bluuebunny/crossref_metadata_2025 huggingface dataset:
Transonic flows of dense gases over finite wings
Authors: Cinnella P.
Published: April 2008

Transonic inviscid flows of dense gases of the Bethe–Zel’dovich–Thompson (BZT) type over finite wings are numerically investigated. BZT gases are fluids of the retrograde type (i.e., that superheat when expanded), which exhibit a region of negative values of the fundamental derivative of gas dynamics Γ. As a consequence, they display, in the transonic and supersonic regime, nonclassical gas dynamic behaviors, such as rarefaction shock waves and mixed shock/fan waves. The peculiar properties of BZT fluids have received increased interest in recent years because of their possible application in energy-conversion cycles. The present research aims at providing insight about the transonic aerodynamics of BZT fluids past finite wings, roughly representative of isolated turbine blades with infinite tip leakage. This represents an important step toward the design of advanced turbine blades by using organic working fluids. An investigation of the flow patterns and aerodynamic performance for several choices of the upstream thermodynamic conditions is provided, and the advantages of using BZT working fluids instead of classical ones are discussed.
Dissipation and enstrophy in isotropic turbulence: Resolution effects and scaling in direct numerical simulations
Authors: Donzis D. A. , Yeung P. K. , Sreenivasan K. R.
Published: April 2008

Existing experimental and numerical data suggest that the turbulence energy dissipation and enstrophy (i.e., the square of vorticity) possess different scaling properties, while available theory suggests that there should be no differences at sufficiently high Reynolds numbers. We have performed a series of direct numerical simulations with up to 20483 grid points where advanced computational power is used to increase the Reynolds number (up to 650 on the Taylor scale) or to resolve the small scales better (down to 1∕4 of a Kolmogorov scale). Our primary goal is to assess the differences and similarities between dissipation and enstrophy. Special attention is paid to the effects of small-scale resolution on the quality and reliability of the data, in view of recent theoretical work [V. Yakhot and K. R. Sreenivasan, “Anomalous scaling of structure functions and dynamic constraints on turbulence simulations,” J. Stat. Phys. 121, 823 (2005)] which stipulates the resolution needed to obtain a moment of a given order. We also provide error estimates as a function of small-scale resolution. Probability density functions of dissipation and enstrophy at high Reynolds number reveal the presence of extreme events several thousands times of the mean. The extreme events in dissipation and enstrophy fields appear to scale alike, substantially overlap in space, and are nearly statistically isotropic, while fluctuations of moderate amplitudes, at least for the present Reynolds numbers, show persistent differences. Conditional sampling shows that intense dissipation is likely to be accompanied by similarly intense enstrophy, but intense enstrophy is not always accompanied by intense dissipation.
Solution for space charge limited field emission current densities with injection velocity and geometric effects corrections
Authors: Feng Y. , Verboncoeur J. P. , Lin M. C.
Published: April 2008

When particles are injected according to the Fowler–Nordheim (FN) field emission equation, the transmitted current density will transition to the space charge limited (SCL) current density, with increasing applied diode voltage. The actual transmitted current density is the so-called SCL-FN current density. In this work, Barbour’s analytic solution for the SCL-FN current density is modified with consideration of injection velocity and also geometric effects, by solving the advanced FN equation with the effective field enhancement factor, the energy conservation equation with an initial velocity term, and Poisson’s equation simultaneously. The solution is also extended to the relativistic regime where similar transition process is found. This solution has been verified using particle-in-cell simulation with varying diode voltage, electron injection velocity, and field enhancement factor.
Limiting efficiency of an intermediate band solar cell under a terrestrial spectrum
Authors: Bremner Stephen P. , Levy Michael Y. , Honsberg Christiana B.
Published: April 2008

The limiting efficiency of an intermediate band (IB) solar cell under the terrestrial AM1.5 spectrum was calculated by detailed balance for various concentration levels. The results show four energy gap combinations giving similar limiting efficiencies. This is in contrast to the more studied case of an IB solar cell under a blackbody spectrum where a single optimum combination is found. A design with a subenergy gap of ∼0.57eV is found to be viable, leading to the conclusion that the design space for an IB solar cell is larger when under the AM1.5 spectrum than when under a Blackbody spectrum.
Improved frequency/voltage converters for fast quartz crystal microbalance applications
Authors: Torres R. , García J. V. , Arnau A. , Perrot H. , Kim L. To Thi , Gabrielli C.
Published: April 2008

The monitoring of frequency changes in fast quartz crystal microbalance (QCM) applications is a real challenge in today’s instrumentation. In these applications, such as ac electrogravimetry, small frequency shifts, in the order of tens of hertz, around the resonance of the sensor can occur up to a frequency modulation of 1kHz. These frequency changes have to be monitored very accurately both in magnitude and phase. Phase-locked loop techniques can be used for obtaining a high performance frequency/voltage converter which can provide reliable measurements. Sensitivity higher than 10mV∕Hz, for a frequency shift resolution of 0.1Hz, with very low distortion in tracking both the magnitude and phase of the frequency variations around the resonance frequency of the sensor are required specifications. Moreover, the resonance frequency can vary in a broad frequency range from 5to10MHz in typical QCM sensors, which introduces an additional difficulty. A new frequency-voltage conversion system based on a double tuning analog-digital phase-locked loop is proposed. The reported electronic characterization and experimental results obtained with conducting polymers prove its reliability for ac-electrogravimetry measurements and, in general, for fast QCM applications.
Magnetic structure and orbital ordering in tetragonal and monoclinic KCrF3 from first-principles calculations
Authors: Xu Yuanhui , Hao Xianfeng , Lv Minfeng , Wu Zhijian , Zhou Defeng , Meng Jian
Published: April 2008

