bluuebunny/crossref_metadata_2025 huggingface dataset:
Unified model for the injection and transport of charge in organic diodes
Authors: Lara Bullejos Pablo , Jiménez Tejada Juan A. , Deen M. J. , Marinov O. , Datars W. R.
Published: March 2008

This paper presents a unified model for charge injection and transport in organic or polymeric diodes. A special focus is placed on charge injection from the contacts, using existing models such as thermionic emission and tunnel injection. These are combined to produce a compact model that includes effects associated with oxidation/reduction reactions at the electrodes. Charges are formed at the electrodes by oxidation or reduction in a process governed by the Nernst equation, and these charges modulate the injection barrier. A current-voltage relationship for organic or polymeric diodes that incorporates these injection phenomena, as well as the charge transport by the drift mechanism, is presented and discussed. The voltage ranges in which these effects are dominant are estimated. Finally, the resulting current-voltage and current-temperature relations are used to explain published experimental data.
A 106-fold enhancement in the conductivity of a discotic liquid crystal doped with only 1% (w∕w) gold nanoparticles
Authors: Holt Lucy A. , Bushby Richard J. , Evans Stephen D. , Burgess Andrew , Seeley Gordon
Published: March 2008

The presence of 1% (w∕w) of methylbenzene thiol coated gold nanoparticles increases the conductivity of the discotic liquid crystal 2,3,6,7,10,11-hexakis(hexyloxy)triphenylene (HAT6) by about two orders of magnitude in all three phases (crystal, columnar liquid crystal, and isotropic liquid). However, when a field (above a certain critical value) is applied to the isotropic phase, the conductivity rapidly increases by another three or four orders of magnitude after which the higher conductivity is maintained regardless of phase, field, or temperature. This increase in conductivity is attributed to the formation of chains of gold nanoparticles. A similar phenomenon is observed for 1% (w∕w) gold nanoparticles in the isotropic phase of hexadecane. However, the liquid crystal/nanoparticle mixture preserves its high conductivity when it is cooled into the crystalline phase whereas that of the hexadecane/nanoparticle mixture is lost. In hexadecane, crystal grain boundaries are expected to form in a random fashion and this disrupts the conductive pathways. However, if HAT6 crystallizes via the homeotropically aligned columnar phase, the grain boundaries form predominantly surface to surface (electrode to electrode) so that the conductive nanoparticle chains are trapped in a stabilizing solid matrix.
Hydrogenic impurity binding energy in self-assembled GaAs∕Ga1−xAlxAs quantum rings
Authors: Wang Guangxin , Zhang Peng
Published: March 2008

Using a variational approach within the effective mass approximation and adiabatic approximation, the binding energy of the ground state of a hydrogenic impurity positioned in a self-assembled GaAs∕Ga1−xAlxAs quantum ring (QR) is studied. The binding energy is calculated as a function with the size (outer radius, height) of the QR, the Al concentration, and the donor impurity position. The results indicate that the binding energy reaches a peak value when the size (outer radius, height) of the QR decreases to a certain value. The binding energy reaches a maximum for an impurity ion positioned at the midplane perpendicular to the symmetry axis of the QR. In addition, the binding energy becomes large as the Al concentration in GaAs∕Ga1−xAlxAs increases. When shifting the impurity ion from the internal surface of the QR to the external surface, the impurity binding energy increases, then decreases to a certain value, indicating that there is a maximum.
Nanomicrointerface to read molecular potentials into current-voltage based electronics
Authors: Rangel Norma L. , Seminario Jorge M.
Published: March 2008

Molecular potentials are unreadable and unaddressable by any present technology. It is known that the proper assembly of molecules can implement an entire numerical processing system based on digital or even analogical computation. In turn, the outputs of this molecular processing unit need to be amplified in order to be useful. We have developed a nanomicrointerface to read information encoded in molecular level potentials and to amplify this signal to microelectronic levels. The amplification is performed by making the output molecular potential slightly twist the torsional angle between two rings of a pyridazine, 3,6-bis(phenylethynyl) (aza-OPE) molecule, requiring only fractions of kcal/mol energies. In addition, even if the signal from the molecular potentials is not enough to turn the ring or even if the angles are the same for different combinations of outputs, still the current output yields results that resemble the device as a field effect transistor, providing the possibility to reduce channel lengths to the range of just 1 or 2nm. The slight change in the torsional angle yields readable changes in the current through the aza-OPE biased by an external applied voltage. Using ab initio methods, we computationally demonstrate the amplification of molecular potential signals into currents that can be read by standard circuits.
Mechanics of nonlinear random wave groups interacting with a vertical wall
Authors: Romolo Alessandra , Arena Felice
Published: March 2008

Nonlinear random wave groups interacting with a vertical wall are investigated. The analytical solution for the second-order free surface displacement and velocity potential when a high crest occurs at some fixed point on, or close to, the vertical wall is obtained. The solution is exact for any water depth, and it is given as a function of the frequency spectrum of the incident waves. It is obtained that the effects of nonlinearity strongly modify the linear structure of wave groups both in the space and the time domain. The maximum effect of nonlinearity occurs when the high wave hits the wall. Furthermore, it is shown that in finite water depth, the nonlinearity increases as the bottom depth decreases. Finally, a validation by means of Monte Carlo simulations of nonlinear random waves in reflection is given.
Calculations of stopping powers of 100eV–30keV electrons in 31 elemental solids
Authors: Tanuma S. , Powell C. J. , Penn D. R.
Published: March 2008

