bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of Reynolds number on the critical mass phenomenon in vortex-induced vibration
Authors: Morse T. L. , Williamson C. H. K.
Published: April 2009

In this study, we investigate the critical mass phenomenon in vortex-induced vibration over a wide range of Reynolds numbers (Re=4000–30 000). We consider an elastically mounted cylinder that is able to vibrate transverse to a fluid flow. If we remove the restoring spring (k=0), then above a certain critical mass ratio (m∗ is oscillating body mass/displaced fluid mass), the cylinder will experience almost no motion, despite its unrestrained freedom to move transverse to the flow. However, when the mass ratio is decreased below a special critical value, without altering anything else in the system, we see a catastrophic increase in amplitude, and the body settles into a large amplitude periodic vibration. This corresponds to a change from a desynchronized wake to a 2P mode of vortex formation, where two pairs of vortices are formed per cycle of motion. Since a system with no restoring force represents a case of infinite normalized velocity (U∗→∞), the observation of high amplitude motion indicates that the regime of U∗ giving resonant vibration extends to infinity, for sufficiently small mass ratio. In this work, we measure the critical mass directly from experiments with no spring stiffness, and we show also how the critical mass may be accurately predicted from force measurements from controlled vibration experiments, or from free vibration measurements of elastically mounted cylinders. Critical mass gradually increases with Reynolds number from a value of 0.36 to 0.54, over the regime Re=4000–30 000. The fact that the critical mass is a function of Reynolds numbers should be expected because it depends on the vortex-induced forces, which are influenced by gradual changes in vortex formation as Re increases. The evaluation of critical mass in this configuration, and indeed in other diverse vortex-induced vibration (VIV) systems, is important because it can predict the regime of normalized velocities that will yield large amplitude vibration, and which one may wish to avoid in practice. The fact that critical mass, at moderate Reynolds numbers, in several diverse VIV systems, including cylinders in one or two degrees of freedom, pivoted bodies, cantilevers, and tethered spheres, are all within a small range 0.36–0.6, remains an interesting question.
The Fermi-level efficiency method and its applications on high interface trap density oxide-semiconductor interfaces
Authors: Lin H. C. , Brammertz Guy , Martens Koen , de Valicourt Guilhem , Negre Laurent , Wang Wei-E , Tsai Wilman , Meuris Marc , Heyns Marc
Published: April 2009

An interface characterization technique, termed the Fermi-level efficiency (FLE) method, is proposed for evaluating the passivation level of high trap density oxide-semiconductor interfaces. Based on the characteristic charge trapping time-energy relation and the conductance method, the FLE method examines the Fermi-level displacement at the oxide-semiconductor interface under applied gate bias. The obtained Fermi-level efficiencies can be used to assess the interface qualities of metal-oxide-semiconductor devices with III-V and other novel substrate materials.
Quantum ion-acoustic double layers in unmagnetized dense electron-positron-ion plasmas
Authors: Khan S. A. , Mahmood S. , Ali S.
Published: April 2009

The existence of small amplitude quantum ion-acoustic double layers is studied in an unmagnetized dense electron-positron-ion plasma. For this purpose, the quantum hydrodynamic model is employed to derive a deformed Korteweg–de Vries (dKdV) equation. The steady state double layer solution of dKdV equation is obtained and its dependence on various parameters is discussed. It is found that only compressive double layers can exist in such plasmas. The analytical and numerical studies reveal that the quantum ion-acoustic double layer structures strongly depend on quantum diffraction effects and positron number density.
Resonant second harmonic generation of a Gaussian electromagnetic beam in a collisional magnetoplasma
Authors: Kaur Sukhdeep , Sharma A. K. , Salih Hyder A.
Published: April 2009

Second harmonic generation of a right circularly polarized Gaussian electromagnetic beam in a magnetized plasma is investigated. The beam causes Ohmic heating of electrons and subsequent redistribution of the plasma, leading to self-defocusing. The radial density gradient, in conjunction with the oscillatory electron velocity, produces density oscillation at the wave frequency. The density oscillation beats with the oscillatory velocity to produce second harmonic current density, giving rise to resonant second harmonic radiation when the wave frequency is one-third of electron cyclotron frequency. The second harmonic field has azimuthal dependence as exp(iθ). The self-defocusing causes a reduction in the efficiency of harmonic generation.
Computation of ion drag force on a static spherical dust grain immersed in rf discharges
Authors: Ikkurthi V. R. , Matyash K. , Melzer A. , Schneider R.
Published: April 2009

The ion drag force on static spherical dust grains located in an argon rf discharge under typical laboratory experiment conditions has been computed using a three-dimensional particle-particle-particle-mesh code. Elastic and inelastic collisions have been included in the current model to obtain realistic rf discharge plasma conditions. The ion drag has been computed for various sizes of dust placed at different locations in the rf discharge under different gas pressures. The orbital drag force is typically found larger than the collection drag force. Ion-neutral collisions increase flux to the dust and hence the total drag force for collisional case is found larger than the collisionless case. Within the pressure range investigated, the drag forces do not vary much with pressure. The size dependence of the drag force is nonlinear and agrees well with the forces computed from the analytical models.
Shape invariance in prepotential approach to exactly solvable models
Authors: Ho Choon-Lin
Published: April 2009

