bluuebunny/crossref_metadata_2025 huggingface dataset:
A combined approach of mass spectrometry, molecular modeling, and site‐directed mutagenesis highlights key structural features responsible for the thermostability ofSulfolobus solfataricuscarboxypeptidase
Authors: Sommaruga Silvia , De Palma Antonella , Mauri Pier Luigi , Trisciani Manuela , Basilico Fabrizio , Martelli Pier Luigi , Casadio Rita , Tortora Paolo , Occhipinti Emanuela
Published: January 2008

Sulfolobus solfataricuscarboxypeptidase (CPSso) is a thermostable zinc‐metalloenzyme, consisting of four identical subunits with aMrof 43,000. In a previous paper (Occhipintiet al., Biophys J 2003; 85:1165–1175), we developed a structure of the enzyme by molecular modeling and validated it by site‐directed mutagenesis and small angle X‐ray scattering. Here, we report investigations aimed at further validating the model, as well as at identifying molecular determinants responsible for thermostability. To this end, we took advantage of mass spectrometry techniques, notably LC‐MS/MS. The structure was confirmed by such approaches, in that they lead to the identification of a disulfide bridge formed by Cys286 and Cys293, whose location in the model is well suited for giving rise to the crosslink. More notably, we also identified a protease‐resistant core consisting of the N‐ and C‐terminal antiparallel α‐helices, which in the model are predicted to interact with each other via hydrophobic quadrants. On the basis of the model, we also tentatively identified the most tightly interacting residues as Leu7, Ala380, and Leu376. Although the replacement of Ala380 by serine did not detectably impair protein stability, a dramatic drop in thermostability was observed when the two leucines were replaced by either aspartate (L7D; L376D) or asparagine (L7N; L376N). We then investigated the kinetic thermal stability of the wild type and the mutants by determining the thermodynamic activation parameters, ΔG‡, ΔH‡, and ΔS‡. Besides highlighting the key role of the hydrophobic core in thermostability, these results suggest clearly different mechanisms of destabilization by the single mutations, depending on whether the leucines are replaced by asparagines or aspartates. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Understanding of known drug‐target interactions in the catalytic pocket of neuraminidase subtype N1
Authors: Malaisree Maturos , Rungrotmongkol Thanyada , Decha Panita , Intharathep Pathumwadee , Aruksakunwong Ornjira , Hannongbua Supot
Published: January 2008

To provide detailed information and insight into the drug‐target interaction, structure, solvation, and dynamic and thermodynamic properties, the three known‐neuraminidase inhibitors—oseltamivir (OTV), zanamivir (ZNV), and peramivir (PRV)—embedded in the catalytic site of neuraminidase (NA) subtype N1 were studied using molecular dynamics simulations. In terms of ligand conformation, there were major differences in the structures of the guanidinium and the bulky groups. The atoms of the guanidinium group of PRV were observed to form many more hydrogen bonds with the surrounded residues and were much less solvated by water molecules, in comparison with the other two inhibitors. Consequently, D151 lying on the 150‐loop (residues 147–152) of group‐1 neuraminidase (N1, N4, N5, and N8) was considerably shifted to form direct hydrogen bonds with the OH group of the PRV, which was located rather far from the 150‐loop. For the bulky group, direct hydrogen bonds were detected only between the hydrophilic side chain of ZNV and residues R224, E276, and E277 of N1 with rather weak binding, 20–70% occupation. This is not the case for OTV and PRV, in which flexibility and steric effects due to the hydrophobic side chain lead to the rearrangement of the surrounded residues, that is, the negatively charged side chain of E276 was shifted and rotated to form hydrogen bonds with the positively charged moiety of R224. Taking into account all the ligand‐enzyme interaction data, the gas phase MM interaction energy of −282.2 kcal/mol as well as the binding free energy (ΔGbinding) of −227.4 kcal/mol for the PRV‐N1 are significantly lower than those of the other inhibitors. The ordering of ΔGbinding of PRV < ZNV < OTV agrees well with the ordering of experimental IC50 value. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Inheritance of resistance in cowpea (Vigna unguiculata) to the pod‐sucking bug Clavigralla tomentosicollis (Hemiptera: Coreidae)
Authors: Olatunde GO , Biobaku IA , Ojo DK , Pitan OOR , Adegbite EA
Published: January 2008

Inheritance of resistance in cowpea to Clavigralla tomentosicollis Stål was studied on F1, F2 and F3 generations produced from crosses made between Ife Brown, a susceptible cultivar (PS), and TVu 3354, a resistant variety (PR), on the pods of which freshly emerged nymphs of C. tomentosicollis were caged. Nymphal weight gain was significantly higher (p < 0.05) on PS. There were no significant differences between the weight gains of nymphs that fed on F1, F2 and F3 pods. Insect mortality was significantly higher on PR (86.7%) and the F2 (70.0%) generation. Total nymphal development period was significantly longer on PR (15.0 days) while that on F1 and F2 generations was significantly longer than on the F3 generation. Nymphal survival and adult emergence were observed on eight plants out of 60 and 19 plants out of 80 from the F2 and F3 generations, respectively. Broad‐sense heritability estimates were 90.3% and 94.3% for the F2 and F3 generations, respectively. The results clearly indicated that TVu 3354 has highly heritable resistance to C. tomentosicollis. Copyright © 2008 John Wiley & Sons, Ltd
Goserelin versus leuprolide before hysterectomy for uterine fibroids
Authors: Lim Soo Soo , Sockalingam Jayanthi K. , Tan Peng Chiong
Published: January 2008

Objective

To compare goserelin and leuprolide given before hysterectomy for symptomatic large fibroid uteri.

