bluuebunny/crossref_metadata_2025 huggingface dataset:
Low‐frequency characteristics of wave group–forced vortices
Authors: Long Joseph W. , Özkan‐Haller H. Tuba
Published: August 2009

The dynamics of vorticity motions forced by wave groups incident on an alongshore‐uniform barred beach are analyzed. For both normally and obliquely incident wave groups, the potential vorticity and enstrophy equations reveal that the temporal variability of wave group–forced vortices is directly linked to the variability in the incoming wave groups rather than bottom friction, as previously hypothesized. Analysis of the lifespan of individual vortices further shows that the wave group forcing is responsible for not only the temporal variations of the vortices but also their eventual demise. Vortices in the simulations persist for 5 to 45 min, which is consistent with recent field observations. For oblique wave groups, the resulting vortices are advected by the mean current, yielding a signature in the frequency–wave number spectrum that is similar to that usually attributed to shear instabilities of the alongshore current. These results may explain previous observations of alongshore‐propagating vorticity motions in the presence of a stable alongshore current. For simulations involving an unstable alongshore current, we find that the inclusion of wave group forcing results in velocity spectra that are much broader compared to the simulations that neglect wave grouping, which could explain discrepancies between previously observed and modeled spectral widths of propagating vorticity motions. Finally, the potential enstrophy balance shows that vorticity production due to wave groups may be as important as that due to the instability process and that not all low‐frequency vortical motions observed during oblique wave incidence should be attributed to shear instabilities of the alongshore current.
Debut of a flexible model for simulating soil respiration–soil temperature relationship: Gamma model
Authors: Khomik Myroslava , Arain M. Altaf , Liaw Kao‐Lee , McCaughey J. Harry
Published: August 2009

A number of empirical models are used in literature to simulate the response of soil respiration (Rs) to soil temperature (Ts). The most widely used ones are the exponential Q10 model and the sigmoid‐shaped Lloyd‐Taylor and logistic models. None of these models are applicable across a wide range of ecosystems or climates, and none allow Rs to decrease at high Ts values. Here we present a new, more flexible, empirical model, the so‐called Gamma model, which can take on the shapes of the three models mentioned above and is mathematically flexible enough to allow for Rs to decrease at high Ts values, as dictated by data. We compared the Gamma model fits to the Q10, Lloyd‐Taylor, and logistic models, using coefficient of determination (R2), residual sum of squares, and Akaike's Information Criterion. The models were tested across a wide Ts range (−18 to 35°C), in five forest ecosystems, spanning three different climate zones: boreal, temperate, and Mediterranean. Compared to the other three models, the Gamma model performed either better or as good as the other models in simulating the Rs‐Ts relationship at all sites. Simulations were carried out using models parameterized by the ordinary least squares and weighted absolute deviation estimation methods. Rs values derived from the two estimation methods were comparable once the proper functional form for the Rs‐Ts model was chosen. We also show how the Gamma model can be expanded, using simple mathematics to help researchers analyze the Rs‐Ts relationship in the context of other environmental factors, such as soil moisture and nutrients.
Bifurcation structure and noise‐assisted transitions in the Pleistocene glacial cycles
Authors: Ditlevsen Peter D.
Published: August 2009

The glacial cycles are attributed to the climatic response of the orbital changes in the irradiance to the Earth. These changes in the forcing are too small to explain the observed climate variations as simple linear responses. Nonlinear amplifications of the orbital forcing are necessary to account for the glacial cycles. Here an empirical model of the nonlinear response is presented. From the model it is possible to assess the role of stochastic noise in comparison to the deterministic orbital forcing of the ice ages. The model is based on the bifurcation structure derived from the climate history. It indicates the dynamical origin of the mid‐Pleistocene transition from the “41 ka world” to the “100 ka world.” The dominant forcing in the latter is still the 41 ka obliquity cycle, but the bifurcation structure of the climate system is changed. The model suggests that transitions between glacial and interglacial climate are assisted by internal stochastic noise in the period prior to the last five glacial cycles, while the last five cycles are deterministic responses to the orbital forcing.
Length scale of braided river morphology
Authors: Hundey E. J. , Ashmore P. E.
Published: August 2009

Pool‐bar topography in single‐channel rivers has a length scale proportional to channel width. In braided rivers confluence‐bifurcation units are analogous to pool‐bar morphology and, in some cases, develop from initial alternate bars. Consequently, confluence‐bifurcation units are expected to have length that scales with the central anabranch width and that constitutes a basic length scale braided channel morphology. This idea was tested using measurements from a physical model of a gravel bed braided river and from aerial photographs of braided rivers. Length (distance from confluence to bifurcation), anabranch width, and confluence angle of confluence‐bifurcation units were measured. A simple length scaling is evident across the range of scales; confluence‐bifurcation length is 4–5 times the channel width. This scaling is a fundamental element of braided river morphology and suggests that braided patterns are created by processes, and have morphological regularity, similar to pool‐bar units of low‐sinuosity single‐thread rivers.
Geomagnetic jerks in the polar regions
Authors: Tozzi R. , De Michelis P. , Meloni A.
Published: August 2009

