bluuebunny/crossref_metadata_2025 huggingface dataset:
Pharmacokinetic‐pharmacodynamic modelling ofS(−)‐atenolol in rats: reduction of isoprenaline‐induced tachycardia as a continuous pharmacodynamic endpoint
Authors: van Steeg T J , Freijer J , Danhof M , de Lange E C M
Published: April 2007

Background and purpose:

For development of mechanism‐based pharmacokinetic‐pharmacodynamic (PK‐PD) models, continuous recording of drug effects is essential. We therefore explored the use of isoprenaline in the continuous measurement of the cardiovascular effects of antagonists of β‐adrenoceptors (β‐blockers). The aim was to validate heart rate as a pharmacodynamic endpoint under continuous isoprenaline‐induced tachycardia by means of PK‐PD modelling ofS(−)‐atenolol.

Experimental approach:

Groups of WKY rats received a 15 min iv infusion of 5 mg kg−1S(−)‐atenolol, with or without iv infusion of 5 μg kg−1h−1isoprenaline. Heart rate was continuously monitored and blood samples were taken.

Key results:

A three‐compartment model best described the pharmacokinetics ofS(−)‐atenolol. The PK–PD relationship was described by a sigmoid Emax model and an effect compartment was used to resolve the observed hysteresis. In the group without isoprenaline, the variability in heart rate (30 b.p.m.) approximated the maximal effect (Emax=43±18 b.p.m.), leaving the parameter estimate of potency (EC50=28±27 ng ml−1) unreliable. Both precise and reliable parameter estimates were obtained during isoprenaline‐induced tachycardia: 517±13 b.p.m. (E0), 168±15 b.p.m. (Emax), 49±14 ng ml−1(EC50), 0.042±0.012 min−1(keo) and 0.95±0.34 (n).

Conclusions and implications:

Reduction of heart rate during isoprenaline‐induced tachycardia is a reliable pharmacodynamic endpoint for β‐blockersin vivoin rats. Consequently this experimental approach will be used to investigate the relationship between drug characteristics andin vivoeffects of different β‐blockers.

British Journal of Pharmacology(2007)151, 356–366; doi:10.1038/sj.bjp.0707234
Thromboxane A2inhibition of SKCaafter NO synthase block in rat middle cerebral artery
Authors: McNeish A J , Garland C J
Published: April 2007

Background and purpose:

NO/prostanoid independent, EDHF‐mediated hyperpolarization and dilation in rat middle cerebral arteries is mediated solely by endothelial cell IKCa. However, when the NO‐pathway is also active, both SKCaand IKCacontribute to EDHF responses. As the SKCacomponent can be inhibited by stimulation of thromboxane A2(TxA2) TP receptors and NO has the potential ability to inhibit thromboxane synthesis, we investigated whether TxA2might explain loss of functional input from SKCaduring NOS inhibition in cerebral arteries.

Experimental approach:

Rat middle cerebral arteries were mounted in a wire myograph. Endothelium‐dependent responses to the PAR2 agonist, SLIGRL were assessed as simultaneous changes in smooth muscle membrane potential and tension.

Key results:

Responses were obtained in the presence ofL‐NAME as appropriate. Inhibition of TP receptors with either ICI 192,605 or SQ 29,548, did not affect EDHF mediated hyperpolarization and relaxation, but in their presence neither TRAM‐34 nor apamin (to block IKCaand SKCarespectively) individually affected the EDHF response. However, in combination they virtually abolished it. Similar effects were obtained in the presence of the thromboxane synthase inhibitor, furegrelate, which additionally revealed an iberiotoxin‐sensitive residual EDHF hyperpolarization and relaxation in the combined presence of TRAM‐34 and apamin.

Conclusions and implications:

In the rat middle cerebral artery, inhibition of NOS leads to a loss of the SKCacomponent of EDHF responses. Either antagonism of TP receptors or block of thromboxane synthase restores an input through SKCa. These data indicate that NO normally enables SKCaactivity in rat middle cerebral arteries.

British Journal of Pharmacology(2007)151, 441–449; doi:10.1038/sj.bjp.0707240
GW3965, a synthetic liver X receptor (LXR) agonist, reduces angiotensin II‐mediated pressor responses in Sprague–Dawley rats
Authors: Leik C E , Carson N L , Hennan J K , Basso M D , Liu Q‐Y , Crandall D L , Nambi P
Published: April 2007

Background and purpose:

Liver X receptors (LXRs) activate genes that regulate lipid and cholesterol metabolism. LXR agonists were shown recently to also increase murine renin gene expression in vivo. To further examine a link between lipid metabolism, the renin‐angiotensin‐aldosterone‐system and blood pressure regulation, we investigated the effect of a LXR agonist (GW3965) on angiotensin II (Ang II)‐mediated vasoreactivity and vascular angiotensin II receptor (ATR) gene expression.

Experimental approach:

Arterial blood pressure (BP) was measured during Ang II infusions (1.5 min duration; 0.001–3 μg kg−1) in pentobarbital‐anesthetized male Sprague–Dawley rats (n = 6‐9) after oral administration of GW3965 (10 mg kg−1, q.d.) or vehicle for 7 – 15 days. Mesenteric arteries and plasma were collected to analyze ATR gene expression and to measure plasma renin activity (PRA) and lipid profile, respectively.

