bluuebunny/crossref_metadata_2025 huggingface dataset:
Anisotropic thermal conductivity of the Aurivillus phase, bismuth titanate (Bi4Ti3O12): A natural nanostructured superlattice
Authors: Shen Yang , Clarke David R. , Fuierer Paul A.
Published: September 2008

The thermal conductivity of c-axis textured polycrystalline perovskite Bi4Ti3O12 and random polycrystalline material is reported up to 1000 °C. Based on measurements of the thermal diffusivity, density, and specific heat, the thermal conductivity is lower along the c-axis than in the a-b plane by almost a factor of 2, and the anisotropy persists up to at least 1000 °C despite a change in the crystal structure at 675 °C. The exceptionally low (1.0 W/mK), temperature-independent conductivity perpendicular to the perovskite layer structure is attributed to the density difference between the pseudoperovskite and fluorite blocks in the unit cell, forming a natural nanostructured superlattice.
Temperature dependence and physical properties of Ga(NAsP)/GaP semiconductor lasers
Authors: Chamings J. , Adams A. R. , Sweeney S. J. , Kunert B. , Volz K. , Stolz W.
Published: September 2008

We report on the properties of GaNAsP/GaP lasers which offer a potential route to producing lasers monolithically on silicon. Lasing has been observed over a wide temperature range with pulsed threshold current density of 2.5 kA/cm2 at 80 K (λ=890 nm). Temperature dependence measurements show that the radiative component of the threshold is relatively temperature stable while the overall threshold current is temperature sensitive. A sublinear variation of spontaneous emission versus current coupled with a decrease in external quantum efficiency with increasing temperature and an increase in threshold current with hydrostatic pressure implies that a carrier leakage path is the dominant carrier recombination mechanism.
Compositional and structural changes at the anodic surface of thermally poled soda-lime float glass
Authors: Ziemath E. C. , Araújo V. D. , Escanhoela C. A.
Published: September 2008

Applying high dc electric fields at elevated temperatures on silicate glasses results in displacement of ions, causing compositional and structural changes in the anodic surface. In this work, the ionic displacement was accompanied by electric current measurements during poling. The thickness of the Na+ depletion layer calculated from the current curves agrees with the thickness measured by EDS only if displacement of Ca2+ and O− are also taken into account. A depletion of Ca2+ in the anodic surface has in fact been observed. Structural changes were confirmed by infrared diffuse and specular reflectance spectroscopies. A narrowing of the band at about 1070 cm−1 can be attributed to an increase in the structural ordering degree. Refractive index measurements confirm compositional changes and contact angle measurements indicate the existence of a negative charge density at the anodic surface.
Lattice thermal conductivity of Si nanowires: Effect of modified phonon density of states
Authors: Lü Xiang
Published: September 2008

We investigate the size-dependent lattice thermal conductivity of silicon (Si) square cross-sectional and cylindrical nanowires. The calculation includes the modifications of the phonon density of states and group velocities due to phonon confinement. The decrease in phonon density of states and group velocities results in further thermal conductivity reduction in Si nanowires. By using suitable values of interface specularity parameters, the calculated thermal conductivities of Si square cross-sectional and cylindrical nanowires are found to be in good agreement with molecular dynamics and experimental results, respectively.
Mapping the thermal response of planar diffusion-type Si photodiodes under different bias conditions using optical microthermography
Authors: Cemine Vernon Julius , Mar Blanca Carlo
Published: September 2008

We map the local thermal progression of the photocurrent across the surface of a planar silicon photodiode at forward and reverse bias operations using optical-feedback laser microscopy. The photocurrent topographies exhibit distinct behavior dependent on the bias mode of the device with the width depletion layer varying with voltage. The maps also reveal local photocurrent behavior in the n-region that decay (at reverse bias) or remain constant (at forward bias) at elevated temperatures. Specific areas on the diode can be enhanced by driving the device in different bias modes which improves site selectivity and augments the method’s sensitivity to the thermal response of regions of interest for a more thorough performance characterization.
High-throughput viscosity determinations
Authors: Ma Jing , Lopez-Pedrosa Jose M. , Bradley Mark
Published: September 2008

A new high-throughput viscosimeter device was designed, built, and tested allowing measurement of the viscosity of 100 different solutions in a single experiment using the falling sphere approach. Using the corrected Stokes’ law, viscosities obtained by the HT device were compared to viscosities of the same solutions obtained on a conventional viscosimeter and showed excellent correlation. The theoretical set of data, correlated with Reynolds numbers, and the viscosities obtained for each sample showed very good correlation with the experimental data, demonstrating the robustness of the device.
A molecular site-site integral equation that yields the dielectric constant
Authors: Dyer Kippi M. , Perkyns John S. , Stell George , Pettitt B. Montgomery
Published: September 2008

Our recent derivation [K. M. Dyer et al., J. Chem. Phys. 127, 194506 (2007)] of a diagrammatically proper, site-site, integral equation theory using molecular angular expansions is extended to polar fluids. With the addition of atomic site charges we take advantage of the formal long-ranged potential field cancellations before renormalization to generate a set of numerically stable equations. Results for calculations in a minimal (spherical) angular basis set are presented for the radial distribution function, the first dipolar (110) projection, and the dielectric constant for two model diatomic systems. All results, when compared to experiment and simulation, are a significant quantitative and qualitative improvement over previous site-site theories. More importantly, the dielectric constant is not trivial and close to simulation and experiment.
Frequency shift in the moving periodic structure
Authors: Dong Tian-lin , Xia Dan
Published: September 2008