K Cr F 3 has been systematically investigated by using the full-potential linearized augmented plane wave plus local orbital method within the generalized gradient approximation and the local spin density approximation plus the on-site Coulomb repulsion approach. The total energies for ferromagnetic and three different antiferromagnetic configurations are calculated in the high-temperature tetragonal and low-temperature monoclinic phases, respectively. It reveals that the ground state is the A-type antiferromagnetic in both phases. Furthermore, the ground states of the two phases are found to be Mott–Hubbard insulators with the G-type orbital ordering pattern. In addition, our calculations show the staggered orbital ordering of the 3dx2 and 3dy2 orbitals for the tetragonal phase and the 3dz2 and 3dx2 orbitals for the monoclinic phase, which is in agreement with the available data. More importantly, the relationship between magnetic structure and orbital ordering as well as the origin of the orbital ordering are analyzed in detail.
On the number of significant mode-mode anharmonic couplings in vibrational calculations: Correlation-corrected vibrational self-consistent field treatment of di-, tri-, and tetrapeptides
Authors: Pele Liat , Gerber R. Benny
Published: April 2008

A computational study is made of the number of important anharmonic mode-mode couplings in the context of vibrational calculations for di-, tri-, and tetrapeptides. The method employed is the correlation-corrected vibrational self-consistent field (CC-VSCF) algorithm, which includes correlation effects between different vibrational modes. It is found that results of good accuracy can be obtained in calculations that include only NlogN mode-mode coupling terms, where N is the number of modes. This simplification significantly accelerates CC-VSCF calculations for large molecules. A criterion based on the characteristics of the normal-mode displacements is employed to predict a priori unimportant coupling terms. The criterion is tested statistically using Spearman’s rank correlation coefficient. The results are illustrated by calculations for several di-, tri-, and tetrapeptides using semiempirical PM3 potential surfaces. These results are analyzed and a statistical model for error estimation is given. The decrease in the number of included coupling from N2 to NlogN opens possibilities of anharmonic vibrational calculations for large peptides.
Depth evaluation of surface-breaking cracks using laser-generated transmitted Rayleigh waves
Authors: Moura André , Lomonosov Alexey M. , Hess Peter
Published: April 2008

A theoretical and experimental study of nondestructive evaluation of surface-breaking cracks with linear surface acoustic wave (SAW) pulses is presented. Schwarz–Christoffel conformal mapping was used to introduce a special orthogonal coordinate system that conserves the profile of the cracked surface. The inverse problem for two dimensions has been solved by means of conformal mapping. Thermoelastically generated broadband SAW pulses were employed to study the scattering of linear SAW pulses by a single crack. The surface wave component transmitted through the isolated microcrack was recorded as a function of distance by the cw laser probe-beam-deflection method. The Fourier transform of the transmitted SAW waveforms provides a stationary solution for any frequency. With this procedure the depth of the crack, produced in a separate experiment with a strongly nonlinear SAW pulse in a silica sample, was evaluated.
A weakly nonlocal anisotropic fluid model for inhomogeneous Stokesian suspensions
Authors: Goddard J. D.
Published: April 2008

A continuum model is proposed for a weakly inhomogeneous Stokesian suspensions, as an extension with minor amendments of a previous work on homogeneous suspensions [J. D. Goddard, J. Fluid Mech. 568, 1 (2006)]. In the present model, stress and particle flux are given as invariant tensor functions of particle volume fraction ϕ, deformation rate E, and second-rank anisotropy tensor A, in a form that is also linear in E and the gradients of ϕ, E, and A. In contrast to models without history dependence, all nonlinear dependence of particle flux on E arises from the evolution of A. Detailed attention is paid to unsteady viscometric flow, where a contribution of streamline curvature to particle migration emerges as a natural consequence of tensorial gradients. The model predicts equal curvature-induced fluxes in gradient and vorticity directions but there is an unexplained disagreement with recent experiments on Couette and torsional flows. A previously proposed corotational evolution equation for A, with a two-mode exponential relaxation, is employed to investigate the transient response following the reversal of shearing in sinusoidal and in steady shear. The model predicts roughly equal response for the two flows if sinusoidal strains are of order unity, which is consistent with some but not all experiments. The model for particle flux admits an asymmetric diffusion tensor which, owing to Stokesian reversibility, can become nonpositive upon abrupt reversal of shearing. This effect is diminished by non-Stokesian response on short strain scales, which, although poorly understood, appears essential to elementary models without dependence on shear history. A synthesis is given of multipolar Stokesian resistance and the associated Stokesian dynamics, showing how these follow from a single grand resistance kernel. In addition to unifying and extending large literature on Stokesian resistance formulae, this provides some justification for the proposed continuum model and possible multipolar extensions.
Some issues concerning large-eddy simulation of inertial particle dispersion in turbulent bounded flows
Authors: Marchioli C. , Salvetti M. V. , Soldati A.
Published: April 2008

