A highly dynamic loop–helix region (α3-α4) of the PhyR-SL domain plays an important role in PhyR∼P binding to NepR in vitro, and in stress-dependent activation of transcription in vivo. This study provides a foundation for understanding the protein-protein interactions and protein structural dynamics that underpin general stress adaptation in a large and metabolically diverse clade of the bacterial kingdom.
Urban land teleconnections and sustainability
Authors: Seto Karen C. , Reenberg Anette , Boone Christopher G. , Fragkias Michail , Haase Dagmar , Langanke Tobias , Marcotullio Peter , Munroe Darla K. , Olah Branislav , Simon David
Published: May 2012

This paper introduces urban land teleconnections as a conceptual framework that explicitly links land changes to underlying urbanization dynamics. We illustrate how three key themes that are currently addressed separately in the urban sustainability and land change literatures can lead to incorrect conclusions and misleading results when they are not examined jointly: the traditional system of land classification that is based on discrete categories and reinforces the false idea of a rural–urban dichotomy; the spatial quantification of land change that is based on place-based relationships, ignoring the connections between distant places, especially between urban functions and rural land uses; and the implicit assumptions about path dependency and sequential land changes that underlie current conceptualizations of land transitions. We then examine several environmental “grand challenges” and discuss how urban land teleconnections could help research communities frame scientific inquiries. Finally, we point to existing analytical approaches that can be used to advance development and application of the concept.
Regulatory effects of mTORC2 complexes in type I IFN signaling and in the generation of IFN responses
Authors: Kaur Surinder , Sassano Antonella , Majchrzak-Kita Beata , Baker Darren P. , Su Bing , Fish Eleanor N. , Platanias Leonidas C.
Published: May 2012

IFNs transduce signals by binding to cell surface receptors and activating cellular pathways and regulatory networks that control transcription of IFN-stimulated genes (ISGs) and mRNA translation, leading to generation of protein products that mediate biological responses. Previous studies have shown that type I IFN receptor-engaged pathways downstream of AKT and mammalian target of rapamycin complex (mTORC) 1 play important roles in mRNA translation of ISGs and the generation of IFN responses, but the roles of mTORC2 complexes in IFN signaling are unknown. We provide evidence that mTORC2 complexes control IFN-induced phosphorylation of AKT on serine 473 and their function is ultimately required for IFN-dependent gene transcription via interferon-stimulated response elements. We also demonstrate that such complexes exhibit regulatory effects on other IFN-dependent mammalian target of rapamycin-mediated signaling events, likely via engagement of the AKT/mTORC1 axis, including IFN-induced phosphorylation of S6 kinase and its effector rpS6, as well as phosphorylation of the translational repressor 4E-binding protein 1. We also show that induction of ISG protein expression and the generation of antiviral responses are defective in Rictor and mLST8-KO cells. Together, our data provide evidence for unique functions of mTORC2 complexes in the induction of type I IFN responses and suggest a critical role for mTORC2-mediated signals in IFN signaling.
Force-specific activation of Smad1/5 regulates vascular endothelial cell cycle progression in response to disturbed flow
Authors: Zhou Jing , Lee Pei-Ling , Tsai Chien-Sung , Lee Chih-I , Yang Tung-Lin , Chuang Han-Sheng , Lin Wei-Wen , Lin Ting-Er , Lim Seh Hong , Wei Shu-Yi , Chen Yuh-Lien , Chien Shu , Chiu Jeng-Jiann
Published: May 2012

