bluuebunny/crossref_metadata_2025 huggingface dataset:
Volume transport and generalized hydrodynamic equations for monatomic fluids
Authors: Eu Byung Chan
Published: October 2008

In this paper, the effects of volume transport on the generalized hydrodynamic equations for a pure simple fluid are examined from the standpoint of statistical mechanics and, in particular, kinetic theory of fluids. First, we derive the generalized hydrodynamic equations, namely, the constitutive equations for the stress tensor and heat flux for a single-component monatomic fluid, from the generalized Boltzmann equation in the presence of volume transport. Then their linear steady-state solutions are derived and examined with regard to the effects of volume transport on them. The generalized hydrodynamic equations and linear constitutive relations obtained for nonconserved variables make it possible to assess Brenner’s proposition [Physica A 349, 11 (2005); Physica A 349, 60 (2005)] for volume transport and attendant mass and volume velocities as well as the effects of volume transport on the Newtonian law of viscosity, compression/dilatation (bulk viscosity) phenomena, and Fourier’s law of heat conduction. On the basis of study made, it is concluded that the notion of volume transport is sufficiently significant to retain in irreversible thermodynamics of fluids and fluid mechanics.
A method to measure the frequencies of individual half cells in a dumbbell cavity
Authors: An Sun , Liping Zhang , Yazhe Tang , Li Ying-min , Cho Yong-Sub
Published: October 2008

Dumbbell fabrication is a midprocess for manufacturing an elliptical superconducting rf cavity. In order to understand how a welding shrinkage affects a dumbbell’s frequencies and length, we need to measure the exact frequencies of each individual half cell of a dumbbell. To improve such a calculation precision and to simplify the calculation formulae, based on a two-coupled oscillator model and a cavity perturbation theory, a new formula to calculate the individual half-cell frequencies of a dumbbell or the individual cavity frequencies of a two-cavity coupling system has been developed, and its performance has been confirmed by using a dumbbell simulation. This formula can be applied to any kind of rf cavities with electric, magnetic, or electromagnetic coupling, if a coupling hole between two coupling cavities is small compared to the wavelength. Compared to other calculation formulae, this formula simplifies the calculation process of the individual resonator frequencies of a coupling system considerably, and it can also improve the calculation precision than that of a normal calculation method. Another advantage of this new method is that we do not need to consider a coupling factor between two resonators during a testing for an individual resonator frequency of an oscillator. The developed formula has been successfully used to tune the PEFP dumbbells.
Low velocity ion stopping in binary ionic mixtures
Authors: Tashev Bekbolat , Baimbetov Fazylkhan , Deutsch Claude , Fromy Patrice
Published: October 2008

Attention is focused on the low ion velocity stopping mechanisms in multicomponent and dense target plasmas built of quasiclassical electron fluids neutralizing binary ionic mixtures, such as, deuterium-tritium of current fusion interest, proton-heliumlike iron in the solar interior or proton-helium ions considered in planetology, as well as other mixtures of fiducial concern in the heavy ion beam production of warm dense matter at Bragg peak conditions. The target plasma is taken in a multicomponent dielectric formulation à la Fried–Conte. The occurrence of projectile ion velocities (so-called critical) for which target electron slowing down equals that of given target ion components is also considered. The corresponding multiquadrature computations, albeit rather heavy, can be monitored analytical through a very compact code operating a PC cluster. Slowing down results are systematically scanned with respect to target temperature and electron density, as well as ion composition.
The influence of C2 dimers on the stability of TimCn metcar clusters
Authors: Joswig Jan-Ole , Springborg Michael
Published: October 2008