The occurrence of geomagnetic jerks over the Arctic and Antarctic regions is here investigated. Maps of geomagnetic secular acceleration over the polar regions are produced from the CM4 and CHAOS models and the occurrence of geomagnetic jerks is associated with jumps in secular acceleration. The obtained results confirm that in Antarctica geomagnetic jerks systematically follow geomagnetic jerks in the Arctic region with a time delay from one to three years. Evidence is found of an abrupt change in secular acceleration in both polar regions around 1985, suggesting that the 1985 local jerk could actually be a worldwide event. Combining our results with the results previously obtained on the occurrence of a geomagnetic jerk at low‐mid latitudes around 2003, we support the hypothesis of a global extension of an event occurred at the beginning of the 21st century.
Spatial and temporal variation patterns of reference evapotranspiration across the Qinghai‐Tibetan Plateau during 1971–2004
Authors: Zhang Xueqin , Ren Yu , Yin Zhi‐Yong , Lin Zhenyao , Zheng Du
Published: August 2009

Reference evapotranspiration (RET), an indicator of atmospheric evaporating capability over a hypothetical reference surface, was calculated using the Penman‐Monteith method for 75 stations across the Qinghai‐Tibetan Plateau between 1971 and 2004. Generally, both annual and seasonal RET decreased for most part of the plateau during the study period. Multivariate linear models were used to determine the contributions of climate factors to RET change, including air temperature, air humidity, solar radiation, and wind speed. Spatial differences in the causes of RET change were detected by K‐means clustering analysis. It indicates that wind speed predominated the changes of RET almost throughout the year, especially in the north of the study region, whereas radiation was the leading factor in the southeast, especially during the summertime. Although the recent warming trend over the plateau would have increased RET, the combined effect of the reduced wind speed and shortened sunshine duration negated the effect of rising temperature and caused RET to decrease in general. The significant decrease in surface wind speed corresponded to the decreasing trends of upper‐air zonal wind and the decline of pressure gradient, possibly as a result of the recent warming.
Recognition of an intra‐chain tandem 14‐3‐3 binding site within PKCε
Authors: Kostelecky Brenda , Saurin Adrian T , Purkiss Andrew , Parker Peter J , McDonald Neil Q
Published: August 2009

The phosphoserine/threonine binding protein 14‐3‐3 stimulates the catalytic activity of protein kinase C‐ε (PKCε) by engaging two tandem phosphoserine‐containing motifs located between the PKCε regulatory and catalytic domains (V3 region). Interaction between 14‐3‐3 and this region of PKCε is essential for the completion of cytokinesis. Here, we report the crystal structure of 14‐3‐3ζ bound to a synthetic diphosphorylated PKCε V3 region revealing how a consensus 14‐3‐3 site and a divergent 14‐3‐3 site cooperate to bind to 14‐3‐3 and so activate PKCε. Thermodynamic data show a markedly enhanced binding affinity for two‐site phosphopeptides over single‐site 14‐3‐3 binding motifs and identifies Ser 368 as a gatekeeper phosphorylation site in this physiologically relevant 14‐3‐3 ligand. This dual‐site intra‐chain recognition has implications for other 14‐3‐3 targets, which seem to have only a single 14‐3‐3 motif, as other lower affinity and cryptic 14‐3‐3 gatekeeper sites might exist.
An Ontology for Designing Models of Epidemics
Authors: Frank Geoffrey , Wheaton William , Bakalov Vesselina , Cooley Phillip , Wagener Diane
Published: August 2009

Models of epidemics allow decision makers to explore the consequences of different interventions. The Models of Infectious Disease Agent Study (MIDAS) project has been collecting studies, models, data supporting the models, and publications providing historical evidence about epidemics.An ontology has been developed for MIDAS to support the collection, documentation, and dissemination of models. It uses relations to link taxonomies (including a subset of the infectious disease ontology) that define the scope of its models and supporting documentation.The ontology is used to aid in the navigation process that is part of the user interface for identifying which studies and publications are available in the MIDAS repository (MREP) that are consistent with the many parameters associated with a particular study.
Exciting Collaboration Turns Cluttering Fascinating: A Story Told by a Person Who Clutters and a Speech and Language Therapist From Norway
Authors: Kvenseth Helene , Sønsterud Hilda
Published: August 2009

The purpose of this article is to describe some ways in which a person who clutters and a speech and language therapist from Norway have worked together to spread awareness about cluttering. The article outlines how a consumer and a therapist can complement each other by combining their perspectives. The content of the article has implications for the development of cluttering awareness programs worldwide.
Strain relaxation in Si/Ge/Si nanoscale bars from molecular dynamics simulations
Authors: Park Yumi , Atkulga Hasan Metin , Grama Ananth , Strachan Alejandro
Published: August 2009

We use molecular dynamics (MD) with the reactive interatomic potential ReaxFF to characterize the local strains of epitaxial Si/Ge/Si nanoscale bars as a function of their width and height. While the longitudinal strain (along the bars length) is independent of geometry, surface relaxation leads to transverse strain relaxation in the Ge section. This strain relaxation increases with increasing height of the Ge section and reduction in its width and is complete (i.e., zero transverse strain) for roughly square cross sections of Ge leading to a uniaxial strain state. Such strain state is desirable in some microelectronics applications. From the MD results, which are in excellent agreement with experiments, we derive a simple model to predict lateral strain as a function of geometry for this class of nanobars.
Sticking properties of an in situ prepared polymer film
Authors: Pires David , Fleury Jean-Baptiste , Galerne Yves
Published: August 2009