Key results:

Basal mean arterial pressure (MAP) was similar between groups. GW3965 dosing blunted the vasopressor effect of Ang II, which was significantly different with the 0.3 and 3 μg kg−1 doses. No difference in heart rate, PRA or lipid profile was observed between groups. A time‐course indicated that ATR type 1 and 2 gene expression of GW3965‐treated vs. vehicle‐treated rats decreased by 50%, reaching significance for ATR type 2, but not for ATR type 1, at time‐points coinciding with BP measurements.

Conclusions and implications:

GW3965 decreased Ang II‐mediated vasopressor responses coincident with a trend toward reduced ATR gene expression, suggesting that LXR agonists could affect vascular reactivity.

British Journal of Pharmacology (2007) 151, 450–456; doi:10.1038/sj.bjp.0707241
Mathematical models of cytotoxic T‐lymphocyte killing
Authors: Regoes Roland R , Yates Andrew , Antia Rustom
Published: April 2007

By killing infected host cells, cytotoxic T lymphocytes (CTL) mediate an important defense mechanism against viruses and other intracellular pathogens. Quantitative aspects of this killing process have been studied for several decades in vitro. More recently, methods have been developed to measure the timescales of CTL killing in vivo. Here, we review the estimates of kinetic rates involved in CTL killing which were obtained in these studies, and elaborate on the differences between them.
Common Pitfalls and Issues during Generic Licensing Negotiations
Authors: Clark Guy , DiCicco Richard L.
Published: April 2007

This paper is about the key points of debate in generic licensing agreements, considering the objectives of the licensor and licensee. It offers compromise solutions that should help business development professionals in the generic industry in the portion of their job requiring negotiations as licensor and licensee, with the common objective to bring affordable medicines to those who need them, while increasing profits.
Monoenergetic and GeV ion acceleration from the laser breakout afterburner using ultrathin targets
Authors: Yin L. , Albright B. J. , Hegelich B. M. , Bowers K. J. , Flippo K. A. , Kwan T. J. T. , Fernández J. C.
Published: April 2007

A new laser-driven ion acceleration mechanism using ultrathin targets has been identified from particle-in-cell simulations. After a brief period of target normal sheath acceleration (TNSA) [S. P. Hatchett et al., Phys. Plasmas 7, 2076 (2000)], two distinct stages follow: first, a period of enhanced TNSA during which the cold electron background converts entirely to hot electrons, and second, the “laser breakout afterburner” (BOA) when the laser penetrates to the rear of the target where a localized longitudinal electric field is generated with the location of the peak field co-moving with the ions. During this process, a relativistic electron beam is produced by the ponderomotive drive of the laser. This beam is unstable to a relativistic Buneman instability, which rapidly converts the electron energy into ion energy. This mechanism accelerates ions to much higher energies using laser intensities comparable to earlier TNSA experiments. At a laser intensity of 1021W∕cm2, the carbon ions accelerate as a quasimonoenergetic bunch to 100s of MeV in the early stages of the BOA with conversion efficiency of order a few percent. Both are an order of magnitude higher than those realized from TNSA in recent experiments [Hegelich et al., Nature 441, 439 (2006)]. The laser-plasma interaction then evolves to produce a quasithermal energy distribution with maximum energy of ∼2GeV.
Inhomogeneities in spin states and magnetization reversal of geometrically identical elongated Co rings
Authors: Gao X. S. , Adeyeye A. O. , Goolaup S. , Singh N. , Jung W. , Castaño F. J. , Ross C. A.
Published: April 2007

The magnetic configurations and magnetic reversal processes in arrays of geometrically identical rounded rectangular Co rings have been investigated. Magnetic imaging reveals a range of configurations, including diagonal onion, horseshoe onion, and vortex states. Reversal from the onion to the vortex state can occur via different routes involving domain wall motion within the rings, and the mechanism depends on the applied field orientation.
Vacancy mediated ferromagnetic interaction in TiO2 doped with magnetic ions
Authors: Cohen G. , Fleurov V. , Kikoin K.
Published: April 2007

We extend the model of ferromagnetic superexchange in dilute magnetic semiconductors to the ferromagnetically ordered highly insulating compounds (dilute magnetic dielectrics). The intrinsic ferromagnetism without free carriers is observed in oxygen-deficient films of anatase TiO2 doped with the transition metal impurities in cation sublattice. We suppose that ferromagnetic order arises due to superexchange between the complexes [oxygen vacancies+magnetic impurities], which are stabilized by a charge transfer from the vacancies to impurities. The Hund rule controls the superexchange via the empty vacancy related levels in the energy gap, so that it becomes possible only for the parallel orientation of impurity magnetic moments. The percolation threshold for magnetic ordering is determined by the radius of vacancy levels, but the exchange mechanism does not require free carriers. The crucial role of the nonstoichiometry in the formation of the ferromagnetism makes the Curie temperature extremely sensitive to the methods of sample preparation.
Sampling diffusive transition paths
Authors: Miller Thomas F. , Predescu Cristian
Published: April 2007

