bluuebunny/crossref_metadata_2025 huggingface dataset:
A procedure for computing accurate ab initio quartic force fields: Application to HO2+ and H2O
Authors: Huang Xinchuan , Lee Timothy J.
Published: July 2008

A procedure for the calculation of molecular quartic force fields (QFFs) is proposed and investigated. The goal is to generate highly accurate ab initio QFFs that include many of the so-called “small” effects that are necessary to achieve high accuracy. The small effects investigated in the present study include correlation of the core electrons (core correlation), extrapolation to the one-particle basis set limit, correction for scalar relativistic contributions, correction for higher-order correlation effects, and inclusion of diffuse functions in the one-particle basis set. The procedure is flexible enough to allow for some effects to be computed directly, while others may be added as corrections. A single grid of points is used and is centered about an initial reference geometry that is designed to be as close as possible to the final ab initio equilibrium structure (with all effects included). It is shown that the least-squares fit of the QFF is not compromised by the added corrections, and the balance between elimination of contamination from higher-order force constants while retaining energy differences large enough to yield meaningful quartic force constants is essentially unchanged from the standard procedures we have used for many years. The initial QFF determined from the least-squares fit is transformed to the exact minimum in order to eliminate gradient terms and allow for the use of second-order perturbation theory for evaluation of spectroscopic constants. It is shown that this step has essentially no effect on the quality of the QFF largely because the initial reference structure is, by design, very close to the final ab initio equilibrium structure. The procedure is used to compute an accurate, purely ab initio QFF for the H2O molecule, which is used as a benchmark test case. The procedure is then applied to the ground and first excited electronic states of the HO2+ molecular cation. Fundamental vibrational frequencies and spectroscopic constants from these highly accurate QFFs are compared and contrasted with previous experiment and theory. It is concluded that the spectroscopic constants determined for the X3A″ and A1A′ states of HO2+ are the most accurately available.
Estimating the temperature dependence of the dielectric constant of multiphased mixed crystals
Authors: Katsika-Tsigourakou Vassiliki , Vassilikou-Dova Aglaia
Published: July 2008

Measurements of the dielectric constant of multiphased binary and ternary mixed alkali halides, which have found a multitude of applications in optical and electronic devices, have been recently reported in the temperature range from room temperature to 423 K. It was found that the temperature variation in the binary mixed crystal (NaCl)0.587 (KBr)0.413 is drastically larger than in any other. We show that this variation can be quantitatively reproduced by means of a simple model, which does not contain any adjustable parameter and solely makes use of the properties of the end members, viz., NaCl and KBr.
Comparison of single neuron models in terms of synchronization propensity
Authors: Sungar N. , Allaria E. , Leyva I. , Arecchi F. T.
Published: July 2008

A plausible model for coherent perception is the synchronization of chaotically distributed neural spike trains over wide cortical areas. A recently introduced propensity criterion provides a tool for a quantitative comparison of different neuron models in terms of their ability to synchronize to an applied perturbation. We explore the propensity of several systems and indicate the requirements to be satisfied by a plausible candidate for modeling neuronal activity. Our results show that the conflicting requirements of stability and sensitivity leading to high propensity to synchronization can be satisfied by a strongly nonuniform attractor made of two distinct regions: a saddle focus plus a sufficiently separated saddle node.
Radial characterization of the electron energy distribution in a helicon source terminated by a double layer
Authors: Takahashi Kazunori , Charles Christine , Boswell Rod , Hatakeyama Rikizo
Published: July 2008

Electron energy probability functions (EEPFs) are measured across the radius (0⩽r<6.85cm) of a low pressure (0.3mTorr) helicon plasma source terminated by a current-free double layer. The source field of about 130G is generated using a Helmholtz coil pair and the radio frequency (rf) power is maintained at 250W. All EEPFs exhibit a distribution with a temperature Tebulk out to a break energy εbreak and a relatively depleted distribution for higher energies with a lower temperature Tetail. Tebulk and Tetail are about 8eV and 5eV, respectively, for r<4cm and increase up to about 14eV and 9eV near the source wall, i.e., near the rf antenna. εbreak is found to correspond to the potential drop of the double layer for the central part of the source and to the sheath potential near the wall.
High-performance C60 thin-film field-effect transistors with parylene gate insulator
Authors: Kubozono Yoshihiro , Haas Simon , Kalb Wolfgang L. , Joris Pierre , Meng Fabian , Fujiwara Akihiko , Batlogg Bertram
Published: July 2008

C 60 field-effect transistors (FETs) have been fabricated with parylene gate dielectric on Si∕SiO2, on polyethylene terephthalate, and commercially available transparent sheet substrates. The best performance of the C60 FET device is achieved with parylene as gate dielectric: field-effect mobility of 0.41cm2V−1s−1 and on-off ratio of ∼107. The excellent FET characteristics are recorded without any annealing, and the devices were kept in He atmosphere after an exposure to air. This result suggests the parylene gate dielectric to be highly H2O repellent. The mechanical flexibility and air-exposure effect were studied for the C60 FET with parylene gate dielectric.
Apparent thickness dependence of mobility in organic thin films analyzed by Gaussian disorder model
Authors: Chu Ta-Ya , Song Ok-Keun
Published: July 2008

