bluuebunny/crossref_metadata_2025 huggingface dataset:
CuInS
2
–
CdS
heterojunction valence band offset measured with near-UV constant final state yield spectroscopy
Authors: Johnson B. , Korte L. , Lußky T. , Klaer J. , Lauermann I.
Published: October 2009

The valence band offset of the heterojunction between CuInS2 (CIS) and chemical bath deposited CdS has been determined both by means of combined x-ray photoelectron spectroscopy (XPS) and ultraviolet photoelectron spectroscopy (UPS) and by near-UV constant final state (CFS) yield spectroscopy. The use of the latter shows that this spectroscopic method is indeed suitable for the investigation of chalcopyrite thin films. The higher information depth due to the low excitation energies (7.5–4.0 eV) used in CFS makes it possible to obtain a signal from the valence band of the CIS substrate even after a relatively thick (∼5 nm) CdS layer has been deposited. The number of samples needed to determine the band offset is reduced from three to one and the effects of chemical changes on the CIS surface can be accounted for because the valence band edges of both materials are measured directly. The valence band offsets with the XPS/UPS and CFS methods were determined to be 1.25±0.20 and 1.45±0.20 eV, respectively.
Switching dynamics in titanium dioxide memristive devices
Authors: Pickett Matthew D. , Strukov Dmitri B. , Borghetti Julien L. , Yang J. Joshua , Snider Gregory S. , Stewart Duncan R. , Williams R. Stanley
Published: October 2009

Memristive devices are promising components for nanoelectronics with applications in nonvolatile memory and storage, defect-tolerant circuitry, and neuromorphic computing. Bipolar resistive switches based on metal oxides such as TiO2 have been identified as memristive devices primarily based on the “pinched hysteresis loop” that is observed in their current-voltage (i-v) characteristics. Here we show that the mathematical definition of a memristive device provides the framework for understanding the physical processes involved in bipolar switching and also yields formulas that can be used to compute and predict important electrical and dynamical properties of the device. We applied an electrical characterization and state-evolution procedure in order to capture the switching dynamics of a device and correlate the response with models for the drift diffusion of ionized dopants (vacancies) in the oxide film. The analysis revealed a notable property of nonlinear memristors: the energy required to switch a metal-oxide device decreases exponentially with increasing applied current.
Arsenic doped p-type zinc oxide films grown by radio frequency magnetron sputtering
Authors: Fan J. C. , Zhu C. Y. , Fung S. , Zhong Y. C. , Wong K. S. , Xie Z. , Brauer G. , Anwand W. , Skorupa W. , To C. K. , Yang B. , Beling C. D. , Ling C. C.
Published: October 2009

As-doped ZnO films were grown by the radio frequency magnetron sputtering method. As the substrate temperature during growth was raised above ∼400 °C, the films changed from n type to p type. Hole concentration and mobility of ∼6×1017 cm−3 and ∼6 cm2 V−1 s−1 were achieved. The ZnO films were studied by secondary ion mass spectroscopy, x-ray photoelectron spectroscopy (XPS), low temperature photoluminescence (PL), and positron annihilation spectroscopy (PAS). The results were consistent with the AsZn–2VZn shallow acceptor model proposed by Limpijumnong et al. [Phys. Rev. Lett. 92, 155504 (2004)]. The results of the XPS, PL, PAS, and thermal studies lead us to suggest a comprehensive picture of the As-related shallow acceptor formation.
Thermal stability and thermoelectric properties of p-type Ba8Ga16Ge30 clathrates
Authors: Cederkrantz D. , Saramat A. , Snyder G. J. , Palmqvist A. E. C.
Published: October 2009

The thermal stability of p-type Ba8Ga16Ge30 clathrates grown from gallium flux has been tested by heat treatment in low pressure Ar atmosphere at 400, 600, and 800 °C. Significant gallium loss was observed for all samples during heat treatment. The treatment at 400 °C does not significantly change the sample properties, and the samples remain p-type and comparable to the untreated, as-prepared, sample. At 600 °C the sample switches from extrinsic p-type to extrinsic n-type, presumably due to significant loss of Ga, and shows a high thermopower but a reduced electrical conductivity compared to as-made n-type samples. Surprisingly, after a thermal treatment at 800 °C, the crystal structure seemingly loses less Ga, only reducing the hole concentration to near intrinsic levels and thus has a negative impact on ZT. Regardless of the heat treatment temperature of the p-type samples the thermal conductivity remained exceptionally low, for some samples 0.9 W/m K. Heat treatment can thus greatly affect the thermoelectric properties of p-type Ba8Ga16Ge30, but the crystal structure remains intact.
Weakly nonlinear ablative Rayleigh–Taylor instability at preheated ablation front
Authors: Fan Zhengfeng , Luo Jisheng , Ye Wenhua
Published: October 2009

