bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimization and scale-freeness for complex networks
Authors: Minnhagen Petter , Bernhardsson Sebastian
Published: June 2007

Complex networks are mapped to a model of boxes and balls where the balls are distinguishable. It is shown that the scale-free size distribution of boxes maximizes the information associated with the boxes provided configurations including boxes containing a finite fraction of the total amount of balls are excluded. It is conjectured that for a connected network with only links between different nodes, the nodes with a finite fraction of links are effectively suppressed. It is hence suggested that for such networks the scale-free node-size distribution maximizes the information encoded on the nodes. The noise associated with the size distributions is also obtained from a maximum entropy principle. Finally, explicit predictions from our least bias approach are found to be borne out by metabolic networks.
Agreement dynamics on interaction networks with diverse topologies
Authors: Barrat Alain , Baronchelli Andrea , Dall’Asta Luca , Loreto Vittorio
Published: June 2007

We review the behavior of a recently introduced model of agreement dynamics, called the “Naming Game.” This model describes the self-organized emergence of linguistic conventions and the establishment of simple communication systems in a population of agents with pairwise local interactions. The mechanisms of convergence towards agreement strongly depend on the network of possible interactions between the agents. In particular, the mean-field case in which all agents communicate with all the others is not efficient, since a large temporary memory is requested for the agents. On the other hand, regular lattice topologies lead to a fast local convergence but to a slow global dynamics similar to coarsening phenomena. The embedding of the agents in a small-world network represents an interesting tradeoff: a local consensus is easily reached, while the long-range links allow to bypass coarsening-like convergence. We also consider alternative adaptive strategies which can lead to faster global convergence.
Spectral densities of scale-free networks
Authors: Kim D. , Kahng B.
Published: June 2007

The spectral densities of the weighted Laplacian, random walk, and weighted adjacency matrices associated with a random complex network are studied using the replica method. The link weights are parametrized by a weight exponent β. Explicit results are obtained for scale-free networks in the limit of large mean degree after the thermodynamic limit, for arbitrary degree exponent and β.
Extreme fluctuations in noisy task-completion landscapes on scale-free networks
Authors: Guclu H. , Korniss G. , Toroczkai Z.
Published: June 2007

We study the statistics and scaling of extreme fluctuations in noisy task-completion landscapes, such as those emerging in synchronized distributed-computing networks, or generic causally constrained queuing networks, with scale-free topology. In these networks the average size of the fluctuations becomes finite (synchronized state) and the extreme fluctuations typically diverge only logarithmically in the large system-size limit ensuring synchronization in a practical sense. Provided that local fluctuations in the network are short tailed, the statistics of the extremes are governed by the Gumbel distribution. We present large-scale simulation results using the exact algorithmic rules, supported by mean-field arguments based on a coarse-grained description.
Electron collection by a negatively charged sphere in a collisionless magnetoplasma
Authors: Patacchini L. , Hutchinson I. H. , Lapenta G.
Published: June 2007

Easy-to-evaluate approximate formulas are presented for the repelled-species current collected by a spherical body in a collisionless, magnetized plasma, valid over the full range of ratio of Larmor radius to sphere radius. The form is an appropriate average of the lower and upper bounds obtained by prior analytic arguments. This formulation enables rapid evaluation of the floating potential in hybrid Boltzmann-particle-in-cell (PIC) codes with a background magnetic field. The treatment is validated by comparison of hybrid PIC (ion particle) code with full PIC (electron and ion particle) code calculations. It is found that typically for no value of magnetic field is it valid to approximate the electrons as fully magnetized but the ions as unmagnetized in the absence of plasma drift.
Ontology of temperature in nonequilibrium systems
Authors: Popov Alexander V. , Hernandez Rigoberto
Published: June 2007

The laws of thermodynamics provide a clear concept of the temperature for an equilibrium system in the continuum limit. Meanwhile, the equipartition theorem allows one to make a connection between the ensemble average of the kinetic energy and the uniform temperature. When a system or its environment is far from equilibrium, however, such an association does not necessarily apply. In small systems, the regression hypothesis may not even apply. Herein, it is shown that in small nonequilibrium systems, the regression hypothesis still holds, though with a generalized definition of the temperature. The latter must now be defined for each such manifestation.
Phase separation in dilute LiCl–H2O solution related to the polyamorphism of liquid water
Authors: Mishima Osamu
Published: June 2007

When an emulsified 4.8mol% LiCl–H2O solution was cooled under a pressure of 0.35 or 0.45GPa and decompressed to 0.1GPa at 142K, slightly above its glass transition temperature (∼140K at 0.1GPa), its volume increased suddenly. This was regarded as an appearance of the low-density amorphous ice in the liquid solution as suggested by x-ray and Raman measurements, and this appearance corresponded to the high-to-low-density polyamorphic transition of pure H2O. Hysteresis was considered to accompany this volumetric change. The hysteresis of the liquid transition proves its first-order nature and, as for the solution, this suggests that the transition is a polyamorphic phase separation.
Electron temperature effects on the eigenmodes of a plasma waveguide
Authors: Aghamir F. M. , Abbas-nejad M.
Published: June 2007