We present calculated electron stopping powers (SPs) for 31 elemental solids (Li, Be, glassy C, graphite, diamond, Na, Mg, K, Sc, Ti, V, Fe, Y, Zr, Nb, Mo, Ru, Rh, In, Sn, Cs, Gd, Tb, Dy, Hf, Ta, W, Re, Os, Ir, and Bi). These SPs were determined with an algorithm previously used for the calculation of electron inelastic mean free paths and from energy-loss functions (ELFs) derived from experimental optical data. The SP calculations were made for electron energies between 100eV and 30keV and supplement our earlier SP calculations for ten additional solids (Al, Si, Cr, Ni, Cu, Ge, Pd, Ag, Pt, and Au). Plots of SP versus atomic number for the group of 41 solids show clear trends. Multiple peaks and shoulders are seen that result from the contributions of valence-electron and various inner-shell excitations. Satisfactory agreement was found between the calculated SPs and values from the relativistic Bethe SP equation with recommended values of the mean excitation energy (MEE) for energies above 10keV. We determined effective MEEs versus maximum excitation energy from the ELFs for each solid. Plots of effective MEE versus atomic number showed the relative contributions of valence-electron and different core-electron excitations to the MEE. For a maximum excitation energy of 30keV, our effective MEEs agreed well for Be, graphite, Na, Al, and Si with recommended MEEs; a difference for Li was attributed to sample oxidation in the SP measurements for the recommended MEE. Substantially different effective MEEs were found for the three carbon allotropes (graphite, diamond, and glassy C).
Fermi level pinning-free interface at metals/homoepitaxial diamond (111) films after oxidation treatments
Authors: Ri Sung-Gi , Takeuchi Daisuke , Tokuda Norio , Okushi Hideyo , Yamasaki Satoshi
Published: March 2008

Schottky barrier heights of metal (Al, Au, Ni, and Pt) contacts on boron (B)-doped (111) homoepitaxial diamond films are investigated as a function of surface oxidation treatments before metal deposition [after wet-chemical oxidation (WO), WO followed by annealing in Ar atmosphere (WO-AN) and air oxidation]. It is found that the Schottky barrier height (ϕB) depends on the metal work function (ϕM) (Sϕ≡dϕB∕dϕM>0.3) on surfaces only after WO-AN, indicating that the interface at metals/B-doped (111) films after WO-AN has fewer defect states which do not pin the Fermi level. Experimental results and the appearance of a p-type surface conductive layer (SCL) are discussed and it is concluded that the pinning-free nature of the Fermi level is related to the appearance of a SCL.
Electronically excited states and visible region photodissociation spectroscopy of Aum+⋅Arn clusters (m=7–9): Molecular dimensionality transition?
Authors: Gloess Alexia N. , Schneider Holger , Weber J. Mathias , Kappes Manfred M.
Published: March 2008

Photodissociation spectra were determined for Aum+⋅Arn (m=7; n=0–3 and m=8,9; n=0,1) in the photon energy range of 2.14–3.02eV. Experimental data were compared with predictions of dipole allowed transitions using time-dependent density functional theory (TDDFT) as applied to cluster structures from both DFT (B3-LYP functional) and ab initio calculations at the MP2 level. Argon adduct formation does not significantly perturb the bare metal cluster core structure, but it does change the metal cluster spectrum for highly symmetric cluster structures. The photodissociation spectra are consistent with a transition from planar to three-dimensional gold cluster core geometries between m=7 and m=8 for both n=0 and 1. TDDFT predictions for favored isomers describe experimental absorption features to within ±0.25eV. We also discuss size-dependent trends in TDDFT transition energies for the lowest energy two- and three-dimensional structures of Aum+(m=3–9).
A density-functional study of the possibility of noncollinear magnetism in small Mn clusters using SIESTA and the generalized gradient approximation to exchange and correlation
Authors: Longo R. C. , Alemany M. M. G. , Ferrer J. , Vega A. , Gallego L. J.
Published: March 2008

We investigated the possibility of noncollinear magnetism in small Mnn clusters (n=2–6) using the density-functional method SIESTA with the generalized gradient approximation (GGA) to exchange and correlation. The lowest-energy states identified were collinear, with the atomic spin magnetic moments pointing in the same direction, for Mn2 and Mn3, and noncollinear for Mn4, Mn5 and, most decidedly, Mn6. These SIESTA/GGA results, which are compared with those of an earlier SIESTA study that used the local spin density approximation, are qualitatively in keeping with the result obtained by VASP/GGA calculations.
Self-consistent Ornstein–Zernike approximation for the Yukawa fluid with improved direct correlation function
Authors: Reiner A. , Høye J. S.
Published: March 2008

Thermodynamic consistency of the mean spherical approximation as well as the self-consistent Ornstein–Zernike approximation (SCOZA) with the virial route to thermodynamics is analyzed in terms of renormalized γ-ordering. For continuum fluids, this suggests the addition of a short-ranged contribution to the usual SCOZA direct correlation function, and the shift of the adjustable parameter from the potential term to this new term. The range of this contribution is fixed by imposing consistency with the virial route at the critical point. Comparison of the results of our theory for the hard-core Yukawa potential with the simulation data show very good agreement for cases where the liquid-vapor transition is stable or not too far into the metastable region with respect to the solid state. In the latter case for extremely short-ranged interactions discrepancies arise.
Tuning morphology and magnetic properties of sputtered permalloy by organic underlayers
Authors: Ahmad S. N. , Rao S. G. , Shaheen S. A. , Magana D. , Strouse G. F.
Published: March 2008