In supersymmetric quantum mechanics, exact solvability of one-dimensional quantum systems can be classified only with an additional assumption of integrability, the so-called shape invariance condition. In this paper we show that in the prepotential approach we proposed previously, shape invariance is automatically satisfied and need not be assumed.
Structures of water-CO2 and methanol-CO2 cluster ions: [H2O•(CO2)n]+ and [CH3OH•(CO2)n]+ (n=1–7)
Authors: Inokuchi Yoshiya , Kobayashi Yusuke , Muraoka Azusa , Nagata Takashi , Ebata Takayuki
Published: April 2009

Infrared photodissociation (IRPD) spectra of [H2O•(CO2)n]+ and [CH3OH•(CO2)n]+ (n=1–7) are measured in the 1100–3800 cm−1 region. At the same time, the solvation characteristics in the clusters are investigated theoretically; the geometry optimization and the vibrational analysis are carried out for the [H2O•(CO2)n]+ (n=1–4) and the [CH3OH•(CO2)n]+ (n=1–3) ions at the MP2/6-31+G* level of theory. The IRPD spectrum of the [H2O•(CO2)1]+ ion shows the free OH and the hydrogen-bonded OH stretching bands of the H2O+ ion core and the antisymmetric CO stretching band of the solvent CO2 molecule, indicating that the solvent CO2 molecule is preferentially solvated to the H2O+ ion core via the O–H•••OCO hydrogen bond. In [H2O•(CO2)2]+, the free OH stretching band is not observed; both of the OH groups of the H2O+ ion core are hydrogen bonded to the solvent CO2 molecules. Spectral features of the IRPD spectra of [H2O•(CO2)n]+ (n=3–7) suggest that the third and the fourth CO2 molecules are bound to the oxygen atom of the H2O+ ion core, and that the first solvation shell of the H2O+ ion core becomes filled with four CO2 molecules. All the IRPD spectra of the [CH3OH•(CO2)n]+ (n=1–7) ions display the hydrogen-bonded OH stretching band of the CH3OH+ ion core, meaning that the solvent CO2 molecule is preferentially bonded to the OH group of the CH3OH+ ion core, similar to the case of [H2O•(CO2)n]+. Quantum chemical calculations for the [CH3OH•(CO2)1–3]+ ions demonstrate that the second and the third solvent CO2 molecules are bonded to the oxygen atom of the CH3OH+ ion core.
Heat generation in plasmonic nanostructures: Influence of morphology
Authors: Baffou G. , Quidant R. , Girard C.
Published: April 2009

Using the Green’s dyadic method, we investigated numerically the heat generation in gold nanoparticles when illuminated at their plasmonic resonance. Two kinds of structures are discussed—colloidal-like nanoparticles and lithographic planar nanostructures—putting special emphasis on the influence of the object’s morphology at a constant metal volume. The mechanism of heating is explained and discussed by mapping the heating power density inside the structures. This work aims at giving an intuitive and original understanding of the relative heating efficiency of a wide set of morphologies and could stand for a basis recipe to design optimized plasmonic nanoheaters.
A system for high-resolution depth-resolved optical imaging of fluorescence and absorption contrast
Authors: Yuan Baohong , Burgess Sean A. , Iranmahboob Amir , Bouchard Matthew B. , Lehrer Nicole , Bordier Clémence , Hillman Elizabeth M. C.
Published: April 2009

Laminar optical tomography (LOT) is a new three-dimensional in vivo functional optical imaging technique. Adopting a microscopy-based setup and diffuse optical tomography (DOT) imaging principles, LOT can perform both absorption- and fluorescence-contrast imaging with higher resolution (100–200 μm) than DOT and deeper penetration (2–3 mm) than laser scanning microscopy. These features, as well as a large field of view and acquisition speeds up to 100 frames per second, make LOT suitable for depth-resolved imaging of stratified tissues such as retina, skin, endothelial tissues and the cortex of the brain. In this paper, we provide a detailed description of a new LOT system design capable of imaging both absorption and fluorescence contrast, and present characterization of its performance using phantom studies.
Magnetically induced martensite transition in freestanding epitaxial Ni–Mn–Ga films
Authors: Heczko O. , Thomas M. , Niemann R. , Schultz L. , Fähler S.
Published: April 2009

The martensitic transformation in freestanding Ni–Mn–Ga films obtained by epitaxial growth on NaCl (001) is analyzed. A temperature-magnetic field phase diagram reveals that the martensitic phase, exhibiting a higher magnetization compared to austenite, is favored by an external field. A shift of martensite temperature of dT/dH=0.36 K/T is observed, in good agreement with the value expected from a Clausius–Clapeyron equation. The practicality and energy input for actuation using magnetically induced martensitic transition is compared with a magnetically induced reorientation of martensitic variants.
Properties and performance of cotton seed oil–diesel blends as a fuel for compression ignition engines
Authors: Murali Krishna B. , Mallikarjuna J. M.
Published: April 2009

