bluuebunny/crossref_metadata_2025 huggingface dataset:
Compact Reconnaissance Imaging Spectrometer observations of water vapor and carbon monoxide
Authors: Smith Michael D. , Wolff Michael J. , Clancy R. Todd , Murchie Scott L.
Published: June 2009

The Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) onboard the Mars Reconnaissance Orbiter (MRO) spacecraft began taking observations in September 2006 and has now collected more than a full Martian year of data. Retrievals performed using the near‐infrared spectra obtained by CRISM are used to characterize the seasonal and spatial variation of the column abundance of water vapor and the column‐averaged mixing ratio of carbon monoxide. CRISM retrievals show nominal behavior in water vapor during northern hemisphere spring and summer with maximum abundance reaching 50 precipitable micrometers. Water vapor abundance during the southern hemisphere spring and summer appears significantly reduced compared to observations by other instruments taken during previous years. The CRISM retrievals show the seasonally and globally averaged carbon monoxide mixing ratio to be 700 ppm, but with strong seasonal variations at high latitudes. The summertime near‐polar carbon monoxide mixing ratio falls to 200 ppm in the south and 400 ppm in the north as carbon dioxide sublimates from the seasonal polar ice caps and dilutes noncondensable species including carbon monoxide. At low latitudes, the carbon monoxide mixing ratio varies in response to the mean seasonal cycle of surface pressure.
Modeling the seasonal distribution of planktonic foraminifera during the Last Glacial Maximum
Authors: Fraile I. , Schulz M. , Mulitza S. , Merkel U. , Prange M. , Paul A.
Published: June 2009

We studied the seasonality of planktonic foraminifera during the Last Glacial Maximum using a foraminifera model coupled to an ecosystem model. The model suggests that the timing of the maximum seasonal production of planktonic foraminifera during the Last Glacial Maximum occurred at a different time of the year from present day. The assumption of “stable” seasonality through time, one of the underlying assumptions in paleoceanographical studies that utilize monospecific samples of planktic foraminifera, is thus mistaken. This finding entails implications for foraminifera‐based paleotemperature reconstructions. The change in the timing of maximum foraminiferal production could lead to a bias in estimated paleotemperature if the change in seasonality is not taken into account. The existence of the potential seasonal bias is not a new concept in paleoceanography, but here we assess this bias for the first time from a comprehensive modeling approach. In tropical waters, where temperature seasonality has a relatively small amplitude, the estimated sea surface temperature is close to the annual mean. Thus, variations in foraminiferal seasonality do not cause a significant change in the recorded temperature. By contrast, changes in seasonality have the largest influence on the temperature signal at high latitudes and midlatitudes. Our model prediction suggests that because of the temperature sensitivity of the considered species, during the Last Glacial Maximum, the largest production of foraminifera occurred during a warmer season of the year. In some regions, the maximum foraminiferal production month shifted by up to 6 months. Our findings may help to reconcile low glacial planktonic δ18O values with proxy evidence for deep‐water formation in the Nordic Seas.
Cohesion influences on erosion and bed load transport
Authors: Jain Rajesh K. , Kothyari Umesh C.
Published: June 2009

Studies on erosion and transport rates of cohesive sediment mixtures containing gravel are not reported so far in the literature to the best of our knowledge. Results from laboratory experiments on the process of erosion of cohesive sediment mixtures by open‐channel flow are presented. The sediment used for experimentation consisted of fine gravel mixed with clay in proportions varying from 10% to 50% and fine gravel, fine sand in equal proportion (by weight) mixed with clay proportions again varying from 10% to 50% by weight. Experimental observations have revealed that the process of detachment of cohesive sediment mixtures containing gravel is significantly different from that of cohesionless sediments. Also, it is different from the detachment process of cohesive sediment mixtures not containing coarser‐size material. Experimental data on transport rates of the bed load of the cohesive sediment mixtures are presented. On the basis of dimensional considerations, a computational procedure is proposed to determine the bed load transport rates generated from erosion of the different size fractions of sediment mixtures. Clay percentage and unconfined compressive strength of the sediment bed were the main parameters controlling bed load transport rate of such sediments. In the absence of cohesion, the proposed method reduces to the Patel and Ranga Raju (1996) method for bed load transport rate computation of nonuniform cohesionless sediments.
Modeling turbidity currents with nonuniform sediment and reverse buoyancy
Authors: Sequeiros Octavio E. , Cantelli Alessandro , Viparelli Enrica , White James D. L. , García Marcelo H. , Parker Gary
Published: June 2009