The effect of finite electron temperature on the excitation of eigenmodes of a plasma loaded cylindrical waveguide is investigated. In the analysis, a nonlinear wave equation is derived using the linearized fluid equations along with Maxwell’s equations. The general result obtained for the annular plasma column is then reduced to be used for the case in which the plasma column fills the entire waveguide as well as for a partially filled configuration. Dispersion relations for electromagnetic and electrostatic modes are solved numerically to study the effect of electron thermal velocity on the characteristics of azimuthally symmetrical eigenmodes. The numerical studies show that the thermal motion of electrons shifts the frequencies of the perturbed transverse magnetic waveguide and those of cyclotron plasma modes toward higher values.
Observation of instabilities during density limit experiments in the Hefei Tokamak-7
Authors: Asif M. ,   HT-7 Team
Published: June 2007

During a recent campaign at the Hefei Tokamak-7 (HT-7) [M. Asif et al., Phys. Plasmas 12, 082502 (2005)], experiments were performed with a moveable graphite limiter to investigate the influence of the horizontal plasma position on the density limit. It has been found that in HT-7 density limits differ by the radiative instability in the plasma boundary and various magnetohydrodynamic (MHD) instabilities, which precedes the disruption. Control of the impurity content, edge, and recycling properties prevents the growth of the multifaceted asymmetric radiation from the edge (MARFE) and makes it possible to exceed the Greenwald limit in HT-7. It has been observed that the m=2, MHD component dominates during almost the whole discharge duration, when the density limit is approached at values of the edge safety factor 3<q(a)<4. The observed sawtooth oscillation shows that oscillation with m=1 and n=1, where m and n are the poloidal and toroidal mode numbers, respectively, triggers m=2 and n=1 in sawtooth collapse, which finally causes disruption in the HT-7 tokamak.
Linear scaling calculation of band edge states and doped semiconductors
Authors: Xiang H. J. , Yang Jinlong , Hou J. G. , Zhu Qingshi
Published: June 2007

Linear scaling methods provide total energy, but no energy levels and canonical wave functions. From the density matrix computed through the density matrix purification methods, we propose an order-N [O(N)] method for calculating both the energies and wave functions of band edge states, which are important for optical properties and chemical reactions. In addition, we also develop an O(N) algorithm to deal with doped semiconductors based on the O(N) method for band edge states calculation. We illustrate the O(N) behavior of the new method by applying it to boron nitride (BN) nanotubes and BN nanotubes with an adsorbed hydrogen atom. The band gap of various BN nanotubes are investigated systematically and the acceptor levels of BN nanotubes with an isolated adsorbed H atom are computed. Our methods are simple, robust, and especially suited for the application in self-consistent field electronic structure theory.
Nonadditive effects in the mixed trimers of HCl and methanethiol
Authors: Balci Mine , Boylu Özgün , Uras-Aytemiz Nevin
Published: June 2007

Ab initio and density functional theory calculations with aug-cc-pVDZ and aug-cc-pVTZ basis sets have been performed on the HCl–CH3SH dimer and HCl–(CH3SH)2 and (HCl)2–CH3SH trimers. Structures, energetics, and infrared frequencies are calculated. The results are discussed in terms of the cooperativity effect which is a characteristic of H-bonded systems and compared to oxygen-containing analogs of the same trimers, HCl–(CH3OH)2 and (HCl)2–CH3OH, which have been published recently.
Phase behavior of attractive and repulsive ramp fluids: Integral equation and computer simulation studies
Authors: Lomba E. , Almarza N. G. , Martín C. , McBride C.
Published: June 2007

Using computer simulations and a thermodynamically self-consistent integral equation we investigate the phase behavior and thermodynamic anomalies of a fluid composed of spherical particles interacting via a two-scale ramp potential (a hard core plus a repulsive and an attractive ramp) and the corresponding purely repulsive model. Both simulation and integral equation results predict a liquid-liquid demixing when attractive forces are present, in addition to a gas-liquid transition. Furthermore, a fluid-solid transition emerges in the neighborhood of the liquid-liquid transition region, leading to a phase diagram with a somewhat complicated topology. This solidification at moderate densities is also present in the repulsive ramp fluid, but in this case inhibits the fluid-fluid separation.
Short-range structure of β-V2D: Pair distribution function analysis of x-ray and neutron diffraction
Authors: Itoh Keiji , Fukunaga Toshiharu
Published: June 2007

X-ray and neutron diffraction experiments using pair distribution function (PDF) analysis were used to elucidate the short-range structure of β-V2D. The PDF obtained by x-ray diffraction indicated the displacement of the vanadium atoms from the ideal body-centered-tetragonal lattice positions; the displacement was evaluated to be 0.008(2) nm. Reverse Monte Carlo simulation based on x-ray and neutron PDFs was also used to determine the locations of the deuterium atoms. Results suggest that the deuterium atoms are displaced from the centers of the octahedral sites and are surrounded by four vanadium atoms at equal average distances.
Depolarized light scattering versus optical Kerr effect. II. Insight into the dynamic susceptibility of molecular liquids
Authors: Brodin Alexander , Rössler Ernst A.
Published: June 2007

We have previously discussed [J. Chem. Phys. 125, 114502 (2006)] that optical Kerr effect (OKE) and depolarized light scattering (DLS) data of molecular liquids reveal, each in their native domain, the same characteristic signatures of the glass transition dynamics; in particular, the intermediate power law of OKE is equivalent with the excess wing of the frequency-domain data, long since known in dielectric spectroscopy. We now extend the discussion to show that the excess wing is an equally common feature in DLS. We further discuss the time-temperature superposition property of OKE data in relation to our DLS and literature dielectric-spectroscopic results, and the merits of their mode coupling theory analyses. Spectroscopic signatures of a liquid-crystal-forming system (nematogen) are discussed in the same frame.
Diffusion lengths of silicon solar cells from luminescence images
Authors: Würfel P. , Trupke T. , Puzzer T. , Schäffer E. , Warta W. , Glunz S. W.
Published: June 2007