The authors report the investigation of thickness dependence of mobility in N, N′-bis(naphthalen-1-yl)-N, N′-bis(phenyl) benzidine (NPB), and tris(8-hydroxyquinoline) aluminum (Alq3) thin films based on the Gaussian disorder model. The energetic disorder of 118 meV at thickness of 50 nm is larger than that of 88 meV at 300 nm in NPB. From the mobility prefactor and intersite distance, the carrier hopping distance between NPB molecules of thinner film is larger than that of thicker film. It suggests that the lower mobility at thinner thickness of NPB is affected by not only the interfacial trap states but also the molecular arrangement on the surface. Contrary to the results of NPB, the energetic disorder of Alq3 at various thicknesses was obtained to be 150±7 meV that is almost independent of the thickness of film. The small changes in hopping distance of Alq3 at different thicknesses have been observed, and this trend is clearly different from the case of NPB.
Hydrogen sensing properties of a Pt-oxide-GaN Schottky diode
Authors: Tsai Yan-Ying , Lin Kun-Wei , Chen Huey-Ing , Liu I-Ping , Hung Ching-Wen , Chen Tzu-Pin , Tsai Tsung-Han , Chen Li-Yang , Chu Kuei-Yi , Liu Wen-Chau
Published: July 2008

The interesting hydrogen sensing properties of a Pt-oxide-GaN metal-oxide-semiconductor-type Schottky diode are comprehensively studied and demonstrated. In the hydrogen-containing environment, the shift in current-voltage curves and decrease in turn-on voltage are found to be caused by the lowering of Schottky barrier height. Also, the corresponding series resistance is decreased from 191.8 (in air) to 155.3 Ω (for a 9970 ppm H2/air gas) at 30 °C. As the carrier gas is replaced by a nitrogen gas, a significant variation of 0.32 V and 19.56 Ω in the turn-on voltage Von and series resistance Rs values, respectively, is obtained at 30 °C, even at an extremely low hydrogen concentration of 4.3 ppm H2/N2. Since the oxygen atoms will be dissolved on the Pt metal surface and react with hydrogen atoms by the formation of hydroxyl and water, the number of adsorbed hydrogen atoms on the Pt surface is reduced. Moreover, the shorter response time constant and the larger initial rate of current density variation are found even at room temperature.
Mechanically robust nanoparticle stabilized transparent liquid marbles
Authors: Bhosale Prasad S. , Panchagnula Mahesh V. , Stretz Holly A.
Published: July 2008

Optically transparent liquid marbles were made from water and glycerol drops embedded in surface-treated fumed silica nanoparticles. The mechanical robustness of such liquid marbles is shown to be greater than similar marbles made from microparticulate poly(tetrafluoroethylene), both under compressive and tensile loading conditions. Using liquid evaporation data and environmental scanning electron microscope images, we demonstrate that their robustness may be attributed to a nanoparticulate elastic thin film that self-assembles on the liquid-vapor interface.
Upconversion photoluminescence of CdS nanocrystals in polymeric film
Authors: He Jun , Scholes Gregory D. , Qu Y. L. , Ji Wei
Published: July 2008

We report on nonlinear upconversion photoluminescence (PL) of CdS nanocrystals (NCs) embedded in a polymeric film. The CdS NCs of 2 nm radius are synthesized by an ion exchange method and highly concentrated in the two layers near the surfaces of a freestanding Nafion film. We observed the differences between the two-photon and one-photon excited PL emissions. The two-photon absorption cross section and quantum yield of CdS NCs were measured with femtosecond laser pulses at 800 nm excitation. The origin of PL, optical nonlinearity, and the figure of merit for optical switching have been discussed.
A miniature effusion cell for the vacuum deposition of organic solids with low vapor pressures in surface science studies
Authors: Yoshinobu Jun , Mukai Kozo , Katayama Tetsuo
Published: July 2008

A miniature effusion cell for the vacuum deposition of volatile organic solids with low vapor pressures has been fabricated and used in surface science studies. The effusion cell is designed to operate at up to 200°C under ultrahigh vacuum (UHV) conditions. The size of this cell is so small that it is attached to the top of a transfer rod and can be introduced from a subchamber into a main UHV chamber (retrievable). In addition, the small heat capacity of this cell means rapid heating and cooling rates. The advantages of this evaporator are its simplicity of design and ease of fabrication, assembly, and operation.
Effects of the compensation level on the carrier lifetime of crystalline silicon
Authors: Dubois S. , Enjalbert N. , Garandet J. P.
Published: July 2008

This study focuses on the evolution of the carrier lifetime with the compensation level in crystalline silicon. Especially we show that an increase in the compensation level reduces the recombination strength of doping species and of some metal impurities. These theoretical results are confirmed by the chemical and electrical characterizations of strongly compensated multicrystalline silicon wafers. These results are of paramount importance since an accurate control of the compensation level can lead to strong improvements in silicon solar cells efficiencies.
Optical reduction of low frequency noise in cryogenic GaAs junction field effect transistor
Authors: Fujiwara M. , Nagata H. , Matsuo H. , Sasaki M.
Published: July 2008