This study focuses on a numerical model of turbidity currents with reversing buoyancy, i.e., flows that are rendered heavier than the ambient water due to the presence of suspended sediment but that as sedimentation progresses become lighter than the ambient water due to a difference in temperature or salinity. The flows considered here may be either pulsed events or continuous flows. It is well known that these flows are subject to a buoyancy reversal. Flows issuing upstream with a sufficient load of suspended sediment are heavier than the ambient water and thus form a bottom underflow. As sediment deposits in the downstream direction, however, the flow gradually loses its density excess, and eventually reverses its buoyancy, detaching upward from the bed. The nature of the sediment deposit emplaced near and downstream of the point of lofting can thus differ significantly from that emplaced upstream. A novel aspect of the work reported here is a mechanistic description of the tendency for the current to sort in the downstream direction a sediment mixture containing a wide range of grain sizes. The numerical model, which is based in the κ − ɛ closure for turbulence, is verified with a unique set of experimental data intended to model sediment sorting associated with turbidity currents created by explosive undersea eruptions. Both cases with nonreversing buoyancy and reversing buoyancy are considered. As such, the model not only provides a detailed description of flows with reversing buoyancy, but also provides a tool to aid sedimentologists in back‐calculating the flow emplaced by turbidity currents from the downstream variation in the grain size distribution of the bed deposit.
Aerosol size distribution modeling with the Community Multiscale Air Quality modeling system in the Pacific Northwest: 2. Parameterizations for ternary nucleation and nucleation mode processes
Authors: Elleman Robert A. , Covert David S.
Published: June 2009

In order to test Community Multiscale Air Quality (CMAQ) model performance for ultrafine particle concentrations in the Pacific Northwest, CMAQ v4.4 was modified for ternary NH3‐H2SO4‐H2O nucleation and for atmospheric processing of ultrafine particles. Sulfuric acid from sulfur dioxide oxidation is iteratively partitioned into gaseous sulfuric acid, newly condensed aerosol sulfate, and aerosol sulfuric acid contained in new 1 nm particles. Freshly nucleated particles are either coagulated to larger particles or grown by sulfuric acid condensation to 10 nm at which point they are included in CMAQ's existing Aitken mode. Multiple nucleation parameterizations were implemented into CMAQ, and one other was investigated in a sensitivity analysis. For a case study in the Pacific Northwest where aerosol number concentration and size distributions were measured, standard binary nucleation in CMAQ produces nearly no particles for this case study. Ternary nucleation can produce millions of 1 nm particles per cm3, but few of these particles survive coagulation loss and grow to 10 nm and into the Aitken mode. There are occasions when the additions to CMAQ increase the number of particles to within an order of magnitude of observations, but it is more common for number concentrations to remain underpredicted by, on average, one order of magnitude. Significant particle nucleation in CMAQ successfully produces a distinct Aitken and accumulation mode and an Aitken mode that is more prominent than the accumulation mode, although errors in the size distribution remain. A more recent ternary nucleation scheme including ammonium bisulfate clusters does not nucleate an appreciable number of particles.
Multicomponent gauge cell method
Authors: Vishnyakov Aleksey , Neimark Alexander V.
Published: June 2009

The gauge cell Monte Carlo method [Neimark and Vishnyakov, J. Chem. Phys. 122, 234108 (2005)] for calculations of chemical potential in dense and strongly inhomogeneous fluids is extended to multicomponent systems. The system of interest is simulated in a sample cell that is placed in chemical contact with several gauge cells of limited capacity, one gauge cell per component. Thus, each component can be exchanged between the sample cell and the respective gauge cell. The sample and gauge cells are immersed into the thermal bath of a given temperature. The size of the gauge cell controls the level of concentration fluctuations for the respective component in the sample cell. The chemical potentials are rigorously calculated from the equilibrium distribution of particles between the system and the gauges, and the results do not depend on the gauge size. For large systems, the chemical potentials can be accurately estimated from the average densities in the gauge cells. The proposed method was tested against the literature data on the vapor-liquid equilibrium in a binary mixture of subcritical and supercritical fluids and against the grand canonical and Widom insertion Monte Carlo methods for a binary mixture confined to a very narrow spherical pore. The method is specifically suitable for simulations of metastable and labile states in multicomponent confined fluids.
General framework about defect creation at the Si∕SiO2 interface
Authors: Guerin C. , Huard V. , Bravaix A.
Published: June 2009

This paper presents a theoretical framework about interface state creation rate from Si–H bonds at the Si∕SiO2 interface. It includes three main ways of bond breaking. In the first case, the bond can be broken, thanks to the bond ground state rising with an electrical field. In two other cases, incident carriers will play the main role either if there are very energetic or very numerous but less energetic. This concept allows one to physically model the reliability of metal oxide semiconductor field effect transistors, and particularly negative bias temperature instability permanent part, and channel hot carrier to cold carrier damage.
Aluminum incorporation in Ti1−xAlxN films studied by x-ray absorption near-edge structure
Authors: Gago R. , Redondo-Cubero A. , Endrino J. L. , Jiménez I. , Shevchenko N.
Published: June 2009

The local bonding structure of titanium aluminum nitride (Ti1−xAlxN) films grown by dc magnetron cosputtering with different AlN molar fractions (x) has been studied by x-ray absorption near-edge structure (XANES) recorded in total electron yield mode. Grazing incidence x-ray diffraction (GIXRD) shows the formation of a ternary solid solution with cubic structure (c-Ti1−xAlxN) that shrinks with the incorporation of Al and that, above a solubility limit of x∼0.7, segregation of w-AlN and c-Ti1−xAlxN phases occurs. The Al incorporation in the cubic structure and lattice shrinkage can also be observed using XANES spectral features. However, contrary to GIXRD, direct evidence of w-AlN formation is not observed, suggesting a dominance and surface enrichment of cubic environments. For x>0.7, XANES shows the formation of Ti–Al bonds, which could be related to the segregation of w-AlN. This study shows the relevance of local-order information to assess the atomic structure of Ti1−xAlxN solutions.
Procedures for determining acoustical physical constants of class 6mm single crystals by ultrasonic microspectroscopy technology
Authors: Kushibiki Jun-ichi , Ohashi Yuji , Arakawa Mototaka , Tanaka Tomoya
Published: June 2009