The authors address the problem of sampling double-ended diffusive paths. The ensemble of paths is expressed using a symmetric version of the Onsager-Machlup formula, which only requires evaluation of the force field and which, upon direct time discretization, gives rise to a symmetric integrator that is accurate to second order. Efficiently sampling this ensemble requires avoiding the well-known stiffness problem associated with the sampling of infinitesimal Brownian increments of the path, as well as a different type of stiffness associated with the sampling of the coarse features of long paths. The fine-feature sampling stiffness is eliminated with the use of the fast sampling algorithm, and the coarse-feature sampling stiffness is avoided by introducing the sliding and sampling (S&S) algorithm. A key feature of the S&S algorithm is that it enables massively parallel computers to sample diffusive trajectories that are long in time. The authors use the algorithm to sample the transition path ensemble for the structural interconversion of the 38-atom Lennard-Jones cluster at low temperature.
Jahn-Teller effect in tetrahedral symmetry: Large-amplitude tunneling motion and rovibronic structure of CH4+ and CD4+
Authors: Wörner H. J. , Qian X. , Merkt F.
Published: April 2007

The energy level structures of the ground vibronic states of C12H4+, C13H4+, and C12D4+ have been measured by pulsed-field-ionization zero-kinetic-energy photoelectron spectroscopy. The nuclear spin symmetries of the tunneling-rotational levels have been determined in double-resonance experiments via selected rotational levels of the v3=1 and v3=2 vibrational levels of the X̃A11 ground state of CH4. The energy level structures of C12H4+, C13H4+, and C12D4+ have been analyzed with an effective tunneling-rotational Hamiltonian. The analysis together with a group theoretical treatment of the T⊗(e+t2) Jahn-Teller effect in the Td(M) group prove that the equilibrium geometry of C12H4+, C13H4+, and C12D4+ has C2v symmetry and characterize the pseudorotational dynamics in these fluxional cations. The tunneling behavior is discussed in terms of the relevant properties of the potential energy surface, some of which have been recalculated at the CCSD(T)/cc-pVTZ level of ab initio theory.
Random sequences with power-law correlations exhibit proteinlike behavior
Authors: Mamasakhlisov Yevgeni Sh. , Hayryan Shura , Hu Chin-Kun
Published: April 2007

We use a replica approach to investigate the thermodynamic properties of the random heteropolymers with persistent power-law correlations in monomer sequence. We show that this type of sequences possess proteinlike properties. In particular, we show that they can fold into stable unique three-dimensional structure (the “native” structure, in protein terminology) through two different types of pathways. One is a fast folding pathway and leads directly to the native structure. Another one, a more slower pathway, passes through the microphase separated (MPS) state and includes a number of intermediate glassy states. The scale and the magnitude of the MPS are calculated. The frozen state can be reached only by sequences with weak long-range correlations. The critical value for the correlation exponent is found, above which (strong correlations) freezing is impossible.
Effect of different sodium halides on the self-association of tertiary butanol in water
Authors: Momo Jeufack Hervé , Suter Dieter
Published: April 2007

The molecular self-association of hydrophobic substances is an important process for many biological systems. Here, the authors study the effect of salt on the molecular self-association of t-butanol in water solution, using NMR techniques. They compare the effects of different sodium halides (NaCl, NaBr, and NaI) as a function of their concentration.
Molecular dynamics simulation of thermal transport at a nanometer scale constriction in silicon
Authors: Saha Sanjoy K. , Shi Li
Published: April 2007

To better understand thermal transport at nanoscale point contacts such as the tip-sample contact of a scanning probe microscope and at the contact between a nanotube and a planar surface, we have used a nonequilibrium molecular dynamics (MD) method to calculate the temperature distribution and thermal resistance of a nanometer scale constriction formed between two planar silicon substrates of different temperatures. Surface reconstruction was observed at the two free silicon surfaces and at the constriction. The radius of the heated zone in the cold substrate was found to approach a limit of about 20 times the average nearest-neighbor distance of boron doping atoms when the constriction radius (a) is reduced below the interdopant distance. The phonon mean free path at the constriction was found to be suppressed by diffuse phonon-surface scattering and phonon-impurity scattering. The MD thermal resistance is close to the ballistic resistance when a is larger than 1nm, suggesting that surface reconstruction does not reduce the phonon transmission coefficient significantly. When a is 0.5nm and comparable to the dominant phonon wavelength, however, the MD result is considerably lower than the calculated ballistic resistance because bulk phonon dispersion and bulk potential are no longer accurate. The MD thermal resistance of the constriction increases slightly with increasing doping concentration due to the increase in the diffusive resistance.
Properties of dominant electron trap center in n-type SiC epilayers by means of deep level transient spectroscopy
Authors: Asghar M. , Hussain I. , Noor H. S. , Iqbal F. , Wahab Q. , Bhatti A. S.
Published: April 2007

Characterization of dominant electron trap in as-grown SiC epilayers has been carried out using deep level transient spectroscopy. Two electron traps E1 and Z1 at Ec−0.21 and Ec−0.61 are observed, respectively; Z1 being the dominant level. Line shape fitting, capture cross section, and insensitivity with doping concentration have revealed interesting features of Z1 center. Spatial distribution discloses that the level is generated in the vicinity of epilayers∕substrate interface and the rest of the overgrown layers is defect-free. Owing to the Si-rich growth conditions, the depth profile of Z1 relates it to carbon vacancy. The alpha particle irradiation transforms Z1 level into Z1∕Z2 center involving silicon and carbon vacancies. Isochronal annealing study further strengthens the proposed origin of the debated level.
Potential distribution theorem for the polymer-induced depletion between colloidal particles
Authors: Li Zhidong , Wu Jianzhong
Published: April 2007