Methods

A randomized study of 66 premenopausal women with fibroid uteri at least 14 weeks of gestation in a gravid uterus. Women were randomized to receive either subcutaneous depot 3.6 mg goserelin or 3.75 mg leuprolide every 4 weeks for a total of 3 doses. Hysterectomy was performed within 1 month of the last dose.

Results

A total of 34 women randomized to the goserelin group and 31 women to the leuprolide group were available for analysis. Preoperative hemoglobin level (P = 0.89), operative blood loss (P = 0.72), and operating time (P = 0.39) were not different between the 2 groups. Postoperative hemoglobin was higher in the leuprolide group (P = 0.003), but blood transfusion requirement was not different between the groups (P = 1.0). Other outcomes and side effects of the drugs were similar.

Conclusions

Goserelin and leuprolide administered before hysterectomy for uterine fibroids have similar perioperative outcomes.
Density- and distance-dependent seedling survival in a ballistically dispersed subtropical tree speciesPhilenoptera sutherlandii
Authors: Boudreau S. , Lawes M. J.
Published: January 2008

We examine the density- and distance-dependent seedling survival ofPhilenoptera sutherlandii, a common pod-bearing and dehiscent legume (Fabaceae) in Ongoye Forest, South Africa. Short-range ballistic dispersal causes seed to fall beneath the parent tree, where density- or distance-dependent mortality effects are expected to be concentrated. One hundred and eighty marked seedlings were monitored in a 0.5-ha plot containing 30 adults. Our survival data do not support the escape hypothesis. Predation levels declined with increasing seedling density (positive density-dependent survival), but seedling survival after 15 mo was not distance-dependent. Nevertheless, a unimodal (hump-shaped) recruitment curve, typically associated with decreasing seedling density and increasing seedling survival with distance, was observed. In the context of ballistic dispersal, this recruitment curve may indicate a hump-shaped dispersal kernel with predator satiation at high seedling densities near a parent tree. This recruitment curve likely arises because generalized insect seedling predators while attracted to the adult trees also tend to forage farther away. Short dispersal distances, in turn generate the high densities needed to satiate seed and seedling predators. Predator satiation results in long-term survival rates inP. sutherlandiisimilar to more widely dispersed and less common tree species.
Effect of perpendicular gradients on the amplification of Auroral Kilometric Radiation in auroral cavities with density depletions
Authors: Pavan J. , Ziebell L. F.
Published: January 2008

The kilometric radiation in the auroral zones of the Earth is investigated with the use of the transfer equation for the intensity of the wave along the trajectory, which is obtained with the formulation of the geometric optics. The components of the dielectric tensor are evaluated along the trajectory, taking into account explicit effects due to the inhomogeneity, and considering both the energetic and the background electron populations. The cyclotron emissivity is evaluated using the locally homogeneous plasma approximation. For frequencies in the vicinity of the electron cyclotron frequency, the calculations are made for a range of initial values of the parallel refractive index which result in significant amplification. The results obtained show that the inclusion of inhomogeneity effects in the evaluation of the components of the dielectric tensor leads to an amplification process which is qualitatively similar to that obtained using the locally homogeneous approximation, in the same range of frequency and initial parallel refractive index, but less efficient, so that the maximum efficiency obtained is nearly 30% of that obtained using the locally homogeneous approximation.
What is the origin of irregular current oscillations in the transfer of ionic surfactants across liquid/liquid interfaces?
Authors: Daikhin Leonid I. , Urbakh Michael
Published: January 2008

We propose a kinetic description of ionic surfactant transfer across an interface between two immiscible electrolyte solutions that includes interfacial processes (charging of the interface, adsorption, and direct ion transfer) as well as characteristics of the electrical circuit. Our model demonstrates that experimentally observed irregular current oscillations may stem from a dynamical instability of the system which is induced by the interplay between a potential-dependent adsorption and direct ionic transfer across the interface. Calculated temporal patterns exhibit dynamical features which agree well with the experimental observations; in particular, we found that current anomalies occur in a vicinity of the standard ion transfer potential, and the presence of the irregular current oscillations depends on the rate and direction of potential scans.
Investigation of water bound to photosystem I with multiquantum filtered O17 nuclear magnetic resonance
Authors: Krzystyniak M. , Shen Gaozhong , Golbeck John H. , Antonkine Mikhail L.
Published: January 2008

A new analytical approach was developed to characterize the properties of water molecules bound to macromolecules in solution using O17 nuclear magnetic resonance (NMR) relaxation. A combination of conventional (single-quantum) and triple-quantum filtered Hahn echo and inversion recovery measurements was employed. From measured relaxation rate constants, the fraction and the correlation time of bound H2O17 molecules and the relaxation rate constant of bulk water in solution were calculated. This was done by solving analytically a set of nonlinear equations describing the overall relaxation rate constants in the presence of chemical exchange between bulk and bound water. The analytical approach shows the uniqueness of the solution for a given set of three relaxation rate constants. This important result sheds light on the data reduction problem from O17 NMR experiments on biological systems. Water bound in photosystem I isolated from the wild type and rubA variant of the cyanobacterium Synechocystis species PCC 7002 was investigated for the first time. The analysis revealed that photosystem I isolated from the wild type binds 1720±110 water molecules, whereas photosystem I isolated from the rubA variant binds only 1310±170. The accuracy of the method proposed can be increased by further O17 enrichment. The methodology, established for the first time in this work, allows the study of a diverse range of biological samples regardless of their size and molecular weight. Applied initially to photosystem I, this novel method has important consequences for the future investigation of the assembly of biological molecules.
Multireference theoretical investigation on selectivity of the bond fissions in photodissociation of acetyl cyanide
Authors: Xiao Hong-Yan , Liu Ya-Jun , Fang Wei-Hai
Published: January 2008

