bluuebunny/crossref_metadata_2025 huggingface dataset:
The development of asymmetry for oscillatory flow within a tube containing sharp edge periodic baffles
Authors: Zheng Mingzhi , Li Jie , Mackley M. R. , Tao Jianjun
Published: November 2007

This paper investigates the evolution of asymmetric patterns for oscillatory flow in a baffled tube. A numerical simulation for three-dimensional flows in an axisymmetric geometry was developed and compared with experimental results obtained using particle image velocimetry (PIV). Sharp edged baffles were used for both numerical simulations and experiments. From the numerical simulation, a stability map of the flow symmetry was obtained as a function of Reynold-Strouhal numbers. The simulations show that for all Strouhal numbers, the flow was axisymmetric at Reynolds numbers less than 100 and asymmetric at Reynolds numbers larger than 225. The flow was less stable to asymmetric disturbances at small or large Strouhal numbers when compared to St=1.0. In particular, the flow in the region St<0.5 and Re>100 was asymmetric. Two mechanisms for vortex instability transition into three dimensions has been identified. At small Strouhal numbers, the primary mechanism is a shear (Kelvin-Helmholtz) instability. At larger Strouhal numbers, the axisymmetry of the flow is broken because of the collision of travelling eddies that have been shed from opposite baffles. The numerical results are in general in agreement quantitatively with the experimental observations and both experiment and simulation assist in understanding the development of unsteadiness in periodic reversing flows.
Granular mixtures: Analogy with chemical solution thermodynamics
Authors: Severson B. L. , Snurr R. Q. , Ottino J. M.
Published: November 2007

Particle dynamics simulations reveal parallels between granular mixtures and chemical solutions. Thermodynamic solution theory provides a connection between the interaction strength of the molecules, the concentration of each species in the solution, and bulk solution behavior. Particle dynamics simulations demonstrate a similar relationship between the interparticle forces, the composition of the granular mixture, and bulk flow behavior. The analogy holds true over different particle interaction types (friction or adhesion) and over different bulk properties (the angle of repose in a rotating drum and the viscosity of particles sheared between parallel plates). A solution theory for granular mixtures would provide a framework to study the properties of granular mixtures.
Modeling of plasma-target interaction during reactive magnetron sputtering of TiN
Authors: Möller W. , Güttler D.
Published: November 2007

The nitrogen incorporation at the target during reactive magnetron sputtering of TiN is described by a simple stationary global model of the magnetron plasma, in combination with an analytical two-layer stationary surface model or dynamic collisional computer simulation (TRIDYN) of the surface processes. Results are shown for different nitrogen gas additions in Ar∕N2 and Xe∕N2 gas mixtures at a total pressure of 0.3Pa and a magnetron current of 0.3A. The nitrogen incorporation predicted by the analytical model is significantly less than obtained from computer simulation. The computer simulation yields nitrogen depth profiles which extend to about 2.5nm, exhibiting a quasirectangular shape in case of stoichiometric saturation with an integrated nitrogen areal density of ∼1.25×1016N∕cm2. The stationary-state nitrogen incorporation results from the balance of surface adsorption in connection with recoil implantation, direct ion implantation, and resputtering. The most relevant species are nitrogen gas molecules for adsorption, molecular nitrogen ions for implantation, and inert gas ions for recoil implantation and sputtering. The model results are in good agreement with experiment provided that nonzero sticking of nitrogen gas molecules is assumed on the unsaturated surface. The analytical surface model is preferable, which favors the picture of a continuous transition to bulk and surface saturation rather than discrete local saturation which is inherent in TRIDYN. Also the relative nitrogen incorporation for Xe∕N2 versus Ar∕N2 gas mixtures is well described.
Complex laterally ordered InGaAs and InAs quantum dots by guided self-organized anisotropic strain engineering on shallow- and deep-patterned GaAs (311)B substrates
Authors: Selçuk E. , Hamhuis G. J. , Nötzel R.
Published: November 2007

Self-organized anisotropic strain engineering guided on shallow- and deep-patterned GaAs (311)B substrates is exploited for formation of complex laterally ordered architectures of connected InGaAs quantum dot (QD) arrays and isolated InAs QD groups by molecular beam epitaxy. The combination of strain and step engineerings on shallow stripe-patterned substrates transforms the periodic spotlike arrangement of the InGaAs QD arrays and InAs QD groups (on planar substrates) into a zigzag arrangement of periodic stripes which are well ordered over macroscopic areas on zigzag mesa-patterned substrates. In contrast, the formation of slow-growing facets on deep-patterned substrates produces QD-free mesa sidewalls, while InGaAs QD arrays and InAs QD groups form on the GaAs (311)B top and bottom planes with arrangements modified only close to the sidewalls depending on the sidewall orientation. The QDs on the shallow- and deep-patterned substrates exhibit excellent optical properties up to room temperature. Therefore, the concept of guided self-organization demonstrated on shallow-patterned (due to steps) and deep-patterned (due to facets) substrates is highlighted for creation of complex architectures of laterally ordered QDs for future quantum functional devices.
Comparing the activation energy of diffusion in bulk and ultrathin fluid films
Authors: Grabowski Christopher A. , Mukhopadhyay Ashis
Published: November 2007