Vascular endothelial cells (ECs) are constantly exposed to blood flow-induced shear stress, but the mechanism of force-specific activation of their signaling to modulate cellular function remains unclear. We have demonstrated that bone morphogenetic protein receptor (BMPR)-specific Smad1/5 can be force-specifically activated by oscillatory shear stress (OSS) in ECs to cause cell cycle progression. Smad1/5 is highly activated in ECs of atherosclerotic lesions in diseased human coronary arteries from patients with end-stage heart failure undergoing heart transplantation and from apolipoprotein E-deficient mice. Application of OSS (0.5 ± 4 dyn/cm
2
) causes the sustained activation of Smad1/5 in ECs through activations of mammalian target of rapamycin and p70S6 kinase, leading to up-regulation of cyclin A and down-regulations of p21
CIP1
and p27
KIP1
and, hence, EC cycle progression.
En face
examination of rat aortas reveals high levels of phospho-Smad1/5 in ECs of the straight segment of thoracic aorta and the inner, but not the outer, curvature of aortic arch. Immunohistochemical and
en face
examinations of the experimentally stenosed abdominal aorta in rats show high levels of phospho-Smad1/5 in ECs at poststenotic sites, where OSS occurs. These OSS activations of EC Smad1/5 in vitro and in vivo are not inhibited by the BMP-specific antagonist Noggin and, hence, are independent of BMP ligand. Transfecting ECs with Smad1/5-specific small interfering RNAs inhibits the OSS-induced EC cycle progression. Our findings demonstrate the force-specificity of the activation of Smad1/5 and its contribution to cell cycle progression in ECs induced by disturbed flow.
Patterns in Catch Per Unit Effort of Native Prey Fish and Alien Piscivorous Fish in 7 Pacific Northwest USA Rivers
Authors: Hughes Robert M , Herlihy Alan T
Published: May 2012

Nonnative or alien invasive species are commonly accorded threats to native biological assemblages; however, it is difficult to separate the effects of aliens from other covarying disturbances. We evaluated the effect of alien piscivorous fish on native prey species in seven Pacific Northwest rivers through the use of a spatially balanced random sample of 20 sites on each river. The rivers lacked large main-stem dams, and point sources, if any, met state and federal water quality standards. Individual sample sites were electrofished a distance equal to 50 times their mean wetted channel widths, and all fish were identified to species, measured, and returned to the rivers alive (except for museum voucher specimens). At nearly all sites in all seven rivers, we found that the catch per unit effort (CPUE) of native prey species varied inversely with the CPUE of alien piscivores. In the two rivers most dominated by alien piscivores, we collected native prey at only 20%–25% of the sites. We conclude that piscivorous alien fish are associated with reduced population sizes of native prey species, at least during the summer low-flow period, and are potential threats to prey species persistence.

RESUMEN

es comúnmente aceptado que las especies no nativas o foráneas constituyen una amenaza para las comunidades biológicas locales; no obstante, resulta complicado separar el efecto que tienen estas especies invasoras frente a otras perturbaciones co-variantes. Se evaluó el efecto de los peces piscívoros foráneos sobre especies nativas en siete ríos del Pacífico Noroeste de los Estados Unidos de Norteamérica, mediante un muestreo al azar espacialmente balanceado en 20 localidades dentro de cada río. Los ríos carecían de drenajes importantes y los existentes, de haber alguno, cumplían con los estándares federales en cuanto a calidad del agua. En cada localidad de muestreo se llevó a cabo una colecta por medios eléctricos (electro-pesca) a una distancia equivalente a 50 veces el ancho del canal de inundación; todos los peces fueron identificados a nivel especie, medidos y devueltos vivos a los ríos (excepto aquellos especímenes destinados a museos). En casi todas las localidades de los siete ríos, se encontró que la captura por unidad de esfuerzo (CPUE) de las especies nativas de peces, varió de manera inversa con respecto a la CPUE de los peces piscívoros foráneos. En los dos ríos que estaban dominados mayormente por especies piscívoras, se colectaron especies nativas sólo en el 20–25% de las localidades. Se concluye que, al menos durante los periodos de flujo reducido en el verano, los peces piscívoros foráneos se relacionan con reducciones poblacionales de las especies nativas y constituyen una amenaza potencial a la persistencia de las especies locales.mentos relacionados a la liberación y los derechos de los animales, pueden tener consecuencias muy importantes para las pesquerías recreativas.
Formulae for Askey-Wilson moments and enumeration of staircase tableaux
Authors: Corteel S. , Stanley R. , Stanton D. , Williams L.
Published: May 2012

We explain how the moments of the (weight function of the) Askey-Wilson polynomials are related to the enumeration of the staircase tableaux introduced by the first and fourth authors. This gives us a direct combinatorial formula for these moments, which is related to, but more elegant than the formula given in their earlier paper. Then we use techniques developed by Ismail and the third author to give explicit formulae for these moments and for the enumeration of staircase tableaux. Finally we study the enumeration of staircase tableaux at various specializations of the parameterizations; for example, we obtain the Catalan numbers, Fibonacci numbers, Eulerian numbers, the number of permutations, and the number of matchings.
What is behind fleet evolution: a framework for flow analysis and application to the French Atlantic fleet
Authors: Quillérou Emmanuelle , Guyader Olivier
Published: May 2012