The selectivity of the C–CH3 and C–CN bond fissions upon excitation of acetyl cyanide at 193nm has been investigated at the theoretical level of multistate complete active space self-consistent field second order perturbation. The calculated results indicated that the initially excited S3 state relaxes to S2 via ultrafast internal conversion. The S2 state could dissociate via two pathways. One, adiabatically dissociates to CH3CO(X̃)+CN(Ã). The other one internally converts to S1 before S1 intersystem crossing to T1. The T1 state subsequently dissociates to two groups of products: CH3(X̃)+OCCN(X̃) and CH3CO(X̃)+CN(X̃). The experimentally observed preference branching of CN elimination over CH3 one and bond selectivity are the results of the competition between the adiabatic and nonadiabatic dynamics of the S2 state.
Accuracy of typical approximations in classical models of intermolecular polarization
Authors: Söderhjelm Pär , Öhrn Anders , Ryde Ulf , Karlström Gunnar
Published: January 2008

One of the largest limitations of standard molecular-mechanics force fields is the neglect of intermolecular polarization. Several attempts to cure this problem have been made, but the results have not always been fully satisfactory. In this paper, we present a quantitative study of the fundamental approximations that underlie polarization models for classical force fields. The induced charge density of a large set of molecular dimers is compared to supermolecular calculations for a hierarchy of simplified models. We study the effect of the Pauli principle, the local inhomogeneity of the electric field, the intramolecular coupling of the polarization response, and the fact that the induced density is a continuous function. We show that standard point-polarizability models work rather well, despite their lack of all these effects, because (1) there is a systematic error cancellation between the neglect of effects of the Pauli principle and the locally inhomogeneous electric field, and (2) the lack of intramolecular coupling and the use of a dipole expansion of the induced density have only minor effects on the polarization. However, the cancellation in (1) is not perfect, and therefore polarizable force-fields could be improved if both effects are explicitly treated.
Study of intercalated Ti atom in tetrahedral or octahedral sites of titanium disulfide (001) surfaces: Theoretical scanning tunneling microscopy images
Authors: Amzallag E. , Baraille I. , Martinez H. , Rérat M. , Gonbeau D.
Published: January 2008

We have performed ab initio linear combination of atomic orbitals-density functional theory calculations on biperiodic supercells to model the electronic and geometrical involvements of Ti intercalated atom in either octahedral or tetrahedral sites of the (001) TiS2 surfaces. For each type of defect, both the relaxed atomic structure and the electronic properties of the defect states were carefully analyzed. For the titanium atom in the van der Waals gap, the partial filling of the conduction band is in agreement with the metallic behavior reported by experimental studies and the last filled states in the bottom of the conduction band—mainly developed on titanium 3d orbitals—permit us to explain the dark defects observed on the scanning tunneling microscopy image of the (001) TiS2 surfaces. On the other hand, the intercalated titanium atom in the tetrahedral site which is just below the top sulfur atom plane governs the electronic density detected by the tip. It permits us to explain the triangular defect with a clear maximum of intensity in its center and dark sides.
Chemical imaging of single 4,7,12,15-tetrakis[2.2]paracyclophane by spatially resolved vibrational spectroscopy
Authors: Liu N. , Silien C. , Ho W. , Maddox J. B. , Mukamel S. , Liu B. , Bazan G. C.
Published: January 2008

Single 4,7,12,15-tetrakis[2.2]paracyclophane were deposited on NiAl(110) surface at 11K. Two adsorbed species with large and small conductivities were detected by the scanning tunneling microscope (STM). Their vibrational properties were investigated by inelastic electron tunneling spectroscopy (IETS) with the STM. Five vibrational modes were observed for the species with the larger conductivity. The spatially resolved vibrational images for the modes show striking differences, depending on the coupling of the vibrations localized on different functional groups within the molecule to the electronic states of the molecule. The vibrational modes are assigned on the basis of ab initio calculations. No IETS signal is resolved from the species with the small conductivity.
Polarization dependence of transition intensities in double resonance experiments: Unresolved spin doublets
Authors: Petrović Vladimir S. , Field Robert W.
Published: January 2008

The polarization dependence of transition intensities in multiple resonance spectroscopic experiments can provide information useful for making rotational assignments. A formalism to describe the polarization dependence of transition intensities in multiple resonance experiments, particularly for cases when two rotational/fine structure quantum numbers are needed to specify the state of the system, is presented. The formalism is presented in a form usable both when the transitions between the underlying fine structure components are experimentally resolved, as well as when they are unresolved, to form composite lines. This sort of treatment is necessary for cases when the two quantum numbers that specify the fine structure differ significantly, such as is the case at low N, when the difference between J and N becomes comparable to the value of J. Ratios of transition intensities in different experimentally convenient polarization arrangements are evaluated for the case of composite N transitions formed by combining the spin components of a doublet system. The formalism is expressed in a form easily extendable to accommodate experimental cases of more than two excitation steps, or a combination of excitation steps and an external static electric field. This polarization diagnostic has been experimentally applied to assign spectral features in double resonance Rydberg spectra of CaF.
Crucial influence on d∕p range in bistable chiral tilted-homeotropic nematic liquid crystal cells
Authors: Liang Bau-Jy , Lin Che-Li
Published: January 2008