We have measured the activation energy (Eact) of translational diffusion for a dissolved fluorescent dye in bulk and within an ultrathin liquid film formed on a solid substrate. The experiments were performed using the single-molecule sensitive technique of fluorescence correlation spectroscopy. From the temperature-dependent measurements, we have determined that the activation energy for a few nanometer thick fluid film increases by a factor of ≈3–4 compared to bulk liquid. The results are confirmed for two distinctly different systems in regard to molecular shape, tetrakis (2-ethylhexoxy) silane and hexadecane.
High resolution selective multilayer laser processing by nanosecond laser ablation of metal nanoparticle films
Authors: Ko Seung H. , Pan Heng , Hwang David J. , Chung Jaewon , Ryu Sangil , Grigoropoulos Costas P. , Poulikakos Dimos
Published: November 2007

Ablation of gold nanoparticle films on polymer was explored using a nanosecond pulsed laser, with the goal to achieve feature size reduction and functionality not amenable with inkjet printing. The ablation threshold fluence for the unsintered nanoparticle deposit was at least ten times lower than the reported threshold for the bulk film. This could be explained by the combined effects of melting temperature depression, lower conductive heat transfer loss, strong absorption of the incident laser beam, and the relatively weak bonding between nanoparticles. The ablation physics were verified by the nanoparticle sintering characterization, ablation threshold measurement, time resolved ablation plume shadowgraphs, analysis of ablation ejecta, and the measurement and calculation of optical properties. High resolution and clean feature fabrication with small energy and selective multilayer processing are demonstrated.
Electronic polarization spectroscopy of metal phthalocyanine chloride compounds in superfluid helium droplets
Authors: Pei Linsen , Zhang Jie , Kong Wei
Published: November 2007

We report the electronic polarization spectroscopy of two metal phthalocyanine chloride compounds (MPcCl, M=Al,Ga) embedded in superfluid helium droplets and oriented in a dc electric field. For both compounds, the laser induced fluorescence spectra show preference for perpendicular excitation relative to the orientation field. This result indicates that the permanent dipoles of both compounds are predominantly perpendicular to the transition dipole. Since the permanent dipole derives from the metal chloride, while the transition dipole derives from the phthalocyanine chromophore, in the plane of phthalocyanine, this qualitative result is not surprising. However, quantitative modeling reveals that this intuitive model is inadequate and that the transition dipole might have tilted away from the molecular plane of phthalocyanine. The out of plane component of the transition dipole amounts to ∼10% if the permanent dipole is assumed to be ∼4debye. The origin for this tilt is puzzling, and we tentatively attribute it to the transition of nonbonding orbitals, either from the chlorine atom or from the bridge nitrogen atom, to the π* orbitals of the phthalocyanine chromophore. On the other hand, although unlikely, we cannot completely exclude the possibility that both our high level density functional theory calculation and ab initio results severely deviate from reality. The droplet matrix induces redshifts in the origin of the electronic transition and produces discrete phonon wings. Nevertheless, in dc electric fields, all phonon wings and the zero phonon line demonstrate the same dependence on the polarization direction of the excitation laser. Although electronic excitation does couple to the superfluid helium matrix and the resulting phonon wings add complications to the electronic spectrum, this coupling does not affect the direction of the electronic transition dipole. Electronic polarization spectroscopy in superfluid helium droplets is thus still informative in revealing the permanent dipole and its relation relative to the transition dipole.
Phase transition and piezoelectric property of (Bi0.5Na0.5)0.94Ba0.06ZryTi1−yO3(y=–0.04) ceramics
Authors: Yao Yi-Quan , Tseng Tseung-Yuen , Chou Chen-Chia , Chen Haydn H. D.
Published: November 2007

The ceramics with the composition of (Bi0.5Na0.5)0.94Ba0.06ZryTi1−yO3 (BNBZ100yT, in which y=0,0.01,0.02,0.04) were prepared successfully by the solid state reaction method. X-ray diffraction studies revealed the perovskite structure in BNBZ100yT ceramics sintered at 1170°C for 2h in air. The relative densities of the sintered ceramics were around 97%–99%. The temperature dependent dielectric properties of BNB6T and BNB6Z4T ceramics showed their relaxor-like behaviors. Decreases in remnant polarization, coercive field, and disappearance of piezoelectric properties were found by the substitution of 2 and 4mol% Zr4+ for Ti4+ in these ceramics. Electron diffraction patterns taken in a transmission electron microscope demonstrated the existence of cubic crystalline phase in the BNB6Z4T ceramics leading to the disappearance of piezoelectric property. Decrease in grain size was also observed with the substitution of Zr4+ for Ti4+ in BNB6T ceramics.
Intrinsic electrostatic resonances of heterostructures with negative permittivity from finite-element calculations: Application to core-shell inclusions
Authors: Mejdoubi Abdelilah , Brosseau Christian
Published: November 2007

