DOI
string | abstract
string | title
string | author
list | URL
string | year
int64 | month
string | vector
list |
|---|---|---|---|---|---|---|---|
10.1063/1.1483369
|
<jats:p>In SrRuO3/PbZr0.52Ti0.48O3/SrRuO3 multilayer thin films on SrTiO3 substrates the different lattice distortion behavior of the top and the bottom SrRuO3 film layer is found and characterized by means of transmission electron microscopy. The bottom SrRuO3 layer is compressively strained in the film plane by a constraint of the SrTiO3 substrate. In contrast, in the interface area of the top SrRuO3 layer, a lattice dilatation is measured not only in the film plane but also parallel to the film normal. The misfit strain, the lead interdiffusion and the oxygen concentration in this area are investigated and discussed as possible reasons for the unexpected lattice dilatation along the film normal direction.</jats:p>
|
Lattice strain and lattice expansion of the SrRuO3 layers in SrRuO3/PbZr0.52Ti0.48O3/SrRuO3 multilayer thin films
|
[
"Jia C. L. ",
"Contreras J. Rodrı́guez ",
"Poppe U. ",
"Kohlstedt H. ",
"Waser R. ",
"Urban K. "
] |
https://doi.org/10.1063/1.1483369
| 2,002 |
July
|
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] |
10.1063/1.1483373
|
<jats:p>Two powerful synchrotron x-ray scattering techniques for residual strain depth-profiling and tomography-like scatter-intensity profiling of materials are presented. The techniques utilize energy dispersive x-ray scattering, from a fixed microvolume, with microscanning of the specimen being used to profile its interior. The tomography-like profiles exploit scattering-cross-section variations, and can be contrast enhanced by separately monitoring scattering from different crystal structures. The strain profiling technique is shown to finely chronicle the internal strain variation over several mm of steel. Detailed strain profiling for a cantilever spring demonstrates the interplay of residual and external stresses in elastic/plastic deformation. Since surface compression, by shot peening, is a classic method to fortify against fatigue failure, the strain profile for a shot-peened, surface-toughened material is determined and discussed in terms of a simple elastic–plastic stress/strain model. Finally the lattice strains in a WC/Co coated steel composite material are discussed.</jats:p>
|
Strain field and scattered intensity profiling with energy dispersive x-ray scattering
|
[
"Croft M. ",
"Zakharchenko I. ",
"Zhong Z. ",
"Gurlak Y. ",
"Hastings J. ",
"Hu J. ",
"Holtz R. ",
"DaSilva M. ",
"Tsakalakos T. "
] |
https://doi.org/10.1063/1.1483373
| 2,002 |
July
|
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] |
10.1063/1.1483374
|
<jats:p>We explore the single-band envelope-function model in the entire Brillouin zone for electronic structure calculation of nanostructures that involve semiconductors with one or more significant valleys in the conduction band. Comparison with the numerically more demanding empirical pseudopotential calculation shows reasonably good accuracy of the method described here, which correctly predicts the quantized state energies, splittings in multivalley semiconductor nanostructures, as well as the intersubband transition derived optical properties. This makes it potentially useful for modeling nanostructures and nanodevices based on Si and other materials.</jats:p>
|
Single-band envelope-function model in the full Brillouin zone for electronic structure calculation in semiconductor nanostructures
|
[
"Mirčetić A. ",
"Ikonić Z. ",
"Milanović V. ",
"Indjin D. "
] |
https://doi.org/10.1063/1.1483374
| 2,002 |
July
|
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] |
10.1063/1.1483380
|
<jats:p>Empirical rules are derived that describe the temperature dependence of the infrared absorption spectra of pure diamond for photons of energy hν=500–4000 cm−1. We show that with increasing temperature in the range 14&lt;T&lt;850 K, all the features in the infrared spectrum shift to lower frequency at very similar fractional rates. The rate for all the features is, to ±13%, Δν/ν=cn(Ee) where c=−0.027 and n(Ee) is the Bose–Einstein population factor with Ee=860 cm−1. The intensities of the optical absorption involving the creation of two phonons of energies E1 and E2 are expected to increase with T in proportion to [1+n(E1)][1+n(E2)]. This expression, combined with the fractional shift rule for the energies of each mode, allows high temperature two-phonon spectra to be simulated accurately from a low temperature spectrum. The temperature dependence of the three-phonon band between 2665 and 3900 cm−1 is precisely fitted without adjustable parameters by using the shift rule in conjunction with a modified density of three-phonon states. Absorption at 10.6 μm is shown to involve the simultaneous destruction and creation of phonons. Its strong temperature dependence in the range 300&lt;T&lt;800 K is accurately described, without any adjustable parameters, in terms of three main components: the destruction of one phonon of 335 cm−1 and the creation of a second of 1275 cm−1; the shift to lower energy of the phonons; and a three-phonon process involving the destruction of one and the creation of two phonons. The analysis demonstrates why diamond has to be effectively cooled when used for the windows of a high-power CO2 laser.</jats:p>
|
Temperature dependence of intrinsic infrared absorption in natural and chemical-vapor deposited diamond
|
[
"Piccirillo Clara ",
"Davies Gordon ",
"Mainwood Alison ",
"Scarle Simon ",
"Penchina C. M. ",
"Mollart T. P. ",
"Lewis K. L. ",
"Nesládek M. ",
"Remes Z. ",
"Pickles C. S. J. "
] |
https://doi.org/10.1063/1.1483380
| 2,002 |
July
|
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] |
10.1063/1.1483394
|
<jats:p>A 248 nm KrF excimer laser was used to ablate the yttria stabilized ZrO2 target in vacuum while an intensified charge coupled device camera was used to get the time-resolved side view images of the induced plume/plasma. Two components, plume and plasma, can be clearly distinguished from the images with delay time less than 300 ns. The center of the plasma is found moving along the direction tilted ∼55°, instead of 90°, from the surface of the target while the processing laser came along ∼40°. The movement velocities and the explosion rates of the plasma during the first 2 μs after the laser strike were calculated. Time- and spatial-resolved emission spectra from excited Zr atoms in the plasma have been measured to determine the corresponding excitation temperature. The dynamic evolution of the plasma is outlined based on the experimental results.</jats:p>
|
Diagnostics of nanosecond dynamics of the plasma produced during KrF excimer laser ablation of zirconia in vacuum
|
[
"Li Peng ",
"Lim Daniel ",
"Mazumder Jyoti "
] |
https://doi.org/10.1063/1.1483394
| 2,002 |
July
|
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-0.5035431385040283,
1.1210007667541504,
-0.19001483917236328,
0.24354608356952667,
0.08839115500450134,
0.4898773729801178,
0.8679555654525757,
0.7277445197105408,
-0.7640376091003418,
-0.2229980230331421,
-0.8500997424125671,
0.47652360796928406,
-0.2821497321128845,
0.21693210303783417,
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0.10626983642578125,
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-0.7330832481384277,
1.0399636030197144,
-0.10425498336553574,
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0.2335202842950821,
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0.8152934908866882,
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0.8624127507209778,
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0.9844446778297424,
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0.1068674772977829
] |
10.1063/1.1483852
|
<jats:p>The potential energy surface for methyl cation is calculated using an extrapolated full coupled-cluster/complete basis set (FCC/CBS) theory. The equilibrium C–H bond length is obtained as 1.0884 Å. The vibrational energy levels of both CH3+ and CD3+ cations are computed using a variational method, based on the accurate potential energy surface. The fundamental frequencies in cm−1 are predicted to be 2942.27 (v1), 1377.82 (v2), 3108.29 (v3), and 1387.01 (v4) for CH3+, and 2082.99 (v1), 1070.31 (v2), 2339.99 (v3), and 1015.70 (v4) for CD3+, respectively.</jats:p>
|
Vibrational energy levels of methyl cation
|
[
"Yu Hua-Gen ",
"Sears Trevor J. "
] |
https://doi.org/10.1063/1.1483852
| 2,002 |
July
|
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] |
10.1063/1.1483912
|
<jats:p>Deep-level transient spectroscopy (DLTS) studies on both p-type unintentionally doped and n-type (Si-doped), 1.05 eV band gap InGaAsN grown by molecular-beam epitaxy are reported. Two majority-carrier hole traps were observed in p-type material, H3′ (0.38 eV) and H4′ (0.51 eV), and no evidence was found for the presence of minority-carrier electron traps. In n-type material, we observed a shallow distribution of electron levels, E1′, as well as a deep electron trap E4′ (0.56 eV) and a deep hole trap H5′ (0.71 eV). All DLTS peaks observed were broad and are thus consistent with continuous defect distributions and/or groups of closely spaced discrete energy levels in the band gap. Comparison of the spectra to previously reported spectra of metalorganic chemical vapor deposition-grown InGaAsN of the same composition revealed some similarities and some differences, suggesting that some of the observed deep levels are due to intrinsic physical sources, whereas others are specific to the growth technique used.</jats:p>
|
Deep-level defects in InGaAsN grown by molecular-beam epitaxy
|
[
"Kaplar R. J. ",
"Ringel S. A. ",
"Kurtz Steven R. ",
"Klem J. F. ",
"Allerman A. A. "
] |
https://doi.org/10.1063/1.1483912
| 2,002 |
July
|
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] |
10.1063/1.1484236
|
<jats:p>In this article a numerical method for an electrical data treatment which is aimed to define the key electrical parameters monitoring the thermal and chemical properties of gas discharges, in particular dielectric barrier discharges is presented. Numerous electrical parameters characterize the electrical discharges: pulses onset voltage, pulse number, pulse height, pulse width, power injected in the discharge cell, etc. Our treatment using Matlab® allows us to get such data, as is shown in the present article for a point-to-plane dielectric barrier discharge. Moreover it shows how a separation between the different components of the current signals remaining after the elimination of the capacitive component can be obtained. Much attention is paid, in particular, to the impulsive components (streamers and Trichel pulses components) and on the nonimpulsive ones constituting what we call the pseudocontinuous components, generally ignored in the literature. So four different categories of charges are considered: for the positive voltage alternation, a positive-pulse charge (Qimp+) and a positive pseudocontinuous charge (Qcont+) and for the negative alternation, a negative-pulse charge (Qimp−) and a negative pseudocontinuous charge (Qcont−). The article also intends to show how the main electrical parameters (current charge and power) can be determined by different ways and how to select the best way for representative measurements in every situation.</jats:p>
|
Electrical characterization of gas discharges using a numerical treatment. Application to dielectric barrier discharges
|
[
"Petit M. ",
"Jidenko N. ",
"Goldman A. ",
"Goldman M. ",
"Borra J. P. "
] |
https://doi.org/10.1063/1.1484236
| 2,002 |
July
|
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] |
10.1063/1.1484255
|
<jats:p>A new form of surface junction thermocouple sensor has been developed and tested. The novel feature of the design is the use of a tapered fit between two coaxial thermocouple elements to form a thin, robust junction. The gauge has a response time on the order of 1 μs and is suitable for measuring large transient heat fluxes in hypervelocity wind tunnels. Asymptotic analysis is used to demonstrate the operating principles and to assess the errors associated with the finite thickness of the surface junction. Spectral deconvolution methods are used to infer a mean square optimal estimate of the surface heat flux from time resolved surface temperature measurements. This improved signal processing method is applicable to transient heat flux gauges of all types. Potential reducible error sources and other systematic errors are described. Measurements of the heat flux about the forebody of a cylindrical body in a hypervelocity flow demonstrate the functioning of the gauge and are used to obtain statistical estimates of the repeatability of the technique. The measured heat fluxes are compared with established theoretical predictions.</jats:p>
|
Transient heat flux measurement using a surface junction thermocouple
|
[
"Sanderson S. R. ",
"Sturtevant B. "
] |
https://doi.org/10.1063/1.1484255
| 2,002 |
July
|
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] |
10.1063/1.1484388
|
<jats:p>The ionization and double-ionization spectra of fluorinated carbanions of various chain lengths are compared with those of their corresponding acids. For the acidic systems we find a dramatic relative shift of the double-ionization spectra to higher energies due to the presence of just one additional proton. The impact of the proton on the ionization spectra is also important, but results in only half of the double-ionization spectra’s shift. A molecular electronic decay mechanism is found to be operative in the valence region of the molecules under investigation. The impact of this decay is more substantial for the anions. The threshold for electronic decay (i.e., the first double-ionization potential) is at much lower energy for the anions than for the acids. Interestingly, the localization pattern of the holes in the decay channels is, in contrast to the decay threshold, only a little affected by protonation. We also compare the impact of electron correlation effects on the ionization and double-ionization spectra of the series of fluorinated carbanions and of their acids.</jats:p>
|
Comparison of electronic decay of valence ionized fluorinated carbanions and their acids
|
[
"Müller I. B. ",
"Zobeley J. ",
"Cederbaum L. S. "
] |
https://doi.org/10.1063/1.1484388
| 2,002 |
July
|
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] |
10.1063/1.1485721
|
<jats:p>The equilibrium structure and potential energy surface of magnesium monohydroxide in its ground doublet state, X 2Σ+ MgOH, have been determined from large-scale ab initio calculations using the spin-restricted coupled-cluster method, RCCSD(T), with basis sets of double-through quintuple-zeta quality. The effects of core-electron correlation on the calculated molecular parameters were investigated. The vibrational-rotational energy levels of various MgOH isotopomers were calculated using the variational method. The spectroscopic constants determined are found to be in remarkably good agreement with experimental data.</jats:p>
|
The <i>ab initio</i> potential energy surface and vibrational-rotational energy levels of X 2Σ+ MgOH
|
[
"Koput Jacek ",
"Carter Stuart ",
"Peterson Kirk A. ",
"Theodorakopoulos Giannoula "
] |
https://doi.org/10.1063/1.1485721
| 2,002 |
July
|
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] |
10.1063/1.1485761
|
<jats:p>The evolution of a vertically falling film in the presence of a simple first-order (exothermic or endothermic) chemical reaction is considered. The heat of reaction sets up surface tension gradients that induce thermocapillary stresses on the free-surface, thus affecting the evolution of the film. By using a long-wave expansion of the equations of motion and associated boundary conditions, we derive a nonlinear partial differential equation of the evolution type for the local film thickness. We demonstrate that, when the surface tension is an increasing function of temperature an exothermic reaction has a stabilizing effect on the free surface while an endothermic reaction is destabilizing. We construct bifurcation diagrams for permanent solitary waves and show that, in all cases the solution branches exhibit limit points and multiplicity with two branches, a lower branch and an upper branch. Time-dependent computations of the free-surface evolution equation show that the system always approaches a train of coherent structures that resemble the lower branch solitary waves. We also examine the absorption characteristics through the interface and we demonstrate that an endothermic reaction enhances absorption and mass transport. The opposite is true for an exothermic reaction.</jats:p>
|
Dynamics of a vertically falling film in the presence of a first-order chemical reaction
|
[
"Trevelyan Philip M. J. ",
"Kalliadasis Serafim ",
"Merkin John H. ",
"Scott Stephen K. "
] |
https://doi.org/10.1063/1.1485761
| 2,002 |
July
|
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] |
10.1063/1.1485963
|