We report the effect of polarity of self-assembled monolayers on magnetic properties and morphology of a deposited magnetic material. Sputtering of permalloy (Ni79Fe21) on a patterned structure of self-assembled monolayers (SAMs), with −COOH and −CH3 terminal groups, results in the formation of a film on −COOH regions and clusters on −CH3 regions. Further investi-gations reveal that the cluster formation gives rise to superparamagnetism, while the film shows usual ferromagnetic behavior. The observed contrast in morphology and magnetism of permalloy is attributed to different growth mechanisms arising from the difference in reactive nature of the terminal functional groups of the SAMs.
High dielectric permittivity silver/polyimide composite films with excellent thermal stability
Authors: Dang Zhi-Min , Peng Bo , Xie Dan , Yao Sheng-Hong , Jiang Mei-Juan , Bai Jinbo
Published: March 2008

Silver/polyimide composite films were prepared through simple ultrasonic dispersion and subsequent in situ polymerization process. Dependence of dielectric properties of the films on volume fraction of Ag particles, frequency, and temperature was investigated. The percolation threshold of the films was only 0.122, which was lower than the theoretical value (0.16). The effective dielectric permittivity of the film with 12.5vol% of Ag fillers achieved 400 at 103Hz. The relative tolerance of dielectric permittivity of the film with 12.0vol% of Ag fillers in wide temperature range was less than 4.0%, which would satisfy the need in practical applications.
Single-file diffusion through inhomogeneous nanopores
Authors: Bandyopadhyay Tusar
Published: March 2008

Strict one-dimensional diffusion, due to geometrical confinement in a nanopore, of an assembly of particles forbids overtaking by each other, giving rise to single-file diffusion (SFD). Smooth carbon nanotube is the epitome of SFD. However, natural nanoporous materials are far from smooth; morphologically, the nanopores’ inner surface may provide an inhomogeneous environment for diffusion to occur, giving rise to subnormal diffusion even for an isolated particle diffusing through this fractal landscape. The realm of fractional diffusion (FD) falls under this paradigm. In order to understand the characteristics of SFD through inhomogeneous nanopores, here, we introduce a fractional SFD (FSFD) formalism that deals with a combination of these two phenomena, namely, SFD of particles, each of which are moving subdiffusively in one dimension. For an infinite system, we obtain the mean square displacement (MSD) of the combined entity and our analysis is based on FD equation for particles moving in concert where the single-file correlation is established through reflection principle. For a finite system, we calculate the transport probabilities based on continuous time random walk model. While both the diffusion mechanisms (SFD and FD) acting separately are responsible for slow dynamics at long times, their combined effect leads to ultraslow diffusion. For example, while the long time asymptote of MSD of SFD scales as t, that for FSFD is tα, where α is the measure of the extent of inhomogeneity. These findings, which are believed to occur in a natural inhomogeneous nanopore, is also important for design and fabrication of nanofluidic devices through which the fluid delivery can be engineered.
Q
factor of dual-tunable microwave resonators based on yttrium iron garnet and barium strontium titanate layered structures
Authors: Ustinov A. B. , Kalinikos B. A. , Tiberkevich V. S. , Slavin A. N. , Srinivasan G.
Published: March 2008

Q factor of dual-tunable ferrite-ferroelectric hybrid wave microwave resonator was studied as a function of bias electric voltage U and bias magnetic field H. The resonator consisted of a thin (7μm) ferromagnetic resonator made of a single-crystal yttrium iron garnet film and a dielectric resonator made of relatively thick (500μm) plate of ceramic barium strontium titanate having similar in-plane sizes. A frequency spectrum of the resonator consisted of two hybridized modes: a quasiferromagnetic mode and a quasidielectric mode. Maximum electric tuning band of 5% of the resonance frequency has been observed for H values corresponding to maximum hybridization of the modes. The Q factor of the resonator was varied from 30–300 depending on both U and H. In general, Q factor decreases with increasing level of modes’ hybridization and electric tuning interval. Thus, Q factor and electric tunability are competing characteristics of hybrid ferrite-ferroelectric microwave resonators.
Pressure-modulated free energy change in piezoelectric and dielectric responses for relaxor ferroelectric solid solution Pb(Mg1∕3Nb2∕3)O3–PbTiO3 binary system single crystal and ceramics near a morphotropic phase boundary composition
Authors: Yasuda Naohiko , Suzuki Satoshi , Rahman Md. M. , Ohwa Hidehiro , Matsushita Mituyoshi , Yamashita Yohachi , Iwata Makoto , Terauchi Hikaru , Ishibashi Yoshihiro
Published: March 2008