The interaction between the electromagnetic wave and the moving periodic structure is analyzed. The main physical effect revealed by theoretical analysis is that the frequency shift of the scattered or transmitted mode is proportional to the speed and the mode order m over the period a. The frequency shift is independent of the incidence direction and the carrier frequency. The physical effect is verified by an experiment. The analysis released here is fundamental in speed measurement and may have certain significance in interdisciplinary fields.
How does sensitivity to dynamical heterogeneity in supercooled colloidal liquids depend on tracer size?
Authors: Sarangapani Prasad , Zhao Jiang , Zhu Yingxi
Published: September 2008

Few experimental investigations have examined the dependence of probe length scale on the evolution of dynamical heterogeneity in supercooled liquids. In this study, we use fluorescent tracer probes, which are smaller than that of the constituent unlabeled particles in the matrix suspension, to investigate the tracer size sensitivity to the onset of dynamical heterogeneity in model hard-sphere colloidal suspensions close to the glass transition. The dynamics of poly(methyl methacrylate) (PMMA) tracer particles of radii aS=137nm embedded into constituent PMMA particles of aL=212 and 637nm with bulk volume fraction ϕ varied from 0.50 to 0.57 is examined using fluorescence correlation spectroscopy (FCS). Upon increasing ϕ for the largest tracer size ratio explored, f (=aS∕aL)=0.646, the onset of dynamic heterogeneity is observed from the broad distribution of characteristic decay times of the tracers, which is extracted from the measured FCS autocorrelation functions. The strong coupling between tracer size and its sensitivity to dynamical heterogeneity is reflected in the dynamic susceptibility, where dynamic correlation lengths are immeasurable for the smallest size ratio and show a marked increase to five tracer particle diameters for the largest size ratio.
Diffusion, aggregation, and the thermal conductivity of nanofluids
Authors: Gharagozloo Patricia E. , Eaton John K. , Goodson Kenneth E.
Published: September 2008

The effects of nanoparticle aggregation and diffusion are difficult to separate using most nanofluid thermal conductivity data, for which the temperature dependence is collected sequentially. The present work captures the instantaneous temperature-dependent thermal conductivity using cross-sectional infrared microscopy and tracks the effects of aggregation and diffusion over time. The resulting data are strongly influenced by spatial and temperature variations in particle size and concentration and are interpreted using a Monte Carlo simulation and rate equations for particle and heat transport. These experiments improve our understanding of nanofluid behavior in practical systems including microscale heat exchangers.
m
=
1
ideal kink modes in a line-tied screw pinch with finite plasma pressure
Authors: Svidzinski V. A. , Mirnov V. V. , Li H.
Published: September 2008

A new method for computing ideal magnetohydrodynamic linear eigenmodes in a cylindrical screw pinch with line-tying boundary conditions at the axial ends is presented. In this method, plasma volume is reflected over one of the end planes, and equations and field components are continued into the extended volume with the continuation rules prescribed by the line-tying boundary conditions. Field components in the combined volume are expanded in Fourier series in the axial coordinate. The resulting set of coupled differential equations is solved numerically in the radial coordinate by a finite difference method yielding growth rates and eigenmodes for the system. An example of an m=1 (m is the poloidal wave number) internal kink instability in a force-free plasma equilibrium with uniform pressure is considered. In contrast to a periodic screw pinch, marginally stable perturbations are essentially compressible in the line-tied geometry. Finite compressibility makes the mode more stable in addition to the usual line-tying stabilization in zero pressure plasma. The critical length corresponding to the marginal stability increases with the increase of plasma beta. A universal axial dependence for marginally stable density perturbations ρ(r,z)=ρ(r)exp[−izμ(r)] is predicted analytically and confirmed numerically, where μ(r) depends on the equilibrium magnetic field components as μ(r)=B¯θ∕rB¯z.
Evolution of convective patterns in a binary-mixture layer subjected to a periodical change of the gravity field
Authors: Smorodin B. L. , Myznikova B. I. , Legros J. C.
Published: September 2008

A theoretical study has been made of the convective stability and developed heat transfer regimes in a horizontal, binary-mixture layer with negative Soret coupling. The system is under temperature gradient and finite-frequency vibration. Both analytical and numerical examinations are presented. The limiting case of long-wave disturbances is studied using the perturbation method. To find instability thresholds in the linear approximation the Floquet theory is applied. The stability borders and characteristics of critical disturbances are determined depending on the vibration frequency for typical gaseous, liquid, and colloidal mixtures. The phase mapping and the Fourier spectra are used to describe the nonlinear evolution of the convective system. It is shown that supercritical flows within the first and second resonance domains develop via soft-mode transitions at critical parameter values which are consistent with the predictions of the linear stability theory. The nonlinear convection patterns demonstrate the synchronous, subharmonic, or quasiperiodic dynamics. The hysteretic transitions between nonlinear regimes are also investigated. The influence of the vibrational Grashof number on the concentration field is discussed for standing wave and traveling wave modes.
Advanced interferometric profile measurements through refractive media
Authors: Koev Stephan T. , Ghodssi Reza
Published: September 2008