<jats:p>A systematic procedure based on the sequential Monte Carlo quantum mechanics (S-MC/QM) methodology has been used to obtain hydrogen bond strength and structures in liquids. The system considered is pyridine in water. The structures are generated by NVT Monte Carlo simulation, of one pyridine molecule and 400 water molecules. The hydrogen bonds are obtained using a geometric and energetic procedure. Detailed analysis shows that 62% of the configurations have one hydrogen bond. In the average, pyridine in liquid water makes 1.1 hydrogen bonds. The sampling of the structures for the quantum mechanical calculations is made using the interval of statistical correlation obtained by the autocorrelation function of the energy. A detailed statistical analysis is presented and converged results are obtained. The QM calculations are performed at the ab initio MP2/6-31+G(d) level and the results are compared with the optimized 1:1 cluster. Our results using QM calculations on 155 structures making one hydrogen bond gives an average binding energy of 3.7 kcal/mol, after correcting for basis set superposition error, indicating that in the liquid the binding energy is about 2/3 of the corresponding binding in the optimized cluster.</jats:p>
|
<i>Ab initio</i> calculation of hydrogen bonds in liquids: A sequential Monte Carlo quantum mechanics study of pyridine in water
|
[
"Malaspina Thaciana ",
"Coutinho Kaline ",
"Canuto Sylvio "
] |
https://doi.org/10.1063/1.1485963
| 2,002 |
July
|
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] |
10.1063/1.1485964
|
<jats:p>A theoretical model has been proposed and applied to explain recent experimental results concerning the external electric field effect on fluorescence quenching due to intramolecular electron transfer in donor–acceptor pairs linked by a spacer. These results show that for some systems with a short length of a spacer and for a very low concentration of donor–acceptor pairs, the fluorescence quenching of the photoexcited donor is reduced by the electric field instead of being enhanced. The model predicts that the reducing effect of the external electric field on the fluorescence quenching alternates with the enhancing effect when the standard free energy change or the donor–acceptor separation is varied. For systems with a high concentration of the donor–acceptor pairs the resultant effect of the field is determined additionally by competition between the intramolecular and intermolecular electron transfers.</jats:p>
|
Electric field effects on fluorescence quenching due to electron transfer. II. Linked donor–acceptor systems
|
[
"Hilczer Maria ",
"Tachiya M. "
] |
https://doi.org/10.1063/1.1485964
| 2,002 |
July
|
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] |
10.1063/1.1486025
|
<jats:p>Co 1−x Cr x /Pt multilayers have been deposited by magnetron sputtering onto different seed layers with simultaneous gradients in both Co1−xCrx thickness and composition x. These gradients make it possible to perform magnetic and structural measurements for different thicknesses and compositions on one single wafer. Hence, the depositions are not sensitive to variations in background conditions such as temperature, pressure, or contaminants that could otherwise vary between runs. The study concluded that the maximum for the coercivity of the multilayers is, in this case, dependent on the microstructure, namely the degree of c-axis orientation in the films. Specifically, the coercivity maximum coincides with the maximum of the x-ray diffraction peak full-width at-half-maximum for the two separate cases shown.</jats:p>
|
CoCr/Pt multilayers with perpendicular anisotropy and texture-controlled coercivity
|
[
"Svedberg Erik B. "
] |
https://doi.org/10.1063/1.1486025
| 2,002 |
July
|
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] |
10.1063/1.1486036
|
<jats:p>Interface reactions in Si/SiOx(Ny)/ZrO2 and Si/SiOx(Ny)/ZrO2/poly-Si gate stacks have been studied by high-resolution transmission electron microscopy. In the case of an uncapped stack ZrSi and ZrSi2 phases form during an ultrahigh vacuum anneal at temperatures above 900 °C. Both phases show an island-type growth with an epitaxial relationship with Si (100). Gate dielectric stacks with a poly-Si cap are found to be thermally unstable at T=1000 °C, so that the reaction is initiated at the ZrO2/poly-Si interface. Here a different reaction mechanism is identified, which involves the reduction of ZrO2 and the growth of a bottom interfacial layer between ZrOx and Si. Replacement of the bottom SiO2 layer by an ultrathin Si oxinitride does not completely suppress these interfacial reactions at T⩾1000 °C. We suggest that control of the poly-Si/ZrO2 interfacial reactions may be an important factor in modifying the thermal stability of a stack. These results shed a new light on understanding the material challenges involved in the integration of ZrO2 for the next generation of complementary metal–oxide–semiconductor technologies.</jats:p>
|
Interface reactions in ZrO2 based gate dielectric stacks
|
[
"Gribelyuk M. A. ",
"Callegari A. ",
"Gusev E. P. ",
"Copel M. ",
"Buchanan D. A. "
] |
https://doi.org/10.1063/1.1486036
| 2,002 |
July
|
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] |
10.1063/1.1486052
|
<jats:p>The axial heat flow within an aligned fiber composite containing matrix cracks bridged by the fibers is analyzed. A unit cell is defined and an exact expression for the constriction resistance of the unit cell is found. For values of fiber volume fraction and crack spacing that occur in actual composites, the thermal interaction between cracks is found to be almost negligible when the fiber/matrix interface is perfect. The asymptotic behavior under conditions of severe interface debonding is found.</jats:p>
|
Effect of cracks on the thermal resistance of aligned fiber composites
|
[
"Dryden J. ",
"Deakin A. ",
"Zok F. "
] |
https://doi.org/10.1063/1.1486052
| 2,002 |
July
|
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] |
10.1063/1.1486253
|
<jats:p>The properties of field effect transistors with organic insulator and semiconducting regions, fabricated with a top-gate architecture, have been investigated. Thin films (d≈30 nm) of regioregular poly(3-dodecylthiophene) were employed as the active semiconductor and the gate insulator was formed by a 500-nm-thick layer of poly(4-vinylphenol). Both were solution-processed on top of poly(ethylenetherephthalate) films, which were used as substrates. The output characteristics show a pronounced saturation behavior with an unconventional nonquadratic saturation current dependence on the gate voltage. Hence the (hole) mobility of 0.002–0.005 cm2/Vs has been estimated from the linear region of the transfer characteristics. The transistor turn-on occurs at a threshold voltage of approximately Vth=0 V, and the device can be operated with a supply voltage of between 15 and 20 V. As is usually observed for organic transistors, the inverse subthreshold slope (S) is very high, in our case S≈7 V/dec, by contrast with S≈200 mV/dec obtained for the similar material poly(3-octylthiophene) (P3OT) with silicon dioxide (SiO2) as an insulator. Furthermore, the subthreshold current depends on the drain voltage even though the transistor is electrically a long channel device with L=2 μm, notwithstanding the fact that this channel length is rather small for the present organic devices. To clarify these peculiarities numerical simulations have been carried out with a systematic variation of the relevant material parameters and assuming the existence of interface or bulk trap states. It turns out that both the high inverse subthreshold slope and the drain voltage dependence can be explained by recharging of trap states either at the interface or in the bulk. Considering the difference to the P3OT device with SiO2 as insulator it is proposed that interface traps are responsible for these effects, although one excludes the possibility that the film formation either on an organic substrate or on SiO2 leads to different bulk properties.</jats:p>
|
Subthreshold characteristics of field effect transistors based on poly(3-dodecylthiophene) and an organic insulator
|
[
"Scheinert S. ",
"Paasch G. ",
"Schrödner M. ",
"Roth H.-K. ",
"Sensfuß S. ",
"Doll Th. "
] |
https://doi.org/10.1063/1.1486253
| 2,002 |
July
|
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10.1063/1.1486257
|
<jats:p>We present experimental data showing a significant dependence of light absorption on temperature in photorefractive LiNbO3:Fe crystals. The results are successfully explained by assuming that the widths of the Fe2+ absorption bands in the visible and in the infrared spectral region depend on temperature. The findings are of relevance for thermal fixing of holograms. Furthermore, a temperature-induced increase of the infrared absorption is promising for improved infrared recording.</jats:p>
|
Temperature dependence of absorption in photorefractive iron-doped lithium niobate crystals
|
[
"Panotopoulos G. ",
"Luennemann M. ",
"Buse K. ",
"Psaltis D. "
] |
https://doi.org/10.1063/1.1486257
| 2,002 |
July
|
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] |
10.1063/1.1486445
|
<jats:p>A density functional theory for polymer solutions is generalized to cases where the monomers have a different diameter to the solvent. An appropriate free energy functional is obtained by integration of the generalized Flory equation of state for such systems. This functional predicts that entropic demixing may occur in polymer solutions in which the solvent particles are smaller than the monomers. Demixing is promoted not only by a large size disparity, but also by a high pressure as well as by polymer length. The existence of two separate phases in the bulk solution suggests the possibility of capillary-induced phase transitions, even when the confining surfaces are hard, but otherwise inert. We examine such phase transitions and their relation to surface forces and colloidal stability. The density functional theory also predicts that under certain conditions, layering transitions will occur at hard and flat surfaces. A transition from a thin to a thick polymer-rich surface layer may take place as the separation between two surfaces is decreased, and we study the concomitant change on the surface force. Stable thick phases are predicted even at very large undersaturations, and they give rise to a profound increase of the range and strength of the surface force. We furthermore include comparisons with predictions from a model in which the solvent only enters the description implicitly. Responses of the surface forces to changes in monomer diameter, solvent diameter, polymer density, and chain length are investigated.</jats:p>
|
Density functional study of surface forces in athermal polymer solutions with additive hard sphere interactions: Solvent effects, capillary condensation, and capillary-induced surface transitions
|
[
"Forsman Jan ",
"Woodward Clifford E. ",
"Freasier Ben C. "
] |
https://doi.org/10.1063/1.1486445
| 2,002 |
July
|
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] |
10.1063/1.1486450
|
<jats:p>The second wake transition occurs in the far wake of a bluff body. This transition destroys the Bénard–von Kármán vortex street originating in the near wake and produces a secondary vortex street with a lower characteristic frequency. We characterize the onset of the second wake for Reynolds numbers 50&lt;Re&lt;800 in a nearly two-dimensional soap film flow. The dimensionless distance between the cylinder and the onset of the second wake decreases with Reynolds number consistently with Re−1/2 power law. Our two-dimensional far-wake numerical simulations are in good agreement with the experiment.</jats:p>
|
Onset of the second wake: Dependence on the Reynolds number
|
[
"Vorobieff Peter ",
"Georgiev Daniel ",
"Ingber Marc S. "
] |
https://doi.org/10.1063/1.1486450
| 2,002 |
July
|
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] |
10.1063/1.1487374
|
<jats:p>The photodissociation dynamics of jet-cooled BrCl molecules have been investigated at four different wavelengths in the range 425–485 nm by high-resolution velocity map ion imaging. Four images of the Cl(2P3/2) atomic fragments are recorded at each photolysis wavelength with the probe laser polarization, respectively, linearly aligned and vertical (i.e., perpendicular to the detection axis), right circularly polarized, horizontally linearly polarized (i.e., parallel to the detection axis) and left circularly polarized on successive laser shots, thereby ensuring automatic mutual self-normalization. Appropriate linear combinations of these images allow quantification of the angular momentum alignment of the Cl(2P3/2o) fragments [i.e., the correlation between their recoil velocity (v) and their electronic angular momentum (J)] in terms of the alignment anisotropy parameters s2, α2, η2, and γ2, and determination of the “alignment-free” recoil anisotropy parameter, β0, as a function of parent excitation wavelength. Both incoherent and coherent contributions to the alignment are identified, with both simultaneous parallel and perpendicular excitations to the B 3Π(0+) and C 1Π(1) states and excitations to the Ω=±1 components of the C state contributing to the latter. The deduced values of the alignment-free β parameters indicate (wavelength dependent) contributions from both parallel and perpendicular parent absorptions in this wavelength range. Such a conclusion accords with approximate deconvolutions of the parent absorption spectrum that are currently available, and with determinations of the orientation parameter γ1′ obtained by fitting the difference image obtained when using left and right circularly polarized radiation to probe the ground state Cl atoms arising in the 480.63 nm photodissociation of BrCl when the photolysis laser radiation is polarized linearly at 45° to the detection axis.</jats:p>
|
Ion imaging studies of Cl(2P3/2) fragments arising in the visible photolysis of BrCl: Measurement of orientation, alignment, and alignment-free anisotropy parameters
|
[
"Wouters Eloy R. ",
"Beckert Marco ",
"Russell Lucy J. ",
"Rosser Keith N. ",
"Orr-Ewing Andrew J. ",
"Ashfold Michael N. R. ",
"Vasyutinskii Oleg S. "
] |
https://doi.org/10.1063/1.1487374
| 2,002 |
July
|
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] |
10.1063/1.1487440
|
<jats:p>Near-field cathodoluminescence (NFCL) has been used to characterize hydride vapor phase epitaxy grown n-GaN films. This technique can obtain high resolution luminescence images and perform local measurements of the diffusion length for minority carriers in different parts of the sample. NFCL contrast observed in round growth hillocks at the sample surface, with a diameter of less than 10 μm, is compared with that observed by conventional cathodoluminescence in scanning electron microscope (CLSEM) techniques. In particular NFCL images reveal features not detected by CLSEM which is explained by the fact that under near field conditions the signal arises from a depth of only several tens of nanometers and is then directly related to the surface hillocks. Diffusion lengths of about 0.4 and 4 μm have been found for the holes in different regions of the samples at room temperature. The order of magnitude of these minority carriers diffusion lengths is in good agreement with previous measurements performed at different GaN samples with other techniques. The NFCL contrast and the differences in the measured diffusion lengths are discussed and explained by variations in local trap concentrations.</jats:p>
|
Near-field cathodoluminescence studies on <i>n</i>-doped gallium nitride films
|
[
"Nogales E. ",
"Joachimsthaler I. ",
"Heiderhoff R. ",
"Piqueras J. ",
"Balk L. J. "
] |
https://doi.org/10.1063/1.1487440
| 2,002 |
July
|
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] |
10.1063/1.1487441
|
<jats:p>Light-switching behavior of reflective reserved-mode polymer-stabilized-cholesteric-texture (PSCT) was analyzed and validated experimentally. Our results indicate that the reflective reversed-mode PSCT offers a much higher contrast ratio and lower operating voltage than its transmissive counterpart. Effects of cell gap, birefringence, and pitch length on the contrast ratios of the reversed-mode PSCT cells were investigated. Potential applications of this device as variable optical attenuator and light shutter for telecommunication are emphasized.</jats:p>
|
Reflective reversed-mode polymer stabilized cholesteric texture light switches
|
[
"Ren Hongwen ",
"Wu Shin-Tson "
] |
https://doi.org/10.1063/1.1487441
| 2,002 |
July
|
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] |
10.1063/1.1487896
|
<jats:p>Recently, we reported the observation of step structure, similar to Coulomb staircase, in the current–voltage characteristic of metal/polyimide(PI)/rhodamine-dendrimer(Rh-G2)/PI/metal junctions prepared by the Langmuir–Blodgett(LB) technique [J. Appl. Phys. 90, 1368 (2001)]. Calculating the additional apparent capacitance formed by electrostatic charge at the interface, the equation of threshold voltage of the step structure was derived and the interfacial space charge effect was pointed out. However, this analysis is not sufficient. In this Addendum, the equation of step voltage is derived taking into account both electrostatic charges and residual charges by electron tunneling. It was found that the derived equation is more satisfactory to explain our previous experimental result.</jats:p>
|
Addendum: “Space charge effect and the step voltages in metal/polyimide/rhodamine–dendorimer/polyimide/metal junctions” [J. Appl. Phys. 90, 1368 (2001)]
|
[
"Noguchi Yutaka ",
"Iwamoto Mitsumasa ",
"Kubota Tohru ",
"Mashiko Shinro "
] |
https://doi.org/10.1063/1.1487896
| 2,002 |
July
|
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] |
10.1063/1.1487911
|