The electromechanical and dielectric responses in transverse and longitudinal modes for relaxor ferroelectric solid solution Pb(Mg1∕3Nb2∕3)O3–PbTiO3 (PMNT) near a morphotropic phase boundary composition were investigated under hydrostatic pressures up to 700MPa at 25°C. The effect of pressure on their responses remarkably appeared. Their electromechanical suppression in PMNT single crystal and ceramics occurs at each pressure, corresponding to electromechanical coupling coefficient k. The permittivity ε increased with pressure-induced electromechanical suppression. The change in ε with such suppression corresponds to k. Such phenomena were considered to be due to the increase in piezoelectric load based on decrease of domain size coming from increase in free energy with pressures.
Some remarks on the Gelfand–Naimark–Segal representations of topological  *-algebras
Authors: Iguri S. M. , Castagnino M. A.
Published: March 2008

After an appropriate restatement of the Gelfand–Naimark–Segal construction for topological  *-algebras we prove that there exists an isomorphism among the set Cycl(A) of weakly continuous strongly cyclic  *-representations of a barreled dual-separable  *-algebra with unit A, the space HilbA(A*) of the Hilbert spaces that are continuously embedded in A* and are  * -invariant under the dual left regular action of A, and the set of the corresponding reproducing kernels. We show that these isomorphisms are cone morphisms and we prove many interesting results that follow from this fact. We discuss how these results can be used to describe cyclic representations on more general inner product spaces.
Microphotoluminescence study of individual suspended ZnO nanowires
Authors: Gao Min , Li Wenliang , Liu Yang , Li Quan , Chen Qing , Peng Lian-Mao
Published: March 2008

We report microphotoluminescence measurements on individually suspended ZnO nanowires attached to nanometer-sized metal tips. This procedure avoids the possible influence of the substrate and enables comprehensive optical, electrical, chemical, and morphological characterizations to be carried on the same individual nanowire. Based on the ZnO nanowires examined, we found that the near band edge emission redshifted with the increasing intensity of the defect-related green emission. The comprehensive characterizations of in situ heated ZnO nanowires suggested a correlation between the defect green emission and the oxygen deficiency, which also affect the carrier density, and thus, the nanowire’s transport property.
Dual-color emitting quantum-dot-quantum-well CdSe-ZnS heteronanocrystals hybridized on InGaN∕GaN light emitting diodes for high-quality white light generation
Authors: Nizamoglu Sedat , Mutlugun Evren , Özel Tuncay , Demir Hilmi Volkan , Sapra Sameer , Gaponik Nikolai , Eychmüller Alexander
Published: March 2008

We report white light generation by hybridizing green-red emitting (CdSe)ZnS∕CdSe (core)shell/shell quantum-dot-quantum-well heteronanocrystals on blue InGaN∕GaN light emitting diodes with the photometric properties of tristimulus coordinates (x,y)=(0.36,0.30), luminous efficacy of optical radiation LE=278lm∕W, correlated color temperature CCT=3929K, and color-rendering index CRI=75.1. We present the photometric analysis and the quantum mechanical design of these dual-color emitting heteronanocrystals synthesized to achieve high-quality white light when hybridized on light emitting diodes. Using such multicolor emitting heteronanocrystals facilitates simple device implementation while providing good photometric properties.
1.6
W
high wall plug efficiency, continuous-wave room temperature quantum cascade laser emitting at 4.6μm
Authors: Lyakh A. , Pflügl C. , Diehl L. , Wang Q. J. , Capasso Federico , Wang X. J. , Fan J. Y. , Tanbun-Ek T. , Maulini R. , Tsekoun A. , Go R. , Kumar N. Patel C.
Published: March 2008

A strain-balanced, InP-based quantum cascade laser structure designed for light emission at 4.6μm was grown by metal-organic chemical vapor deposition. A maximum total optical power of 1.6W was obtained in continuous-wave mode at 300K for uncoated devices processed in buried heterostructure geometry with stripe dimensions of 5mm by 9.5μm. Corresponding maximum wall plug efficiency and threshold current density were measured to be 8.8% and 1.05kA∕cm2, respectively. Fully hermetically packaged laser of identical dimensions produced in excess of 1.5W under the same conditions.
Creep-resistant composites of alumina and single-wall carbon nanotubes
Authors: Zapata-Solvas Eugenio , Poyato Rosalía , Gómez-García Diego , Domínguez-Rodríguez Arturo , Radmilovic Velimir , Padture Nitin P.
Published: March 2008

Composites of alumina (Al2O3) ceramic and single-wall carbon nanotubes (SWNTs) have been tested in uniaxial compression at 1300 and 1350°C (Ar atmosphere), and they have been found to be about two orders of magnitude more creep-resistant compared to a pure alumina of about the same grain size (0.5μm). This is attributed to partial blocking of grain-boundary sliding by SWNTs in the composites. Since the grain boundaries in the ceramic/SWNTs composites are amenable to being engineered, this constitutes an attractive approach to the design of creep-resistant ceramic composites.
Diode-pumped polymeric dye lasers operating at a pump power level of 10mW
Authors: Sakata Hajime , Takeuchi Hideki
Published: March 2008

We present a low-threshold vertical-cavity dye laser that is pumped by an InGaN laser diode. This vertical-cavity laser has a 1.2-μm-thick poly-N-vinylcarbazole active layer doped with coumarin 540A. The threshold pump power depended on the dye concentration and showed the minimum value of 16mW/pulse with the dye concentration of 4.0%. Single-mode laser action is attained at around 550nm and the output intensity decreases to half of the initial value after the emission of 8×105 pulses. This concept helps to realize a highly compact dye laser that can be operated in the entire range of visible wavelengths.
Contrasting water-use strategies in two sympatric cool-temperate rainforest species, Nothofagus cunninghamii (Nothofagaceae) and Atherosperma moschatum (Atherospermataceae)
Authors: Sommerville Katy E. , Read Jennifer
Published: March 2008