This paper presents the evaluation of properties of straight vegetable cotton seed oil (CSO) and its blends with diesel fuel in various proportions to evaluate the performance and emission characteristics of a single cylinder compression ignition (CI) engine at constant speed of 1500rev∕min. Diesel and CSO oil fuel blends (10%, 30%, 50%, and 70%) were used to conduct engine performance and smoke emission tests at varying loads of 0%, 20%, 40%, 60%, 80%, and 100% of full load in addition to their straight CSO and diesel fuel. The performance parameters of brake specific energy consumption (BSFC), brake thermal efficiency (BTE), mechanical efficiency (ME), exhaust gas temperature (EGT), and exhaust emission (smoke) were evaluated to find the optimum CSO and diesel fuel blend. From the experimental results, the CSO10D90 blend fuel showed 3.7% reduction in BSFC, 1.7% increase in BTE, 6.7% increase in ME, and 21.7% reduction in the smoke emissions in comparison with conventional diesel operated engine. Finally, it is concluded that CSO10D90 can be used straight away in CI engines without any major modifications to the engine as it showed good performance and improved emission compared to all other fuels tested for the entire range of engine operation in comparison with diesel.
Scaling of the surface migration length in nanoscale patterned growth
Authors: Lee S. C. , Brueck S. R. J.
Published: April 2009

Scaling of the surface migration length in nanoscale patterned growth (NPG) is investigated as a function of the lateral dimension LM of a mask film fabricated on a substrate for selective epitaxy. By reducing LM below the surface migration length, any nucleation on the mask is avoided through the evaporation and surface out-diffusion of adatoms. The upper limit of LM for NPG LM,c corresponds to the surface migration length on the mask. An equation, identical to that for two-dimensional step-flow growth, is derived for NPG. However, the boundary conditions at the substrate-mask interface are affected by the surface potential difference and are different from those at the terrace edges of a homogeneous stepped surface. This results in a scaling law for surface migration length, which is proportional to the diffusion constant D and the critical incident flux Fc in the form (D/Fc)1/α with α decreasing from 4 to 2 as evaporation becomes dominant. NPG of GaAs for LM,c∼200 nm(α∼3.8) is demonstrated at ∼600 °C with molecular beam epitaxy.
General theory of excitation energy transfer in donor-mediator-acceptor systems
Authors: Kimura Akihiro
Published: April 2009

General theory of the excitation energy transfer (EET) in the case of donor-mediator-acceptor system was constructed by using generalized master equation (GME). In this theory, we consider the direct and indirect transitions in the EET consistently. Hence, our theory includes the quantum mechanical interference between the direct and indirect transitions automatically. Memory functions in the GME were expressed by the overlap integrals among the time-dependent emission spectrum of the donor, the absorption spectrum of the mediator, the time-dependent emission spectrum of the mediator, and the absorption spectrum of the acceptor. In the Markov limit of the memory functions, we obtained the rate of EET which consists of three terms due to the direct transition, the indirect transition, and the interference between them. We found that the interference works effectively in the limit of slow thermalization at the intermediate state. The formula of EET rate in this limit was expressed by the convolution of the EET interaction and optical spectra. The interference effect strongly depends on the width of the absorption spectrum of mediator molecule and the energy gap between the donor and the mediator molecules.
Relaxor behavior in nanostructured Pb(Zn1/3Nb2/3)O3–Pb(Fe1/2Nb1/2)O3–PbTiO3 ceramics
Authors: Amorín H. , Jiménez R. , Hungría T. , Castro A. , Algueró M.
Published: April 2009

There is controversy about the persistence or not of the relaxor state in the nanoscale. We report here the dielectric properties of nanostructured ceramics of the Pb(Zn1/3Nb2/3)O3–Pb(Fe1/2Nb1/2)O3–PbTiO3 ternary system with an average grain size of 20 nm, which clearly indicate that it persists as long as correlations among polar nanoregions are possible across grain boundaries. Two independent Vogel–Fulcher type relaxations are found in the materials that have a non-negligible width of the size distribution, which are proposed to be associated with intra- and intergranular correlations that show freezing at different temperatures.
A moment model with variable length scale for the motion of a vortex pair in two-dimensional incompressible flows
Authors: Matsumoto Yuko , Ueno Kazuyuki , Saito Tsunenari
Published: April 2009

A simple model for the motion of a vortex pair in two-dimensional inviscid flows is presented. In this model the motion of the vortex pair is expressed by a set of ordinary differential equations for the dipole moment, the length scale, and the centroid position. The length scale is the distance between the positive vortex and the negative vortex in the pair. A self-propelling velocity of the model vortex pair is introduced in response to a wide range of the length scale. If a background flow is a linear function of the position, the dipole moment and the length scale of the model are exact. This model works well for a separated vortex pair, although it is not applicable to an asymmetrically deformed vortex pair.
Stable field-induced ferrielectric liquid crystal phases in devices
Authors: Jaradat S. , Brimicombe P. D. , Southern C. , Siemianowski S. D. , DiMasi E. , Pindak R. , Gleeson H. F.
Published: April 2009

The field-induced transitions between ferri-, antiferro-, and ferroelectric liquid crystal phases are interesting because although there are only small thermodynamic differences between them, each of these phases has different electrical and optical properties. We report an irreversible field-induced transition from an antiferroelectric phase to the ferrielectric phase in a liquid crystal device, and compare it to a system in which the transition is reversible. The two systems differ mainly in their spontaneous polarization (120 nC cm−2 for the former and 60 nC cm−2 for the latter) while the optical tilt is comparable (29° and 25°, respectively). We explain the observed transitions based on the relative magnitudes of the discrete flexoelectric and spontaneous polarizations.
ZnO tetrapod p-n junction diodes
Authors: Newton Marcus C. , Shaikhaidarov Rais
Published: April 2009