We theoretically and numerically investigated procedures for accurately determining the acoustical physical constants of piezoelectric hexagonal (class 6mm) crystals, taking ZnO as an example, using bulk-wave velocities and leaky surface acoustic wave (LSAW) velocities acquired by ultrasonic microspectroscopy technology. Selection of appropriate propagation modes and directions for eight velocity measurements to facilitate accurately determining five elastic constants (c11E, c12E, c13E, c33E, and c44E) and three piezoelectric constants (e15, e31, and e33) was discussed in addition to measurements of two dielectric constants (ε11S and ε33S) and the density (ρ). Several determination procedures were obtained. Using only bulk-wave velocities measured for Y-cut, Z-cut, and several rotated Y-cut crystalline plane specimens provided the best determination accuracies for constants c13E, c33E, e31, and e33. Favorable determination accuracies were also achieved using several sets of two rotated Y-cut crystalline plane specimens such as (101) and (102). Conductive specimens of (001) and (102) with a resistive (103) specimen made the bulk-wave measurements simpler, resulting in greatly improved determination accuracies. The additional use of LSAW velocity with one conductive (001) specimen enabled the determination procedures to be simplified, resulting in acceptable accuracy for c13E. Measurements of bulk-wave velocities and LSAW velocities for just two resistive Y-cut and Z-cut specimens could determine all the constants, albeit with some deterioration in accuracy, especially for e31 and e33. This will be useful for preliminary determination of the constants for precious crystals.
Anomalous photoresponse of GaN x-ray Schottky detectors
Authors: Duboz Jean-Yves , Beaumont Bernard , Reverchon Jean-Luc , Wieck Andreas D.
Published: June 2009

GaN based materials are believed to be very stable materials, in particular, under irradiation by high energy photons such as x rays. We have studied x-ray detectors based on GaN Schottky diodes. Vertical Schottky diodes were fabricated based on a 20μm thick undoped GaN layer grown on a conductive GaN substrate. Their photoresponse to near UV light and to x rays was measured. While the response to near UV light was fast and linear as expected, anomalous behaviors were observed under x-ray illumination. The photocurrent increases as the third power of the incident x-ray flux. The photocurrent transient when the x rays is turned on are long and nonexponential (S shape) and strongly differs from the off transient which is fast and exponential. Also, a very strong quenching of the x-ray photoresponse is observed when the detector is simultaneously illuminated with visible light. All of these anomalous behaviors are explained in the frame of a complete model involving traps and tunnel currents. A reasonable quantitative agreement between the model and the experimental data is obtained.
Effect of in-plane misfit strains on dielectric and pyroelectric response of poly(vinylidene fluoride-trifluoroethylene) ferroelectric polymer
Authors: Liu P. F. , Meng X. J. , Chu J. H. , Geneste G. , Dkhil B.
Published: June 2009

Using Landau–Devonshire (LD) phenomenological model, we investigate the dielectric and pyroelectric behaviors of poly(vinylidene fluoride-trifluoroethylene) [P(VDF-TrFE)] ferroelectric Langmuir–Blodgett super thin films. Effects of homogeneous in-plane misfit strains and external electric field on the dielectric properties are combined to be investigated. The theoretical analysis indicates that phase transition temperature can be changed by in-plane misfit strains. Furthermore results show in-plane strains only change the position of peak but value of dielectric constant and pyroelectric coefficient. At one temperature (below phase transition temperature), compressive strain is more beneficial. Consequently the dielectric and pyroelectric responses can be optimized to satisfy various demands by the applied electric fields and tuning in-plane misfit strains.
Direct-current-induced transformation at the interface between platinum anode and holmium-doped ceria electrolyte
Authors: Ou Ding Rong , Mori Toshiyuki , Ye Fei , Zou Jin , Drennan John
Published: June 2009

Under the influence of a direct current (dc), phase transformation could take place at the interface between platinum anode and holmium-doped ceria (HDC) electrolyte at temperature ≥600 °C. This transformation is insensitive to the doping concentration and the sintering temperature, but strongly depends on the testing temperature. As a result of the dc-induced transformation, products with a size up to hundreds of microns were separated from the anode-side surface and, correspondingly, circular holes with diameters varied from tens to hundreds of microns remained on the surface. Compared with original HDC samples, a high degree of local ordering of oxygen vacancies was found in most of the products. Based on structural and compositional studies, it is suggested that the dc-induced transformation could be attributed to the electrochemical reaction at the anode/electrolyte interface and the mobility of Ho cations promoted by the current.
Continuum-plasma solution surrounding nonemitting spherical bodies
Authors: Patacchini Leonardo , Hutchinson Ian H.
Published: June 2009