A method for spatially resolved measurement of the minority carrier diffusion length in silicon wafers and in silicon solar cells is introduced. The method, which is based on measuring the ratio of two luminescence images taken with two different spectral filters, is applicable, in principle, to both photoluminescence and electroluminescence measurements and is demonstrated experimentally by electroluminescence measurements on a multicrystalline silicon solar cell. Good agreement is observed with the diffusion length distribution obtained from a spectrally resolved light beam induced current map. In contrast to the determination of diffusion lengths from one single luminescence image, the method proposed here gives absolute values of the diffusion length and, in comparison, it is much less sensitive to lateral voltage variations across the cell area as caused by local variations of the series resistance. It is also shown that measuring the ratio of two luminescence images allows distinguishing shunts or surface defects from bulk defects.
Microstructural analysis of Ga(NAs)/GaP heterostructures
Authors: Németh I. , Torunski T. , Kunert B. , Stolz W. , Volz K.
Published: June 2007

We have investigated the microstructure of compressively strained Ga(NAs)/GaP quantum wells (QWs) with different N contents. This material system is a promising candidate for future integration of photonics on silicon substrates. N-induced microscopic strain fields are detected applying strain sensitive transmission electron microscopy dark-field (DF-TEM) imaging. Exceeding 7% of N concentration, we find a deterioration of the upper QW interface despite a reduction of the macroscopic strain for compositions with increasing N content. These nitrogen-induced structural characteristics of the ternary alloy are presumably correlated with the optical properties as observed by photoluminescence spectroscopy.
Development of advanced x-ray imaging crystal spectrometer utilizing a large area segmented proportional counter for KSTAR
Authors: Lee S. G. , Bak J. G. , Nam U. W. , Moon M. K. , Cheon J. K.
Published: June 2007

An advanced x-ray imaging crystal spectrometer (XICS) for KSTAR tokamak has been developed by utilizing a segmented two dimensional (2D) position-sensitive multiwire proportional counter. The XICS for the KSTAR tokamak provides time-resolved measurements of the radial ion and electron temperature profiles, toroidal plasma rotation velocity, and ionization equilibrium. The segmented 2D detector with delay-line readout and supporting electronics has been adopted to improve the photon count rate capability. The current fabrication status of the XICS for the KSTAR tokamak and the first performance test results of the prototype segmented 2D detector are presented.
Determination of the R-line luminescence spatial resolution of a near-field optical spectroscopy system for piezospectroscopy
Authors: Tomimatsu T. , Kagawa Y. , Clarke D. R.
Published: June 2007

The spatial resolution of a near-field optical spectroscopy system in the R-line photoluminescence mode has been evaluated to assess the resolution with which stress measurements can be made by piezospectroscopy. The effect of the probe tip–sample distance as well as the aperture size of the near-field probe on the luminescence R-line intensity was obtained. The luminescence intensity was found to increase linearly with the third power of the aperture size, whereas the lateral spatial resolution was proportional to the aperture size. These findings are consistent with a simple model for the electric dipole moment interaction between the tip and the sample. The minimum lateral spatial resolution was found to be 160nm using the smallest available aperture size of ∼100nm. Images of the stress distribution in a polycrystalline alumina are presented, showing variations at this scale.
Real time spectroscopic ellipsometry on ultrathin (<50Å) hydrogenated amorphous silicon films on Si(100) and GaAs(100)
Authors: van den Oever P. J. , van de Sanden M. C. M. , Kessels W. M. M.
Published: June 2007

Real time spectroscopic ellipsometry was used to determine the time evolution of the dielectric function, bulk thickness, and surface roughness during hot-wire chemical vapor deposition of hydrogenated amorphous silicon (a-Si:H). The amorphous silicon films were deposited on native-oxide-covered c-Si(100) and GaAs(100) substrates at temperatures in the range from 70to350°C. Data analysis by a three layer optical model, consisting of substrate, bulk, and surface roughness layer, revealed that the dielectric function of the a-Si:H film changes in the initial growth regime (d<50Å), which can be attributed to a higher optical band gap for films with a smaller thickness. It is argued that the origin of this higher band gap lies most likely in quantum confinement effects of the electron wave function in the ultrathin film, with possibly a small contribution of a higher hydrogen content in the ultrathin film. In addition, we show that the trends in surface roughness and bulk thickness are only marginally affected, regardless of whether the change in dielectric function with film thickness is incorporated in the data analysis.
Charge trapping and retention behaviors of Ge nanocrystals distributed in the gate oxide near the gate synthesized by low-energy ion implantation
Authors: Yang M. , Chen T. P. , Wong J. I. , Ng C. Y. , Liu Y. , Ding L. , Fung S. , Trigg A. D. , Tung C. H. , Li C. M.
Published: June 2007