<jats:p>Deposition of hafnium silicate films with various hafnium contents was tried by plasma-enhanced chemical vapor deposition using tetraethoxysilane and a hafnium alkoxide. From x-ray photoelectron spectroscopy, the deposited films are confirmed to be silicate with Hf–O–Si bonds but without any Hf–Si bonds. The permittivity calculated from the capacitance of the accumulation layer increases monotonically with an increase in the hafnium content, whereas the optical band gap energy estimated from vacuum ultraviolet absorption spectra decreases. Similar results were obtained from zirconium silicate films deposited using tetraethoxysilane and a zirconium alkoxide. If we compare the films with the same hafnium or zirconium content, the hafnium silicate exhibits a higher permittivity and a larger band gap energy than the zirconium silicate.</jats:p>
|
Plasma-enhanced chemical vapor deposition and characterization of high-permittivity hafnium and zirconium silicate films
|
[
"Kato Hiromitsu ",
"Nango Tomohiro ",
"Miyagawa Takeshi ",
"Katagiri Takahiro ",
"Seol Kwang Soo ",
"Ohki Yoshimichi "
] |
https://doi.org/10.1063/1.1487911
| 2,002 |
July
|
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] |
10.1063/1.1487916
|
<jats:p>Dipolar molecules have been grafted on the surface of indium–tin–oxide plates. Using these modified substrates as anodes for organic diodes made from poly–vinylcarbazole enhances the hole current by 1–2 orders of magnitude as compared to diodes with nonmodified anodes. The organization and surface concentration of the grafted monolayer, determined by infrared spectroscopy, show that the grafted layer is not densely packed. The influence of the dipolar molecules on the energy barrier height for the injection of hole current into the organic layer is also measured by internal photoemission, evidencing that the barrier is lowered by the molecular grafting. The free space around the grafted molecules allows for their reorientation under electric field. The energy barrier height has been measured as a function of time during this reorientation.</jats:p>
|
Barrier lowering and reorientation of dipoles grafted at indium–tin–oxide/polymer interfaces
|
[
"Sigaud Philippe ",
"Chazalviel Jean-Noël ",
"Ozanam François "
] |
https://doi.org/10.1063/1.1487916
| 2,002 |
July
|
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] |
10.1063/1.1488245
|
<jats:p>The fundamentals of low-energy physical sputtering currently attract increasing interest in relation to ion-based and plasma-based micro- and nanofabrication technologies. However, explaining sputtering in the sub-keV bombardment regime has long been a challenge for the kinetic theory, partly because of a simplistic treatment of the surface. Here, transport theory of sputtering is formulated, which includes a more realistic analytical model of the surface in a semi-infinite target. In contrast to the traditional theory, which is based on the linearized Boltzmann equation, the new approach uses the discrete-path master equation for particle transport in matter. Starting from the discrete-path formalism, the deflection of incoming projectiles and focusing of emitted particles when they pass the surface are described by a unified few-collision approach and combined with the bulk master equation through sophisticated boundary conditions. The numerical results are compared with available experiments. Major anisotropies that affect differential sputtering yields in the sub-keV bombardment regime are considered as obtained from the kinetic modeling.</jats:p>
|
Discrete-path transport theory of physical sputtering
|
[
"Stepanova M. ",
"Dew S. K. "
] |
https://doi.org/10.1063/1.1488245
| 2,002 |
July
|
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] |
10.1063/1.1488246
|
<jats:p>A recently developed model that unifies the ballistic and diffusive transport mechanisms is applied to the carrier transport across potential barriers at grain boundaries in microcrystalline semiconducting materials. In the unified model, the conductance depends on the detailed structure of the band edge profile and in a nonlinear way on the carrier mean free path. Equilibrium band edge profiles are calculated within the trapping model for samples made up of a linear chain of identical grains. Quantum corrections allowing for tunneling are included in the calculation of electron mobilities. The dependence of the mobilities on carrier mean free path, grain length, number of grains, and temperature is examined, and appreciable departures from the results of the thermionic-field-emission model are found. Specifically, the unified model is applied in an analysis of Hall mobility data for n-type μc-Si thin films in the range of thermally activated transport. Owing mainly to the effect of tunneling, potential barrier heights derived from the data are substantially larger than the activation energies of the Hall mobilities. The specific features of the unified model, however, cannot be resolved within the rather large uncertainties of the analysis.</jats:p>
|
Barrier-controlled carrier transport in microcrystalline semiconducting materials: Description within a unified model
|
[
"Weis T. ",
"Lipperheide R. ",
"Wille U. ",
"Brehme S. "
] |
https://doi.org/10.1063/1.1488246
| 2,002 |
July
|
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] |
10.1063/1.1488575
|
<jats:p>A full dimensional variational algorithm to calculate vibrational energies of penta-atomic molecules is presented. The quantum mechanical Hamiltonian of the system for J=0 is derived in a set of orthogonal polyspherical coordinates in the body-fixed frame without any dynamical approximation. The vibrational Hamiltonian has been obtained in an explicitly Hermitian form. Variational calculations are performed in a direct product discrete variable representation basis set. The sine functions are used for the radial coordinates, whereas the Legendre polynomials are employed for the polar angles. For the azimuthal angles, the symmetrically adapted Fourier–Chebyshev basis functions are utilized. The eigenvalue problem is solved by a Lanczos iterative diagonalization algorithm. The preliminary application to methane is given. A comparison with previous results is made.</jats:p>
|
An exact variational method to calculate vibrational energies of five atom molecules beyond the normal mode approach
|
[
"Yu Hua-Gen "
] |
https://doi.org/10.1063/1.1488575
| 2,002 |
July
|
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] |
10.1063/1.1488586
|
<jats:p>The reorientational relaxation of nonlinear molecules in liquids is treated using the site–site generalized Langevin/mode-coupling theory. We found an inconsistency between the rank-1 reorientational correlation functions of different vectors on a molecule when the molecule is nearly planar. We show that it is because the coupling between the torque and the acceleration of different rotational modes is missing in the theory. A modification of the theory is proposed to incorporate this coupling, and the inconsistency between the reorientational correlation functions is remedied by the modification. We also apply the modified theory to the reorientational motion of water. The rotational part of the memory function becomes greater compared with the conventional theory, and it approaches to that from the molecular dynamics simulation. The charge-current spectrum of water is also shown to be improved by the modification.</jats:p>
|
Interaction-site model description of the reorientational relaxation of molecular liquids: Incorporation of the interaxial coupling into the site–site generalized Langevin/mode-coupling theory
|
[
"Yamaguchi T. ",
"Hirata F. "
] |
https://doi.org/10.1063/1.1488586
| 2,002 |
July
|
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] |
10.1063/1.1488690
|
<jats:p>A method for positioning colloidal particles on surfaces in any designed pattern is described. Optical tweezers are used to bring particles from a reservoir to the substrate where opposite surface charges are used to immobilize particles on the surface. Both chemical surface modification and polyelectrolyte coating of either substrate or colloids make the method generally applicable. We show that using this technique large, two-dimensional patterns can be created that can be dried without distortions by critical point drying. As an example we show the positioning of 79 nm radius metallodielectric particles and we show how two-dimensional patterns can be used to direct three-dimensional epitaxial crystal growth. The method is inexpensive, relatively fast, and can be fully automated.</jats:p>
|
Patterning surfaces with colloidal particles using optical tweezers
|
[
"Hoogenboom J. P. ",
"Vossen D. L. J. ",
"Faivre-Moskalenko C. ",
"Dogterom M. ",
"van Blaaderen A. "
] |
https://doi.org/10.1063/1.1488690
| 2,002 |
July
|
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] |
10.1063/1.1488922
|
<jats:p>Resonantly-enhanced two photon ionization and mass-analyzed threshold ionization (MATI) spectra of 2-aminopyridine (2AP–NH2) and its deuterated analogs have been obtained using two-photon (1+1′) excitation process via S1 intermediate states for ionization. Ionization energies of 2AP–NH2 and 2AP–ND2 are both precisely and accurately determined to be 8.1086±0.0005 and 8.1027±0.0005 eV, respectively. Two geometrical isomers, 2AP–NHD or 2AP–NDH, of which H or D is hydrogen-bonded to the nitrogen atom on the pyridine ring, respectively, are spectroscopically well isolated using the hole-burning spectroscopy in the S1 states. Corresponding ionization energies are thus separately determined to be 8.1067±0.0005 or 8.1048±0.0005 eV for 2AP–NHD or 2AP–NDH, respectively. Vibrational bands of 2-aminopyridine ions associated with various aromatic ring-skeletal modes are identified in the MATI spectra and appropriately assigned with the aid of ab initio calculation. All of the ring-skeletal vibrational frequencies observed in this work become slightly higher than those in the S1 states when the molecules are ionized, consistent with the fact that the S1–S0 excitation is due to π*–π transition. According to ab initio calculation, the amino group is in the molecular plane both in the S1 and D0 states, while it is slightly distorted in the ground state of 2-aminopyridine. Inversion modes in 2AP–ND2 and 2AP–NDH in S1 states are split into two bands due to their strong coupling with the other mode, which is most probably due to torsional motion of the amino group. Strong mode couplings are clearly manifested in interferencelike patterns observed in vibrational band structures of MATI spectra taken via those two bands in S1 states as intermediate states. A new spectroscopic scheme, in which MATI signals are used for obtaining mode-resolved spectra for the intermediate state is introduced. The vibrational band at 911 cm−1 from the S1–S0 origin that has been previously assigned as the inversion mode of 2AP–NH2 is found to actually consist of two closely-spaced different modes giving two clearly-resolved different Franck–Condon active modes in corresponding MATI spectra.</jats:p>
|
Resonant-enhanced two photon ionization and mass-analyzed threshold ionization spectroscopy of jet-cooled 2-aminopyridines (2AP–NH2,–NHD,–NDH,–ND2)
|
[
"Baek Sun Jong ",
"Choi Kyo-Won ",
"Choi Young S. ",
"Kim Sang Kyu "
] |
https://doi.org/10.1063/1.1488922
| 2,002 |
July
|
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] |
10.1063/1.1488929
|
<jats:p>In order to analyze the properties of the ideal lines of thermodynamic parameters use is made of some analytical equations of state, approximate integral equations of the theory of liquids, and computer simulations data. The findings of this study reveal that the ideal lines are not linear functions in the density–temperature phase diagram as was previously believed. It is also shown that the nonlinear behavior of the ideal lines is associated with the structure of the fluid, that is with the inherent features of correlation functions in different domains of the phase diagram. Changes from one linear branch of the ideal line to another are found to occur in the vicinity of the Fisher–Widom line, around which the asymptotically monotonic damping of the total correlation function alters to damping oscillations.</jats:p>
|
On the behavior of the ideal lines of thermodynamic functions
|
[
"Sarkisov G. N. "
] |
https://doi.org/10.1063/1.1488929
| 2,002 |
July
|
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] |
10.1063/1.1489495
|
<jats:p>We present a theoretical study, within the effective-mass approximation, of the magnetoabsorption spectra of intraexcitonic terahertz transitions of light-hole and heavy-hole confined magnetoexcitons in GaAs-(Ga,Al)As quantum wells. The semiconductor quantum wells are studied under magnetic fields applied in the growth direction of the semiconductor heterostructure. The various magnetoexciton states are obtained in the effective-mass approximation by an expansion of the exciton-envelope wave functions in terms of products of hole and electron quantum-well states with appropriate Gaussian functions for the various excitonic states. Intramagnetoexciton transitions are theoretically studied by exciting the allowed excitonic transitions with σ+ (or σ−) far-infrared radiation circularly polarized in the plane of the GaAs-(Ga,Al)As quantum well. Theoretical results are obtained for the intramagnetoexciton transition energies and magneto-absorption spectra associated with excitations from 1s-like to 2p±, and 3p±-like magnetoexciton states, and found in overall agreement with optically detected resonance measurements.</jats:p>
|
Magnetoabsorption spectra of intraexcitonic transitions in GaAs-(Ga,Al)As semiconductor quantum wells
|
[
"Barticevic Z. ",
"Pacheco M. ",
"Duque C. A. ",
"Oliveira L. E. "
] |
https://doi.org/10.1063/1.1489495
| 2,002 |
July
|
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] |
10.1063/1.1489715
|
<jats:p>Carbon often appears in Si in concentrations above its solubility. In this article, we propose a comprehensive model that, taking diffusion and clustering into account, is able to reproduce a variety of experimental results. Simulations have been performed by implementing this model in a Monte-Carlo atomistic simulator. The initial path for clustering included in the model is consistent with experimental observations regarding the formation and dissolution of substitutional C–interstitial C pairs (Cs–Ci). In addition, carbon diffusion profiles at 850 and 900 °C in carbon-doping superlattice structures are well reproduced. Finally, under conditions of thermal generation of intrinsic point defects, the weak temperature dependence of the Si interstitial undersaturation and the vacancy supersaturation in carbon-rich regions also agree with experimental measurements.</jats:p>
|
Carbon in silicon: Modeling of diffusion and clustering mechanisms
|
[
"Pinacho R. ",
"Castrillo P. ",
"Jaraiz M. ",
"Martin-Bragado I. ",
"Barbolla J. ",
"Gossmann H.-J. ",
"Gilmer G.-H. ",
"Benton J.-L. "
] |
https://doi.org/10.1063/1.1489715
| 2,002 |
July
|
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10.1063/1.1489904
|
<jats:p>The thermal effects on the ClCH2CN+Cl−SN2 reaction at 300 K have been studied by ab initio molecular dynamics. The role of the cyano-substituent is explained by the formation of a hydrogen bond and is discussed by comparison with the reactions of ClCH3 and Cl2CH2. It is shown that the interactions occurring in the prereactive complex are sufficiently strong to be effective also at high temperature. It is also shown that the temperature effects on the activation barrier are significant.</jats:p>
|
Thermal effects on the Cl−+ClCH2CN reaction by Car-Parrinello molecular dynamics
|
[
"Pagliai Marco ",
"Raugei Simone ",
"Cardini Gianni ",
"Schettino Vincenzo "
] |
https://doi.org/10.1063/1.1489904
| 2,002 |
July
|
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] |
10.1063/1.1490156
|
<jats:p>Oscillations stimulated by an S-shaped negative differential resistance originating from the self-assembly and decay of a self-organized space charge configuration in front of the anode of a dc gas discharge were observed. The oscillations appear in a resonant circuit, appropriate for the discharge, which contains a capacitor having a plate charged by secondary electron emission. The plate can be a metallic or a dielectric one because the negative differential resistance operates at zero dc current to the plate.</jats:p>
|
Negative differential resistance related to self-organization phenomena in a dc gas discharge
|
[
"Lozneanu E. ",
"Popescu V. ",
"Sanduloviciu M. "
] |
https://doi.org/10.1063/1.1490156
| 2,002 |
July
|
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] |
10.1063/1.1490394
|
<jats:p>The photovoltaic performance of solid-state dye-sensitized solar cells based on 2,2′7,7′-tetrakis(N,N-di-p-methoxyphenyl-amine)-9,9′-spiro-bifluorene has been improved to 3.2% overall conversion efficiency under air mass (AM) 1.5 illumination by performing the dye adsorption in the presence of silver ions in the dye solution. The enhancement in overall device efficiency is a result of increased open circuit potential and short circuit current. Different spectroscopic methods, such as x-ray photoelectron, Fourier-transform infrared and UV-visible spectroscopy have been employed to scrutinize the impact of the silver on the dye-sensitized device. From spectroscopic evidence it is inferred that the silver is mainly binding to the sensitizer via the amphidentate thiocyanate, allowing the formation of ligand-bridged dye complexes.</jats:p>
