bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic delamination of patterned thin films
Authors: Kandula Soma S. V. , Tran Phuong , Geubelle Philippe H. , Sottos Nancy R.
Published: December 2008

We investigate laser-induced dynamic delamination of a patterned thin film on a substrate. Controlled delamination results from our insertion of a weak adhesion region beneath the film. The inertial forces acting on the weakly bonded portion of the film lead to stable propagation of a crack along the film/substrate interface. Through a simple energy balance, we extract the critical energy for interfacial failure, a quantity that is difficult and sometimes impossible to characterize by more conventional methods for many thin film/substrate combinations.
Raman spectroscopy of (K,Na)NbO3 and (K,Na)1−xLixNbO3
Authors: Trodahl H. J. , Klein N. , Damjanovic D. , Setter N. , Ludbrook B. , Rytz D. , Kuball M.
Published: December 2008

We report Raman spectroscopy in all four phases of a (K0.5+δNa0.5−δ)NbO3 (δ∼0.03) crystal and ((K0.5+δNa0.5−δ)1−xLix)NbO3 for x=0.02 and 0.03. The phase transitions in the Li-free crystal are homogeneous and hysteretic, with no mixed-phase region between the rhombohedral and orthorhombic phases. Raman spectra in the lowest-temperature phase in the Li-doped material differ significantly from those at x=0 and suggest a structural phase boundary at a Li concentration of less than 2%.
Geometrical effects in the energy transfer mechanism for silicon nanocrystals and Er3+
Authors: Choy K. , Lenz F. , Liang X. X. , Marsiglio F. , Meldrum A.
Published: December 2008

Silicon nanoclusters (NCs) strongly sensitize the luminescence of Er3+ ions. Attempts to calculate the interaction distance have assumed that the Förster [Ann. Phys. 437, 55 (1948)] and Dexter [J. Chem. Phys. 21, 836 (1953)] relationships for point-to-point energy transfer can be applied to experiments based on multilayered thin-film specimens. Here, the effective finite plane-to-plane relationships are derived for both interaction mechanisms. These relationships show that energy transfer can result from the Förster interaction despite the fact that the measured luminescence intensity varies much more weakly with NC-Er3+ separation than predicted by theory for point dipoles. An effective energy transfer distance is found for the NC-Er3+ system.
Simple two-dimensional-imaging spectrograph with wedged narrow band filters
Authors: Divoký Martin , Straka Petr
Published: December 2008

A minute, yet practical, modification of a well-known spectrograph based on a set of wedged narrow band filters is presented. It makes possible two-dimensional-imaging spectral measurements with a potential subpixel precision of a few micrometers. The simple spectroscopic device can evaluate dispersion of quantities which can be transformed into an image, e.g., into a spatial beam distribution. The spectrograph was used to measure angular dispersion of both a laser oscillator producing femtosecond pulses and a simple dispersive optical system, an optical wedge.
Experimental quality factor determination of guided-mode resonances in photonic crystal slabs
Authors: Nazirizadeh Yousef , Lemmer Uli , Gerken Martina
Published: December 2008

We report on a method how quality factors of guided-mode resonances in photonic crystal slabs (PCSs) can be determined in the reciprocal space. Transmission measurements through PCSs are performed using crossed polarization filters before and after the PCS. Consequently the unwanted illumination source is suppressed and only the guided-mode resonances are revealed. This method allows for a spatially resolved quality factor determination in the reciprocal space. As an example we scan a two-dimensional PCS and visualize its inhomogeneities. Although the resonance wavelength variations were only ≈3 nm, the quality factor varies from 100 to 350.
Temperature compensated overdrive in vertically aligned liquid crystal displays
Authors: Vanbrabant Pieter J. M. , Velthoven-Dessaud Nathalie , Strömer Jan F. , Neyts Kristiaan
Published: December 2008

The occurrence of backflow in vertically aligned liquid crystal displays (VA-LCDs) inhibits application of conventional overdrive techniques to achieve faster switching. This (hydro)dynamic behavior is simulated accurately by using the Leslie–Ericksen theory in a one-dimensional model. Taking the limitations due to backflow into account from these simulations, we designed overdrive schemes for VA-LCDs. The temperature sensitivity of a fixed overdrive table was eliminated by adapting the scheme to the simulated temperature variations in the dynamic behavior. Experimental verification in the 25–75 °C range shows that the resulting temperature compensated overdrive leads to faster switching, which is expected to be artifact free.
Domain control in ferroelectric nanodots through surface charges
Authors: Wang Jie , Kamlah Marc
Published: December 2008

Stable polarization distributions of freestanding ferroelectric nanodots with different surface charges are investigated numerically using a phase field model. The out-of-plane components of polarizations are found to be proportional to the density of surface charge. When the density of surface charge exceeds a critical value, the in-plane components of polarizations disappear. It makes ferroelectric nanodots experience an unusual transition from a vortex state to a single-domain state. Simulation results also show that regular multidomain structures can be obtained by means of specified surface charges, which suggests a way to tailor the physical properties for specific applications.
Partial confinement photonic crystal waveguides
Authors: Saini S. , Hong C.-Y. , Pfaff N. , Kimerling L. C. , Michel J.
Published: December 2008