The problem of accurate Eulerian–Lagrangian modeling of inertial particle dispersion in large-eddy simulation (LES) of turbulent wall-bounded flows is addressed. We run direct numerical simulation (DNS) of turbulent channel flow at shear Reynolds number Reτ=150 and corresponding a priori and a posteriori LES on two coarser grids. For each flow field, we tracked swarms of particles with different inertia to examine the behavior of particle statistics, specifically focusing on particle preferential segregation and accumulation at the wall. Our object is to discuss the necessity of a closure model for the particle equations when using LES and we verify if the influence of the subgrid turbulence filtered by LES is an important effect on particle motion according to particle size. The results show that well-resolved LES gives particle velocity statistics in satisfactory agreement with DNS. However, independent of the grid, quantitatively inaccurate predictions are obtained for local particle preferential segregation, particularly in the near-wall region. Inaccuracies are observed for the entire range of particle size considered in this study, even when the particle response time is much larger than the flow time scales not resolved in LES. The satisfactory behavior of LES in reproducing particle velocity statistics is thus counterbalanced by the inaccurate representation of local segregation phenomena, indicating that closure models supplying the particle motion equation with an adequate rendering of the flow field might be needed. Finally, we remark that recovering the level of fluid and particle velocity fluctuations in the particle equations does not ensure a quantitative replica of the subgrid turbulence effects, thus implying that accurate subgrid closure models for particles may require information also proportional to the higher-order moments of the velocity fluctuations.
Numerical investigation of three-dimensional cloud cavitation with special emphasis on collapse induced shock dynamics
Authors: Schnerr Günter H. , Sezal Ismail H. , Schmidt Steffen J.
Published: April 2008

The aim of the present investigation is to model and analyze compressible three-dimensional (3D) cavitating liquid flows with special emphasis on the detection of shock formation and propagation. We recently developed the conservative finite volume method CATUM (Cavitation Technische Universität München), which enables us to simulate unsteady 3D liquid flows with phase transition at all Mach numbers. The compressible formulation of the governing equations together with the thermodynamic closure relations are solved by a modified Riemann approach by using time steps down to nanoseconds. This high temporal resolution is necessary to resolve the wave dynamics that leads to acoustic cavitation as well as to detect regions of instantaneous high pressure loads. The proposed two-phase model based on the integral average properties of thermodynamic quantities is first validated against the solution of the Rayleigh–Plesset equation for the collapse of a single bubble. The computational fluid dynamics tool CATUM is then applied to the numerical simulation of the highly unsteady two-phase flow around a 3D twisted hydrofoil. This specific hydrofoil allows a detailed study of sheet and cloud cavitation structures related to 3D shock dynamics emerging from collapsing vapor regions. The time dependent development of vapor clouds, their shedding mechanism, and the resulting unsteady variation of lift and drag are discussed in detail. We identify instantaneous local pressure peaks of the order of 100bar, which are thought to be responsible for the erosive damage of the surface of the hydrofoil.
Interacting two-dimensional bubbles and droplets in a yield-stress fluid
Authors: Singh John P. , Denn Morton M.
Published: April 2008

We study the buoyancy-driven motion of two-dimensional bubbles and droplets in a Bingham fluid using a regularization method. The finite-element computations are carried out using the method of level sets to track the interface. We find that multiple bubbles and droplets can move in a body force field under conditions where a single bubble or droplet with the same physical properties would be unable to overcome the integrated yield stress and would be trapped. The finite yielded region around a single bubble or droplet in a Bingham fluid causes a backflow, resulting in unyielded “ears” that rotate and exchange material points with the yielded fluid to maintain a fixed position on the equatorial plane as the bubble rises or the droplet falls. The backflow flattens the tail of the trailing bubble or droplet in a pair and, at a sufficiently high level of interfacial tension, causes a splitting of the tail and the creation of a cusp. Three bubbles in a triangular configuration interact in a manner that is qualitatively predictable by considering pair interactions. Despite important differences in detail, the general shape evolution of bubbles and droplets in a Bingham fluid is similar to that in a Newtonian liquid when time scales are considered on a comparable basis.
Statistical equilibrium of bubble oscillations in dilute bubbly flows
Authors: Colonius Tim , Hagmeijer Rob , Ando Keita , Brennen Christopher E.
Published: April 2008

The problem of predicting the moments of the distribution of bubble radius in bubbly flows is considered. The particular case where bubble oscillations occur due to a rapid (impulsive or step change) change in pressure is analyzed, and it is mathematically shown that in this case, inviscid bubble oscillations reach a stationary statistical equilibrium, whereby phase cancellations among bubbles with different sizes lead to time-invariant values of the statistics. It is also shown that at statistical equilibrium, moments of the bubble radius may be computed using the period-averaged bubble radius in place of the instantaneous one. For sufficiently broad distributions of bubble equilibrium (or initial) radius, it is demonstrated that bubble statistics reach equilibrium on a time scale that is fast compared to physical damping of bubble oscillations due to viscosity, heat transfer, and liquid compressibility. The period-averaged bubble radius may then be used to predict the slow changes in the moments caused by the damping. A benefit is that period averaging gives a much smoother integrand, and accurate statistics can be obtained by tracking as few as five bubbles from the broad distribution. The period-averaged formula may therefore prove useful in reducing computational effort in models of dilute bubbly flow wherein bubbles are forced by shock waves or other rapid pressure changes, for which, at present, the strong effects caused by a distribution in bubble size can only be accurately predicted by tracking thousands of bubbles. Some challenges associated with extending the results to more general (nonimpulsive) forcing and strong two-way coupled bubbly flows are briefly discussed.
Simultaneous analytical optimization of variational parameters in Gaussian-type functions with full configuration interaction of multicomponent molecular orbital method by elimination of translational and rotational motions: Application to isotopomers of the hydrogen molecule
Authors: Ishimoto Takayoshi , Tachikawa Masanori , Nagashima Umpei
Published: April 2008