A layer of Ge nanocrystals (nc-Ge) distributed in the gate oxide near the gate of a metal-oxide-semiconductor structure is synthesized with low-energy Ge ion implantation followed by thermal annealing at 800°C. The behaviors of charge trapping and charge retention in the nc-Ge have been studied. For a positive charging voltage, only electron trapping occurs, and the trapped electrons show a long retention time. However, for a negative charging voltage, both the hole trapping and electron trapping occur simultaneously, and the hole trapping is dominant if the magnitude of the charging voltage is small or the charging time is short. Due to the relatively easier loss of the trapped holes, the net charge trapping in the nc-Ge exhibits a continuous shift toward a more negative value with the waiting time.
Solid solubility of Ir and Rh at the Co sites of skutterudites
Authors: Shi X. , Zhou Z. , Zhang W. , Chen L. D. , Yang J. , Uher C.
Published: June 2007

Phase diagrams for skutterudite solid solutions made by alloying at the Co site of CoSb3 skutterudite structure are studied by density functional theory. A limited solid solubility is observed for IrxCo1−xSb3 and RhxCo1−xSb3, showing good agreement with experimental reports. A correlation between solubility and material preparation procedure is discussed. A simple method to synthesize skutterudite nanocomposites is proposed. Our calculations also demonstrate that IrxRh1−xSb3 is a compound with ordered structure rather than a random solid solution.
Charge- and orbital-ordering patterns in Bi1∕2Sr1∕2MnO3 thin films studied by Raman scattering
Authors: Kawasaki T. , Ogimoto Y. , Ogawa N. , Miyano K. , Tamaru H. , Izumi M.
Published: June 2007

Polarized Raman spectroscopy has been applied for Bi1∕2Sr1∕2MnO3 thin films on SrTiO3(001) substrate in order to clarify the charge- and orbital-ordering patterns. From the mode assignment on the basis of group theoretical analysis and the lattice dynamical calculations previously reported, it is concluded that the conventional checkerboard charge-order model is more appropriate than the Zener polaron model. It is also confirmed that the major peaks are activated by charge and orbital ordering from the comparison between the temperature dependence of the intensity of the (1120) superlattice reflection peak in synchrotron x-ray powder diffraction and that of the intensity of the phonon peaks observed in the Raman spectra.
Lasing characteristics of GaSb∕GaAs self-assembled quantum dots embedded in an InGaAs quantum well
Authors: Tatebayashi J. , Khoshakhlagh A. , Huang S. H. , Balakrishnan G. , Dawson L. R. , Huffaker D. L. , Bussian D. A. , Htoon H. , Klimov V.
Published: June 2007

The authors report the optical characteristics of GaSb∕GaAs self-assembled quantum dots (QDs) embedded in an InGaAs quantum well (QW). Variations in the In composition of the QW can significantly alter the emission wavelength up to 1.3μm and emission efficiency. Lasing operation at room temperature is obtained from a 2-mm-long device containing five stacked GaSb QDs in In0.13Ga0.87As QWs at 1.026μm with a threshold current density of 860A∕cm2. The probable lasing transition involves electrons and holes confined in the QW and QDs, respectively, resulting in a large peak modal gain of 45cm−1. A significant blueshift of the electroluminescence peak is observed with increased injection current and suggests a type-II band structure.
Graphitization of polymer surfaces by low-energy ion irradiation
Authors: Lazareva I. , Koval Y. , Alam M. , Strömsdörfer S. , Müller P.
Published: June 2007

The surface of several polymers was graphitized by low-energy ion irradiation. Their conducting properties were studied as a function of the energy of the ions and the irradiation temperature. It was found that at rather modest ion energies (∼1000eV) and irradiation temperatures (<400°C), polymer surfaces transform to a graphitized state. The graphitized layer consists of overlapping graphite islands with a diameter of 1–3nm and exhibits a semimetallic conductivity. Gradually reducing the energy of the ions and the irradiation temperature, the authors observed a transition from semimetallic to variable range hopping conductivity.
Above room-temperature operation of InAs∕AlGaSb superlattice quantum cascade lasers emitting at 12μm
Authors: Ohtani K. , Moriyasu Y. , Ohnishi H. , Ohno H.
Published: June 2007

The authors report on above-room-temperature operation of InAs∕AlGaSb quantum cascade lasers emitting at 12μm. The laser structures are grown on a n-InAs (100) substrate using solid-source molecular beam epitaxy. An InAs∕AlGaSb superlattice is used as an active part and an InAs double plasmon waveguide is used for optical confinement. Results show that increased doping concentration in the injection part of the active region expands the current operation range of the devices, allowing laser operation at and above room temperature. The observed threshold current density is 4.0kA∕cm2 at 300K; the maximum operation temperature is 340K.
Study of ferroelectric and reproducible bistable switching properties in CdMnS thin films for nonvolatile memory applications
Authors: Lee J. C. , Subramaniam N. G. , Lee J. W. , Kang T. W.
Published: June 2007

CdMnS thin films grown on indium tin oxide substrate exhibit a ferroelectric property. The remnant polarization of CdMnS films was around 0.025μC∕cm2 for 10% of manganese with a sustained polarization endurance for several cycles. Persisting and highly reproducible bistable switching of about five orders in magnitude between low and high impedance states was observed in current voltage measurements. Nondestructive readout measurement with a short pulse width of 20μs resulted in a resistance difference of two orders between two read levels with a good retention time. Possible use of CdMnS for nonvolatile memory applications is explored.
Soil amendments modify phosphate sorption in an acid soil: the importance of P source (KH2PO4, TSP, DAP)
Authors: Schefe C. R. , Patti A. F. , Clune T. S. , Jackson W. R.
Published: June 2007