|
Improvement of the photovoltaic performance of solid-state dye-sensitized device by silver complexation of the sensitizer cis-bis(4,4′-dicarboxy-2,2′bipyridine)-bis(isothiocyanato) ruthenium(II)
|
[
"Krüger Jessica ",
"Plass Robert ",
"Grätzel Michael ",
"Matthieu Hans-Jörg "
] |
https://doi.org/10.1063/1.1490394
| 2,002 |
July
|
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] |
10.1063/1.1490626
|
<jats:p>We present anisotropic magnetoresistance measurements of magnetic switching processes in narrow ferromagnetic permalloy rings fabricated with six nonmagnetic electrical contacts. We demonstrate that measuring the resistance between different contacts allows the determination of the domain wall positions. Furthermore, these measurements also yield the possibility of determining the local switching fields of different parts of the ring. This provides a very useful tool to explore the complete switching process of a single ring. We show that, by using notches of suitable size and by applying fields along appropriate directions, it is possible to select the circulation direction of the vortex state using a uniform field only.</jats:p>
|
Controlled magnetic switching in single narrow rings probed by magnetoresistance measurements
|
[
"Kläui M. ",
"Vaz C. A. F. ",
"Bland J. A. C. ",
"Wernsdorfer W. ",
"Faini G. ",
"Cambril E. "
] |
https://doi.org/10.1063/1.1490626
| 2,002 |
July
|
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] |
10.1063/1.1490632
|
<jats:p>We have investigated magnetization reversal of ultrathin Co/Pd (111) films via in situ determination of three-dimensional magnetization orientations using magneto-optical Kerr effects of p and s waves. We find that with increasing the Co thickness the easy axis of magnetization is switching from normal-to-plane to in-plane through a stable canted phase and magnetization reversal under an applied magnetic field shows very contrastive behavior depending on the easy axis of magnetization. In particular, magnetization reversal via spiral motion is observed in the Co film of the canted phase which could be explained by an existence of in-plane anisotropy and an applied field slightly tilted from the film normal.</jats:p>
|
<i>In situ</i> vectorial magnetization reversal study of ultrathin Co films on Pd (111) using magneto-optical Kerr effects
|
[
"Shin Sung-Chul ",
"Lee Jeong-Won ",
"Kim Sang-Koog ",
"Kim Jonggeol "
] |
https://doi.org/10.1063/1.1490632
| 2,002 |
July
|
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-0.5951168537139893,
0.4838177263736725,
0.5048505067825317,
1.0912247896194458,
-0.03522680327296257,
-0.999132513999939,
-0.5616708993911743
] |
10.1063/1.1491002
|
<jats:p>Temperature dependence of electroluminescence degradation is studied in organic light emitting devices containing an emitting layer composed of a mixture of N,N′-di(naphthalene-1-yl)-N,N′-diphenyl-benzidine and tris(8-hydroxyquinoline)aluminum (AlQ3), doped with quinacridone green emitter. The emitting layer is sandwiched between hole and electron transport layers. Electroluminescence degradation in time is measured on devices operated at temperatures ranging from 22 to 100 °C. The devices demonstrated remarkable stability, even at elevated temperatures. From accelerated degradation tests, a device half-life of about 78 500, 18 700, and 8600 h can be projected for devices operated at 22, 70, and 100 °C, respectively, at an initial device luminance of 100 cd/m2. Activation energy for device degradation of 0.27 eV is consistent with the recently proposed degradation mechanism based on the unstable cationic AlQ3 species.</jats:p>
|
Organic light emitting devices with enhanced operational stability at elevated temperatures
|
[
"Aziz Hany ",
"Popovic Zoran D. ",
"Hu Nan-Xing "
] |
https://doi.org/10.1063/1.1491002
| 2,002 |
July
|
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] |
10.1063/1.1491175
|
<jats:p>The temperature dependence of the complex magnetic susceptibility χ′+χ″ of various YBCO films is investigated at different amplitudes of the exciting field Hac. It is found that when the temperature Tm at which the maximum is observed on the χ″(T) curve is plotted as a function of Hacα (the parameter α=1, 1/2, or 2/3, depending on the character of the coupling between crystallites), a kink appears at a certain field Hac=H1*. It is suggested that the temperature Tc1 obtained by extrapolating the Tm(Hac2/3) curve from the high-field region to zero field is the Berezinskii–Kosterlitz–Thouless transition temperature TBKT. This suggestion is based on a comparison of the present results with published data from a study of the complex susceptibility of a GdBa2Cu3O6.75 single crystal for directions of Hac parallel to the c axis of the single crystal and in its ab plane, and also on the coincidence of the calculated values of certain characteristic temperatures near the BKT transition with our experimental values.</jats:p>
|
Manifestation of two-dimensional behavior of YBCO films in a study of their complex susceptibility
|
[
"Khokhlov A. V. ",
"Prokhorov A. Yu. ",
"Drobotko V. F. ",
"Levchenko G. G. ",
"Klimov A. V. "
] |
https://doi.org/10.1063/1.1491175
| 2,002 |
July
|
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] |
10.1063/1.1491181
|
<jats:p>A two-quantum process of electron spin–lattice relaxation in amorphous solids is investigated. A relaxation mechanism involving two-level tunneling systems and phonons from the region of the boson peak is considered. It is shown that this mechanism is effective under certain conditions.</jats:p>
|
Two-quantum electron spin–lattice relaxation in amorphous solids
|
[
"G. Zakharov L. ",
"Chotorlishvili L. L. ",
"Buishvili T. L. "
] |
https://doi.org/10.1063/1.1491181
| 2,002 |
July
|
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] |
10.1063/1.1491184
|
<jats:p>A self-consistent field (SCF) model is constructed for spatially inhomogeneous Bose systems with broken symmetry. A system of self-consistent equations is obtained for the wave functions of the quasiparticles and the wave function of the condensate particles and another system of equations for the normal and anomalous single-particle density matrices. The many-particle wave function is found. The thermodynamics of multiparticle Bose systems is constructed on the basis of a microscopic treatment in the SCF approximation. It is stressed that Bose condensation in the ideal gas model is substantially different from Bose condensation in a system of interacting Bose particles because a pair condensate is necessarily present as well as the single-particle condensate, even for an arbitrarily weak interaction. The role of single-particle and collective excitations in Bose systems is discussed.</jats:p>
|
Self-consistent field model for spatially inhomogeneous Bose systems
|
[
"Poluéktov Yu. M. "
] |
https://doi.org/10.1063/1.1491184
| 2,002 |
July
|
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] |
10.1063/1.1491186
|
<jats:p>Nonlinear shear waves in two-dimensional systems (in particular, surface waves) are investigated with allowance for the spatial dispersion of the elastic medium. It is shown that the dispersion plays an important role in the structural and modulational stability of the nonlinear waves and to a large degree determines the directions of localization of phonons in a nonlinear localized wave and, in particular, the possibility of existence of elastic surface solitons. By means of an asymptotic procedure, solutions are found for small-amplitude two-dimensional elastic shear solitons of the one-parameter stationary-profile type and for envelope solitons and also for surface solitons localized near an ideal surface of an elastic half space. Localized excitations of this kind can exist only in a medium with a “focusing” (soft) nonlinearity and positive dispersion ∂2ω/∂k2&gt;0, where ω(k) is the dispersion relation for linear waves. A procedure is proposed for finding solutions for surface envelope solitons localized near a surface covered with a layer of another substance. A comparison is made between the structures of the surface shear solitons at an ideal surface and at a surface with a film coating.</jats:p>
|
Multidimensional and surface solitons in a nonlinear elastic medium
|
[
"Kovalev A. S. ",
"Syrkin E. S. ",
"Maugin J. A. "
] |
https://doi.org/10.1063/1.1491186
| 2,002 |
July
|
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] |
10.1063/1.1491587
|
<jats:p>Several new iridium based cyclometalated complexes were investigated as phosphorescent dopants for molecularly doped polymeric organic light-emitting diodes. Specifically, the complexes used in this study were iridium (III) bis(2-phenylpyridinato-N,C2′) (acetylacetonate) [ppy], iridium (III) bis(7,8-benzoquinolinato-N,C3′) (acetylacetonate) [bzq], iridium (III) bis(2-phenylbenzothiazolato-N,C2′) (acetylacetonate) [bt], iridium (III) bis(2-(2′-naphthyl)benzothiazolato-N,C2′) (acetylacetonate) [bsn] and iridium (III) bis(2-(2′-benzo[4,5-a]thienyl)pyridinato-N,C3′) (acetylacetonate) [btp]. Single layer devices of doped polyvinylcarbazole: 2-(4-biphenyl)-5-(4-tert-butylphenyl)-1,3,4-oxadiazole give maximum external quantum efficiencies that varied from 3.5% for the ppy dopant to 0.4% for the btp dopant. Several different device heterostructure architectures were explored, and the best quantum efficiency of the devices reached 4.2% for the heterostructures.</jats:p>
|
Cyclometalated Ir complexes in polymer organic light-emitting devices
|
[
"Lamansky Sergey ",
"Djurovich Peter I. ",
"Abdel-Razzaq Feras ",
"Garon Simona ",
"Murphy Drew L. ",
"Thompson Mark E. "
] |
https://doi.org/10.1063/1.1491587
| 2,002 |
July
|
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] |
10.1063/1.1492021
|
<jats:p>One of the major loss mechanisms leading to low energy conversion efficiencies of solar cells is the thermalization of charge carriers generated by the absorption of high-energy photons. These losses can largely be reduced in a solar cell if more than one electron–hole pair can be generated per incident photon. A method to realize multiple electron–hole pair generation per incident photon is proposed in this article. Incident photons with energies larger than twice the band gap of the solar cell are absorbed by a luminescence converter, which transforms them into two or more lower energy photons. The theoretical efficiency limit of this system for nonconcentrated sunlight is determined as a function of the solar cell’s band gap using detailed balance calculations. It is shown that a maximum conversion efficiency of 39.63% can be achieved for a 6000 K blackbody spectrum and for a luminescence converter with one intermediate level. This is a substantial improvement over the limiting efficiency of 30.9%, which a solar cell exposed directly to nonconcentrated radiation may have under the same assumption of radiative recombination only.</jats:p>
|
Improving solar cell efficiencies by down-conversion of high-energy photons
|
[
"Trupke T. ",
"Green M. A. ",
"Würfel P. "
] |
https://doi.org/10.1063/1.1492021
| 2,002 |
July
|
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] |
10.1063/1.1492022
|
<jats:p>We report pseudodielectric function data 〈ε〉=〈εa1〉+i〈εa2〉 and 〈ε〉=〈εc1〉+i〈εc2〉 for the optically uniaxial material ZnGeP2, critical point energies of structures in these data, and dielectric function data for the natural oxide. Annealing reduces the values of the peaks of 〈εa2〉.</jats:p>
|
Pseudodielectric function of ZnGeP2 from 1.5 to 6 eV
|
[
"Blickle V. ",
"Flock K. ",
"Dietz N. ",
"Aspnes D. E. "
] |
https://doi.org/10.1063/1.1492022
| 2,002 |
July
|
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] |
10.1063/1.1492854
|
<jats:p>Epitaxial Na0.5K0.5NbO3 (NKN) thin films have been grown on LaAlO3 substrates by rf magnetron sputtering of a stoichiometric, high-density, ceramic target. X-ray diffraction analysis showed c-axis oriented cube-on-cube growth. Micrometer size interdigital capacitor (IDC) structures were defined on the surface of the NKN film using photolithography. The electrical characterization at 1 MHz showed dissipation factor tan δ of 0.010, tunability 16.5% at 200 kV/cm and dielectric permittivity εr=470. The frequency dispersion of εr between 1 kHz and 1 MHz was 8.5% and the IDCs showed very good insulating properties with leakage current density on the order of 30 nA/cm2 at 400 kV/cm. The polarization loop exhibits weak ferroelectric hysteresis with maximum polarization 23.5 μC/cm2 at 600 kV/cm. These results are promising for tunable microwave devices based on rf sputtered NKN thin films.</jats:p>
|
High-performance epitaxial Na0.5K0.5NbO3 thin films by magnetron sputtering
|
[
"Blomqvist Mats ",
"Koh Jung-Hyuk ",
"Khartsev Sergey ",
"Grishin Alex ",
"Andréasson Johanna "
] |
https://doi.org/10.1063/1.1492854
| 2,002 |
July
|
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] |
10.1063/1.1493230
|
<jats:p>Cd 1−x Zn x Te wafers used for x-ray detector arrays have been failure analyzed using x-ray diffraction, x-ray electron spectroscopy (XPS), energy dispersive spectroscopy (EDS), and surface photovoltage spectroscopy (SPS). The last shows ZnTe segregation in failed pixels while the precipitant phase is too small to be observed by the other techniques. The Zn concentration, measured using EDS and XPS, was higher than that deduced from SPS data, confirming the conclusion. The segregation can be revealed only by SPS since it is sensitive to the electronic structure and thus to x in each phase while the other techniques average x over their measurement volume.</jats:p>
|
Studies of phase segregation in Cd1−xZnxTe using surface photovoltage spectroscopy
|
[
"Zidon Y. ",
"Yang Jihua ",
"Shapira Yoram "
] |
https://doi.org/10.1063/1.1493230
| 2,002 |
July
|
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] |
10.1063/1.1494109
|
<jats:p>Electronic transport and magnetic properties of La0.477Bi0.193Ca0.33MnO3 have been experimentally studied. Different resistive behaviors are observed in the cooling and warming processes. The system first stays at a high resistive state, and switches to a state of lower resistivity when it is cooled below a critical temperature. However, keeping the sample at a temperature below ∼60 K, a relaxation to the high resistive state takes place. This process is current dependent, and the application of a large current slows down the relaxation greatly. There is a strong competition between the two resistive states, which causes a switch of the system between states.</jats:p>
|
State switching in Bi-doped La0.67Ca0.33MnO3 and the effects of current
|
[
"Sun J. R. ",
"Gao J. ",
"Kang L. "
] |
https://doi.org/10.1063/1.1494109
| 2,002 |
July
|
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] |
10.1063/1.1494115
|
<jats:p>We propose a sub-millimeter-scale vapor-cell atomic-frequency reference based on a micromachined vapor cell, all-optical excitation, and advanced diode-laser technology. We analyze theoretically the performance of such a device as a function of cell size. Initial measurements on small-scale vapor cells support the theoretical treatment.</jats:p>
|
Miniature vapor-cell atomic-frequency references
|
[
"Kitching J. ",
"Knappe S. ",
"Hollberg L. "
] |
https://doi.org/10.1063/1.1494115
| 2,002 |
July
|
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] |
10.1063/1.1494120
|
<jats:p>The electronic behavior of gold nanoparticles (NPs) of ∼2 nm capped with dendrimer and thiol molecules was studied with Au L3,2-edge x-ray absorption near-edge structure (XANES). The results reveal the tunability of the d-electron distribution in the Au NPs by selective capping. That is, that the Au atoms in the NPs gain 5d electrons (relative to the bulk) when capped with weakly interacting dendrimers and lose 5d electrons when capped with strongly interacting thiol molecules. A semiquantitative analysis of the d-charge (holes) distribution is presented. This work demonstrates the important role of the capping molecules in the d-charge distribution of Au NPs and the usefulness of XANES in probing the electronic behavior of transition metal NPs.</jats:p>
|
Tuning the electronic behavior of Au nanoparticles with capping molecules
|
[
"Zhang P. ",
"Sham T. K. "
] |
https://doi.org/10.1063/1.1494120
| 2,002 |
July
|
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] |
10.1063/1.1494454
|
<jats:p>Based on different photonic band structures of TE and TM polarization modes in periodic multilayers, a method to realize the waveguide polarizer is proposed. The waveguide structure contains a SiO2 core layer sandwiched between two multilayers of alternately stacked poly-Si and SiO2, and the whole structure can be grown on a Si substrate. Its propagation characteristics are studied theoretically. High extinction ratio over 40 dB at a light wavelength of 1.3 μm is expected in the waveguide of only 40 μm long, accompanied with very low propagation loss of the passive TE mode. These characteristics are very suitable for the applications in integrated optics. The fabrication of this polarizer structure by using the magnetron sputtering method is demonstrated.</jats:p>
|
Silicon-based optical waveguide polarizer using photonic band gap
|
[
"Zhao Dengtao ",
"Shi Bin ",
"Jiang Zuimin ",
"Fan Yongliang ",
"Wang Xun "
] |
https://doi.org/10.1063/1.1494454
| 2,002 |
July
|
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] |
