bluuebunny/crossref_metadata_2025 huggingface dataset:
SUSTAINED MONITORING OF THE SOUTHERN OCEAN AT DRAKE PASSAGE: PAST ACHIEVEMENTS AND FUTURE PRIORITIES
Authors: Meredith Michael P. , Woodworth Philip L. , Chereskin Teresa K. , Marshall David P. , Allison Lesley C. , Bigg Grant R. , Donohue Kathy , Heywood Karen J. , Hughes Chris W. , Hibbert Angela , Hogg Andrew McC. , Johnson Helen L. , Jullion Loïc , King Brian A. , Leach Harry , Lenn Yueng‐Djern , Morales Maqueda Miguel A. , Munday David R. , Naveira Garabato Alberto C. , Provost Christine , Sallée Jean‐Baptiste , Sprintall Janet
Published: September 2011

Drake Passage is the narrowest constriction of the Antarctic Circumpolar Current (ACC) in the Southern Ocean, with implications for global ocean circulation and climate. We review the long‐term sustained monitoring programs that have been conducted at Drake Passage, dating back to the early part of the twentieth century. Attention is drawn to numerous breakthroughs that have been made from these programs, including (1) the first determinations of the complex ACC structure and early quantifications of its transport; (2) realization that the ACC transport is remarkably steady over interannual and longer periods, and a growing understanding of the processes responsible for this; (3) recognition of the role of coupled climate modes in dictating the horizontal transport and the role of anthropogenic processes in this; and (4) understanding of mechanisms driving changes in both the upper and lower limbs of the Southern Ocean overturning circulation and their impacts. It is argued that monitoring of this passage remains a high priority for oceanographic and climate research but that strategic improvements could be made concerning how this is conducted. In particular, long‐term programs should concentrate on delivering quantifications of key variables of direct relevance to large‐scale environmental issues: In this context, the time‐varying overturning circulation is, if anything, even more compelling a target than the ACC flow. Further, there is a need for better international resource sharing and improved spatiotemporal coordination of the measurements. If achieved, the improvements in understanding of important climatic issues deriving from Drake Passage monitoring can be sustained into the future.
Modeling surf zone tracer plumes: 2. Transport and dispersion
Authors: Clark David B. , Feddersen Falk , Guza R. T.
Published: September 2011

Five surf zone dye tracer releases from the HB06 experiment are simulated with a tracer advection diffusion model coupled to a Boussinesq surf zone model (funwaveC). Model tracer is transported and stirred by currents and eddies and diffused with a breaking wave eddy diffusivity, set equal to the breaking wave eddy viscosity, and a small (0.01 m2 s−1) background diffusivity. Observed and modeled alongshore parallel tracer plumes, transported by the wave driven alongshore current, have qualitatively similar cross‐shore structures. Although the model skill for mean tracer concentration is variable (from negative to 0.73) depending upon release, cross‐shore integrated tracer moments (normalized by the cross‐shore tracer integral) have consistently high skills (≈0.9). Modeled and observed bulk surf zone cross‐shore diffusivity estimates are also similar, with 0.72 squared correlation and skill of 0.4. Similar to the observations, the model bulk (absolute) cross‐shore diffusivity is consistent with a mixing length parameterization based on low‐frequency (0.001–0.03 Hz) eddies. The model absolute cross‐shore dispersion is dominated by stirring from surf zone eddies and does not depend upon the presence of the breaking wave eddy diffusivity. Given only the bathymetry and incident wave field, the coupled Boussinesq‐tracer model qualitatively reproduces the observed cross‐shore absolute tracer dispersion, suggesting that the model can be used to study surf zone tracer dispersion mechanisms.
Closure modeling and direct simulation of vegetation drag in flow through emergent vegetation
Authors: Kim Su Jin , Stoesser Thorsten
Published: September 2011

This paper presents numerical simulations of flow through emergent vegetation. Two simulation strategies are evaluated, (1) Reynolds‐averaged Navier‐Stokes (RANS)‐ based simulations employing a vegetation closure model and (2) low‐resolution large‐eddy simulation (LES). RANS‐based models offer efficiency in terms of computational resources, however, it is demonstrated herein that the accuracy of RANS models depends strongly on empirical parameters of the corresponding vegetation closure model. The method of low‐resolution LES is an efficient alternative to a fully resolved LES, simulates vegetation drag directly, and does not require empirical parameter input. Predictions of the vegetative flow resistance of emergent vegetation using low‐resolution LES are in fairly good agreement with measurements, in particular for low and moderate vegetation densities. This is because prevailing stream‐ and spanwise‐velocity gradients, vertical velocity profiles, and recirculation zones are calculated with reasonable accuracy.
JSBML update
Authors: Dräger Andreas , Rodriguez Nicolas
Published: September 2011

This presentation gives an overview about the major changes in JSBML since the release of version 0.8-b1, which will become part of the first release candidate.
Distribution of ABO blood groups and Rh(D) factor among the Brahmin and Kushwaha populations of Jhansi District(U.P)
Authors: Dar Nawab John , Srivastava Ankit , Dar Farooq
Published: September 2011