Soil acidity is a widespread problem in Victoria, Australia, affecting at least 4 million ha of agricultural land. Soil amendments such as lime and organic materials may ameliorate acid soils, resulting in raised soil pH and increased availability of plant nutrients such as phosphorus (P). The addition of lime, lignite, and compost significantly modified P sorption in an acid soil, with the degree of change highly dependent upon the source of P applied. The application of 2.5 t/ha of lime increased P sorption for all P sources, while P sorption was decreased in the lignite and compost treatments when di-ammonium phosphate (DAP) was applied. Lime and compost addition increased the solution pH, with no change in pH in the lignite treatment. Addition of TSP decreased the pH in all treatments, while DAP addition only increased solution pH in the untreated soil and the lignite treatment. The addition of soil amendments had a significant effect on solution cation concentrations, due to both the influx of cations, and the resultant changes in solution pH. The source of P applied (KH2PO4, TSP (triple superphosphate), DAP) also had a significant effect due to both the counter-ions present and the pH of each P source (e.g. TSP pH 2.7; DAP pH 7.4). The lignite treatment decreased total P sorption relative to the other amendments. The combination of lignite and DAP resulted in both the greatest decrease in P sorption, and the formation of soluble Al–organic complexes. Therefore, a combination of lignite and DAP may be of use in decreasing P sorption in acid soils.
Converting reactive iron, reactive aluminium, and phosphorus retention index (PRI) to the phosphorus buffering index (PBI) for sandy soils of south-western Australia
Authors: Bolland M. D. A. , Windsor D. P.
Published: June 2007

The recently developed phosphorus (P) buffering index (PBI) is now the national single-point P sorption index to rank the capacity of soil to sorb P. However, before PBI was developed, P sorption was routinely measured by 2 simple procedures in Western Australia: (i) since the mid 1970s, reactive iron (Fe), which is the concentration of Fe extracted from soil by ammonium oxalate; and (ii) since the mid 1980s, the P retention index (PRI), a single-point P sorption index. Both reactive Fe and aluminium (Al) extracted from soil by ammonium oxalalate (reactive Al) have been measured in experiments conducted in Western Australia. Because PBI is now routinely measured in Western Australia there is the need to convert historical reactive Fe, reactive Al, and PRI values to PBI values. In this study we used soil samples collected from 2 field studies and a study of 96 paddocks, all on sandy soil types common in the region, to measure PBI, reactive Fe, reactive Al (not measured in the paddock study), and PRI. We related PBI (dimensionless), as the dependent (y-axis), to reactive Fe (mg/kg), reactive Al (mg/kg), or PRI (mL/g), as the independent (x-axis). The relationships for all data were good for reactive Al (47 data points from the 2 field studies) and PRI (133 data points for the 2 field studies and the paddock study):

-->
However, the relationships was poor for reactive Fe (133 data points) and differed for each of the 2 field studies and the paddock study, so no consistent, reliable approach for converting reactive Fe to PBI values could be determined. We recommend that reactive Fe is no longer used in the region, and that only PBI is used to estimate P sorption.
Occurrence of Angiostrongylus species (Nematoda) in populations of Rattus rattus and Rattus fuscipes in coastal forests of south-eastern Australia
Authors: Stokes Vicki L. , Spratt David M. , Banks Peter B. , Pech Roger P. , Williams Richard L.
Published: June 2007

The distributions of the introduced nematode parasite, Angiostrongylus cantonensis, and the native Angiostrongylus mackerrasae in Australia are poorly understood. We sampled rodents and/or their faeces, and intermediate gastropod hosts for the presence of Angiostrongylus species in coastal forests surrounding Jervis Bay in south-eastern Australia. We found A. cantonensis in populations of introduced Rattus rattus in forests to the north of Jervis Bay, and A. mackerrasae in native Rattus fuscipes in forests to the south of Jervis Bay. The apparent geographical separation of these lungworm species may be a consequence of host specificity and negative associations between R. rattus and R. fuscipes that results from interspecific competition. A. cantonensis was regularly found in R. rattus or their faeces across 9 of 12 study sites north of Jervis Bay, and three species of snail common to the area were suitable intermediate hosts. This has potential negative implications for native wildlife and human visitors to these forests, because A. cantonensis infection causes zoonotic disease (neuro-angiostrongyliasis) in humans and a wide range of bird and mammal hosts. Management of pest rodents in the study area is warranted.
Propagation of olfactory information in
Drosophila
Authors: Root Cory M. , Semmelhack Julia L. , Wong Allan M. , Flores Jorge , Wang Jing W.
Published: June 2007