The classical problem of the interaction of a nonemitting spherical body with a zero mean-free-path continuum plasma is solved numerically in the full range of physically allowed free parameters (electron Debye length to body radius ratio, ion to electron temperature ratio, and body bias), and analytically in rigorously defined asymptotic regimes (weak and strong bias, weak and strong shielding, thin and thick sheath). Results include current-voltage characteristics as well as floating potential and capacitance, for both continuum and collisionless electrons. Our numerical computations show that for most combinations of physical parameters, there exists a closest asymptotic regime whose analytic solutions are accurate to 15% or better.
Convex-set description of quantum phase transitions in the transverse Ising model using reduced-density-matrix theory
Authors: Schwerdtfeger Christine A. , Mazziotti David A.
Published: June 2009

Quantum phase transitions in N-particle systems can be identified and characterized by the movement of the two-particle reduced density matrix (2-RDM) along the boundary of its N-representable convex set as a function of the Hamiltonian parameter controlling the phase transition [G. Gidofalvi and D. A. Mazziotti, Phys. Rev. A 74, 012501 (2006)]. For the one-dimensional transverse Ising model quantum phase transitions as well as their finite-lattice analogs are computed and characterized by the 2-RDM movement with respect to the transverse magnetic field strength g. The definition of a 2-RDM “speed” quantifies the movement of the 2-RDM per unit of g, which reaches its maximum at the critical point of the phase transition. For the infinite lattice the convex set of 2-RDMs and the 2-RDM speed are computed from the exact solution of the 2-RDM in the thermodynamic limit of infinite N [P. Pfeuty, Ann. Phys. 57, 79 (1970)]. For the finite lattices we compute the 2-RDM convex set and its speed by the variational 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 93, 213001 (2004)] in which approximate ground-state 2-RDMs are calculated without N-particle wave functions by using constraints, known as N-representability conditions, to restrict the 2-RDMs to represent quantum system of N fermions. Advantages of the method include: (i) rigorous lower bounds on the ground-state energies, (ii) polynomial scaling of the calculation with N, and (iii) independence of the N-representability conditions from a reference wave function, which enables the modeling of multiple quantum phases. Comparing the 2-RDM convex sets for the finite- and infinite-site lattices reveals that the variational 2-RDM method accurately captures the shape of the convex set and the signature of the phase transition in the 2-RDM movement. From the 2-RDM all one- and two-particle expectation values (or order parameters) of the quantum Ising model can also be computed including the pair correlation function, which decays rapidly around the critical field strength g.
On the calculation of puckering free energy surfaces
Authors: Sega M. , Autieri E. , Pederiva F.
Published: June 2009

Cremer–Pople puckering coordinates appear to be the natural candidate variables to explore the conformational space of cyclic compounds and in literature different parametrizations have been used to this end. However, while every parametrization is equivalent in identifying conformations, it is not obvious that they can also act as proper collective variables for the exploration of the puckered conformations free energy surface. It is shown that only the polar parametrization is fit to produce an unbiased estimate of the free energy landscape. As an example, the case of a six-membered ring, glucuronic acid, is presented, showing the artifacts that are generated when a wrong parametrization is used.
Nanograin crystalline transformation enhanced UV transparency of annealing refined indium tin oxide film
Authors: Hsu Wei-Lun , Pai Yi-Hao , Meng Fan-Shuen , Liu Chee-Wee , Lin Gong-Ru
Published: June 2009

This work investigates enhancing UV transmittance and resistivity of indium tin oxide (ITO) film via nanograin crystalline transformation. After annealing, the ITO transforms its crystallinity from amorphous to columnar nanograins, and enriches the Sn–O bonds with absorption at 572 cm−1 to greatly reduce its resistivity to 1.2×10−4 Ω cm. Long-term annealing beyond 475 °C transforms ITO crystallinity to equiaxed nanograins, promoting high UV transmittance of 50%–76% at 325–405 nm but increasing resistivity up to 1.6×10−3 Ω cm. A compromised UV transmittance of >50% and resistivity of <2×10−4 Ω cm can be simultaneously achieved in annealed ITO with hybrid crystallinity of columnar and equiaxed grains.
Ion thermal double layers in a pair-ion warm magnetized plasma containing charged dust impurities
Authors: El-Labany S. K. , El-Bedwehy N. A. , El-Shamy E. F.
Published: June 2009

In this paper the formation and the dynamics of ion thermal double layers (ITDLs) in a magnetized plasma, composed of positive and negative ions as well as a fraction of stationary charged (positive or negative) dust impurities have been studied. Using plasma hydrodynamics and Poisson equations for the two ion species, a modified Zakharov–Kuznetsov equation has been derived. The effects of the external magnetic field, the concentration of charged dust impurities, and the negative to positive ion temperature ratio on the ITDLs structure are investigated.
Efficient light harvesting in hybrid CdTe nanocrystal/bulk GaAs p-i-n photovoltaic devices
Authors: Chanyawadee Soontorn , Harley Richard T. , Taylor David , Henini Mohamed , Susha Andrei S. , Rogach Andrey L. , Lagoudakis Pavlos G.
Published: June 2009

A hybrid colloidal CdTe nanocrystal/bulk GaAs p-i-n heterostructure is demonstrated to have potential for highly efficient light harvesting photovoltaic devices. An array of rectangular channels is fabricated on the surface of the GaAs heterostructure penetrating through its active layer and subsequently filled with water soluble CdTe nanocrystals emitting in the near infrared. Photogenerated carriers in the highly absorbing colloidal nanocrystals are efficiently transferred by means of nonradiative energy transfer to the patterned heterostructure possessing high carrier mobility and converted to electrical current. A threefold enhancement of both photocurrent and monochromatic power conversion efficiency has been achieved.
Electronic, magnetic, and physical structure of cobalt deposited on aluminum tris(8-hydroxy quinoline)
Authors: Xu Weihao , Brauer Jonathan , Szulczewski Greg , Sky Driver M. , Caruso A. N.
Published: June 2009