Optical profilers are valuable tools for the characterization of microelectromechanical systems (MEMSs). They use phase sifting interferometry (PSI) or vertical scanning interferometry to measure the topography of microscale structures with nanometer resolution. However, for many emerging MEMS applications, the sample needs to be imaged while placed in a liquid or in a package with a glass window. The increased refractive index of the transparent medium degrades the interference image contrast and prevents any measurement of the sample. We report on the modification of a Veeco NT1100 optical profiler to enable PSI measurements through refractive media. This approach can be applied to any other optical profiler with PSI capability. The modification consists in replacing the original illumination source with a custom-built narrow linewidth source, which increases the coherence length of the light and the contrast of the interference image. We present measurements taken with the modified configuration on samples covered with 3 mm water or 500 μm glass, and we compare them to measurements of uncovered samples. We show that the measurement precision is only slightly reduced by the water and glass, and that it is still sufficiently high for typical MEMS applications. The described method can be readily used for measuring through other types and thicknesses of refractive materials.
Grain size reduction for perpendicular magnetic recording media using an Ar-ion etched Ru seedlayer
Authors: Yuan Hua , Laughlin David E.
Published: September 2008

We report an approach to reduce grain size for perpendicular media by using an Ar-ion etched Ru seedlayer. The surface etching affects the microstructure of the subsequent high pressure deposited Ru2+SiO2 interlayer and magnetic layer, whose grain size can be controlled. SiO2 in the interlayer plays a more important role in grain size reduction on the etched seedlayer than the as-grown seedlayer. Small Ru2 grains ∼3.9 nm and magnetic grains ∼5.3 nm with uniform distribution have been obtained. Thinner Ru grain boundaries with reduced size could be the cause of nonideal one-to-one grain growth and degraded magnetic properties.
Evidence for ion irradiation induced dissociation and reconstruction of Si–H bonds in hydrogen-implanted silicon
Authors: Di Z. F. , Wang Y. Q. , Nastasi M. , Shao L. , Lee J. K. , Theodore N. D.
Published: September 2008

We observe that H-related chemical bonds formed in H-implanted Si will evolve under subsequent ion irradiation. During ion irradiation hydrogen is inclined to dissociate from simple H-related defect complexes (i.e., VHx and IHx), diffuse, and attach to vacancy-type defects resulting in new platelet formation, which facilitate surface blistering after annealing, a process completely inhibited in the absence of ion irradiation. The understanding of our results provides insight into the structure and stability of hydrogen-related defects in silicon.
Enhanced electroluminescence intensity of InGaN∕GaN multi-quantum-wells based on Mg-doped GaN annealed in O2
Authors: Ma Ping , Gai Yanqin , Wang Junxi , Yang Fuhua , Zeng Yiping , Li Jinmin , Li Jingbo
Published: September 2008

In Ga N ∕ Ga N multi-quantum-well blue (461±4nm) light emitting diodes with higher electroluminescence intensity are obtained by postgrowth thermal annealing at 720°C in O2-ambient. Based on our first-principle total-energy calculations, we conclude that besides dissociating the Mg–H complex by forming H2O, annealing in O2 has another positive effect on the activation of acceptor Mg in GaN. Mg can be further activated by the formation of an impurity band above the valence band maximum of host GaN from the passivated MgGa–ON complex. Our calculated ionization energy for acceptor Mg in the passivated system is about 30meV shallower than that in pure GaN, in good agreement with previous experimental measurement. Our model can explain that the enhanced electroluminescence intensity of InGaN∕GaN MQWs based on Mg-doped p-type GaN is due to a decrease in the ionization energy of Mg acceptor with the presence of oxygen.
Visualization and investigation of Si–C covalent bonding of single carbon nanotube grown on silicon substrate
Authors: You YuMeng , Yu Ting , Kasim Johnson , Song Hang , Fan XiaoFeng , Ni ZhenHua , Cao LianZhen , Jiang Hong , Shen DeZhen , Kuo JerLai , Shen ZeXiang
Published: September 2008

It has been predicted that the electronic properties of carbon nanotubes (CNTs) can be dramatically tuned by forming Si–C bonds with a silicon surface. Thus, the realization of Si–C bonds will broaden future applications of CNTs on nanodevices. In this paper, we use micro-Raman imaging and spectroscopy to investigate the interaction between individual CNTs and silicon substrate. We show that covalent bonds were formed between certain CNTs and the substrate, and visualized such Si-CNT bonds using micro-Raman imaging. Polarized Raman results further reveal that the Si–C bonds are arranged orderly along the long axis of the Si-CNT. We thus show that Raman imaging is a very useful technique to study properties of such Si-CNTs.
Heterodyne-detected electronic sum frequency generation: “Up” versus “down” alignment of interfacial molecules
Authors: Yamaguchi Shoichi , Tahara Tahei
Published: September 2008

Heterodyne-detected electronic sum frequency generation (HD-ESFG) spectroscopy is newly developed to obtain complex electronic χ(2) spectra of interfaces for a simultaneous detection bandwidth broader than 100 nm. HD-ESFG provides linear χ(2) spectra that have unambiguous information on the “up” versus “down” alignment of interfacial molecules. It is demonstrated for p-nitroaniline, a prototypical molecule of nonlinear optical materials, that the up versus down alignment at an air/fused silica interface is critically influenced by a fine modification of the molecule.
Evanescent field response to immunoassay layer thickness on planar waveguides
Authors: Yan Rongjin , Yuan Guangwei , Stephens Matthew D. , He Xinya , Henry Charles S. , Dandy David S. , Lear Kevin L.
Published: September 2008