We demonstrated optical low frequency noise reduction in a n-type SONY GaAs junction field effect transistor (JFET) (gate width: 5μm; length: 1μm) operating at 4.2K. At 1Hz, a 6dB decrease and a 10dB increase in noise were observed when the JFET (band gap: 1.51eV) was illuminated by light with wavelengths of 1650 and 1550nm, respectively, for a drain voltage of 0.5V and drain current of 0.25μA. When the drain current was 0.5μA, 1650nm illumination increased the noise; moreover, hysteretic behavior in response to the illumination was also observed. These results show that deep level trapped charges apparently affect low frequency noise, which can be controlled by illumination using photons whose energies are below the band gap energy at cryogenic temperatures.
Ultrasensitive immunoassay for prostate specific antigen using scanning tunneling microscopy-based electrical detection
Authors: Choi Jeong-Woo , Oh Byung-Keun , Jang Yong-Hark , Kang Da-Yeon
Published: July 2008

We characterized a vertically configured electrical detection system that used scanning tunneling microscopy (STM) to detect antigen-antibody binding. This technique could be used to easily construct a multiple measurement system in a protein chip. We utilized immunocomplexes comprised of our model protein, prostate specific antigen (PSA), corresponding antibody fragments, and gold nanoparticle-antibody conjugates. The electrical tunneling current between the STM tip and these complexes exhibited a peaklike pulse, the frequency of which depended on the surface density of the bound complexes. We could therefore quantitatively measure PSA concentrations as low as 10fg∕mL using periodogram analysis of this peak frequency.
Lateral epitaxial growth of germanium on silicon oxide
Authors: Cammilleri V. D. , Yam V. , Fossard F. , Renard C. , Bouchier D. , Fazzini P. F. , Ortolani L. , Houdellier F. , Hÿtch M.
Published: July 2008

We have developed a method using local oxidation on silicon to create nanoscale silicon seeds for the lateral epitaxial overgrowth of germanium on silicon oxide. The germanium growth starts selectively from silicon seed lines, proceeds by wetting the SiO2 layer and coalesces without formation of grain boundary. Analysis by high resolution transmission electron microscopy have shown that Ge layers grown above silicon oxide are perfectly monocrystalline and are free of defect. The only detected defects are situated at the Ge∕Si interface. Geometrical phase analyses of the microscopy images have shown that the Ge layer is fully relaxed and homogeneous.
Structure and mechanical properties of osmium carbide: First-principles calculations
Authors: Guo Xiaoju , Xu Bo , He Julong , Yu Dongli , Liu Zhongyuan , Tian Yongjun
Published: July 2008

Synthesized osmium carbide (OsC) was reported in tungsten carbide (WC) structure, inconsistent with recent theoretical finding that the WC-structured OsC does not satisfy the mechanical stability criteria. The first-principles calculations of osmium carbide for nine hypothetical structures indicate that OsC with FeSi structure, NiAs structure, and CoSn structure satisfy the mechanical stability criteria. Based on the simulated x-ray diffraction data of WC structure and NiAs structure, we consider that the experimentally synthesized OsC is of the NiAs structure rather than the WC structure. In addition, the Os–C bond in NiAs-structured OsC has metallic feature, responsible for low hardness.
p
-channel thin-film transistor using p-type oxide semiconductor, SnO
Authors: Ogo Yoichi , Hiramatsu Hidenori , Nomura Kenji , Yanagi Hiroshi , Kamiya Toshio , Hirano Masahiro , Hosono Hideo
Published: July 2008

This paper reports that among known p-type oxide semiconductors, tin monoxide (SnO) has a high hole mobility and produces good p-type oxide thin-film transistors (TFTs). Device-quality SnO films were grown epitaxially on (001) yttria-stabilized zirconia substrates at 575°C by pulsed laser deposition. These exhibited a Hall mobility of 2.4cm2V−1s−1 at room temperature. Top-gated TFTs, using epitaxial SnO channels, exhibited field-effect mobilities of 1.3cm2V−1s−1, on/off current ratios of ∼102, and threshold voltages of 4.8V.
Elasticity of ideal single-walled carbon nanotubes via symmetry-adapted tight-binding objective modeling
Authors: Zhang D.-B. , Dumitrică T.
Published: July 2008

The elastic response for a large catalog of carbon nanotubes subjected to axial and torsional strain is derived from atomistic calculations that rely on an accurate tight-binding description of the covalent binding. The application of the computationally expensive quantum treatment is possible due to the simplification in the number of atoms introduced by accounting for the helical and angular symmetries exhibited by the elastically deformed nanotubes. The elasticity of nanotubes larger than ∼1.25nm in diameter can be represented with an isotropic elastic continuum.
The use of thermal initiator to make organic bulk heterojunction solar cells with a good percolation path
Authors: Tong S. W. , Zhang C. F. , Jiang C. Y. , Ling Q. D. , Kang E. T. , Chan D. S. H. , Zhu Chunxiang
Published: July 2008

A simple method is developed to make an interpenetrating network of poly(3-hexylthiophene-2,5-diyl) (P3HT) and fullerene (C60) by mixing P3HT solution with a thermal initiator 2,2′-azobis(isobutyronitrile) (AIBN). After mild annealing, the release of nitrogen from AIBN increases the roughness of P3HT dramatically. Significant photoluminescence quenching between the roughened donor P3HT and overlaying acceptor C60 is related to the significant increment of donor-acceptor interfacial areas. Based on this interpenetrated network of P3HT/C60, more than threefold increase in the photovoltaic efficiency of devices is achieved compared with bilayer structure. Fill factor is also improved, implying good percolation path in this heterojunction structure.
Electron mobility in N-polar GaN/AlGaN/GaN heterostructuress
Authors: Brown David F. , Rajan Siddharth , Keller Stacia , Hsieh Yun-Hao , DenBaars Steven P. , Mishra Umesh K.
Published: July 2008