Investigating how information propagates between layers in the olfactory system is an important step toward understanding the olfactory code. Each glomerular output projection neuron (PN) receives two sources of input: the olfactory receptor neurons (ORNs) of the same glomerulus and interneurons that innervate many glomeruli. We therefore asked how these inputs interact to produce PN output. We used receptor gene mutations to silence all of the ORNs innervating a specific glomerulus and recorded PN activity with two-photon calcium imaging and electrophysiology. We found evidence for balanced excitatory and inhibitory synaptic inputs but saw little or no response in the absence of direct ORN input. We next asked whether any transformation of activity occurs at successive layers of the antennal lobe. We found a strong link between PN firing and dendritic calcium elevation, the latter of which is tightly correlated with calcium activity in ORN axons, supporting the idea of glomerular propagation of olfactory information. Finally, we showed that odors are represented by a sparse population of PNs. Together, these results are consistent with the idea that direct receptor input provides the main excitatory drive to PNs, whereas interneurons modulate PN output. Balanced excitatory and inhibitory interneuron input may provide a mechanism to adjust PN sensitivity.
LEKTI Fragments Specifically Inhibit KLK5, KLK7, and KLK14 and Control Desquamation through a pH-dependent Interaction
Authors: Deraison Celine , Bonnart Chrystelle , Lopez Frederic , Besson Celine , Robinson Ross , Jayakumar Arumugam , Wagberg Fredrik , Brattsand Maria , Hachem Jean Pierre , Leonardsson Goran , Hovnanian Alain
Published: June 2007

LEKTI is a 15-domain serine proteinase inhibitor whose defective expression underlies the severe autosomal recessive ichthyosiform skin disease, Netherton syndrome. Here, we show that LEKTI is produced as a precursor rapidly cleaved by furin, generating a variety of single or multidomain LEKTI fragments secreted in cultured keratinocytes and in the epidermis. The identity of these biological fragments (D1, D5, D6, D8–D11, and D9–D15) was inferred from biochemical analysis, using a panel of LEKTI antibodies. The functional inhibitory capacity of each fragment was tested on a panel of serine proteases. All LEKTI fragments, except D1, showed specific and differential inhibition of human kallikreins 5, 7, and 14. The strongest inhibition was observed with D8–D11, toward KLK5. Kinetics analysis revealed that this interaction is rapid and irreversible, reflecting an extremely tight binding complex. We demonstrated that pH variations govern this interaction, leading to the release of active KLK5 from the complex at acidic pH. These results identify KLK5, a key actor of the desquamation process, as the major target of LEKTI. They disclose a new mechanism of skin homeostasis by which the epidermal pH gradient allows precisely regulated KLK5 activity and corneodesmosomal cleavage in the most superficial layers of the stratum corneum.
An Elaborate Classification of SNARE Proteins Sheds Light on the Conservation of the Eukaryotic Endomembrane System
Authors: Kloepper Tobias H. , Kienle C. Nickias , Fasshauer Dirk
Published: June 2007

Proteins of the SNARE (soluble N-ethylmalemide–sensitive factor attachment protein receptor) family are essential for the fusion of transport vesicles with an acceptor membrane. Despite considerable sequence divergence, their mechanism of action is conserved: heterologous sets assemble into membrane-bridging SNARE complexes, in effect driving membrane fusion. Within the cell, distinct functional SNARE units are involved in different trafficking steps. These functional units are conserved across species and probably reflect the conservation of the particular transport step. Here, we have systematically analyzed SNARE sequences from 145 different species and have established a highly accurate classification for all SNARE proteins. Principally, all SNAREs split into four basic types, reflecting their position in the four-helix bundle complex. Among these four basic types, we established 20 SNARE subclasses that probably represent the original repertoire of a eukaryotic cenancestor. This repertoire has been modulated independently in different lines of organisms. Our data are in line with the notion that the ur-eukaryotic cell was already equipped with the various compartments found in contemporary cells. Possibly, the development of these compartments is closely intertwined with episodes of duplication and divergence of a prototypic SNARE unit.
Penalized and weightedK-means for clustering with scattered objects and prior information in high-throughput biological data
Authors: Tseng George C.
Published: June 2007

Motivation: Cluster analysis is one of the most important data mining tools for investigating high-throughput biological data. The existence of many scattered objects that should not be clustered has been found to hinder performance of most traditional clustering algorithms in such a high-dimensional complex situation. Very often, additional prior knowledge from databases or previous experiments is also available in the analysis. Excluding scattered objects and incorporating existing prior information are desirable to enhance the clustering performance.

Results: In this article, a class of loss functions is proposed for cluster analysis and applied in high-throughput genomic and proteomic data. Two major extensions from K-means are involved: penalization and weighting. The additive penalty term is used to allow a set of scattered objects without being clustered. Weights are introduced to account for prior information of preferred or prohibited cluster patterns to be identified. Their relationship with the classification likelihood of Gaussian mixture models is explored. Incorporation of good prior information is also shown to improve the global optimization issue in clustering. Applications of the proposed method on simulated data as well as high-throughput data sets from tandem mass spectrometry (MS/MS) and microarray experiments are presented. Our results demonstrate its superior performance over most existing methods and its computational simplicity and extensibility in the application of large complex biological data sets.