Wedge bistable chiral tilted-homeotropic nematic liquid crystal (BHN LC) cells with various pretilt angles are experimentally manufactured. The bistable ranges were determined experimentally and by simulation. The crucial influence of BHN LC cells on the d∕p (thickness to pitch ratio of LC cell) range in the BHN cell is determined in detail by dynamic simulation. The onset of bistability is determined by the relaxing elastic restoring force, and the relevant physical mechanism is elucidated as well.
Ballistic electron emission spectroscopy/microscopy of self-assembled InAs quantum dots of different sizes embedded in GaAs∕AlGaAs heterostructure
Authors: Walachová J. , Zelinka J. , Malina V. , Vaniš J. , Šroubek F. , Pangrác J. , Melichar K. , Hulicius E.
Published: January 2008

Self-assembled InAs quantum dots embedded in GaAs∕GaAlAs heterostructure were visualized by ballistic electron emission microscopy. The spectroscopic characteristics on individual quantum dots were examined. Quantum dots had images of elliptical shapes. Their length was from about 10to20nm. Below one-electron p1-like state, one-electron and two-electron ground states and excited two-electron states were observed. The Coulomb interaction and exchange energies between two electrons in quantum dots were determined and compared with the previously published theoretical results.
Plasmon-enhanced solar energy conversion in organic bulk heterojunction photovoltaics
Authors: Morfa Anthony J. , Rowlen Kathy L. , Reilly Thomas H. , Romero Manuel J. , van de Lagemaat Jao
Published: January 2008

Plasmon-active silver nanoparticle layers were included in solution-processed bulk-heterojunction solar cells. Nanoparticle layers were fabricated using vapor-phase deposition on indium tin oxide electrodes. Owing to the increase in optical electrical field inside the photoactive layer, the inclusion of such particle films lead to increased optical absorption and consequently increased photoconversion at solar-conversion relevant wavelengths. The resulting solar energy conversion efficiency for a bulk heterojunction photovoltaic device of poly(3-hexylthiophene)/[6,6]-phenyl C61 butyric acid methyl ester was found to increase from 1.3%±0.2% to 2.2%±0.1% for devices employing thin plasmon-active layers. Based on six measurements, the improvement factor of 1.7 was demonstrated to be statistically significant.
Three-dimensional simulations of compressible tearing instability
Authors: Landi Simone , Londrillo Pasquale , Velli Marco , Bettarini Lapo
Published: January 2008

Three-dimensional numerical simulations of the tearing instability in the framework of compressible and resistive magnetohydrodynamics are presented. Simulations have been performed with a novel Eulerian conservative high order code, including an explicit resistivity, which uses implicit high order numerical schemes having higher spectral resolution than classical schemes. The linear and non linear evolution of the tearing instability has been followed for force-free and pressure-balanced initial equilibrium configurations. Pressure equilibrium configurations are subject to a secondary instability which drives the system toward a quasi two dimensional structure oriented perpendicularly to the initial configuration. The development of secondary instabilities is suppressed by a guide field allowing the coalescence instability to fully develop in the system. Force-free initial configurations follow an intermediate path with respect the previous cases: Strong coalescence of magnetic islands, due to the non linear evolution of the tearing instability, is observed before the system enters in a phase dominated by 3D modes. The histories of the differing initial current-sheet equilibria have counterparts in the energy spectra that, for all three cases, are observed to be strongly anisotropic.
Electroporation chip for adherent cells on photochemically modified polymer surfaces
Authors: Olbrich Michael , Rebollar Esther , Heitz Johannes , Frischauf Irene , Romanin Christoph
Published: January 2008

We present a polytetrafluoroethylene electroporation microchip with integrated electrodes for transfection of adherent biological cells. For fabrication, UV-surface modification was employed in combination with metal deposition. UV irradiation in reactive atmosphere resulted in introduction of polar chemical groups into the polytetrafluoroethylene surface for significant adhesion enhancement of both biological cells as well as metal electrodes thereon. Electroporation was demonstrated by transfection of human embryonic kidney cells with the enhanced green fluorescent protein. Transparent, working at low voltages, and easy to handle, this chip yields the potential to reduce the amount of sequential working steps necessary for transfection.
High-resolution transmission electron microscopy analysis of L1 ordering process in Fe/Pd thin layers
Authors: Kovács András , Sato Kazuhisa , Hirotsu Yoshihiko
Published: January 2008