The authors investigated the polymer-mediated colloidal interactions in a good solvent wherein the particle size varies from that much smaller than the polymer radius of gyration up to macroscopic and the polymer concentration varies from that corresponding to a dilute solution to that close to a melt. At conditions directly accessible to molecular simulations, the theoretical predictions agree favorably with the simulation results for the distributions of polymer segments and for the polymer-mediated colloidal interactions. The theoretical methods were then exploited to examine the polymer structure and colloidal interactions when the particle∕polymer size ratio changes from the “protein” limit to the “colloid” limit at different regimes of the polymer concentration (i.e., dilute, semidilute, and concentrated). The authors found that the surface curvature plays a significant role on the distribution of polymer segments near the particle surface at low polymer concentration, but this effect diminishes as the polymer concentration increases. The Derjaguin approximation works reasonably well at high polymer concentration even in the protein limit, but it may fail qualitatively at low polymer concentration where the polymer-induced colloidal force becomes long range.
Large-scale molecular dynamics simulation of magnetic properties of amorphous iron under pressure
Authors: Ma Pui-Wai , Liu W. C. , Woo C. H. , Dudarev S. L.
Published: April 2007

We perform large-scale molecular dynamics simulations to study the magnetic properties of amorphous iron under pressure. Simulations, exceeding by at least two orders of magnitude those accessible to density functional calculations, use the recently developed magnetic interatomic potential for iron. The distributions of the size of atomic magnetic moments and parameters characterizing the structure of amorphous iron, such as radial distribution functions, are calculated as a function of the applied hydrostatic stress. As the density increases, there is a reduction in the magnitude of the mean magnetic moment of individual atoms, accompanied by the transformation of an increasing proportion of atoms from a magnetic to a nonmagnetic configuration. Beyond a critical density the proportion of nonmagnetic atoms increases sharply, yet homogeneously. The local magnetic moment of an atom correlates with the local Voronoi volume via a logarithmic relation. In addition, we observe a complex dependence of the local magnetic moment on the topological arrangement of neighboring atoms.
Structural evolution and characterization of heteroepitaxial GaSb thin films on Si(111) substrates
Authors: Nguyen Thang , Varhue Walter , Cross Michael , Pino Robinson , Adams Edward , Lavoie Mark , Lee Jaichan
Published: April 2007

This paper describes the structural evolution and characterization of heteroepitaxial GaSb thin films on Si(111) substrates. The growth process used a combination of atomic sources which included the rf sputtering of Sb and the thermal effusion of Ga. The formation of crystalline GaSb thin films required that initially a monolayer thick Sb buffer layer be applied directly to a clean H-passivated Si(111) substrate surface. The resulting film was characterized by high resolution x-ray diffraction, Rutherford backscattering spectrometry, transmission electron microscopy, secondary ion mass spectroscopy, and atomic force microscopy (AFM). The AFM images were taken from the material after several periods of growth to determine the evolution of crystal structure with thickness. Atomic force microscopy images of the film surface showed that the heteroepitaxial layers were formed via the Stranski-Krastanov growth mechanism. This result is consistent with the heteroepitaxial growth of systems representing large differences in lattice constant. The hole mobility and carrier concentration in the deposited material were determined by the Hall measurement, performed at room temperature and on a 140nm thick sample, to be 66cm2∕Vsec and 3×1019cm−3, respectively. The carrier mobility was relatively low as expected for measurements taken at room temperature.
Study of the B″B¯Σu+1 state of H2: Transition probabilities from the ground state, dissociative widths, and Fano parameters
Authors: Glass-Maujean M. , Klumpp S. , Werner L. , Ehresmann A. , Schmoranzer H.
Published: April 2007

The transition probabilities, the dissociation widths, and the associated Fano parameters for rovibronic lines with J″=0,…,3 of the absorption bands of the B″B¯Σu+1 state out of the XΣg+1 v″=0 ground state were measured over the complete vibrational progression, showing clearly that only the inner-well state with B″ 4pσ character can absorb vuv light and predissociate efficiently. The absolute values of these transition probablities, predissociation widths, and Fano parameters were found to agree well with ab initio calculations if one takes into account that the calculations neglect nonadiabatic couplings.
Source and sink potentials for the description of open systems with a stationary current passing through
Authors: Goyer Francois , Ernzerhof Matthias , Zhuang Min
Published: April 2007

The authors present a model Hamiltonian for the description of open systems that exchange probability current density with their surroundings. The complex potentials appearing in this Hamiltonian act as source and sink, respectively, of probability current density. The primary applications of the theory of source and sink potentials are molecular electronic devices (MEDs), in the description of which the semi-infinite contacts are replaced by complex potentials. This is done in a rigorous manner, i.e., the exact wave function is recovered in the interior of the MED. To illustrate the approach, certain prototypical molecular conductors are considered in the Hückel approximation. The authors show that, for the examples considered, there exist almost isolated molecular states in the continuum of contact states that manifest themselves as Fano resonances in the transmission probability. The findings are confirmed by density functional theory calculations that also yield the predicted molecular states that are nearly decoupled from the contacts.
Extending molecular dynamics time scales with milestoning: Example of complex kinetics in a solvated peptide
Authors: West Anthony M. A. , Elber Ron , Shalloway David
Published: April 2007