The drift mobility of two-dimensional electron gasses in N-polar GaN/AlGaN/GaN heterostructures was measured with capacitance and resistance measurements using gated transmission line method structures. A decrease in mobility with increasing reverse bias of the gate was observed. A variational wave function was used to calculate the mobility limited by optical phonon, alloy disorder, and ionized impurity scattering as a function of gate bias, and found to match the experimental data well. Three distinct regimes where phonon, alloy, and impurity scattering are dominant were observed.
Scale bridging method to characterize mechanical properties of nanoparticle/polymer nanocomposites
Authors: Yang Seunghwa , Cho Maenghyo
Published: July 2008

Multiscale analysis to characterize the size effect of silica nanoparticles on the mechanical properties of nanoparticle/polymer nanocomposites is developed and verified through a molecular dynamics simulation and continuum micromechanics model. In the micromechanics model, the particle-matrix interface mechanical property is incorporated, and the thickness and elastic properties of the interface are extracted from the atomistic structures. The proposed multiscale micromechanics model accurately reflects the size effect of the nanoparticle. The prediction by the current multiscale model at various volume fractions is compared to the results of the molecular dynamics simulations in order to validate the present multiscale analysis model.
Current percolation in ultrathin channel nanocrystalline silicon transistors
Authors: Guo X. , Silva S. R. P. , Ishii T.
Published: July 2008

The ultrathin channel nanocrystalline silicon transistor shows greatly improved switching performance and has demonstrated its candidacy for low power applications. In this work, by careful observation of the current-voltage and threshold voltage characteristics, we find that current percolation occurs when the channel is thinner than 3.0nm due to strong quantum confinement induced large potential variations over the channel. We show that the device channel width must be at least 0.3μm to avoid percolative “pinch off” for 0.5μm channel length devices. Theoretical analysis performed on the devices agrees well with the experimental data and provides important guidelines to model and optimize the devices for circuit design.
Enhanced directional optical transmission
Authors: Dobrzynski L. , Akjouj A.
Published: July 2008

The system presented here enables transmission of almost all the light intensities injected in four input channels into one output channel. It is conceived in the form of a metallic wire with one central hole and four other holes parallel to the central one. The incident light is injected in the four external holes and transmitted to the central one, thanks to appropriate resonant mechanisms between the central hole and each of the four other holes. Each of these mechanisms is constituted by two coupled cavities.
Monitoring leaf pigment status with hyperspectral remote sensing in wheat
Authors: Feng Wei , Yao Xia , Tian Yongchao , Cao Weixing , Zhu Yan
Published: July 2008

Leaf pigment status within a canopy is a key index for evaluating photosynthetic efficiency and nutritional stress in crop plants. Non-destructive and quick assessment of leaf pigment status is needed for growth diagnosis, yield prediction, and nitrogen (N) management in crop production. The objectives of this study were to analyse quantitative relationships of leaf pigment concentration on a dry weight basis and leaf pigment density per unit soil area to ground-based canopy hyperspectral reflectance and derivative parameters, and to establish estimation models for real-time monitoring of leaf pigment status with key hyperspectral bands and indices in wheat (Triticum aestivum L.). Two field experiments were conducted with different N application rates and wheat cultivars across two growing seasons, and time-course measurements were taken on canopy hyperspectral reflectance over 350−2500 nm, leaf pigment concentrations, and leaf dry weights under the various treatments at different growth stages. The results showed that different pigment concentrations and densities of chlorophyll a (Chla), chlorophyll b (Chlb), total chlorophyll (Chla+b), and carotenoids (Car) in two cultivars, Ningmai 9 (low grain protein concentration) and Yumai 34 (high grain protein concentration), tended to increase with increasing N rates, and differed with genotypes and growth stages. The analyses on the relationships between vegetation indices and leaf pigment concentrations and densities indicated that the pigment concentrations and pigment densities, respectively, were highly correlated with eight spectral parameters selected. The leaf chlorophyll concentrations were highly correlated with red edge position, with highest coefficients of determination (R2) for REPLE, while R2 between Car and spectral indices decreased. The chlorophyll densities were highly correlated with VOG2, VOG3, RVI(810,560), Dr/Db, and SDr/SDb, but the correlation was also reduced for carotenoids. Testing of the monitoring equations with independent datasets indicated that the red edge position was the best hyperspectral parameter to estimate leaf pigment concentrations, with no significant difference between REPLE and REPIG for Chla, Chla+b, and Car, although better performance with REPIG than with REPIE for estimation of Chlb. The VOG2, VOG3, Dr/Db, and SDr/SDb were the best hyperspectral parameters to estimate leaf pigment densities, but with lower estimation accuracy for Chlb and lower estimation precision for Car. The overall results suggested that the pigment concentrations and densities in wheat leaves, especially for Chla and Chla+b, could be reliably estimated with the hyperspectral parameters established in this study.
A quantitative approach detects three QTLs involved in powdery mildew resistance at the seedling stage in the winter wheat line RE714
Authors: Muranty H. , Pavoine M.-T. , Jaudeau B. , Radek W. , Doussinault G. , Barloy D.
Published: July 2008