Colloidal silica particles of micrometric size are dispersed in 5CB, a nonionic nematic liquid crystal, and are glued on a glass-indium-tin-oxide substrate by means of an in situ synthesized acrylate polymer film. In order to evaluate the gluing properties of the film, we address pull-off forces in the piconewton range on the beads on applying small electric fields. This provides us with an extremely sensitive tool for studying the adhesion of the beads on the substrate. We thus determine their pull-off statistics. We show that the gluing properties of the film depend on whether the polymerization of the film is initiated via volume or surface nucleation, and whether the film is synthesized before or after the beads are deposited on the substrate. Typically, the adhesion is measured around 25pN which nevertheless could be interesting for particular applications.
Spinor fields without Lorentz frames in curved space-time using complexified quaternions
Authors: Fredsted John
Published: August 2009

Using complexified quaternions, a formalism without Lorentz frames, and therefore also without vierbeins, for dealing with tensor and spinor fields in curved space-time is presented. A local U(1) gauge symmetry, which, it is speculated, might be related to electromagnetism, emerges naturally.
Berry phase and entanglement of three qubits in a new Yang–Baxter system
Authors: Hu Taotao , Xue Kang , Wu Chunfeng
Published: August 2009

In this paper we construct a new 8×8 M matrix from the 4×4 M matrix, where M/M is the image of the braid group representation. The 8×8 M matrix and the 4×4 M matrix both satisfy extraspecial 2-group algebra relations. By Yang–Baxteration approach, we derive a unitary R̆(θ,φ) matrix from the M matrix with parameters φ and θ. Three-qubit entangled states can be generated by using the R̆(θ,φ) matrix. A Hamiltonian for three qubits is constructed from the unitary R̆(θ,φ) matrix. We then study the entanglement and Berry phase of the Yang–Baxter system.
Flexible electronics sensors for tactile multiscanning
Authors: Chang Wen-Yang , Fang Te-Hua , Shen Yu-Tang , Lin Yu-Cheng
Published: August 2009

Flexible electronics sensors are designed and fabricated for tactile multiscanning and large area applications. The algorithm matrix is derived for multiscanning switch of tactile sensing. The thixotropy materials, bump, and resistance material are printed on the polyimide substrate. A gap between the top electrode and the resistance layers provides a buffer distance to increase the radius of curvature for large bending. Experiment results show that a flexible electronics sensor with a printed a resistance layer and an algorithm matrix performed the multiscanning functions. The membrane without a bump had a delay time of about 0.2 s at the transient response and took a longer time to reach the stable state after a force is applied. For printing thick structures on the flexible substrates, diffusion effects, and dimensional shrinkages can be reduced by using a thixotropy material with a high viscosity. The probability distribution density of the printed resistance values, a thickness of about 23.2 μm, at two standard deviations from the mean values is about 81.2%. Feasibility studies show that screen printing is appropriate for large area applications and is a low-cost technology for fabricating flexible electronics sensors.
Chemical and physical sputtering effects on the surface morphology of carbon films grown by plasma chemical vapor deposition
Authors: Vázquez Luis , Buijnsters Josephus G.
Published: August 2009

We have studied the influence of chemical and physical sputtering on the surface morphology of hydrogenated carbon films deposited on silicon substrates by bias-enhanced electron cyclotron resonance chemical vapor deposition. Atomic force microscopy based power spectrum density (PSD) and roughness analysis have been used to investigate the film morphology. This study has been possible due to the appropriate choice of the experimental variables, in particular, gas mixture, resulting in either nitrogen-free (a-C:H) or nitrogenated carbon (a-CN:H) films, and substrate bias (Vb). Under these conditions, chemical sputtering is present for a-CN:H deposition but it is negligible for a-C:H film growth, while physical sputtering processes appear for both systems for Vb≤−85 V. When physical sputtering does not operate, the film growth with simultaneous chemical sputtering leads to a characteristic a-CN:H granular surface morphology. Furthermore, PSD analysis reveals that a spatial correlation of the a-CN:H film surface roughness, up to distances ∼300 nm, becomes a fingerprint of the coexistence of growth and chemical erosion processes on the film morphology. However, once physical sputtering takes place, the influence of chemical sputtering by reactive nitrogen species on the final surface morphology becomes negligible and both a-CN:H and a-C:H film morphologies are ultrasmooth.
Explicit polynomial formulas for solutions of the matrix equation AX−XA=C
Authors: Demenchuk Alexandr K. , Makarov Evgeniĭ K.
Published: August 2009

We provide some mathematical tool to analyze the possible theoretical structure of Hamiltonian reconstructed from von Neumann or Heisenberg’s equation for a finite-dimensional quantum system. To this end, we give an explicit polynomial representation for the general solution of the matrix equation AX−XA=C together with some (also polynomial) solvability conditions when A and C are some complex square matrices of the same size and the matrix A is semisimple. When the matrix A is normal, we derive a polynomial existence condition for Hermitian solutions and a similar formula for all solutions of this type.
General decay for quasilinear viscoelastic equations with nonlinear weak damping
Authors: Park Jong Yeoul , Park Sun Hye
Published: August 2009