10.1063/1.1494864
|
<jats:p>We investigate the strength of the coupling of the electronic states with the electromagnetic field in ZnO nanospheres, taking into account the retardation effect. We show that the coupling strength is particularly strong: the bulk properties are so enhanced that the radiative decay time can reach some 200 ps for quantum dot sizes of some 30 nm.</jats:p>
|
Giant exciton-light coupling in ZnO quantum dots
|
[
"Gil Bernard ",
"Kavokin Alexey V. "
] |
https://doi.org/10.1063/1.1494864
| 2,002 |
July
|
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] |
10.1063/1.1495089
|
<jats:p>Electron-heating measurements are used to compare the form of the electron–phonon interaction in two-dimensional, and quasi-one-dimensional, InGaAs quantum wires. Evidence for a strongly enhanced interaction is found in the quasi-one-dimensional wire, and is suggested to result from the presence of the singularities in its electronic density of states. The Bloch–Gruneisen criterion is easily violated in this wire, and its energy-loss function is found to show a weak temperature dependence, which is argued to result from a saturation of scattering processes in the uppermost one-dimensional subband.</jats:p>
|
Experimental studies of the electron–phonon interaction in InGaAs quantum wires
|
[
"Sugaya T. ",
"Bird J. P. ",
"Ferry D. K. ",
"Sergeev A. ",
"Mitin V. ",
"Jang K.-Y. ",
"Ogura M. ",
"Sugiyama Y. "
] |
https://doi.org/10.1063/1.1495089
| 2,002 |
July
|
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] |
10.1063/1.1495545
|
<jats:p>A torus knot model is presented to analyze the chiral wave propagation of photonic quantum-ring lasers in a three-dimensional Rayleigh–Fabry–Perot toroidal cavity. The Rayleigh–Fabry–Perot cavity gives rise to peculiar multichromatic spectra with nonequal intermode spacings. In particular, the knot model analysis suggests a strange three-dimensional effective index ellipsoid for the cavity with a large birefringence of neff3D(z)−neff2D(x,y)≈0.4–0.5.</jats:p>
|
Chiral wave propagation manifold of the photonic quantum-ring laser
|
[
"Park B. H. ",
"Bae J. ",
"Kim M. J. ",
"Kwon O’Dae "
] |
https://doi.org/10.1063/1.1495545
| 2,002 |
July
|
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] |
10.1063/1.1495902
|
<jats:p>Ordered three-dimensional macroporous SiO2 films were fabricated by colloidal crystal templating. Scanning electron microscope measurements showed that the size of the air sphere replicates that of the initial polystyrene spheres, and that the porous sample exhibits long-range order. Optical measurements show that the macroporous sample exhibits the behavior of a photonic band gap, indicating crystalline order in the sample. Fourier-transform infrared measurements revealed that a strong network of Si–O–Si bonds have been formed throughout the voids of the template before the solidification of the gel. It is proposed that this network hinders the large volume shrinkage during the subsequent heat treatment, and thus high-quality large-scale ordered macroporous films can be obtained.</jats:p>
|
Large-scale ordered macroporous SiO2 thin films by a template-directed method
|
[
"Ye Yong-Hong ",
"Badilescu Simona ",
"Truong Vo-Van "
] |
https://doi.org/10.1063/1.1495902
| 2,002 |
July
|
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] |
10.1063/1.1496131
|
<jats:p>The barrier thickness in magnetic spin-dependent tunnel junctions with Al2O3 barriers has been measured using grazing incidence x-ray reflectivity and by fitting the tunneling current to the Simmons model. We have studied the effect of glow discharge oxidation time on the barrier structure, revealing a substantial increase in Al2O3 thickness with oxidation. The greater thickness of barrier measured using grazing incidence x-ray reflectivity compared with that obtained by fitting current density–voltage to the Simmons electron tunneling model suggests that electron tunneling is localized to specific regions across the barrier, where the thickness is reduced by fluctuations due to nonconformal roughness.</jats:p>
|
Determination of the thickness of Al2O3 barriers in magnetic tunnel junctions
|
[
"Buchanan J. D. R. ",
"Hase T. P. A. ",
"Tanner B. K. ",
"Hughes N. D. ",
"Hicken R. J. "
] |
https://doi.org/10.1063/1.1496131
| 2,002 |
July
|
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] |
10.1073/pnas.082148899
|
<jats:p>This paper reports a computational method, the quantized elastic deformational model, that can reliably describe the conformational flexibility of a protein in the absence of the amino acid sequence and atomic coordinates. The essence of this method lies in the fact that, in modeling the functionally important conformational changes such as domain movements, it is possible to abandon the traditional concepts of protein structure (bonds, angles, dihedrals, etc.) and treat the protein as an elastic object. The shape and mass distribution of the object are described by the electron density maps, at various resolutions, from methods such as x-ray diffraction or cryo-electron microscopy. The amplitudes and directionality of the elastic deformational modes of a protein, whose patterns match the biologically relevant conformational changes, can then be derived solely based on the electron density map. The method yields an accurate description of protein dynamics over a wide range of resolutions even as low as 15–20 Å at which there is nearly no visually distinguishable internal structures. Therefore, this method dramatically enhances the capability of studying protein motions in structural biology. It is also expected to have ample applications in related fields such as bioinformatics, structural genomics, and proteomics, in which one's ability to extract functional information from the not-so-well-defined structural models is vitally important.</jats:p>
|
How to describe protein motion without amino acid sequence and atomic coordinates
|
[
"Ming Dengming ",
"Kong Yifei ",
"Lambert Maxime A. ",
"Huang Zhong ",
"Ma Jianpeng "
] |
https://doi.org/10.1073/pnas.082148899
| 2,002 |
July
|
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] |
10.1073/pnas.082223899
|
<jats:p>
Binding of CBF3, a protein complex consisting of Ndc10p, Cep3p, Ctf13p, and Skp1p, to the centromere DNA nucleates kinetochore formation in budding yeast. Here, we investigate how the Ctf13p/Skp1p complex becomes competent to form the CBF3-centromere DNA complex. As revealed by mass spectrometry, Ctf13p and Skp1p carry two and four phosphate groups, respectively. Complete dephosphorylation of Ctf13p and Skp1p does not interfere with the formation of CBF3-centromere DNA complexes
<jats:italic>in vitro</jats:italic>
. Furthermore, deletion of corresponding phosphorylation sites results in viable cells. Thus, in contrast to the current view, phosphorylation of Ctf13p and Skp1p is not essential for the formation of CBF3-centromere DNA complexes. Instead, the formation of active Ctf13p/Skp1p requires Hsp90. Several lines of evidence support this conclusion: activation of heterologous Ctf13p/Skp1p by reticulocyte lysate is inhibited by geldanamycin and Hsp90 depletion. skp1 mutants exhibit growth defects on media containing geldanamycin. A skp1 mutation together with Hsp90 mutations exhibits synthetic lethality. An Hsp90 mutant contains decreased levels of active Ctf13p/Skp1p.
</jats:p>
|
Hsp90 enables Ctf13p/Skp1p to nucleate the budding yeast kinetochore
|
[
"Stemmann Olaf ",
"Neidig Anke ",
"Köcher Thomas ",
"Wilm Matthias ",
"Lechner Johannes "
] |
https://doi.org/10.1073/pnas.082223899
| 2,002 |
July
|
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] |
10.1073/pnas.092025499
|
<jats:p>
The general transcription factor TFIID facilitates recruitment of the transcription machinery to gene promoters and regulates initiation of transcription by RNA polymerase II. hTAF
<jats:sub>II</jats:sub>
130, a component of TFIID, interacts with and serves as a coactivator for multiple transcriptional regulatory proteins, including Sp1 and CREB. A yeast two-hybrid screen has identified an interaction between hTAF
<jats:sub>II</jats:sub>
130 and heterochromatin protein 1 (HP1), a chromatin-associated protein whose function has been implicated in gene silencing. We find that hTAF
<jats:sub>II</jats:sub>
130 associates with HP1 in an isoform-specific manner: HP1α and HP1γ bind to hTAF
<jats:sub>II</jats:sub>
130, but not HP1β. In addition, we show that endogenous hTAF
<jats:sub>II</jats:sub>
130 and components of TFIID in HeLa nuclear extracts associate with glutathione
<jats:italic>S</jats:italic>
-transferase-HP1α and -HP1γ. hTAF
<jats:sub>II</jats:sub>
130 possesses a pentapeptide HP1-binding motif, and mutation of the hTAF
<jats:sub>II</jats:sub>
130 HP1 box compromises the interaction of hTAF
<jats:sub>II</jats:sub>
130 with HP1. We demonstrate that Gal4-HP1 proteins interfere with hTAF
<jats:sub>II</jats:sub>
130-mediated activation of transcription. Our results suggest that HP1α and HP1γ associate with hTAF
<jats:sub>II</jats:sub>
130 to mediate repression of transcription, supporting a new model of transcriptional repression involving a specific interaction between a component of TFIID and chromatin.
</jats:p>
|
Isoform-specific interaction of HP1 with human TAF
<sub>II</sub>
130
|
[
"Vassallo Milo F. ",
"Tanese Naoko "
] |
https://doi.org/10.1073/pnas.092025499
| 2,002 |
July
|
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] |
10.1073/pnas.092129899
|
<jats:p>TH1 memory T cells derived from T cell receptor transgenic mice, in which the T cell antigen receptor is specific for a cytochrome C peptide in association with I-E<jats:sup>k</jats:sup>, were transferred into normal B10.A mice and allowed to adopt a resting phenotype. When challenged, 30–60 days after transfer, with i.v. cytochrome C, the transgenic cells rapidly became activated, expressed mRNA for IFNγ, and began to divide. However, after 48 h, the frequency of the cells fell progressively, reaching levels only slightly above the limit of detection by day 8 and thereafter remain depressed for up to 90 days. The remaining cells were anergic as shown by limitation in proliferation and IFNγ production in response to<jats:italic>in vitro</jats:italic>antigen stimulation. Even if challenged with antigen emulsified in complete Freund's adjuvant, the overall pattern was similar, except that in the draining lymph nodes, the surviving antigen-specific cells were not anergic, although spleen cells were still strikingly anergic. Thus, antigenic challenge of mice possessing resting memory TH1 CD4 T cells leads to the unanticipated loss of most of the specific cells and an apparent depletion rather than enhancement of immunologic memory.</jats:p>
|
Antigen challenge leads to<i>in vivo</i>activation and elimination of highly polarized TH1 memory T cells
|
[
"Hayashi Nobuki ",
"Liu Dacai ",
"Min Booki ",
"Ben-Sasson Shlomo Z. ",
"Paul William E. "
] |
https://doi.org/10.1073/pnas.092129899
| 2,002 |
July
|
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] |
10.1073/pnas.102291599
|
<jats:p>
The G
<jats:sub>12</jats:sub>
subfamily of heterotrimeric G-proteins consists of two members, G
<jats:sub>12</jats:sub>
and G
<jats:sub>13</jats:sub>
. Gene-targeting studies have revealed a role for G
<jats:sub>13</jats:sub>
in blood vessel development. Mice lacking the α subunit of G
<jats:sub>13</jats:sub>
die around embryonic day 10 as the result of an angiogenic defect. On the other hand, the physiological role of G
<jats:sub>12</jats:sub>
is still unclear. To address this issue, we generated Gα
<jats:sub>12</jats:sub>
-deficient mice. In contrast to the Gα
<jats:sub>13</jats:sub>
-deficient mice, Gα
<jats:sub>12</jats:sub>
-deficient mice are viable, fertile, and do not show apparent abnormalities. However, Gα
<jats:sub>12</jats:sub>
does not seem to be entirely redundant, because in the offspring generated from Gα
<jats:sub>12</jats:sub>
± Gα
<jats:sub>13</jats:sub>
± intercrosses, at least one intact Gα
<jats:sub>12</jats:sub>
allele is required for the survival of animals with only one Gα
<jats:sub>13</jats:sub>
allele. In addition, Gα
<jats:sub>12</jats:sub>
and Gα
<jats:sub>13</jats:sub>
showed a difference in mediating cell migratory response to lysophosphatidic acid in embryonic fibroblast cells. Furthermore, mice lacking both Gα
<jats:sub>12</jats:sub>
and Gα
<jats:sub>q</jats:sub>
die
<jats:italic>in utero</jats:italic>
at about embryonic day 13. These data indicate that the Gα
<jats:sub>12</jats:sub>
-mediated signaling pathway functionally interacts not only with the Gα
<jats:sub>13</jats:sub>
- but also with the Gα
<jats:sub>q/11</jats:sub>
-mediated signaling systems.
</jats:p>
|
Interaction of Gα
<sub>12</sub>
with Gα
<sub>13</sub>
and Gα
<sub>q</sub>
signaling pathways
|
[
"Gu Jennifer L. ",
"Müller Stefan ",
"Mancino Valeria ",
"Offermanns Stefan ",
"Simon Melvin I. "
] |
https://doi.org/10.1073/pnas.102291599
| 2,002 |
July
|
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] |
10.1073/pnas.102304299
|
<jats:p>Prp8 is the largest and most highly conserved protein in the spliceosome yet its mechanism of function is poorly understood. Our previous studies implicate Prp8 in control of spliceosome activation for the first catalytic step of splicing, because substitutions in five distinct regions (a–e) of Prp8 suppress a cold-sensitive block to activation caused by a mutation in U4 RNA. Catalytic activation of the spliceosome is thought to require unwinding of the U1 RNA/5′ splice site and U4/U6 RNA helices by the Prp28 and Prp44/Brr2 DExD/H-box helicases, respectively. Here we show that mutations in regions a, d, and e of Prp8 exhibit allele-specific genetic interactions with mutations in Prp28, Prp44/Brr2, and U6 RNA, respectively. These results indicate that Prp8 coordinates multiple processes in spliceosome activation and enable an initial correlation of Prp8 structure and function. Furthermore, additional genetic interactions with U4-cs1 support a two-state model for this RNA conformational switch and implicate another splicing factor, Prp31, in Prp8-mediated spliceosome activation.</jats:p>
|
Distinct domains of splicing factor Prp8 mediate different aspects of spliceosome activation
|
[
"Kuhn Andreas N. ",
"Reichl Elizabeth M. ",
"Brow David A. "
] |
https://doi.org/10.1073/pnas.102304299
| 2,002 |
July
|
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] |
10.1073/pnas.102306999
|
<jats:p>The turnover of linear and cyclic electron flows has been determined in fragments of dark-adapted spinach leaf by measuring the kinetics of fluorescence yield and of the transmembrane electrical potential changes under saturating illumination. When Photosystem (PS) II is inhibited, a cyclic electron flow around PSI operates transiently at a rate close to the maximum turnover of photosynthesis. When PSII is active, the cyclic flow operates with a similar rate during the first seconds of illumination. The high efficiency of the cyclic pathway implies that the cyclic and the linear transfer chains are structurally isolated one from the other. We propose that the cyclic pathway operates within a supercomplex including one PSI, one cytochrome bf complex, one plastocyanin, and one ferredoxin. The cyclic process induces the synthesis of ATP needed for the activation of the Benson–Calvin cycle. A fraction of PSI (∼50%), not included in the supercomplexes, participates in the linear pathway. The illumination would induce a dissociation of the supercomplexes that progressively increases the fraction of PSI involved in the linear pathway.</jats:p>
|
Cyclic electron transfer in plant leaf
|
[
"Joliot Pierre ",
"Joliot Anne "
] |
https://doi.org/10.1073/pnas.102306999
| 2,002 |
July
|
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] |
10.1073/pnas.112217899
|
<jats:p>
A method for inverting measurements made on the surfaces of tissues for recovery of interior optical property maps is demonstrated for sparse near-infrared (NIR) fluorescence measurement sets on large tissue-simulating volumes with highly variable signal-to-noise ratio. A Bayesian minimum-variance reconstruction algorithm compensates for the spatial variability in signal-to-noise ratio that must be expected to occur in actual NIR contrast-enhanced diagnostic medical imaging. Image reconstruction is demonstrated by using frequency-domain photon migration measurements on 256-cm
<jats:sup>3</jats:sup>
tissue-mimicking phantoms containing none, one, or two 1-cm
<jats:sup>3</jats:sup>
heterogeneities with 50- to 100-fold greater concentration of Indocyanine Green dye over background levels. The spatial parameter estimate of absorption owing to the dye was reconstructed from only 160 to 296 surface measurements of emission light at 830 nm in response to incident 785-nm excitation light modulated at 100 MHz. Measurement error of acquired fluence at fluorescent emission wavelengths is shown to be highly variable. Convergence and quality of image reconstructions are improved by Bayesian conditioning incorporating (
<jats:italic>i</jats:italic>
) experimentally determined measurement error variance, (
<jats:italic>ii</jats:italic>
) recursively updated estimates of parameter uncertainty, and (
<jats:italic>iii</jats:italic>
) dynamic zonation. The results demonstrate that, to employ NIR fluorescence-enhanced optical imaging for large volumes, reconstruction approaches must account for the large range of signal-to-noise ratio associated with the measurements.