Quillérou, E. and Guyader, O. 2012. What is behind fleet evolution: a framework for flow analysis and application to the French Atlantic fleet – ICES Journal of Marine Science, 69: 1069–1077. The study of fishery dynamics considers national-level fleet evolution. It has, however, failed to consider the flows behind fleet evolution as well as the impact of the dynamics of owners of invested capital on fleet evolution. This paper establishes a general conceptual framework which identifies different vessel and owner flows behind fleet evolution and some relationships between these flows. This descriptive conceptual framework aims to change the current focus on drivers of fleet evolution to drivers of the flows behind fleet evolution. We identify a direct impact of vessel flows on the fleet size and nature, and an indirect impact of the movements of capital owners on the fleet evolution (size and nature). This conceptual framework is illustrated using French Atlantic fleet data over a 15-year period (1994–2008). It is shown that the identified flows vary in size and nature and therefore impact differently on the fleet evolution. This description also shows some dependence of vessel flows on owner dynamics. This relationship should be better taken into account for more effective capacity management.
Identification and Characterization of the Defensin-Like Gene Family of Grapevine
Authors: Giacomelli Lisa , Nanni Valentina , Lenzi Luisa , Zhuang Jun , Serra Mauro Dalla , Banfield Mark J. , Town Christopher D. , Silverstein Kevin A. T. , Baraldi Elena , Moser Claudio
Published: May 2012

Defensins are a class of small and diverse cysteine-rich proteins found in plants, insects, and vertebrates, which share a common tertiary structure and usually exert broad-spectrum antimicrobial activities. We used a bioinformatic approach to scan the Vitis vinifera genome and identified 79 defensin-like sequences (DEFL) corresponding to 46 genes and allelic variants, plus 33 pseudogenes and gene fragments. Expansion and diversification of grapevine DEFL has occurred after the split from the last common ancestor with the genera Medicago and Arabidopsis. Grapevine DEFL localization on the ‘Pinot Noir’ genome revealed the presence of several clusters likely evolved through local duplications. By sequencing reverse-transcription polymerase chain reaction products, we could demonstrate the expression of grapevine DEFL with no previously reported record of expression. Many of these genes are predominantly or exclusively expressed in tissues linked to plant reproduction, consistent with findings in other plant species, and some of them accumulated at fruit ripening. The transcripts of five DEFL were also significantly upregulated in tissues infected with Botrytis cinerea, a necrotrophic mold, suggesting a role of these genes in defense against this pathogen. Finally, three novel defensins were discovered among the identified DEFL. They inhibit B. cinerea conidia germination when expressed as recombinant proteins.
Physiologic Specialization of Puccinia triticina on Wheat in the United States in 2010
Authors: Kolmer J. A. , Long D. L. , Hughes M. E.
Published: May 2012

Collections of Puccinia triticina were obtained from rust-infected leaves provided by cooperators throughout the United States and from wheat fields and breeding plots by United States Department of Agriculture–Agricultural Research Service personnel and cooperators in the Great Plains, Ohio River Valley, southeastern states, Oregon, and Washington State in order to determine the virulence of the wheat leaf rust population in 2010. Single uredinial isolates (537 total) were derived from the collections and tested for virulence phenotype on 19 lines of ‘Thatcher’ wheat and a winter wheat line that are near-isogenic for 20 leaf rust resistance genes. In 2010, 38 virulence phenotypes were described in the United States. Virulence phenotypes MLDSD, TDBJG, and TCRKG were the three most common phenotypes. Phenotype MLDSD is virulent to Lr17 and Lr39/Lr41 and was widely distributed throughout the United States. Phenotype TDBJG is virulent to Lr24 and was found in both the soft red winter wheat and hard red winter wheat regions. Phenotype TCRKG is virulent to Lr11, Lr18, and Lr26 and was found mostly in the soft red winter wheat region in the eastern United States. Virulence to Lr21 was found for the first time in North America in isolates collected from spring wheat cultivars in North Dakota and Minnesota.
Data from selective harvests underestimate temporal trends in quantitative traits
Authors: Pelletier Fanie , Festa-Bianchet Marco , Jorgenson Jon T.
Published: May 2012