The response of a compact photonic immunoassay biosensor based on a planar waveguide to variation in antigen (C-reactive protein) concentration as well as waveguide ridge height has been investigated. Near-field scanning optical microscope measurements indicate 1.7%∕nm and 3.3%∕nm top surface optical intensity modulation due to changes in effective adlayer thickness on waveguides with 16.5 and 10nm ridge heights, respectively. Beam propagation method simulations are in good agreement with the experimental sensitivities as well as the observation of leaky mode interference both within and after the adlayer region.
Improved light harvesting in tin-doped indum oxide (ITO)-free inverted bulk-heterojunction organic solar cells using capping layers
Authors: Meiss J. , Allinger N. , Riede M. K. , Leo K.
Published: September 2008

We show that ultrathin metal layers (Ag or Al/Ag) are feasible as transparent top contacts for zinc phthalocyanine: C60 bulk-heterojunction inverted organic solar cells thermally evaporated on glass substrates. Furthermore, it is demonstrated that the introduction of an organic capping layer drastically increases light incoupling and photon harvesting, in accordance with optical simulations. Proof of principle tin-doped indium oxide (ITO)-free solar cells employing a transparent metal contact and a capping layer reach efficiencies of 1.06%, compared to 0.69% without addition of the capping layer.
Nanopencil as a wear-tolerant probe for ultrahigh density data storage
Authors: Tayebi Noureddine , Narui Yoshie , Chen Robert J. , Collier C. Patrick , Giapis Konstantinos P. , Zhang Yuegang
Published: September 2008

A dielectric-sheathed carbon nanotube probe, resembling a “nanopencil,” has been fabricated by conformal deposition of silicon-oxide on a carbon nanotube and subsequent “sharpening” to expose its tip. The high aspect-ratio nanopencil probe takes advantage of the small nanotube electrode size, while avoiding bending and buckling issues encountered with naked or polymer-coated carbon nanotube probes. Since the effective electrode diameter of the probe would not change even after significant wear, it is capable of long-lasting read/write operations in contact mode with a bit size of several nanometers.
DNA molecules resolved by electrical double layer force spectroscopy imaging
Authors: Sotres J. , Baró A. M.
Published: September 2008

This paper deals with spatially resolved force spectroscopy applied to the imaging of the electrical double layer (EDL) force. It is focused on an important point that has not been elucidated yet, the resolution that can be achieved. For this purpose, single plasmid DNA molecules have been studied with an atomic force microscope operated in the force spectroscopy imaging mode. With this approach, important quantities deduced from the force spectra can be simultaneously mapped along with the topography image. Single DNA molecules have been probed obtaining a lateral resolution in the EDL force similar to that of the topography.
Small-signal modeling of the transistor laser including the quantum capture and escape lifetimes
Authors: Faraji B. , Pulfrey D. L. , Chrostowski L.
Published: September 2008

The authors report the analytical small-signal modeling of the distribution of minority carriers in the base of a transistor laser and of the high-speed dynamics of the device. The modeling is based on analytically solving the continuity equation and the rate equations, which incorporate the virtual states as a conversion mechanism. Wide-band operation of the transistor laser along with the suppression of the relaxation oscillation frequency peak is demonstrated.
Evanescent coupling in arrays of type II femtosecond laser-written waveguides in bulk x-cut lithium niobate
Authors: Heinrich Matthias , Szameit Alexander , Dreisow Felix , Döring Sven , Thomas Jens , Nolte Stefan , Tünnermann Andreas , Ancona Antonio
Published: September 2008

We report on the first fabrication of evanescently coupled planar arrays of type II waveguides in x-cut lithium niobate (LiNbO3) by femtosecond laser inscription. A particular choice of writing parameters allows the evanescent field of the individual waveguide modes to extend significantly beyond the damage lines into the neighboring guides, thus realizing a coupling constant of 2.2 cm−1 at a wavelength of 633 nm.
The
Salmonella
virulence protein SifA is a G protein antagonist
Authors: Jackson Laurie K. , Nawabi Parwez , Hentea Cristiana , Roark Everett A. , Haldar Kasturi
Published: September 2008

Salmonella
's success at proliferating intracellularly and causing disease depends on the translocation of a major virulence protein, SifA, into the host cell. SifA recruits membranes enriched in lysosome associated membrane protein 1 (LAMP1) and is needed for growth of
Salmonella
induced filaments (Sifs) and the
Salmonella
containing vacuole (SCV). It directly binds a host protein called SKIP (SifA and kinesin interacting protein) which is critical for membrane stability and motor dynamics at the SCV. SifA also contains a WxxxE motif, predictive of G protein mimicry in bacterial effectors, but whether and how it mimics the action of a host G protein is not known. We show that SKIP's pleckstrin homology domain, which directly binds SifA, also binds to the late endosomal GTPase Rab9. Knockdown studies suggest that both SKIP and Rab9 function to maintain peripheral LAMP1 distribution in cells. The Rab9:SKIP interaction is GTP-dependent and is inhibited by SifA binding to the SKIP pleckstrin homology domain, suggesting that SifA may be a Rab9 antagonist. SifA:SKIP binding is significantly tighter than Rab9:SKIP binding and may thus allow SifA to bring SKIP to the SCV via SKIP's Rab9-binding site. Rab9 can measurably reverse SifA-dependent LAMP1 recruitment and the perinuclear location of the SCV in cells. Importantly, binding to SKIP requires SifA residues W197 and E201 of the conserved WxxxE signature sequence, leading to the speculation that bacterial G protein mimicry may result in G protein antagonism.
β-Blockers alprenolol and carvedilol stimulate β-arrestin-mediated EGFR transactivation
Authors: Kim Il-Man , Tilley Douglas G. , Chen Juhsien , Salazar Natasha C. , Whalen Erin J. , Violin Jonathan D. , Rockman Howard A.
Published: September 2008