Herein, we report finite-element calculations of the effective (relative) permittivity of composite materials consisting of inclusions and inclusion arrays with a core-shell structure embedded in a surrounding host. The material making up the core of the two-dimensional structures, or cross sections of infinite three-dimensional objects (parallel, infinitely long, and identical cylinders) where the properties and characteristics are invariant along the perpendicular cross sectional plane, is assumed to have a negative real part of the permittivity, while the coating material (annular shell) is considered to be lossless. While strictly valid only in a dc situation, our analysis can be extended to treat electric fields that oscillate with time, provided that the wavelengths and attenuation lengths associated with the fields are much larger than the microstructure dimension in order that the homogeneous (effective-medium) representation of the composite structure makes sense. While one may identify features of the electrostatic resonance (ER) which are common to core-shell structures characterized by permittivities with real parts of opposite signs, it appears that the predicted ER positions are sensitive to the shell thickness and can be tuned through varying this geometric parameter. For example, we observe that the ER is broadened and shifted as the loss and the shell thickness are increased, respectively. We also argue that such core shell may also be valuable in controlling ER characteristics via polarization in an external electric field. In addition, by considering calculations of the electric field distribution, we find that the ER results in very strong and local-field enhancements into small parts of the shell perimeter. Our findings open up possibilities for the development of hybrid structures that could exploit the ER features for a particular application.
Carrier transport mechanisms of the writing and the erasing processes for Al∕ZnO nanoparticles embedded in a polyimide layer/p-Si diodes
Authors: Jung J. H. , Kim H. J. , Kim B. J. , Kim T. W. , Kim Y.-H.
Published: November 2007

Capacitance-voltage measurements on Al∕ZnO nanocrystals embedded in polyimide (PI) layer/p-Si diodes at 300K showed a metal-insulator-semiconductor behavior with a flatband voltage shift. Current-voltage (I-V) measurements on the diodes showed that carrier transport processes were attributed to the Poole-Frenkel effect and to thermionic emission. Possible carrier transport mechanisms of the writing and the erasing processes for the Al∕ZnO nanocrystals embedded in PI layer/p-Si diodes are described on the basis of the I-V results.
Enlarging the bandwidth of nanoscale propagating plasmonic modes in deep-subwavelength cylindrical holes
Authors: Catrysse Peter B. , Fan Shanhui
Published: November 2007

Subwavelength cylindrical holes in optically thick metallic films always support a propagating HE11 mode near the surface plasmon frequency, regardless of how small the holes are. For holes filled with a uniform dielectric material, the bandwidth of the HE11 mode asymptotically approaches zero as the hole size is reduced to deep-subwavelength scales. We show that it is possible to create nanoscale propagating plasmonic modes with a very large bandwidth in holes that are concentrically filled with two different dielectric materials, even when the hole radius goes to zero.
Memory and Coulomb blockade effects in germanium nanocrystals embedded in amorphous silicon on silicon dioxide
Authors: Gacem K. , El Hdiy A. , Troyon M. , Berbezier I. , Szkutnik P. D. , Karmous A. , Ronda A.
Published: November 2007

Germanium nanocrystals embedded in amorphous silicon and self-organized on a tunnel silicon dioxide layer thermally grown on (100) p-doped silicon substrate have been electrically studied at different temperatures by using current-voltage and capacitance-voltage measurements. Results showed a carrier exchange between the gate and isolated germanium nanocrystals via amorphous silicon. Hysteresis loops observed in the capacitance-voltage curves were attributed to electron injection∕emission process in germanium nanocrystals, which indicated a memory effect behavior. Resonant tunneling effect through germanium nanocrystals with large voltage gaps was observed at room temperature in these ultradense Ge nanocrystals of ∼3.5nm mean size. It appeared for increasingly low voltages when the temperature decreases. All these results are consistent with a Coulomb blockade effect in ultrasmall Ge nanocrystals in which an effective number of electrons transported by each tunneling step varied between 1.8 and 3.81.
Generally covariant quantum mechanics on noncommutative configuration spaces
Authors: Kopf Tomáš , Paschke Mario
Published: November 2007

We generalize the previously given algebraic version of “Feynman’s proof of Maxwell’s equations” to noncommutative configuration spaces. By doing so, we also obtain an axiomatic formulation of nonrelativistic quantum mechanics over such spaces, which, in contrast to most examples discussed in the literature, does not rely on a distinguished set of coordinates. We give a detailed account of several examples, e.g., C∞(Q)⊗Mn(C) which leads to non-Abelian Yang-Mills theories, and of noncommutative tori Tθd. Moreover, we examine models over the Moyal-deformed plane Rθ2. Assuming the conservation of electrical charges, we show that in this case the canonical uncertainty relation [xk,ẋl]=igkl with metric gkl is only consistent if gkl is constant.
Detection of low energy single ion impacts in micron scale transistors at room temperature
Authors: Batra A. , Weis C. D. , Reijonen J. , Persaud A. , Schenkel T. , Cabrini S. , Lo C. C. , Bokor J.
Published: November 2007

We report the detection of single ion impacts through monitoring of changes in the source-drain currents of field effect transistors at room temperature. Implant apertures are formed in the interlayer dielectrics and gate electrodes of planar, microscale transistors by electron beam assisted etching. Device currents increase due to the generation of positively charged defects in gate oxides when ions (Sb12+,14+121 and Xe6+; 50–70keV) impinge into channel regions. Implant damage is repaired by rapid thermal annealing, enabling iterative cycles of device doping and electrical characterization for the development of single atom devices and studies of dopant fluctuation effects.
Conduction band offset of HfO2 on GaAs
Authors: Seguini G. , Perego M. , Spiga S. , Fanciulli M. , Dimoulas A.
Published: November 2007