We have extended the multicomponent molecular orbital (MC̱MO) method to the full-configuration interaction (full-CI) fully variational molecular orbital method by elimination of translational and rotational motion components from total Hamiltonian. In the MC̱MO scheme, the quantum effects of protons and deuterons as well as electrons can be directly taken into account. All variational parameters in the full-CI scheme, i.e., exponents and centers (α and R) in the Gaussian-type function (GTF) basis set as well as the CI coefficients, are simultaneously optimized by using their analytical gradients. The total energy of the H2 molecule calculated using the electronic [6s3p2d1f] and nuclear [1s1p1d1f] GTFs is −1.161726hartree, which can be compared to the energy of −1.164025hartree reported using a 512 term-explicitly correlated GTF calculation. Although the d- and f-type nuclear GTFs contribute to the improvement of energy convergence, the convergence of electron-nucleus correlation energy is slower than that of electron-electron one. The nuclear wave functions are delocalized due to the electron-nucleus correlation effect compared to the result of Hartree–Fock level of MC̱MO method. In addition, the average internuclear distances of all diatomic molecules are within 0.001Å of the previously reported experimental results. The dipole moment of the HD molecule estimated by our method is 8.4×10−4D, which is in excellent agreement with the experimental result of (8–10)×10−4D.
Ion core structure in (CS2)n+ and (CS2)n− (n=3–10) studied by infrared photodissociation spectroscopy
Authors: Kobayashi Yusuke , Inokuchi Yoshiya , Ebata Takayuki
Published: April 2008

Infrared photodissociation spectra of (CS2)n+ and (CS2)n− with n=3–10 are measured in the 1100–2000cm−1 region. All the (CS2)n+ clusters exhibit three bands at ∼1410, ∼1490, and ∼1540cm−1. The intensity of the 1540cm−1 band relative to those of the other bands increases with increasing the cluster size, indicating that the band at 1540cm−1 is assignable to the antisymmetric CS stretching vibration of solvent CS2 molecules in the clusters. On the basis of density functional theory calculations, the 1410 and 1490cm−1 bands of (CS2)n+ are assigned to CS stretching vibrations of the C2S4+ cation core with a C2 form. The (CS2)n− clusters show two bands at around 1215 and 1530cm−1. Similar to the case of cation clusters, the latter band is ascribed to the antisymmetric CS stretching vibration of solvent CS2 molecules. Vibrational frequency analysis of CS2− and C2S4− suggests that the 1215cm−1 band is attributed to the antisymmetric CS stretching vibration of the CS2− anion core with a C2v structure.
Optical determination of the flexural rigidity of carbon nanotube ensembles
Authors: Ni C. , Deck C. , Vecchio K. S. , Bandaru P. R.
Published: April 2008

We demonstrate two simple and consistent optical methods for quantitatively determining the flexural rigidity EI (where E is the elastic modulus and I the moment of inertia), a quantity of practical importance in determining the deflection and buckling characteristics of carbon nanotubes (CNTs). This is done through monitoring the deflection of patterned arrays of CNTs, which are subject to fluid flow. In addition to mechanical characterization of filamentous nanostructures, the implications of our work extend to the monitoring of nanoscale fluid flows for tactile and shear force sensors and the characterization of the mechanosensor response of cilia in physiology.
Piezoelectric properties of lithium modified silver niobate perovskite single crystals
Authors: Fu Desheng , Endo Makoto , Taniguchi Hiroki , Taniyama Tomoyasu , Koshihara Shin-ya , Itoh Mitsuru
Published: April 2008

We report the growth and the piezoelectric properties of lead-free perovskite single crystals of Ag1−xLixNbO3. It possesses a rhombohedral structure with high ferroelectric phase transition (Tc=548K for x=0.086) and large spontaneous polarization (Ps∼40μC∕cm2 for x=0.062) along the ⟨111⟩c direction of pseudocubic perovskite structure for x>0.05–0.06. High quasistatic d33∼210pC∕N and low dielectric constant have lead to a very large value of piezoelectric voltage constant g33∼53.9×10−3Vm∕N for the ⟨001⟩c-cut crystal of this simple perovskite. It has been shown that Li substitution might enhance the piezoelectric coefficient of the crystal. The excellent piezo-/ferroelectricity of this system are considered to be facilitated by the strong polarization nature of both Ag and Li in the perovskite structure. Our findings may stimulate further interests in the development of lead-free piezoelectrics.
Spin-polarized current and spin accumulation in a three-terminal two quantum dots ring
Authors: Chi Feng , Zheng Jun , Sun Lian-Liang
Published: April 2008

We study the coexistence of the spin-polarized current and the spin accumulation in a three-terminal quantum ring structure, in which two quantum dots (QDs) are inserted in one arm of the ring and the Rashba spin-orbit interaction (RSOI) exists in the other. We find that by properly adjusting the applied voltages in the three leads, the RSOI-induced phase factor and the parameters relevant to the QDs, the spin-polarization efficiency in the leads can achieve either 100% or infinite, and the electrons of the same or different spin directions can accumulate in the two dots, respectively. The manipulation of the electron spin in the present device relies on the RSOI and the electric fields, thus making it realizable with the currently existing technologies.
Organic anions in the rhizosphere of Al-tolerant and Al-sensitive wheat lines grown in an acid soil in controlled and field environments
Authors: Schefe C. R. , Watt M. , Slattery W. J. , Mele P. M.
Published: April 2008