Powdery mildew (Blumeria graminis f. sp. tritici) is one of the major diseases of wheat (Triticum aestivum). The objective of the present study was to describe the quantitative resistance to powdery mildew of the winter wheat line RE714 at the seedling stage and to identify microsatellite markers tightly linked to the RE714 resistance QTL, which could be used in marker-assisted selection. A population of 160 recombinant inbred lines obtained from the cross between RE714 (resistant) and Hardi (susceptible) was genotyped with microsatellite and AFLP markers. Fifteen powdery mildew isolates were used to test the resistance of these lines at the seedling stage. QTL analysis enabled us to identify three major QTLs controlling powdery mildew resistance in RE714: a QTL located on chromosome 2A, corresponding to the Pm4b gene, explaining 76–93% of the phenotypic variance for resistance to six isolates; two QTLs located on chromosomes 5D and 6A, each explaining 20–67% of the phenotypic variance for resistance to five isolates. A minor QTL for resistance to four of the six isolates revealing Pm4b was detected in the same region as the 5D QTL. Other minor QTLs were detected on chromosomes 2A and 6B, explaining, respectively, 10.9 and 11.5% of the phenotypic variance for resistance to isolate 96-27. The maps around the three major QTLs were enriched with microsatellite markers that could be used in marker-assisted selection of these QTLs.
Characterisation of genetic diversity and DNA fingerprinting of Australian chickpea (Cicer arietinum L.) cultivars using MFLP markers
Authors: Lin R. , Yang H. , Khan T. N. , Siddique K. H. M. , Yan G.
Published: July 2008

Chickpea (Cicer arietinum L.) is one of the major grain legume crops in the world. In this study, the genetic diversity of 24 Australian chickpea cultivars released between 1987 and 2005 was investigated with microsatellite-anchored fragment length polymorphism (MFLP) DNA markers. Among the cultivars examined, 30 cultivar-specific markers were identified and all were unequivocally identified using the DNA fingerprints developed in this study. Most of the cultivars were grouped into two major clusters; cv. Flipper was separated from the rest based on total character differences of DNA polymorphism. The MFLP approach proved suitable in the analysis of genetic diversity among the chickpea cultivars studied and the genetic relationship identified will be useful for chickpea breeding programs in selecting parent materials.
Systems analysis of the single photon response in invertebrate photoreceptors
Authors: Pumir Alain , Graves Jennifer , Ranganathan Rama , Shraiman Boris I.
Published: July 2008

Photoreceptors of
Drosophila
compound eye employ a G protein-mediated signaling pathway that transduces single photons into transient electrical responses called “quantum bumps” (QB). Although most of the molecular components of this pathway are already known, the system-level understanding of the mechanism of QB generation has remained elusive. Here, we present a quantitative model explaining how QBs emerge from stochastic nonlinear dynamics of the signaling cascade. The model shows that the cascade acts as an “integrate and fire” device and explains how photoreceptors achieve reliable responses to light although keeping low background in the dark. The model predicts the nontrivial behavior of mutants that enhance or suppress signaling and explains the dependence on external calcium, which controls feedback regulation. The results provide insight into physiological questions such as single-photon response efficiency and the adaptation of response to high incident-light level. The system-level analysis enabled by modeling phototransduction provides a foundation for understanding G protein signaling pathways less amenable to quantitative approaches.
Conformational dynamics of an intact virus: Order parameters for the coat protein of Pf1 bacteriophage
Authors: Lorieau Justin L. , Day Loren A. , McDermott Ann E.
Published: July 2008

This study has examined the atomic-level dynamics of the protein in the capsid of filamentous phage Pf1. This capsid consists of ≈7,300 small subunits of only 46 aa in a helical array around a highly extended, circular single-stranded DNA molecule of 7,349 nt. Measurements were made of site-specific, solid-state NMR order parameters, 〈
S
〉, the values which are dimensionless quantities between 0 (mobile) and 1 (static) that characterize the amplitudes of molecular bond angular motions that are faster than microseconds. It was found that the protein subunit backbone is very static, and of particular interest, it appears to be static at residues glycine 15 and glutamine 16 where it had been previously thought to be mobile. In contrast to the backbone, several side chains display large-amplitude angular motions. Side chains on the virion exterior that interact with solvent are highly mobile, but surprisingly, the side chains of residues arginine 44 and lysine 45 near the DNA deep in the interior of the virion are also highly mobile. The large-amplitude dynamic motion of these positively charged side chains in their interactions with the DNA were not previously expected. The results reveal a highly dynamic aspect of a DNA–protein interface within a virus.
Chronic intake of fermented floral nectar by wild treeshrews
Authors: Wiens Frank , Zitzmann Annette , Lachance Marc-André , Yegles Michel , Pragst Fritz , Wurst Friedrich M. , von Holst Dietrich , Guan Saw Leng , Spanagel Rainer
Published: July 2008