</jats:p>
|
Three-dimensional, Bayesian image reconstruction from sparse and noisy data sets: Near-infrared fluorescence tomography
|
[
"Eppstein Margaret J. ",
"Hawrysz Daniel J. ",
"Godavarty Anuradha ",
"Sevick-Muraca Eva M. "
] |
https://doi.org/10.1073/pnas.112217899
| 2,002 |
July
|
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] |
10.1073/pnas.122061399
|
<jats:p>
Ebselen [2-phenyl-1,2-benzisoselenazol-3(2
<jats:italic>H</jats:italic>
)-one], a seleno-organic compound with glutathione peroxidase-like activity is used in clinical trials against stroke. Human and bovine TrxR catalyzed the reduction of ebselen to ebselen selenol by NADPH with an apparent
<jats:italic>K</jats:italic>
<jats:sub>M</jats:sub>
-value of 2.5 μM and a
<jats:italic>k</jats:italic>
<jats:sub>cat</jats:sub>
of 588 min
<jats:sup>−1</jats:sup>
. The addition of thioredoxin (Trx) stimulated the TrxR-catalyzed reduction of ebselen several-fold. This result was caused by a very fast oxidation of reduced Trx by ebselen with a rate constant in excess of 2 × 10
<jats:sup>7</jats:sup>
M
<jats:sup>−1</jats:sup>
s
<jats:sup>−1</jats:sup>
. This rate is orders of magnitude faster than the reaction of dithiol Trx with insulin disulfides. Ebselen competed with disulfide substrates for reduction by Trx and, therefore, acted as an inhibitor of protein disulfide reduction by the Trx system. The inherent H
<jats:sub>2</jats:sub>
O
<jats:sub>2</jats:sub>
reductase activity of mammalian TrxR dependent on its active-site selenocysteine residue was stimulated 10-fold by 2 μM ebselen and 25-fold in the additional presence of 5 μM Trx. Furthermore, the apparent
<jats:italic>K</jats:italic>
<jats:sub>M</jats:sub>
-value of TrxR for H
<jats:sub>2</jats:sub>
O
<jats:sub>2</jats:sub>
was lowered 25-fold to about 100 μM. Our results demonstrate that ebselen is a TrxR peroxidase which, in the presence of Trx, acted as a mimic of a peroxiredoxin. The activity with TrxR and oxidation of reduced Trx offer mechanistic explanations for the
<jats:italic>in vivo</jats:italic>
effects of ebselen as an antioxidant and anti-inflammatory agent. Our results demonstrate that the mechanism of action of ebselen may be predominantly via the Trx system rather than via glutathione.
</jats:p>
|
Ebselen: A substrate for human thioredoxin reductase strongly stimulating its hydroperoxide reductase activity and a superfast thioredoxin oxidant
|
[
"Zhao Rong ",
"Masayasu Hiroyuki ",
"Holmgren Arne "
] |
https://doi.org/10.1073/pnas.122061399
| 2,002 |
July
|
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] |
10.1073/pnas.132178099
|
<jats:p>Molecular surveillance of pathogenic microbes works by genotyping isolates with DNA fingerprinting techniques and then using these genotypes to assign individuals to populations. Clonality is assumed in many fingerprinting studies, although this assumption has been shown to be false for many organisms. To accommodate recombining organisms into surveillance programs, methods using population allele frequencies in combination with individual multilocus genotypes are necessary. Here, we develop a statistical method appropriate for haploid recombining microbes that allows individuals to be assigned to populations. We illustrate the usefulness of this technique by inferring the source populations for<jats:italic>Coccidioides</jats:italic>isolates recovered from patients treated outside the endemic area of<jats:italic>Coccidioides</jats:italic>sp., the etiological agents of human coccidioidomycosis, but with a travel history including visits to one or more endemic areas.</jats:p>
|
Disease surveillance in recombining pathogens: Multilocus genotypes identify sources of human<i>Coccidioides</i>infections
|
[
"Fisher Matthew C. ",
"Rannala Bruce ",
"Chaturvedi Vishnu ",
"Taylor John W. "
] |
https://doi.org/10.1073/pnas.132178099
| 2,002 |
July
|
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] |
10.1073/pnas.132253599
|
<jats:p>
The natural history of follicular lymphoma (FL) is frequently characterized by transformation to a more aggressive diffuse large B cell lymphoma (DLBCL). We compared the gene-expression profiles between transformed DLBCL and their antecedent FL. No genes were observed to increase or decrease their expression in all of the cases of histological transformation. However, two different gene-expression profiles associated with the transformation process were defined, one in which
<jats:italic>c-myc</jats:italic>
and genes regulated by
<jats:italic>c-myc</jats:italic>
showed increased expression and one in which these same genes showed decreased expression. Further, there was a striking difference in gene-expression profiles between transformed DLBCL and
<jats:italic>de novo</jats:italic>
DLBCL, because the gene-expression profile of transformed DLBCL was more similar to their antecedent FL than to
<jats:italic>de novo</jats:italic>
DLBCL. This study demonstrates that transformation from FL to DLBCL can occur by alternative pathways and that transformed DLBCL and
<jats:italic>de novo</jats:italic>
DLBCL have very different gene-expression profiles that may underlie the different clinical behaviors of these two types of morphologically similar lymphomas.
</jats:p>
|
Transformation of follicular lymphoma to diffuse large-cell lymphoma: Alternative patterns with increased or decreased expression of
<i>c</i>
-
<i>myc</i>
and its regulated genes
|
[
"Lossos Izidore S. ",
"Alizadeh Ash A. ",
"Diehn Maximilian ",
"Warnke Roger ",
"Thorstenson Yvonne ",
"Oefner Peter J. ",
"Brown Patrick O. ",
"Botstein David ",
"Levy Ronald "
] |
https://doi.org/10.1073/pnas.132253599
| 2,002 |
July
|
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] |
10.1073/pnas.132259899
|
<jats:p>
During paroxysmal neocortical oscillations, sudden depolarization leading to the next cycle occurs when the majority of cortical neurons are hyperpolarized. Both the Ca
<jats:sup>2+</jats:sup>
-dependent K
<jats:sup>+</jats:sup>
currents (
<jats:italic>I</jats:italic>
<jats:sub>K(Ca)</jats:sub>
) and disfacilitation play critical roles in the generation of hyperpolarizing potentials.
<jats:italic>In vivo</jats:italic>
experiments and computational models are used here to investigate whether the hyperpolarization-activated depolarizing current (
<jats:italic>I</jats:italic>
<jats:sub>h</jats:sub>
) in cortical neurons also contributes to the generation of paroxysmal onsets. Hyperpolarizing current pulses revealed a depolarizing sag in ≈20% of cortical neurons. Intracellular recordings from glial cells indirectly indicated an increase in extracellular potassium concentration ([K
<jats:sup>+</jats:sup>
]
<jats:sub>o</jats:sub>
) during paroxysmal activities, leading to a positive shift in the reversal potential of K
<jats:sup>+</jats:sup>
-mediated currents, including
<jats:italic>I</jats:italic>
<jats:sub>h</jats:sub>
. In the paroxysmal neocortex, ≈20% of neurons show repolarizing potentials originating from hyperpolarizations associated with depth-electroencephalogram positive waves of spike-wave complexes. The onset of these repolarizing potentials corresponds to maximal [K
<jats:sup>+</jats:sup>
]
<jats:sub>o</jats:sub>
as estimated from dual simultaneous impalements from neurons and glial cells. Computational models showed how, after the increased [K
<jats:sup>+</jats:sup>
]
<jats:sub>o</jats:sub>
, the interplay between
<jats:italic>I</jats:italic>
<jats:sub>h</jats:sub>
,
<jats:italic>I</jats:italic>
<jats:sub>K(Ca)</jats:sub>
, and a persistent Na
<jats:sup>+</jats:sup>
current,
<jats:italic>I</jats:italic>
<jats:sub>Na(P)</jats:sub>
, could organize paroxysmal oscillations at a frequency of 2–3 Hz.
</jats:p>
|
Cortical hyperpolarization-activated depolarizing current takes part in the generation of focal paroxysmal activities
|
[
"Timofeev Igor ",
"Bazhenov Maxim ",
"Sejnowski Terrence ",
"Steriade Mircea "
] |
https://doi.org/10.1073/pnas.132259899
| 2,002 |
July
|
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] |
10.1073/pnas.132275399
|
<jats:p>
Prokaryotic repressor–operator systems provide exemplars for the sequence-specific interactions between DNA and protein. The crucial atomic contacts of the two macromolecules are attained in a compact, geometrically defined structure of the DNA–protein complex. The pitch of the DNA interface seems an especially sensitive part of this architecture because changes in its length introduce new spacing and rotational relations in one step. We discovered a natural system that may serve as a model for investigating this problem: the repressor of the
<jats:italic>16</jats:italic>
-
<jats:italic>3</jats:italic>
phage of
<jats:italic>Rhizobium meliloti</jats:italic>
(helix-turn-helix class protein) possesses inherent ability to accommodate to various DNA twistings. It binds the cognate operators, which are 5′-ACAA-4 bp-TTGT-3′ (O
<jats:sub>L</jats:sub>
) and 5′-ACAA-6 bp-TTGT-3′ (O
<jats:sub>R</jats:sub>
) and thus differ 2 bp in length, and consequently the two half-sites will be rotated with respect to each other by 72° in the idealized B-DNA (64° by dinucleotide steps calculations). Furthermore, a synthetic intermediate (DNA sequence) 5′-ACAA-5 bp-TTGT-3′ (O
<jats:sub>5</jats:sub>
) also binds specifically the repressor. The natural operators and bound repressors can form higher order DNA–protein complexes and perform efficient repression, whereas the synthetic operator-repressor complex cannot do either. The natural operators are bent when complexed with the repressor, whereas the O
<jats:sub>5</jats:sub>
operator does not show bending in electrophoretic mobility assay. Possible structures of the complexes are discussed.
</jats:p>
|
Binding sites of different geometries for the
<i>16</i>
-
<i>3</i>
phage repressor
|
[
"Papp Péter P. ",
"Nagy Tibor ",
"Ferenczi Szilamér ",
"Élõ Péter ",
"Csiszovszki Zsolt ",
"Buzás Zsuzsanna ",
"Patthy András ",
"Orosz László "
] |
https://doi.org/10.1073/pnas.132275399
| 2,002 |
July
|
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] |
10.1073/pnas.132277799
|
<jats:p>Quantitative evolutionary design involves the numerical relationships, evolved through natural selection, of biological capacities to each other and to natural loads. Here we study the relation of nutrient-processing capacities of the intestine and of organs beyond it (such as liver and kidneys) to each other and to natural loads of nutrients normally consumed. To control experimentally the rate of nutrient delivery to organs beyond the intestine, we administered nutrients directly into the veins of rats by the method of total parenteral nutrition (TPN). Control rats consuming the TPN solution by mouth ingested glucose at 42 mmol/day and processed it completely, as gauged by negligible appearance of glucose in urine and feces. Experimental rats receiving TPN were able to process infused glucose completely at rates up to 92 mmol/day. At higher infusion rates, they were unable to process further glucose, as gauged by rises in serum and urinary glucose levels and serum osmolality. At the highest infusion rates, they exhibited diuresis, dehydration, and both decreased weight gain and survival. These symptoms closely resemble the human diabetic condition known as nonketotic hypertonicity. Thus, a rat's body has a safety factor of 2.2 (=92/42) for glucose processing: it can process glucose at a rate 2.2 times its voluntary intake. This safety factor represents apparent excess capacity that may have evolved to process other nutrients converted into glucose, to minimize the risk of loads swamping capacities, to handle suddenly increased nutrient requirements, or to effect rapid mobilization of glucose.</jats:p>
|
Quantitative evolutionary design of nutrient processing: Glucose
|
[
"Steyermark Anthony C. ",
"Lam Mandy M. ",
"Diamond Jared "
] |
https://doi.org/10.1073/pnas.132277799
| 2,002 |
July
|
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] |
10.1073/pnas.132630999
|
<jats:p>Cell metabolism self-organizes into two types of dissipative structures: chemical oscillations and traveling metabolic waves. In the present study we test the hypothesis that traveling NAD(P)H waves within neutrophils are associated spatially and temporally with the release of reactive oxygen metabolites (ROMs). Using high-speed optical microscopy and taking advantage of the autofluorescence of NAD(P)H, we have observed the propagation of NAD(P)H waves within cells. When NAD(P)H waves reach the lamellipodium of morphologically polarized neutrophils, a diffusing plume of superoxide is released as evidenced by the conversion of hydroethidine in the extracellular environment to ethidium bromide. Parallel results were obtained by using high-speed emission microspectrophotometry. These experiments indicate that the spatial and temporal properties of NAD(P)H waves are transformed into ROM pulses in the extracellular environment. Propagating NAD(P)H waves allow neutrophils to specifically deliver substrate to the lamellipodium at high concentrations, thus facilitating the local and periodic release of ROMs in the direction of cell movement and/or a target.</jats:p>
|
Apparent role of traveling metabolic waves in oxidant release by living neutrophils
|
[
"Kindzelskii Andrei L. ",
"Petty Howard R. "
] |
https://doi.org/10.1073/pnas.132630999
| 2,002 |
July
|
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] |
10.1073/pnas.132711799
|
<jats:p>Actin-myosin (actomyosin) generates mechanical force by consuming ATP molecules. We apply the energy landscape perspective to address a controversial issue as to whether the myosin head moves with multiple steps after a single ATP hydrolysis or only a single mechanical event of the lever-arm swinging follows a single ATP hydrolysis. Here we propose a theoretical model in which the refolding of the partially unfolded actomyosin complex and the movement of the myosin head along the actin filament are coupled. A single ATP hydrolysis is followed by the formation of a high free-energy partially unfolded actomyosin complex, which then gradually refolds with a concomitant multiple stepping movement on the way to the lowest free-energy rigor state. The model quantitatively explains the single-molecular observation of the multiple stepping movement and is consistent with structural observations of the disorder in the actomyosin-binding process. The model also explains the observed variety in dwell time before each step, which is not accounted for by previous models, such as the lever-arm or ratchet models.</jats:p>
|
Conformational change of the actomyosin complex drives the multiple stepping movement
|
[
"Terada Tomoki P. ",
"Sasai Masaki ",
"Yomo Tetsuya "
] |
https://doi.org/10.1073/pnas.132711799
| 2,002 |
July
|
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] |
10.1073/pnas.142100999
|
<jats:p>
Lymphocyte homeostasis is the result of a critical balance between cell proliferation and death. Disruption of this subtle equilibrium can lead to the onset of leukemia, an increase in the number of lymphocytes being potentially due to both of these parameters. The relative importance of cell proliferation vs. apoptosis during pathogenesis induced by the primate T cell lymphotropic viruses and bovine leukemia virus (BLV) has been difficult to assess because of conflicting data from a range of
<jats:italic>in vitro</jats:italic>
and
<jats:italic>ex vivo</jats:italic>
experimental systems. Here, we aim to resolve this issue by measuring the rates of cell proliferation and death in the BLV-ovine system, an animal model of human T lymphotropic virus (HTLV-1). We use a method based on the i.v. injection of 5-bromodeoxyuridine into BLV-infected sheep. We show that B lymphocytes in BLV
<jats:sup>+</jats:sup>
asymptomatic sheep proliferate significantly faster than in uninfected controls (average proliferation rate: 0.020 per day vs. 0.011 per day). In contrast, the rates of cell death were not significantly different between aleukemic BLV-infected and control sheep (average death rate 0.089 per day vs. 0.094 per day, respectively). We conclude that the increase in the number of B cells during BLV-induced lymphocytosis results from higher proliferation rates but is not due to a significant decrease in apoptosis, in contrast to data from
<jats:italic>in vitro</jats:italic>
(
<jats:italic>ex vivo</jats:italic>
) experiments. The imbalance created by the net increase in proliferation in the absence of compensating cell death reveals a complex mechanism of feedback regulation controlling homeostasis in the blood compartment.