Several sampling methods were investigated for the quantification of organic anions in the rhizosphere of Al-tolerant (ET8) and Al-sensitive (ES8) wheat plants in soil systems. Controlled environment studies used anion exchange membranes to collect rhizosphere organic anions (from root tips and mature regions of nodal roots) from ET8 and ES8 plants at the 6-leaf stage in a glasshouse environment. Using the anion exchange membranes, a selection of organic anions were detected on the tips and mature regions of roots, with ET8 and ES8 having similar rhizosphere organic anion profiles. The field experiment used 2 established methods of organic anion collection: rhizosphere soil and root washings. The ET8 and ES8 wheat lines had similar levels of organic anions, including malate, in the rhizosphere (using soil shaken from roots and root washings) at 3 sampling times (4 and 6 leaves, and flowering). The rhizosphere organic anions differed significantly from the bulk soil, with the concentration and range of organic anions in the rhizosphere decreasing towards flowering, presumably due to physiological changes in plant and root growth. This study used several techniques to investigate organic anion exudation by roots, with organic anions detected using all techniques. However, technical limitations of these techniques were recognised: (i) the lack of simultaneous exposure of root tips to both the anion exchange membrane and the chemical stimulant, e.g. Al3+; and (ii) the inability to derive the origin of organic anions measured in rhizosphere soil and root washings. The challenge for future soil-based organic anion research is to identify the dominant stress that has triggered an exudation response (i.e. Al toxicity, P deficiency), and to clearly differentiate between plant- and microbial-derived contributions to exudation.
β-Arrestin-1 mediates glucagon-like peptide-1 signaling to insulin secretion in cultured pancreatic β cells
Authors: Sonoda Noriyuki , Imamura Takeshi , Yoshizaki Takeshi , Babendure Jennie L. , Lu Juu-Chin , Olefsky Jerrold M.
Published: April 2008

Glucagon-like peptide-1 (GLP-1) is a polypeptide hormone secreted from enteroendocrine L cells and potentiates glucose-dependent insulin secretion in pancreatic β cells. Recently the GLP-1 receptor (GLP-1 R) has been a focus for new anti-diabetic therapy with the introduction of GLP-1 analogues and DPP-IV inhibitors, and this has stimulated additional interest in the mechanisms of GLP-1 signaling. Here we identify a mechanism for GLP-1 action, showing that the scaffold protein β-arrestin-1 mediates the effects of GLP-1 to stimulate cAMP production and insulin secretion in β cells. Using a coimmunoprecipitation technique, we also found a physical association between the GLP-1 R and β-arrestin-1 in cultured INS-1 pancreatic β cells. β-Arrestin-1 knockdown broadly attenuated GLP-1 signaling, causing decreased ERK and CREB activation and IRS-2 expression as well as reduced cAMP levels and impaired insulin secretion. However, β-arrestin-1 knockdown did not affect GLP-1 R surface expression and ligand-induced GLP-1 R internalization/desensitization. Taken together, these studies indicate that β-arrestin-1 plays a role in GLP-1 signaling leading to insulin secretion, defining a previously undescribed mechanism for GLP-1 action.
Design of protein function leaps by directed domain interface evolution
Authors: Huang Jin , Koide Akiko , Makabe Koki , Koide Shohei
Published: April 2008

Most natural proteins performing sophisticated tasks contain multiple domains where an active site is located at the domain interface. Comparative structural analyses suggest that major leaps in protein function occur through gene recombination events that connect two or more protein domains to generate a new active site, frequently occurring at the newly created domain interface. However, such functional leaps by combination of unrelated domains have not been directly demonstrated. Here we show that highly specific and complex protein functions can be generated by joining a low-affinity peptide-binding domain with a functionally inert second domain and subsequently optimizing the domain interface. These directed evolution processes dramatically enhanced both affinity and specificity to a level unattainable with a single domain, corresponding to >500-fold and >2,000-fold increases of affinity and specificity, respectively. An x-ray crystal structure revealed that the resulting “affinity clamp” had clamshell architecture as designed, with large additional binding surface contributed by the second domain. The affinity clamps having a single-nanomolar dissociation constant outperformed a monoclonal antibody in immunochemical applications. This work establishes evolutionary paths from isolated domains with primitive function to multidomain proteins with sophisticated function and introduces a new protein-engineering concept that allows for the generation of highly functional affinity reagents to a predefined target. The prevalence and variety of natural interaction domains suggest that numerous new functions can be designed by using directed domain interface evolution.
National and ethnic identity markers
Authors: Starks Donna
Published: April 2008