A detailed analysis of the band alignment between molecular beam deposited amorphous HfO2 and GaAs is reported. The conduction band offset, measured by internal photoemission (IPE), is 1.9±0.2eV. The valence band offset (VBO) is probed by x-ray photoelectron spectroscopy (XPS). The accurate determination of the VBO requires a careful evaluation of differential charging phenomena and consequently a proper correction of the energy scale. The measured VBO value is 2.1±0.1eV. Since the HfO2 gap is 5.6eV, as detected by photoconductivity analysis, the results obtained by IPE and XPS are in excellent agreement.
Isotropic frequency selective surfaces made of cubic resonators
Authors: Baena J. D. , Jelinek L. , Marqués R. , Mock J. J. , Gollub J. , Smith D. R.
Published: November 2007

Isotropic frequency selective surface (FSS) made of cubic arrangements of split ring resonators (SRRs) is proposed and analyzed. For this purpose, a suitable isotropic modification of the SRR was used in the design of a cubic unit element invariant under the tetrahedral point symmetry group. It was experimentally demonstrated that the transmission through such a FSS is angle and polarization independent. For comparison, another FSS, whose unit elements do not satisfy necessary symmetries, was measured, showing clearly anisotropic behavior. We feel then that symmetries play an important role. Potential device applications are envisioned for antenna technology at microwave and terahertz frequencies.
Origins of high radiative efficiency and wideband emission from InAs quantum dots
Authors: Ngo C. Y. , Yoon S. F. , Fan W. J. , Chua S. J.
Published: November 2007

Origins of high radiative efficiency and wideband emission from InAs quantum dots (QDs) were studied experimentally and theoretically. Radiative efficiency was found to depend strongly on the absence of large nonradiative islands. Theoretical calculations were performed to determine the combined effects of QD size and its fluctuation on the energy range. Good agreement between the theoretical and experimental results was obtained. Recognizing that high output power and large optical bandwidth are key figures of merit for QD superluminescent diodes (SLDs), we believe that the findings from our work will be beneficial for those working on QD-SLDs.
High performance n-channel thin-film transistors with an amorphous phase C60 film on plastic substrate
Authors: Na Jong H. , Kitamura M. , Arakawa Y.
Published: November 2007

We fabricated high mobility, low voltage n-channel transistors on plastic substrates by combining an amorphous phase C60 film and a high dielectric constant gate insulator titanium silicon oxide (TiSiO2). The transistors exhibited high performance with a threshold voltage of 1.13V, an inverse subthreshold swing of 252mV/decade, and a field-effect mobility up to 1cm2∕Vs at an operating voltage as low as 5V. The amorphous phase C60 films can be formed at room temperature, implying that this transistor is suitable for corresponding n-channel transistors in flexible organic logic devices.
Animation uses old physics to new effect
Authors: Feder Toni
Published: November 2007

Achieving visual realism with physically based simulations while taming the result to fit artists' imaginations is the goal in animated filmmaking and gaming.
The rubidium atomic clock and basic research
Authors: Camparo James
Published: November 2007

The vapor-cell atomic clock finds application today in the global positioning system and telecommunications. To improve and miniaturize the humble device for future applications will require a deeper understanding of atomic and chemical physics.
Organoboron Reagents in the Preparation of Functionalized ?-Amino Acids
Authors: Kaiser Peter F. , Churches Quentin I. , Hutton Craig A.
Published: November 2007

Over the past decade, major advances in the preparation and utilization of organoboron reagents have been applied to virtually all areas of organic synthesis. The present review collates recent examples of the use of organoboron reagents in the synthesis of α-amino acids and their derivatives. Aryl- and alkenylboronic acids have been used in the asymmetric synthesis of α-amino acids through conjugate addition to unsaturated amino acids and the Petasis three-component coupling reaction. Additionally, α-amino acid derivatives with organoboron functionality on the side-chain have been prepared and used in metal-catalyzed cross-coupling reactions to prepare cross-linked amino acids and complex cyclic peptide natural products.
Tapping into Boron/?-Hydroxycarboxylic Acid Interactions in Sensing and Catalysis
Authors: Houston Todd A. , Levonis Stephan M. , Kiefel Milton J.
Published: November 2007

Whereas interaction of boron acids (boric and boronic) with diols and neutral sugar ligands has received much global research attention in recent years, the binding of simple α-hydroxycarboxylic and sugar acids by boron has received less attention. Applications of boron-based fluorescent sensors and chemoselective catalysts targeting this functional motif have appeared only in the past 5 years. The present synopsis will focus on rapid developments that have occurred in both areas during this half decade.
Phototransformation of Perchlorate to Chloride in the Presence of Polysilanes
Authors: Lazar Carmen , Halasz Annamaria , Beaulieu Chantale , Thiboutot Sonia , Ampleman Guy , Hawari Jalal
Published: November 2007

Perchlorate is a uniquely stable chemical described as an emerging thyroid disrupting agent that is presently detected in several terrestrial and aquatic matrices. The present study was undertaken to deoxygenate perchlorate to the chloride anion photolytically in the presence of dodecamethylcyclohexasilane (Me2Si)6 1. It is found that photolysis of 1 in the presence of dry NaClO4 in tetrahydrofuran (THF) at 254 nm leads to the disappearance of the salt. The removal of ClO4– occurred with the concurrent formation of ClO3– and ClO2–, which disappear to eventually produce the chloride anion quantitatively. The two cyclic silanes (Me2Si)5 3 and (Me2Si)4 4 in addition to several other siloxanes that include (Me2SiO)3, (Me2SiO)4, and (Me2Si)xO2 (x = 4 and 5) were also detected. When the reaction was repeated using uniformly labelled 18O-[ClO4–] it was found that oxygen incorporated in the siloxane products was derived from perchlorate. Mixing 1 with perchlorate in THF in the dark or adding the salt to 1 after the latter being photolyzed in THF did not deoxygenate ClO4–. Based on experimental evidence gathered thus far it is concluded that dimethylsilylene, Me2Si: 2, a reactive intermediate produced by the photolysis of 1, is in part responsible for the deoxygenation of perchlorate. Direct oxygen transfer from ClO4– to the silanes during photolysis is also suggested as a potential route of deoxygenating ClO4–.
Expanding Roles for Organoboron Compounds – Versatile and Valuable Molecules for Synthetic, Biological and Medicinal Chemistry
Authors: Petasis Nicos A.
Published: November 2007