For humans alcohol consumption often has devastating consequences. Wild mammals may also be behaviorally and physiologically challenged by alcohol in their food. Here, we provide a detailed account of chronic alcohol intake by mammals as part of a coevolved relationship with a plant. We discovered that seven mammalian species in a West Malaysian rainforest consume alcoholic nectar daily from flower buds of the bertam palm (
Eugeissona tristis
), which they pollinate. The 3.8% maximum alcohol concentration (mean: 0.6%; median: 0.5%) that we recorded is among the highest ever reported in a natural food. Nectar high in alcohol is facilitated by specialized flower buds that harbor a fermenting yeast community, including several species new to science. Pentailed treeshrews (
Ptilocercus lowii
) frequently consume alcohol doses from the inflorescences that would intoxicate humans. Yet, the flower-visiting mammals showed no signs of intoxication. Analysis of an alcohol metabolite (ethyl glucuronide) in their hair yielded concentrations higher than those in humans with similarly high alcohol intake. The pentailed treeshrew is considered a living model for extinct mammals representing the stock from which all extinct and living treeshrews and primates radiated. Therefore, we hypothesize that moderate to high alcohol intake was present early on in the evolution of these closely related lineages. It is yet unclear to what extent treeshrews benefit from ingested alcohol
per se
and how they mitigate the risk of continuous high blood alcohol concentrations.
Native 3D intermediates of membrane fusion in herpes simplex virus 1 entry
Authors: Maurer Ulrike E. , Sodeik Beate , Grünewald Kay
Published: July 2008

The concerted action of four viral glycoproteins and at least one cellular receptor is required to catalyze herpes simplex virus 1 entry into host cells either by fusion at the plasma membrane or intracellularly after internalization by endocytosis. Here, we applied cryo electron tomography to capture 3D intermediates from Herpes simplex virus 1 fusion at the plasma membrane in their native environment by using two model systems: adherent cells and synaptosomes. The fusion process was delineated as a series of structurally different steps. The incoming capsid separated from the tegument and was closely surrounded by the cortical cytoskeleton. After entry, the viral membrane curvature changed concomitantly with a reorganization of the envelope glycoprotein spikes. Individual glycoprotein complexes in transitional conformations during pore formation and dilation revealed the complex viral fusion mechanism in action. Snapshots of the fusion intermediates provide unprecedented details concerning the overall structural changes occurring during herpesvirus entry. Moreover, our data suggest that there are two functional “poles” of the asymmetric herpesvirion: one related to cell entry, and the other formed during virus assembly.
Statistical analysis of the National Institutes of Health peer review system
Authors: Johnson Valen E.
Published: July 2008

A statistical model is proposed for the analysis of peer-review ratings of R01 grant applications submitted to the National Institutes of Health. Innovations of this model include parameters that reflect differences in reviewer scoring patterns, a mechanism to account for the transfer of information from an application's preliminary ratings and group discussion to final ratings provided by all panel members and posterior estimates of the uncertainty associated with proposal ratings. Application of this model to recent R01 rating data suggests that statistical adjustments to panel rating data would lead to a 25% change in the pool of funded proposals. Viewed more broadly, the methodology proposed in this article provides a general framework for the analysis of data collected interactively from expert panels through the use of the Delphi method and related procedures.
Effective inhibition in animals of viral pathogenesis by a ribozyme derived from RNase P catalytic RNA
Authors: Bai Yong , Trang Phong , Li Hongjian , Kim Kihoon , Zhou Tianhong , Liu Fenyong
Published: July 2008

A functional RNase P ribozyme (M1GS RNA) was constructed to target the overlapping mRNA region of two murine cytomegalovirus (MCMV) capsid proteins essential for viral replication: the assembly protein (mAP) and M80. The customized ribozyme efficiently cleaved the target mRNA sequence
in vitro
. Moreover, 80% reduction in the expression of mAP and M80 and a 2,000-fold reduction in viral growth were observed in cells expressing the ribozyme. In contrast, there was no significant reduction in viral gene expression and growth in cells that either did not express the ribozyme or produced a “disabled” ribozyme carrying mutations that abolished its catalytic activity. When the ribozyme-expressing constructs were delivered into MCMV-infected SCID mice via a modified “hydrodynamic transfection” procedure, expression of ribozymes was observed in the livers and spleens. Compared with the control animals that did not receive any M1GS constructs or received the disabled ribozyme construct, animals receiving the functional ribozyme construct exhibited a significant reduction of viral gene expression and infection. Viral titers in the spleens, livers, lungs, and salivary glands of the functional ribozyme-treated SCID mice at 21 days after infection were 200- to 2,000-fold lower than those in the control animals. Moreover, survival of the infected animals significantly improved upon receiving the functional ribozyme construct. Our study examines the use of M1GS ribozymes for inhibition of gene expression in animals and demonstrates the utility of RNase P ribozymes for gene targeting applications
in vivo
.
NIK overexpression amplifies, whereas ablation of its TRAF3-binding domain replaces BAFF:BAFF-R-mediated survival signals in B cells
Authors: Sasaki Yoshiteru , Calado Dinis P. , Derudder Emmanuel , Zhang Baochun , Shimizu Yuri , Mackay Fabienne , Nishikawa Shin-ichi , Rajewsky Klaus , Schmidt-Supprian Marc
Published: July 2008

BAFF-R-dependent activation of the alternative NF-κB pathway plays an essential role in mature B cell survival. Mutations leading to overexpression of NIK and deletion of the
TRAF3
gene are implicated in human multiple myeloma. We show that overexpression of NIK in mouse B lymphocytes amplifies alternative NF-κB activation and peripheral B cell numbers in a BAFF-R-dependent manner, whereas uncoupling NIK from TRAF3-mediated control causes maximal p100 processing and dramatic hyperplasia of BAFF-R-independent B cells. NIK controls alternative NF-κB signaling by increasing the protein levels of its negative regulator TRAF3 in a dose-dependent fashion. This mechanism keeps NIK protein levels below detection even when they cause B cell hyperplasia, so that contributions of NIK to B cell pathologies can easily be overlooked.
Children's patterns of composition and their reflections on their composing processes
Authors: Myhill Debra
Published: July 2008