Recent evidence suggests that binding of agonist to its cognate receptor initiates not only classical G protein-mediated signaling, but also β-arrestin-dependent signaling. One such β-arrestin-mediated pathway uses the β1-adrenergic receptor (β1AR) to transactivate the EGFR. To determine whether β-adrenergic ligands that do not activate G protein signaling (i.e., β-blockers) can stabilize the β1AR in a signaling conformation, we screened 20 β-blockers for their ability to stimulate β-arrestin-mediated EGFR transactivation. Here we show that only alprenolol (Alp) and carvedilol (Car) induce β1AR-mediated transactivation of the EGFR and downstream ERK activation. By using mutants of the β1AR lacking G protein-coupled receptor kinase phosphorylation sites and siRNA directed against β-arrestin, we show that Alp- and Car-stimulated EGFR transactivation requires β1AR phosphorylation at consensus G protein-coupled receptor kinase sites and β-arrestin recruitment to the ligand-occupied receptor. Moreover, pharmacological inhibition of Src and EGFR blocked Alp- and Car-stimulated EGFR transactivation. Our findings demonstrate that Alp and Car are ligands that not only act as classical receptor antagonists, but can also stimulate signaling pathways in a G protein-independent, β-arrestin-dependent fashion.
The infinite sites model of genome evolution
Authors: Ma Jian , Ratan Aakrosh , Raney Brian J. , Suh Bernard B. , Miller Webb , Haussler David
Published: September 2008

We formalize the problem of recovering the evolutionary history of a set of genomes that are related to an unseen common ancestor genome by operations of speciation, deletion, insertion, duplication, and rearrangement of segments of bases. The problem is examined in the limit as the number of bases in each genome goes to infinity. In this limit, the chromosomes are represented by continuous circles or line segments. For such an infinite-sites model, we present a polynomial-time algorithm to find the most parsimonious evolutionary history of any set of related present-day genomes.
A refined two-hybrid system reveals that SCF
Cdc4
-dependent degradation of Swi5 contributes to the regulatory mechanism of S-phase entry
Authors: Kishi Tsutomu , Ikeda Akemi , Koyama Noriko , Fukada Junji , Nagao Rina
Published: September 2008

Ubiquitin-dependent degradation is implicated in various cellular regulatory mechanisms. The SCF
Cdc4
(Skp1, Cullin/Cdc53, and the F-box protein Cdc4) complex is an ubiquitin ligase complex that acts as a regulator of cell cycle, signal transduction, and transcription. These regulatory mechanisms are not well defined because of the difficulty in identifying the interaction between ubiquitin ligases and their substrates. To identify substrates of the yeast SCF
Cdc4
ubiquitin ligase complex, we refined the yeast two-hybrid system to allow screening Cdc4-substrate interactions under conditions of substrate stabilization, and identified Swi5 as a substrate of the SCF
Cdc4
complex. Swi5 is the transcriptional activator of Sic1, the inhibitor of
S
phase cyclin-dependent kinases (CDKs). We showed that Swi5 is indeed ubiquitinated and degraded through the SCF
Cdc4
complex. Furthermore, the SCF
Cdc4
-dependent degradation of Swi5 was required to terminate
SIC1
transcription at early G
1
phase, which ensured efficient entry into
S
phase: Hyperaccumulation of Sic1 was noted in cells expressing stabilized Swi5, and expression of stabilized Swi5 delayed
S
phase entry, which was dominantly suppressed by
SIC1
deletion. These findings indicate that the SCF
Cdc4
complex regulates
S
phase entry not only through degradation of Sic1, but also through degradation of Swi5.
CD4 memory T cells divide poorly in response to antigen because of their cytokine profile
Authors: MacLeod Megan K. L. , McKee Amy , Crawford Frances , White Janice , Kappler John , Marrack Philippa
Published: September 2008

Immunological memory is a hallmark of adaptive immunity, and understanding T cell memory will be central to the development of effective cell-mediated vaccines. The characteristics and functions of CD4 memory cells have not been well defined. Here we demonstrate that the increased size of the secondary response is solely a consequence of the increased antigen-specific precursor frequency within the memory pool. Memory cells proliferated less than primary responding cells, even within the same host. By analyzing the entry of primary and memory cells into the cell cycle, we found that the two populations proliferated similarly until day 5; after this time, fewer of the reactivated memory cells proliferated. At this time, fewer of the reactivated memory cells made IL-2 than primary responding cells, but more made IFNγ. Both these factors affected the low proliferation of the memory cells, because either exogenous IL-2 or inhibition of IFNγ increased the proliferation of the memory cells.
Art and Mithāl: Reading Geometry as Visual Commentary
Authors: Bier Carol
Published: September 2008

This article seeks to develop an interpretation of ornament as geometric pattern that embodies metaphysical intent in Iranian monuments of the fifth/eleventh century. The proposed argument elucidates cultural meaning relevant to a particular time and specific place, with implications for broader application.1 Reading geometric patterns as visual commentary, this approach relates the presence of patterns in art accompanied by a Qur'anic inscription to both the practice of pattern-making and the contemporary discourse concerning mathematics, philosophy, and the Islamic sciences in Iran. Particular emphasis is placed on the use of a passage from the Qur'an (59:21–24) inscribed on the tomb towers at Kharraqān, in which the Qur'anic term, amthāl, is taken literally to refer to the patterns executed on the monuments.
Treatment with Aspirin and Dipyridamole is More Effective than Aspirin in Reducing Low Shear Blood Viscosity
Authors: ROSENSON ROBERT S.
Published: September 2008

Objective: Investigate effects of aspirin/dipyridamole and aspirin on blood viscosity (BV) in subjects with hyperhomocystememia (>14 μmol/L) and stable cardiovascular disease (CVD) or ≥ 20% risk for CVD were the aims of this study.