In this paper, we investigate general decay rates of solutions for a quasilinear viscoelastic equation with nonlinear weak damping.
Droplet formation in a T-shaped microfluidic junction
Authors: Liu Haihu , Zhang Yonghao
Published: August 2009

Using a phase-field model to describe fluid/fluid interfacial dynamics and a lattice Boltzmann model to address hydrodynamics, two dimensional (2D) numerical simulations have been performed to understand the mechanisms of droplet formation in microfluidic T-junction. Although 2D simulations may not capture underlying physics quantitatively, our findings will help to clarify controversial experimental observations and identify new physical mechanisms. We have systematically examined the influence of capillary number, flow rate ratio, viscosity ratio, and contact angle in the droplet generation process. We clearly observe that the transition from the squeezing regime to the dripping regime occurs at a critical capillary number of 0.018, which is independent of flow rate ratio, viscosity ratio, and contact angle. In the squeezing regime, the squeezing pressure plays a dominant role in the droplet breakup process, which arises when the emerging interface obstructs the main channel. The droplet size depends on both the capillary number and the flow rate ratio, but is independent of the viscosity ratio under completely hydrophobic wetting conditions. In the dripping regime, the droplet size will be significantly influenced by the viscosity ratio as well as the built-up squeezing pressure. When the capillary number increases, the droplet size becomes less dependent on the flow rate ratio. The contact angle also affects the droplet shape, size, and detachment point, especially at small capillary numbers. More hydrophobic wetting properties are expected to produce smaller droplets. Interestingly, the droplet size is dependent on the viscosity ratio in the squeezing regime for less hydrophobic wetting conditions.
A geometry interface for gyrokinetic microturbulence investigations in toroidal configurations
Authors: Xanthopoulos P. , Cooper W. A. , Jenko F. , Turkin Yu. , Runov A. , Geiger J.
Published: August 2009

The GENE/GIST code package is developed for the investigation of plasma microturbulence, suitable for both stellarator and tokamak configurations. The geometry module is able to process typical equilibrium files and create the interface for the gyrokinetic solver. The analytical description of the method for constructing the geometric elements is documented, together with several numerical evaluation tests. As a concrete application of this product, a cross-machine comparison of the anomalous ion heat diffusivity is presented.
Shock compression of cubic boron nitride
Authors: Kawai Nobuaki , Yokoo Manabu , Kondo Ken-ichi , Taniguchi Takashi , Saito Fumikazu
Published: August 2009

Hugoniot measurements have been performed on high-purity cubic boron nitride polycrystals in the pressure range up to 296GPa using a two-stage light-gas gun. Hugoniot parameters have been measured by a line reflection method and Fabry–Pérot velocimetry. The Hugoniot elastic limit (HEL) is determined to be 44.3GPa, which is the second highest value after that of diamond. Above the HEL, the Hugoniot compression curve shows a considerable offset from its hydrodynamic compression curve, which is calculated from static-compression data. This result shows that cubic boron nitride preserves its shear strength in the plastic region. Hugoniot data indicate that the cubic phase of boron nitride is stable in the pressure range up to 296GPa.
Steady state, time resolved, and circular dichroism spectroscopic studies to reveal the nature of interactions of zinc oxide nanoparticles with transport protein bovine serum albumin and to monitor the possible protein conformational changes
Authors: Bardhan Munmun , Mandal Gopa , Ganguly Tapan
Published: August 2009

In this paper, the interaction between bovine serum albumin (BSA) and zinc oxide (ZnO) nanoparticles was investigated by fluorescence quenching spectra, circular dichroism (CD), and synchronous spectra under physiological conditions. From the analysis of the steady state and time resolved fluorescence quenching of BSA in aqueous solution in presence of ZnO it was observed that the nature of the quenching is of static-type quenching. The Stern–Volmer quenching constant KS at different temperatures were determined and the thermodynamic parameters ΔH, ΔG, and ΔS were computed. The experiment revealed that the electrostatic interaction was the predominant force in stabilizing the complex. The effect of ZnO on the conformation of BSA has been analyzed by synchronous spectra and CD spectrum. Although the observed results demonstrate some conformational changes in BSA in presence of ZnO nanoparticles, the secondary structure of BSA, predominantly of α-helix, is found to retain its identity.
The influence of temporal phase difference of m=±2 oscillations on surface frequency analysis for levitated droplets
Authors: Ozawa S. , Koda T. , Adachi M. , Morohoshi K. , Watanabe M. , Hibiya T.
Published: August 2009

The oscillations of an electromagnetically levitated molten silicon droplet were analyzed. Analysis was carried out under a superimposed static magnetic field, where the m=±2 oscillation is dominant and the droplet rotates. A phase unwrapping method was used to reveal sample rotation. The oscillation frequency of the longest diameter Dmax and difference of radii along the X and Y axes, R−, were analyzed using an image of the droplet as seen from the top of the sample. The m=+2 and m=−2 oscillations were analyzed theoretically using spherical harmonics, and it was found that a temporal phase difference between m=+2 and −2 oscillations causes apparent rotation of the samples, which causes unequal intensities of the m=±2 peaks which are split by the droplet rotation.
A comparative study of single and double pulse laser induced breakdown spectroscopy
Authors: Ahmed Rizwan , Baig M. Aslam
Published: August 2009