ZnO nanocrystals hold the potential for use in a wide range of applications particularly in optoelectronics. We report on the fabrication of a highly sensitive p-n junction diode structure based on a single ZnO tetrapod shaped nanocrystal. This device shows a noted response to ultraviolet light with high internal gain. The high reponsivities we have observed exceed 104 A/W and are likely due to impact-ionization effects at the p-n junction interface.
Near-midgap deep levels in Al0.26Ga0.74N grown by metal-organic chemical vapor deposition
Authors: Sugawara Katsuya , Kotani Junji , Hashizume Tamotsu
Published: April 2009

A deep level with an activation energy of 1.0 eV in n-type Al0.26Ga0.74N grown by metal-organic chemical vapor deposition was detected by deep-level transient spectroscopy (DLTS) with a sampling time window of several seconds. The deep-level density was 6×1015 cm−3. At the temperatures around which the DLTS peaks were observed, capacitance transient was measured. Under the dark condition, a capacitance increase was observed, corresponding to the thermal emission of electrons from the level with 1.0 eV activation energy. After that, we observed a large capacitance increase under illumination with 2.3 eV photon energy. On the basis of potential simulation taking account of deep levels, we found that the photoinduced capacitance change arose from electron emission from additional near-midgap levels in energy ranging from EC−1.5 to EC−2.3 eV.
White phosphorescent organic light-emitting devices with dual triple-doped emissive layers
Authors: Eom Sang-Hyun , Zheng Ying , Wrzesniewski Edward , Lee Jaewon , Chopra Neetu , So Franky , Xue Jiangeng
Published: April 2009

We demonstrate high efficiency white organic light-emitting devices with two adjacent emissive layers each doped with three phosphorescent emitters (blue, green, and red). Efficient charge and exciton confinement is realized by employing charge transport layers with high triplet energy, leading to a maximum external quantum efficiency of (19±1)%. Using the p-i-n device structure, we have achieved a peak power efficiency of (40±2) lm/W and (36±2) lm/W at 100 cd/m2, a color rendering index of 79, and Commission Internationale de L’Eclairage coordinates of (0.37, 0.40) for the white light emission.
Near-field visualization of focal depth modulation by step corrugated plasmonic slits
Authors: Jia Baohua , Shi Haofei , Li Jiafang , Fu Yongqi , Du Chunlei , Gu Min
Published: April 2009

Nanometric plasmonic slits with stepped corrugations have been designed and fabricated to achieve plasmonic focusing and focal depth modulation. A scanning near-field optical microscope is employed to directly visualize the transmitted light from the slits. The near-field and far-field two-dimensional images taken at different planes parallel to the slit surface unambiguously demonstrated the focusing effect of the nanoslits. Furthermore, by forming stepped corrugations with either a concave or a convex profile on both sides of the slits, the phase of the transmitted beam can be effectively manipulated, thus allowing an accurate tuning of the focal depth.
Photoelectrochemical etching of p-type GaN heterostructures
Authors: Tamboli Adele C. , Hirai Asako , Nakamura Shuji , DenBaars Steven P. , Hu Evelyn L.
Published: April 2009

We have developed a method for photoelectrochemical etching of p-type semiconductors, including GaN, that relies on the built-in bandbending already inherent to optical devices. Electron-hole pairs are generated by filtered light in a buried small bandgap layer, and a pn junction separates the charge. Electrons are sent into the n-type layer, where they are extracted, and holes to the surface, where they participate in etching reactions. This technique is rapid and inexpensive, and it requires no applied bias or elevated temperatures. This technique has widespread applications to GaN optical devices where ion-damage-free etching or wide tunability of etch parameters is desired.
Hydrogenation of passivated aluminum with hydrogen fluid
Authors: Saitoh H. , Machida A. , Katayama Y. , Aoki K.
Published: April 2009

Hydrogenation conditions of passivated aluminum were examined in a pressure and temperature range of 6–10 GPa and 300–800 °C, respectively. The relationship between the hydrogenation reaction yields and holding time was analyzed by Johnson–Mehl–Avrami equation. An Avrami exponent n of 0.3 indicated that the reaction decreased with time due to the low diffusivity of hydrogen in AlH3. The oxide layer on passivated aluminum seemed to be partly removed or modified by pressure-temperature treatment above 6 GPa and 600 °C in hydrogen fluid. The hydrogenation pressure of 9 GPa for the passivated aluminum was reduced to 6 GPa.
Oscillation spectrums and beat phenomenon of a water droplet driven by electrowetting
Authors: Lai Mei-Feng , Lee Chiun-Peng , Liao Chun-Neng , Wei Zung-Hang
Published: April 2009

Droplet oscillation is an intriguing study that has inspired researches in many fields, and it becomes increasingly important on biochip applications. In this study, amplitude and phase spectrums and beat phenomenon of water droplet oscillation driven by ac electrowetting are studied using frequency scanning method. It is observed by experiment that at resonant frequencies of water droplets phase differences between the driving voltage and the droplet motion are ±90°. In addition, near resonant frequencies beat phenomenon of water droplet oscillation is also observed by experiment.
Atomic scale study of strain relaxation in Sn islands on Sn-induced Si(111)-(23×23) surface
Authors: Wang L. L. , Ma X. C. , Ning Y. X. , Ji S. H. , Fu Y. S. , Jia J. F. , Kelly K. F. , Xue Q. K.
Published: April 2009