Method: Forty‐seven subjects were treated with 14 days of either aspirin/dipyridamole (25 mg/200 mg twice‐daily) or aspirin (81 mg daily). BV was measured from fasting specimens at 37°C from whole blood at shear rates ranging from 1,000 to 1s−1 by using a scanning capillary viscometer (Rheolog™ Rheologics Inc., Exton, Pennsylvania, USA).

Results: Aspirin/dipyridamole was more effective than aspirin therapy in reducing BV at shear rates of 1 s−1 (−3.03 [−3.88, −2.17] mPas vs. −0.07 [−1.06, 0.92] mPas; P<0.0001) and 2 s−1 (−1.86 [−2.72, −1.01] mPas vs. −0.21 [−1.20, 0.79] mPas; P=0.0136); however, there were no significant differences in blood viscosity at shear rates of 5 s−1 to 1000 s−1. Changes in hematocrit, a major determinant of whole BV, were greater in the aspirin/dipyridamole group than the aspirin group (P=0.043). After hematocrit adjustment, differences in BV between aspirin/dipyridamole and aspirin remained significant at 1s−1 (−2.78 [−3.68, −1.88] mPas vs. −0.04 [−1.05, 0.98] mPas; P<0.0001) and 2 s−1 (−1.62 [−2.52, −0.72] mPas vs. −0.17 [−1.19, 0.85] mPas; P=0.0315).

Conclusion: These findings may have important clinical benefits in the CVD prevention and treatment due to the contribution of BV in tissue perfusion and thrombus formation.
Pathotypes of Colletotrichum sublineolum in Arkansas
Authors: Moore J. W. , Ditmore M. , TeBeest D. O.
Published: September 2008

Sorghum anthracnose, caused by Colletotrichum sublineolum, is widely distributed in most grain sorghum-producing areas in Arkansas, and localized epidemics continue to occur across the state. The objectives of this research were to determine the number of pathotypes of C. sublineolum in Arkansas and to determine where these pathotypes are located within the state. Ninety-eight isolates were collected from research stations and production fields located in the Delta region of Arkansas from 2003 through 2005 and were tested for virulence to eight differential grain sorghum breeding lines. Of these, 11 isolates produced conflicting and unreliable results and were excluded from further analysis. Among the remaining 87 isolates, 13 pathotypes were identified. Eleven of these pathotypes were previously unreported, with 53% of the isolates consisting of pathotype 9. Pathotype 9 was distinguished from all other pathotypes by its virulence to all eight differential lines. Pathotype diversity appeared to be more closely associated with the year than with the locations where isolates were collected. Although all host differential lines were susceptible to at least 50% of the isolates evaluated, inbred lines SC326-6, TAM428, and TX2536 were susceptible to more than 90% of the 87 isolates evaluated. These results showed that the C. sublineolum populations in Arkansas are diverse based on the comparisons of pathogenicity to previously published host differentials, and it appears that these field populations varied from year to year.
Colletotrichum fragariae Is a Pathogen on Hosts Other Than Strawberry
Authors: MacKenzie S. J. , Mertely J. C. , Seijo T. E. , Peres N. A.
Published: September 2008

Evidence that Colletotrichum fragariae causes disease on hosts other than strawberry is limited. In the fall of 2006, fungal isolates from silver date palm with leaf spot symptoms and from cyclamen with leaf spot and stem rot symptoms were identified as C. fragariae. After confirming the pathogenicity of the isolates on their host of origin, a representative isolate from each host was compared to C. fragariae and to C. gloeosporioides/Glomerella cingulata isolates from strawberry. Date palm and cyclamen isolates bore conidia on setae, and conidia were tapered and in the size range of C. fragariae reference isolates. Sequence data from the combined internal transcribed spacer (ITS) regions 1 and 2 and the gene for the 5.8 ribosomal RNA from the cyclamen and date palm isolates matched the sequence for C. fragariae reference isolates. Based on these characteristics, it was concluded that the C. fragariae species designation was correct for both isolates. However, the date palm isolate was a weak pathogen on strawberry compared with other isolates and had a distinct AT-rich DNA banding pattern. The ability of the cyclamen isolate to cause crown rot on strawberry was comparable with the strawberry reference isolates, and the AT-rich DNA banding pattern of the cyclamen isolate was identical to the C. fragariae isolates from strawberry. The results indicate that C. fragariae is a pathogen on hosts other than strawberry and that there is more diversity among C. fragariae isolates than previously reported.
Characterization of Erwinia chrysanthemi from a Bacterial Heart Rot of Pineapple Outbreak in Hawaii
Authors: Kaneshiro Wendy S. , Burger Maren , Vine Benjamin G. , de Silva Asoka S. , Alvarez Anne M.
Published: September 2008