Nothofagus cunninghamii (Hook.) Oerst. and Atherosperma moschatum Labill. co-occur in cool-temperate rainforest across the wetter parts of Tasmania and Victoria, Australia, but A. moschatum extends to drier areas than N. cunninghamii. Possible reasons include differential tolerance of drought and fire or dispersal capacity. Here, we compare these species in their responses to water deficits. Differences in seedling survival, leaf tissue damage, shoot water relations, stomatal sensitivity, allocation of biomass and the long-term water-use efficiency of each species in response to water stress were investigated. N. cunninghamii showed traits typical of a high-water-use species, such as high stomatal conductance, a strategy that is not surprising in a rainforest species. However, it also displayed an exceptional ability to draw water from the soil and longer seedling roots, allowing replacement of water lost, at least in the short term. A. moschatum showed a more conservative water-use strategy, surviving greater internal dehydration with less damage, and displaying greater stomatal sensitivity to drought and long-term water-use efficiency in trees. The apparently superior long-term drought resistance of A. moschatum may in part explain its more common occurrence in drier regions than N. cunninghamii, at least in Tasmania, while the capacity of N. cunninghamii to survive short but severe periods of water stress correlates well with its higher position in the canopy and greater exposure to sunlight and desiccating winds. However, there is little evidence to suggest that the absence of N. cunninghamii from the rainforests of eastern Victoria is due to drought. We also suggest that the water-use strategy of N. cunninghamii may relate not just to surviving water deficits, but to maximising annual carbon gain in a temperate climate that is, on average, driest during the warmest time of the year.
Plant-growth-promoting rhizobacteria and arbuscular mycorrhizal fungi modify alleviation biochemical mechanisms in water-stressed plants
Authors: Kohler Josef , Hernández José Antonio , Caravaca Fuensanta , Roldán Antonio
Published: March 2008

This study examined the effect of inoculation with the plant-growth-promoting rhizobacterium (PGPR) Pseudomonas mendocina Palleroni, alone or in combination with an arbuscular mycorrhizal (AM) fungus, Glomus intraradices (Schenk & Smith) or Glomus mosseae (Nicol & Gerd.) Gerd. & Trappe, on antioxidant enzyme activities (superoxide dismutase, catalase and total peroxidase activities), phosphatase and nitrate reductase activities and solute accumulation in leaves of Lactuca sativa L. cv. Tafalla affected by three different levels of water stress. At moderate drought, bacterial inoculation and mycorrhizal inoculation with G. intraradices, alone or in combination, stimulated significantly nitrate reductase activity. At severe drought, fertilisation and P. mendocina inoculation, alone or in combination with either of the selected AM fungi, increased significantly phosphatase activity in lettuce roots and proline accumulation in leaves. Total peroxidase (POX) and catalase (CAT) activities increased in response to drought, whereas superoxide dismutase activity decreased. Inorganic fertilisation and both combined treatments of PGPR and AM fungus showed the highest values of leaf POX activity under severe drought. The highest CAT activity was recorded in the fertilised plants followed by the P. mendocina-inoculated plants grown under severe stress conditions. These results support the potential use of a PGPR as an inoculant to alleviate the oxidative damage produced under water stress.
Evolution of malaria parasite plastid targeting sequences
Authors: Tonkin Christopher J. , Foth Bernardo J. , Ralph Stuart A. , Struck Nicole , Cowman Alan F. , McFadden Geoffrey I.
Published: March 2008

The transfer of genes from an endosymbiont to its host typically requires acquisition of targeting signals by the gene product to ensure its return to the endosymbiont for function. Many hundreds of plastid-derived genes must have acquired transit peptides for successful relocation to the nucleus. Here, we explore potential evolutionary origins of plastid transit peptides in the malaria parasite
Plasmodium falciparum
. We show that exons of the
P. falciparum
genome could serve as transit peptides after exon shuffling. We further demonstrate that numerous randomized peptides and even whimsical sequences based on English words can also function as transit peptides
in vivo
. Thus, facile acquisition of transit peptides from existing sequence likely expedited endosymbiont integration through intracellular gene transfer.
Motion vision is independent of color in
Drosophila
Authors: Yamaguchi Satoko , Wolf Reinhard , Desplan Claude , Heisenberg Martin
Published: March 2008

Whether motion vision uses color contrast is a controversial issue that has been investigated in several species, from insects to humans. We used
Drosophila
to answer this question, monitoring the optomotor response to moving color stimuli in WT and genetic variants. In the fly eye, a motion channel (outer photoreceptors R1–R6) and a color channel (inner photoreceptors R7 and R8) have been distinguished. With moving bars of alternating colors and high color contrast, a brightness ratio of the two colors can be found, at which the optomotor response is largely missing (point of equiluminance). Under these conditions, mutant flies lacking functional rhodopsin in R1–R6 cells do not respond at all. Furthermore, genetically eliminating the function of photoreceptors R7 and R8 neither alters the strength of the optomotor response nor shifts the point of equiluminance. We conclude that the color channel (R7/R8) does not contribute to motion detection as monitored by the optomotor response.
Calcium Regulation of Myogenesis by Differential Calmodulin Inhibition of Basic Helix-Loop-Helix Transcription Factors
Authors: Hauser Jannek , Saarikettu Juha , Grundström Thomas
Published: March 2008