The distribution of ABO blood groups and Rh(D) factor has been studied among the Brahmin and Kushwaha populations of Jhansi Uttar Pradesh. The A,B,O and AB blood group percentage in Brahmins was recorded as 20.88%, 36.64%, 37.02% and 10.44% .The Rh(D) positive percentage was 96.20% and Rh(d) negative 3.79%. In Kushwaha population the percentage of A,B,O and AB was recorded as 25.65%, 30.26%, 31.25% and 12.82% respectively. The Rh (D) positive was recorded as 97.36% and Rh(d) negative as 2.63%. The allele frequency of ABO among Brahmins was 0.198, 0.266, 0.536 and in Kushwaha the allele frequency of ABO was recorded as 0.251, 0.278, and 0.471 respectively. So the prevalence of the ABO from the area under study can be shown with a general formula as O>B>A>AB.
The System Biology Format Converter
Authors: Jalowicki Gaël , Rodriguez Nicolas , Kutmon Martina , Pettit Jean-Baptiste , Li Lu , Henry Arnaud , Nath Natarajan Kedar , Laibe Camille , Evelo Chris T. , Le Novère Nicolas
Published: September 2011

The System Biology Format Converter (SBFC) aims is to provide a generic framework that potentially allows any conversion between two formats. Interoperability between formats is a recurring issue in Systems Biology. Although there are various tools available to convert models from one format to another, most of them have been independently developed and cannot easily be combined, specially to provide support for more formats. The framework is written in Java and can be used as a standalone executable. This is a collaborative project and we hope that developers will provide support for more formats by creating new modules.SBFC allows anyone to easily add new converters and to integrate existing converters with a minimum of changes. We will also allow to combine several existing converters.
Electronic Nose Technology to Measure Soil Microbial Activity and Classify Soil Metabolic Status
Authors: De Cesare Fabrizio , Di Mattia Elena , Pantalei Simone , Zampetti Emiliano , Vinciguerra Vittorio , Macagnano Antonella
Published: September 2011

The electronic nose (E-nose) is a sensing technology that has been widely used to monitor environments in the last decade. In the present study, the capability of an E-nose, in combination with biochemical and microbiological techniques, of both detecting the microbial activity and estimating the metabolic status of soil ecosystems, was tested by measuring on one side respiration, enzyme activities and growth of bacteria in natural but simplified soil ecosystems over 23 days of incubation through traditional methodologies, and on the other side VOCs and/or gases evolution in their headspace during the same period through the E-nose. Both kinds of measurements, i.e. biochemical-microbiological and sensorial, succeeded in discriminating between inoculated and non-inoculated microcosms and in distinguishing different phases of bacterial growth and activity during the incubation. E-nose responses were highly and significantly correlated with all catalytic activities, respiration and different phases of bacterial growth. Hence, the E-nose was proved able to detect microbial activity in natural soil ecosystems. The metabolic status of these soil ecosystems was calculated on the base of some of the parameters previously tested in order to obtain a metabolic index (MI), ranging between 0 and 1. These MIs were then grouped into 3 classes, corresponding to a low, medium and high metabolic status. All the other measures were used as a multi-type data set in a partial least square discriminant analysis to generate a model capable of classifying the soil microcosms at different sampling dates according to the 3 classes of MIs. The resulting outcomes confirmed that the E-nose technology combined with both metabolic and biomass parameters can altogether represent reliable indicators of the metabolic status of soil ecosystems.
ABC transporters, mechanisms and biology: an overview
Authors: Holland I. Barry
Published: September 2011

This chapter concentrates mainly on structural and mechanistic aspects of ABC (ATP-binding cassette) transporters and, as an example of the physiological significance of these proteins, on lipid transport, vitally important for human health. The chapter considers those aspects of ABC transporter function that appear reasonably well established, those that remain controversial and what appear to be emerging themes. Although we have seen dramatic progress in ABC protein studies in the last 20 years, we are still far from a detailed molecular understanding of function. Nevertheless two critical steps – capture and release of allocrites (transport substrates) involving a binding cavity in the membrane domain, and hydrolysis of ATP by the NBD (nucleotide-binding domain) dimer – are now described by persuasive and testable models: alternating access, and sequential firing of catalysis sites respectively. However, these need to be tested rigorously by more structural and biochemical studies. Other aspects considered include the level at which ATP binding and dimer activation are controlled, the nature of the power stroke delivering mechanical energy for transport, and some unexpected and intriguing differences between importers and exporters. The chapter also emphasizes that some ABC transporters, although important for elimination of toxic compounds (xenobiotics), are also increasingly seen to play crucial roles in homoeostatic regulation of membrane biogenesis and function through translocation of endogenous allocrites such as cholesterol. Another emerging theme is the identification of accessory domains and partners for ABC proteins, resulting in a corresponding widening of the range of activities. Finally, what are the prospects for translational research and ABC transporters?
ABC proteins in yeast and fungal pathogens
Authors: Klein Cornelia , Kuchler Karl , Valachovic Martin
Published: September 2011

All fungal genomes harbour numerous ABC (ATP-binding cassette) proteins located in various cellular compartments such as the plasma membrane, vacuoles, peroxisomes and mitochondria. Most of them have initially been discovered through their ability to confer resistance to a multitude of drugs, a phenomenon called PDR (pleiotropic drug resistance) or MDR (multidrug resistance). Studying the mechanisms underlying PDR/MDR in yeast is of importance in two ways: first, ABC proteins can confer drug resistance on pathogenic fungi such as Candida spp., Aspergillus spp. or Cryptococcus neoformans; secondly, the well-established genetic, biochemical and cell biological tractability of Saccharomyces cerevisiae makes it an ideal tool to study basic mechanisms of drug transport by ABC proteins. In the past, knowledge from yeast has complemented work on human ABC transporters involved in anticancer drug resistance or genetic diseases. Interestingly, increasing evidence available from yeast and other organisms suggests that ABC proteins play a physiological role in membrane homoeostasis and lipid distribution, although this is being intensely debated in the literature.
ABC transporters involved in drug resistance in human parasites
Authors: Leprohon Philippe , Légaré Danielle , Ouellette Marc
Published: September 2011