Stuart’s weakly nonlinear theory is generalized to study single-mode ablative Rayleigh–Taylor instability (ARTI) at a broad ablation front caused by preheating. The thickness effect of the ablation front is considered and the spatial amplitude distributions of density, temperature, and velocity for harmonic modes are obtained in the present model. It is confirmed that the modified Lindl formula [W. H. Ye et al., Phys. Rev. E 65, 057401 (2002)] is valid for predicting the linear growth rate when the ablation front is broad. It is shown by the present model that the mass ablation of the shell is enhanced obviously due to the generation of harmonics while the harmonics’ effect on the mass asymmetry of the shell is weaker than the expectation given by the classical theory. It is also indicated by the present model that ARTI is stabilized by the nonlinear correction for all modes. This conclusion is physical and different from the sharp boundary model where ARTI is enhanced by the nonlinear correction for the short wavelength case. The reason for this difference is due to the thickness effect of the ablation front.
3 W continuous-wave room temperature single-facet emission from quantum cascade lasers based on nonresonant extraction design approach
Authors: Lyakh A. , Maulini R. , Tsekoun A. , Go R. , Pflügl C. , Diehl L. , Wang Q. J. , Capasso Federico , Patel C. Kumar N.
Published: October 2009

A strain-balanced, InP-based quantum cascade laser structure, designed for light emission at 4.6 μm using a new nonresonant extraction design approach, was grown by molecular beam epitaxy. Removal of the restrictive two-phonon resonant condition, currently used in most structure designs, allows simultaneous optimization of several design parameters influencing laser performance. Following the growth, the structure was processed in buried heterostructure. Maximum single-ended continuous-wave optical power of 3 W was obtained at 293 K for devices with stripe dimensions of 5 mm×11.6 μm. Corresponding maximum wallplug efficiency and threshold current density were measured to be 12.7% and 0.86 kA/cm2.
Nonmagnetic thin layers of Ni3N
Authors: Vempaire D. , Fettar F. , Ortega L. , Pierre F. , Miraglia S. , Sulpice A. , Pelletier J. , Hlil E. K. , Fruchart D.
Published: October 2009

From structural analysis by x-ray diffraction, Rutherford backscattering spectroscopy, and physical investigations (magnetization and resistance), reactive sputtering assisted by microwave multidipolar plasma appears to be a powerful means for tailoring the stoichiometry of transition metal nitrides. Reactive sputtered nitride Ni layers were elaborated while keeping the Ar partial pressure constant (∼1.5 μbar) and varying the N2 partial pressure in the 0.1–0.5 μbar range. A mixing of Ni2N and Ni3N and a single-phase Ni3N are stabilized in thin layers for high and low p(N2), respectively. For the first time, an optimization of the crystallization of Ni3N pure layers is obtained for intermediate p(N2) (0.23 μbar). Both nitrided phases Ni2N and Ni3N, elaborated with appropriate deposition parameters, do not present ferromagnetic behavior in contrast to experimental results in the literature. Theoretical results using the full-potential linearized augmented plane wave method confirm the nonferromagnetic behavior of nitrided phases. Ni3N could be used as nonmagnetic spacer layer in spintronic devices.
Atomic hydrogen interactions with amorphous carbon thin films
Authors: Jariwala Bhavin N. , Ciobanu Cristian V. , Agarwal Sumit
Published: October 2009

The atomic-scale interactions of H atoms with hydrogenated amorphous carbon (a-C:H) films were identified using molecular dynamics (MD) simulations and experiments based on surface characterization tools. Realistic a-C:H films developed using MD simulations were impinged with H atoms with a kinetic energy corresponding to a temperature of 700 K. The specific chemical reactions of the H atoms with the a-C:H surface were identified through a detailed analysis of the MD trajectories. The MD simulations showed that hydrogenation occurs primarily at the sp2 sites and converts them to sp3-hybridized C atoms. Depending on the hybridization of the next-nearest neighbor, a dangling bond may or may not be created. The hydrogenation reaction is highly exothermic, >2.5 eV, and proceeds with a negligible activation energy barrier via a mechanism similar to Eley–Rideal. In certain cases hydrogenation may also cleave a C–C bond. The reaction events observed through MD simulations are consistent with the surface characterization of D-exposed a-C:H films using Raman spectroscopy, spectroscopic ellipsometry, and in situ attenuated total reflection Fourier-transform infrared spectroscopy.
Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach
Authors: Cheng Li-Tien , Wang Zhongming , Setny Piotr , Dzubiella Joachim , Li Bo , McCammon J. Andrew
Published: October 2009

A model nanometer-sized hydrophobic receptor-ligand system in aqueous solution is studied by the recently developed level-set variational implicit solvent model (VISM). This approach is compared to all-atom computer simulations. The simulations reveal complex hydration effects within the (concave) receptor pocket, sensitive to the distance of the (convex) approaching ligand. The ligand induces and controls an intermittent switching between dry and wet states of the hosting pocket, which determines the range and magnitude of the pocket-ligand attraction. In the level-set VISM, a geometric free-energy functional of all possible solute-solvent interfaces coupled to the local dispersion potential is minimized numerically. This approach captures the distinct metastable states that correspond to topologically different solute-solvent interfaces, and thereby reproduces the bimodal hydration behavior observed in the all-atom simulation. Geometrical singularities formed during the interface relaxation are found to contribute significantly to the energy barrier between different metastable states. While the hydration phenomena can thus be explained by capillary effects, the explicit inclusion of dispersion and curvature corrections seems to be essential for a quantitative description of hydrophobically confined systems on nanoscales. This study may shed more light onto the tight connection between geometric and energetic aspects of biomolecular hydration and may represent a valuable step toward the proper interpretation of experimental receptor-ligand binding rates.
Spatially resolved scanning probe electron energy spectroscopy for Ag islands on a graphite surface
Authors: Xu ChunKai , Chen XiangJun , Zhou Xia , Wei Zheng , Liu WenJie , Li JiWei , Williams J. F. , Xu KeZun
Published: October 2009