One-dimensional photonic crystal waveguides with an incomplete photonic band gap are modeled and proposed for an integration application that exploits their property of partial angular confinement. Planar apodized photonic crystal structures are deposited by plasma enhanced chemical vapor deposition and characterized by reflectivity as a function of angle and polarization, validating a partial confinement design for light at 850 nm wavelength. Partial confinement identifies an approach for tailoring waveguide properties by the exploitation of conformal film deposition over a substrate with angularly dependent topology. An application for an optoelectronic transceiver is demonstrated.
Engineering piezoresistivity using biaxially strained silicon
Authors: Pedersen Jesper Goor , Richter Jacob , Brandbyge Mads , Thomsen Erik V. , Hansen Ole
Published: December 2008

We calculate the shear piezocoefficient of p-type silicon with grown-in biaxial strain using a 6×6 k⋅p method. We find a significant increase in the value of the shear piezocoefficient for compressive grown-in biaxial strain, while tensile strain decreases the piezocoefficient. The dependence of the piezocoefficient on temperature and dopant density is altered qualitatively for strained silicon. In particular, we find that a vanishing temperature coefficient may result for silicon with grown-in biaxial tensile strain. These results suggest that strained silicon may be used to engineer the piezoresistivity to enhance the performance of piezoresistive stress sensors.
Unliganded gating of acetylcholine receptor channels
Authors: Purohit Prasad , Auerbach Anthony
Published: December 2008

We estimated the unliganded opening and closing rate constants of neuromuscular acetylcholine receptor-channels (AChRs) having mutations that increased the gating equilibrium constant. For some mutant combinations, spontaneous openings occurred in clusters. For 25 different constructs, the unliganded gating equilibrium constant (
E
0
) was correlated with the product of the predicted fold-increase in the diliganded gating equilibrium constant caused by each mutation alone. We estimate that (
i
)
E
0
for mouse, wild-type α
2
βδε AChRs is ≈1.15 × 10
−7
; (
ii
) unliganded AChRs open for ≈80 μs, once every ≈15 min; (
iii
) the affinity for ACh of the O(pen) conformation is ≈10 nM, or ≈15,600 times greater than for the C(losed) conformation; (
iv
) the ACh-monoliganded gating equilibrium constant is ≈1.7 × 10
−3
; (
v
) the C→O isomerization reduces substantially ACh dissociation, but only slightly increases association; and (
vi
) ACh provides only ≈0.9 k
B
T more binding energy per site than carbamylcholine but ≈3.1 k
B
T more than choline, mainly because of a low O conformation affinity. Most mutations of binding site residue αW149 increase
E
0
. We estimate that the mutation αW149F reduces the ACh affinity of C only by 13-fold, but of O by 190-fold. Rate–equilibrium free-energy relationships for different regions of the protein show similar slopes (Φ values) for un- vs. diliganded gating, which suggests that the conformational pathway of the gating structural change is fundamentally the same with and without agonists. Agonist binding is a perturbation that (like most mutations) changes the energy, but not the mechanism, of the gating conformational change.
The yeast Sup35NM domain propagates as a prion in mammalian cells
Authors: Krammer Carmen , Kryndushkin Dmitry , Suhre Michael H. , Kremmer Elisabeth , Hofmann Andreas , Pfeifer Alexander , Scheibel Thomas , Wickner Reed B. , Schätzl Hermann M. , Vorberg Ina
Published: December 2008

Prions are infectious, self-propagating amyloid-like protein aggregates of mammals and fungi. We have studied aggregation propensities of a yeast prion domain in cell culture to gain insights into general mechanisms of prion replication in mammalian cells. Here, we report the artificial transmission of a yeast prion across a phylogenetic kingdom. HA epitope-tagged yeast Sup35p prion domain NM was stably expressed in murine neuroblastoma cells. Although cytosolically expressed NM-HA remained soluble, addition of fibrils of bacterially produced Sup35NM to the medium efficiently induced appearance of phenotypically and biochemically distinct NM-HA aggregates that were inherited by daughter cells. Importantly, NM-HA aggregates also were infectious to recipient mammalian cells expressing soluble NM-HA and, to a lesser extent, to yeast. The fact that the yeast Sup35NM domain can propagate as a prion in neuroblastoma cells strongly argues that cellular mechanisms support prion-like inheritance in the mammalian cytosol.
Evaluation of new generationSalmonella entericaserovar Typhimurium vaccines with regulated delayed attenuation to induce immune responses against PspA
Authors: Li Yuhua , Wang Shifeng , Scarpellini Giorgio , Gunn Bronwyn , Xin Wei , Wanda Soo-Young , Roland Kenneth L. , Curtiss Roy
Published: December 2008

Increasing the immunogenicity to delivered antigens by recombinant attenuatedSalmonellavaccines (RASV) has been the subject of intensive study. With this goal in mind, we have designed and constructed a new generation of RASV that exhibit regulated delayed attenuation. These vaccine strains are phenotypically wild type at the time of immunization and become attenuated after colonization of host tissues. The vaccine strains are grown under conditions that allow expression of genes required for optimal invasion and colonization of host tissues. Once established in the host, these virulence genes are turned off, fully attenuating the vaccine strain. In this study, we compared 2 of our newly developed regulated delayed attenuationSalmonella entericaserovar Typhimurium strains χ9088 and χ9558 with the ΔcyaΔcrpΔasd strain χ8133, for their abilities to express and present a secreted form of the α-helical region of pneumococcal surface protein A (PspA) to the mouse immune system. All 3 strains induced high levels of serum antibodies specific for PspA as well as toSalmonellaantigens in orally immunized mice. However, both RASVs expressing delayed attenuation elicited significantly greater anti-PspA immune responses, including serum IgG and T cell secretion of IL-4 and IFN-γ, than other groups. Also, vaccination with delayed attenuation strains resulted in a greater degree of protection againstStreptococcus pneumoniaechallenge than in mice vaccinated with χ8133 (71–86% vs. 21% survival,P≤ 0.006). Together, the results demonstrate that the regulated attenuation strategy results in highly immunogenic antigen delivery vectors for oral vaccination.
Blocking Pore-open Mutants of CLC-0 by Amphiphilic Blockers
Authors: Zhang Xiao-Dong , Tseng Pang-Yen , Yu Wei-Ping , Chen Tsung-Yu
Published: December 2008