We present results of an investigation of small TimCn clusters with different stoichiometries in order to throw light on the occurrence of carbon dimers in these structures. Previous studies of transition metal (M) metallocarbohedrene (metcar) clusters MmCn have proposed that C2 dimers play a special role. In the special case of TimCn metcars these dimers have been observed in several studies. We shall show that clusters containing C2 dimers are energetically favored with respect to those containing only single carbon atoms or trimers, especially when the dimers occupy the corner positions of cubic clusters. Moreover, we find that cubic structures are more stable than corresponding double-cage metcars. Finally, a highly symmetric Ti6C10 metcar cluster is presented and proposed to be the global-minimum structure of this stoichiometry.
Structural and elastic properties of LaAlO3 from first-principles calculations
Authors: Luo Xin , Wang Biao
Published: October 2008

Using the first-principles linearized augmented plane wave calculations within density functional theory, the stable structure, the phase transition, and elastic properties of the LaAlO3 are investigated. At low temperature, our calculation indicates that the rhombohedral R-3C phase is the most energetically stable structure among the three proposed structures: R-3C (No. 167), R-3M (No. 166), and R3C (No. 161). It is found that the LaAlO3 transforms from rhombohedral R-3C phase to cubic PM-3M phase with a volume change of 1% when the applied hydrostatic pressure is 15.4 GPa, which is consistent with the experimental value. The elastic constants, shear modulus, bulk modulus, and Poisson’s ratio of LaAlO3 are calculated and compared with corresponding experimental data. Our result shows that the rotation of the AlO6 octahedra in LaAlO3 has a large influence on the anisotropic elastic constants. From the calculated Debye temperature and elastic constants, the R-3C phase of LaAlO3 is predicted to be more thermostable and to exhibit higher fracture toughness than the high-pressured PM-3M phase.
Cyclic loading of an elastic-plastic adhesive spherical microcontact
Authors: Kadin Y. , Kligerman Y. , Etsion I.
Published: October 2008

A previous study of a single load-unload cycle of an adhesive contact between an elastic-plastic microscopic sphere and a rigid flat is extended here for several load-unload cycles. The interacting forces between the sphere and the flat obey the Lennard–Jones potential. Kinematic hardening is assumed for the sphere material to account for possible plastic shakedown, and the difference between kinematic and isotropic hardenings is discussed. The main goal of the current work is to investigate the evolution of the load-approach curves for the elastic-plastic spherical contact during its cyclic loading-unloading. These curves are presented for different physical conditions, represented by three main dimensionless parameters, which affect the behavior of the elastic-plastic adhesive contact. A transition value of the Tabor parameter is found, below which the load-approach curves are always continuous and jump-in and jump-out instabilities are not expected.
Investigation of lateral exciton transfer of coexistent quantum dot systems
Authors: Lee Jia-Ren , Lu Chien-Rong , Jen Jen-Yi
Published: October 2008

The optical characterization of the ZnCdSe/ZnSe quantum dot (QDs) system is studied by photoluminescence (PL) spectrum measured at temperatures from 22 to 300 K. The distinct quenching rates of spectral integrated intensity demonstrate that there are divergent lateral exciton transfer modes between two types of coexistent QDs with different sizes and densities. The smaller and denser QD assemblies are advantageous to trigger lateral migration of thermally activated excitons due to their shallower localization and more coupling channels. However, the carrier repopulation-induced redistribution of excitonic emission energy is contrarily observed in the deepest localized case. The extra redshift of transition energy with increasing temperature is attributed to the incompletely three-dimensional excitonic confinement induced by the morphological features. In contrast with scanning probe techniques, using PL as spectral probe is a nondestructive way to explore inner morphology of capped multiple quantum structure.
Defect-free ZnSe nanowire and nanoneedle nanostructures
Authors: Aichele Thomas , Tribu Adrien , Bougerol Catherine , Kheng Kuntheak , André Régis , Tatarenko Serge
Published: October 2008

We report the growth of ZnSe nanowires and nanoneedles using molecular beam epitaxy (MBE). Different growth regimes were found, depending on growth temperature and the Zn–Se flux ratio. By employing a combined MBE growth of nanowires and nanoneedles without any postprocessing of the sample, we achieved an efficient suppression of stacking fault defects. This is confirmed by transmission electron microscopy and by photoluminescence studies.
Response to “Comment on ‘Nonlinear properties of small amplitude dust ion acoustic solitary waves’” [Phys. Plasmas 15, 104703 (2008)]
Authors: Gupta M. R. , Sarkar S. , Khan Manoranjan , Ghosh Samiran
Published: October 2008