The scanning probe electron energy spectra for micron-sized Ag islands on highly ordered pyrolytic graphite substrate are measured. One- and two-dimensional relative intensity distributions for Ag or graphite plasmon peaks have been acquired and a lateral resolution of 4.8±2.4 μm has been achieved. It is the first time for the scanning probe electron energy spectroscopy technique to obtain the spatially resolved electron energy spectra with elemental contrast for a surface, which demonstrates the possibility of the element identification for the scanning tunneling microscope.
Nonlinear development of inertial instability in a barotropic shear
Authors: Plougonven Riwal , Zeitlin Vladimir
Published: October 2009

Inertial instability is investigated numerically in a two-dimensional setting in order to understand its nonlinear stage and saturation. To focus on fundamental mechanisms, a simple barotropic shear U(y)=tanh y on the f-plane is considered. The linear stability problem is first solved analytically, and the analytical solutions are used to benchmark numerical simulations. A simple scenario of the nonlinear development of the most unstable mode was recurrently observed in the case of substantial diffusivity: while reaching finite amplitude the unstable mode spreads laterally, distorting the initially vertical instability zone. This process produces strong vertical gradients which are subsequently annihilated by diffusion, making the flow barotropic again but with the shear spread over a wider region. In the course of such evolution, unexpectedly, strong negative absolute vorticity anomalies are produced. In weakly diffusive simulations, the horizontal spreading of the unstable motions and the enhancement of the anticyclonic vorticity extremum persist, but small-scale motions/instabilities render the flow considerably more complex. It is known that the barotropic component of the final state can be predicted from the conservation of momentum. Our simulations confirm the relevance of this simple prediction in the cases investigated regardless of resolution and diffusion. The baroclinic component of the final state is also analyzed and three types of structures are identified: persistent stationary stratification layers, subinertial waves trapped in the anticyclonic shear, and freely propagating inertia-gravity waves. The subinertial waves and the stratification staircase have clear signatures and can therefore help to identify the regions that have undergone inertial instability.
High depth resolution analysis of Si/SiGe multilayers with the atom probe
Authors: Koelling Sebastian , Gilbert Matthieu , Goossens Jozefien , Hikavyy Andriy , Richard Olivier , Vandervorst Wilfried
Published: October 2009

The laser assisted atom probe has been proposed as a metrology tool for next generation semiconductor technologies requiring subnanometer depth resolution. In order to support its routine application, we carried out a quantitative assessment of the performance of the atom probe on semiconductor stacks. We analyzed a silicon, silicon-germanium multilayer-structure with atom-probe tomography (APT), secondary ion mass spectroscopy (SIMS), transmission electron microscopy (TEM), and high-resolution x-ray diffraction (HRXRD). We demonstrate that APT outperforms SIMS by a factor of 3 in terms of depth-resolution providing a decay length of 0.2–0.6 nm/decade whereas the compositions and layer thicknesses are in close agreement with SIMS, HRXRD, and TEM.
Nonlinear motion of coupled magnetic vortices in ferromagnetic/nonmagnetic/ferromagnetic trilayer
Authors: Jun Su-Hyeong , Shim Je-Ho , Oh Suhk-Kun , Yu Seong-Cho , Kim Dong-Hyun , Mesler Brooke , Fischer Peter
Published: October 2009

We have investigated a coupled motion of two parallel vortex cores in ferromagnetic/nonmagnetic/ferromagnetic trilayer cylinders by means of micromagnetic simulation. Dynamic motion of two vortices with parallel and antiparallel relative chiralities of curling spins around the vortex cores have been examined after excitation by 1 ns pulsed external field, revealing a nontrivial coupled vortices motion.
Accuracy assessment of strain mapping from Z-contrast images of strained nanostructures
Authors: Guerrero E. , Galindo P. L. , Yáñez A. , Pizarro J. , Guerrero-Lebrero M. P. , Molina S. I.
Published: October 2009

Geometric phase and peak pairs strain mapping techniques have been applied to high angular annular dark field scanning transmission electron microscopy (HAADF-STEM) simulated images of an InAs/InP strained nanowire at different sample thicknesses. Strain values determined from HAADF-STEM images have been compared to theoretical values obtained by solving the elastic theory equation by finite element analysis, in order to analyze and assess both techniques in terms of accuracy of the predictions.
Effect of ion temperature on oblique propagation of large amplitude solitary kinetic Alfvén waves
Authors: Chatterjee Prasanta , Saha Taraknath , Muniandy S. V. , Wong C. S.
Published: October 2009

The effect of ion temperature on the existence of large amplitude solitary kinetic Alfvén waves and double layers are investigated in a two-fluid model using Sagdeev’s pseudopotential technique. The ion temperature, obliqueness parameter, and the ratio of cyclotron frequency to ion frequency are found to play significant roles in the formation and the shape of solitary kinetic Alfvén waves and double layers. Hump-type solitary waves and dip-type double layers are also observed. Conditions for the existence of solitary waves and double layers are discussed.
On the use of a chaotic cavity transducer in nonlinear elastic imaging
Authors: Bou Matar O. , Li Y. F. , Van Den Abeele K.
Published: October 2009