Human harvests can select against phenotypes favoured by natural selection, and natural resource managers should evaluate possible artificial selection on wild populations. Because the required genetic data are extremely difficult to gather, however, managers typically rely on harvested animals to document temporal trends. It is usually unknown whether these data are unbiased. We explore our ability to detect a decline in horn size of bighorn sheep (
Ovis canadensis
) by comparing harvested males with all males in a population where evolutionary changes owing to trophy hunting were previously reported. Hunting records underestimated the temporal decline, partly because of an increasing proportion of rams that could not be harvested because their horns were smaller than the threshold set by hunting regulations. If harvests are selective, temporal trends measured from harvest records will underestimate the magnitude of changes in wild populations.
The structure of a bottlenose dolphin society is coupled to a unique foraging cooperation with artisanal fishermen
Authors: Daura-Jorge F. G. , Cantor M. , Ingram S. N. , Lusseau D. , Simões-Lopes P. C.
Published: May 2012

Diverse and localized foraging behaviours have been reported in isolated populations of many animal species around the world. In Laguna, southern Brazil, a subset of resident bottlenose dolphins (
Tursiops truncatus
) uses a foraging tactic involving cooperative interactions with local, beach-casting fishermen. We used individual photo-identification data to assess whether cooperative and non-cooperative dolphins were socially segregated. The social structure of the population was found to be a fission–fusion system with few non-random associations, typical for this species. However, association values were greater among cooperative dolphins than among non-cooperative dolphins or between dolphins from different foraging classes. Furthermore, the dolphin social network was divided into three modules, clustering individuals that shared or lacked the cooperative foraging tactic. Space-use patterns were not sufficient to explain this partitioning, indicating a behavioural factor. The segregation of dolphins using different foraging tactics could result from foraging behaviour driving social structure, while the closer association between dolphins engaged in the cooperation could facilitate the transmission and learning of this behavioural trait from conspecifics. This unique case of a dolphin–human interaction represents a valuable opportunity to explore hypotheses on the role of social learning in wild cetaceans.
Bottom-up regulation of a pelagic community through spatial aggregations
Authors: Benoit-Bird Kelly J. , McManus Margaret A.
Published: May 2012

The importance of spatial pattern in ecosystems has long been recognized. However, incorporating patchiness into our understanding of forces regulating ecosystems has proved challenging. We used a combination of continuously sampling moored sensors, complemented by shipboard sampling, to measure the temporal variation, abundance and vertical distribution of four trophic levels in Hawaii's near shore pelagic ecosystem. Using an analysis approach from trophic dynamics, we found that the frequency and intensity of spatial aggregations—rather than total biomass—in each step of a food chain involving phytoplankton, copepods, mesopelagic micronekton and spinner dolphins (Stenella longirostris) were the most significant predictors of variation in adjacent trophic levels. Patches of organisms had impacts disproportionate to the biomass of organisms within them. Our results are in accordance with resource limitation—mediated by patch dynamics—regulating structure at each trophic step in this ecosystem, as well as the foraging behaviour of the top predator. Because of their high degree of heterogeneity, ecosystem-level effects of patchiness such as this may be common in many pelagic marine systems.
Structure and physical properties of silkworm cocoons
Authors: Chen Fujia , Porter David , Vollrath Fritz
Published: May 2012

Silkworm cocoons have evolved a wide range of different structures and combinations of physical and chemical properties in order to cope with different threats and environmental conditions. We present our observations and measurements on 25 diverse types of cocoons in a first attempt to correlate physical properties with the structure and morphology of the cocoons. These two architectural parameters appear to be far more important than the material properties of the silk fibres themselves. We consider tensile and compressive mechanical properties and gas permeation of the cocoon walls, and in each case identify mechanisms or models that relate these properties to cocoon structure, usually based upon non-woven fibre composites. These properties are of relevance also for synthetic non-woven composite materials and our studies will help formulate bio-inspired design principles for new materials.