A comparative study of single and double pulse laser induced breakdown spectroscopy (LIBS) using the fundamental (1064 nm) and the second harmonics (532 nm) of Nd:YAG lasers is presented. The double pulse collinear configuration yields more than three hundred times signal enhancement in the singly ionized aluminum lines as compared to the single pulse LIBS spectrum. The effect of interpulse delay between the two laser pulses and the laser pulses energies ratio in the double pulse spectrum are studied. A comparison of variations of plasma parameters along the plume axis in the single and the double pulse has also been studied.
Competing tetragonal and monoclinic phases in Ni2.2Mn0.80Ga
Authors: Ranjan Rajeev , Singh Sanjay , Boysen Hans , Trots Dmytro , Banik S. , Awasthi A. M. , Mukhopadhyay P. K. , Barman S. R.
Published: August 2009

Temperature dependent synchrotron x-ray powder diffraction, differential scanning calorimetry, and magnetic measurements were performed on Ni2+xMn1−xGa (x=0.20 and 0.35) magnetic shape memory alloys. For x=0.20, though the monoclinic phase is thermodynamically stable, a trace of residual stress can stabilize a tetragonal phase. The residual-stress-induced tetragonal phase transforms to the cubic austenite phase over an unusually large temperature range (348 K≤T≤693 K), suggesting extremely slow kinetics of transformation. In contrast to x=0.20, the thermodynamically stable phase of x=0.35 is tetragonal and this composition exhibits the usual features of a reversible martensitic transformation. The results suggest that for x=0.20 the monoclinic and tetragonal phases are nearly degenerate.
Concentration-dependent two-photon absorption and subsequent excited-state absorption in 4-methoxy-2-nitroaniline
Authors: Gu Bing , Ji Wei , Huang Xiao-Qin , Patil P. S. , Dharmaprakash S. M.
Published: August 2009

By performing both open-aperture Z-scan and transient transmission measurements with femtosecond laser pulses in the near infrared region, the concentration dependence of two-photon absorption (2PA) and subsequent excited-state absorption (ESA) are investigated in acetone solution of 4-methoxy-2-nitroaniline (4M2N). Owing to the high tendency of forming aggregation molecules in solution, a considerable dependence of the nonlinear optical response on the concentration is observable at a 4M2N concentration of 10−3 M and beyond. It is found that both effective 2PA and ESA cross sections decrease with increasing concentration, while the effective lifetime of 2PA-induced excited states lengthens.
New correction factor for the estimation of solar radiation
Authors: Aggarwal R. K.
Published: August 2009

A new correction factor (CFyear) depending upon the longitude and altitude of a location has been introduced in place of the clearness index (Kt year) used for the estimation of solar irradiation H. Thirty different geographical locations have been taken for comparing the values of Kt year and CFyear. The results show that the values of Kt year and CFyear are in close agreement, having variation within 10%. The estimated values of H for Kt year and CFyear have also been compared using 15 year measured data of 11 Indian cities to establish the accuracy of the CF over Kt. The annual mean percentage error between the estimated and measured values of these locations has been found to be within 10%. The monthwise variation in the estimated values of the 11 Indian cities compared with their measured values also proved the better accuracy of CF than Kt. The study reveals that solar radiation can be estimated using CF without applying any meteorological parameters for the locations having a longitude range of ±70 to ±125.
Electrostatic and thermal fluctuations are the source of magnetic fields in unmagnetized inhomogeneous plasmas
Authors: Saleem Hamid
Published: August 2009

It is pointed out that electron thermal fluctuations can couple with the ion acoustic mode in an inhomogeneous plasma to generate a low frequency ion time scale electromagnetic wave. This electromagnetic wave can become unstable if the temperature and density gradients are parallel to each other, which can be the case in laser-plasmas similar to stellar cores. The comparisons of the present theoretical model with the previous investigations are also presented. The final result is applied to a classical laser induced plasma for illustration.
A low-impedance transit-time oscillator without foils
Authors: Cao Yibing , Zhang Jiande , He Juntao
Published: August 2009

A low-impedance transit-time oscillator (LITTO) without foils is proposed and studied by simulation. By using a coaxial structure, the space-charge limiting current can be improved significantly, thus allowing higher input and output powers. With no foils to erode, the only factor limiting the repetition rate is the ability to maintain an adequate vacuum. By contrast with conventional transit-time oscillators, the proposed LITTO has the advantages of low diode impedance, rapid saturation time, and a possibility of repetitive operation. As indicated in PIC simulation, the average microwave output power is over 5.0 GW at the main frequency of 1.6 GHz, with an input electron beam of 36.0 kA current and 600 kV voltage, and an external magnetic field of 0.45 Tesla.
ER membrane-localized oxidoreductase Ero1 is required for disulfide bond formation in the rice endosperm
Authors: Onda Yayoi , Kumamaru Toshihiro , Kawagoe Yasushi
Published: August 2009