X-ray and ultraviolet photoemission of Co deposited onto aluminum tris(8-hydroxyquinoline) (Alq3) is investigated in situ. The initial Co deposited onto Alq3 reacts to form a complex. After 1 nm of Co is deposited core level and valence band spectra show evidence for the formation of metallic cobalt. After 2 nm of Co is deposited onto Alq3 x-ray magnetic circular dichroism spectra reveals the Co is ferromagnetic at 300 K. Transmission electron microscopy images show an abrupt interface between Co and Alq3 with minimal intermixing. These results provide valuable insight into the electronic, magnetic, and physical structure of the Co/Alq3 interface.
Linewidth properties of active-passive coupled monolithic InGaAs semiconductor ring lasers
Authors: Choi Muhan , Tanaka Tomoko , Sunada Satoshi , Harayama Takahisa
Published: June 2009

We report linewidth properties of active-passive coupled monolithic InGaAs semiconductor ring lasers with various length of passive waveguide. It is experimentally confirmed that the linewidth of the lasers is proportional to the square of the ratio of the length of active part of the cavity over the total length of the cavity. The lasers are applicable for communication and sensing devices, which need the narrow linewidth.
Raman spectroscopy of rare earth doped silver halide crystals
Authors: Shafir I. , Nagli L. , Katzir A
Published: June 2009

The phonon energy of rare earth doped silver halide crystals was investigated using Raman spectroscopy. An additional phonon vibrational mode was observed and attributed to localized defect vibrational modes. Good agreement was found between the measured and the predicted frequencies of the local modes. These additional low energy (65–80 cm−1) vibrational modes do not increase the thermal quenching of mid-IR luminescence of the rare earth ions in silver halide crystals. The rare earth doped silver halide crystals are suitable for the fabrication of mid-IR solid state lasers and fiber lasers due to their extremely low phonon energies.
The structure of phenol-Arn (n=1,2) clusters in their S and S1 states
Authors: Kalkman Ivo , Brand Christian , Vu Thi-Bao Chau , Meerts W. Leo , Svartsov Yuriy N. , Dopfer Otto , Tong Xin , Müller-Dethlefs Klaus , Grimme Stefan , Schmitt Michael
Published: June 2009

The structures of the van der Waals bonded complexes of phenol with one and two argon atoms have been determined using rotationally resolved electronic spectroscopy of the S1←S0 transition. The experimentally determined structural parameters were compared to the results of quantum chemical calculations that are capable of properly describing dispersive interactions in the clusters. It was found that both complexes have π-bound configurations, with the phenol-Ar2 complex adopting a symmetric (1∣1) structure. The distances of the argon atoms to the aromatic plane in the electronic ground state of the n=1 and n=2 clusters are 353 and 355 pm, respectively. Resonance-enhanced multiphoton ionization spectroscopy was used to measure intermolecular vibrational frequencies in the S1 state and Franck–Condon simulations were performed to confirm the structure of the phenol-Ar2 cluster. These were found to be in excellent agreement with the (1∣1) configuration.
High-energy negative ion beam obtained from pulsed inductively coupled plasma for charge-free etching process
Authors: Vozniy O. V. , Yeom G. Y.
Published: June 2009

Negative ions in conventional inductively coupled plasma are often more chemically active than positive ions (for example, in CF4 or SF6 plasmas), but inconveniently they are trapped inside the sheath and cannot be used for high-energy surface etching in sources with a grid-type acceleration system. In this work we describe a method of positive and negative ion extraction that allows the energy and flux of oppositely charged particles to be varied independently. Then by scattering the ions off from a metal surface, it is possible to form a high-energy beam of neutrals from the negative ions by using the low-energy positive component of the beam current for better charge compensation.
Size-dependent effective Young’s modulus of silicon nitride cantilevers
Authors: Babaei Gavan Khashayar , Westra Hidde J. R. , van der Drift Emile W. J. M. , Venstra Warner J. , van der Zant Herre S. J.
Published: June 2009

The effective Young’s modulus of silicon nitride cantilevers is determined for thicknesses in the range of 20–684 nm by measuring resonance frequencies from thermal noise spectra. A significant deviation from the bulk value is observed for cantilevers thinner than 150 nm. To explain the observations we have compared the thickness dependence of the effective Young’s modulus for the first and second flexural resonance mode and measured the static curvature profiles of the cantilevers. We conclude that surface stress cannot explain the observed behavior. A surface elasticity model fits the experimental data consistently.
Surface stress-induced change in overall elastic behavior and self-bending of ultrathin cantilever plates
Authors: Sadeghian H. , Goosen J. F. L. , Bossche A. , van Keulen F.
Published: June 2009