The hard magnetic L10 ordered phase formation in thin Pd and Fe bilayers prepared on MgO (001) substrate has been investigated by transmission electron microscopy using in situ annealing. The structures of as-deposited Fe/Pd and Pd/MgO interfaces were characterized by high-resolution transmission electron microscopy. Fast intermixing of Fe and Pd layers and immediate L10 phase formation within the alloyed area was found at 673 K. The high-resolution observations indicated that the ordered region of the L10-FePd phase was formed in dispersed areas without a predetermined nucleation site. At 773 K, the growing ordered areas occasionally formed antiphase boundaries between the adjacent parts. The ordered L10-FePd thin layer contained translational domains with tetragonal c axis perpendicular to the substrate.
Toggle magnetic random access memory cells scalable to a capacity of over 100 megabits
Authors: Fukumoto Yoshiyuki , Nebashi Ryusuke , Mukai Tomonori , Tsuji Kiyotaka , Suzuki Tetsuhiro
Published: January 2008

We investigated the toggle-writing characteristics of magnetic tunnel junctions (MTJs) with minimum bit widths as narrow as 90 nm. The MTJs were fabricated using electron-beam lithography and a 0.24 μm complementary metal-oxide semiconductor process. Here, we discuss the scalability in bit writing of toggle magnetic random access memories (MRAMs) with toggle cells consisting of two soft magnetic layers ferromagnetically coupled with synthetic antiferromagnets (2SL-FC-SAFs). The effect of the structures of 2SL-FC-SAFs on toggle writing against a reduction in bit width was examined. Taking account of the distributions of seven standard deviations, 2SL-FC-SAFs were shown to decrease the writing current to around 3 mA when a Cu yoke wire was used for writing lines, while maintaining the writing margin in both 110 and 170 nm wide MTJs. The thermal activation robustness of these cells, which was measured by the direct switching probability versus the pulse field duration, ensures 10-year retentions. These writing characteristics make toggle MRAMs with a density of over 100 megabits possible.
High perpendicular anisotropy in copper ferrite thin films
Authors: Ahmad M. , Desai M. , Khatirkar R.
Published: January 2008

Copper ferrite thin films, radio-frequency sputtered at 200 W, on fused quartz substrates, postannealed at about 800 °C and slow cooled, exhibited a tetragonal copper ferrite phase, but with a preferred orientation of mainly a (311) or (400) peak. The films show a perpendicular coercivity of about 3000 Oe or more, almost two times the parallel coercivity. Magnetocrystalline anisotropy is the major cause of the high coercivity observed in these films. The perpendicular anisotropy of these films is attributed to the texture with the hard axis in the film plane as seen by texture measurement.
Rollover instability due to double diffusion in a stably stratified cylindrical tank
Authors: Zimmerman William B. , Rees Julia M.
Published: January 2008

Double diffusion of a viscous fluid is simulated for heat leakage driven by buoyant convection under cryogenic storage conditions in a cylindrical tank with laminar flow. If the tank is stably stratified, there is a potential instability due to the inability of the fluid in the lower layer to release heat to the top vapor space, whereas the upper liquid layer can exchange heat and mass through sensible heat transfer and evaporation with the vapor space. Eventually, the lower layer becomes less dense due to thermal expansion and is no longer constrained in the stratification. The rapid rise and overturning of the fluid is termed rollover, and can be accompanied by a potentially explosive release of vapor. In this paper, hydrodynamics and heat and mass transport are used to study the stability characteristics of rollover. The transient state is used as a base state for a linear stability analysis which shows the transition from a “corner eddy” mode spinning down to spinning up is the driver for the rollover instability. Four different vapor-liquid interfacial boundary conditions are tested, with similar results for the time to rollover. Surprisingly, the long time prerollover state is dominated in the laminar flow regime by heat conduction and diffusion, as the expected double roll structure is suppressed and advection plays a small roll in the majority of the prerollover period. Scalings are suggested for controlling dimensionless groups on this prerollover basis that can be used as a guideline to determine the regime of double diffusion—a single roll or a double roll stratification, as well as the severity of the eventual rollover event. An energy analysis demonstrates the switch from practically advection free to free convection regimes.
Polarized spectral analysis and laser demonstration of Nd3+:Bi2(MoO4)3 biaxial crystal
Authors: Gong Xinghong , Chen Yujin , Lin Yanfu , Tan Qiguang , Luo Zundu , Huang Yidong
Published: January 2008

Nd 3 + : Bi 2 ( Mo O 4 ) 3 single crystal grown by the Czochralski technique was oriented and the orientation relationship between the principal axes of the optical indicatrix (X, Y, Z) and the crystallographic axes (a, b, c) was determined. The polarized absorption spectra, polarized fluorescence spectra, and fluorescence decay curve of the crystal were measured at room temperature. The Judd-Ofelt theory and the Fuchtbauer-Landenburg formula were applied to analyze the spectroscopic parameters. The relation between the spectral properties and the crystal structure was discussed. A primary laser output of about 235mW at 1064nm with the slope efficiency of 25% has been obtained under a Ti:sapphire laser pumping.
All-optical delay line using semiconductor cavity solitons
Authors: Pedaci F. , Barland S. , Caboche E. , Genevet P. , Giudici M. , Tredicce J. R. , Ackemann T. , Scroggie A. J. , Firth W. J. , Oppo G.-L. , Tissoni G. , Jäger R.
Published: January 2008

An all-optical delay line based on the lateral drift of cavity solitons in semiconductor microresonators is proposed and experimentally demonstrated. The functionalities of the device proposed as well as its performance is analyzed and compared with recent alternative methods based on the decrease of group velocity in the vicinity of resonances. We show that the current limitations can be overcome using broader devices with tailored material responses.
Selective formation of Ohmic junctions and Schottky barriers with electrodeposited ZnO
Authors: Chatman Shawn , Ryan Bernard J. , Poduska Kristin M.
Published: January 2008