The developing endosperm of rice (
Oryza sativa
, Os) synthesizes a large amount of storage proteins on the rough (r)ER. The major storage proteins, glutelins and prolamins, contain either intra or intermolecular disulfide bonds, and oxidative protein folding is necessary for the sorting of the proteins to the protein bodies. Here, we investigated an electron transfer pathway for the formation of protein disulfide bonds in the rER of the rice endosperm, focusing on the roles of the thiol-disulfide oxidoreductase, OsEro1. Confocal microscopic analysis revealed that
N
-glycosylated OsEro1 is localized to the rER membrane in the subaleurone cells, and that targeting of OsEro1 to the rER membrane depends on the N-terminal region from Met-1 to Ser-55. The RNAi knockdown of
OsERO1
inhibited the formation of native disulfide bonds in the glutelin precursors (proglutelins) and promoted aggregation of the proglutelins through nonnative intermolecular disulfide bonds in the rER. Inhibition of the formation of native disulfide bonds was also observed in the seeds of the
esp2
mutant, which lacks protein disulfide isomerase-like (PDIL)1;1, but shows enhanced OsEro1 expression. We detected the generation of H
2
O
2
in the rER of the WT subaleurone cells, whereas the rER-derived H
2
O
2
levels decreased markedly in EM49 homozygous mutant seeds, which have fewer sulfhydryl groups than the WT seeds. Together, we propose that the formation of native disulfide bonds in proglutelins depends on an electron transfer pathway involving OsEro1 and OsPDIL.
Inoculation of killed
Leishmania major
into immune mice rapidly disrupts immunity to a secondary challenge via IL-10-mediated process
Authors: Okwor Ifeoma , Liu Dong , Beverley Stephen M. , Uzonna Jude E.
Published: August 2009

Recovery from natural or experimental
Leishmania major
infection, the causative agent of cutaneous leishmaniasis, results in development of durable immunity in mice and humans that is manifested as rapid control of parasite replication and resolution of cutaneous lesion after secondary challenge. This form of “infection-induced” immunity is thought to occur naturally in endemic areas and is generally considered the gold standard for any effective vaccine against cutaneous leishmaniasis. To determine factors that might heighten or abrogate infection-induced immunity, we investigated the impact of inoculating dead antigen in the form of killed
Leishmania
parasites to healed mice. We show that inoculation of killed parasites into mice that resolved their primary virulent
L. major
infection results in rapid and relatively sustained loss of infection-induced immunity. This loss of immunity was not due to the inability of killed parasites to induce inflammatory responses (such as delayed type hypersensitivity), but it was related to their failure to induce robust IFN-γ response. Furthermore, inoculation of killed
Leishmania
parasites into healed mice led to rapid expansion of IL-10-producing CD4
+
CD25
+
Foxp3
+
T cells in lymph nodes draining the primary infection site. Treatment with anti-CD25 or anti-IL-10R mAb abolished killed parasite-induced loss of immunity. Our study suggests that vaccination with killed parasites could predispose naturally immune individuals to become susceptible to new infections and/or disease reactivation. This may account for the lack of efficacy of such vaccines in field trials in endemic regions. These findings have important implications for vaccine design and vaccination strategies against human cutaneous leishmaniasis.
Roland Barthes and the Grain of Panzéra's Voice
Authors: Dunsby Jonathan
Published: August 2009

Roland Barthes's perception of voice having a ‘grain’ is one of the best-known legacies of the last century's history of ideas, especially in discussions of popular music. His evidence, the singing of Charles Panzéra, compared with that of Dietrich Fischer-Dieskau, is explored and illustrated here in the context of a discussion of the origin of ‘grain’ and its wider implications. It is only rhetorically that one may consider the ‘geno’-song separately from the ‘pheno’-song, but the implied interplay of structure and effect is a powerful critical resource, neglected to date because Barthes's vision requires explanation, as proposed here.
Improving phylogenetic analyses by incorporating additional information from genetic sequence databases
Authors: Liang Li-Jung , Weiss Robert E. , Redelings Benjamin , Suchard Marc A.
Published: August 2009

Motivation: Statistical analyses of phylogenetic data culminate in uncertain estimates of underlying model parameters. Lack of additional data hinders the ability to reduce this uncertainty, as the original phylogenetic dataset is often complete, containing the entire gene or genome information available for the given set of taxa. Informative priors in a Bayesian analysis can reduce posterior uncertainty; however, publicly available phylogenetic software specifies vague priors for model parameters by default. We build objective and informative priors using hierarchical random effect models that combine additional datasets whose parameters are not of direct interest but are similar to the analysis of interest.

Results: We propose principled statistical methods that permit more precise parameter estimates in phylogenetic analyses by creating informative priors for parameters of interest. Using additional sequence datasets from our lab or public databases, we construct a fully Bayesian semiparametric hierarchical model to combine datasets. A dynamic iteratively reweighted Markov chain Monte Carlo algorithm conveniently recycles posterior samples from the individual analyses. We demonstrate the value of our approach by examining the insertion–deletion (indel) process in the enolase gene across the Tree of Life using the phylogenetic software BALI-PHY; we incorporate prior information about indels from 82 curated alignments downloaded from the BAliBASE database.