This article reports on an Economic and Social Research Council‐funded study into secondary‐aged writers' compositional processes, both as observed in a naturalistic classroom setting and as gathered through post hoc reflections. The sample comprised 38 children drawn from Year 9 and Year 11 who were observed, using an annotated timeline, responding to a writing task in the classroom and were subsequently interviewed, using stimulated recall. The initial analysis of the pause and writing patterns observed during the writing task revealed different writing profiles for different writers, and subsequent analysis suggests tentatively that writers of different proficiency may present differing writing profiles. These patterns of composition are then illustrated further through use of the interview data, indicating the writers' awareness of their own composing processes. Finally, the article considers the pedagogic and theoretical implications of these findings, in particular the need for further confirmatory research.
A Flexible Stochastic Automaton-Based Algorithm for Network Self-Partitioning
Authors: Wan Yan , Roy Sandip , Saberi Ali , Lesieutre Bernard
Published: July 2008

This article proposes a flexible and distributed stochastic automaton-based network partitioning algorithm that is capable of finding the optimal k-way partition with respect to a broad range of cost functions, and given various constraints, in directed and weighted graphs. Specifically, we motivate the distributed partitioning (self-partitioning) problem, introduce the stochastic automaton-based partitioning algorithm, and show that the algorithm finds the optimal partition with probability 1 for a large class of partitioning tasks. Also, a discussion of why the algorithm can be expected to find good partitions quickly is included, and its performance is further illustrated through examples. Finally, applications to mobile/sensor classification in ad hoc networks, fault-isolation in electric power systems, and control of autonomous vehicle teams are pursued in detail.
Exploring the Interplay between Virology and Molecular Crystallography
Authors: Janner Aloysio
Published: July 2008

Polyhedra with icosahedral symmetry and vertices labelled by rational indices of points of a six‐dimensional lattice left invariant by the icosahedral group allow a morphological characterization of icosahedral viruses which includes the Caspar–Klug classification as a special case. Scaling transformations relating the indexed polyhedron enclosing the surface with the one delimiting the central cavity lead to models of viral capsids observed in nature. Similar scaling relations can be obtained from projected images in three dimensions of higher‐dimensional crystallographic point groups having the icosahedral group as a subgroup. This crystallographic approach can be extended to axial‐symmetric clusters of coat proteins around icosahedral axes of the capsid. One then gets enclosing forms with vertices at points of lattices left invariant by the corresponding point group and having additional crystallographic properties also observed in natural crystals, but not explained by the known crystallographic laws.
DNA Knotting in Spooling Like Conformations in Bacteriophages
Authors: Arsuaga J. , Diao Y.
Published: July 2008

A number of idealized models have been proposed to explain the long range organization of the DNA in bacteriophages. However, none of these models can account for the distributions of complex knots found when examining DNA extracted from bacteriophage P4 capsids. Furthermore, these models do not consider possible chirality biases in the arrangement of the DNA molecule inside the capsid. In this paper, we address these two issues by proposing a randomized version of one of the most popular models: the coaxially spooled model. We present analytical and numerical results for the properties of the random polygons (knots) generated using this model. We show that such model can easily generate complex knotted conformations and although it accounts for some chirality of the organization of the DNA molecules inside bacteriophage capsids does not fully explain the experimental data.
Polyomaviridae Assembly Polymorphism from an Energy Landscape Perspective
Authors: ElSawy Karim M. , Caves Leo S. D. , Twarock Reidun
Published: July 2008

Polyomaviridae assemble in vitro into different aggregates depending on experimental conditions. We use an energy landscape approach using empirical energy calculations to quantify how the formation of these different aggregates depends on pH, the presence of bound calcium ions and disulfide linkages. Computations are carried out for SV40, a member of the Polyomaviridae family and are based on the binding free energy landscape of three distinct trimers of pentamers that correspond to the different bonding configurations between the capsid proteins observed in its crystal structure. Our computational analysis shows that the energetics of one of these environments is pivotal for the polymorphic assembly behaviour of SV40, whilst the binding energy landscapes of the other two environments are broadly funnel‐shaped and thus contribute little to the formation of particles other than virus‐like particles (VLP). We have quantified how the existence of bound calcium ions in the absence of disulfide linkages enhances the binding free energies of all three environments and hence, favours the assembly of VLPs. Moreover, estimation of the relative binding free energies of the three environments at pH 5 and pH 8 reveals that they are destabilized at pH 5 relative to pH 8. The extent of this destabilization is dependent on the presence of disulfide linkages and bound calcium ions and accounts for the experimentally observed polymorphic behaviour of VP1 proteins at pH 5. Interestingly, concurrent existence of bound calcium ions and disulfide linkages is found to be destabilizing and thus may disrupt the assembly of VLPs at pH 8.
New Insights into Viral Architecture via Affine Extended Symmetry Groups
Authors: Keef T. , Twarock R.
Published: July 2008