Surface structure of the Sn islands 5 ML high, prepared on Si(111)-(23×23)-Sn substrate, is investigated by low temperature scanning tunneling microscopy/spectroscopy. Due to the elastic strain relaxation in the islands, the in-plane unit cell structure distorts and the apparent height of the surface atoms varies regularly to form an overall modulated strip structure. The quantum well states are observed to depend on the relative position within this structure, which implies the change of the surface chemical potential induced by the elastic strain relaxation as well.
Ultrathin CuSiN/p-SiC:H bilayer capping barrier for Cu/ultralow-k dielectric integration
Authors: Liu B. , Yang J. J. , Liu C. H. , Wang Y.
Published: April 2009

Different amount of porosity, which leads to the change in the dielectric constant of films from 4.1 to 2.9, can be created in amorphous SiC:H (a-SiC:H) films. The resultant CuSiN/a-SiC:H bilayered structure, as a copper capping barrier, shows improved thermal stability properties, lower leakage current density, and a low effective dielectric constant (keff) for the integrated ultralow-k a-SiOC:H film. This integrated film structure has the potential to meet the need of the 45 nm and lower technology node. Detailed characterizations of the integrated films were conducted to illustrate the possible mechanisms in the improvement of the film properties.
Single crystalline microribbons of perylo[1,12-b,c,d]selenophene for high performance transistors
Authors: Tan Lin , Jiang Wei , Jiang Lang , Jiang Shidong , Wang Zhaohui , Yan Shouke , Hu Wenping
Published: April 2009

Micrometer sized single crystalline ribbons of a Se-heterocyclic annelated perylene were prepared by drop casting and physical vapor transport techniques. The crystals of the Se-heterocyclic annelated perylene showed near planar molecular conformation, which regularly stacked along b-axis with Se⋯Se contacts at 3.49 Å. Single crystal transistors of individual ribbon were fabricated by “gold layer glue” technique. Over 90% transistors exhibited mobility >1.6 cm2 V−1 s−1, the highest mobility approaching 2.66 cm2 V−1 s−1. The top performance indicated the bright prospect of this material in organic electronics.
Tailoring the local density of states of nonradiative field at the surface of nanolayered materials
Authors: Ben-Abdallah Philippe , Joulain Karl , Drevillon Jérémie , Domingues Gilberto
Published: April 2009

The ability to artificially grow in a controllable manner at nanoscale, from modern deposition techniques, complex structural configurations made with metallic, polar, and semiconductor materials raises today the issue of the “best” achievable inner structure to tailor the near-field properties of a nanostructured medium. In the present work we make a step toward the rational design of these materials by reporting numerical experimentations demonstrating the possibility of identifying structural configurations of layered metallodielectric media specifically designed to control the electromagnetic density of states in the close vicinity of their surface. These results could find broad applications in near-field technologies.
Reproductive biotechniques in buffaloes (Bubalus bubalis): status, prospects and challenges
Authors: Singh B. , Chauhan M. S. , Singla S. K. , Gautam S. K. , Verma V. , Manik R. S. , Singh A. K. , Sodhi M. , Mukesh M.
Published: April 2009

The swamp buffalo holds tremendous potential in the livestock sector in Asian and Mediterranean countries. Current needs are the faster multiplication of superior genotypes and the conservation of endangered buffalo breeds. Recent advances in assisted reproductive technologies, including in vitro embryo production methodologies, offer enormous opportunities to not only improve productivity, but also to use buffaloes to produce novel products for applications to human health and nutrition. The use of molecular genomics will undoubtedly advance these technologies for their large-scale application and resolve the key problems currently associated with advanced reproductive techniques, such as animal cloning, stem cell technology and transgenesis. Preliminary success in the application of modern reproductive technologies warrants further research at the cellular and molecular levels before their commercial exploitation in buffalo breeding programmes.
Site-specific integration of adeno-associated virus involves partial duplication of the target locus
Authors: Henckaerts Els , Dutheil Nathalie , Zeltner Nadja , Kattman Steven , Kohlbrenner Erik , Ward Peter , Clément Nathalie , Rebollo Patricia , Kennedy Marion , Keller Gordon M. , Linden R. Michael
Published: April 2009

A variety of viruses establish latency by integrating their genome into the host genome. The integration event generally occurs in a nonspecific manner, precluding the prediction of functional consequences from resulting disruptions of affected host genes. The nonpathogenic adeno-associated virus (AAV) is unique in its ability to stably integrate in a site-specific manner into the human
MBS85
gene. To gain a better understanding of the integration mechanism and the consequences of
MBS85
disruption, we analyzed the molecular structure of AAV integrants in various latently infected human cell lines. Our study led to the observation that AAV integration causes an extensive but partial duplication of the target gene. Intriguingly, the molecular organization of the integrant leaves the possibility that a functional copy of the disrupted target gene could potentially be preserved despite the resulting rearrangements. A latently infected,
Mbs85
-targeted mouse ES cell line was generated to study the functional consequences of the observed duplication-based integration mechanism. AAV-modified ES cell lines continued to self-renew, maintained their multilineage differentiation potential and contributed successfully to mouse development when injected into blastocysts. Thus, our study reveals a viral strategy for targeted genome addition with the apparent absence of functional consequences.
Endocytosis is required for E-cadherin redistribution at mature
adherens
junctions
Authors: de Beco Simon , Gueudry Charles , Amblard François , Coscoy Sylvie
Published: April 2009