The objections are not justified. It should have been noted that ion charge number zi=1 throughout the referred paper [Ghosh et al., Phys. Plasmas 7, 3594 (2000)]. There is no inconsistency in the formulation of the referred paper as explained in the text.
Alfvén cascade modes at high β in the National Spherical Torus Experiment
Authors: Crocker N. A. , Fredrickson E. D. , Gorelenkov N. N. , Kramer G. J. , Darrow D. S. , Heidbrink W. W. , Kubota S. , Levinton F. M. , Yuh H. , Menard J. E. , LeBlanc B. P. , Bell R. E.
Published: October 2008

Alfvén cascade (AC) modes are observed in the National Spherical Torus Experiment [M. Ono et al., Nucl. Fusion 40, 557 (2000)] reversed shear plasmas over a wide range (up to ∼25% on axis, or ∼11% at minimum q) of β (ratio of kinetic pressure to magnetic pressure). At low β, the AC mode spectrum shows characteristics similar to conventional tokamaks. At higher β, distinct β and ∇β effects are observed in the spectrum, including a significant reduction in the relative size of the frequency sweep and a toroidal mode number dependence in the minimum mode frequency. AC mode structure is obtained using reflectometry. Fast-ion loss associated with AC mode activity is observed. AC mode polarization at the plasma edge is consistent with expectation. Magnetohydrodynamic (MHD) spectroscopy is shown to be usable to determine qmin at both low β and high β. Observed AC mode structure and frequency are found to be consistent with calculations for the same plasma conditions and geometry using the linear, ideal MHD hybrid kinetic code NOVA-K [C. Z. Cheng, Phys. Rep. 211, 1 (1992)].
Plasma jet acceleration of dust particles to hypervelocities
Authors: Ticoş C. M. , Wang Zhehui , Wurden G. A. , Kline J. L. , Montgomery D. S.
Published: October 2008

A convenient method to accelerate simultaneously hundreds of micron-size dust particles to a few km/s over a distance of about 1m is based on plasma drag. Plasma jets which can deliver sufficient momentum to the dust particles need to have speeds of at least several tens of km/s, densities of the order of 1022m−3 or higher, and low temperature ∼1eV, in order to prevent dust destruction. An experimental demonstration of dust particles acceleration to hypervelocities by plasma produced in a coaxial gun is presented here. The plasma flow speed is deduced from photodiode signals while the plasma density is measured by streaked spectroscopy. As a result of the interaction with the plasma jet, the dust grains are also heated to high temperatures and emit visible light. A hypervelocity dust shower is imaged in situ with a high speed video camera at some distance from the coaxial gun, where light emission from the plasma flow is less intense. The bright traces of the flying microparticles are used to infer their speed and acceleration by employing the time-of-flight technique. A simple model for plasma drag which accounts for ion collection on the grain surface gives predictions for dust accelerations which are in good agreement with the experimental observations.
Ferroelectric domain wall pinning at a bicrystal grain boundary in bismuth ferrite
Authors: Rodriguez Brian J. , Chu Y. H. , Ramesh R. , Kalinin Sergei V.
Published: October 2008

The ferroelectric polarization switching behavior at the 24° (100) tilt grain boundary (GB) in an epitaxial multiferroic BiFeO3 bicrystal film is studied using piezoresponse force microscopy (PFM). The PFM amplitudes across positively and negatively poled GB regions suggest the presence of a frozen polarization component at the interface. The switching experiments demonstrate that the GB attracts the domain wall and acts as a pinning center. The PFM results are compared with conductive atomic force microscopy and spectroscopy, which suggest domain wall pinning at the GB can be partially attributed to increased conductance at the GB.
Artificial electrical dipole in polymer multilayers for nonvolatile thin film transistor memory
Authors: Chang Chia-Chieh , Pei Zingway , Chan Yi-Jen
Published: October 2008