The present essay offers an overview of the latest developments in the chemistry of organoboron compounds. The unique structural characteristics and the versatile reactivity profile of organoboron compounds continue to expand their roles in several areas of chemistry. A growing number of boron-mediated reactions have become vital tools for synthetic chemistry, particularly in asymmetric synthesis, metal-catalyzed processes, acid catalysis, and multicomponent reactions. As a result, boronic acids and related molecules have now evolved as major players in synthetic and medicinal chemistry. Moreover, their remnant electrophilic reactivity, even under physiological conditions, has allowed their incorporation in a growing number of bioactive molecules, including bortezomib, a clinically approved anticancer agent. Finally, the sensitive and selective binding of boronic acids to diols and carbohydrates has led to the development of a growing number of novel chemosensors for the detection, quantification, and imaging of glucose and other carbohydrates. There is no doubt that the chemistry of organoboron compounds will continue to expand into new discoveries and new applications in several fields of science.
Patterns of morphological leaf traits among pteridophytes along humidity and temperature gradients in the Bolivian Andes
Authors: Kessler Michael , Siorak Yvonne , Wunderlich Meike , Wegner Caroline
Published: November 2007

Macroecological patterns of leaf traits can be used to assess adaptive responses of plants to environmental stress. Here we present the first such study on a large number of fern species (403) along gradients of elevation (temperature) and humidity. To assess how the representation of traits such as degree of lamina dissection, leaf length, leaf mass per area (LMA), trichome density, venation density, stomatal density, and of adaptive strategies such as poikilohydry vary at the community and species levels in response to changes in humidity and temperature in the Bolivian Andes, we (1) compared whole pteridophyte communities at 14 sites, and (2) analysed intraspecific variation of the morphological traits of 17 fern species along an elevational gradient at 1700–3400 m in humid forest. Among the fern communities of the 14 sites, leaf length decreased with elevation and aridity, LMA increased with elevation, and trichome density and venation density increased with aridity. The study of intraspecific variation among 17 species showed an increase of stomatal density with elevation in six of 11 species (filmy ferns lacked stomata), an increase of specific weight in 15 species, a decrease of trichome density in seven of 10 species (other species lacked hairs), and a decrease of venation density in seven of 10 cases. Some of these trends can be interpreted adaptively: leaf thickness appears to increase in situations with low nutrient availability rather than with low water availability, whereas a dense cover of scales or hairs serves as a protection against insolation or as a vehicle for the absorption of water in poikilohydric species. In arid areas, trichome density increased with elevation, while it decreased with elevation in cloudy and humid regions. For most traits, variation was more pronounced at the community than at the species level, except for stomatal density, which varied much more strongly within than between species. Several of these morphological and anatomical characters can be used to infer palaeoclimatic conditions based on fossil pteridophyte floras.
The sun-exposed peel of apple fruit has a higher photosynthetic capacity than the shaded peel
Authors: Chen Li-Song , Cheng Lailiang
Published: November 2007

To determine whether the sun-exposed peel of apple fruit has a higher photosynthetic capacity than the shaded peel, fruit peel samples were taken in both early July and early September from the exterior part of the canopy of mature ‘Liberty’/M.9 trees for measuring oxygen evolution, key enzymes and metabolites involved in photosynthesis, and chlorophyll fluorescence. Compared with the shaded peel, the sun-exposed peel had higher light-saturated oxygen evolution rate and higher light saturation point, but lower apparent and true quantum yields. The activity of ribulose-1,5-bisphosphate carboxylase/oxygenase, glyceraldehyde-3-phosphate dehydrogenase, phosphoribulokinase, stromal fructose-1,6-bisphosphatase, ADP-glucose pyrophosphorylase and sucrose-phosphate synthase (SPS) were higher in the sun-exposed peel than in the shaded peel on both sampling dates except that no significant difference was found in SPS activity between the two peel types in September. No significant difference was detected in the concentration of key metabolites (G6P, F6P, G1P, and PGA) between the sun-exposed peel and the shaded peel, suggesting that the response of the key enzymes to light exposure is well coordinated. Chlorophyll fluorescence quenching analysis showed that the sun-exposed peel had higher PSII quantum efficiency than the shaded peel at each given PFD, which resulted mainly from the higher photochemical quenching coefficient (qP). The sun-exposed peel had higher thermal dissipation capacity, as indicated by larger NPQ and Fo quenching, than the shaded peel at high PFD. In conclusion, the sun-exposed peel of apple fruit has higher activities of the Calvin cycle enzymes and higher rate of electron transport, leading to higher photosynthetic O2 evolution capacity. It appears that the acclimation of the Calvin cycle activities, thermal dissipation, and electron transport in apple peel are well coordinated in response to light exposure.
Corrigendum to: Elastic properties of the forisome
Authors: Warmann Stephen A. , Pickard William F. , Shen Amy Q.
Published: November 2007