The blockade of CLC-0 chloride channels by p-chlorophenoxy acetate (CPA) has been thought to be state dependent; the conformational change of the channel pore during the “fast gating” alters the CPA binding affinity. Here, we examine the mechanism of CPA blocking in pore-open mutants of CLC-0 in which the residue E166 was replaced by various amino acids. We find that the CPA-blocking affinities depend upon the volume and the hydrophobicity of the side chain of the introduced residue; CPA affinity can vary by three orders of magnitude in these mutants. On the other hand, mutations at the intracellular pore entrance, although affecting the association and dissociation rates of the CPA block, generate only a modest effect on the steady-state blocking affinity. In addition, various amphiphilic compounds, including fatty acids and alkyl sulfonates, can also block the pore-open mutants of CLC-0 through a similar mechanism. The blocking affinity of fatty acids and alkyl sulfonates increases with the length of these amphiphilic blockers, a phenomenon similar to the block of the Shaker K+ channel by long-chain quaternary ammonium (QA) ions. These observations lead us to propose that the CPA block of the open pore of CLC-0 is similar to the blockade of voltage-gated K+ channels by long-chain QAs or by the inactivation ball peptide: the blocker first uses the hydrophilic end to “dock” at the pore entrance, and the hydrophobic part of the blocker then enters the pore to interact with a more hydrophobic region of the pore. This blocking mechanism appears to be very general because the block does not require a precise structural fit between the blocker and the pore, and the blocking mechanism applies to the cation and anion channels with unrelated pore architectures.
Amphiphilic Blockers Punch through a Mutant CLC-0 Pore
Authors: Zhang Xiao-Dong , Chen Tsung-Yu
Published: December 2008

Intracellularly applied amphiphilic molecules, such as p-chlorophenoxy acetate (CPA) and octanoate, block various pore-open mutants of CLC-0. The voltage-dependent block of a particular pore-open mutant, E166G, was found to be multiphasic. In symmetrical 140 mM Cl−, the apparent affinity of the blocker in this mutant increased with a negative membrane potential but, paradoxically, decreased when the negative membrane potential was greater than −80 mV, a phenomenon similar to the blocker “punch-through” shown in many blocker studies of cation channels. To provide further evidence of the punch-through of CPA and octanoate, we studied the dissociation rate of the blocker from the pore by measuring the time constant of relief from the block under various voltage and ionic conditions. Consistent with the voltage dependence of the effect on the steady-state current, the rate of CPA dissociation from the E166G pore reached a minimum at −80 mV in symmetrical 140 mM Cl−, and the direction of current recovery suggested that the bound CPA in the pore can dissociate into both intracellular and extracellular solutions. Moreover, the CPA dissociation depends upon the Cl− reversal potential with a minimal dissociation rate at a voltage 80 mV more negative than the Cl− reversal potential. That the shift of the CPA-dissociation rate follows the Cl− gradient across the membrane argues that these blockers can indeed punch through the channel pore. Furthermore, a minimal CPA-dissociation rate at a voltage 80 mV more negative than the Cl− reversal potential suggests that the outward blocker movement through the CLC-0 pore is more difficult than the inward movement.
Functional Proteomics ofArabidopsis thalianaGuard Cells Uncovers New Stomatal Signaling Pathways
Authors: Zhao Zhixin , Zhang Wei , Stanley Bruce A. , Assmann Sarah M.
Published: December 2008

We isolated a total of 3 × 108 guard cell protoplasts from 22,000 Arabidopsis thaliana plants and identified 1734 unique proteins using three complementary proteomic methods: protein spot identification from broad and narrow pH range two-dimensional (2D) gels, and 2D liquid chromatography–matrix assisted laser desorption/ionization multidimensional protein identification technology. This extensive single-cell-type proteome includes 336 proteins not previously represented in transcriptome analyses of guard cells and 52 proteins classified as signaling proteins by Gene Ontology analysis, of which only two have been previously assessed in the context of guard cell function. THIOGLUCOSIDE GLUCOHYDROLASE1 (TGG1), a myrosinase that catalyzes the production of toxic isothiocyanates from glucosinolates, showed striking abundance in the guard cell proteome. tgg1 mutants were hyposensitive to abscisic acid (ABA) inhibition of guard cell inward K+ channels and stomatal opening, revealing that the glucosinolate-myrosinase system, previously identified as a defense against biotic invaders, is required for key ABA responses of guard cells. Our results also suggest a mechanism whereby exposure to abiotic stresses may enhance plant defense against subsequent biotic stressors and exemplify how enhanced knowledge of the signaling networks of a specific cell type can be gained by proteomics approaches.
Sustaining the Ark: the challenges faced by zoos in maintaining viable populations
Authors: LEES C. M. , WILCKEN J.
Published: December 2008