In this letter, an organic nonvolatile thin film transistor (TFT) memory on a plastic substrate is reported. The cross-linked poly-4-vinyl phenol (PVP) is used as a polymer dielectric layer in the form of a triple layer structure to achieve the memory function. Two interfaces between the PVP triple layers are the main trapping centers for electrons and holes, respectively, which are verified by the capacitance-voltage analysis. The electric dipole is established by the separated electrons and holes in the two interfaces of the PVP triple layer structure and results in an 11V memory window for the TFT nonvolatile memory.
Coherent trapping of x-ray photons in crystal cavities in the picosecond regime
Authors: Chen S.-Y. , Wu H.-H. , Chang Y.-Y. , Lee Y.-R. , Sun W.-H. , Chang S.-L. , Stetsko Yu. P. , Tang M.-T. , Yabashi M. , Ishikawa T.
Published: October 2008

We report on the trapping of 14keV photons in periods of 1.11–1.67ps by the 12 4 0 backdiffraction in two- and multiplate silicon single-crystal cavities of a few hundred micrometer size. The formation of standing waves inside the cavities ensures better coherence for the x rays. We anticipate that the transmitted x rays through this type of cavities can be used as a quasicoherent x-ray source for probing the dynamic structures of solids, liquids, and biological substances.
Differential surface stress sensor for detection of chemical and biological species
Authors: Kang K. , Nilsen-Hamilton M. , Shrotriya P.
Published: October 2008

We report a sensor consisting of two micromachined cantilevers (a sensing/reference pair) that is suitable for detection of chemical and biological species. The sensing strategy involves coating the sensing cantilever with receptors that have high affinities for the analyte. The presence of analyte is detected by determining the differential surface stress associated with its adsorption/absorption to the sensing cantilever. An interferometric technique is utilized to measure the differential bending of the sensing cantilever with respect to reference. Surface stress associated with hybridization of single stranded DNA is measured to demonstrate the unique advantages of the sensor.
Subterahertz excitations and magnetoelectric effects in hexaferrite-piezoelectric bilayers
Authors: Ustinov Alexey B. , Srinivasan G.
Published: October 2008

A frequency-agile hexaferrite-piezoelectric composite for potential device applications at subterahertz frequencies is studied. The bilayer is composed of aluminum substituted barium hexagonal ferrite (BaAl2Fe10O19) and lead zirconate titanate (PZT). A dc electric field applied to PZT results in mechanical deformation of the ferrite, leading to a frequency shift in ferromagnetic resonance. The bilayer demonstrates magnetoelectric interaction coefficient of about 0.37Oecm∕kV.
Trimolecular recombination in polythiophene: fullerene bulk heterojunction solar cells
Authors: Juška G. , Genevičius K. , Nekrašas N. , Sliaužys G. , Dennler G.
Published: October 2008

In this work, reduced Langevin recombination in poly(3-hexylthiophene): 1-(3-methoxycarbonyl) propyl-1-phenyl[6,6]C61 blends has been studied with various methods. Using photogenerated charge carrier extraction by linearly increasing voltage technique, it was observed that charge carrier recombination transient corresponds to trimolecular recombination. By double injection current transient technique, it was shown that the influence of deep charge carrier trapping is insignificant and that trimolecular recombination coefficient γ is independent of the electric field. Finally, the temperature dependence of γ was measured by integral time-of-flight method.
Gated armchair nanotube and metallic field effect
Authors: Ren Wei , Cho T. H. , Leung T. C. , Chan C. T.
Published: October 2008