The first reported outbreak of bacterial heart rot of pineapple (Ananas comosus var. comosus) in Hawaii occurred in December 2003. Of immediate concern was the differentiation of heart rot caused by Erwinia chrysanthemi from a soft rot caused by E. carotovora subsp. carotovora because of regulatory issues. Presumptive identifications of the isolated bacteria were made using bacteriological tests (including reactivity with an Erwinia-specific monoclonal antibody, E2) and compared with identifications obtained by two general methods: carbon source utilization profiling (Biolog) and 16S rDNA sequence analysis. The panel of bacteriological tests consistently differentiated E. chrysanthemi from E. carotovora subsp. carotovora and other nonquarantine organisms. BOX-polymerase chain reaction fingerprint patterns further differentiated the pineapple-isolated E. chrysanthemi strains from those obtained from other plants and irrigation water. Pineapple leaf inoculations revealed that only E. chrysanthemi from pineapple produced watersoaking and rot similar to that observed on the original symptomatic plants, thus identifying these strains as the causal agents of the outbreak. In this situation, where rapid identification of an unknown pathogen was necessary, standard bacteriological tests then available in the laboratory provided reliable differentiation of E. chrysanthemi from E. carotovora subsp. carotovora. Additional strain characterization is needed before the pineapple-isolated E. chrysanthemi strains can be classified into a species of the new genus Dickeya.
Viability ofPhakopsora pachyrhiziUrediniospores Under Simulated Southern Louisiana Winter Temperature Conditions
Authors: Park S. , Chen Z.-Y. , Chanda A. K. , Schneider R. W. , Hollier C. A.
Published: September 2008

Soybean rust, caused by Phakopsora pachyrhizi, originally occurred in Asia. It has now spread to South America and the continental United States. This disease has the potential to cause severe economic losses to U.S. soybean growers, especially in the south, where the environmental conditions are more favorable to P. pachyrhizi survival during winter. In the present study, the effect of simulated southern Louisiana winter temperature conditions (12°C, 14-h days and 1°C, 10-h nights with 75% relative humidity) on soybean rust urediniospore viability was examined. It was found that urediniospore viability declined rapidly from 72 to 40% after 1 day and then decreased gradually to 17% after 7 days and 11% after 60 days. Spores stored under southern Louisiana winter conditions for 60 days still produced pustules on inoculated leaves. In comparison, the viability of spores stored at room temperature decreased gradually and reached 0% at the end of 60 days. Winter temperature treatment not only reduced spore viability but also decreased germ tube growth. In addition, soybean rust spores recovered from overwintered dry kudzu leaves were also found viable. This study indicates that soybean rust spores could survive southern Louisiana winter conditions and initiate a new cycle of infection in the next growing season.
First Report of Phytophthora Stem Rot on Gloxinia in Bulgaria
Authors: Bobev S. G. , Van Poucke K. , Maes M.
Published: September 2008

Severe stem base necrosis was observed on potted gloxinia (Sinningia speciosa) plants in a greenhouse in the Plovdiv Region of Bulgaria in the spring of 2006 and sporadically in 2007. Initial symptoms were water-soaked lesions at the stem base; eventually the lesions spread upward and downward until the entire stem was affected, resulting in withered leaves and plant collapse. Disease foci were sometimes apparent in rows of plants because of water splash. White, fungal-like colonies with arachnoid, aerial mycelia were obtained from affected plant tissue placed on potato dextrose agar (PDA) at 24 to 25°C in the dark. Pyriform to ellipsoid sporangia, 30 to 55 × 23 to 40 μm (average 38 × 27 μm), with a prominent papilla (sometimes two) and a short pedicel were observed. Chlamydospores were intercalary or terminal, spherical, and 15 to 55 μm in diameter. Oogonia and antheridia were not observed. On the basis of morphological features, the pathogen was tentatively identified as Phytophthora nicotianae (2). Pathogenicity was tested by placing 3-mm-diameter discs from 7-day-old PDA cultures onto wounded petioles of visibly healthy 3-month-old gloxinia potted plants (three replicates). Sterile PDA plugs were placed onto similar wounds of three control plants. The inoculated wounds were covered with Parafilm. Three days after inoculation, water-soaked lesions began to spread longitudinally in both directions on inoculated petioles. The pathogen was recovered from the inoculated tissue but not from the control plants. Molecular identification of the pathogen was achieved with PCR-restriction fragment length polymorphism of the internal transcribed spacer regions ITS1 and ITS2 of the ribosomal DNA (1). The restriction patterns obtained with the enzymes AluI, MspI, and TaqIα were identical to those of P. nicotianae, confirming the morphological identification. To our knowledge, this is the first report of P. nicotianae on gloxinia in Bulgaria.

References: (1) D. E. L. Cooke and J. M. Duncan. Mycol. Res. 101:667, 1997. (2) D. C. Erwin and O. K. Ribeiro. Phytophthora Diseases Worldwide. The American Phytopathological Society, St. Paul, MN, 1996.
First Report of Bitter Rot Caused by Colletotrichum acutatum on Apple in China
Authors: Zhang R. , Wang S. F. , Cui J. Q. , Sun G. Y. , Gleason M. L.
Published: September 2008