A recently introduced computational algorithm to extend time scales of atomically detailed simulations is illustrated. The algorithm, milestoning, is based on partitioning the dynamics to a sequence of trajectories between “milestones” and constructing a non-Markovian model for the motion along a reaction coordinate. The kinetics of a conformational transition in a blocked alanine is computed and shown to be accurate, more efficient than straightforward molecular dynamics by a factor of about 9, and nonexponential. A general scaling argument predicts a linear speedup with the number of milestones for diffusive processes and an exponential speedup for transitions over barriers. The algorithm is also trivial to parallelize. As a side result, milestoning also produces the free energy profile along the reaction coordinate and is able to describe nonequilibrium motions along one (or a few) degrees of freedom.
Edge effects in an electrochemical reaction: HCOOH oxidation on a Pt ribbon
Authors: Lee Jaeyoung , Christoph Johannes , Noh Taegeun , Eiswirth Markus , Ertl Gerhard
Published: April 2007

The use of a ribbon-shaped Pt electrode gives rise to edge effects of the interfacial potential, as is predicted from the potential theory in the form of the corresponding reaction-migration equation. They are studied in the bistable region of formic acid oxidation. Essentially, the edges tend to be more passive than the bulk of the electrode, which also causes a passivation (activation) transition to originate from the edges (center) of the ribbon. The experimental results are in agreement with simulations of the reaction-migration system.
Energy level alignment at metal/organic semiconductor interfaces: “Pillow” effect, induced density of interface states, and charge neutrality level
Authors: Vázquez H. , Dappe Y. J. , Ortega J. , Flores F.
Published: April 2007

A unified model, embodying the “pillow” effect and the induced density of interface states (IDIS) model, is presented for describing the level alignment at a metal/organic interface. The pillow effect, which originates from the orthogonalization of the metal and organic wave functions, is calculated using a many-body linear combination of atomic orbitals Hamiltonian, whereby electron long-range interactions are obtained using an expansion in the metal/organic wave function overlap, while the electronic charge of both materials remains unchanged. This approach yields the pillow dipole and represents the first effect induced by the metal/organic interaction, resulting in a reduction of the metal work function. In a second step, we consider how charge is transferred between the metal and the organic material by means of the IDIS model: Charge transfer is determined by the relative position of the metal work function (corrected by the pillow effect) and the organic charge neutrality level, as well as by an interface parameter S, which measures how this potential difference is screened. In our approach, we show that the combined IDIS-pillow effects can be described in terms of the original IDIS alignment corrected by a screened pillow dipole. For the organic materials considered in this paper, we see that the IDIS dipole already represents most of the realignment induced at the metal/organic interface. We therefore conclude that the pillow effect yields minor corrections to the IDIS model.
Strong Aharonov-Bohm oscillations in GaAs two-dimensional holes
Authors: Habib B. , Tutuc E. , Shayegan M.
Published: April 2007

The authors measured Aharonov-Bohm resistance oscillations [Phys. Rev. 115, 485 (1959)] in a shallow two-dimensional GaAs hole ring structure, defined by local anodic surface oxidation. The amplitude of the oscillations is about 10% of the ring resistance, the strongest seen in a hole system. In addition the authors observe resistance oscillations as a function of front gate bias at zero magnetic field. They authors discuss the results in light of spin interference in the ring and possible applications to spintronics.
Bipolar charge transport in an organic photorefractive composite
Authors: Salvador Michael , Gallego-Gomez Francisco , Köber Sebastian , Meerholz Klaus
Published: April 2007

The authors report on tuning the near-infrared holographic recording speed in a poly(N-vinylcarbazole) based photorefractive composite by illuminating it at a wavelength of very strong absorption. Due to the small penetration depth of the light under these conditions this approach allows to flood the material with charge carriers from the side of the sample. Even at light levels much stronger than the write beams, this additional illumination does allow for grating recording. However, under these conditions competition between positive and negative charges leads to sign inversion of the two-beam coupling gain coefficient during recording. An improvement of the recording speed is demonstrated.
Origin of the slow photoresponse in an individual sol-gel synthesized ZnO nanowire
Authors: Ahn Seung-Eon , Ji Hyun Jin , Kim Kanghyun , Kim Gyu Tae , Bae Chang Hyun , Park Seung Min , Kim Yong-Kwan , Ha Jeong Sook
Published: April 2007

Photocurrent of a single ZnO nanowire synthesized by a sol-gel route was investigated. In vacuum, the dark current was bigger but the photoresponse was slower than that in air, attributed to the release of the available charge carriers by the desorption of water molecules and the decrease of the exchange rates of molecular ions. Under the steady radiation of the ultraviolet light (λ=325nm), a gradual decrease of the photocurrent was noticeable, which can be explained in terms of the annihilation of the carriers by the replacement of hydroxyl groups (OH−) by O2−, resulting in the decrease of charge carriers.
Significant enhancement of Si oxidation rate at low temperatures by atmospheric pressure Ar∕O2 plasma
Authors: Kakiuchi Hiroaki , Ohmi Hiromasa , Harada Makoto , Watanabe Heiji , Yasutake Kiyoshi
Published: April 2007

Using stable atmospheric pressure plasma, the effect of inert gas (He, Ar, and Kr) mixed with O2 on the oxidation process of Si(001) wafers was investigated. Ar∕O2 plasma was shown capable of generating atomic oxygen most efficiently and significantly enhanced the oxidation rate in comparison with He∕O2 plasma, while Kr∕O2 plasma was not suitable for the low-temperature and high-rate oxidation of Si. As a result, by using Ar∕O2 plasma, oxide layers having equivalent quality to that by He∕O2 plasma could be formed with a drastically high initial oxidation rate of 28.0nm∕min.
Two-dimensional analytical Mott-Gurney law for a trap-filled solid
Authors: Chandra W. , Ang L. K. , Pey K. L. , Ng C. M.
Published: April 2007