The ABC (ATP-binding cassette) protein superfamily is a ubiquitous and functionally versatile family of proteins that is conserved from archaea to humans. In eukaryotes, most of these proteins are implicated in the transport of a variety of molecules across cellular membranes, whereas the remaining ones are involved in biological processes unrelated to transport. The biological functions of several ABC proteins have been described in clinically important parasites and nematode worms and include vesicular trafficking, phospholipid movement, translation and drug resistance. This chapter reviews our current understanding of the role of ABC proteins in drug resistance and treatment failure in apicomplexan, trypanosomatid and amitochondriate parasites of medical relevance as well as in helminths.
Functions of ABC transporters in plants
Authors: Kretzschmar Tobias , Burla Bo , Lee Youngsook , Martinoia Enrico , Nagy Réka
Published: September 2011

ABC (ATP-binding cassette) proteins are ubiquitously found in prokaryotes and eukaryotes and generally serve as membrane-intrinsic primary active pumps. In higher plants, ABC proteins constitute a large family, grouped phylogenetically into eight clusters, subfamilies ABCA–ABCI (ABCH is not found in plants). ABC transporters shuttle substrates as diverse as lipids, phytohormones, carboxylates, heavy metals, chlorophyll catabolites and xenobiotic conjugates across a variety of biological membranes. To date, the largest proportions of characterized members have been localized to the plasma membrane and the tonoplast, with dominant implications in cellular secretion and vacuolar sequestration, but they are also found in mitochondrial, plastidal and peroxisomal membranes. Originally identified as tonoplast-intrinsic proteins that shuttle xenobiotic conjugates from the cytosol into the vacuole, thus being an integral part of the detoxification machinery, ABC transporters are now recognized to participate in a multitude of physiological processes that allow the plant to adapt to changing environments and cope with biotic and abiotic stresses.
The P-glycoprotein multidrug transporter
Authors: Sharom Frances J.
Published: September 2011

Pgp (P-glycoprotein) (ABCB1) is an ATP-powered efflux pump which can transport hundreds of structurally unrelated hydrophobic amphipathic compounds, including therapeutic drugs, peptides and lipid-like compounds. This 170 kDa polypeptide plays a crucial physiological role in protecting tissues from toxic xenobiotics and endogenous metabolites, and also affects the uptake and distribution of many clinically important drugs. It forms a major component of the blood–brain barrier and restricts the uptake of drugs from the intestine. The protein is also expressed in many human cancers, where it probably contributes to resistance to chemotherapy treatment. Many chemical modulators have been identified that block the action of Pgp, and may have clinical applications in improving drug delivery and treating cancer. Pgp substrates are generally lipid-soluble, and partition into the membrane before the transporter expels them into the aqueous phase, much like a ‘hydrophobic vacuum cleaner’. The transporter may also act as a ‘flippase’, moving its substrates from the inner to the outer membrane leaflet. An X-ray crystal structure shows that drugs interact with Pgp within the transmembrane regions by fitting into a large flexible binding pocket, which can accommodate several substrate molecules simultaneously. The nucleotide-binding domains of Pgp appear to hydrolyse ATP in an alternating manner; however, it is still not clear whether transport is driven by ATP hydrolysis or ATP binding. Details of the steps involved in the drug-transport process, and how it is coupled to ATP hydrolysis, remain the object of intensive study.
VEGF increases the proliferative capacity and eNOS/NO levels of endothelial progenitor cells through the calcineurin/NFAT signalling pathway
Authors: Yang Long , Guan Hongshan , He Jionghong , Zeng Liqun , Yuan Zhengqiang , Xu Min , Zhang Wenhui , Wu Xiaole , Guan Jing
Published: September 2011

We have investigated whether VEGF (vascular endothelial growth factor) regulates the proliferative capacity and eNOS (endothelial nitric oxide synthase)/NO (nitric oxide) pathway of EPCs (endothelial progenitor cells) by activating CaN (calcineurin)/NFAT (nuclear factor of activated T‐cells) signalling. EPCs were obtained from cultured mononuclear cells isolated from the peripheral blood of healthy adults. Treatment with VEGF (50 ng/ml) potently promoted CaN enzymatic activity, activation of NFAT2, cell proliferation, eNOS protein expression and NO production. Pretreatment with cyclosporin A (10 μg/ml), a pharmacological inhibitor of CaN or 11R‐VIVIT, a special inhibitor of NFAT, completely abrogated the aforementioned effects of VEGF treatment and increased apoptosis. The results indicate that VEGF treatment promotes the proliferative capacity of human EPCs by activating CaN/NFAT signalling leading to increased eNOS protein expression and NO production.
AP‐1 and NF‐κB transcriptionally regulate interleukin‐8 in EA.Hy926 cells under shear stress
Authors: Zhang Yi , Lai Yi , Chen Huai‐Qing , Liu Ying‐Feng
Published: September 2011