We discuss the advantages of “chaotic cavity transducer focusing” to enhance the localization of microdamage in conjunction with nonlinear elastic wave spectroscopy methods. Chaotic cavity transducer focusing is defined as the hardware-software combination of a piezoelectric ceramic glued on a cavity of chaotic shape on the one hand with the reciprocal time reversal (or inverse filter) technique on the other hand. Additional optimization through the use of sweeps and inverse filtering techniques are discussed as well. The technique is applied to image a crack in a steel sample.
Free vibration of microscaled Timoshenko beams
Authors: Abbasion Saeed , Rafsanjani Ahmad , Avazmohammadi Reza , Farshidianfar Anoushiravan
Published: October 2009

In this paper, a comprehensive model is presented to investigate the influence of surface elasticity and residual surface tension on the natural frequency of flexural vibrations of microbeams in the presence of rotary inertia and shear deformation effects. An explicit solution is derived for the natural oscillations of microscaled Timoshenko beams considering surface effects. The analytical results are illustrated with numerical examples in which two types of microbeams are configured based on Euler–Bernoulli and Timoshenko beam theory considering surface elasticity and residual surface tension. The natural frequencies of vibration are calculated for selected beam length on the order of nanometer to microns and the results are compared with those corresponding to the classical beam models, emphasizing the differences occurring when the surface effects are significant. It is found that the nondimensional natural frequency of the vibration of micro and nanoscaled beams is size dependent and for limiting case in which the beam length increases, the results tends to the results obtained by classical beam models. This study might be helpful for the design of high-precision measurement devices such as chemical and biological sensors.
Spectral dependence of time-resolved photoreflectance of InN epitaxial films
Authors: Tsai Tsong-Ru , Chang Cheng-Yu , Kuo Chih-Wei , Hwang Jih-Shang , Lin Tai-Yuan , Gwo Shangjr
Published: October 2009

Femtosecond pulses at wavelengths ranging from 750to900nm (1.38–1.65eV) were used in the excitation and probing of ultrafast carrier dynamics in InN epitaxial films. Experimental results show that the hot electron relaxation rate increases with increasing electron energy, which is measured as E0.53. This observation agrees with the prediction of electron-electron scattering relaxation mechanism. In addition, the electron-hole recombination rates are independent of the electron energy and have values of ∼7×109Hz. We attribute this result to the Auger recombination in InN being insensitive to temperature.
Use of AlGaN in the notch region of GaN Gunn diodes
Authors: Yang Linan , Hao Yue , Zhang Jincheng
Published: October 2009

The wurtzite gallium nitride (GaN) Gunn diodes with aluminum gallium nitride (AlGaN) as launcher in the notch region are investigated by negative-differential-mobility model based simulation. Under the operation of self-excitation oscillation with dipole domain mode, the simulations show that the diode with two-step-graded AlGaN launcher structure can yield the maximal rf power of 1.95 W and dc/rf conversion efficiency of 1.72% at the fundamental oscillation frequency of around 215 GHz. This kind of Gunn diode structure without the low doping process is convenient for accurately controlling the dopant concentration of GaN epitaxial growth.
Engineering anatomically shaped human bone grafts
Authors: Grayson Warren L. , Fröhlich Mirjam , Yeager Keith , Bhumiratana Sarindr , Chan M. Ete , Cannizzaro Christopher , Wan Leo Q. , Liu X. Sherry , Guo X. Edward , Vunjak-Novakovic Gordana
Published: October 2009

The ability to engineer anatomically correct pieces of viable and functional human bone would have tremendous potential for bone reconstructions after congenital defects, cancer resections, and trauma. We report that clinically sized, anatomically shaped, viable human bone grafts can be engineered by using human mesenchymal stem cells (hMSCs) and a “biomimetic” scaffold-bioreactor system. We selected the temporomandibular joint (TMJ) condylar bone as our tissue model, because of its clinical importance and the challenges associated with its complex shape. Anatomically shaped scaffolds were generated from fully decellularized trabecular bone by using digitized clinical images, seeded with hMSCs, and cultured with interstitial flow of culture medium. A bioreactor with a chamber in the exact shape of a human TMJ was designed for controllable perfusion throughout the engineered construct. By 5 weeks of cultivation, tissue growth was evidenced by the formation of confluent layers of lamellar bone (by scanning electron microscopy), markedly increased volume of mineralized matrix (by quantitative microcomputer tomography), and the formation of osteoids (histologically). Within bone grafts of this size and complexity cells were fully viable at a physiologic density, likely an important factor of graft function. Moreover, the density and architecture of bone matrix correlated with the intensity and pattern of the interstitial flow, as determined in experimental and modeling studies. This approach has potential to overcome a critical hurdle—in vitro cultivation of viable bone grafts of complex geometries—to provide patient-specific bone grafts for craniofacial and orthopedic reconstructions.
Gray and white matter changes associated with tool-use learning in macaque monkeys
Authors: Quallo M. M. , Price C. J. , Ueno K. , Asamizuya T. , Cheng K. , Lemon R. N. , Iriki A.
Published: October 2009