Constant-potential electrochemical synthesis of ZnO on metal substrates enables selective formation of either Ohmic or Schottky-barrier contacts. Using a mildly acidic nitrate-based aqueous electrolyte, there is a substrate-dependent deposition potential below which electrodeposited ZnO heterojunctions display Schottky response with high contact resistances (∼105Ω) and above which Ohmic behavior and low contact resistances (∼1Ω) occur. Voltammetric evidence for Zn metal deposition, in conjunction with Schottky-barrier heights that are consistent with values expected for a ZnO–Zn junction, suggests that more negative deposition potentials create a Zn-based interface between the substrate and ZnO that leads to rectifying behavior.
Band bending and the thermochemistry of oxygen vacancies in ionic metal oxide thin films
Authors: Guha S. , Solomon P.
Published: January 2008

We address the problem of band bending in a metal oxide thin film/electrode layer and derive equations relating the voltage drop across the oxide to the oxygen activity of the ambient in equilibrium with the oxide. Applied to the case of oxygen vacancies, the results predict situations where the vacancy charge is strongly localized adjacent to the metal interface. Comparing predictions to experimental results for the specific case of HfO2, we find that the free energy of formation of the oxygen vacancies are of the order of ∼3eV, significantly smaller than the numbers theoretically predicted for bulk HfO2.
Erasure of stored optical information in a Pr3+:Y2SiO5 crystal
Authors: Wang Hai-Hua , Kang Zhi-Hui , Jiang Yun , Li Ya-Juan , Du Dun-Mao , Wei Xiao-Gang , Wu Jin-Hui , Gao Jin-Yue
Published: January 2008

We experimentally demonstrate an erasure of stored optical information in a Pr3+:Y2SiO5 crystal by applying an erasing pulse to destroy atomic spin coherence. We observed an erasing efficiency of about 85%. Such an erasing operation of stored optical information may have practical applications in the field of information processing and all-optical network.
Polarization microscopy probe for applications in a high magnetic field
Authors: Konijnenberg Peter J. , Ziemons Arndt , Molodov Dmitri A. , Gottstein Günter
Published: January 2008

A microscopy probe designed for use in high field magnets is presented. It was developed to observe and continuously measure the position and shape of a magnetically driven grain boundary in a magnetically anisotropic material. The approach utilizes the anisotropy of reflectivity of visible light for orientation contrast to determine the boundary location. The major components of the system are the polarizing microscope with video camera and the sample chamber with a resistive heater for annealing at elevated temperatures up to 500°C in an inert gas atmosphere. The results of test measurements are presented.
Giant piezoelectric d33 coefficient in ferroelectric vanadium doped ZnO films
Authors: Yang Y. C. , Song C. , Wang X. H. , Zeng F. , Pan F.
Published: January 2008

A giant electromechanical d33 coefficient 110pC∕N is obtained in ferroelectric V-doped ZnO films, which is nearly one order of magnitude higher than that of undoped samples. It is considered that the switchable spontaneous polarization induced by V dopants and the accompanying relatively high permittivity should be responsible for the enhancement of piezoelectric response. Moreover, from another point of view, an easier rotation of V–O bonds which are noncollinear with c axis under electric field might be the microscopic origin of this anomaly. The improved piezoelectric properties could make V-doped ZnO a promising candidate for piezoelectric devices.
The highest-energy cosmic rays appear to come from nearby active galactic nuclei
Authors: Schwarzschild Bertram
Published: January 2008

Though it’s more reassuring than surprising, this new result from the enormous Auger ground array suggests the discovery potential of cosmic-ray astronomy.
Charge-transfer measurements provide new angle on diamond surface conductivity
Authors: Miller Johanna
Published: January 2008

Diamond submerged in water can lose some of its electrons and acquire p-type charge carriers, but only at low pH.
Universities face cap on indirect costs for Pentagon-funded research
Authors: Kramer David
Published: January 2008

Academic institutions fear that an Appropriations rider could undermine the long-established system for recovering research costs and financing new laboratories.
Planning NASA’s future
Authors: Guinnessy Paul
Published: January 2008

How do you run NASA effectively? Physics Today asks agency head Michael Griffin.
With Domenici’s departure, DOE labs to lose their top Hill advocate
Authors: Kramer David
Published: January 2008

No successor is apparent for “St. Pete,” who showered funding and new programs on the labs.
Cryo-electron microscopy of biological nanostructures
Authors: Glaeser Robert M.
Published: January 2008

The imaging of unstained and fully hydrated biological specimens embedded in vitreous ice is leading to powerful advances in understanding the structural basis of biological phenomena.
Dioxin-mediated tumor progression through activation of mitochondria-to-nucleus stress signaling
Authors: Biswas Gopa , Srinivasan Satish , Anandatheerthavarada Hindupur K. , Avadhani Narayan G.
Published: January 2008