Cardiovascular and cerebrovascular diseases remain the leading cause of death in the world. AS (atherosclerosis) is not only an inflammatory disease in which chemokines play the main role but also a disorder that is related to blood SS (shear stress). We have investigated the action of IL‐8 (interleukin‐8) mRNA expression in human endothelial cells line‐EA.Hy926 under SS at different intensities and duration. Expression increases with time in an intensity dependent manner. With regard to the transcriptional mechanism involved, transient transfection of the human wild‐type IL‐8 promoter (–162/+44)/luciferase reporter plasmid, or site mutation of one of the binding sites [AP‐1 (activator protein 1) or NF‐κB (nuclear factor κB)] in the IL‐8 promoter region was investigated. Both AP‐1 and NF‐κB were essential for SS‐activated transcription, with the cells responding to NF‐κB activation within minutes. After stimulated at low SS (4.20 dyne/cm2) for 30 min, the P65 subunit was translocated from the cytoplasm to nucleus for at least 60 min, while the cytoplasmic level of IκB (inhibitory κB) gradually decreased. The combined activation of NF‐κB and AP‐1 are the upstream regulators of low SS‐induced IL‐8 production in EA.Hy926 cells, which subsequently trigger an inflammatory reaction in endothelium.
Robust outer synchronization between two complex networks with fractional order dynamics
Authors: Asheghan Mohammad Mostafa , Míguez Joaquín , Hamidi-Beheshti Mohammad T. , Tavazoei Mohammad Saleh
Published: September 2011

Synchronization between two coupled complex networks with fractional-order dynamics, hereafter referred to as outer synchronization, is investigated in this work. In particular, we consider two systems consisting of interconnected nodes. The state variables of each node evolve with time according to a set of (possibly nonlinear and chaotic) fractional-order differential equations. One of the networks plays the role of a master system and drives the second network by way of an open-plus-closed-loop (OPCL) scheme. Starting from a simple analysis of the synchronization error and a basic lemma on the eigenvalues of matrices resulting from Kronecker products, we establish various sets of conditions for outer synchronization, i.e., for ensuring that the errors between the state variables of the master and response systems can asymptotically vanish with time. Then, we address the problem of robust outer synchronization, i.e., how to guarantee that the states of the nodes converge to common values when the parameters of the master and response networks are not identical, but present some perturbations. Assuming that these perturbations are bounded, we also find conditions for outer synchronization, this time given in terms of sets of linear matrix inequalities (LMIs). Most of the analytical results in this paper are valid both for fractional-order and integer-order dynamics. The assumptions on the inner (coupling) structure of the networks are mild, involving, at most, symmetry and diffusivity. The analytical results are complemented with numerical examples. In particular, we show examples of generalized and robust outer synchronization for networks whose nodes are governed by fractional-order Lorenz dynamics.
Geometrical effects on the thermoelectric properties of ballistic graphene antidot lattices
Authors: Karamitaheri Hossein , Pourfath Mahdi , Faez Rahim , Kosina Hans
Published: September 2011

The thermoelectric properties of graphene-based antidot lattices are theoretically investigated. A third nearest-neighbor tight-binding model and a fourth nearest-neighbor force constant model are employed to study the electronic and phononic band structures of graphene antidot lattices with circular, rectangular, hexagonal, and triangular antidot shapes. Ballistic transport models are used to evaluate transport coefficients. Methods to reduce the thermal conductance and to increase the thermoelectric power factor of such structures are studied. Our results indicate that triangular antidot lattices have the smallest thermal conductance due to longer boundaries and the smallest distance between the neighboring antidots. Among them, iso-triangular antidot lattices have also a large power factor and as a result a large figure of merit.
Self-focusing media using graded photonic crystals: Focusing, Fourier transforming and imaging, directive emission, and directional cloaking
Authors: Vasić Borislav , Gajić Radoš
Published: September 2011

Using numerical simulations, we investigate the realization of self-focusing media using two-dimensional graded photonic crystals and their applications for imaging and non-imaging purposes. The two-dimensional graded photonic crystals consist of spatially varying cylindrical holes drilled in a dielectric host. By controlling the gradient of the refractive index and the thickness of the self-focusing medium, it is possible to obtain either a focusing lens with Fourier transforming capabilities or an imaging lens, which produces inverted images. Non-imaging applications include a simple antenna for directive emission obtained from the focusing lens, whereas a directional cloak is obtained by modifying the imaging lens. Graded photonic crystal based devices work well up to the Bragg frequencies. They are compact, made from lossless dielectrics, and compatible with planar lithographic techniques, so they can find applications in a broad frequency range, even at the optical frequencies.
Intrinsic and external strains modulated electronic properties of GaN/InN core/shell nanowires
Authors: Xiao M. X. , Zhao M. , Jiang Q.
Published: September 2011

We investigate influence of the intrinsic and external uniaxial strains on the electronic properties of GaN/InN core/shell nanowires (CSNWs) with hexagonal and triangular shapes using the first-principle density functional theory. It is found that the band gap of the GaN core in CSNW differs from that of the pure GaN nanowire due to the intrinsic strain ɛi between GaN and InN layers. When the external uniaxial strain ɛe is applied on GaN/InN CSNWs, the direct band gap changes and the efficient creation and dissociation of excitons is improved. ɛi and ɛe substantially influence electronic and optical properties of CSNWs, which may benefit for the efficiency of GaN and InN based photovoltaic devices.
Electrical characteristics of gadolinium gallium oxide/gallium oxide insulators on GaAs and In0.53Ga0.47As in metal-oxide-semiconductor field effect transistors - admittance and subthreshold characteristics
Authors: Paterson G. W. , Bentley S. J. , Holland M. C. , Thayne I. G. , Long A. R.
Published: September 2011