Bitter rot of apple caused by Colletotrichum gloeosporioides was first reported in China in 1985 (3). In China, apples are grown on approximately 2 million ha, and bitter rot occurs in almost all production areas, with crop damage ranging from 30 to 70%. During the summer of 2007, fungi were isolated from apple fruit exhibiting bitter rot symptoms in 12 and 9 orchards in Shaanxi and Henan provinces, respectively, in China. Symptoms included 2- to 3-cm-diameter, sunken, brown lesions on the fruit surface that contained black, pinhead-size fruiting structures producing orange conidial masses under high humidity, similar to that of C. gloeosporioides. On potato dextrose agar (PDA), colonies were white, pale gray, or pale orange when grown at 25°C. Conidia were 8 to 16 × 2.5 to 4 μm, fusiform, pointed at one or both ends, one celled, thin walled, aseptate, and hyaline. Appressoria were 6.5 to 11 × 4.5 to 7.5 μm, clavate to circular, and light to dark brown. These characteristics matched published descriptions of C. acutatum (2). To confirm pathogenicity, three mature, healthy apples (cv. Fuji) were surface disinfested with 70% ethanol and then wounded with a sterile needle. After being inoculated with a spore suspension (1 × 105 conidia/ml) prepared from a 2-week-old culture on PDA, these apples were sealed in a plastic bag and incubated at 25°C. Symptoms appeared 3 to 5 days after inoculation and began to enlarge 7 days later, forming lesions with fruiting structures. Under high humidity, cream-to-salmon pink spore masses were produced on lesions. As the lesions enlarged, the rot progressed to the core of the fruit in a V-shaped pattern. When the pathogen was reisolated from lesions of inoculated fruit onto PDA and incubated at 25°C, colony and conidial morphology were identical to those of the original isolates. Tests were performed three times with similar results. PCR with species-specific primer pair CaInt2/ITS4 (1) of genomic DNA from the isolates resulted in an amplification product of approximately 490 bp, which is specific for C. acutatum. The sequences exhibited 99% similarity with those of C. acutatum isolates AB273195 from GenBank. Approximately 20 of 103 symptomatic fruit from the field survey yielded fungal cultures whose morphology was consistent with that of C. acutatum, whereas the other cultures were C. gloeosporioides and Botryosphaeria dothidea. To our knowledge, this is the first report of bitter rot of apple caused by Colletotrichum acutatum in China.

References: (1) S. Sreenivasaprasad et al. Plant Pathol. 45:650, 1996. (2) B. C. Sutton. Page 523 in: The Coelomycetes. Commonwealth Mycological Institute, Kew, Surrey, England, 1980. (3) X. M. Wang. M.S. thesis. (In Chinese). College of Northwest Agriculture, Shaanxi Province, China, 1985.
Conserved main‐chain peptide distortions: A proposed role for Ile203 in catalysis by dihydrodipicolinate synthase
Authors: Dobson Renwick C.J. , Griffin Michael D.W. , Devenish Sean R.A. , Pearce F. Grant , Hutton Craig A. , Gerrard Juliet A. , Jameson Geoffrey B. , Perugini Matthew A.
Published: September 2008

In recent years, dihydrodipicolinate synthase (DHDPS, E.C. 4.2.1.52) has received considerable attention from a mechanistic and structural viewpoint. DHDPS catalyzes the reaction of (S)‐aspartate‐β‐semialdehyde with pyruvate, which is bound via a Schiff base to a conserved active‐site lysine (Lys161 in the enzyme from Escherichia coli). To probe the mechanism of DHDPS, we have studied the inhibition of E. coli DHDPS by the substrate analog, β‐hydroxypyruvate. The K i was determined to be 0.21 (±0.02) mM, similar to that of the allosteric inhibitor, (S)‐lysine, and β‐hydroxypyruvate was observed to cause time‐dependent inhibition. The inhibitory reaction with β‐hydroxypyruvate could be qualitatively followed by mass spectrometry, which showed initial noncovalent adduct formation, followed by the slow formation of the covalent adduct. It is unclear whether β‐hydroxypyruvate plays a role in regulating the biosynthesis of meso‐diaminopimelate and (S)‐lysine in E. coli, although we note that it is present in vivo. The crystal structure of DHDPS complexed with β‐hydroxypyruvate was solved. The active site clearly showed the presence of the inhibitor covalently bound to the Lys161. Interestingly, the hydroxyl group of β‐hydroxypyruvate was hydrogen‐bonded to the main‐chain carbonyl of Ile203. This provides insight into the possible catalytic role played by this peptide unit, which has a highly strained torsion angle (ω ∼201°). A survey of the known DHDPS structures from other organisms shows this distortion to be a highly conserved feature of the DHDPS active site, and we propose that this peptide unit plays a critical role in catalysis.
Subaqueous hydrochory: open‐channel hydraulic modelling of non‐buoyant seed movement
Authors: MARKWITH SCOTT H. , LEIGH DAVID S.
Published: September 2008

1. Subaqueous transport may be a significant dispersal and migration mechanism of non‐buoyant seeds of aquatic and riparian plants, and also secondary transport of seeds once they have lost buoyancy, but the efficiency of this difficult to observe process is largely unexamined. This study uses hydraulic modelling to establish the discharges that move the non‐buoyant seeds of Hymenocallis coronaria as bedload or suspended load; uses stream gauge data to examine the frequency of effective discharges from late June to late September, the seed maturation and germination period; and the potential transport distance of the seeds.

2. The results show that the majority of non‐buoyant seeds of H. coronaria can be transported as bedload through entire modelled stream reaches of lengths 10.8, 18 and 14.4 km with the 0.5 year return interval flow. Bedload apparently has the ability to move seeds over great distances, and may be a substantial factor determining the genetic structure, demography and dynamics of populations and communities. However, prolonged movement of non‐buoyant seeds in suspension appears to be quite rare.

3. Although insect mediated pollination and biochory occur concurrently with bedload transport, bedload transport alone may be sufficient to account for the established gene flow rate of H. coronaria. The potential transport distance of many of the seeds exceed that between populations, and migration may occur more frequently than the species’ generation time.

4. This is the first known study to use open‐channel hydraulic modelling and sediment transport analysis to determine the effectiveness of non‐buoyant seed transport. This method of analysis shows promise for application in other contexts, and especially where flow management is a critical issue for maintenance of rare species.