In the World Zoo and Aquarium Conservation Strategy, the world's leading zoos commit to focusing their efforts on conserving wildlife. Such a commitment is made as human activities are driving many species of wildlife towards extinction. The world's leading zoos aim to act as a counterbalance to activities that undermine the sustainability of wild populations of threatened species. However, to date, this same group of zoos has largely failed to manage its own populations of wildlife sustainably despite distinguished calls to action over the past 25 years, significant scientific input and much organizational effort. This paper explores the efforts of the global zoo community to bring sustainability and conservation value to its animal populations. It looks at where we have come from, where we are now and where we need to go from here.
Breeding and maintenance of the Central rock‐rat Zyzomys pedunculatus at Perth Zoo
Authors: GAIKHORST G. , LAMBERT C.
Published: December 2008

The Central rock‐rat Zyzomys pedunculatus is a native Australian rodent, thought to be extinct until its rediscovery near Alice Springs in 1996. Classified as Critically Endangered, recovery actions include the study and maintenance of the species in captivity. Between mid‐2001 and mid‐2002, eight litters were produced at Perth Zoo, with 26 young surviving to weaning. Females were shown to be capable of producing three to four young every 37–44 days. The husbandry protocols, reproductive parameters, reproductive behaviour, and birth and development of young Z. pedunculatus are described in this article.
Inner Workings of Aerodynamic Sweep
Authors: Wadia A. R. , Szucs P. N. , Crall D. W.
Published: December 2008

The recent trend in using aerodynamic sweep to improve the performance of transonic blading has been one of the more significant technological evolutions for compression components in turbomachinery. This paper reports on the experimental and analytical assessment of the pay-off derived from both aft and forward sweep technology with respect to aerodynamic performance and stability. The single-stage experimental investigation includes two aft-swept rotors with varying degree and type of aerodynamic sweep and one swept forward rotor. On a back-to-back test basis, the results are compared with an unswept rotor with excellent performance and adequate stall margin. Although designed to satisfy identical design speed requirements as the unswept rotor, the experimental results reveal significant variations in efficiency and stall margin with the swept rotors. At design speed, all the swept rotors demonstrated a peak stage efficiency level that was equal to that of the unswept rotor. However, the forward-swept rotor achieved the highest rotor-alone peak efficiency. At the same time, the forward-swept rotor demonstrated a significant improvement in stall margin relative to the already satisfactory level achieved by the unswept rotor. Increasing the level of aft swept adversely affected the stall margin. A three-dimensional viscous flow analysis was used to assist in the interpretation of the data. The reduced shock/boundary layer interaction, resulting from reduced axial flow diffusion and less accumulation of centrifuged blade surface boundary layer at the tip, was identified as the prime contributor to the enhanced performance with forward sweep. The impact of tip clearance on the performance and stability for one of the aft-swept rotors was also assessed.
Effects of Stream Surface Inclination on Tip Leakage Flow Fields in Compressor Rotors
Authors: Furukawa M. , Saiki K. , Nagayoshi K. , Kuroumaru M. , Inoue M.
Published: December 2008

Experimental and computational results of tip leakage flow fields in a diagonal flow rotor at the design flow rate are compared with those in an axial flow rotor. In the diagonal flow rotor, the casing and hub walls are inclined at 25 deg and 45 deg, respectively, to the axis of rotation, and the blade has airfoil sections with almost the same tip solidity as that of the axial flow rotor. It is found out that “breakdown” of the tip leakage vortex occurs at the aft part of the passage in the diagonal flow rotor. The “vortex breakdown” causes significant changes in the nature of the tip leakage vortex: disappearance of the vortex core, large expansion of the vortex, and appearance of low relative velocity region in the vortex. These changes result in a behavior of the tip leakage flow that is substantially different from that in the axial flow rotor: no rolling-up of the leakage vortex downstream of the rotor, disappearance of the casing pressure trough at the aft part of the rotor passage, large spread of the low-energy fluid due to the leakage flow, much larger growth of the casing wall boundary layer, and considerable increase in the absolute tangential velocity in the casing wall boundary layer. The vortex breakdown influences the overall performance, also: large reduction of efficiency with the tip clearance, and low level of noise.
The Influence of Wake–Wake Interactions on Loss Fluctuations of a Downstream Axial Compressor Blade Row
Authors: Walker G. J. , Hughes J. D. , Ko¨hler I. , Solomon W. J.
Published: December 2008

The interaction between wakes of an adjacent rotor–stator or stator–rotor blade row pair in an axial turbomachine is known to produce regular spatial variations in both the time-mean and unsteady flow fields in a frame relative to the upstream member of the pair. This paper examines the influence of such changes in the free-stream disturbance field on the viscous losses of a following blade row. Hot-wire measurements are carried out downstream of the outlet stator in a 1.5-stage axial compressor having equal blade numbers in the inlet guide vane (IGV) and stator rows. Clocking of the IGV row is used to vary the disturbance field experienced by the stator blades; the influence on stator wake properties is evaluated. The magnitude of periodic fluctuations in ensemble-averaged stator wake thickness is significantly influenced by IGV wake-rotor wake interaction effects. The changes in time-mean stator losses appear marginal.
On the Design Criteria for Suppression of Secondary Flows in Centrifugal and Mixed Flow Impellers
Authors: Zangeneh M. , Goto A. , Harada H.
Published: December 2008