Forisomes are elongate Ca2+-responsive contractile protein bodies and act as flow blocking gates within the phloem of legumes. Because an understanding of their mechanical properties in vitro underpins understanding of their physiology in vivo, we undertook, using a microcantilever method, microscopic tensile tests (incremental stress-relaxation measurements) on forisomes from Canavalia gladiata (Jacq.) DC Akanata Mame and Vicia faba L. Witkiem Major. Viscoelastic properties of forisomes in their longitudinal direction were investigated before and after Ca2+-induced contraction, but in the radial direction only before contraction. Forisomes showed mechanical properties typical of a biological material with a unidirectional fibrous structure, i.e. the modulus of elasticity in the direction of their fibers is much greater than in the radial direction. Creep data were collected in all tensile tests and fit with a three parameter viscoelastic model. The pre-contraction longitudinal elastic moduli of the forisomes were not differentiable between the two species (V. faba, 660���360�kPa; C. gladiata, 600���360�kPa). Both species showed a direction-dependent mechanical response: the elastic modulus was dramatically smaller in the radial direction than in the longitudinal direction, suggesting a weak protein cross-linking amongst longitudinal protein fibers. Activation of forisomes decreased forisome stiffness longitudinally, as evidenced by the loss of toe-region in the stress strain curve, suggesting that the forisome may have dispersed or disordered its protein structure in a controlled fashion. Contractile forces generated by single forisomes undergoing activation were also measured for V. faba (510���390�nN) and C. gladiata (570���310�nN).
Bicarbonate blocks the expression of several genes involved in the physiological responses to Fe deficiency of Strategy I plants
Authors: Lucena Carlos , Romera Francisco J. , Rojas Carmen L. , García María J. , Alcántara Esteban , Pérez-Vicente Rafael
Published: November 2007

Bicarbonate is considered one of the most important factors causing Fe chlorosis in Strategy I plants, mainly on calcareous soils. Most of its negative effects have been attributed to its capacity to buffer a high pH in soils, which can diminish both Fe solubility and root ferric reductase activity. Besides its pH-mediated effects, previous work has shown that bicarbonate can inhibit the induction of enhanced ferric reductase activity in Fe-deficient Strategy I plants. However, to date it is not known whether bicarbonate affects the upregulation of the ferric reductase gene and other genes involved in Fe acquisition. The objective of this work has been to study the effect of bicarbonate on the expression of several Fe acquisition genes in Arabidopsis (Arabidopsis thaliana L.), pea (Pisum sativum L.), tomato (Lycopersicon esculentum Mill.) and cucumber (Cucumis sativus L.) plants. Genes for ferric reductases AtFRO2, PsFRO1, LeFRO1 and CsFRO1; iron transporters AtITR1, PsRIT1, LeIRT1 and CsIRT1; H+-ATPases CsHA1 and CsHA2; and transcription factors AtFIT and LeFER have been examined. The results showed that bicarbonate could induce Fe chlorosis by inhibiting the expression of the ferric reductase, the iron transporter and the H+-ATPase genes, probably through alteration of the expression of Fe efficiency reactions (FER) (or FER-like) transcription factors.
On the 16O/18O isotope effect associated with photosynthetic O2 production
Authors: Tcherkez Guillaume , Farquhar Graham D.
Published: November 2007

While photosynthetically evolved O2 has been repeatedly shown to have nearly the same oxygen isotope composition as source water so that there is no corresponding 16O/18O isotope effect, some recent 18O-enrichment studies suggest that a large isotope effect may occur, thus feeding a debate in the literature. Here, the classical theory of isotope effects was applied to show that a very small isotope effect is indeed expected during O2 production. Explanations of the conflicting results are briefly discussed.
Geographical and environmental correlates of big and small game in Andalusia (southern Spain)
Authors: Vargas J. M. , Farfán M. A. , Guerrero J. C. , Barbosa A. M. , Real R.
Published: November 2007

In Andalusia, southern Spain, each game estate applies its own rules and presents its results in annual hunting reports, which have been mandatory for Spanish game estates since 1989. We used the information about hunting yields, included in 32 134 annual hunting reports produced during the period 1993/94 to 2001/02 by 6049 game estates, to determine the current distribution of hunting yields of big and small game species in Andalusia. Using generalised linear models and a geographic information system, we determined the most favourable municipalities to big and small game, respectively, and delimited potential areas to attain good hunting yields for big and small game at a 1-km2 resolution. Municipalities and areas favourable to big game are mainly located in the Sierra Morena and the westernmost fringe of the Betic Range, while those favourable to small game occupy the upper Guadalquivir River valley. There is a clear segregation between big and small game species according to the physiography and land uses of the territory. Big game species are typical of Mediterranean woodland areas, while the most emblematic small game species prefer agricultural areas. Our results provide a territorial ordination of hunting yields in southern Spain and have several potential applications in strategic planning for hunting activities and biodiversity conservation in Andalusia that can be extrapolated to other regions.
Do feathertail gliders show a preference for nest box design?
Authors: Goldingay Ross L. , Grimson Matthew J. , Smith Geoffrey C.
Published: November 2007