Availability:  http://www.pitt.edu/~ctseng/research/software.html

Contact:  ctseng@pitt.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
A novel and major association ofHLA-Cin Graves' disease that eclipses the classicalHLA-DRB1effect
Authors: Simmonds Matthew J. , Howson Joanna M.M. , Heward Joanne M. , Carr-Smith Jackie , Franklyn Jayne A. , Todd John A. , Gough Stephen C.L.
Published: June 2007

Association of the major histocompatibility complex (MHC) class II-encoded HLA-DRB1-DQA1-DQB1 haplotype with Graves' disease (GD) has been known for several years. Recent evidence from other autoimmune diseases has suggested that the HLA class I encoded HLA-B/-C molecules could be conferring HLA-DRB1-DQA1-DQB1 independent effects on disease. The aim of this study was to determine the effect of HLA-B and HLA-C in GD in a white ethnic group of 806 patients with GD and 487 control subjects from the UK. Of the five loci (HLA-B, -C, -DRB1, -DQA1, -DQB1), HLA-C demonstrated the strongest association (P = 1.20 × 10−20) with HLA-C*07 predisposing [OR = 1.63, 95% CI (1.23–2.17)] and both HLA-C*03 [OR = 0.54, 95% CI (0.38–0.77)], HLA-C*16 [OR = 0.36, 95% CI (0.21–0.61)] protective. The other loci were then tested for HLA-C-independent associations. HLA-B was found to be associated independently of HLA-C (P = 1.54 × 10−6) with the other three loci, HLA-DRB1, HLA-DQB1 and HLA-DQA1, also improving the model but with less confidence (P > 10−5). This study has for the first time provided evidence of a primary association of HLA-C, and to a lesser extent HLA-B, with GD. Class II loci could still have effects on GD, but they appear smaller than the HLA-C association. A full investigation of the MHC region, including all class I and II loci is now required. Our results point to a primary role for class I-mediated responses in GD, a condition classically assumed to be a straightforward HLA-class II-restricted autoantibody response to the thyroid stimulating hormone receptor.
What does integrability of finite-gap or soliton potentials mean?
Authors: Brezhnev Yurii V
Published: June 2007

In the example of the Schrödinger/KdV equation, we treat the theory as equivalence of two concepts of Liouvillian integrability: quadrature integrability of linear differential equations with a parameter (spectral problem) and Liouville's integrability of finite-dimensional Hamiltonian systems (stationary KdV equations). Three key objects in this field—new explicitΨ-function, trace formula and the Jacobi problem—provide a complete solution. TheΘ-function language is derivable from these objects and used for ultimate representation of a solution to the inversion problem. Relations with non-integrable equations are also discussed.
Filling of artificial lateral canals and microleakage and flow of five endodontic sealers
Authors: Almeida J. F. A. , Gomes B. P. F. A. , Ferraz C. C. R. , Souza‐Filho F. J. , Zaia A. A.
Published: June 2007

Aim  To evaluate the flow characteristics of AH Plus, Epiphany Root Canal Sealant, Endométhasone, Pulp Canal Sealer (EWT) and Sealapex and their ability to fill artificial lateral canals and prevent microleakage.

Methodology  Flow of the sealers was analysed using the American Dental Association (ADA) 57 and the International Standards Organization (ISO) 6876 specifications. Two lateral canals were produced in the middle and apical third of 64 roots using 0.1 mm cylindrical drills. Lateral condensation of gutta‐percha or Resilon and one or other of the sealers were used to fill the root canals. Buccal‐lingual digital radiographs were exposed. After the sealer had set, the roots were immersed in Indian ink and cleared in methyl salicylate. The extent of filling and dye penetration were measured on the buccal and lingual root surfaces under 30× magnification with a stereoscope.

Results  AH Plus, Epiphany and Pulp Canal Sealer (EWT) complied with ADA 57 and ISO 6876 specifications. Sealapex complied with the ADA 57 specification but not with ISO 6876. Endométhasone did not comply with either specification. Filling of lateral canals was similar for the five sealers tested. Dye leakage demonstrated that AH Plus, Epiphany and Sealapex permitted less leakage than Pulp Canal Sealer (EWT) (P < 0.05).

Conclusions  All the sealers flowed into the 0.1 mm artificial lateral canals. AH Plus, Epiphany and Sealapex allowed less linear leakage than Pulp Canal Sealer (EWT). The flow of Endométhasone did not comply with either ADA 57 or ISO 6876 specifications and Sealapex did not comply with ISO 6876.
Seen but not heard: a systematic review of the place of the child in 21st‐century dental research
Authors: MARSHMAN ZOE , GIBSON BARRY J. , OWENS JANINE , RODD HELEN D. , MAZEY HUW , BAKER SARAH R. , BENSON PHILIP E. , ROBINSON PETER G.
Published: June 2007

Background.  The position of children in society has changed with increasing emphasis on children's rights and child‐centred services. This study aimed to describe the extent to which contemporary oral health research has been conducted with or on children.

Design.  A systematic review of the child dental literature from 2000–2005 was conducted. A purposive sample was used to develop categories describing the level of involvement of children in research. Four main categories were developed: children as the objects of research, proxies used on behalf of children, children as the subjects of research with some involvement and children as active participants with their perspectives explored.

Electronic databases were searched and exclusion criteria applied. Each of the resulting papers was examined and categorised. The frequency distribution in each category and the distribution of these categories according to subject were calculated.

Results.  The search revealed 3266 papers after application of the exclusion criteria. Of these, 87.1% were categorised as research where children were used as objects, 5.7% were found to involve proxies (parents or clinicians), 7.0% involved children to some extent and 0.3% involved children actively.

Conclusion.  Most oral health research is conducted on children, in future research should strive to be conducted with children, involving them as fully as possible.
Caries experience in a severely obese adolescent population
Authors: BAILLEUL‐FORESTIER ISABELLE , LOPES KARINE , SOUAMES MOURAD , AZOGUY‐LEVY SYLVIE , FRELUT MARIE‐LAURE , BOY‐LEFEVRE MARIE‐LAURE
Published: June 2007

Aim.  The present study assessed caries experience in an adolescent population being treated for severe obesity. The DMFT indices of a group of obese adolescents (n = 41) and a group of nonobese adolescents (n = 41) were compared.