In this paper, for the first time, a set of guidelines is presented for the systematic design of mixed flow and centrifugal compressors and pumps with suppressed secondary flows and a uniform exit flow field. The paper describes the shape of the optimum pressure distribution for the suppression of secondary flows in the impeller with reference to classical secondary flow theory. The feasibility of achieving this pressure distribution is then demonstrated by deriving guidelines for the design specifications of a three-dimensional inverse design method, in which the blades are designed subject to a specified circulation distribution or 2πrVθ. The guidelines will define the optimum choice of the blade loading or ∂rVθ/∂m and the stacking condition for the blades. These guidelines are then used in the design of three different low specific speed centrifugal pump impellers and a high specific speed industrial centrifugal compressor impellers. The flows through all the designed impellers are computed numerically by a three-dimensional viscous code and the resulting flow field is compared to that obtained in the corresponding conventional impeller. The results show consistent suppression of secondary flows in all cases. The design guidelines are validated experimentally by comparing the performance of the inverse designed centrifugal compressor impeller with the corresponding conventional impeller. The overall performance of the stage with the inverse designed impeller with suppressed secondary flows was found to be 5 percent higher than the conventional impeller at the peak efficiency point. Exit flow traverse results at the impeller exit indicate a more uniform exit flow than that measured at the exit from the conventional impeller.
Measurements in Film Cooling Flows: Hole L/D and Turbulence Intensity Effects
Authors: Burd S. W. , Kaszeta R. W. , Simon T. W.
Published: December 2008

Hot-wire anemometry measurements of simulated film cooling are presented to document the influence of the free-stream turbulence intensity and film cooling hole length-to-diameter ratio on mean velocity and on turbulence intensity. Measurements are taken in the zone where the coolant and free-stream flows mix. Flow from one row of film cooling holes with a streamwise injection of 35 deg and no lateral injection and with a coolant-to-free-stream flow velocity ratio of 1.0 is investigated under free-stream turbulence levels of 0.5 and 12 percent. The coolant-to-free-stream density ratio is unity. Two length-to-diameter ratios for the film cooling holes, 2.3 and 7.0, are tested. The Measurements document that under low free-stream turbulence conditions pronounced differences exist in the flowfield between L/D= 7.0 and 2.3. The difference between L/D cases are less prominent at high free-stream turbulence intensities. Generally, Short-L/D injection results in “jetting” of the coolant farther into the free-stream flow and enhanced mixing. Other changes in the flowfield attributable to a rise in free-stream turbulence intensity to engine-representative conditions are documented.
Heat Transfer in a Rotating Cavity With a Peripheral Inflow and Outflow of Cooling Air
Authors: Mirzaee I. , Gan X. , Wilson M. , Owen J. M.
Published: December 2008

This paper describes a combined computational and experimental study of the heat transfer in a rotating cavity with a peripheral inflow and outflow of cooling air for a range of rotational speeds and flow rates. Measurements are made in a purpose-built rig, with one of the two rotating discs heated, and computations are conducted using an axisymmetric elliptic solver incorporating the Launder-Sharma low-Reynolds-number k–ε turbulence model. Measured values of the tangential component of velocity, Vπ, exhibit Rankine-vortex behaviour which is not accurately modelled by the computations. Both computed and measured values of the radial component of velocity, Vr, confirm the recirculating nature of the flow. In the outflow region, agreement between computed and measured values of Vr is mainly good, but in the inflow region the computations exhibit a “peaky” distribution which is not shown by the measurements. The measured and computed Nusselt numbers show that Nu increases as the magnitudes of the flow rate and the rotational speed increase. The computed Nusselt numbers (allowing for the effects of conduction through and radiation to the unheated disk) reproduce the measured trends but tend to underestimate the experimental values at the larger radii.
Prediction of the Becalmed Region for LP Turbine Profile Design
Authors: Schulte V. , Hodson H. P.
Published: December 2008

Recent attention has focused on the so-called “becalmed region” that is observed inside the boundary layers of turbomachinery blading and is associated with the process of wake-induced transition. Significant reductions of profile loss have been shown for high lift LP turbine blades at low Reynolds numbers due the effects of the becalmed region on the diffusing flow at the rear of the suction surface. In this paper the nature and the significance of the becalmed region are examined using experimental observations and computational studies. It is shown that the becalmed region may be modeled using the unsteady laminar boundary layer equations. Therefore, it is predictable independent of the transition or turbulence models employed. The effect of the becalmed region on the transition process is modeled using a spot-based intermittency transition model. An unsteady differential boundary layer code was used to simulate a deterministic experiment involving an isolated turbulent spot numerically. The predictability of the becalmed region means that the rate of entropy production can be calculated in that region. It is found to be of the order of that in a laminar boundary layer. It is for this reason and because the becalmed region may be encroached upon by pursuing turbulent flows that for attached boundary layers, wake-induced transition cannot significantly reduce the profile loss. However, the becalmed region is less prone to separation than a conventional laminar boundary layer. Therefore, the becalmed region may be exploited in order to prevent boundary layer separation and the increase in loss that this entails. It is shown that it should now be possible to design efficient high lift LP turbine blades.
Direct Full Surface Skin Friction Measurement Using Nematic Liquid Crystal Techniques
Authors: Buttsworth D. R. , Elston S. J. , Jones T. V.
Published: December 2008