The New Zealand (NZ) short front vowels are often considered as a defining feature of New Zealand English (NZE), yet research which has considered data from both the Pakeha (NZ European) and the NZ Maori communities has noted slightly different patterns in the realisations of the vowel in the KIT lexical set in the respective communities (Bell 1997a, b; Warren and Bauer 2004). This paper compares the short front vowel series of NZ Maori students with that of NZ Samoan, Tongan, Cook Island and Niuean students and demonstrates how the NZ short front vowel series mark both similarity and difference across NZ communities. Our findings show that NZ Maori students have a greater degree of centralisation in their KIT vowel and a greater degree of raising of their DRESS and TRAP vowels than their NZ Pasifika counterparts. However, the manner in which the vowels raise and centralise distinguishes NZ Maori and Cook Island students from their NZ Samoan, Tongan and Niuean cohorts. The latter observation highlights problems with the pan-ethnic “Pasifika” label used to distinguish NZ Maori from other NZ Polynesian communities.
Diuron Lacks Promoting Potential in a Rat Liver Bioassay
Authors: Grassi Tony Fernando , Tararam Cibele Aparecida , Spinardi-Barbisan Ana Lúcia Tozzi , Domingues Maria Aparecida Custódio , de Camargo João Lauro Viana , Barbisan Luís Fernando
Published: April 2008

The promoting activity of the herbicide Diuron was evaluated in a medium-term rat liver carcinogenesis bioassay that uses as endpoint immunohistochemically identified glutathione S-transferase positive (GST-P+) foci. Male Wistar rats were allocated to the following groups: G1 to G6 were initiated for liver carcinogenesis by a single dose of diethylnitrosamine (DEN, 200 mg/kg) while groups G7 and G8 received only 0.9% NaCl (DEN vehicle). From the 2nd week animals were fed a basal diet (G1 and G7) or a diet added with Diuron at 125, 500, 1250, 2500 and 2500 ppm (G2 to G5 and G8, respectively) or 200 ppm Hexaclorobenzene (HCB; G6). The animals were submitted to 70% partial hepatectomy at the 3rd week and sacrificed at the 8th week. The herbicide did not alter ALT or creatinine serum levels. No conspicuous GST-P+ foci development was registered in non-initiated rats fed Diuron at 2500 ppm. While DEN-initiated animals fed Diuron at 1250 or 2500 ppm developed mild centrilobular hypertrophy, DEN-initiated HCB-fed animals showed severe liver centrilobular hypertrophy and significant GST-P+ foci development. These findings indicate that the medium-term assay adopted in this study does not reveal any liver carcinogenesis initiating or promoting potential of Diuron in the rat.
Differential Tumor Biology Effects of Double-Initiation in a Mouse Skin Chemical Carcinogenesis Model Comparing Wild Type versus Protein Kinase Cepsilon Overexpression Mice
Authors: Li Yafan , Wheeler Deric L. , Ananthaswamy Honnavara N. , Verma Ajit K. , Oberley Terry D.
Published: April 2008

Our previous studies showed that protein kinase Cepsilon (PKCɛ) verexpression in mouse skin resulted in metastatic squamous cell carcinoma (SCC) elicited by single 7,12-dimethylbenz(a)anthracene (DMBA)-initiation and 12-O-tetradecanoylphorbol-13-acetate (TPA)-promotion in the absence of preceding papilloma formation as is typically observed in wild type mice. The present study demonstrates that double-DMBA initiation modulates tumor incidence, multiplicity, and latency period in both wild type and PKCɛoverexpression transgenic (PKCɛ-Tg) mice. After 17 weeks (wks) of tumor promotion, a reduction in papilloma multiplicity was observed in double- versus single-DMBA initiated wild type mice. Papilloma multiplicity was inversely correlated with cell death indices of interfollicular keratinocytes, indicating decreased papilloma formation was caused by increased cell death and suggesting the origin of papillomas is in interfollicular epidermis. Double-initiated PKCɛ-Tg mice had accelerated carcinoma formation and cancer incidence in comparison to single-initiated PKCɛ-Tg mice. Morphologic analysis of mouse skin following double initiation and tumor promotion showed a similar if not identical series of events to those previously observed following single initiation and tumor promotion: putative preneoplastic cells were observed arising from hyperplastic hair follicles (HFs) with subsequent cancer cell infiltration into the dermis. Single-initiated PKCɛ-Tg mice exhibited increased mitosis in epidermal cells of HFs during tumor promotion.
The Demonstration of Immunohistochemical Biomarkers in Methyl Methacrylate-Embedded Plucked Human Hair Follicles
Authors: Randall Kevin J , Foster John R.
Published: April 2008

Plucked human hair follicles have been proposed as a potential surrogate for tumour tissue for measuring the effect of drugs on pharmacodynamic biomarkers in drug intervention studies. We describe a new technique of embedding plucked hair follicles in the acrylic resin, methyl methacrylate, and the immunohistochemical demonstration of six potential biomarkers (Ki67, EGFR, phospho-p27, phospho-histone H3, phospho-MAPK and phospho-Rb) in de-plasticised sections. The advantages of this technique over those that have been used in support of clinical drug trials, such as skin and tumour biopsies, whole blood and whole hair samples is discussed.
Temporal Clinical Chemistry and Microscopic Renal Effects Following Acute Uranyl Acetate Exposure
Authors: Zimmerman Kurt L. , Barber David S. , Ehrich Marion F. , Tobias Lynette , Hancock Sandra , Hinckley J. , Binder Ellen M. , Jortner Bernard S.
Published: April 2008