The environmental toxin 2,3,7,8-tetrachlorodibenzodioxin (TCDD) is a known human carcinogen; however, its precise mechanism of action remains unclear. Here we show that TCDD induces mitochondrial dysfunction, stress signaling, and tumor invasion by a mechanism similar to that described for mtDNA-depleted cells. Treatment of C2C12 cells with TCDD disrupted mitochondrial transmembrane potential in a time-dependent fashion and inhibited mitochondrial transcription and translation. TCDD also increased cytosolic [Ca
2+
]
c
and RyR1-specific Ca
2+
release. These changes were associated with increased calcineurin (CnA) levels and activation of CnA-sensitive NF-κB/Rel (IκBβ-dependent) factors. Cells treated with TCDD displayed resistance to apoptosis, increased expression of the tumor marker cathepsin L, and a high degree of invasiveness as tested by the Matrigel membrane invasion assay. These effects were reversed by the CnA inhibitor FK506, and CnA mRNA silencing suggesting that TCDD triggers a signaling pathway similar to mtDNA depletion. Taken together, these results reveal that TCDD may promote tumor progression
in vivo
by directly targeting mitochondrial transcription and induction of mitochondrial stress signaling.
Mycobacterium tuberculosis
Rv2224c modulates innate immune responses
Authors: Rengarajan Jyothi , Murphy Elissa , Park Arnold , Krone Cassandra L. , Hett Erik C. , Bloom Barry R. , Glimcher Laurie H. , Rubin Eric J.
Published: January 2008

Tuberculosis remains a major global health problem that kills up to 2 million people annually. Central to the success of
Mycobacterium tuberculosis
(
Mtb
) as a pathogen is its ability to evade host immunity and to establish a chronic infection. Although its primary intracellular niche is within macrophages, the underlying molecular mechanisms are poorly understood. Here we show that Rv2224c, a cell envelope-associated predicted protease, is critical for
Mtb
virulence. Disruption of
Rv2224c
led to prolonged survival of infected mice and highly reduced lung pathology. Absence of
Rv2224c
enhanced host innate immune responses, compromised the intracellular survival of
Mtb
in macrophages, and increased its susceptibility to lysozyme. We provide insights into the molecular basis for Rv2224c function by showing that Rv2224c activity promotes processing and extracellular release of the
Mtb
protein, GroEL2. Inhibition of Rv2224c and its targets offers opportunities for therapeutic interventions and immune-modulatory strategies.
A combined transcriptome and proteome survey of malaria parasite liver stages
Authors: Tarun Alice S. , Peng Xinxia , Dumpit Ronald F. , Ogata Yuko , Silva-Rivera Hilda , Camargo Nelly , Daly Thomas M. , Bergman Lawrence W. , Kappe Stefan H. I.
Published: January 2008

For 50 years since their discovery, the malaria parasite liver stages (LS) have been difficult to analyze, impeding their utilization as a critical target for antiinfection vaccines and drugs. We have undertaken a comprehensive transcriptome analysis in combination with a proteomic survey of LS. Green fluorescent protein-tagged
Plasmodium yoelii
(PyGFP) was used to efficiently isolate LS-infected hepatocytes from the rodent host. Genome-wide LS gene expression was profiled and compared with other parasite life cycle stages. The analysis revealed ≈2,000 genes active during LS development, and proteomic analysis identified 816 proteins. A subset of proteins appeared to be expressed in LS only. The data revealed exported parasite proteins and LS metabolic pathways including expression of FASII pathway enzymes. The FASII inhibitor hexachlorophene and the antibiotics, tetracycline and rifampicin, that target the apicoplast inhibited LS development, identifying FASII and other pathways localized in the apicoplast as potential drug targets to prevent malaria infection.
Ecclesiastical petrology: the building stones of Brixworth Church
Authors: SUTHERLAND DIANA
Published: January 2008

Brixworth church in Northamptonshire has been aptly described as a museum of rock–types. An archaeological assignment involving the identification of every stone in one of the oldest of our English churches has led to some surprising discoveries – about how the church was built, and the lengthy journeys undertaken by the Saxons in their search for stone.
Kaolin: a servant of humanity
Authors: KELLER W.D.
Published: January 2008

Kaolinite, an aristocrat of minerals, serves as the medium on which is printed the records of scholarly human culture from the oldest known to the present. It also serves as a refractory to confine ultra–high temperatures and protect furnaces used in modern industry and technology. Produced by reaction between rigid igneous silicates and physically yielding but chemically potent water, kaolin crystals reveal a graphic story, shown in scanning electron micrographs, of most diverse properties, geneses and potential applications.
Geology in the Pyrenees
Authors: MCMILLAN A.A.
Published: January 2008

M.D. Jones runs special–interest, geology and natural history holidays to the Pyrenees, Spain, North Africa, Iceland and elsewhere, and is a part–time tutor in the Department of Adult Education at the University of Leicester.
Layered intrusions – a fluid situation?
Authors: WADSWORTH W. J.
Published: January 2008

Recent research into layered intrusions (intrusive bodies in which there are layers of different mineralogical composition) provides an interesting example of ‘role–reversal’. Traditionally, crystal settling has been regarded as the main agent of differentiation, with magma convection as a useful subsidiary factor. Now the behaviour of the fluid phase – before, during and after the main crystallisation period – is assuming increasing importance, even to the extent of eliminating the need for crystal settling altogether. The ‘new wave’ of ideas is stimulating and challenging, but by no means sounds the death–knell of conventional magmatic sedimentation.
The lying stones of Eibelstadt
Authors: NIELD TED
Published: January 2008

In 1725 Dr Johann Beringer became the butt of a malicious academic hoax. But in his disgrace he rendered no small service to the emerging science of palaeontology.
Fossil sharks
Authors: DICK JOHN R.F. , COATES M.I. , ROLFE W.D.I.
Published: January 2008