Contact:  liangl@ucla.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
The role of marine habitat mapping in ecosystem-based management
Authors: Cogan Christopher B. , Todd Brian J. , Lawton Peter , Noji Thomas T.
Published: August 2009

Cogan, C. B., Todd, B. J., Lawton, P., and Noji, T. T. 2009. The role of marine habitat mapping in ecosystem-based management. – ICES Journal of Marine Science, 66: 2033–2042. Ecosystem-based management (EBM) and the related concept of large marine ecosystems (LMEs) are sometimes criticized as being too broad for many management and research applications. At the same time, there is a great need to develop more effectively some substantive scientific methods to empower EBM. Marine habitat mapping (MHM) is an example of an applied set of field methods that support EBM directly and contribute essential elements for conducting integrated ecosystem assessments. This manuscript places MHM practices in context with biodiversity models and EBM. We build the case for MHM being incorporated as an explicit and early process following initial goal-setting within larger EBM programmes. Advances in MHM and EBM are dependent on evolving technological and modelling capabilities, conservation targets, and policy priorities within a spatial planning framework. In both cases, the evolving and adaptive nature of these sciences requires explicit spatial parameters, clear objectives, combinations of social and scientific considerations, and multiple parameters to assess overlapping viewpoints and ecosystem functions. To examine the commonalities between MHM and EBM, we also address issues of implicit and explicit linkages between classification, mapping, and elements of biodiversity with management goals. Policy objectives such as sustainability, ecosystem health, or the design of marine protected areas are also placed in the combined MHM–EBM context.
The Evolution of a ‘Memeplex’ in Late Mozart: Replicated Structures in Pamina's ‘Ach ich fühl's’
Authors: Jan Steven
Published: August 2009

‘Memetics’, a concept most elegantly expounded by Richard Dawkins inThe Selfish Gene, asserts that human culture consists of a multitude of units transmitted between individuals by imitation and subject to evolutionary pressures. Such particles, ‘memes’, are broadly analogous to the genes of biological transmission. Four late pieces of Mozart's, including Pamina's aria ‘Ach ich fühl's’ fromDie Zauberflöte, are examined in terms of the meme concept and a conglomeration, or ‘memeplex’, consisting of seven memes is identified within them. The nature of the musical memeplex, in this specific case and also more generally, is considered, particularly from the perspective of its location at different levels of the structural hierarchy. The evolutionary history of some of Mozart's memes is examined with reference to selected passages from works of the eighteenth and nineteenth centuries. Finally, relationships between the musical memes under investigation and memes in the verbal-conceptual realm are explored.
BioXTAS RAW, a software program for high-throughput automated small-angle X-ray scattering data reduction and preliminary analysis
Authors: Nielsen S. S. , Toft K. Noergaard , Snakenborg D. , Jeppesen M. G. , Jacobsen J. K. , Vestergaard B. , Kutter J. P. , Arleth L.
Published: August 2009

A fully open source software program for automated two-dimensional and one-dimensional data reduction and preliminary analysis of isotropic small-angle X-ray scattering (SAXS) data is presented. The program is freely distributed, following the open-source philosophy, and does not rely on any commercial software packages.BioXTAS RAWis a fully automated program that,viaan online feature, reads raw two-dimensional SAXS detector output files and processes and plots data as the data files are created during measurement sessions. The software handles all steps in the data reduction. This includes mask creation, radial averaging, error bar calculation, artifact removal, normalization andqcalibration. Further data reduction such as background subtraction and absolute intensity scaling is fast and easyviathe graphical user interface.BioXTAS RAWalso provides preliminary analysis of one-dimensional data in terms of the indirect Fourier transform using the objective Bayesian approach to obtain the pair-distance distribution function, PDDF, and is thereby a free and open-source alternative to existing PDDF estimation software. Apart from the TIFF input format, the program also accepts ASCII-format input files and is currently compatible with one-dimensional data files from SAXS beamlines at a number of synchrotron facilities.BioXTAS RAWis written in Python with C++ extensions.
PolySNAP3: a computer program for analysing and visualizing high-throughput data from diffraction and spectroscopic sources
Authors: Barr Gordon , Dong Wei , Gilmore Christopher J.
Published: August 2009

PolySNAP3is a computer program for the classification of powder diffraction, spectroscopic and numerical data either separately or combined. A correlation matrix is generated by matching full data profiles; for numerical data the standard Euclidean distance is calculated. The matrices are combined by the INDSCAL method [Carroll & Chang (1970).Psychometria,35, 283–319] to give either a single interpretation of the data or combinations of any of the data types. Cluster analysis, multivariate data analysis and extensive data visualization routines are used to automatically classify the patterns into groups, validate the classification, and thus identify polymorphs, mixtures and salts.
Evidence for oxazepam as anin vivoprobe of UGT2B15: oxazepam clearance is reduced byUGT2B15D85Y polymorphism but unaffected byUGT2B17deletion
Authors: He Xi , Hesse Leah M. , Hazarika Suwagmani , Masse Gina , Harmatz Jerold S. , Greenblatt David J. , Court Michael H.
Published: August 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• UDP‐glucuronosyltransferase (UGT) 2B15 is a major drug glucuronidation enzyme expressed in human liver.

• Oxazepam is an isoform‐selective probe drug that is being used forin vitrostudies of UGT2B15.

• The most commonUGT2B15missense polymorphisms (D85Y and K523T) are correlated with variable oxazepam glucuronidation in human liver bank samples.

• UGT2B17 is also expressed in liver and has high sequence homology and substrate specificity overlap with UGT2B15.