The letter presents a two-dimensional analytical model of the space charge limited (SCL) current injection in a solid with exponentially distributed trap energy state. By considering that the electrons are injected from an infinitely long emission strip of width W, the one-dimensional SCL current density is enhanced by a factor of 1+F(4∕π)∕(W∕L), where F=1∕(l+2) measures the mean position of the injected electrons in the solid of length L, and l is the ratio of the distribution of the traps to the free carriers. The analytical formula is verified by using a two-dimensional device simulator.
Improvement of thermal stability and composition changes of atomic layer deposited HfO2 on Si by in situ O3 pretreatment
Authors: Park Tae Joo , Kim Jeong Hwan , Seo Min Ha , Jang Jae Hyuck , Hwang Cheol Seong
Published: April 2007

The influence of thick (1.4nm) and thin (0.6nm) SiO2 interfacial layers grown by an O3 predeposition treatment during atomic layer deposition of high-k HfO2 films on the thermal stability and chemical structure of the film was investigated. It was found that the HfO2/thick SiO2 stack maintained a good thermal stability up to the postdeposition annealing at 1000°C because Hf silicate formation was accompanied by the consumption of the interfacial SiO2 layer. On the other hand, the HfO2/thin SiO2 layer stack showed an inferior stability because Hf silicate was formed by enhanced Si diffusion from the Si substrate during the same postdeposition annealing.
Thermally stable luminescence of KSrPO4:Eu2+ phosphor for white light UV light-emitting diodes
Authors: Tang Yu-Sheng , Hu Shu-Fen , Lin Chun Che , Bagkar Nitin C. , Liu Ru-Shi
Published: April 2007

A novel blue phosphor based on phosphate host matrix, KSrPO4 doped with Eu2+, was prepared by solid state reaction. The phosphor invariably emits blue luminescence with a peak wavelength at 424nm under ultraviolet excitation at 360nm. Eu2+-doped KSrPO4 phosphors show higher thermally stable luminescence which was found to be better than commercially available Y3Al5O12:Ce3+ phosphor at temperature higher than 225°C.
Semen quality detection using time of flight and acoustic wave sensors
Authors: Newton M. I. , Evans C. R. , Simons J. J. , Hughes D. C.
Published: April 2007

The authors report a real-time technique for assessing the number of motile sperm in a semen sample. The time of flight technique uses a flow channel with detection at the end of the channel using quartz crystal microbalances. Data presented suggest that a simple rigid mass model may be used in interpreting the change in resonant frequency using an effective mass for the sperm.
Low thermal conductivity of the negative thermal expansion material, HfMo2O8
Authors: Kennedy Catherine A. , White Mary Anne , Wilkinson Angus P. , Varga Tamas
Published: April 2007

The thermal conductivity of the cubic polymorph of hafnium molybdate, HfMo2O8, was determined over the temperature range of 2–400K. The values of thermal conductivity were low (0.64±0.15Wm−1K−1 at T=300K for a fully dense sample), with a positive temperature coefficient throughout the temperature range examined. Calculations of the theoretical minimum thermal conductivity and the effective phonon mean free path show that the heat-carrying phonons are nearly fully coupled in HfMo2O8, consistent with the rather large magnitude of its Grüneisen parameter. The low-frequency optic modes which lead to negative thermal expansion in HfMo2O8 are likely responsible for the low thermal conductivity.
Direct measurements of the lifetimes of longitudinal optical phonon modes and their dynamics in InN
Authors: Tsen K. T. , Kiang Juliann G. , Ferry D. K. , Lu Hai , Schaff William J. , Lin Hon-Way , Gwo Shangjr
Published: April 2007

Longitudinal optical phonons in InN have been studied by time-resolved Raman spectroscopy on a subpicosecond time scale. The lifetimes of both the A1(LO) and E1(LO) phonons have been directly measured. From the temperature dependence of their lifetimes, the authors demonstrate that both phonons decay primarily into a large wave vector TO phonon and a large wave vector TA/LA phonon, consistent with the accepted phonon dispersion relationship for wurtzite InN.
Mutation of the MAP kinase DYF-5 affects docking and undocking of kinesin-2 motors and reduces their speed in the cilia of
Caenorhabditis elegans
Authors: Burghoorn Jan , Dekkers Martijn P. J. , Rademakers Suzanne , de Jong Ton , Willemsen Rob , Jansen Gert
Published: April 2007

In the cilia of the nematode
Caenorhabditis elegans
, anterograde intraflagellar transport (IFT) is mediated by two kinesin-2 complexes, kinesin II and OSM-3 kinesin. These complexes function together in the cilia middle segments, whereas OSM-3 alone mediates transport in the distal segments. Not much is known about the mechanisms that compartmentalize the kinesin-2 complexes or how transport by both kinesins is coordinated. Here, we identify DYF-5, a conserved MAP kinase that plays a role in these processes. Fluorescence microscopy and EM revealed that the cilia of
dyf-5
loss-of-function (lf) animals are elongated and are not properly aligned into the amphid channel. Some cilia do enter the amphid channel, but the distal ends of these cilia show accumulation of proteins. Consistent with these observations, we found that six IFT proteins accumulate in the cilia of
dyf-5(lf)
mutants. In addition, using genetic analyses and live imaging to measure the motility of IFT proteins, we show that
dyf-5
is required to restrict kinesin II to the cilia middle segments. Finally, we show that, in
dyf-5(lf)
mutants, OSM-3 moves at a reduced speed and is not attached to IFT particles. We propose that DYF-5 plays a role in the undocking of kinesin II from IFT particles and in the docking of OSM-3 onto IFT particles.
A cationic host displaying positive cooperativity in water
Authors: Hughes Andrew D. , Anslyn Eric V.
Published: April 2007