New techniques for the direct measurement of skin friction using nematic liquid crystal layers are demonstrated. Skin friction measurements can be made using a molecular rotation time technique or an equilibrium orientation technique. A mathematical model describing the molecular dynamics of the nematic liquid crystal layer has been introduced. Theoretical results from the proposed mathematical model are in excellent agreement with the current experimental measurements. It is thus demonstrated that the present model captures the essential physics of the nematic liquid crystal measurement techniques. Estimates based on the variance of the liquid crystal calibration data indicate that skin friction measurements to within ±4 percent should certainly be possible. The techniques offer the considerable advantage of simplicity, without any compromise on the accuracy, relative to other surface shear stress measurement techniques. The full surface measurement capacity of the equilibrium orientation technique is demonstrated by measuring the skin friction distribution around a cylindrical obstruction in a fully developed laminar flow.
Regulation of Dendritic Cell Migration by CD74, the MHC Class II-Associated Invariant Chain
Authors: Faure-André Gabrielle , Vargas Pablo , Yuseff Maria-Isabel , Heuzé Mélina , Diaz Jheimmy , Lankar Danielle , Steri Veronica , Manry Jeremy , Hugues Stéphanie , Vascotto Fulvia , Boulanger Jérôme , Raposo Graça , Bono Maria-Rosa , Rosemblatt Mario , Piel Matthieu , Lennon-Duménil Ana-Maria
Published: December 2008

Dendritic cells (DCs) sample peripheral tissues of the body in search of antigens to present to T cells. This requires two processes, antigen processing and cell motility, originally thought to occur independently. We found that the major histocompatibility complex II–associated invariant chain (Ii or CD74), a known regulator of antigen processing, negatively regulates DC motility in vivo. By using microfabricated channels to mimic the confined environment of peripheral tissues, we found that wild-type DCs alternate between high and low motility, whereas Ii-deficient cells moved in a faster and more uniform manner. The regulation of cell motility by Ii depended on the actin-based motor protein myosin II. Coupling antigen processing and cell motility may enable DCs to more efficiently detect and process antigens within a defined space.
A Null Mutation in Human
APOC3
Confers a Favorable Plasma Lipid Profile and Apparent Cardioprotection
Authors: Pollin Toni I. , Damcott Coleen M. , Shen Haiqing , Ott Sandra H. , Shelton John , Horenstein Richard B. , Post Wendy , McLenithan John C. , Bielak Lawrence F. , Peyser Patricia A. , Mitchell Braxton D. , Miller Michael , O'Connell Jeffrey R. , Shuldiner Alan R.
Published: December 2008

Apolipoprotein C-III (apoC-III) inhibits triglyceride hydrolysis and has been implicated in coronary artery disease. Through a genome-wide association study, we have found that about 5% of the Lancaster Amish are heterozygous carriers of a null mutation (R19X) in the gene encoding apoC-III (
APOC3
) and, as a result, express half the amount of apoC-III present in noncarriers. Mutation carriers compared with noncarriers had lower fasting and postprandial serum triglycerides, higher levels of HDL-cholesterol and lower levels of LDL-cholesterol. Subclinical atherosclerosis, as measured by coronary artery calcification, was less common in carriers than noncarriers, which suggests that lifelong deficiency of apoC-III has a cardioprotective effect.
The Emerging Nature of Nurture
Authors: Sur Mriganka
Published: December 2008

The Fundamentals of Brain Development
. Integrating Nature and Nurture.
By Joan Stiles
. Harvard University Press, Cambridge, MA, 2008. 433 pp. $49.95, £32.95, €37.50. ISBN 9780674026742.

Stiles draws on the findings of the past two decades to provide an inclusive and accessible account of the complexities and dynamism of brain development.
Traction Dynamics of Filopodia on Compliant Substrates
Authors: Chan Clarence E. , Odde David J.
Published: December 2008

Cells sense the environment's mechanical stiffness to control their own shape, migration, and fate. To better understand stiffness sensing, we constructed a stochastic model of the “motor-clutch” force transmission system, where molecular clutches link F-actin to the substrate and mechanically resist myosin-driven F-actin retrograde flow. The model predicts two distinct regimes: (i) “frictional slippage,” with fast retrograde flow and low traction forces on stiff substrates and (ii) oscillatory “load-and-fail” dynamics, with slower retrograde flow and higher traction forces on soft substrates. We experimentally confirmed these model predictions in embryonic chick forebrain neurons by measuring the nanoscale dynamics of single–growth-cone filopodia. Furthermore, we experimentally observed a model-predicted switch in F-actin dynamics around an elastic modulus of 1 kilopascal. Thus, a motor-clutch system inherently senses and responds to the mechanical stiffness of the local environment.
Structure and Functional Role of Dynein's Microtubule-Binding Domain
Authors: Carter Andrew P. , Garbarino Joan E. , Wilson-Kubalek Elizabeth M. , Shipley Wesley E. , Cho Carol , Milligan Ronald A. , Vale Ronald D. , Gibbons I. R.
Published: December 2008

Dynein motors move various cargos along microtubules within the cytoplasm and power the beating of cilia and flagella. An unusual feature of dynein is that its microtubule-binding domain (MTBD) is separated from its ring-shaped AAA+ adenosine triphosphatase (ATPase) domain by a 15-nanometer coiled-coil stalk. We report the crystal structure of the mouse cytoplasmic dynein MTBD and a portion of the coiled coil, which supports a mechanism by which the ATPase domain and MTBD may communicate through a shift in the heptad registry of the coiled coil. Surprisingly, functional data suggest that the MTBD, and not the ATPase domain, is the main determinant of the direction of dynein motility.
Modafinil Shifts Human Locus Coeruleus to Low-Tonic, High-Phasic Activity During Functional MRI
Authors: Minzenberg Michael J. , Watrous Andrew J. , Yoon Jong H. , Ursu Stefan , Carter Cameron S.
Published: December 2008