The admittances and subthreshold characteristics of capacitors and MOSFETs on buried InxGa1-xAs channel wafers with a dielectric stack of Gd0.25Ga0.15O0.6/Ga2O3 deposited on GaAs and In0.53Ga0.47As are reported. Both the GaAs and InGaAs interface samples show admittance characteristics indicative of the presence of defect states within the oxide, in agreement with previously reported data from the same oxides on n+ substrates. The interface state model is applied to the admittance data to extract an apparent interface state density (Dit) that includes interface and oxide states. The Dit profiles are very different and have pronounced effects on the device performance. The device subthreshold swings (SS) at low source-drain voltages are also used to extract an apparent Dit. A simple method is used to estimate the Fermi-level position within the bandgap (Et) at threshold, and the resulting Dit(Et) are found to be in good agreement with the admittance data. The importance of proper interpretation of SS and Dit in general and in GaAs interface devices in particular is emphasized. A model that accounts for the logarithmic sweep rate dependence of the extracted Dit due to the presence of oxide states is reported and used to estimate their density from SS measurements. The implications of the band parameters of an oxide with defect states within it for the comparison of different oxides on the same substrate and the issues around the comparison of results in general are discussed.
Five picocoulomb electron bunch generation by ultrafast laser-induced field emission from metallic nano-tip arrays
Authors: Mustonen Anna , Beaud Paul , Kirk Eugenie , Feurer Thomas , Tsujino Soichiro
Published: September 2011

Laser-induced field emission from metallic field emitter array cathodes excited by femtosecond near infrared laser pulses is explored. When 50 fs laser pulses irradiated a 1.2 × 105-tip emitter array under a DC field emission bias, electron bunches with bunch charge up to 5.2 pC were observed. The variation of the bunch charge at different laser intensities and polarizations indicated that electrons were produced from the field emitters by a photofield emission process. The result demonstrates the feasibility of metallic field emitter array cathodes for high-charge short-pulse electron source applications.
Thermoelectric figure of merit as a function of carrier propagation angle in semiconducting superlattices
Authors: Liu Shuo , Carlson E. W.
Published: September 2011

Superlattices have been a fruitful approach for enhancing the figure of merit, ZT, of thermoelectric materials. Generally, superlattice transport is measured either parallel or perpendicular to the superlattice planes. We show here that the figure of merit is a function of carrier propagation angle in the superlattice and that ZT generically exhibits a maximum at an oblique angle, near θ ≈ π/6.
Electrical calcium test for moisture barrier evaluation for organic devices
Authors: Schubert S. , Klumbies H. , Müller-Meskamp L. , Leo K.
Published: September 2011

We discuss the electrical calcium test – a method to measure very small rates of water vapor permeation through barrier films with high throughput. The sensitivity range for our design is found to be 10−5 to 15 g/(m2 d). Moreover, a closer look at the importance of electrodes series resistance is taken: We show that permeation rates are underestimated if it is neglected. Taking this series resistance and Fickian diffusion into account not only the steady, but also the transient state of the permeation curve can be fitted. Using this approach, permeation barriers with different permeabilities are evaluated leading to water vapor transmission rates well comparable to coulometric measurements. The calcium layer morphology is investigated by atomic force microscopy measurements indicating microscopical inhomogeneities during degradation. Variations of electrode material and calcium layer thickness are carried out to examine their influence on the measured permeation. Additionally, optical and electrical calcium tests are compared. Small differences in the time dependence are observed and discussed.
Broadband slow-wave systems of subwavelength thickness excited by a metal wire
Authors: Jin Zhou Yong , Jun Cui Tie
Published: September 2011

We propose a broadband slow-wave system based on metallic graded grating structures of subwavelength thickness. A metal wire is used to excite the slow waves propagating along the gratings. The analysis and full-wave simulations show that the electromagnetic waves could be stopped at designed positions under different frequencies. Experiments are conducted in the microwave frequencies to verify the proposed system. The measured results show very good agreements to the full-wave simulations. We have further modeled a broadband slow-wave system of subwavelength thickness in the terahertz (THz) frequencies to demonstrate its validity.
Spatial hole burning degradation of AlGaAs/GaAs laser diodes
Authors: Qiao Y. B. , Feng S. W. , Xiong C. , Wang X. W. , Ma X. Y. , Zhu H. , Wei G. H.
Published: September 2011

The degradation of AlGaAs/GaAs laser diodes is studied in detail using laser scanning confocal microscopy, cathodoluminescence images, and x-ray diffraction (XRD) techniques. Our analysis has identified a degradation mechanism that results from the periodic distribution of the carrier density and the near-field intensity originating from periodic spatial hole burning. Based on the XRD measurements, we find that the epitaxial layer enters a polycrystalline phase during degradation due to the dark line defects, and the out-of-plane strain and in-plane compressive stress are induced by degradation.
Suppression in the negative bias illumination instability of Zn-Sn-O transistor using oxygen plasma treatment
Authors: Yang Shinhyuk , Hwan Ji Kwang , Ki Kim Un , Seong Hwang Cheol , Ko Park Sang-Hee , Hwang Chi-Sun , Jang Jin , Kyeong Jeong Jae
Published: September 2011