We used noninvasive MRI and voxel-based morphometry (VBM) to detect changes in brain structure in three adult Japanese macaques trained to use a rake to retrieve food rewards. Monkeys, who were naive to any previous tool use, were scanned repeatedly in a 4-T scanner over 6 weeks, comprising 2 weeks of habituation followed by 2 weeks of intensive daily training and a 2-week posttraining period. VBM analysis revealed significant increases in gray matter with rake performance across the three monkeys. The effects were most significant (P< 0.05 corrected for multiple comparisons across the whole brain) in the right superior temporal sulcus, right second somatosensory area, and right intraparietal sulcus, with less significant effects (P< 0.001 uncorrected) in these same regions of the left hemisphere. Bilateral increases were also observed in the white matter of the cerebellar hemisphere in lobule 5. In two of the monkeys who exhibited rapid learning of the rake task, gray matter volume in peak voxels increased by up to 17% during the intensive training period; the earliest changes were seen after 1 week of intensive training, and they generally peaked when performance on the task plateaued. In the third monkey, who was slower to learn the task, peak voxels showed no systematic changes. Thus, VBM can detect significant brain changes in individual trained monkeys exposed to tool-use training for the first time. This approach could open up a means of investigating the underlying neurobiology of motor learning and other higher brain functions in individual animals.
A Bayesian approach to the alignment of mass spectra
Authors: Kong Xiaoxiao , Reilly Cavan
Published: October 2009

Motivation: The need to align spectra to correct for mass-to-charge experimental variation is a problem that arises in mass spectrometry (MS). Most of the MS-based proteomic data analysis methods involve a two-step approach, identify peaks first and then do the alignment and statistical inference on these identified peaks only. However, the peak identification step relies on prior information on the proteins of interest or a peak detection model, which are subject to error. Also numerous additional features such as peak shape and peak width are lost in simple peak detection, and these are informative for correcting mass variation in the alignment step.

Results: Here, we present a novel Bayesian approach to align the complete spectra. The approach is based on a parametric model which assumes that the spectrum and alignment function are Gaussian processes, but the alignment function is monotone. We show how to use the expectation–maximization algorithm to find the posterior mode of the set of alignment functions and the mean spectrum for a patient population. After alignment, we conduct tests while controlling for error attributable to multiple comparisons on the level of the peaks identified from the absolute mean spectra difference of two patient populations.

Contact:  cavanr@biostat.umn.edu
Inferring relative proportions of DNA variants from sequencing electropherograms
Authors: Carr I. M. , Robinson J. I. , Dimitriou R. , Markham A. F. , Morgan A. W. , Bonthron D. T.
Published: October 2009

Motivation: Determination of the relative copy number of single-nucleotide sequence variants (SNVs) within a DNA sample is a frequent experimental goal. Various methods can be applied to this problem, although hybridization-based approaches tend to suffer from high-setup cost and poor adaptability, while others (such as pyrosequencing) may not be accessible to all laboratories. The potential to extract relative copy number information from standard dye-terminator electropherograms has been little explored, yet this technology is cheap and widely accessible. Since several biologically important loci have paralogous copies that interfere with genotyping, and which may also display copy number variation (CNV), there are many situations in which determination of the relative copy number of SNVs is desirable.

Results: We have developed a desktop application, QSVanalyzer, which allows high-throughput quantification of the proportions of DNA sequences containing SNVs. In reconstruction experiments, QSVanalyzer accurately estimated the known relative proportions of SNVs. By analyzing a large panel of genomic DNA samples, we demonstrate the ability of the software to analyze not only common biallelic SNVs, but also SNVs within a locus at which gene conversion between four genomic paralogs operates, and within another that is subject to CNV.

Availability and Implementation: QSVanalyzer is freely available at http://dna.leeds.ac.uk/qsv/. It requires the Microsoft .NET framework version 2.0, which can be installed on all Microsoft operating systems from Windows 98 onwards.

Contact:  msjimc@leeds.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cod, haddock, saithe, herring, and capelin in the Barents Sea and adjacent waters: a review of the biological value of the area
Authors: Olsen Erik , Aanes Sondre , Mehl Sigbjørn , Holst Jens Christian , Aglen Asgeir , Gjøsæter Harald
Published: October 2009

Olsen, E., Aanes, S., Mehl, S., Holst, J. C., Aglen, A., and Gjøsæter, H. 2010. Cod, haddock, saithe, herring, and capelin in the Barents Sea and adjacent waters: a review of the biological value of the area. – ICES Journal of Marine Science, 67: 87–101. Cod, haddock, saithe, herring, and capelin are the most important fish species in the Barents Sea and adjacent waters. Ecosystem-based management requires species-specific knowledge of the biological value and vulnerability throughout their life history and distributional range. For each of the five species and four annual quarters, the spawning (egg) areas, nursery areas for larvae and juveniles, and feeding grounds for adults are described and mapped. Areas of eggs (spawning) and larvae were the most important because these are the life stages when fish are most vulnerable to anthropogenic impact. The greatest overlap of spawning areas was from Røstbanken in the south to the Varanger Peninsula in the northeast, and overlap of larval distribution was more extensive.
What controls the spatial distribution of the North Sea plaice spawning population? Confronting ecological hypotheses through a model selection framework
Authors: Loots Christophe , Vaz Sandrine , Planque Benjamin , Koubbi Philippe
Published: October 2009