Models of cognitive control posit a key modulatory role for the pontine locus coeruleus–norepinephrine (LC-NE) system. In nonhuman primates, phasic LC-NE activity confers adaptive adjustments in cortical gain in task-relevant brain networks, and in performance, on a trial-by-trial basis. This model has remained untested in humans. We used the pharmacological agent modafinil to promote low-tonic/high-phasic LC-NE activity in healthy humans performing a cognitive control task during event-related functional magnetic resonance imaging (fMRI). Modafanil administration was associated with decreased task-independent, tonic LC activity, increased task-related LC and prefrontal cortex (PFC) activity, and enhanced LC-PFC functional connectivity. These results confirm in humans the role of the LC-NE system in PFC function and cognitive control and suggest a mechanism for therapeutic action of procognitive noradrenergic agents.
Developmental Patterning by Mechanical Signals inArabidopsis
Authors: Hamant Olivier , Heisler Marcus G. , Jönsson Henrik , Krupinski Pawel , Uyttewaal Magalie , Bokov Plamen , Corson Francis , Sahlin Patrik , Boudaoud Arezki , Meyerowitz Elliot M. , Couder Yves , Traas Jan
Published: December 2008

A central question in developmental biology is whether and how mechanical forces serve as cues for cellular behavior and thereby regulate morphogenesis. We found that morphogenesis at theArabidopsisshoot apex depends on the microtubule cytoskeleton, which in turn is regulated by mechanical stress. A combination of experiments and modeling shows that a feedback loop encompassing tissue morphology, stress patterns, and microtubule-mediated cellular properties is sufficient to account for the coordinated patterns of microtubule arrays observed in epidermal cells, as well as for patterns of apical morphogenesis.
A 10-Year Survey of Antifungal Susceptibility of Candidemia Isolates from Intensive Care Unit Patients in Greece
Authors: Dimopoulos George , Velegraki Aristea , Falagas Matthew E.
Published: December 2008

This study retrospectively reviews the susceptibility of 135 baseline ICU candidemia isolates (from 1997 to 2007) to nine antifungals as determined by the AFST-EUCAST microdilution method and identifies the most frequent causative agents of confirmed point-source candidemia outbreaks in local intensive care units. A minority of common and rare
Candida
species displayed decreased susceptibility to all antifungals.
Molecular Diversity of a North Carolina Wastewater Treatment Plant as Revealed by Pyrosequencing
Authors: Sanapareddy Nina , Hamp Timothy J. , Gonzalez Luis C. , Hilger Helene A. , Fodor Anthony A. , Clinton Sandra M.
Published: December 2008

We report the results of pyrosequencing of DNA collected from the activated sludge basin of a wastewater treatment plant in Charlotte, NC. Using the 454-FLX technology, we generated 378,601 sequences with an average read length of 250.4 bp. Running the 454 assembly algorithm over our sequences yielded very poor assembly, with only 0.3% of our sequences participating in assembly of significant contigs. Of the 117 contigs greater than 500 bp long that were assembled, the most common annotations were to transposases and hypothetical proteins. Comparing our sequences to known microbial genomes showed nonspecific recruitment, indicating that previously described taxa are only distantly related to the most abundant microbes in this treatment plant. A comparison of proteins generated by translating our sequence set to translations of other sequenced microbiomes shows a distinct metabolic profile for activated sludge with high counts for genes involved in metabolism of aromatic compounds and low counts for genes involved in photosynthesis. Taken together, these data document the substantial levels of microbial diversity within activated sludge and further establish the great utility of pyrosequencing for investigating diversity in complex ecosystems.
High-Level Diversity of Dinoflagellates in the Natural Environment, Revealed by Assessment of Mitochondrial
cox1
and
cob
Genes for Dinoflagellate DNA Barcoding
Authors: Lin Senjie , Zhang Huan , Hou Yubo , Zhuang Yunyun , Miranda Lilibeth
Published: December 2008

DNA barcoding is a diagnostic technique for species identification using a short, standardized DNA. An effective DNA barcoding marker would be very helpful for unraveling the poorly understood species diversity of dinoflagellates in the natural environment. In this study, the potential utility for DNA barcoding of mitochondrial cytochrome
c
oxidase 1 (
cox1
) and cytochrome
b
(
cob
) was assessed. Among several primer sets examined, the one amplifying a 385-bp
cob
fragment was most effective for dinoflagellates. This short
cob
fragment is easy to sequence and yet possess reasonable taxon resolution. While the lack of a uniform gap between interspecific and intraspecific distances poses difficulties in establishing a phylum-wide species-discriminating distance threshold, the variability of
cob
allows recognition of species within particular lineages. The potential of this
cob
fragment as a dinoflagellate species marker was further tested by applying it to an analysis of the dinoflagellate assemblages in Long Island Sound (LIS) and Mirror Lake in Connecticut. In LIS, a highly diverse assemblage of dinoflagellates was detected. Some taxa can be identified to the species and some to the genus level, including a taxon distinctly related to the bipolar species
Polarella glacialis
, and the large number of others cannot be clearly identified, due to the inadequate database. In Mirror Lake, a
Ceratium
species and an unresolved taxon were detected, exhibiting a temporal transition from one to the other. We demonstrate that this 385-bp
cob
fragment is promising for lineage-wise dinoflagellate species identification, given an adequate database.
Growth-Regulated Expression of a Bacteriocin, Produced by the Sweet Potato Pathogen
Streptomyces ipomoeae
, That Exhibits Interstrain Inhibition
Authors: Wang Jing , Schully Kevin L. , Pettis Gregg S.
Published: December 2008