Although nest boxes have considerable application in the research and management of hollow-using arboreal marsupials, few studies have assessed whether species show a preference for particular nest box designs. This study aimed to determine whether the feathertail glider (Acrobates pygmaeus) showed a preference when offered four different designs, each of which had been used in earlier studies. We established one of each design in 45 plots across five locations, spanning north-east New South Wales and south-east Queensland. Feathertail gliders used 34 nest boxes at four locations but avoided a medium-sized rear-entry box with a 45-mm-diameter entrance. No clear preference was shown for three designs with narrow (≤25 mm) entrances. Feathertail gliders used 15 small rear-entry boxes, 10 large slit-entrance boxes and 9 wedge-shaped bat boxes. A slight preference was shown by breeding groups to occur in the non-wedge boxes compared with the wedge boxes. Squirrel gliders (Petaurus norfolcensis) used 51% of medium rear-entry boxes at four locations. This may account for the avoidance of this box design by feathertail gliders at these locations. Breeding and prolonged use of nest boxes by resident feathertail gliders and squirrel gliders at two locations in eucalypt plantations suggest that nest boxes can support local populations of arboreal marsupials where tree hollows are absent or scarce.
Adult spinal cord progenitor cells are repelled by netrin-1 in the embryonic and injured adult spinal cord
Authors: Petit Audrey , Sellers Drew L. , Liebl Daniel J. , Tessier-Lavigne Marc , Kennedy Timothy E. , Horner Philip J.
Published: November 2007

Adult neural progenitor cells (aNPCs) exhibit limited migration
in vivo
with the exception of the rostral migratory stream and injury-induced movement. Surprisingly little is known regarding those signals regulating attraction or inhibition of the aNPC. These studies demonstrate that aNPCs respond principally to a repulsive cue expressed at the embryonic floor plate (FP) and also the injured adult CNS. Adult spinal cord progenitor cells (aSCPs) were seeded onto organotypic slice preparations of the intact embryonic or injured adult spinal cord. Cell migration assays combined with genetic and molecular perturbation of FP-derived migration cues or aSCP receptors establish netrin-1 (Ntn-1) but not Slit-2, Shh, or Ephrin-B3 as the primary FP-derived repellant. When slices were prepared from injured spinal cord, aSCP migration away from the injury core was Ntn-1-dependent. These studies establish Ntn-1 as a critical regulator of aSCP migration in the intact and injured CNS.
The auxiliary subunit γ
1
of the skeletal muscle L-type Ca
2+
channel is an endogenous Ca
2+
antagonist
Authors: Andronache Zoita , Ursu Daniel , Lehnert Simone , Freichel Marc , Flockerzi Veit , Melzer Werner
Published: November 2007

Ca
2+
channels play crucial roles in cellular signal transduction and are important targets of pharmacological agents. They are also associated with auxiliary subunits exhibiting functions that are still incompletely resolved. Skeletal muscle L-type Ca
2+
channels (dihydropyridine receptors, DHPRs) are specialized for the remote voltage control of type 1 ryanodine receptors (RyR1) to release stored Ca
2+
. The skeletal muscle-specific γ subunit of the DHPR (γ
1
) down-modulates availability by altering its steady state voltage dependence. The effect resembles the action of certain Ca
2+
antagonistic drugs that are thought to stabilize inactivated states of the DHPR. In the present study we investigated the cross influence of γ
1
and Ca
2+
antagonists by using wild-type (γ+/+) and γ
1
knockout (γ−/−) mice. We studied voltage-dependent gating of both L-type Ca
2+
current and Ca
2+
release and the allosteric modulation of drug binding. We found that 10 μM diltiazem, a benzothiazepine drug, more than compensated for the reduction in high-affinity binding of the dihydropyridine agent isradipine caused by γ
1
elimination; 5 μM devapamil [(−)D888], a phenylalkylamine Ca
2+
antagonist, approximately reversed the right-shifted voltage dependence of availability and the accelerated recovery kinetics of Ca
2+
current and Ca
2+
release. Moreover, the presence of γ
1
altered the effect of D888 on availability and strongly enhanced its impact on recovery kinetics demonstrating that γ
1
and the drug do not act independently of each other. We propose that the γ
1
subunit of the DHPR functions as an endogenous Ca
2+
antagonist whose task may be to minimize Ca
2+
entry and Ca
2+
release under stress-induced conditions favoring plasmalemma depolarization.
Disruption of maternal DNA repair increases sperm-derived chromosomal aberrations
Authors: Marchetti F. , Essers J. , Kanaar R. , Wyrobek A. J.
Published: November 2007

Male and female germ cells can transmit genetic defects that lead to pregnancy loss, infant mortality, birth defects, and genetic diseases in offspring; however, the parental origins of transmitted defects are not random, with
de novo
mutations and chromosomal structural aberrations transmitted predominantly by sperm. We tested the hypotheses that paternal mutagenic exposure during late spermatogenesis can induce damage that persists in the fertilizing sperm and that the risk of embryos with paternally transmitted chromosomal aberrations depends on the efficiency of maternal DNA repair during the first cycle after fertilization. We show that female mice with defective DNA double-strand break repair had significantly increased frequencies of zygotes with sperm-derived chromosomal aberrations after matings with wild-type males irradiated 7 days earlier with 4 Gy of ionizing radiation. These findings demonstrate that mutagenic exposures during late spermatogenesis can induce damage that persists for at least 7 days in the fertilizing sperm and that maternal genotype plays a major role in determining the risks for pregnancy loss and frequencies of offspring with chromosomal defects of paternal origin.
The emergence of HIV/AIDS in the Americas and beyond
Authors: Gilbert M. Thomas P. , Rambaut Andrew , Wlasiuk Gabriela , Spira Thomas J. , Pitchenik Arthur E. , Worobey Michael
Published: November 2007