Military use of depleted uranium (DU) has renewed interest in the toxicology of this metal. In this study, the nephrotoxicity of single exposure DU was assessed with and without pre-exposure stress. Adult male Sprague–Dawley rats (n = 288) were administered a single IM dose of 0, 0.1, 0.3 or 1.0 mg/kg DU. Corticosterone concentrations (ng/ml, mean ± SD) were 763.65 ± 130.94 and 189.80 ± 90.81 for swim stressed and unstressed rats. Serum and kidney uranium concentration, hematocrit, chemistry, and renal histology were assessed on sacrifice days 1, 3, 7 and 30 post-DU-dosing. Dose related increases in serum and kidney uranium were noted. DU concentration peaked day 1 in the kidney and days 3–7, in the serum. Dose-related elevations of Cr and BUN concentrations were seen on days 3 and 7. A decline in serum albumin coincided with Cr and BUN suggesting protein losing nephropathy. Dose related acute tubular necrosis and proliferative glomulonephritis were seen. Tubular regeneration in low dose rats was almost complete by day 30. High dose rats had extensive tubular necrosis and delayed regeneration with focal residual chronic interstitial nephritis and cortical scarring. Glomular changes were reversed in all treatment groups by day 30. Stress exposure had no impact on any measured renal parameter.
nuScore: a web-interface for nucleosome positioning predictions
Authors: Tolstorukov Michael Y. , Choudhary Vidhu , Olson Wilma K. , Zhurkin Victor B. , Park Peter J.
Published: April 2008

Summary: Sequence-directed mapping of nucleosome positions is of major biological interest. Here, we present a web-interface for estimation of the affinity of the histone core to DNA and prediction of nucleosome arrangement on a given sequence. Our approach is based on assessment of the energy cost of imposing the deformations required to wrap DNA around the histone surface. The interface allows the user to specify a number of options such as selecting from several structural templates for threading calculations and adding random sequences to the analysis.

Availability: The nuScore interface is freely available for use at http://compbio.med.harvard.edu/nuScore.

Contact:  peter_park@harvard.edu; tolstorukov@gmail.com

Supplementary information: The site contains user manual, description of the methodology and examples.
jSquid: a Java applet for graphical on-line network exploration
Authors: Klammer Martin , Roopra Sanjit , Sonnhammer Erik L. L.
Published: April 2008

Summary: jSquid is a graph visualization tool for exploring graphs from protein–protein interaction or functional coupling networks. The tool was designed for the FunCoup web site, but can be used for any similar network exploring purpose. The program offers various visualization and graph manipulation techniques to increase the utility for the user.

Availability: jSquid is available for direct usage and download at http://jSquid.sbc.su.se including source code under the GPLv3 license, and input examples. It requires Java version 5 or higher to run properly.

Contact:  erik.sonnhammer@sbc.su.se

Supplementary information:  Supplementary data are available at Bioinformatics online.
Viability of brown trout embryos positively linked to melanin-based but negatively to carotenoid-based colours of their fathers
Authors: Wedekind Claus , Jacob Alain , Evanno Guillaume , Nusslé Sébastien , Müller Rudolf
Published: April 2008

‘Good-genes’ models of sexual selection predict significant additive genetic variation for fitness-correlated traits within populations to be revealed by phenotypic traits. To test this prediction, we sampled brown trout (Salmo trutta) from their natural spawning place, analysed their carotenoid-based red and melanin-based dark skin colours and tested whether these colours can be used to predict offspring viability. We produced half-sib families byin vitrofertilization, reared the resulting embryos under standardized conditions, released the hatchlings into a streamlet and identified the surviving juveniles 20 months later with microsatellite markers. Embryo viability was revealed by the sires' dark pigmentation: darker males sired more viable offspring. However, the sires' red coloration correlated negatively with embryo survival. Our study demonstrates that genetic variation for fitness-correlated traits is revealed by male colour traits in our study population, but contrary to predictions from other studies, intense red colours do not signal good genes.
Community extinction patterns in coloured environments
Authors: Ruokolainen Lasse , Fowler Mike S
Published: April 2008

Understanding community responses to environmental variation is a fundamental aspect of ecological research, with direct ecological, conservation and economic implications. Here, we examined the role of the magnitude, correlation and autocorrelation structures of environmental variation on species' extinction risk (ER), and the probability of actual extinction events in model competitive communities. Both ER and probability increased with increasing positive autocorrelation when species responded independently to the environment, yet both decreased with a strong correlation between species-specific responses. These results are framed in terms of the synchrony between—and magnitude of variation within—species population sizes and are explained in terms of differences in noise amplification under different conditions. The simulation results are robust to changes in the strength of interspecific density dependence, and whether noise affects density-independent or density-dependent population processes. Similar patterns arose under different ranges of noise severity when these different model assumptions were examined. We compared our results with those from an analytically derived solution, which failed to capture many features of the simulation results.
Bacterioferritin from Mycobacterium smegmatis contains zinc in its di‐nuclear site
Authors: Janowski Robert , Auerbach‐Nevo Tamar , Weiss Manfred S.
Published: April 2008

Bacterioferritins, also known as cytochrome b 1, are oligomeric iron‐storage proteins consisting of 24 identical amino acid chains, which form spherical particles consisting of 24 subunits and exhibiting 432 point‐group symmetry. They contain one haem b molecule at the interface between two subunits and a di‐nuclear metal binding center. The X‐ray structure of bacterioferritin from Mycobacterium smegmatis (Ms‐Bfr) was determined to a resolution of 2.7 Å in the monoclinic space group C2. The asymmetric unit of the crystals contains 12 protein molecules: five dimers and two half‐dimers located along the crystallographic twofold axis. Unexpectedly, the di‐nuclear metal binding center contains zinc ions instead of the typically observed iron ions in other bacterioferritins.
Toward chaperone‐assisted crystallography: Protein engineering enhancement of crystal packing and X‐ray phasing capabilities of a camelid single‐domain antibody (VHH) scaffold
Authors: Tereshko Valentina , Uysal Serdar , Koide Akiko , Margalef Katrina , Koide Shohei , Kossiakoff Anthony A.
Published: April 2008