The members of the MyoD family of basic helix-loop-helix (bHLH) transcription factors are critical regulators of skeletal muscle differentiation that function as heterodimers with ubiquitously expressed E-protein bHLH transcription factors. These heterodimers must compete successfully with homodimers of E12 and other E-proteins to enable myogenesis. Here, we show that E12 mutants resistant to Ca2+-loaded calmodulin (CaM) inhibit MyoD-initiated myogenic conversion of transfected fibroblasts. Ca2+channel blockers reduce, and Ca2+stimulation increases, transcription by coexpressed MyoD and wild-type E12 but not CaM-resistant mutant E12. Furthermore, CaM-resistant E12 gives lower MyoD binding and higher E12 binding to a MyoD-responsive promoter in vivo and cannot rescue myogenic differentiation that has been inhibited by siRNA against E12 and E47. Our data support the concept that Ca2+-loaded CaM enables myogenesis by inhibiting DNA binding of E-protein homodimers, thereby promoting occupancy of myogenic bHLH protein/E-protein heterodimers on promoters of myogenic target genes.
Ubiquitin–Proteasome-dependent Degradation of a Mitofusin, a Critical Regulator of Mitochondrial Fusion
Authors: Cohen Mickael M.J. , Leboucher Guillaume P. , Livnat-Levanon Nurit , Glickman Michael H. , Weissman Allan M.
Published: March 2008

The mitochondrion is a dynamic membranous network whose morphology is conditioned by the equilibrium between ongoing fusion and fission of mitochondrial membranes. In the budding yeast, Saccharomyces cerevisiae, the transmembrane GTPase Fzo1p controls fusion of mitochondrial outer membranes. Deletion or overexpression of Fzo1p have both been shown to alter the mitochondrial fusion process indicating that maintenance of steady-state levels of Fzo1p are required for efficient mitochondrial fusion. Cellular levels of Fzo1p are regulated through degradation of Fzo1p by the F-box protein Mdm30p. How Mdm30p promotes degradation of Fzo1p is currently unknown. We have now determined that during vegetative growth Mdm30p mediates ubiquitylation of Fzo1p and that degradation of Fzo1p is an ubiquitin-proteasome–dependent process. In vivo, Mdm30p associates through its F-box motif with other core components of Skp1-Cullin-F-box (SCF) ubiquitin ligases. We show that the resulting SCFMdm30p ligase promotes ubiquitylation of Fzo1p at mitochondria and its subsequent degradation by the 26S proteasome. These results provide the first demonstration that a cytosolic ubiquitin ligase targets a critical regulatory molecule at the mitochondrial outer membrane. This study provides a framework for developing an understanding of the function of Mdm30p-mediated Fzo1p degradation in the multistep process of mitochondrial fusion.
The Origins and Evolution of Homo sapiens
Authors: Lurquin Paul F. , Stone Linda
Published: March 2008

The notions of natural selection and drift also apply to humans and their biological and cultural evolution. The science of paleoanthropology explains human evolution through the study of intermediate fossil forms. In addition, geneticists have been able to retrace, through the study of mitochondrial DNA and Y-chromosome DNA, the origin and migrations of prehistoric humans. The understanding of human cultural evolution has greatly benefited from the application of evolutionary thinking.
Integrating ARC grid middleware with Taverna workflows
Authors: Krabbenhöft Hajo N. , Möller Steffen , Bayer Daniel
Published: March 2008

Summary: This work presents two independent approaches for a seamless integration of computational grids with the bioinformatics workflow suite Taverna. These are supported by a unique relational database to link applications with grid resources and presents those as workflow elements. A web portal facilitates its collaborative maintenance. The first approach implements a gateway service to handle authentication certificates and all communication with the grid. It reads the database to spawn web services for workflow elements which are in turn used by Taverna. The second approach lets Taverna communicate with the grid on its own, by means of a newly developed plug-in. It reads the database and executes the needed tasks directly on the grid. While the gateway service is non-intrusive, the plug-in has technical advantages, e.g. by allowing data to remain on the grid while being passed between workflow elements.

Availability:  http://grid.inb.uni-luebeck.de/

Contact:  bayer@inb.uni-luebeck.de
Combining statistical alignment and phylogenetic footprinting to detect regulatory elements
Authors: Satija Rahul , Pachter Lior , Hein Jotun
Published: March 2008

Motivation: Traditional alignment-based phylogenetic footprinting approaches make predictions on the basis of a single assumed alignment. The predictions are therefore highly sensitive to alignment errors or regions of alignment uncertainty. Alternatively, statistical alignment methods provide a framework for performing phylogenetic analyses by examining a distribution of alignments.

Results: We developed a novel algorithm for predicting functional elements by combining statistical alignment and phylogenetic footprinting (SAPF). SAPF simultaneously performs both alignment and annotation by combining phylogenetic footprinting techniques with an hidden Markov model (HMM) transducer-based multiple alignment model, and can analyze sequence data from multiple sequences. We assessed SAPF's predictive performance on two simulated datasets and three well-annotated cis-regulatory modules from newly sequenced Drosophila genomes. The results demonstrate that removing the traditional dependence on a single alignment can significantly augment the predictive performance, especially when there is uncertainty in the alignment of functional regions.