In this letter, the dominant role of surface stress and surface elasticity on the overall elastic behavior of ultrathin cantilever plates is studied. A general framework based on two-dimensional plane-stress analysis is presented. Because of either surface reconstruction or molecular adsorption, there exists a surface stress and a surface elasticity imbalance between top and bottom surface of the cantilever. The surface elasticity imbalance creates an extra bending-extensional coupling which has not been taken into account previously. This leads to a modified extensional stiffness, bending stiffness and bending-extensional coupling stiffness. Due to the surface stress imbalance, an extended Stoney’s formula for self-bending of ultrathin cantilevers is derived.
A Brief and Informationally Rich Naming System for Oligosaccharide Motifs of Heteroxylans Found in Plant Cell Walls
Authors: Fauré Régis , Courtin Christophe M. , Delcour Jan A. , Dumon Claire , Faulds Craig B. , Fincher Geoffrey B. , Fort Sébastien , Fry Stephen C. , Halila Sami , Kabel Mirjam A. , Pouvreau Laurice , Quemener Bernard , Rivet Alain , Saulnier Luc , Schols Henk A. , Driguez Hugues , O'Donohue Michael J.
Published: June 2009

The one-letter code system proposed here is a simple method to accurately describe structurally diverse oligosaccharides derived from heteroxylans. Substitutions or ‘molecular decoration(s)’ of main-chain d-xylosyl moieties are designated by unique letters. Hence, an oligosaccharide is described by a series of single letters, beginning with the non-reducing d-xylosyl unit. Superscripted numbers are used to indicate the linkage position(s) of main-chain substitution(s) and, where necessary, superscripted lowercase letter(s) indicate the nature of non-glycosidic groups (e.g., methyl, acetyl, or phenolic derivative moieties) that can be present on the substituents. Although relatively simple and practical to use, this abbreviated system lends itself to the naming of a large number of different combinations of structural building blocks and substituents. In its present state, this system is, therefore, adequate to name and differentiate all currently known complex oligosaccharides derived from heteroxylans and is sufficiently flexible to accommodate new structures as they become available.
Synthesis of Naturally Occurring Arsenic-Containing Carbohydrates
Authors: Traar Pedro , Rumpler Alice , Madl Tobias , Saischek Gerald , Francesconi Kevin A.
Published: June 2009

We report the synthesis of (S)-2′-hydroxy-3′-sulfonylpropyl 5-deoxy-5-dimethylarsinoyl-β-d-riboside ammonium salt and (S)-2′-hydroxy-3′-sulfooxypropyl 5-deoxy-5-dimethylarsinoyl-β-d-riboside ammonium salt, two common naturally occurring arsenicals.
An Improved Synthetic Route to the Potent Angiogenesis Inhibitor Benzyl Manα(1→3)-Manα(1→3)-Manα(1→3)-Manα(1→2)-Man Hexadecasulfate
Authors: Liu Ligong , Johnstone Ken D. , Fairweather Jon K. , Dredge Keith , Ferro Vito
Published: June 2009

An improved synthetic route to α(1→3)/α(1→2)-linked mannooligosaccharides has been developed and applied to a more efficient preparation of the potent anti-angiogenic sulfated pentasaccharide, benzyl Manα(1→3)-Manα(1→3)-Manα(1→3)-Manα(1→2)-Man hexadecasulfate, using only two monosaccharide building blocks. Of particular note are improvements in the preparation of both building blocks and a simpler, final deprotection strategy. The route also provides common intermediates for the introduction of aglycones other than benzyl, either at the building block stage or after oligosaccharide assembly. The anti-angiogenic activity of the synthesized target compound was confirmed via the rat aortic assay.
Synthesis and Biological Evaluation of 1,5-Dideoxy-1,5-iminoxylitol–Amino Acid Hybrids as Xylosidase Inhibitors
Authors: Steiner Andreas J. , Stütz Arnold E. , Tarling Chris A. , Withers Stephen G. , Wrodnigg Tanja M.
Published: June 2009

1,5-Dideoxy-1,5-iminoxylitol–amino acid hybrids have been synthesized by cyclisation via a double reductive amination of xylo-pentodialdose and the respective amino groups of lysine as well as serine components. Further modification with aromatic substituents gave access to lipophilic derivatives. Kinetic studies revealed that all compounds exhibited better inhibitory properties against β-xylosidase from Thermoanaerobacterium sacharolyticum than the parent iminosugar.
Synthesis of ABO Histo-Blood Group Type V and VI Antigens
Authors: Meloncelli Peter J. , Lowary Todd L.
Published: June 2009

The ABO histo-blood group antigens have long been of interest to chemists, biochemists, and evolutionary biologists. However, to date, a complete synthesis of all ABO histo-blood group antigens has not been conducted, despite the potential for such a panel to provide a more detailed understanding of the biological roles of these glycan motifs. Here we report the chemical synthesis of the A, B, and H type V and VI antigens in multi-milligramme quantities as part of an overall goal to prepare all 18 A, B, and H antigens. The A and B type V and VI antigens were prepared with a 7-octen-1-yl linker, to enable future conjugation to a protein or solid support. The H type V and VI antigens were prepared as the octyl glycoside, to facilitate detailed enzyme kinetics studies.
Activation of Sugar Hydroxyl Groups Prior to Glycosylation
Authors: Ferrier Robert J. , Furneaux Richard H.
Published: June 2009