Since the seminal work of Caspar and Klug on the structure of the protein containers that encapsulate and hence protect the viral genome, it has been recognized that icosahedral symmetry is crucial for the structural organization of viruses. In particular, icosahedral symmetry has been invoked in order to predict the surface structures of viral capsids in terms of tessellations or tilings that schematically encode the locations of the protein subunits in the capsids. Whilst this approach is capable of predicting the relative locations of the proteins in the capsids, a prediction on the relative sizes of different virus particles in a family cannot be made. Moreover, information on the full 3D structure of viral particles, including the tertiary structures of the capsid proteins and the organization of the viral genome within the capsid are inaccessible with their approach. We develop here a mathematical framework based on affine extensions of the icosahedral group that allows us to address these issues. In particular, we show that the relative radii of viruses in the family of Polyomaviridae and the material boundaries in simple RNA viruses can be determined with our approach. The results complement Caspar and Klug′s theory of quasi‐equivalence and provide details on virus structure that have not been accessible with previous methods, implying that icosahedral symmetry is more important for virus architecture than previously appreciated.
Computer Simulations of DNA Packing inside Bacteriophages: Elasticity, Electrostatics and Entropy
Authors: Marenduzzo D.
Published: July 2008

There is now a considerable literature on computer simulations of DNA packaging inside bacteriophage capsids. While most studies have reached a semiquantitative or qualitative agreement with single molecule packaging and ejection studies, several quantitative answers are to date still lacking, needing either more accurate measurements or more realistic or difficult simulations. Here, I briefly review the outstanding questions in this field and report some new numerical results on DNA packaging inside the phi29 phage, modelled either as a capped sphero‐cylinder or as a sphere with the same internal volume. These simulations include electrostatics and a realistic genome length, and contribute to seriously questioning the inverse spool model, which arises from a purely continuum mechanics view of the problem, and is still commonly adopted to describe the shape of the packaged genome.
RNA Packing Specificity and Folding during Assembly of the Bacteriophage MS2
Authors: Rolfsson Ottar , Toropova Katerina , Morton Victoria , Francese Simona , Basnak Gabriella , Thompson Gary S. , Homans Stephen W. , Ashcroft Alison E. , Stonehouse Nicola J. , Ranson Neil A. , Stockley Peter G.
Published: July 2008

Using a combination of biochemistry, mass spectrometry, NMR spectroscopy and cryo‐electron microscopy (cryo‐EM), we have been able to show that quasi‐equivalent conformer switching in the coat protein (CP) of an RNA bacteriophage (MS2) is controlled by a sequence‐specific RNA–protein interaction. The RNA component of this complex is an RNA stem‐loop encompassing just 19 nts from the phage genomic RNA, which is 3569 nts in length. This binding results in the conversion of a CP dimer from a symmetrical conformation to an asymmetric one. Only when both symmetrical and asymmetrical dimers are present in solution is assembly of the T = 3 phage capsid efficient. This implies that the conformers, we have characterized by NMR correspond to the two distinct quasi‐equivalent conformers seen in the 3D structure of the virion. An icosahedrally‐averaged single particle cryo‐EM reconstruction of the wild‐type phage (to ∼9 Å resolution) has revealed icosahedrally ordered density encompassing up to 90% of the single‐stranded RNA genome. The RNA is seen with a novel arrangement of two concentric shells, with connections between them along the 5‐fold symmetry axes. RNA in the outer shell interacts with each of the 90 CP dimers in the T = 3 capsid and although the density is icosahedrally averaged, there appears to be a different average contact at the different quasi‐equivalent protein dimers: precisely the result that would be expected if protein conformer switching is RNA‐mediated throughout the assembly pathway. This unprecedented RNA structure provides new constraints for models of viral assembly and we describe experiments aimed at probing these. Together, these results suggest that viral genomic RNA folding is an important factor in efficient assembly, and further suggest that RNAs that could sequester viral CPs but not fold appropriately could act as potent inhibitors of viral assembly.
Metalloproteinase regulation improves in vitro generation of efficacious platelets from mouse embryonic stem cells
Authors: Nishikii Hidekazu , Eto Koji , Tamura Noriko , Hattori Koichi , Heissig Beate , Kanaji Taisuke , Sawaguchi Akira , Goto Shinya , Ware Jerry , Nakauchi Hiromitsu
Published: July 2008

Embryonic stem cells (ESCs) could potentially compensate for the lack of blood platelets available for use in transfusions. Here, we describe a new method for generating mouse ESC-derived platelets (ESPs) that can contribute to hemostasis in vivo. Flow cytometric sorting of cells from embryoid bodies on day 6 demonstrated that c-Kit+ integrin αIIb (αIIb)+ cells, but not CD31+ cells or vascular endothelial cadherin+ cells, are capable of megakaryopoiesis and the release of platelet-like structures by day 12. αIIbβ3-expressing ESPs exhibited ectodomain shedding of glycoprotein (GP)Ibα, GPV, and GPVI, but not αIIbβ3 or GPIbβ. ESPs showed impaired αIIbβ3 activation and integrin-mediated actin reorganization, critical events for normal platelet function. However, the administration of metalloproteinase inhibitors GM6001 or TAPI-1 during differentiation increased the expression of GPIbα, improving both thrombogenesis in vitro and posttransfusion recovery in vivo. Thus, the regulation of metalloproteinases in culture could be useful for obtaining high-quality, efficacious ESPs as an alternative platelet source for transfusions.