Availability: SAPF is freely available to download online at http://www.stats.ox.ac.uk/~satija/SAPF/

Contact:  satija@stats.ox.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
A method for the possible species discrimination of juvenile gadoids by broad-bandwidth backscattering spectra vs. angle of incidence
Authors: Lundgren Bo , Nielsen J. Rasmus
Published: March 2008

Lundgren, B., and Nielsen, J. R. 2008. A method for the possible species discrimination of juvenile gadoids by broad-bandwidth backscattering spectra vs. angle of incidence. – ICES Journal of Marine Science, 65: 581–593. Measurements were made of the broad-bandwidth (80–220 kHz) acoustic backscattering from free-swimming juvenile gadoids at various orientations and positions in an acoustic beam, under controlled conditions. The experimental apparatus consisted of a stereo-video camera system, a broad-bandwidth echosounder and echo-processor system, a narrowband 120 kHz split-beam echosounder, a large tank, and a fishnet cage. The net cage was centred on the acoustic beams and was virtually transparent, both acoustically and optically. Accurate three-dimensional positions and angular orientations of individual fish were estimated from stereo-images captured synchronously when broad-bandwidth echoes were received from passing fish. Fish positions were also estimated from data collected with a synchronized split-beam echosounder. Software was developed for image analysis and modelling, including calibration, alignment of acoustic and optical-reference frames, and automatic position-fitting of fish models to manually marked fix-points on fish images. The software also performs Fourier spectrum analysis and pulse-shape analysis of broad-bandwidth echoes. Therefore, several measurement series on free-swimming juvenile gadoids were evaluated. The method and data may be used to improve the acoustic identification of fish species and sizes, and thereby improve investigations of spatial prey–predator relationships, and the accuracy and efficiency of acoustic surveys.
Foam: a multiphase system with many facets
Authors: Hilgenfeldt Sascha , Arif Shehla , Tsai Jih-Chiang
Published: March 2008

Liquid foams are an extreme case of multiphase flow systems: capable of flow despite a very high dispersed phase volume fraction, yet exhibiting many characteristics of not only viscoelastic materials but also elastic solids. The non-trivial, well-defined geometry of foam bubbles is at the heart of a plethora of dynamical processes on widely varying length and time scales. We highlight recent developments in foam drainage (liquid dynamics) and foam rheology (flow of the entire gas–liquid system), emphasizing that many poorly understood features of other materials have precisely defined and quantifiable analogues in aqueous foams, where the only ingredients are well-known material parameters of Newtonian fluids and bubble geometry, together with subtle but important information on the surface mobility of the foam. Not only does this make foams an ideal model system for the theorist, but also an exciting object for experimental studies, in which dynamical processes span length scales from nanometres (thin films) to metres (foam continuum flows) and time scales from microseconds (film rupture) to minutes (foam rheology).
Lift, drag and added mass of a hemispherical bubble sliding and growing on a wall in a viscous linear shear flow
Authors: Legendre Dominique , Colin Catherine , Coquard Typhaine
Published: March 2008

The three-dimensional flow around a hemispherical bubble sliding and growing on a wall in a viscous linear shear flow is studied numerically by solving the full Navier–Stokes equations in a boundary-fitted domain. The main goal of the present study is to provide a complete description of the forces experienced by the bubble (drag, lift and added mass) over a wide range of sliding and shear Reynolds numbers (0.01≤
Re
b
,
Re
α
≤2000) and shear rate (0≤
Sr
≤5). The drag and lift forces are computed successively for the following situations: an immobile bubble in a linear shear flow; a bubble sliding on the wall in a fluid at rest; and a bubble sliding in a linear shear flow. The added-mass force is studied by considering an unsteady motion relative to the wall or a time-dependent radius.
Increasing power in association studies by using linkage disequilibrium structure and molecular function as prior information
Authors: Eskin Eleazar
Published: March 2008

The availability of various types of genomic data provides an opportunity to incorporate this data as prior information in genetic association studies. This information includes knowledge of linkage disequilibrium structure as well as which regions are likely to be involved in disease. In this paper, we present an approach for incorporating this information by revisiting how we perform multiple-hypothesis correction. In a traditional association study, in order to correct for multiple-hypothesis testing, the significance threshold at each marker, t, is set to control the total false-positive rate. In our framework, we vary the threshold at each marker ti and use these thresholds to incorporate prior information. We present a numerical procedure for solving for thresholds that maximizes association study power using prior information. We also present the results of benchmark simulation experiments using the HapMap data, which demonstrate a significant increase in association study power under this framework. We provide a Web server for performing association studies using our method and provide thresholds optimized for the Affymetrix 500k and Illumina HumanHap 550 chips and demonstrate the application of our framework to the analysis of the Wellcome Trust Case Control Consortium data.
Panel construction for mapping in admixed populations via expected mutual information
Authors: Bercovici Sivan , Geiger Dan , Shlush Liran , Skorecki Karl , Templeton Alan
Published: March 2008

Mapping by admixture linkage disequilibrium (MALD) is an economical and powerful approach for the identification of genomic regions harboring disease susceptibility genes in recently admixed populations. We develop an information-theory-based measure, called expected mutual information (EMI), which computes the impact of a set of markers on the ability to infer ancestry at each chromosomal location. We then present a simple and effective algorithm for the selection of panels that strives to maximize the EMI score. Finally, we demonstrate via well-established simulation tools that our panels provide more power and accuracy for inferring disease gene loci via the MALD method in comparison to previous methods.
The Arabidopsis Putative Selenium-Binding Protein Family: Expression Study and Characterization of SBP1 as a Potential New Player in Cadmium Detoxification Processes
Authors: Dutilleul Christelle , Jourdain Agnès , Bourguignon Jacques , Hugouvieux Véronique
Published: March 2008