E-cadherin plays a key role at
adherens
junctions between epithelial cells, but the mechanisms controlling its assembly, maintenance, and dissociation from junctions remain poorly understood. In particular, it is not known to what extent the number of E-cadherins engaged at junctions is regulated by endocytosis, or by dissociation of adhesive bonds and redistribution within the membrane from a pool of diffusive cadherins. To determine whether cadherin levels at mature junctions are regulated by endocytosis or dissociation and membrane diffusion, the dynamics of E-cadherin were quantitatively analyzed by a new approach combining 2-photon fluorescence recovery after photobleaching (FRAP) and fast 3D wide-field fluorescence microscopy. Image analysis of fluorescence recovery indicates that most E-cadherin did not diffuse in the membrane along mature junctions, but followed a first order turn-over process that was rate-limited by endocytosis. In confluent cultures of MCF7 or MDCK cells, stably expressed EGFP-E-cadherin was rapidly recycled with spatially uniform kinetics (50 s in MCF7 and 4 min in MDCK). In addition, when endocytosis was pharmacologically blocked by dynasore or MiTMAB, no fluorescence recovery was observed, suggesting that no endocytosis-independent membrane redistribution was occurring. Our data show that membrane redistribution of E-cadherin molecules engaged in mature junctions requires endocytosis and subsequent exocytosis, and lead to the notion that E-cadherins engaged at junctions do not directly revert to free membrane diffusion. Our results point to the possibility that a direct mechanical coupling between endocytosis efficiency and cadherin-mediated forces at junctions could help to regulate intercellular adhesion and locally stabilize epithelia.
Examination of the contributions of size and avidity to the neutralization mechanisms of the anti-HIV antibodies b12 and 4E10
Authors: Klein Joshua S. , Gnanapragasam Priyanthi N. P. , Galimidi Rachel P. , Foglesong Christopher P. , West Anthony P. , Bjorkman Pamela J.
Published: April 2009

Monoclonal antibodies b12 and 4E10 are broadly neutralizing against a variety of strains of the human immunodeficiency virus type 1 (HIV-1). The epitope for b12 maps to the CD4-binding site in the gp120 subunit of HIV-1's trimeric gp120-gp41 envelope spike, whereas 4E10 recognizes the membrane-proximal external region (MPER) of gp41. Here, we constructed and compared a series of architectures for the b12 and 4E10 combining sites that differed in size, valency, and flexibility. In a comparative analysis of the ability of the b12 and 4E10 constructs to neutralize a panel of clade B HIV-1 strains, we observed that the ability of bivalent constructs to cross-link envelope spikes on the virion surface made a greater contribution to neutralization by b12 than by 4E10. Increased distance and flexibility between antibody combining sites correlated with enhanced neutralization for both antibodies, suggesting restricted mobility for the trimeric spikes embedded in the virion surface. The size of a construct did not appear to be correlated with neutralization potency for b12, but larger 4E10 constructs exhibited a steric occlusion effect, which we interpret as evidence for restricted access to its gp41 epitope. The combination of limited avidity and steric occlusion suggests a mechanism for evading neutralization by antibodies that target epitopes in the highly conserved MPER of gp41.
Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development
Authors: Ji Zhe , Lee Ju Youn , Pan Zhenhua , Jiang Bingjun , Tian Bin
Published: April 2009

The 3′ untranslated regions (3′ UTRs) of mRNAs contain
cis
-acting elements for posttranscriptional regulation of gene expression. Here, we report that mouse genes tend to express mRNAs with longer 3′ UTRs as embryonic development progresses. This global regulation is controlled by alternative polyadenylation and coordinates with initiation of organogenesis and aspects of embryonic development, including morphogenesis, differentiation, and proliferation. Using myogenesis of C2C12 myoblast cells as a model, we recapitulated this process in vitro and found that 3′ UTR lengthening is likely caused by weakening of mRNA polyadenylation activity. Because alternative 3′ UTR sequences are typically longer and have higher AU content than constitutive ones, our results suggest that lengthening of 3′ UTR can significantly augment posttranscriptional control of gene expression during embryonic development, such as microRNA-mediated regulation.
Newcomer insulin secretory granules as a highly calcium-sensitive pool
Authors: Pedersen Morten Gram , Sherman Arthur
Published: April 2009

Insulin secretion is biphasic in response to a step in glucose stimulation. Recent experiments suggest that 2 different mechanisms operate during the 2 phases, with transient first-phase secretion due to exocytosis of docked granules but the second sustained phase due largely to newcomer granules. Another line of research has shown that there exist 2 pools of releasable granules with different Ca
2+
sensitivities. An immediately releasable pool (IRP) is located in the vicinity of Ca
2+
channels, whereas a highly Ca
2+
-sensitive pool (HCSP) resides mainly away from Ca
2+
channels. We extend a previous model of exocytosis and insulin release by adding an HCSP and show that the inclusion of this pool naturally leads to insulin secretion mainly from newcomer granules during the second phase of secretion. We show that the model is compatible with data from single cells on the HCSP and from stimulation of islets by glucose, including L- and R-type Ca
2+
channel knockouts, as well as from Syntaxin-1A-deficient cells. We also use the model to investigate the relative contribution of calcium signaling and pool depletion in controlling biphasic secretion.
Traditional waveform based spike sorting yields biased rate code estimates
Authors: Ventura Valérie
Published: April 2009