The hydroxyl groups of phenols and alcohols, including sugar alcohols, may be activated to make them more susceptible to glycosylation, but frequently activation is not formally carried out before such substitution. The present review considers methods that can be used to bring about hydroxyl group activation and thereby to facilitate glycosylation.
Evolution of the south-western Pacific genus Melicytus (Violaceae): evidence from DNA sequence data, cytology and sex expression
Authors: Mitchell A. D. , Heenan P. B. , Murray B. G. , Molloy B. P. J. , de Lange P. J.
Published: June 2009

Phylogenetic analyses of nuclear DNA external transcribed spacer (ETS) and chloroplast DNA trnL–trnF markers were undertaken to reconstruct the evolutionary history of the South Pacific genus Melicytus. Bayesian analyses of the ETS sequence data produced a phylogenetic tree with several well supported groups, including clades comprising: (1) species from Australia, Tasmania and Lord Howe Island; (2) the Norfolk Island M. latifolius and New Zealand off-shore island M. novae-zelandiae subsp. novae-zelandiae; (3) the large-leaved M. ramiflorus complex; (4) M. fasciger and M. micranthus; and (5) M. obovatus and allies from the Cook Strait region. Phylogenetic analysis of trnL–trnF sequence data also retrieved some of these groups although, in general, was not as well resolved. The relationships of M. lanceolatus are equivocal, as in the ETS phylogeny it is sister to a clade comprising the large-leaved tree species M. fasciger and M. ramiflorus complex and the small-leaved M. micranthus, whereas in the trnL–trnF phylogeny it is sister to a clade of small-leaved shrub species such as M. alpinus and M. crassifolius. Several biogeographic patterns are evident, with dispersal to the west from New Zealand, to Australia, involving small-leaved shrub species. Dispersal to the north from New Zealand, to Norfolk Island and Fiji, involves large-leaved tree species. The sex expression is documented for all named species and undescribed entities, with these being either hermaphroditic or dioecious. When sex expression is mapped onto the phylogeny, the hermaphroditic system is inferred to have evolved from the dioecious system. New chromosome counts are presented for M. angustifolius (2n = 64) and M. dentatus (2n = 32), and earlier counts of 2n = 64 are confirmed for M. crassifolius and M. alpinus. An additional 17 counts are provided for two natural hybrids and several undescribed entities from Australia and New Zealand. The polyploid chromosome number of 2n = 64 occurs most frequently in small-leaved divariate plants with hermaphroditic flowers. When chromosome numbers are plotted onto the phylogeny it is inferred that high polyploids (e.g. 2n = 64) and small-leaved shrubs have evolved from large-leaved trees with functional diploid (e.g. 2n = 32) chromosome numbers.
Characteristic numbers of algebraic varieties
Authors: Kotschick D.
Published: June 2009

A rational linear combination of Chern numbers is an oriented diffeomorphism invariant of smooth complex projective varieties if and only if it is a linear combination of the Euler and Pontryagin numbers. In dimension at least 3, only multiples of the top Chern number, which is the Euler characteristic, are invariant under diffeomorphisms that are not necessarily orientation preserving. In the space of Chern numbers, there are 2 distinguished subspaces, one spanned by the Euler and Pontryagin numbers, and the other spanned by the Hirzebruch–Todd numbers. Their intersection is the span of the Euler number and the signature.
Development regulates a switch between post- and presynaptic strengthening in response to activity deprivation
Authors: Han Edward B. , Stevens Charles F.
Published: June 2009

In response to decreased activity, neurons make global compensatory increases in excitatory synaptic strength. However, how neuronal maturity affects this process is unclear. We silenced cultured hippocampal neurons with TTX at 7 days in vitro, during rapid synaptogenesis, and at 14 days, when major synaptogenesis is complete. For each age, we have explored the effects of short (1 day) and longer (2 days) periods of silencing. We have confirmed that the changes in synaptic strength depend on 2 main mechanisms, one presynaptic and the other postsynaptic. The presynaptic mechanism involves an increase in the probability of neurotransmitter release, mostly arising through an increase in the number of synaptic vesicles available for release. The postsynaptic mechanism operates through an increase in the number of postsynaptic receptors for the excitatory neurotransmitter glutamate. When neurons are silenced for 1 day, young neurons employ the postsynaptic mechanism, whereas more mature neurons increase their strength through the presynaptic mechanism. The postsynaptic strengthening in young neurons does not depend on gene transcription, whereas the presynaptic mechanism does. If neurons are silenced for 2 days, younger and older neurons employ both pre and postsynaptic mechanisms for synaptic strengthening. We also found evidence for 2 additional mechanisms that increased the effective synaptic coupling between neurons after 2 days of silencing: an increase in the number of synapses, and an increase in the electrotonic length of dendrites. These results expand our basic understanding of neuronal homeostasis, and reveal the developmental regulation of its expression mechanisms.
Evidence for light perception in a bioluminescent organ
Authors: Tong Deyan , Rozas Natalia S. , Oakley Todd H. , Mitchell Jane , Colley Nansi J. , McFall-Ngai Margaret J.
Published: June 2009