Sharks were around as early as the Silurian and were most abundant during the Carboniferous. During the Eocene, some of them were even larger than today's Great White Shark.
Marine geology at the World Court
Authors: WHITE ROBERT S.
Published: January 2008

Huge areas of the world's seafloor are being carved up among the nations, ignoring scientific knowledge of the geology, geophysics and geomorphology of the seabed.
Cambrian enigmas
Authors: MORRIS SIMON CONWAY
Published: January 2008

Bizarre soft‐bodied animals from the Cambrian, principally the Burgess Shale of British Columbia, are throwing new light on the major diversification of early metazoans. A distinctive range of new body‐plans hint at explosive rates of evolution, but the underlying mechanisms are still a matter for conjecture. Whether these unusual fossils suffered extinction because of bad design or bad luck is uncertain, but some evidence suggests that chance factors played an important role.
A new ‘Solenhofen’ in Mexico
Authors: MARTILL DAVID M.
Published: January 2008

A new site has recently been discovered near Puebla, Mexico, at which fossils are found in a beautiful state of preservation in Cretaceous limestones. Most of the fossils are of new or little‐known fish, but there is also a wide variety of invertebrates. The fossils have been found in a platy limestone that splits easily along the bedding planes containing the fossils. This type of preservation is very similar to that found at the world‐famous fossil site at Solenhofen in Bavaria, Federal Republic of Germany, and may shed light on the community structure of this Cretaceous part of the geological column.
Ayers Rock
Authors: SELBY JONATHAN
Published: January 2008

For years the world's most famous inselberg was plagued by the deleterious effects of human activity. Now a massive investment, stimulated by the international tourist industry, has ensured preservation of the rock's unique geomorphological features and its fragile ecology.
The Chalk sea‐urchin Micraster: microevolution, adaptation and predation
Authors: ROSE EDWARD P. F. , CROSS NIGEL E.
Published: January 2008

Serial variation between Micraster populations from successive zones in the Upper Cretaceous Chalk of Europe is widely cited as evidence for evolution at the species level, whether changes between species are interpreted as gradual or punctuational. That these changes were adaptive and represent an improved functional efficiency with time is also now widely agreed, if not whether the changes were independent of environmental change or a response to it. Dead specimens of Micraster were commonly encrusted by a wide variety of small invertebrates, presumably because they provided islands of hard substrate on an otherwise soft, muddy sea floor. Less commonly, there is evidence that living specimens of Micraster were susceptible to predation by gastropods and other organisms, one of the natural selection pressures favouring adaptation to a burrowing mode of life.
Mines in the sky
Authors: OPPENHEIMER CLIVE
Published: January 2008

The highest working mines in the world extract bright yellow deposits of sulphur from the peaks of towering volcanoes in the Central Andes. Workers and machinery must cope with the extreme environment at up to 6000 metres above sea level.
Carruthers and the theory of glacial undermelt: lessons from a pamphleteer?
Authors: BENNETT MATTHEW R. , DOYLE PETER
Published: January 2008

In 1953, R. G. Carruthers, a respected geologist, published a private scientific pamphlet which challenged the established view of British Quaternary stratigraphy. Carruthers had no other route but private publication. Why was this, and what was the foundation for his ideas? We explore Carruthers' theory in the light of current knowledge and consider the lessons for scientific publication provided by it.
The Grand Canyon of the Colorado
Authors: FORD TREVOR D.
Published: January 2008

The Grand Canyon is not only one of the greatest erosional features on Earth, it also reveals one of the finest stratigraphic records anywhere.
Geological excursion guide 10: The volcanic geology of La Palma, Canary Islands
Authors: DUNCAN ANGUS , NOTCUTT GEOFF
Published: January 2008

The island of La Palma in the Canary Islands provides an excellent opportunity to examine the products of basaltic volcanism. In contrast to Tenerife, the volcanic activity of La Palma has been more effusive, and the island has largely escaped the impact of package tourism. The scenery is impressive, in particular the classic Caldera de Taburiente.
A short walk in the Himalayas
Authors: BRISTOW CHARLIE
Published: January 2008

Last April I spent three weeks in Nepal, most of the time walking up to the Annapurna Sanctuary, north of Pokhara in western Nepal. This is a popular area for trekking, with spectacular scenery; and I will try to give an impression of what can be found there, with some explanation of the geology and scenery. This is a general overview of what is on offer for the amateur geologist and dedicated walker and not a detailed field guide.
HYDROPHOBIC STACKING OF BASES AND THE SOLVENT DENATURATION OF DNA*
Authors: Sínanoĝlu O. , Abdulnur S.
Published: January 2008

Summary The DNA double helix stable in water is denatured by solvents with widely varing properties. To understand quantitatively the role of water in keeping the helix together, the solvent contributions to the unitary free energy difference between random single strands and the helix are calculated for water, MeOH, glycol, formamide, glycerol, ethanol, n‐propanol, and n‐butanol. The property of solvent crucial in denaturation is found to be mainly the enthalpy part of surface tension. The number of molecules solvating the A, T, G, C bases, hence their energy is drastically reduced in going from random coils to the helix. ‘Hydrophobic bonding’ thus results to a large extent from the large surface enthalpy of water. The same interactions may cause the ‘stacking’ of adjacent bases in a single strand of DNA in water. Such stacking may be what makes thymine photodimerization under the action of uv favorable in some thymine hydrate crystals and in aqueous single strand DNA.