A crystallization chaperone is an auxiliary protein that binds to a target of interest, enhances and modulates crystal packing, and provides high‐quality phasing information. We critically evaluated the effectiveness of a camelid single‐domain antibody (VHH) as a crystallization chaperone. By using a yeast surface display system for VHH, we successfully introduced additional Met residues in the core of the VHH scaffold. We identified a set of SeMet‐labeled VHH variants that collectively produced six new crystal forms as the complex with the model antigen, RNase A. The crystals exhibited monoclinic, orthorhombic, triclinic, and tetragonal symmetry and have one or two complexes in the asymmetric unit, some of which diffracted to an atomic resolution. The phasing power of the Met‐enriched VHH chaperone allowed for auto‐building the entire complex using single‐anomalous dispersion technique (SAD) without the need for introducing SeMet into the target protein. We show that phases produced by combining SAD and VHH model‐based phases are accurate enough to easily solve structures of the size reported here, eliminating the need to collect multiple wavelength multiple‐anomalous dispersion (MAD) data. Together with the presence of high‐throughput selection systems (e.g., phage display libraries) for VHH, the enhanced VHH domain described here will be an excellent scaffold for producing effective crystallization chaperones.
Frequent silencing of a putative tumor suppressor gene melatonin receptor 1 A (MTNR1A) in oral squamous‐cell carcinoma
Authors: Nakamura Erina , Kozaki Ken‐ichi , Tsuda Hitoshi , Suzuki Emina , Pimkhaokham Atiphan , Yamamoto Gou , Irie Tarou , Tachikawa Tetsuhiko , Amagasa Teruo , Inazawa Johji , Imoto Issei
Published: April 2008

Array‐based comparative genomic hybridization (array‐CGH) has good potential for the high‐throughput identification of genetic aberrations in cell genomes. In the course of a program to screen a panel of 21 oral squamous‐cell carcinoma (OSCC) cell lines for genome‐wide copy‐number aberrations by array‐CGH using our in‐house bacterial artificial chromosome arrays, we identified a frequent homozygous deletion at 4q35 loci with approximately 1 Mb in extent. Among the seven genes located within this region, the expression of the melatonin receptor 1 A (MTNR1A) messenger RNA (mRNA) was not detected or decreased in 35 out of the 39 (89%) OSCC cell lines, but was detected in immortalized normal oral epithelial cell line, and was restored in gene‐silenced OSCC cells without its homozygous loss after treatment with 5‐aza‐2′‐deoxycytidine. The hypermethylation of the CpG (cytosine and guanine separated by phosphate) island in the promoter region of MTNR1A was inversely correlated with its expression in OSCC lines without a homozygous deletion. Methylation of this CpG island was also observed in primary OSCC tissues. In an immunohistochemical analysis of 50 primary OSCC tumors, the absence of immunoreactive MTNR1A was significantly associated with tumor size and a shorter overall survival in patients with OSCC tumors, and seems to be an independent prognosticator in a multivariate analysis. Exogenous restoration of MTNR1A expression inhibited the growth of OSCC cells lacking its expression. Together with the known tumor‐suppressive function of melatonin and MTNR1A in various tumors, our results indicate MTNR1A to be the most likely target for epigenetic silencing at 4q35 and to play a pivotal role during oral carcinogenesis. (Cancer Sci 2008; 99: 1390–1400)
Identification of a CD4 T‐cell epitope in tumor rejection antigen RLakt on BALB/c radiation‐leukemia RL male 1
Authors: Kaya Savas , Uenaka Akiko , Sato Shuichiro , Ono Toshiro , Aji Toshiki , Nakayama Eiichi
Published: April 2008

We have previously shown that the RLakt antigen was predominantly recognized by CD8 cytotoxic T lymphocytes (CTL) in RL male 1‐bearing or ‐rejected syngeneic BALB/c mice. CD8 CTL were directed to the octamer pRL1a peptide IPGLPLSL of which recognition was H‐2Ld‐restricted. In this study, we identified a CD4 T‐cell epitope peptide in the tumor rejection antigen RLakt on BALB/c radiation‐leukemia RL male 1. Analyses of the recognition of a bulk CD4 T‐cell line using several recombinant RLakt proteins suggested the presence of multiple CD4 T‐cell epitopes in the molecule. However, cloning from a bulk CD4 T‐cell line resulted in only two clones from 200 wells seeded at three cells per well, and those two CD4 T‐cell clones recognized the same epitope peptide in RLakt. The epitope peptide was 14‐mer p12‐25, AYREETLSIIPGLP, and its recognition was H‐2IAd‐restricted. This sequence overlapped with the CD8 T‐cell epitope pRL1a in its N‐terminal 5 amino acid residues. The relationship of the epitope to the pRL1a peptide predominantly recognized by CD8 CTL suggests that the 14‐mer epitope is predominantly recognized by CD4 T‐cells. (Cancer Sci 2008; 99: 1441–1447)