</jats:p>
|
Increased cell proliferation, but not reduced cell death, induces lymphocytosis in bovine leukemia virus-infected sheep
|
[
"Debacq Christophe ",
"Asquith Becca ",
"Kerkhofs Pierre ",
"Portetelle Daniel ",
"Burny Arsène ",
"Kettmann Richard ",
"Willems Luc "
] |
https://doi.org/10.1073/pnas.142100999
| 2,002 |
July
|
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] |
10.1073/pnas.152085999
|
<jats:p>
The regulators of G protein signaling (RGS) proteins modulate heterotrimeric G protein signaling. RGS8 is a brain-specific RGS protein of 180 aa. Here we identified a short isoform of RGS8, RGS8S, that arises by alternative splicing. RGS8S cDNA encodes a N terminus of 7 aa instead of amino acids 1–9 of RGS8 and 10–180 of RGS8. The subcellular distribution of RGS8 and RGS8S did not differ significantly in transfected cells. RGS8S accelerated, not as efficiently as RGS8, the turning on and off of Gi/o-mediated modulation of G protein-gated inwardly rectifying K
<jats:sup>+</jats:sup>
channels in
<jats:italic>Xenopus</jats:italic>
oocytes. We next examined the effects of RGS8 and RGS8S on Gq-mediated signaling. RGS8 decreased the amplitude of the response upon activation of m1 muscarinic or substance P receptors, but did not remarkably inhibit signaling from m3 muscarinic receptors. In contrast, RGS8S showed much less inhibition of the response of either of these Gq-coupled receptors. By quantitative analysis of the inhibitory effect and the protein expression level, we confirmed that the difference of inhibitory effect is caused by both the qualitative difference between RGS8 and RGS8S and the quantitative difference of the protein expression level. We also confirmed that the receptor-type specificity of inhibition is not caused by the difference of the expression level of the receptors. In summary, we showed that 9 aa in the N terminus of RGS8 contribute to the function to inhibit Gq-coupled signaling in a receptor type-specific manner and that the regulatory function of RGS8S is especially diminished on Gq-coupled responses.
</jats:p>
|
Alternative splicing of RGS8 gene determines inhibitory function of receptor type-specific Gq signaling
|
[
"Saitoh Osamu ",
"Murata Yoshimichi ",
"Odagiri Megumi ",
"Itoh Masayuki ",
"Itoh Hiroshi ",
"Misaka Takumi ",
"Kubo Yoshihiro "
] |
https://doi.org/10.1073/pnas.152085999
| 2,002 |
July
|
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] |
10.1073/pnas.152318799
|
<jats:p>An explanation, based on simple analysis of the spatiotemporal variations of the visual environment, is given to the automatic capture and focusing of visual attention. It is assumed that the transmittance for the sensory signals is modulated by separate control circuits that sample input from the same area of the visual field but at a lower resolution. When these circuits detect significant spatial and/or temporal variations, they “open gates” for the more accurate information arising from the same area. If the variations are related to the spatial resolution, which varies within wide limits over the retina, the visual field is “opened” up to a radius where it captures the most salient structures of the image. If the temporal variations of the signals are further emphasized, the high spatial frequencies begin to dominate. If then the gaze is moved by a small amount, the transmittance of the foveal signal paths is activated strongest.</jats:p>
|
Modeling of automatic capture and focusing of visual attention
|
[
"Kohonen Teuvo "
] |
https://doi.org/10.1073/pnas.152318799
| 2,002 |
July
|
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10.1073/pnas.152321699
|
<jats:p>
<jats:italic>F</jats:italic>
lap
<jats:italic>e</jats:italic>
ndo
<jats:italic>n</jats:italic>
uclease (Fen1) is required for DNA replication and repair, and defects in the gene encoding Fen1 cause increased accumulation of mutations and genome rearrangements. Because mutations in some genes involved in these processes cause cancer predisposition, we investigated the possibility that Fen1 may function in tumorigenesis of the gastrointestinal tract. Using gene knockout approaches, we introduced a null mutation into murine
<jats:italic>Fen1</jats:italic>
. Mice homozygous for the
<jats:italic>Fen1</jats:italic>
mutation were not obtained, suggesting absence of
<jats:italic>Fen1</jats:italic>
expression leads to embryonic lethality. Most
<jats:italic>Fen1</jats:italic>
heterozygous animals appear normal. However, when combined with a mutation in the adenomatous polyposis coli (
<jats:italic>Apc</jats:italic>
) gene, double heterozygous animals have increased numbers of adenocarcinomas and decreased survival. The tumors from these mice show microsatellite instability. Because one copy of the
<jats:italic>Fen1</jats:italic>
gene remained intact in tumors,
<jats:italic>Fen1</jats:italic>
haploinsufficiency appears to lead to rapid progression of cancer.
</jats:p>
|
Haploinsufficiency of Flap endonuclease (
<i>Fen1</i>
) leads to rapid tumor progression
|
[
"Kucherlapati Melanie ",
"Yang Kan ",
"Kuraguchi Mari ",
"Zhao Jie ",
"Lia Maria ",
"Heyer Joerg ",
"Kane Michael F. ",
"Fan Kunhua ",
"Russell Robert ",
"Brown Anthony M. C. ",
"Kneitz Burkhard ",
"Edelmann Winfried ",
"Kolodner Richard D. ",
"Lipkin Martin ",
"Kucherlapati Raju "
] |
https://doi.org/10.1073/pnas.152321699
| 2,002 |
July
|
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] |
10.1073/pnas.152324399
|
<jats:p>
The activity of the two dominant K
<jats:sup>+</jats:sup>
channels in the plasma membrane of
<jats:italic>Vicia faba</jats:italic>
guard cell protoplasts was examined during pressure-driven swelling. For this purpose, the K
<jats:sup>+</jats:sup>
currents and the membrane capacitance (C
<jats:sub>m</jats:sub>
) of guard cell protoplasts were recorded in parallel. A rise in C
<jats:sub>m</jats:sub>
, reflecting an increase of the membrane surface area, was coupled to a proportional rise in conductance of both the K
<jats:sup>+</jats:sup>
inward and K
<jats:sup>+</jats:sup>
outward rectifier. The activation kinetics of the K
<jats:sup>+</jats:sup>
channels were not affected during this process. The quantitative and temporal coupling of C
<jats:sub>m</jats:sub>
and K
<jats:sup>+</jats:sup>
conductance can hence be interpreted as the result of the addition of active inward and outward rectifier K
<jats:sup>+</jats:sup>
channels to the plasma membrane during an increase in surface area.
</jats:p>
|
The number of K
<sup>+</sup>
channels in the plasma membrane of guard cell protoplasts changes in parallel with the surface area
|
[
"Homann Ulrike ",
"Thiel Gerhard "
] |
https://doi.org/10.1073/pnas.152324399
| 2,002 |
July
|
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] |
10.1080/00071310220133313
|
<jats:title>ABSTRACT</jats:title><jats:p>Against the backdrop of discussions about the ‘Information Society’, the ‘Informational Economy’ and the role of IT in realizing organizational change we examine how representations of ‘organizational knowledge’ are constructed and used in work settings. We do this through the explication of ethnographic materials that detail the realization and use of Management Information (MI) in a major UK retail bank undergoing massive organizational change. We focus in particular on explicating how existing metric information was drawn upon to construct a representation of the work of the bank for those involved in managing that work. Systems designers have been increasingly interested in offering ways of conceptualizing the problem of ‘knowledge’ with a view to embedding these properties in systems. In the quest to develop representations of procedural knowledge to support work we argue that it is first necessary to understand how representations are actually created and used in work to support existing work practices.</jats:p>
|
Representing knowledge: instances of management information
|
[
"Hughes John A. ",
"Rouncefield Mark ",
"Tolmie Peter "
] |
https://doi.org/10.1080/00071310220133313
| 2,002 |
July
|
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] |
10.1080/00207590143000315
|
<jats:p><jats:italic>T</jats:italic>he status of efforts to indigenize psychology in the Philippines is reviewed. We address progress in four aspects of indigenization: theoretical/conceptual, methodological, topical, and institutional. Much, but not all, of this progress is the result of efforts associated with the indigenous Sikolohiyang Pilipino (Filipino psychology) movement, which emphasizes (a) the development of a Filipino psychology that reflects the unique experiences and orientations of Filipinos, (b) Filipino identity and national consciousness, (c) explicit socio‐political considerations, (d) application of psychology to societal problems, (e) the study of less elite Filipinos, (f) interdisciplinary efforts, and (g) the use of indigenous languages in the development and dissemination of indigenous psychology. We note considerable progress, but also controversy, in the selection and interpretation of indigenous concepts and less progress in the formulation of indigenous theories. Existing theories are narrow in scope, only partially specified, and have uncertain heuristic value in generating verifiable predictions. Filipino psychologists have also adapted or further specified Western theoretical frameworks to make them more sensitive to Philippine contextual factors. Many indigenous measures have been developed, but more information is needed on their psychometric properties. Several indigenous research methods have been described and these methods typically emphasize the importance of the researcher‐participant relationship. There remain questions about the objectivity and cultural uniqueness of these methods, however, many of which involve (a) unstructured conversations and discussions in lieu of structured interviews, (b) varying degrees of participant observation, or (c) qualitative phenomenological methods. Extensive topical indigenization is evident in studies that focus on everyday Filipinos and Philippine societal concerns. Institutional indigenization is reflected in courses, theses and dissertations, journals, books, conferences, and professional organizations with an indigenous focus. Potential limitations or risks to the indigenous movement include insularity and the limited research culture. Implications of the Philippine case for indigenization efforts in other cultures are discussed.</jats:p>
|
Indigenization of psychology in the Philippines
|
[
"Church A. Timothy ",
"Katigbak Marcia S. "
] |
https://doi.org/10.1080/00207590143000315
| 2,002 |
July
|
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] |
10.1080/10427710050025358
|
<jats:p>There is great variety within contemporary economics. As Coats (2000) points out, not only are there several schools of thought that would conventionally be labeled “heterodox,” there are numerous economists whose work is in a significant sense unorthodox or unconventional. How, then, can a dividing line be drawn between dissent within orthodoxy and dissent from orthodoxy? The suggestion I make here is that a heterodox school of thought has to satisfy three criteria.</jats:p>
|
Progress in Heterodox Economics
|
[
"Backhouse Roger E. "
] |
https://doi.org/10.1080/10427710050025358
| 2,002 |
July
|
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] |
10.1080/10427710050025385
|
<jats:p>This topic is more in contemporary economics than in the history of economics, but in this case an historical perspective does help us to understand the present day. Roger Backhouse and Sheila Dow have approached the progress of heterodox economics mainly through the philosophy and methodology of the discipline. I take a more sociological approach. I see the issue as external to the discipline at least as much as internal.</jats:p>
|
Comment: It's the Homogeneity, Stupid!
|
[
"Goodwin Craufurd D. "
] |
https://doi.org/10.1080/10427710050025385
| 2,002 |
July
|
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] |
10.1080/14616690220130991
|
<jats:p>Since the breakdown of communism, Germany has experienced a major influx of Aussiedler who are basically migrants originating from Eastern European countries. In this article, we use data from the German Socio-Economic Panel of the year 1998 to analyse the labour market performance of this group of migrants. Our key hypothesis guiding the empirical investigations is that in occupational labour markets, such as the German one, migrants are faced with specific problems when transferring their educational and vocational skills acquired in other countries. Only if they gain access to their trained occupations are they able to perform well in the labour market. Otherwise, occupational closure hinders them from receiving returns to their educational and vocational qualifications.</jats:p>
|
The performance of migrants in occupational labour markets
|
[
"Kreyenfeld Michaela ",
"Konietzka Dirk "
] |
https://doi.org/10.1080/14616690220130991
| 2,002 |
July
|
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] |
10.1083/jcb.200202058
|
<jats:p>KIFC3, a microtubule (MT) minus end–directed kinesin superfamily protein, is expressed abundantly and is associated with the Golgi apparatus in adrenocortical cells. We report here that disruption of the kifC3 gene induced fragmentation of the Golgi apparatus when cholesterol was depleted. Analysis of the reassembly process of the Golgi apparatus revealed bidirectional movement of the Golgi fragments in both wild-type and kifC3−/− cells. However, we observed a markedly reduced inwardly directed motility of the Golgi fragments in cholesterol-depleted kifC3−/− cells compared with either cholesterol-depleted wild-type cells or cholesterol-replenished kifC3−/− cells. These results suggest that (a) under the cholesterol-depleted condition, reduced inwardly directed motility of the Golgi apparatus results in the observed Golgi scattering phenotype in kifC3−/− cells, and (b) cholesterol is necessary for the Golgi fragments to attain sufficient inwardly directed motility by MT minus end–directed motors other than KIFC3, such as dynein, in kifC3−/− cells. Furthermore, we showed that Golgi scattering was much more drastic in kifC3−/− cells than in wild-type cells to the exogenous dynamitin expression even in the presence of cholesterol. These results collectively demonstrate that KIFC3 plays a complementary role in Golgi positioning and integration with cytoplasmic dynein.</jats:p>
|
Role of KIFC3 motor protein in Golgi positioning and integration
|
[
"Xu Ying ",
"Takeda Sen ",
"Nakata Takao ",
"Noda Yasuko ",
"Tanaka Yosuke ",
"Hirokawa Nobutaka "
] |
https://doi.org/10.1083/jcb.200202058
| 2,002 |
July
|
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] |
10.1083/jcb.200202082
|
<jats:p>Characterization of mammalian NSF (G274E) and Drosophila NSF (comatose) mutants revealed an evolutionarily conserved NSF activity distinct from ATPase-dependent SNARE disassembly that was essential for Golgi membrane fusion. Analysis of mammalian NSF function during cell-free assembly of Golgi cisternae from mitotic Golgi fragments revealed that NSF disassembles Golgi SNAREs during mitotic Golgi fragmentation. A subsequent ATPase-independent NSF activity restricted to the reassembly phase is essential for membrane fusion. NSF/α-SNAP catalyze the binding of GATE-16 to GOS-28, a Golgi v-SNARE, in a manner that requires ATP but not ATP hydrolysis. GATE-16 is essential for NSF-driven Golgi reassembly and precludes GOS-28 from binding to its cognate t-SNARE, syntaxin-5. We suggest that this occurs at the inception of Golgi reassembly to protect the v-SNARE and regulate SNARE function.</jats:p>
|
Sequential SNARE disassembly and GATE-16–GOS-28 complex assembly mediated by distinct NSF activities drives Golgi membrane fusion
|
[
"Müller Joyce M.M. ",
"Shorter James ",
"Newman Richard ",
"Deinhardt Katrin ",
"Sagiv Yuval ",
"Elazar Zvulun ",
"Warren Graham ",
"Shima David T. "
] |
https://doi.org/10.1083/jcb.200202082
| 2,002 |
July
|
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] |
10.1083/jcb.200206094
|
<jats:p>Lysophosphatidic acid (LPA) is a serum phospholipid that evokes growth factor–like responses in many cell types through the activation of its G protein–coupled receptors. Although much is known about LPA signaling, it has remained unclear where and how bioactive LPA is produced. Umezu-Goto et al. (2002)(this issue, page 227) have purified a serum lysophospholipase D that generates LPA from lysophosphatidylcholine and found it to be identical to autotaxin, a cell motility–stimulating ectophosphodiesterase implicated in tumor progression. This result is surprising, as there was previously no indication that autotaxin could act as a phospholipase.</jats:p>
|
Lysophospholipids in the limelight
|
[
"Moolenaar Wouter H. "
] |
https://doi.org/10.1083/jcb.200206094
| 2,002 |
July
|
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10.1084/jem.20011470
|