Loots, C., Vaz, S., Planque, B., and Koubbi, P. 2010. What controls the spatial distribution of the North Sea plaice spawning population? Confronting ecological hypotheses through a model selection framework. – ICES Journal of Marine Science, 67: 244–257. The spatial dynamics of spawning fish are crucial because they influence the survival rates of eggs and larvae and ultimately impact the reproductive success of populations. The factors that control these dynamics are complex and potentially many, and they interact. A model-selection-based approach was developed to confront various hypotheses of control of the spatial distribution of spawning population of North Sea plaice (Pleuronectes platessa). For each hypothesis or combination thereof, statistical models were constructed. These were then ranked and selected based on their ability to adjust and predict observed spatial distributions. The North Sea plaice population seems to have developed strong attachment to specific spawning sites, where geographic location and population memory are important controlling factors. Temporal changes in spatial distribution patterns appear to be influenced primarily by population size and demography. Variations in hydrographic conditions such as temperature and salinity do not appear to control interannual fluctuations in spatial distribution. This means that, for reproduction, applying conventional habitat models may falsely attribute major controlling effects to environmental conditions. It is concluded that a multiple-hypothesis approach is essential to understanding and predicting the present and future distribution of the North Sea plaice population during its spawning season.
Windshield splatter analysis with the Galaxy metagenomic pipeline
Authors: Kosakovsky Pond Sergei , Wadhawan Samir , Chiaromonte Francesca , Ananda Guruprasad , Chung Wen-Yu , Taylor James , Nekrutenko Anton ,   The Galaxy Team
Published: October 2009

How many species inhabit our immediate surroundings? A straightforward collection technique suitable for answering this question is known to anyone who has ever driven a car at highway speeds. The windshield of a moving vehicle is subjected to numerous insect strikes and can be used as a collection device for representative sampling. Unfortunately the analysis of biological material collected in that manner, as with most metagenomic studies, proves to be rather demanding due to the large number of required tools and considerable computational infrastructure. In this study, we use organic matter collected by a moving vehicle to design and test a comprehensive pipeline for phylogenetic profiling of metagenomic samples that includes all steps from processing and quality control of data generated by next-generation sequencing technologies to statistical analyses and data visualization. To the best of our knowledge, this is also the first publication that features a live online supplement providing access to exact analyses and workflows used in the article.
The Impact of Water Deficiency on Leaf Cuticle Lipids of Arabidopsis
Authors: Kosma Dylan K. , Bourdenx Brice , Bernard Amélie , Parsons Eugene P. , Lü Shiyou , Joubès Jérôme , Jenks Matthew A.
Published: October 2009

Arabidopsis (Arabidopsis thaliana) plants subjected to water deficit, sodium chloride (NaCl), or abscisic acid treatments were shown to exhibit a significant increase in the amount of leaf cuticular lipids. These stress treatments led to increases in cuticular wax amount per unit area of 32% to 80%, due primarily to 29% to 98% increases in wax alkanes. Of these treatments, only water deficit increased the total cutin monomer amount (by 65%), whereas both water deficit and NaCl altered the proportional amounts of cutin monomers. Abscisic acid had little effect on cutin composition. Water deficit, but not NaCl, increased leaf cuticle thickness (by 49%). Electron micrographs revealed that both water-deprived and NaCl-treated plants had elevated osmium accumulation in their cuticles. The abundance of cuticle-associated gene transcripts in leaves was altered by all treatments, including those performed in both pot-grown and in vitro conditions. Notably, the abundance of the ECERIFERUM1 gene transcript, predicted to function in alkane synthesis, was highly induced by all treatments, results consistent with the elevated alkane amounts observed in all treatments. Further, this induction of cuticle lipids was associated with reduced cuticle permeability and may be important for plant acclimation to subsequent water-limited conditions. Taken together, these results show that Arabidopsis provides an excellent model system to study the role of the cuticle in plant response to drought and related stresses, and its associated genetic and cellular regulation.
Plant MetGenMAP: An Integrative Analysis System for Plant Systems Biology
Authors: Joung Je-Gun , Corbett Anthony M. , Fellman Shanna Moore , Tieman Denise M. , Klee Harry J. , Giovannoni James J. , Fei Zhangjun
Published: October 2009

The information and resources generated from diverse “omics” technologies provide opportunities for producing novel biological knowledge. It is essential to integrate various kinds of biological information and large-scale omics data sets through systematic analysis in order to describe and understand complex biological phenomena. For this purpose, we have developed a Web-based system, Plant MetGenMAP, which can comprehensively integrate and analyze large-scale gene expression and metabolite profile data sets along with diverse biological information. Using this system, significantly altered biochemical pathways and biological processes under given conditions can be retrieved rapidly and efficiently, and transcriptional events and/or metabolic changes in a pathway can be easily visualized. In addition, the system provides a unique function that can identify candidate promoter motifs associated with the regulation of specific biochemical pathways. We demonstrate the functions and application of the system using data sets from Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum), respectively. The results obtained by Plant MetGenMAP can aid in a better understanding of the mechanisms that underlie interesting biological phenomena and provide novel insights into the biochemical changes associated with them at the gene and metabolite levels. Plant MetGenMAP is freely available at http://bioinfo.bti.cornell.edu/tool/MetGenMAP.
Phenotypic Plasticity of Adventitious Rooting in Arabidopsis Is Controlled by Complex Regulation of AUXIN RESPONSE FACTOR Transcripts and MicroRNA Abundance
Authors: Gutierrez Laurent , Bussell John D. , Păcurar Daniel I. , Schwambach Josèli , Păcurar Monica , Bellini Catherine
Published: October 2009