We propose a useful metallic field effect element based on the electric field control of armchair single-wall carbon nanotube. The electron conduction channels are enhanced by imposing a transverse gate voltage. Multiple Dirac points have been revealed theoretically by our density functional and tight binding calculations. Our electron transport results show that the performance of such unique transistors depends mainly on the diameter of nanotube exploited. The critical field strength required decreases rapidly with the tube diameter.
Magnetoelectric bistabilities in ferromagnetic resonant tunneling structures
Authors: Ertler Christian
Published: October 2008

The conditions for the occurrence of pronounced magnetoelectric bistabilities in the resonant tunneling through a ferromagnetic quantum well are theoretically investigated. The bistability appears due to the mutual feedback of the carriers Coulomb interaction and the carriers exchange coupling with magnetic impurities in the well. It is shown that the well Curie temperature depends strongly on the relative alignment of the quantum well level and the reservoirs chemical potentials, which can be modified electrically. Switching between a “current-on/magnetism-off” and a “current-off/magnetism-on” mode becomes possible if the well temperature lies in-between the bistable values of the well Curie temperature.
Assessment of nitrogen losses from urea and an organic manure with and without nitrification inhibitor, dicyandiamide, applied to lettuce under glasshouse conditions
Authors: Asing Janice , Saggar S. , Singh Jagrati , Bolan Nanthi S.
Published: October 2008

Urea and organic manures such as ‘Garden galore’ (GG) are used to supply nitrogen (N) in vegetable farming and floriculture systems in New Zealand. However, a significant amount of the applied N is lost to the atmosphere via nitrous oxide (N2O) and ammonia (NH3) emissions, and leached to surface and ground water as nitrate (NO3–) contributing to environmental degradation such as global warming and eutrophication. One of the mitigation options to reduce these losses is to use nitrification inhibitors (NI). Glasshouse and laboratory incubation experiments were conducted under controlled moisture and temperature conditions to determine the effects of an NI, dicyandiamide (DCD), on N losses from urea and GG applied to lettuce grown in a Manawatu sandy soil. Nitrogen and DCD were applied at the rates of 9 and 1.3 g/m2, respectively, and the gaseous emission of N2O and NH3 were monitored over a 5-week period using a closed-chamber technique. At the end of the experiment the lettuce plant shoots and roots were harvested, and analysed for N concentration. Soils were leached with deionised water and leachates were analysed for ammonium (NH4+) and NO3–. The results showed greater loss of N as NH3 than N2O and the effect was more pronounced in the case of urea. Addition of DCD significantly reduced N2O emissions from both urea and GG, and increased NH3 emissions from both urea and GG, with the increase being significant only for urea. Addition of DCD maintained higher soil NH4+ concentration and lower NO3– concentration than without DCD. Overall, DCD was effective in reducing N losses of N2O emissions and NO3– leaching. Urea application resulted in shoot tip burning and the symptoms were enhanced with the addition of DCD. There was no significant effect of DCD addition on lettuce yield.
Analysis of the evolution of soil erosion classes using multitemporal Landsat imagery
Authors: Marquínez J. , Wozniak E. , Fernández S. , Martínez R.
Published: October 2008

A cartographic method based on satellite images was completed in order to analyse the evolution of soil erosion in areas under humid climate conditions that experience frequent small forest fires. The method uses indicators, recognisable in the images, for the spatial and temporal analysis of the soil erosion status in burnt areas where the vegetation recovers quickly after fires. The continuity of the organic horizon, the surface stoniness and the vegetation cover degradation or regeneration were the indicators of the erosive soil class used in the multitemporal analysis of nine Landsat images. The study area is located in the western sector of the Cantabrian Range (NW Spain). The indicators selected were useful to show clearly the erosive status of the soils. Also, the use of multitemporal satellite image analysis seems to be a suitable method for studying soil erosion evolution in areas prone to forest fire. The application of the proposed method showed that in a study area of 48 857 ha, the soil cover was recovering in 7377 ha owing to the smaller frequency of forest fires, and degrading in 2326 ha.
Soil temperatures during autumn prescribed burning: implications for the germination of fire responsive species?
Authors: Penman T. D. , Towerton A. L.
Published: October 2008