Here we show that bioluminescent organs of the squid
Euprymna scolopes
possess the molecular, biochemical, and physiological capability for light detection. Transcriptome analyses revealed expression of genes encoding key visual transduction proteins in light-organ tissues, including the same isoform of opsin that occurs in the retina. Electroretinograms demonstrated that the organ responds physiologically to light, and immunocytochemistry experiments localized multiple proteins of visual transduction cascades to tissues housing light-producing bacterial symbionts. These data provide evidence that the light-organ tissues harboring the symbionts serve as extraocular photoreceptors, with the potential to perceive directly the bioluminescence produced by their bacterial partners.
Satellite-measured seasonal variations in primary production in the scallop-farming region of the Okhotsk Sea
Authors: Mustapha M. A. , Sei-Ichi S. , Lihan T.
Published: June 2009

Mustapha, M. A., Sei-Ichi, S., and Lihan, T. 2009. Satellite-measured seasonal variations in primary production in the scallop-farming region of the Okhotsk Sea. – ICES Journal of Marine Science, 66: 1557–1569. Seasonal variation in primary production after a retreat of the sea ice in the scallop-farming region along the Hokkaido coast of the Okhotsk Sea (1998–2004) was determined using satellite images. Annual variability in primary production was caused by variability in the physical processes associated with retreat of the sea ice, advection of the Sōya Warm Current (SWC), and intrusion of the East Sakhalin Current (ESC). Variability in primary production resulted in variability in the Chl a concentration, which was also demonstrated with an empirical orthogonal function (EOF) analysis. Enhancement of Chl a concentration in the frontal area in late spring was demonstrated by the second EOF mode of Chl a concentration (14.2% of variance), in parallel with the generation of a well-developed frontal area resulting from the advection of warm waters of the SWC along the coast in late spring, as indicated by the second EOF mode of sea surface temperature (SST; 1.8% of variance). Elevated Chl a concentration and the presence of cold water of the ESC in late autumn were also highlighted by the third EOF mode of Chl a concentration (9.0% of variance) and SST (1.5% of variance). Prolonged high primary production within the scallop-farming region after spring is supported by the development of a frontal area in summer and strengthening of the ESC in autumn.
River plume fronts off NW Iberia from satellite observations and model data
Authors: Otero P. , Ruiz-Villarreal M. , Peliz Á.
Published: June 2009

Otero, P., Ruiz-Villarreal, M., and Peliz, Á. 2009. River plume fronts off NW Iberia from satellite observations and model data. – ICES Journal of Marine Science, 66: 1853–1864. River plume fronts off NW Iberia during autumn 2002 are examined based on the gradient of the mixed layer depth (MLD) in three-dimensional model data and on sea surface temperature gradients in Advanced Very High Resolution Radiometer (AVHRR) imagery. The method reveals new aspects of the dynamics of fronts in the area. The strong gradient of the MLD between the plume and the adjacent ocean serves as a physical indicator of the maximum extension of the river plume and takes into account its three-dimensional structure as well as its surface signal. Differences in the position of river plume fronts are associated with local upwelling/downwelling conditions and their relaxation. During expansions of the plume induced by upwelling in late autumn, the shallower plume waters become colder and the thermal gradient with offshore waters increases. The model simulation also illustrates the existence of instabilities at the plume front and cross-shore variations in plume width that could induce the appearance of thermal gradients which can be resolved with AVHRR. Our simulations also show regional differences in front location, structure, and probability north (Galicia) and south (north Portugal) on the shelf, where bathymetry differs in shape and depth.
Female reproductive biology, and age of deep-sea squid Histioteuthis miranda from southern Africa
Authors: Hoving Hendrik Jan T. , Lipiński Marek R.
Published: June 2009

Hoving, H. J. T., and Lipiński, M. R. 2009. Female reproductive biology, and age of deep-sea squid Histioteuthis miranda from southern Africa. – ICES Journal of Marine Science, 66: 1868–1872. Data on female reproductive strategy and male and female length–weight relationships and age are presented for the mesopelagic squid Histioteuthis miranda. Females exhibit synchronous ovulation, indicating that eggs are spawned at once or over a short period. The maximum potential fecundity seems to range from 89 000 to 148 000 oocytes. Assuming daily deposition of statolith increments, maturing females were 10–15 months old. Male H. miranda mature young (∼6 months) and reach at least 15 months old.
Tracking the past: Interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius
Authors: Zhao Fangqing , Qi Ji , Schuster Stephan C.
Published: June 2009

The woolly mammoth (Mammuthus primigenius) died out about several thousand years ago, yet recent paleogenomic studies have successfully recovered genetic information from both the mitochondrial and nuclear genomes of this extinct species. Mammoths belong to Afrotheria, a group of mammals exhibiting extreme morphological diversity and large genome sizes. In this study, we found that the mammoth genome contains a larger proportion of interspersed repeats than any other mammalian genome reported so far, in which the proliferation of the RTE family of retrotransposons (covering 12% of the genome) may be the main reason for an increased genome size. Phylogenetic analysis showed that RTEs in mammoth are closely related to the family BovB/RTE. The incongruence of the reconstructed RTE phylogeny indicates that RTEs in mammoth may be acquired through an ancient lateral gene transfer event. A recent proliferation of SINEs was also found in the probocidean lineage, whereas the Afrotherian-wide SINEs in mammoth have undergone a rather flat and stepwise expansion. Comparisons of the transposable elements (TEs) between mammoth and other mammals may shed light on the evolutionary history of TEs in various mammalian lineages.