The development of shoot-borne roots, or adventitious roots, is indispensable for mass propagation of elite genotypes. It is a complex genetic trait with a high phenotypic plasticity due to multiple endogenous and environmental regulatory factors. We demonstrate here that a subtle balance of activator and repressor AUXIN RESPONSE FACTOR (ARF) transcripts controls adventitious root initiation. Moreover, microRNA activity appears to be required for fine-tuning of this process. Thus, ARF17, a target of miR160, is a negative regulator, and ARF6 and ARF8, targets of miR167, are positive regulators of adventitious rooting. The three ARFs display overlapping expression domains, interact genetically, and regulate each other's expression at both transcriptional and posttranscriptional levels by modulating miR160 and miR167 availability. This complex regulatory network includes an unexpected feedback regulation of microRNA homeostasis by direct and nondirect target transcription factors. These results provide evidence of microRNA control of phenotypic variability and are a significant step forward in understanding the molecular mechanisms regulating adventitious rooting.
MOSAIC FLORAL ORGANS1, anAGL6-Like MADS Box Gene, Regulates Floral Organ Identity and Meristem Fate in Rice
Authors: Ohmori Shinnosuke , Kimizu Mayumi , Sugita Maiko , Miyao Akio , Hirochika Hirohiko , Uchida Eiji , Nagato Yasuo , Yoshida Hitoshi
Published: October 2009

Floral organ identity and meristem determinacy in plants are controlled by combinations of activities mediated by MADS box genes. AGAMOUS-LIKE6 (AGL6)-like genes are MADS box genes expressed in floral tissues, but their biological functions are mostly unknown. Here, we describe an AGL6-like gene in rice (Oryza sativa), MOSAIC FLORAL ORGANS1 (MFO1/MADS6), that regulates floral organ identity and floral meristem determinacy. In the flower of mfo1 mutants, the identities of palea and lodicule are disturbed, and mosaic organs were observed. Furthermore, the determinacy of the floral meristem was lost, and extra carpels or spikelets developed in mfo1 florets. The expression patterns of floral MADS box genes were disturbed in the mutant florets. Suppression of another rice AGL6-like gene, MADS17, caused no morphological abnormalities in the wild-type background, but it enhanced the phenotype in the mfo1 background, indicating that MADS17 has a minor but redundant function with that of MFO1. Whereas single mutants in either MFO1 or the SEPALLATA-like gene LHS1 showed moderate phenotypes, the mfo1 lhs1 double mutant showed a severe phenotype, including the loss of spikelet meristem determinacy. We propose that rice AGL6-like genes help to control floral organ identity and the establishment and determinacy of the floral meristem redundantly with LHS1.
Endogenous, Tissue-Specific Short Interfering RNAs Silence the Chalcone Synthase Gene Family inGlycine maxSeed Coats
Authors: Tuteja Jigyasa H. , Zabala Gracia , Varala Kranthi , Hudson Matthew , Vodkin Lila O.
Published: October 2009

Two dominant alleles of the I locus in Glycine max silence nine chalcone synthase (CHS) genes to inhibit function of the flavonoid pathway in the seed coat. We describe here the intricacies of this naturally occurring silencing mechanism based on results from small RNA gel blots and high-throughput sequencing of small RNA populations. The two dominant alleles of the I locus encompass a 27-kb region containing two perfectly repeated and inverted clusters of three chalcone synthase genes (CHS1, CHS3, and CHS4). This structure silences the expression of all CHS genes, including CHS7 and CHS8, located on other chromosomes. The CHS short interfering RNAs (siRNAs) sequenced support a mechanism by which RNAs transcribed from the CHS inverted repeat form aberrant double-stranded RNAs that become substrates for dicer-like ribonuclease. The resulting primary siRNAs become guides that target the mRNAs of the nonlinked, highly expressed CHS7 and CHS8 genes, followed by subsequent amplification of CHS7 and CHS8 secondary siRNAs by RNA-dependent RNA polymerase. Most remarkably, this silencing mechanism occurs only in one tissue, the seed coat, as shown by the lack of CHS siRNAs in cotyledons and vegetative tissues. Thus, production of the trigger double-stranded RNA that initiates the process occurs in a specific tissue and represents an example of naturally occurring inhibition of a metabolic pathway by siRNAs in one tissue while allowing expression of the pathway and synthesis of valuable secondary metabolites in all other organs/tissues of the plant.
If SWORD is the answer, what is the question?
Authors: Lewis Stuart , Hayes Leonie , Newton‐Wade Vanessa , Corfield Antony , Davis Richard , Donohue Tim , Wilson Scott
Published: October 2009

Purpose

The purpose of this paper is to describe the repository deposit protocol, Simple Web‐service Offering Repository Deposit (SWORD), its development iteration, and some of its potential use cases. In addition, seven case studies of institutional use of SWORD are provided.