Prescribed fire is a widely applied management tool in native forests. There have been concerns raised about the ecological impacts of prescribed fire on native flora. One aspect of the debate is the extent to which prescribed fire heats the soil to levels reported to trigger germination in the soil seed banks. We used Thermochrons to test soil temperatures at 2 and 5 cm in prescribed burns in dry sclerophyll forests. Soil temperatures during the burns were generally low (<40°C) with less than 5% of sites being exposed to temperatures necessary for the germination of fire-dependent shrub species. High temperatures were associated with high fuel consumption and large woody debris. This information suggests that prescribed fires, carried out according to standard practices, in these forests are unlikely to trigger germination in the majority of the soil-stored seed banks. If ecological burns in these forests are aimed at promoting populations of senescing obligate seeder species, they need to be hotter than standard practice if they are to achieve their objectives, although we acknowledge that there are inherent risks associated with hotter burns.
Biocatalyst activity in nonaqueous environments correlates with centisecond-range protein motions
Authors: Eppler Ross K. , Hudson Elton P. , Chase Shannon D. , Dordick Jonathan S. , Reimer Jeffrey A. , Clark Douglas S.
Published: October 2008

Recent studies exploring the relationship between enzymatic catalysis and protein dynamics in the aqueous phase have yielded evidence that dynamics and enzyme activity are strongly correlated. Given that protein dynamics are significantly attenuated in organic solvents and that proteins exhibit a wide range of motions depending on the specific solvent environment, the nonaqueous milieu provides a unique opportunity to examine the role of protein dynamics in enzyme activity. Variable-temperature kinetic measurements, X-band electron spin resonance spectroscopy,
1
H NMR relaxation, and
19
F NMR spectroscopy experiments were performed on subtilisin Carlsberg colyophilized with several inorganic salts and suspended in organic solvents. The results indicate that salt activation induces a greater degree of transition-state flexibility, reflected by a more positive ΔΔS
†
, for the more active biocatalyst preparations in organic solvents. In contrast, ΔΔH
†
was negligible regardless of salt type or salt content. Electron spin resonance spectroscopy and
1
H NMR relaxation measurements, including spin-lattice relaxation, spin-lattice relaxation in the rotating frame, and longitudinal magnetization exchange, revealed that the enzyme's turnover number (
k
cat
) was strongly correlated with protein motions in the centisecond time regime, weakly correlated with protein motions in the millisecond regime, and uncorrelated with protein motions on the piconanosecond timescale. In addition,
19
F chemical shift measurements and hyperfine tensor measurements of biocatalyst formulations inhibited with 4-fluorobenzenesulfonyl fluoride and 4-ethoxyfluorophosphinyl-oxy-TEMPO, respectively, suggest that enzyme activation was only weakly affected by changes in active-site polarity.
Role of Rab27 in synaptic transmission at the squid giant synapse
Authors: Yu Eunah , Kanno Eiko , Choi Soonwook , Sugimori Mutsuyuki , Moreira Jorge E. , Llinás Rodolfo R. , Fukuda Mitsunori
Published: October 2008

Small GTPase Rab is a member of a large family of Ras-related proteins, highly conserved in eukaryotic cells, and thought to regulate specific type(s) and/or specific step(s) in intracellular membrane trafficking. Given our interest in synaptic transmission, we addressed the possibility that Rab27 (a close isoform of Rab3) could be involved in cytosolic synaptic vesicle mobilization. Indeed, preterminal injection of a specific antibody against squid Rab27 (anti-sqRab27 antibody) combined with confocal microscopy demonstrated that Rab27 is present on squid synaptic vesicles. Electrophysiological study of injected synapses showed that the anti-sqRab27 antibody inhibited synaptic release in a stimulation-dependent manner without affecting presynaptic action potentials or inward Ca
2+
current. This result was confirmed in
in vitro
synaptosomes by using total internal reflection fluorescence microscopy. Thus, synaptosomal Ca
2+
-stimulated release of FM1-43 dye was greatly impaired by intraterminal anti-sqRab27 antibody. Ultrastructural analysis of the injected giant preterminal further showed a reduced number of docked synaptic vesicles and an increase in nondocked vesicular profiles distant from the active zone. These results, taken together, indicate that Rab27 is primarily involved in the maturation of recycled vesicles and/or their transport to the presynaptic active zone in the squid giant synapse.
Photoferrotrophs thrive in an Archean Ocean analogue
Authors: Crowe Sean A. , Jones CarriAyne , Katsev Sergei , Magen Cédric , O'Neill Andrew H. , Sturm Arne , Canfield Donald E. , Haffner G. Douglas , Mucci Alfonso , Sundby Bjørn , Fowle David A.
Published: October 2008