<jats:p>Fas and the tumor necrosis factor receptor (TNFR)1 regulate the programmed cell death of lymphocytes. The death domain kinase, receptor interacting protein (rip), is recruited to the TNFR1 upon receptor activation. In vitro, rip−/− fibroblasts are sensitive to TNF-induced cell death due to an impaired nuclear factor κB response. Because rip−/− mice die at birth, we were unable to examine the effects of a targeted rip mutation on lymphocyte survival. To address the contribution of RIP to immune homeostasis, we examined lethally irradiated mice reconstituted with rip−/− hematopoietic precursors. We observed a decrease in rip−/− thymocytes and T cells in both wild-type C57BL/6 and recombination activating gene 1−/− irradiated hosts. In contrast, the B cell and myeloid lineages are unaffected by the absence of rip. Thus, the death domain kinase rip is required for T cell development. Unlike Fas-associated death domain, rip does not regulate T cell proliferation, as rip−/− T cells respond to polyclonal activators. However, rip-deficient mice contain few viable CD4+ and CD8+ thymocytes, and rip−/− thymocytes are sensitive to TNF-induced cell death. Surprisingly, the rip-associated thymocyte apoptosis was not rescued by the absence of TNFR1, but appears to be rescued by an absence of TNFR2. Taken together, this study implicates RIP and TNFR2 in thymocyte survival.</jats:p>
|
The Death Domain Kinase RIP Protects Thymocytes from Tumor Necrosis Factor Receptor Type 2–induced Cell Death
|
[
"Cusson Nicole ",
"Oikemus Sarah ",
"Kilpatrick Elizabeth D. ",
"Cunningham Leslie ",
"Kelliher Michelle "
] |
https://doi.org/10.1084/jem.20011470
| 2,002 |
July
|
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] |
10.1084/jem.20011682
|
<jats:p>Accumulating evidence has shown the importance of Stat6-mediated signaling in allergic diseases. In this study, we show a novel regulatory mechanism of Stat6-mediated signaling in mast cells. When Stat6 is activated by interleukin (IL)-4 and translocated to the nucleus, Stat6 is cleaved by a nucleus-associated protease in mast cells. The cleaved 65-kD Stat6 lacks the COOH-terminal transactivation domain and functions as a dominant-negative molecule to Stat6-mediated transcription. The retrovirus-mediated expression of cleavage-resistant Stat6 mutants prolongs the nuclear accumulation of Stat6 upon IL-4 stimulation and enhances IL-4–induced gene expression and growth inhibition in mast cells. These results indicate that the proteolytic processing of Stat6 functions as a lineage-specific negative regulator of Stat6-dependent signaling in mast cells, and thus suggest that it may account for the limited role of Stat6 in IL-4 signaling in mast cells.</jats:p>
|
Proteolytic Processing of Stat6 Signaling in Mast Cells as a Negative Regulatory Mechanism
|
[
"Suzuki Kotaro ",
"Nakajima Hiroshi ",
"Kagami Shin-ichiro ",
"Suto Akira ",
"Ikeda Kei ",
"Hirose Koichi ",
"Hiwasa Takaki ",
"Takeda Kiyoshi ",
"Saito Yasushi ",
"Akira Shizuo ",
"Iwamoto Itsuo "
] |
https://doi.org/10.1084/jem.20011682
| 2,002 |
July
|
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] |
10.1084/jem.20020063
|
<jats:p>The immunosurveillance of transformed cells by the immune system remains one of the most controversial and poorly understood areas of immunity. Gene-targeted mice have greatly aided our understanding of the key effector molecules in tumor immunity. Herein, we describe spontaneous tumor development in gene-targeted mice lacking interferon (IFN)-γ and/or perforin (pfp), or the immunoregulatory cytokines, interleukin (IL)-12, IL-18, and tumor necrosis factor (TNF). Both IFN-γ and pfp were critical for suppression of lymphomagenesis, however the level of protection afforded by IFN-γ was strain specific. Lymphomas arising in IFN-γ-deficient mice were very nonimmunogenic compared with those derived from pfp-deficient mice, suggesting a comparatively weaker immunoselection pressure by IFN-γ. Single loss of IL-12, IL-18, or TNF was not sufficient for spontaneous tumor development. A significant incidence of late onset adenocarcinoma observed in both IFN-γ– and pfp-deficient mice indicated that some epithelial tissues were also subject to immunosurveillance.</jats:p>
|
Suppression of Lymphoma and Epithelial Malignancies Effected by Interferon γ
|
[
"Street Shayna E.A. ",
"Trapani Joseph A. ",
"MacGregor Duncan ",
"Smyth Mark J. "
] |
https://doi.org/10.1084/jem.20020063
| 2,002 |
July
|
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] |
10.1084/jem.20020773
|
<jats:p>Unmethylated CpG motifs present in bacterial DNA stimulate a strong innate immune response. There is evidence that DNA-dependent protein kinase (DNA-PK) mediates CpG signaling. Specifically, wortmannin (an inhibitor of phosphatidylinositol 3 kinase [PI3]-kinases including DNA-PK) interferes with CpG-dependent cell activation, and DNA-PK knockout (KO) mice fail to respond to CpG stimulation. Current studies establish that wortmannin actually inhibits the uptake and colocalization of CpG DNA with toll-like receptor (TLR)-9 in endocytic vesicles, thereby preventing CpG-induced activation of the NF-κB signaling cascade. We find that DNA-PK is not involved in this process, since three strains of DNA-PK KO mice responded normally to CpG DNA. These results support a model in which CpG signaling is mediated through TLR-9 but not DNA-PK, and suggest that wortmannin-sensitive member(s) of the PI3-kinase family play a critical role in shuttling CpG DNA to TLR-9.</jats:p>
|
Potential Role of Phosphatidylinositol 3 Kinase, rather than DNA-dependent Protein Kinase, in CpG DNA–induced Immune Activation
|
[
"Ishii Ken J. ",
"Takeshita Fumihiko ",
"Gursel Ihsan ",
"Gursel Mayda ",
"Conover Jacqueline ",
"Nussenzweig Andre ",
"Klinman Dennis M. "
] |
https://doi.org/10.1084/jem.20020773
| 2,002 |
July
|
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10.1085/jgp.20028535
|
<jats:p>ATP-gated P2X channels are the simplest of the three families of transmitter-gated ion channels. Some P2X channels display a time- and activation-dependent change in permeability as they undergo the transition from the relatively Na+-selective I1 state to the I2 state, which is also permeable to organic cations. We report that the previously reported permeability change of rat P2X2 (rP2X2) channels does not occur at mouse P2X2 (mP2X2) channels expressed in oocytes. Domain swaps, species chimeras, and point mutations were employed to determine that two specific amino acid residues in the cytosolic tail domain govern this difference in behavior between the two orthologous channels. The change in pore diameter was characterized using reversal potential measurements and excluded field theory for several organic ions; both rP2X2 and mP2X2 channels have a pore diameter of ∼11 Å in the I1 state, but the transition to the I2 state increases the rP2X2 diameter by at least 3 Å. The I1 to I2 transition occurs with a rate constant of ∼0.5 s−1. The data focus attention on specific residues of P2X2 channel cytoplasmic domains as determinants of permeation in a state-specific manner.</jats:p>
|
Control of P2X2 Channel Permeability by the Cytosolic Domain
|
[
"Eickhorst Angela N. ",
"Berson Amy ",
"Cockayne Debra ",
"Lester Henry A. ",
"Khakh Baljit S. "
] |
https://doi.org/10.1085/jgp.20028535
| 2,002 |
July
|
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] |
10.1085/jgp.20028576
|
<jats:p>Inward rectification in strong inward rectifiers such as Kir2.1 is attributed to voltage-dependent block by intracellular polyamines and Mg2+. Block by the polyamine spermine has a complex voltage dependence with shallow and steep components and complex concentration dependence. To understand the mechanism, we measured macroscopic Kir2.1 currents in excised inside-out giant patches from Xenopus oocytes expressing Kir2.1, and single channel currents in the inside-out patches from COS7 cells transfected with Kir2.1. We found that as spermine concentration or voltage increased, the shallow voltage-dependent component of spermine block at more negative voltages was caused by progressive reduction in the single channel current amplitude, without a decrease in open probability. We attributed this effect to spermine screening negative surface charges involving E224 and E299 near the inner vestibule of the channel, thereby reducing K ion permeation rate. This idea was further supported by experiments in which increasing ionic strength also decreased Kir2.1 single channel amplitude, and by mutagenesis experiments showing that this component of spermine block decreased when E224 and E299, but not D172, were neutralized. The steep voltage-dependent component of block at more depolarized voltages was attributed to spermine migrating deeper into the pore and causing fast open channel block. A quantitative model incorporating both features showed excellent agreement with the steady-state and kinetic data. In addition, this model accounts for previously described substate behavior induced by a variety of Kir2.1 channel blockers.</jats:p>
|
Spermine Block of the Strong Inward Rectifier Potassium Channel Kir2.1
|
[
"Xie Lai-Hua ",
"John Scott A. ",
"Weiss James N. "
] |
https://doi.org/10.1085/jgp.20028576
| 2,002 |
July
|
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] |
10.1085/jgp.20028607
|
<jats:p>Tumor cell membranes have multiple components that participate in the process of metastasis. The present study investigates the physical association of β1-integrins and Kv1.3 voltage-gated potassium channels in melanoma cell membranes using resonance energy transfer (RET) techniques. RET between donor-labeled anti–β1-integrin and acceptor-labeled anti-Kv1.3 channels was detected on LOX cells adherent to glass and fibronectin-coated coverslips. However, RET was not observed on LOX cells in suspension, indicating that molecular proximity of these membrane molecules is adherence-related. Several K+ channel blockers, including tetraethylammonium, 4-aminopyridine, and verapamil, inhibited RET between β1-integrins and Kv1.3 channels. However, the irrelevant K+ channel blocker apamin had no effect on RET between β1-integrins and Kv1.3 channels. Based on these findings, we speculate that the lateral association of Kv1.3 channels with β1-integrins contributes to the regulation of integrin function and that channel blockers might affect tumor cell behavior by influencing the assembly of supramolecular structures containing integrins.</jats:p>
|
Molecular Proximity of Kv1.3 Voltage-gated Potassium Channels and β1-Integrins on the Plasma Membrane of Melanoma Cells
|
[
"Artym Vira V. ",
"Petty Howard R. "
] |
https://doi.org/10.1085/jgp.20028607
| 2,002 |
July
|
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] |
10.1091/mbc.01-12-0572
|
<jats:p>Ionizing radiation (1–5 Gy) activates the epidermal growth factor receptor (EGFR), a major effector of the p42/44 mitogen-activated protein kinase (MAPK) pathway. MAPK and its downstream effector, p90 ribosomal S6 kinase (p90RSK), phosphorylate transcription factors involved in cell proliferation. To establish the role of the EGFR/MAPK pathway in radiation-induced transcription factor activation, MDA-MB-231 human breast carcinoma cells were examined using specific inhibitors of signaling pathways. Gel-shift analysis revealed three different profile groups: 1) transcription factors that responded to both radiation (2 Gy) and epidermal growth factor (EGF) (CREB, Egr, Ets, and Stat3); 2) factors that responded to radiation, but not EGF (C/EBP and Stat1); and 3) those that did not respond significantly to either radiation or EGF (AP-1 and Myc). Within groups 1 and 2, a two- to fivefold maximum stimulation of binding activity was observed at 30–60 min after irradiation. Interestingly, only transcription factors that responded to EGF had radiation responses significantly inhibited by the EGFR tyrosine kinase inhibitor, AG1478; these responses were also abrogated by farnesyltransferase inhibitor (FTI) or PD98059, inhibitors of Ras and MEK1/2, respectively. Moreover, radiation-induced increases in CREB and p90RSK phosphorylation and activation of Stat3 and Egr-1 reporter constructs by radiation were all abolished by AG1478. These data demonstrate a distinct radiation response profile at the transcriptional level that is dependent on enhanced EGFR/Ras/MAPK signaling.</jats:p>
|
Epidermal Growth Factor Receptor Dependence of Radiation-induced Transcription Factor Activation in Human Breast Carcinoma Cells
|
[
"Amorino George P. ",
"Hamilton Virginia M. ",
"Valerie Kristoffer ",
"Dent Paul ",
"Lammering Guido ",
"Schmidt-Ullrich Rupert K. "
] |
https://doi.org/10.1091/mbc.01-12-0572
| 2,002 |
July
|
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10.1091/mbc.e01-10-0096
|
<jats:p>To investigate the importance of tyrosine recognition by the AP-1B clathrin adaptor subunit μ1B for basolateral sorting of integral membrane proteins in polarized epithelial cells, we have produced and characterized a mutant form of μ1B. The mutant (M-μ1B) contains alanine substitutions of each of the four conserved residues, which in the AP-2 adaptor subunit μ2 are critical for interacting with tyrosine-based endocytosis signals. We show M-μ1B is defective for tyrosine binding in vitro, but is nevertheless incorporated into AP-1 complexes in transfected cells. Using LLC-PK1 cells expressing either wild type or M-μ1B, we find that there is inefficient basolateral expression of membrane proteins whose basolateral targeting signals share critical tyrosines with signals for endocytosis. In contrast, membrane proteins whose basolateral targeting signals are distinct from their endocytosis signals (transferrin and low-density lipoprotein receptors) accumulate at the basolateral domain normally, although in a manner that is strictly dependent on μ1B or M-μ1B expression. Our results suggest that μ1B interacts with different classes of basolateral targeting signals in distinct ways.</jats:p>
|
Differential Recognition of Tyrosine-based Basolateral Signals by AP-1B Subunit μ1B in Polarized Epithelial Cells
|
[
"Sugimoto Hisashi ",
"Sugahara Masayuki ",
"Fölsch Heike ",
"Koide Yasuhiro ",
"Nakatsu Fubito ",
"Tanaka Naotaka ",
"Nishimura Toshiro ",
"Furukawa Mitsuru ",
"Mullins Chris ",
"Nakamura Nobuhiro ",
"Mellman Ira ",
"Ohno Hiroshi "
] |
https://doi.org/10.1091/mbc.e01-10-0096
| 2,002 |
July
|
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] |
10.1093/bioinformatics/18.7.939
|
<jats:title>Abstract</jats:title>
<jats:p>Classical molecular interaction potentials, in conjunction with other theoretical techniques, are used to analyze the dependence of the binding sites of representative proteins on the bound ligand. It is found that the ligand bound introduces in general small structural perturbations at the binding site of the protein. However, such small structural changes can lead to important alterations in the recognition pattern of the protein. The impact of these findings in docking procedures is discussed.</jats:p>
<jats:p>Contact: [email protected]; [email protected]</jats:p>
<jats:p>* To whom correspondence should be addressed.</jats:p>
|
Ligand-induced changes in the binding sites of proteins
|
[
"Fradera Xavier ",
"de la Cruz Xavier ",
"Silva Carlos H. T. P. ",
"Gelpí Jose Luis ",
"Luque F.J. ",
"Orozco Modesto "
] |
https://doi.org/10.1093/bioinformatics/18.7.939
| 2,002 |
July
|
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] |
10.1093/bioinformatics/18.7.961
|
<jats:title>Abstract</jats:title>
<jats:p>Motivation: The last few years have seen the development of DNA microarray technology that allows simultaneous measurement of the expression levels of thousands of genes. While many methods have been developed to analyze such data, most have been visualization-based. Methods that yield quantitative conclusions have been diverse and complex.</jats:p>
<jats:p>Results: We present two straightforward methods for identifying specific genes whose expression is linked with a phenotype or outcome variable as well as for systematically predicting sample class membership: (1) a conservative, permutation-based approach to identifying differentially expressed genes; (2) an augmentation of K-nearest-neighbor pattern classification. Our analyses replicate the quantitative conclusions of Golub et al. (1999; Science, 286, 531–537) on leukemia data, with better classification results, using far simpler methods. With the breast tumor data of Perou et al. (2000; Nature, 406, 747–752), the methods lend rigorous quantitative support to the conclusions of the original paper. In the case of the lymphoma data in Alizadeh et al. (2000; Nature, 403, 503–511), our analyses only partially support the conclusions of the original authors.</jats:p>
<jats:p>Availability: The software and supplementary information are available freely to researchers at academic and non-profit institutions at http://cc.ucsf.edu/jain/public</jats:p>
<jats:p>Contact: [email protected]</jats:p>
<jats:p>* To whom correspondence should be addressed.</jats:p>
|
Deriving quantitative conclusions from microarray expression data
|
[
"Olshen Adam B. ",
"Jain Ajay N. "
] |
https://doi.org/10.1093/bioinformatics/18.7.961
| 2,002 |
July
|
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