Design/methodology/approach

The paper describes the recent development cycle of the SWORD standard, with issues being identified and overcome with a subsequent version. Use cases and case studies of the new standard in action are included to demonstrate the wide range of practical uses of the SWORD standard.

Findings

SWORD has many potential use cases and has quickly become the de facto standard for depositing items into repositories. By making use of a widely‐supported interoperable standard, tools can be created that start to overcome some of the problems of gathering content for deposit into institutional repositories. They can do this by changing the submission process from a “one‐size‐fits‐all” solution, as provided by the repository's own user interface, to customised solutions for different users.

Originality/value

Many of the case studies described in this paper are new and unpublished, and describe methods of creating novel interoperable tools for depositing items into repositories. The description of SWORD version 1.3 and its development give an insight into the processes involved with the development of a new standard.
Emotional intelligence and marketing effectiveness
Authors: Gladson Nwokah N. , Ahiauzu Augustine I.
Published: October 2009

Purpose

While much empirical work has centered on marketing effectiveness, the generalizability of its relationship to emotional intelligence in the Nigerian context has been under‐researched. The purpose of this paper is to assess the impact of emotional intelligence on the marketing effectiveness of the organization.

Design/methodology/approach

A 31‐item survey questionnaire is developed and 108 corporate organizations in Nigeria are selected from the 2007 edition of the Nigerian Stock Exchange Gazette as a sample for this study. Hand delivery survey is conducted from key informants in the organizations. Returned instruments are analyzed using non‐parametric correlation through the use of the Statistical Package for Social Sciences.

Findings

The results of the study validate the instruments on emotional intelligence and the earlier instruments for marketing effectiveness and find a strong association between emotional intelligence and marketing effectiveness of corporate organizations in the Nigerian context. The main finding is that emotional intelligence leads to marketing effectiveness in corporate organizations in Nigeria.

Practical implications

The implications of the results are clear for scholars and managers. For managers, the paper has implications for the investigation of the link between emotional intelligence and marketing effectiveness of corporate organizations in Nigeria. In the first place, the paper provides a direct test of the applicability of a western paradigm to the Nigerian economic system different from other cultures.

Originality/value

The paper significantly refines the body of knowledge concerning the impact of emotional intelligence on marketing effectiveness in the Nigerian context. It will, without doubt, contribute to the body of existing literature on emotional intelligence and marketing effectiveness.
Reaching and influencing consumers in the prescription medicine market
Authors: Peters Julia , Nel Deon , Adam Stewart
Published: October 2009

Purpose

Celebrex became the first of a new class of drugs known as COX‐2 selective non‐steroidal anti‐inflammatory drugs. It improves treatment for arthritis sufferers without compromising the protective lining of the stomach. The purpose of this paper is to illustrate how direct‐to‐consumer advertising (DTCA) of prescription medicines can be used to rebuild faith in the cyclooxygenase‐2 (COX‐2) product category.

Design/methodology/approach

The case is developed using published sources and no input is required from company representatives. The presentation style follows the classic comprehensive case format used in postgraduate teaching programmes.

Findings

Business executives and strategic marketing students would benefit from a discussion on how external environmental factors can suddenly impose a review of marketing strategy. The reader learns how management addresses the business dilemma using DTCA.

Research limitations/implications

A blockbuster rival drug Vioxx is withdrawn due to cardiovascular (CV) health safety concerns. A resulting dominant market situation soon becomes a business dilemma. The Federal Drug Administration calls for a “black box” warning label on Celebrex, the most serious type of warning.

Practical implications

The implications are that having a product in a class of its own is not enough. It highlights the need to communicate to different audiences, to both the medical profession and the end‐user. Getting doctors to recommend the medicine and pulling the product through the channel by stimulating patient demand after a health scare are paramount.

Originality/value

This is the first pharmaceutical business case where the withdrawal of a rival product leaves the dominant competitor in a monopoly situation. Contrary to expectation, market share plummets despite the absence of competition.
Mathematical model of variable volume diafiltration with time dependent water adding
Authors: Takači A. , Žikić‐Došenović T. , Zavargó Z.
Published: October 2009

Purpose

The purpose of this paper is to introduce a mathematical model, an algorithm and numerical procedure for determining the duration of a diafiltration process with variable volume. This model should decrease diafiltration time and water usage.

Design/methodology/approach

A mathematical model of a diafiltration process, with constant water adding is considered, as well as the relationships between macro‐ and micro‐solute and the equation for process duration. By introducing α (t)=QD/QF, i.e. time dependent ratio of diafiltration water flow and filtrate flow rate, a mathematical model of diafiltration process with time dependent water adding is proposed. In order to solve this model, an algorithm is suggested, based on the simulation of single time dependent water adding process with a sequence of constant water adding processes. The algorithm is applied for developing both a numerical procedure and simple QBASIC‐program that are tested on one illustrative example.

Findings

The results obtained by the algorithm improve the diafiltration process time around 10 percent and are a step towards finding an optimal dependence function α (t).

Research limitations/implications

Further on, the analysis of water usage in variable volume diafiltration needs to be done. Also, the problem of finding the optimal α (t) is still open.

Practical implications

The suggested algorithm is applicable to various membrane filtration processes and can be applied with little modification of the existing filtration equitment.

Originality/value

This paper is the first to view ALFA as a continuous function of time. Previous authors have considered step functions but never used this general approach.