Considerable discussion surrounds the potential role of anoxygenic phototrophic Fe(II)-oxidizing bacteria in both the genesis of Banded Iron Formations (BIFs) and early marine productivity. However, anoxygenic phototrophs have yet to be identified in modern environments with comparable chemistry and physical structure to the ancient Fe(II)-rich (ferruginous) oceans from which BIFs deposited. Lake Matano, Indonesia, the eighth deepest lake in the world, is such an environment. Here, sulfate is scarce (<20 μmol·liter
−1
), and it is completely removed by sulfate reduction within the deep, Fe(II)-rich chemocline. The sulfide produced is efficiently scavenged by the formation and precipitation of FeS, thereby maintaining very low sulfide concentrations within the chemocline and the deep ferruginous bottom waters. Low productivity in the surface water allows sunlight to penetrate to the >100-m-deep chemocline. Within this sulfide-poor, Fe(II)-rich, illuminated chemocline, we find a populous assemblage of anoxygenic phototrophic green sulfur bacteria (GSB). These GSB represent a large component of the Lake Matano phototrophic community, and bacteriochlorophyll
e
, a pigment produced by low-light-adapted GSB, is nearly as abundant as chlorophyll
a
in the lake's euphotic surface waters. The dearth of sulfide in the chemocline requires that the GSB are sustained by phototrophic oxidation of Fe(II), which is in abundant supply. By analogy, we propose that similar microbial communities, including populations of sulfate reducers and photoferrotrophic GSB, likely populated the chemoclines of ancient ferruginous oceans, driving the genesis of BIFs and fueling early marine productivity.
Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes
Authors: Janga Sarath Chandra , Collado-Vides Julio , Babu M. Madan
Published: October 2008

Genetic material in eukaryotes is tightly packaged in a hierarchical manner into multiple linear chromosomes within the nucleus. Although it is known that eukaryotic transcriptional regulation is complex and requires an intricate coordination of several molecular events both in space and time, whether the complexity of this process constrains genome organization is still unknown. Here, we present evidence for the existence of a higher-order organization of genes across and within chromosomes that is constrained by transcriptional regulation. In particular, we reveal that the target genes (TGs) of transcription factors (TFs) for the yeast,
Saccharomyces cerevisiae
, are encoded in a highly ordered manner both across and within the 16 chromosomes. We show that (
i
) the TGs of a majority of TFs show a strong preference to be encoded on specific chromosomes, (
ii
) the TGs of a significant number of TFs display a strong preference (or avoidance) to be encoded in regions containing particular chromosomal landmarks such as telomeres and centromeres, and (
iii
) the TGs of most TFs are positionally clustered within a chromosome. Our results demonstrate that specific organization of genes that allowed for efficient control of transcription within the nuclear space has been selected during evolution. We anticipate that uncovering such higher-order organization of genes in other eukaryotes will provide insights into nuclear architecture, and will have implications in genetic engineering experiments, gene therapy, and understanding disease conditions that involve chromosomal aberrations.
Antibodies targeted to TRAIL receptor-2 and ErbB-2 synergize
in vivo
and induce an antitumor immune response
Authors: Stagg John , Sharkey Janelle , Pommey Sandra , Young Richard , Takeda Kazuyoshi , Yagita Hideo , Johnstone Ricky W. , Smyth Mark J.
Published: October 2008