Much of neuroscience has to do with relating neural activity and behavior or environment. One common measure of this relationship is the firing rates of neurons as functions of behavioral or environmental parameters, often called tuning functions and receptive fields. Firing rates are estimated from the spike trains of neurons recorded by electrodes implanted in the brain. Individual neurons' spike trains are not typically readily available, because the signal collected at an electrode is often a mixture of activities from different neurons and noise. Extracting individual neurons' spike trains from voltage signals, which is known as spike sorting, is one of the most important data analysis problems in neuroscience, because it has to be undertaken prior to any analysis of neurophysiological data in which more than one neuron is believed to be recorded on a single electrode. All current spike-sorting methods consist of clustering the characteristic spike waveforms of neurons. The sequence of first spike sorting based on waveforms, then estimating tuning functions, has long been the accepted way to proceed. Here, we argue that the covariates that modulate tuning functions also contain information about spike identities, and that if tuning information is ignored for spike sorting, the resulting tuning function estimates are biased and inconsistent, unless spikes can be classified with perfect accuracy. This means, for example, that the commonly used peristimulus time histogram is a biased estimate of the firing rate of a neuron that is not perfectly isolated. We further argue that the correct conceptual way to view the problem out is to note that spike sorting provides information about rate estimation and vice versa, so that the two relationships should be considered simultaneously rather than sequentially. Indeed we show that when spike sorting and tuning-curve estimation are performed in parallel, unbiased estimates of tuning curves can be recovered even from imperfectly sorted neurons.
Insulin-modulated Akt subcellular localization determines Akt isoform-specific signaling
Authors: Gonzalez Eva , McGraw Timothy E.
Published: April 2009

The 3 Akt protein kinase isoforms have critical and distinct functions in the regulation of metabolism, cell growth, and apoptosis, yet the mechanisms by which their signaling specificity is achieved remain largely unclear. Here, we investigated potential mechanisms underlying Akt isoform functional specificity by using Akt2-specific regulation of glucose transport in insulin-stimulated adipocytes as a model system. We found that insulin activates both Akt1 and Akt2 in adipocytes, but differentially regulates the subcellular distribution of these Akt isoforms. The greater accumulation of Akt2 at the plasma membrane (PM) of insulin-stimulated adipocytes correlates with Akt2-specific regulation of the trafficking of the GLUT4 glucose transporter. Consistent with this pattern, Akt constructs that do not accumulate at the PM to the same degree as Akt2 fail to regulate GLUT4 translocation to the PM, whereas enhancement of Akt1 PM association through mutation in Akt1 PH domain is sufficient to overcome Akt-isoform specificity in GLUT4 regulation. Indeed, we found that this distinct insulin-induced PM accumulation of Akt kinases is translated into a differential regulation by the Akt isoforms of AS160, a RabGAP that regulates GLUT4 trafficking. Our data show that Akt2 specifically regulates AS160 phosphorylation and membrane association providing molecular basis for Akt2 specificity in the modulation of GLUT4 trafficking. Together, our findings reveal the stimulus-induced subcellular compartmentalization of Akt kinases as a mechanism contributing to specify Akt isoform functions.
A transcriptomic analysis of superhybrid rice
LYP9
and its parents
Authors: Wei Gang , Tao Yong , Liu Guozhen , Chen Chen , Luo Renyuan , Xia Hongai , Gan Qiang , Zeng Haipan , Lu Zhike , Han Yuning , Li Xiaobing , Song Guisheng , Zhai Hongli , Peng Yonggang , Li Dayong , Xu Honglin , Wei Xiaoli , Cao Mengliang , Deng Huafeng , Xin Yeyun , Fu Xiqin , Yuan Longping , Yu Jun , Zhu Zhen , Zhu Lihuang
Published: April 2009

By using a whole-genome oligonucleotide microarray, designed based on known and predicted
indica
rice genes, we investigated transcriptome profiles in developing leaves and panicles of superhybrid rice
LYP9
and its parental cultivars
93-11
and
PA64s
. We detected 22,266 expressed genes out of 36,926 total genes set collectively from 7 tissues, including leaves at seedling and tillering stages, flag leaves at booting, heading, flowering, and filling stages, and panicles at filling stage. Clustering results showed that the F1 hybrid's expression profiles resembled those of its parental lines more than that which lies between the 2 parental lines. Out of the total gene set, 7,078 genes are shared by all sampled tissues and 3,926 genes (10.6% of the total gene set) are differentially expressed genes (DG). As we divided DG into those between the parents (DG
PP
) and between the hybrid and its parents (DG
HP
), the comparative results showed that genes in the categories of energy metabolism and transport are enriched in DG
HP
rather than in DG
PP
. In addition, we correlated the concurrence of DG and yield-related quantitative trait loci, providing a potential group of heterosis-related genes.
Hv1 proton channels are required for high-level NADPH oxidase-dependent superoxide production during the phagocyte respiratory burst
Authors: Ramsey I. Scott , Ruchti Evelyne , Kaczmarek J. Stefan , Clapham David E.
Published: April 2009