The affinity of guanidinium and Cu(II) containing hosts for polycarboxylate guests is studied in water by using UV-visible spectroscopy and isothermal titration calorimetry. By combining a Cu(II) coordination site and a diguanidinium moiety around a single scaffold it is found that the Gibbs free-energy release upon binding is greater than could be expected based on the sum of the free energy released by the binding functional groups when operating in isolation. This effect is known as positive cooperativity and has rarely been observed with synthetic hosts in water. The isothermal titration calorimetry data suggest that the source of this positive cooperativity is enthalpic in origin. We propose that covalently positioning the cationic binding moieties in close proximity destabilizes the unbound host, and thereby the stabilizing effect of binding the anionic carboxylates is exothermic and also, the source of positive cooperativity observed herein.
A mechanism for transcriptional repression dependent on the BRCA1 E3 ubiquitin ligase
Authors: Horwitz Andrew A. , Affar El Bachir , Heine George F. , Shi Yang , Parvin Jeffrey D.
Published: April 2007

Loss of function of the tumor suppressor protein BRCA1 is responsible for a high percentage of familial and also sporadic breast cancers. Early work identified a stimulatory transcriptional coactivator function for the BRCA1 protein, and more recently, BRCA1 has been implicated in transcriptional repression, although few examples of repressed genes have been characterized. We recently used an
in vitro
transcription assay to identify a biochemical mechanism that explained the BRCA1 stimulatory activity. In this study, we identified an ubiquitin-dependent mechanism by which BRCA1 inhibits transcription. BRCA1 ubiquitinates the transcriptional preinitiation complex, preventing stable association of TFIIE and TFIIH, and thus blocks the initiation of mRNA synthesis. What is striking about this mechanism of regulation by BRCA1 is that the ubiquitination of the preinitiation complex is not targeting proteins for degradation by the proteasome, nor are ubiquitin receptors modifying the activity, but rather the ubiquitin moiety itself interferes with the assembly of basal transcription factors at the promoter. Using RNAi to knockdown expression of the endogenous BRCA1 protein, we assessed the level of repression dependent on BRCA1 in the cell, and we found that BRCA1 is at least as significant a transcriptional repressor as it is an activator. These results define a biochemical mechanism by which the BRCA1 enzymatic activity regulates a key cellular process.
SGT1 is essential for Nod1 activation
Authors: da Silva Correia Jean , Miranda Yvonne , Leonard Nikki , Ulevitch Richard
Published: April 2007

The Nod-like receptor family in man contains proteins that recognize invasive bacteria. Nod1, a member of this family, is activated by specific peptidoglycan-derived muropeptides that contain meso-diaminopimelic acid. Plants contain a large family of proteins known as resistance (R) proteins that have common structural features with the Nod-like receptors and are essential for protection against a variety of plant pathogens. Extensive genetic studies have shown that the R protein function is determined by multiple proteins including SGT1, Rar1, and HSP90. Here we show that SGT1 positively regulates Nod1 activation. Depletion of SGT1 with siRNA did not affect stability of Nod1 protein or of downstream signaling molecules but did prevent multiple cellular responses associated with Nod1 activation. In contrast, depletion of the mammalian orthologue of Rar1, Chp1, had no effect on Nod1-dependent cellular activation. Finally, depletion of HSP90 or addition of a pharmacologic inhibitor of HSP90 resulted in loss of Nod1 protein. Thus, we show common regulatory pathways in plant R protein and human Nod1-dependent pathways and provide the basis for understanding the Nod1 pathway.
Quantifying the genetic influence on mammalian vascular tree structure
Authors: Glenny Robb , Bernard Susan , Neradilek Blazej , Polissar Nayak
Published: April 2007

The ubiquity of fractal vascular trees throughout the plant and animal kingdoms is postulated to be due to evolutionary advantages conferred through efficient distribution of nutrients to multicellular organisms. The implicit, and untested, assertion in this theory is that the geometry of vascular trees is heritable. Because vascular trees are constructed through the iterative use of signaling pathways modified by local factors at each step of the branching process, we sought to investigate how genetic and nongenetic influences are balanced to create vascular trees and the regional distribution of nutrients through them. We studied the spatial distribution of organ blood flow in armadillos because they have genetically identical littermates, allowing us to quantify the genetic influence. We determined that the regional distribution of blood flow is strongly correlated between littermates (
r
2
= 0.56) and less correlated between unrelated animals (
r
2
= 0.36). Using an ANOVA model, we estimate that 67% of the regional variability in organ blood flow is genetically controlled. We also used fractal analysis to characterize the distribution of organ blood flow and found shared patterns within the lungs and hearts of related animals, suggesting common control over the vascular development of these two organs. We conclude that the geometries of fractal vascular trees are heritable and could be selected through evolutionary pressures. Furthermore, considerable postgenetic modifications may allow vascular trees to adapt to local factors and provide a flexibility that would not be possible in a rigid system.
Geochemical proxies of North American freshwater routing during the Younger Dryas cold event
Authors: Carlson Anders E. , Clark Peter U. , Haley Brian A. , Klinkhammer Gary P. , Simmons Kathleen , Brook Edward J. , Meissner Katrin J.
Published: April 2007