Design.  The parameters examined in this transversal study were body mass index (BMI) and the number of decayed, missing, and filled teeth (DMFT). The obese and nonobese groups were matched by age, gender, and parental socio‐occupational category. Differences between the two groups were assessed using nonparametric tests.

Results.  There was a significant association between BMI and DMFT indices (P = 0.01) in the severely obese group. The obese adolescents were more likely to have caries than the nonobese ones.

Conclusions.  The severely obese children (n = 16) had a high level of caries experience. Given the tremendous increase in the prevalence of obesity in children, dentists should promote a healthy diet not only to prevent dental decay but also to reduce the risk for obesity. Dentists should participate in multidisciplinary medical teams managing obese adolescents.
Rapid detection of Actinobacillus actinomycetemcomitans using a loop‐mediated isothermal amplification method
Authors: Osawa R. , Yoshida A. , Masakiyo Y. , Nagashima S. , Ansai T. , Watari H. , Notomi T. , Takehara T.
Published: June 2007

Introduction:  Actinobacillus actinomycetemcomitans has been implicated in the etiology of aggressive periodontitis. In this study, we applied a novel nucleic acid amplification method, called loop‐mediated isothermal amplification (LAMP), which amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions, allowing the rapid detection of A. actinomycetemcomitans.

Methods:  We designed the primers for detecting A. actinomycetemcomitans and evaluated the specificity and sensitivity of the assay.

Results:  The LAMP primers used in this study successfully amplified serotypes a–e of A. actinomycetemcomitans, while other oral bacteria were not amplified. By measuring the precipitation of magnesium pyrophosphate, we could quantify the chromosomal DNA of A. actinomycetemcomitans. The detection limits using the real‐time turbidimetry analysis were 5.8 × 102–5.8 × 107 copies of A. actinomycetemcomitans template DNA per reaction tube. In addition, the LAMP assay was used for the rapid detection of A. actinomycetemcomitans in clinical specimens from eight individuals. The results with the LAMP method were similar to those using conventional polymerase chain reaction.

Conclusion:  Our results suggest that the LAMP‐based assay is very useful for the rapid detection of A. actinomycetemcomitans.
Quantification and characterization of Synergistes in endodontic infections
Authors: Vianna M. E. , Conrads G. , Gomes B. P. F. A. , Horz H. P.
Published: June 2007

Introduction:  Bacterial species belonging to the poorly characterized division Synergistes have recently been reported in endodontic infections, and therefore may be part of the etiology of periradicular diseases. The objective of this study was to characterize and quantify the predominant Synergistes phylotypes in infected root canals.

Methods:  We analyzed 32 necrotic teeth, each from a different patient, with radiographic evidence of apical periodontitis and with primary endodontic infections.

Results:  Using real‐time quantitative polymerase chain reaction based on Synergistes‐specific primers, seven of the 32 cases were found to be positive. Comparative sequence analysis showed that each of the seven samples was infected by one numerically dominant phylotype. Diversity among phylotypes was such that they could be grouped into three major evolutionary branches within the Synergistes division. The size of the total Synergistes population ranged from 4.5 × 104 to 1.5 × 106 16S rRNA gene copies, and the median proportion accounted for 0.79% of the total bacterial community. For comparison, we also quantified such recognized endodontic pathogens as Prevotella intermedia, Porphyromonas gingivalis, and Treponema. The first two species were found in five and nine cases, respectively, with a median proportion below 0.01%, while Treponema was found in 18 cases with a median proportion of 1.48%.

Conclusion:  Thus, the prevalence and quantity of Synergistes was clearly within the range of the other analyzed pathogens, suggesting their clinical relevance in endodontic infections. Furthermore, the diversity of Synergistes found at the diseased sites designates infected root canals as an important human ecosystem providing several unique micro‐niches for this novel group of bacteria.
α‐Synuclein involvement in hippocampal synaptic plasticity: role of NO, cGMP, cGK and CaMKII
Authors: Liu Shumin , Fa Mauro , Ninan Ipe , Trinchese Fabrizio , Dauer William , Arancio Ottavio
Published: June 2007

Synaptic plasticity involves a series of coordinate changes occurring both pre‐ and postsynaptically, of which α‐synuclein is an integral part. We have investigated on mouse primary hippocampal neurons in culture whether redistribution of α‐synuclein during plasticity involves retrograde signaling activation through nitric oxide (NO), cGMP, cGMP‐dependent protein kinase (cGK) and calmodulin‐dependent protein kinase II. We have found that deletion of the α‐synuclein gene blocks both the long‐lasting enhancement of evoked and miniature transmitter release and the increase in the number of functional presynaptic boutons evoked through the NO donor, DEA/NO, and the cGMP analog, 8‐Br‐cGMP. In agreement with these findings both DEA/NO and 8‐Br‐cGMP were capable of producing a long‐lasting increase in number of clusters for α‐synuclein through activation of soluble guanylyl cyclase, cGK and calcium/calmodulin‐dependent protein kinase IIα. Thus, our results suggest that NO, cGMP, GMP‐dependent protein kinase and calmodulin‐dependent protein kinase II play a key role in the redistribution of α‐synuclein during plasticity.