This study examined the effect of oxygen plasma treatment on light-enhanced bias instability in Zn-Sn-O (ZTO) thin film transistors (TFTs). The treated ZTO TFT exhibited only a threshold voltage (Vth) shift of −2.05 V under negative bias illumination stress (NBIS) conditions, whereas the pristine device suffered from a negative Vth shift of 3.76 V under identical conditions. X-ray photoelectron spectroscopic analysis revealed that the oxygen vacancy defect density was diminished via the oxygen plasma treatment. This suggests the Vth degradation under NBIS is due to photo-transition of oxygen vacancy defects.
Influence of the semiconductor oxidation potential on the operational stability of organic field-effect transistors
Authors: Sharma A. , Mathijssen S. G. J. , Bobbert P. A. , de Leeuw D. M.
Published: September 2011

During prolonged application of a gate bias, organic field-effect transistors show a gradual shift of the threshold voltage towards the applied gate bias voltage. The shift follows a stretched-exponential time dependence governed by a relaxation time. Here, we show that a thermodynamic analysis reproduces the observed exponential dependence of the relaxation time on the oxidation potential of the semiconductor. The good fit with the experimental data validates the underlying assumptions. It demonstrates that this operational instability is a straightforward thermodynamically driven process that can only be eliminated by eliminating water from the transistor.
Absence of Casimir regime in two-dimensional nanoribbon phonon conduction
Authors: Wang Zhao , Mingo Natalio
Published: September 2011

In stark contrast with three-dimensional (3D) nanostructures, we show that boundary scattering in two-dimensional (2D) nanoribbons alone does not lead to a finite phonon mean free path. If combined with an intrinsic scattering mechanism, 2D boundary scattering does reduce the overall mean free path; however, the latter does not scale proportionally to the ribbon width, unlike the well known Casimir regime occurring in 3D nanowires. We show that boundary scattering can be accounted for by a simple Mathiessen-type approach for many different 3D nanowire cross sectional shapes; however, this is not possible in the 2D nanoribbon case, where a complete solution of the Boltzmann transport equation is required. These facts have strong implications for the thermal conductivity of suspended nanostructures.
Measurement of electric field across individual wurtzite GaN quantum dots using electron holography
Authors: Zhou Lin , Smith David J. , McCartney Martha R. , Xu Tao , Moustakas Theodore D.
Published: September 2011

Electrostatic potential profiles across wurtzite AlN/GaN quantum dot (QD) superlattices grown by molecular beam epitaxy have been measured using off-axis electron holography. The profiles for individual GaN QDs show large phase shifts which can be understood in terms of spontaneous polarization and piezoelectric fields and the accumulation of positive and negative charge at the GaN/AlN interfaces. An electric field with magnitude of ∼7.8 ± 2 MV/cm was measured across the center of a GaN QD, in reasonable agreement with reported simulations.
Circadian transcriptional regulation by the posttranslational oscillator without de novo clock gene expression in
Synechococcus
Authors: Hosokawa Norimune , Hatakeyama Tetsuhiro S. , Kojima Takashi , Kikuchi Yoshiyuki , Ito Hiroshi , Iwasaki Hideo
Published: September 2011

Circadian rhythms are a fundamental property of most organisms, from cyanobacteria to humans. In the unicellular obligately photoautotrophic cyanobacterium
Synechococcus elongatus
PCC 7942, essentially all promoter activities are controlled by the KaiABC-based clock under continuous light conditions. When
Synechococcus
cells are transferred from the light to continuous dark (DD) conditions, the expression of most genes, including the clock genes
kaiA
and
kaiBC
, is rapidly down-regulated, whereas the KaiC phosphorylation cycle persists. Therefore, we speculated that the posttranslational oscillator might not drive the transcriptional circadian output without de novo expression of the
kai
genes. Here we show that the cyanobacterial clock regulates the transcriptional output even in the dark. The expression of a subset of genes in the genomes of cells grown in the dark was dramatically affected by
kaiABC
nullification, and the magnitude of dark induction was dependent on the time at which the cells were transferred from the light to the dark. Moreover, under DD conditions, the expression of some dark-induced gene transcripts exhibited temperature-compensated damped oscillations, which were nullified in
kaiABC
-null strains and were affected by a
kaiC
period mutation. These results indicate that the Kai protein-based posttranslational oscillator can drive the circadian transcriptional output even without the de novo expression of the clock genes.
Expression of the Sendai (murine parainfluenza) virus C protein alleviates restriction of measles virus growth in mouse cells
Authors: Iwasaki Masaharu , Yanagi Yusuke
Published: September 2011

Measles virus (MV), a human pathogen, uses the signaling lymphocyte activation molecule (SLAM) or CD46 as an entry receptor. Although several transgenic mice expressing these receptors have been generated as small animal models for measles, these mice usually have to be made defective in IFN-α/β signaling to facilitate MV replication. Similarly, when functional receptors are expressed by transfection, mouse cells do not allow MV growth as efficiently as primate cells. In this study, we demonstrate that MV efficiently grows in SLAM-expressing mouse cells in which the Sendai virus (SeV) C protein is transiently expressed. We developed a SLAM-expressing mouse cell line whose genome also encodes the SeV C protein downstream of the sequence flanked with loxP sequences. When this cell line was infected with the recombinant MV expressing the Cre recombinase, the SeV C protein was readily expressed. Importantly, the Cre recombinase-encoding MV grew in this cell line much more efficiently than it did in the parental cell. The minigenome assay demonstrated that the SeV C protein does not modulate MV RNA synthesis. Analyses using the mutant proteins with the defined functional defects revealed that the IFN-antagonist function, but not the budding-accelerating function, of the SeV C protein was critical for supporting efficient MV growth in mouse cells. Our results indicate that insufficient IFN antagonism can be an important determinant of the host range of viruses, and the system described here may be useful to overcome the species barrier of other human viruses.
Interdomain movements in metabotropic glutamate receptor activation
Authors: Huang Siluo , Cao Jianhua , Jiang Ming , Labesse Gilles , Liu Jianfeng , Pin Jean-Philippe , Rondard Philippe
Published: September 2011