Certain strains of the bacterial sweet potato pathogen
Streptomyces ipomoeae
produce the bacteriocin ipomicin, which inhibits other sensitive strains of the same species. Within the signal-sequence-encoding portion of the ipomicin structural gene
ipoA
exists a single rare TTA codon, which is recognized in
Streptomyces
bacteria by the temporally accumulating
bldA
leucyl tRNA. In this study, ipomicin was shown to stably accumulate in culture supernatants of
S. ipomoeae
in a growth-regulated manner that did not coincide with the pattern of
ipoA
expression. Similar growth-regulated production of ipomicin in
Streptomyces coelicolor
containing the cloned
ipoA
gene was found to be directly dependent on translation of the
ipoA
TTA codon by the
bldA
leucyl tRNA. The results here suggest that
bldA
-dependent translation of the
S. ipomoeae ipoA
gene leads to growth-regulated production of the ipomicin precursor, which upon processing to the mature form and secretion stably accumulates in the extracellular environment. To our knowledge, this is the first example of
bldA
regulation of a bacteriocin in the streptomycetes.
Acid and Base Stress and Transcriptomic Responses in
Bacillus subtilis
Authors: Wilks Jessica C. , Kitko Ryan D. , Cleeton Sarah H. , Lee Grace E. , Ugwu Chinagozi S. , Jones Brian D. , BonDurant Sandra S. , Slonczewski Joan L.
Published: December 2008

Acid and base environmental stress responses were investigated in
Bacillus subtilis. B. subtilis
AG174 cultures in buffered potassium-modified Luria broth were switched from pH 8.5 to pH 6.0 and recovered growth rapidly, whereas cultures switched from pH 6.0 to pH 8.5 showed a long lag time. Log-phase cultures at pH 6.0 survived 60 to 100% at pH 4.5, whereas cells grown at pH 7.0 survived <15%. Cells grown at pH 9.0 survived 40 to 100% at pH 10, whereas cells grown at pH 7.0 survived <5%. Thus, growth in a moderate acid or base induced adaptation to a more extreme acid or base, respectively. Expression indices from Affymetrix chip hybridization were obtained for 4,095 protein-encoding open reading frames of
B. subtilis
grown at external pH 6, pH 7, and pH 9. Growth at pH 6 upregulated acetoin production (
alsDS
), dehydrogenases (
adhA
,
ald
,
fdhD
, and
gabD
), and decarboxylases (
psd
and
speA
). Acid upregulated malate metabolism (
maeN
), metal export (
czcDO
and
cadA
), oxidative stress (catalase
katA
; OYE family
namA
), and the SigX extracytoplasmic stress regulon. Growth at pH 9 upregulated arginine catabolism (
roc
), which generates organic acids, glutamate synthase (
gltAB
), polyamine acetylation and transport (
blt
), the K
+
/H
+
antiporter (
yhaTU
), and cytochrome oxidoreductases (
cyd
,
ctaACE
, and
qcrC
). The SigH, SigL, and SigW regulons were upregulated at high pH. Overall, greater genetic adaptation was seen at pH 9 than at pH 6, which may explain the lag time required for growth shift to high pH. Low external pH favored dehydrogenases and decarboxylases that may consume acids and generate basic amines, whereas high external pH favored catabolism-generating acids.
Intraspecies Genomic Diversity and Natural Population Structure of the Meat-Borne Lactic Acid Bacterium
Lactobacillus sakei
Authors: Chaillou Stéphane , Daty Marie , Baraige Fabienne , Dudez Anne-Marie , Anglade Patricia , Jones Rhys , Alpert Carl-Alfred , Champomier-Vergès Marie-Christine , Zagorec Monique
Published: December 2008

Lactobacillus sakei
is a food-borne bacterium naturally found in meat and fish products. A study was performed to examine the intraspecies diversity among 73 isolates sourced from laboratory collections in several different countries. Pulsed-field gel electrophoresis analysis demonstrated a 25% variation in genome size between isolates, ranging from 1,815 kb to 2,310 kb. The relatedness between isolates was then determined using a PCR-based method that detects the possession of 60 chromosomal genes belonging to the flexible gene pool. Ten different strain clusters were identified that had noticeable differences in their average genome size reflecting the natural population structure. The results show that many different genotypes may be isolated from similar types of meat products, suggesting a complex ecological habitat in which intraspecies diversity may be required for successful adaptation. Finally, proteomic analysis revealed a slight difference between the migration patterns of highly abundant GapA isoforms of the two prevailing
L. sakei
subspecies (
sakei
and
carnosus
). This analysis was used to affiliate the genotypic clusters with the corresponding subspecies. These findings reveal for the first time the extent of intraspecies genomic diversity in
L. sakei
. Consequently, identification of molecular subtypes may in the future prove valuable for a better understanding of microbial ecosystems in food products.