The Younger Dryas cold interval represents a time when much of the Northern Hemisphere cooled from ≈12.9 to 11.5 kiloyears B.P. The cause of this event, which has long been viewed as the canonical example of abrupt climate change, was initially attributed to the routing of freshwater to the St. Lawrence River with an attendant reduction in Atlantic meridional overturning circulation. However, this mechanism has recently been questioned because current proxies and dating techniques have been unable to confirm that eastward routing with an increase in freshwater flux occurred during the Younger Dryas. Here we use new geochemical proxies (ΔMg/Ca, U/Ca, and
87
Sr/
86
Sr) measured in planktonic foraminifera at the mouth of the St. Lawrence estuary as tracers of freshwater sources to further evaluate this question. Our proxies, combined with planktonic δ
18
O
seawater
and δ
13
C, confirm that routing of runoff from western Canada to the St. Lawrence River occurred at the start of the Younger Dryas, with an attendant increase in freshwater flux of 0.06 ± 0.02 Sverdrup (1 Sverdrup = 10
6
m
3
·s
−1
). This base discharge increase is sufficient to have reduced Atlantic meridional overturning circulation and caused the Younger Dryas cold interval. In addition, our data indicate subsequent fluctuations in the freshwater flux to the St. Lawrence River of ≈0.06–0.12 Sverdrup, thus explaining the variability in the overturning circulation and climate during the Younger Dryas.
Fronts and pulses in an enzymatic reaction catalyzed by glucose oxidase
Authors: Míguez David G. , Vanag Vladimir K. , Epstein Irving R.
Published: April 2007

Waves and patterns in living systems are often driven by biochemical reactions with enzymes as catalysts and regulators. We present a reaction–diffusion system catalyzed by the enzyme glucose oxidase that exhibits traveling wave patterns in a spatially extended medium. Fronts and pulses propagate as a result of the coupling between the enzyme-catalyzed autocatalytic production and diffusion of hydrogen ions. A mathematical model qualitatively explains the experimental observations.
Omics-based identification of
Arabidopsis
Myb transcription factors regulating aliphatic glucosinolate biosynthesis
Authors: Hirai Masami Yokota , Sugiyama Kenjiro , Sawada Yuji , Tohge Takayuki , Obayashi Takeshi , Suzuki Akane , Araki Ryoichi , Sakurai Nozomu , Suzuki Hideyuki , Aoki Koh , Goda Hideki , Nishizawa Osamu Ishizaki , Shibata Daisuke , Saito Kazuki
Published: April 2007

Understanding plant metabolism as an integrated system is essential for metabolic engineering aimed at the effective production of compounds useful to human life and the global environment. The “omics” approach integrates transcriptome and metabolome data into a single data set and can lead to the identification of unknown genes and their regulatory networks involved in metabolic pathways of interest. One of the intriguing, although poorly described metabolic pathways in plants is the biosynthesis of glucosinolates (GSLs), a group of bioactive secondary products derived from amino acids that are found in the family Brassicaceae. Here we report the discovery of two R2R3-Myb transcription factors that positively control the biosynthesis of GSLs in
Arabidopsis thaliana
by an integrated omics approach. Combined transcriptome coexpression analysis of publicly available, condition-independent data and the condition-specific (i.e., sulfur-deficiency) data identified
Myb28
and
Myb29
as candidate transcription factor genes specifically involved in the regulation of aliphatic GSL production. Analysis of a knockout mutant and ectopic expression of the gene demonstrated that
Myb28
is a positive regulator for basal-level production of aliphatic GSLs.
Myb29
presumably plays an accessory function for methyl jasmonate-mediated induction of a set of aliphatic GSL biosynthetic genes. Overexpression of
Myb28
in
Arabidopsis
-cultured suspension cells, which do not normally synthesize GSLs, resulted in the production of large amounts of GSLs, suggesting the possibility of efficient industrial production of GSLs by manipulation of these transcription factors. A working model for regulation of GSL production involving these genes, renamed
Production of Methionine-Derived Glucosinolate
(
PMG
)
1
and
2
, are postulated.
Algorithm for model validation: Theory and applications
Authors: Sornette D. , Davis A. B. , Ide K. , Vixie K. R. , Pisarenko V. , Kamm J. R.
Published: April 2007

Validation is often defined as the process of determining the degree to which a model is an accurate representation of the real world from the perspective of its intended uses. Validation is crucial as industries and governments depend increasingly on predictions by computer models to justify their decisions. We propose to formulate the validation of a given model as an iterative construction process that mimics the often implicit process occurring in the minds of scientists. We offer a formal representation of the progressive build-up of trust in the model. Thus, we replace static claims on the impossibility of validating a given model by a dynamic process of constructive approximation. This approach is better adapted to the fuzzy, coarse-grained nature of validation. Our procedure factors in the degree of redundancy versus novelty of the experiments used for validation as well as the degree to which the model predicts the observations. We illustrate the methodology first with the maturation of quantum mechanics as the arguably best established physics theory and then with several concrete examples drawn from some of our primary scientific interests: a cellular automaton model for earthquakes, a multifractal random walk model for financial time series, an anomalous diffusion model for solar radiation transport in the cloudy atmosphere, and a computational fluid dynamics code for the Richtmyer–Meshkov instability.