In Arabidopsis (Arabidopsis thaliana), the putative selenium-binding protein (SBP) gene family is composed of three members (SBP1–SBP3). Reverse transcription-polymerase chain reaction analyses showed that SBP1 expression was ubiquitous. SBP2 was expressed at a lower level in flowers and roots, whereas SBP3 transcripts were only detected in young seedling tissues. In cadmium (Cd)-treated seedlings, SBP1 level of expression was rapidly increased in roots. In shoots, SBP1 transcripts accumulated later and for higher Cd doses. SBP2 and SBP3 expression showed delayed or no responsiveness to Cd. In addition, luciferase (LUC) activity recorded on Arabidopsis lines expressing the LUC gene under the control of the SBP1 promoter further showed dynamic regulation of SBP1 expression during development and in response to Cd stress. Western-blot analysis using polyclonal antibodies raised against SBP1 showed that SBP1 protein accumulated in Cd-exposed tissues in correlation with SBP1 transcript amount. The sbp1 null mutant displayed no visible phenotype under normal and stress conditions that was explained by the up-regulation of SBP2 expression. SBP1 overexpression enhanced Cd accumulation in roots and reduced sensitivity to Cd in wild type and, more significantly, in Cd-hypersensitive cad mutants that lack phytochelatins. Similarly, in Saccharomyces cerevisiae, SBP1 expression led to increased Cd tolerance of the Cd-hypersensitive ycf1 mutant. In vitro experiments showed that SBP1 has the ability to bind Cd. These data highlight the importance of maintaining the adequate SBP protein level under healthy and stress conditions and suggest that, during Cd stress, SBP1 accumulation efficiently helps to detoxify Cd potentially through direct binding.
Further Characterization of a Rice AGL12 Group MADS-Box Gene,OsMADS26
Authors: Lee Shinyoung , Woo Young-Min , Ryu Sung-Il , Shin Young-Duck , Kim Woo Taek , Park Ky Young , Lee In-Jung , An Gynheung
Published: March 2008

Plant MADS-box genes can be divided into 11 groups. Genetic analysis has revealed that most of them function in flowering-time control, reproductive organ development, and vegetative growth. Here, we elucidated the role of OsMADS26, a member of the AGL12 group. Transcript levels of OsMADS26 were increased in an age-dependent manner in the shoots and roots. Transgenic plants of both rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) overexpressing this gene manifested phenotypes related to stress responses, such as chlorosis, cell death, pigment accumulation, and defective root/shoot growth. In addition, apical hook development was significantly suppressed in Arabidopsis. Plants transformed with the OsMADS26-GR (glucocorticoid receptor) fusion construct displayed those stress-related phenotypes when treated with dexamethasone. Microarray analyses using this inducible system showed that biosynthesis genes for jasmonate, ethylene, and reactive oxygen species, as well as putative downstream targets involved in the stress-related process, were up-regulated in OsMADS26-overexpressing plants. These results suggest that OsMADS26 induces multiple responses that are related to various stresses.
Annotating Genes of Known and Unknown Function by Large-Scale Coexpression Analysis
Authors: Horan Kevin , Jang Charles , Bailey-Serres Julia , Mittler Ron , Shelton Christian , Harper Jeff F. , Zhu Jian-Kang , Cushman John C. , Gollery Martin , Girke Thomas
Published: March 2008

About 40% of the proteins encoded in eukaryotic genomes are proteins of unknown function (PUFs). Their functional characterization remains one of the main challenges in modern biology. In this study we identified the PUF encoding genes from Arabidopsis (Arabidopsis thaliana) using a combination of sequence similarity, domain-based, and empirical approaches. Large-scale gene expression analyses of 1,310 publicly available Affymetrix chips were performed to associate the identified PUF genes with regulatory networks and biological processes of known function. To generate quality results, the study was restricted to expression sets with replicated samples. First, genome-wide clustering and gene function enrichment analysis of clusters allowed us to associate 1,541 PUF genes with tightly coexpressed genes for proteins of known function (PKFs). Over 70% of them could be assigned to more specific biological process annotations than the ones available in the current Gene Ontology release. The most highly overrepresented functional categories in the obtained clusters were ribosome assembly, photosynthesis, and cell wall pathways. Interestingly, the majority of the PUF genes appeared to be controlled by the same regulatory networks as most PKF genes, because clusters enriched in PUF genes were extremely rare. Second, large-scale analysis of differentially expressed genes was applied to identify a comprehensive set of abiotic stress-response genes. This analysis resulted in the identification of 269 PKF and 104 PUF genes that responded to a wide variety of abiotic stresses, whereas 608 PKF and 206 PUF genes responded predominantly to specific stress treatments. The provided coexpression and differentially expressed gene data represent an important resource for guiding future functional characterization experiments of PUF and PKF genes. Finally, the public Plant Gene Expression Database (http://bioweb.ucr.edu/PED) was developed as part of this project to provide efficient access and mining tools for the vast gene expression data of this study.