WHAT THIS STUDY ADDS

• UGT2B15D85Y polymorphism is identified as a major determinant of oxazepam disposition, accounting for as much as 34% of interindividual variability in oxazepam apparent oral clearance.

• An effect of theUGT2B15K523T or theUGT2B17deletion polymorphisms on oxazepam disposition could not be detected.

• Provides evidence supporting the use of oxazepam as an isoform‐selectivein vivoprobe for studies of variability in UGT2B15 activity.

AIMS

Althoughin vitrostudies indicate that oxazepam is an isoform‐selective substrate probe for UDP‐glucuronosyltransferase 2B15, the utility of this drug as anin vivoprobe is uncertain. The main aim of this study was to determine whether common missense polymorphisms in theUGT2B15gene (D85Y and K523T) are associated with altered oxazepam pharmacokinetics and pharmacodynamics. We also determined the possible influence of a common deletion polymorphism in the gene encoding UGT2B17, which shows substantial substrate specificity overlap with UGT2B15.

METHODS

Thirty healthy male subjects were administered 15 mg of oxazepam by mouth followed by plasma oxazepam concentration monitoring for 36 h, and pharmacodynamic testing for 8 h. Genotypes were determined by genomic polymerase chain reaction and commercial 5′‐nuclease assays.

RESULTS

Allele frequencies for D85Y, K523T,UGT2B17del were 47%, 23% and 19%, respectively. Median oxazepam apparent oral clearance was significantly lower in 85YY subjects (1.62 ml min−1 kg−1) compared with 85DD subjects (3.35 ml min−1 kg−1;P= 0.003, Student–Newman–Keuls test), whereas 85DY subjects were intermediate (2.34 ml min−1 kg−1;P= 0.018vs.85DD,P= 0.034vs.85YY). Regression analysis indicated thatUGT2B15D85Y genotype accounted for 34% of interindividual variability. However, neitherUGT2B15K523T norUGT2B17del was associated with altered oxazepam disposition. Furthermore, no differences in pharmacodynamic measures, including quantitative electroencephalography, digit‐symbol substitution test, self‐ or observer‐rated visual analogue scales, could be demonstrated for any of the polymorphisms evaluated.

CONCLUSIONS

These results identifyUGT2B15D85Y as a major determinant of oxazepam clearance, and indicate that oxazepam may be useful as anin vivoprobe for glucuronidation by UGT2B15.
Obesity treatment: novel peripheral targets
Authors: Field Benjamin C. T. , Chaudhri Owais B. , Bloom Stephen R.
Published: August 2009

Our knowledge of the complex mechanisms underlying energy homeostasis has expanded enormously in recent years. Food intake and body weight are tightly regulated by the hypothalamus, brainstem and reward circuits, on the basis both of cognitive inputs and of diverse humoral and neuronal signals of nutritional status. Several gut hormones, including cholecystokinin, glucagon‐like peptide‐1, peptide YY, oxyntomodulin, amylin, pancreatic polypeptide and ghrelin, have been shown to play an important role in regulating short‐term food intake. These hormones therefore represent potential targets in the development of novel anti‐obesity drugs. This review focuses on the role of gut hormones in short‐ and long‐term regulation of food intake, and on the current state of development of gut hormone‐based obesity therapies.
Effects of aquatic macrophytes on organic matter deposition, resuspension and phosphorus entrainment in a lowland river
Authors: KLEEBERG ANDREAS , KÖHLER JAN , SUKHODOLOVA TATIANA , SUKHODOLOV ALEXANDER
Published: August 2009

1. Although macrophytes play a key role in the structure and functioning of lowland rivers, most of the basic plant, hydrodynamic and sediment‐water interactions have only been described qualitatively. We therefore studied quantitatively, the seasonal dynamics of matter deposition and mobilisation inside and outside (free path) a representative patch of arrowhead, Sagittaria sagittifolia, in the lowland River Spree, NE Germany, in August 2006. Our in situ study combined resuspension experiments, a hydrodynamically calibrated erosion chamber and concurrent measurements of the prevailing flow characteristics and bed load.

2. Increasing entrainment rates (E) of particles (ESPM) and total P (ETP), with increments of shear velocity (U*) from 0.53 to 2.42 cm s−1, were significantly higher inside the plant patch than outside. Indeed, ESPM and ETP at the lowest U* were 8‐ and 12‐fold higher inside than outside the patch, reflecting the resuspension potential of the upper nutrient‐enriched layer and the extent of pulsed P inputs even at small increases in U*.

3. Vertical distribution of velocity (u) revealed a flow pattern of a mixing layer inside the S. sagittifolia patch, and that of a boundary layer in the free path. The highest gradient of u in the mixing layer was located in the water column at about 0.5 m depth, whereas the highest gradient of u for the boundary layer was found near the riverbed. The maximum of U* (1.65 cm s−1) was only 4 mm above the sediment.

4. A plant mosaic provides a low‐energetic environment promoting extensive particle trapping and the accumulation of a fine‐grained, nutrient‐enriched sediment, and forming a large resuspension potential. Consequently, after plant decay and the concomitant increase of U* this material is preferentially entrained at higher rates. Hence, the key role of submerged macrophytes in lowland rivers is more directly related to modifying the dynamic equilibria between vegetation trapping and resuspension, than to the retention of nutrients, particularly P, and the reduction of P loads downstream to other waters.