HIV-1 group M subtype B was the first HIV discovered and is the predominant variant of AIDS virus in most countries outside of sub-Saharan Africa. However, the circumstances of its origin and emergence remain unresolved. Here we propose a geographic sequence and time line for the origin of subtype B and the emergence of pandemic HIV/AIDS out of Africa. Using HIV-1 gene sequences recovered from archival samples from some of the earliest known Haitian AIDS patients, we find that subtype B likely moved from Africa to Haiti in or around 1966 (1962–1970) and then spread there for some years before successfully dispersing elsewhere. A “pandemic” clade, encompassing the vast majority of non-Haitian subtype B infections in the United States and elsewhere around the world, subsequently emerged after a single migration of the virus out of Haiti in or around 1969 (1966–1972). Haiti appears to have the oldest HIV/AIDS epidemic outside sub-Saharan Africa and the most genetically diverse subtype B epidemic, which might present challenges for HIV-1 vaccine design and testing. The emergence of the pandemic variant of subtype B was an important turning point in the history of AIDS, but its spread was likely driven by ecological rather than evolutionary factors. Our results suggest that HIV-1 circulated cryptically in the United States for ≈12 years before the recognition of AIDS in 1981.
Genome-wide analyses of human perisylvian cerebral cortical patterning
Authors: Abrahams B. S. , Tentler D. , Perederiy J. V. , Oldham M. C. , Coppola G. , Geschwind D. H.
Published: November 2007

Despite the well established role of the frontal and posterior perisylvian cortices in many facets of human-cognitive specializations, including language, little is known about the developmental patterning of these regions in the human brain. We performed a genome-wide analysis of human cerebral patterning during midgestation, a critical epoch in cortical regionalization. A total of 345 genes were identified as differentially expressed between superior temporal gyrus (STG) and the remaining cerebral cortex. Gene ontology categories representing transcription factors were enriched in STG, whereas cell-adhesion and extracellular matrix molecules were enriched in the other cortical regions. Quantitative RT-PCR or
in situ
hybridization was performed to validate differential expression in a subset of 32 genes, most of which were confirmed. LIM domain-binding 1 (
LDB1
), which we show to be enriched in the STG, is a recently identified interactor of LIM domain only 4 (
LMO4
), a gene known to be involved in the asymmetric pattering of the perisylvian region in the developing human brain. Protocadherin 17 (
PCDH17
), a neuronal cell adhesion molecule, was highly enriched in focal regions of the human prefrontal cortex. Contactin associated protein-like 2 (
CNTNAP2
), in which mutations are known to cause autism, epilepsy, and language delay, showed a remarkable pattern of anterior-enriched cortical expression in human that was not observed in mouse or rat. These data highlight the importance of expression analysis of human brain and the utility of cross-species comparisons of gene expression. Genes identified here provide a foundation for understanding molecular aspects of human-cognitive specializations and the disorders that disrupt them.
Accretion of ferromanganese nodules that form pavement in Second Connecticut Lake, New Hampshire
Authors: Asikainen Celeste A. , Werle Sean F.
Published: November 2007

We discovered ferromanganese nodules that measure up to 46 cm in diameter with stromatolitic growth patterns in the western central near-shore portion of Second Connecticut Lake, Pittsburg, New Hampshire. They occur as four distinct morphotypes: irregular laminated convex plates that form concentric rings around a nucleating center (“domed-plate”), continuous pustular pavements that extend >10 m
2
(“pustular”), nonlaminated and nonnucleated masses with pebbles scattered throughout the matrix (“lattice”), and small nonnucleated laminated structures >2 cm (“cup”) in water depths between 5 and 12 m. An estimated growth rate of 26 mm/100 years was determined from oxide deposits on datable debris. X-ray fluorescence showed an elemental composition comparable with that of nodule structures in other lakes. These sedimentary structures, the first seen in any of the six New England states, are the most morphologically distinct and varied lacustrine ferromanganese nodules known so far.
Identification of prostate cancer modifier pathways using parental strain expression mapping
Authors: Xu Qing , Majumder Pradip K. , Ross Kenneth , Shim Yeonju , Golub Todd R. , Loda Massimo , Sellers William R.
Published: November 2007

Inherited genetic risk factors play an important role in cancer. However, other than the Mendelian fashion cancer susceptibility genes found in familial cancer syndromes, little is known about risk modifiers that control individual susceptibility. Here we developed a strategy, parental strain expression mapping, that utilizes the homogeneity of inbred mice and genome-wide mRNA expression analyses to directly identify candidate germ-line modifier genes and pathways underlying phenotypic differences among murine strains exposed to transgenic activation of
AKT1
. We identified multiple candidate modifier pathways and, specifically, the glycolysis pathway as a candidate negative modulator of
AKT1
-induced proliferation. In keeping with the findings in the murine models, in multiple human prostate expression data set, we found that enrichment of glycolysis pathways in normal tissues was associated with decreased rates of cancer recurrence after prostatectomy. Together, these data suggest that parental strain expression mapping can directly identify germ-line modifier pathways of relevance to human disease.