Many cell surface receptors are multimeric proteins, composed of several structural domains, some involved in ligand recognition, whereas others are responsible for signal transduction. In most cases, the mechanism of how ligand interaction in the extracellular domains leads to the activation of effector domains remains largely unknown. Here we examined how the extracellular ligand binding to the venus flytrap (VFT) domains of the dimeric metabotropic glutamate receptors activate the seven transmembrane (7TM) domains responsible for G protein activation. These two domains are interconnected by a cysteine-rich domain (CRD). We show that any of the four disulfide bridges of the CRD are required for the allosteric coupling between the VFT and the 7TM domains. More importantly, we show that a specific association of the two CRDs corresponds to the active state of the receptor. Indeed, a specific crosslinking of the CRDs with intersubunit disulfide bridges leads to fully constitutively active receptors, no longer activated by agonists nor by allosteric modulators. These data demonstrate that intersubunit movement at the level of the CRDs represents a key step in metabotropic glutamate receptor activation.
Inhibition of influenza virus replication via small molecules that induce the formation of higher-order nucleoprotein oligomers
Authors: Gerritz Samuel W. , Cianci Christopher , Kim Sean , Pearce Bradley C. , Deminie Carol , Discotto Linda , McAuliffe Brian , Minassian Beatrice F. , Shi Shuhao , Zhu Shirong , Zhai Weixu , Pendri Annapurna , Li Guo , Poss Michael A. , Edavettal Suzanne , McDonnell Patricia A. , Lewis Hal A. , Maskos Klaus , Mörtl Mario , Kiefersauer Reiner , Steinbacher Stefan , Baldwin Eric T. , Metzler William , Bryson James , Healy Matthew D. , Philip Thomas , Zoeckler Mary , Schartman Richard , Sinz Michael , Leyva-Grado Victor H. , Hoffmann Hans-Heinrich , Langley David R. , Meanwell Nicholas A. , Krystal Mark
Published: September 2011

Influenza nucleoprotein (NP) plays multiple roles in the virus life cycle, including an essential function in viral replication as an integral component of the ribonucleoprotein complex, associating with viral RNA and polymerase within the viral core. The multifunctional nature of NP makes it an attractive target for antiviral intervention, and inhibitors targeting this protein have recently been reported. In a parallel effort, we discovered a structurally similar series of influenza replication inhibitors and show that they interfere with NP-dependent processes via formation of higher-order NP oligomers. Support for this unique mechanism is provided by site-directed mutagenesis studies, biophysical characterization of the oligomeric ligand:NP complex, and an X-ray cocrystal structure of an NP dimer of trimers (or hexamer) comprising three NP_A:NP_B dimeric subunits. Each NP_A:NP_B dimeric subunit contains two ligands that bridge two composite, protein-spanning binding sites in an antiparallel orientation to form a stable quaternary complex. Optimization of the initial screening hit produced an analog that protects mice from influenza-induced weight loss and mortality by reducing viral titers to undetectable levels throughout the course of treatment.
Alternative splicing of a single transcription factor drives selfish reproductive behavior in honeybee workers (
Apis mellifera
)
Authors: Jarosch Antje , Stolle Eckart , Crewe Robin M. , Moritz Robin F. A.
Published: September 2011

In eusocial insects the production of daughters is generally restricted to mated queens, and unmated workers are functionally sterile. The evolution of this worker sterility has been plausibly explained by kin selection theory [Hamilton W (1964)
J Theor Biol
7:1–52], and many traits have evolved to prevent conflict over reproduction among the females in an insect colony. In honeybees (
Apis mellifera
), worker reproduction is regulated by the queen, brood pheromones, and worker policing. However, workers of the Cape honeybee,
Apis mellifera capensis
, can evade this control and establish themselves as social parasites by activating their ovaries, parthenogenetically producing diploid female offspring (thelytoky) and producing queen-like amounts of queen pheromones. All these traits have been shown to be strongly influenced by a single locus on chromosome 13 [Lattorff HMG, et al. (2007)
Biol Lett
3:292–295]. We screened this region for candidate genes and found that alternative splicing of a gene homologous to the
gemini
transcription factor of
Drosophila
controls worker sterility. Knocking out the critical exon in a series of RNAi experiments resulted in rapid worker ovary activation—one of the traits characteristic of the social parasites. This genetic switch may be controlled by a short intronic splice enhancer motif of nine nucleotides attached to the alternative splice site. The lack of this motif in parasitic Cape honeybee clones suggests that the removal of nine nucleotides from the altruistic worker genome may be sufficient to turn a honeybee from an altruistic worker into a parasite.
Oxygen-coupled redox regulation of the skeletal muscle ryanodine receptor-Ca
2+
release channel by NADPH oxidase 4
Authors: Sun Qi-An , Hess Douglas T. , Nogueira Leonardo , Yong Sandro , Bowles Dawn E. , Eu Jerry , Laurita Kenneth R. , Meissner Gerhard , Stamler Jonathan S.
Published: September 2011