Granulocytes generate a “respiratory burst” of NADPH oxidase-dependent superoxide anion (O
2
−∙
) production that is required for efficient clearance of bacterial pathogens. Hv1 mediates a voltage-gated H
+
channel activity that is proposed to serve a charge-balancing role in granulocytic phagocytes such as neutrophils and eosinophils. Using mice in which the gene encoding Hv1 is replaced by β-Geo reporter protein sequence, we show that Hv1 expression is required for measurable voltage-gated H
+
current in unstimulated phagocytes. O
2
−∙
production is substantially reduced in the absence of Hv1, suggesting that Hv1 contributes a majority of the charge compensation required for optimal NADPH oxidase activity. Despite significant reduction in superoxide production,
Hv1
−/−
mice are able to clear several types of bacterial infections.
Pitching it right? Selection and learning at a music conservatoire
Authors: Burt‐Perkins Rosie , Mills Janet
Published: April 2009

This article focuses on an oversubscribed UK higher education music conservatoire that centres its selection procedures on individual performance auditions. In this mixed‐method study, centrally‐held assessment scores are used to show that A‐level music grades are a more effective predictor of final degree result than performance at audition. This context is then used to consider the learning of two students at the conservatoire who defy the expectations implied by the statistical results. Through six interviews with each student, their stories are probed through the lens of their trajectories of participation. Drawing on the notion of expansive and restrictive learning, the role that depth and breadth plays in learning to perform is unpacked, and it is suggested that both may be of central importance in shaping musical expertise. The authors discuss the results in terms of the specific challenges that the conservatoire faces in broadening its access, and consider the implications for learners of musical performance.
Diel migration and swimbladder resonance of small fish: some implications for analyses of multifrequency echo data
Authors: Godø Olav Rune , Patel Ruben , Pedersen Geir
Published: April 2009

Godø, O. R., Patel, R., and Pedersen, G. 2009. Diel migration and swimbladder resonance of small fish: some implications for analyses of multifrequency echo data. – ICES Journal of Marine Science, 66: 1143–1148. Many fish with swimbladders exhibit diel vertical migrations (DVM). Ascents and descents of hundreds of metres occur, and altered swimbladder volume and buoyancy can result from incomplete secretion and resorption of gas. When acoustic observations are made near the resonance frequency of the swimbladder, the estimated fish biomass can be positively biased. When multiple-frequency echosounders are used, the frequency response of the backscatter might vary temporally and spatially and compromise the effectiveness of conventional target-identification methods. In this paper, variations in backscatter from mesopelagic fish are studied using data collected west of the British Isles with a five-frequency echosounder (Simrad EK60). Two acoustic layers, one dominated by pearlsides (Maurolicus muelleri) and the other by myctophids (Myctophidae), were monitored during their DVM. The frequency responses of the layers changed systematically, mainly characterized by increases in the nautical-area-backscattering coefficient (sA) values at 18 kHz relative to those at 38 kHz. This could have been caused by changes in the resonance frequencies of fish swimbladders, as they expanded and contracted during ascent and descent. Two sA maxima in the myctophids layer suggest the presence of two types of target with different scattering characteristics. Models of sound scatter from myctophid swimbladders suggest that these peaks have resulted from resonance scattering. The sA at 18 kHz attributed to M. muelleri also peaked, but at the maximum depth of their distribution. Spatial and temporal changes in the frequency responses of fish should be taken into account when pelagic fish communities are surveyed with multiple-frequency echosounders.
microRNA-24a is required to repress apoptosis in the developing neural retina
Authors: Walker James C. , Harland Richard M.
Published: April 2009

Programmed cell death is important for the proper development of the retina, and microRNAs (miRNAs) may be critical for its regulation. Here, we report that miR-24a is expressed in the neural retina and is required for correct eye morphogenesis in Xenopus. Inhibition of miR-24a during development causes a reduction in eye size due to a significant increase in apoptosis in the retina, whereas overexpression of miR-24a is sufficient to prevent apoptosis. We show that miR-24a negatively regulates the proapoptotic factors caspase9 and apaf1, demonstrating a role for miRNAs in the regulation of apoptosis during normal development.
Dynamic reprogramming of transcription factors to and from the subtelomere
Authors: Mak H. Craig , Pillus Lorraine , Ideker Trey
Published: April 2009

Transcription factors are most commonly thought of as proteins that regulate expression of specific genes, independently of the order of those genes along the chromosome. By screening genome-wide chromatin immunoprecipitation (ChIP) profiles in yeast, we find that more than 10% of DNA-binding transcription factors concentrate at the subtelomeric regions near to chromosome ends. None of the proteins identified were previously implicated in regulation at telomeres, yet genomic and proteomic studies reveal that a subset of factors show many interactions with established telomere binding complexes. For many factors, the subtelomeric binding pattern is dynamic and undergoes flux toward or away from the telomere as physiological conditions shift. We find that subtelomeric binding is dependent on environmental conditions and correlates with the induction of gene expression in response to stress. Taken together, these results underscore the importance of genome structure in understanding the regulatory dynamics of transcriptional networks.