Physiological sensing of O
2
tension (partial O
2
pressure, pO
2
) plays an important role in some mammalian cellular systems, but striated muscle generally is not considered to be among them. Here we describe a molecular mechanism in skeletal muscle that acutely couples changes in pO
2
to altered calcium release through the ryanodine receptor–Ca
2+
-release channel (RyR1). Reactive oxygen species are generated in proportion to pO
2
by NADPH oxidase 4 (Nox4) in the sarcoplasmic reticulum, and the consequent oxidation of a small set of RyR1 cysteine thiols results in increased RyR1 activity and Ca
2+
release in isolated sarcoplasmic reticulum and in cultured myofibers and enhanced contractility of intact muscle. Thus, Nox4 is an O
2
sensor in skeletal muscle, and O
2
-coupled hydrogen peroxide production by Nox4 governs the redox state of regulatory RyR1 thiols and thereby governs muscle performance. These findings reveal a molecular mechanism for O
2
-based signaling by an NADPH oxidase and demonstrate a physiological role for oxidative modification of RyR1.
Direct measurements of DNA-mediated colloidal interactions and their quantitative modeling
Authors: Rogers W. Benjamin , Crocker John C.
Published: September 2011

DNA bridging can be used to induce specific attractions between small particles, providing a highly versatile approach to creating unique particle-based materials having a variety of periodic structures. Surprisingly, given the fact that the thermodynamics of DNA strands in solution are completely understood, existing models for DNA-induced particle interactions are typically in error by more than an order of magnitude in strength and a factor of two in their temperature dependence. This discrepancy has stymied efforts to design the complex temperature, sequence and time-dependent interactions needed for the most interesting applications, such as materials having highly complex or multicomponent microstructures or the ability to reconfigure or self-replicate. Here we report high-spatial resolution measurements of DNA-induced interactions between pairs of polystyrene microspheres at binding strengths comparable to those used in self-assembly experiments, up to 6 
k
B
T
. We also describe a conceptually straightforward and numerically tractable model that quantitatively captures the separation dependence and temperature-dependent strength of these DNA-induced interactions, without empirical corrections. This model was equally successful when describing the more complex and practically relevant case of grafted DNA brushes with self-interactions that compete with interparticle bridge formation. Together, our findings motivate a nanomaterial design approach where unique functional structures can be found computationally and then reliably realized in experiment.
3D lithography by rapid curing of the liquid instabilities at nanoscale
Authors: Grilli Simonetta , Coppola Sara , Vespini Veronica , Merola Francesco , Finizio Andrea , Ferraro Pietro
Published: September 2011

In liquids realm, surface tension and capillarity are the key forces driving the formation of the shapes pervading the nature. The steady dew drops appearing on plant leaves and spider webs result from the minimization of the overall surface energy [Zheng Y, et al. (2010)
Nature
463:640–643]. Thanks to the surface tension, the interfaces of such spontaneous structures exhibit extremely good spherical shape and consequently worthy optical quality. Also nanofluidic instabilities generate a variety of fascinating liquid silhouettes, but they are however intrinsically short-lived. Here we show that such unsteady liquid structures, shaped in polymeric liquids by an electrohydrodynamic pressure, can be rapidly cured by appropriate thermal treatments. The fabrication of many solid microstructures exploitable in photonics is demonstrated, thus leading to a new concept in 3D lithography. The applicability of specific structures as optical tweezers and as novel remotely excitable quantum dots–embedded microresonators is presented.
Hydrogen peroxide differentially modulates cardiac myocyte nitric oxide synthesis
Authors: Sartoretto Juliano L. , Kalwa Hermann , Pluth Michael D. , Lippard Stephen J. , Michel Thomas
Published: September 2011

Nitric oxide (NO) and hydrogen peroxide (H
2
O
2
) are synthesized within cardiac myocytes and play key roles in modulating cardiovascular signaling. Cardiac myocytes contain both the endothelial (eNOS) and neuronal (nNOS) NO synthases, but the differential roles of these NOS isoforms and the interplay of reactive oxygen species and reactive nitrogen species in cardiac signaling pathways are poorly understood. Using a recently developed NO chemical sensor [Cu
2
(FL2E)] to study adult cardiac myocytes from wild-type, eNOS
null
, and nNOS
null
mice, we discovered that physiological concentrations of H
2
O
2
activate eNOS but not nNOS. H
2
O
2
-stimulated eNOS activation depends on phosphorylation of both the AMP-activated protein kinase and kinase Akt, and leads to the robust phosphorylation of eNOS. Cardiac myocytes isolated from mice infected with lentivirus expressing the recently developed H
2
O
2
biosensor HyPer2 show marked H
2
O
2
synthesis when stimulated by angiotensin II, but not following β-adrenergic receptor activation. We discovered that the angiotensin-II-promoted increase in cardiac myocyte contractility is dependent on H
2
O
2
, whereas β-adrenergic contractile responses occur independently of H
2
O
2
signaling. These studies establish differential roles for H
2
O
2
in control of cardiac contractility and receptor-dependent NOS activation in the heart, and they identify new points for modulation of NO signaling responses by oxidant stress.