Despite the development of human epidermal growth factor receptor-2 (ErbB-2/HER2)-targeted therapies, there remains an unmet medical need for breast cancer patients with ErbB-2 overexpression. We investigated the therapeutic activity of an agonist mAb to mouse tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) receptor-2 (DR5) against ErbB2-driven breast cancer. Established tumors in BALB/c transgenic mice expressing a constitutively active ErbB-2/neuT were treated with anti-DR5 mAb and/or anti-ErbB-2 mAb and monitored for tumor progression. Treatment with anti-DR5 or anti-ErbB2 mAb as single agents significantly delayed tumor growth, although all tumors eventually progressed. Remarkably, treatment with a combination of anti-DR5 and anti-ErbB-2 mAbs induced complete response in a majority of mice.
In vivo
blockade of CD11b
+
cells, but not natural killer cell depletion, significantly abrogated the early antitumor response. Notably, depletion of CD8
+
T cells provoked primary and secondary tumor relapse, revealing the induction of antitumor immunity by the combination treatment. Combined therapy with anti-DR5 and anti-ErbB-2 mAbs further significantly suppressed the growth of advanced spontaneous tumors in ErbB-2/neuT transgenic mice, even when treatment was delayed until tumors were palpable. We thus demonstrated that the combination of anti-DR5 and anti-ErbB2 mAbs might be an effective form of treatment for ErbB-2-overexpressing breast cancer.
A role for atmospheric CO
2
in preindustrial climate forcing
Authors: van Hoof Thomas B. , Wagner-Cremer Friederike , Kürschner Wolfram M. , Visscher Henk
Published: October 2008

Complementary to measurements in Antarctic ice cores, stomatal frequency analysis of leaves of land plants preserved in peat and lake deposits can provide a proxy record of preindustrial atmospheric CO
2
concentration. CO
2
trends based on leaf remains of
Quercus robur
(English oak) from the Netherlands support the presence of significant CO
2
variability during the first half of the last millennium. The amplitude of the reconstructed multidecadal fluctuations, up to 34 parts per million by volume, considerably exceeds maximum shifts measured in Antarctic ice. Inferred changes in CO
2
radiative forcing are of a magnitude similar to variations ascribed to other mechanisms, particularly solar irradiance and volcanic activity, and may therefore call into question the concept of the Intergovernmental Panel on Climate Change, which assumes an insignificant role of CO
2
as a preindustrial climate-forcing factor. The stomata-based CO
2
trends correlate with coeval sea-surface temperature trends in the North Atlantic Ocean, suggesting the possibility of an oceanic source/sink mechanism for the recorded CO
2
changes.
An oligosaccharide-based HIV-1 2G12 mimotope vaccine induces carbohydrate-specific antibodies that fail to neutralize HIV-1 virions
Authors: Joyce Joseph G. , Krauss Isaac J. , Song Hong C. , Opalka David W. , Grimm Karen M. , Nahas Deborah D. , Esser Mark T. , Hrin Renee , Feng Meizhen , Dudkin Vadim Y. , Chastain Michael , Shiver John W. , Danishefsky Samuel J.
Published: October 2008

The conserved oligomannose epitope, Man9GlcNAc2, recognized by the broadly neutralizing human mAb 2G12 is an attractive prophylactic vaccine candidate for the prevention of HIV-1 infection. We recently reported total chemical synthesis of a series of glycopeptides incorporating one to three copies of Man9GlcNAc2coupled to a cyclic peptide scaffold. Surface plasmon resonance studies showed that divalent and trivalent, but not monovalent, compounds were capable of binding 2G12. To test the efficacy of the divalent glycopeptide as an immunogen capable of inducing a 2G12-like neutralizing antibody response, we covalently coupled the molecule to a powerful immune-stimulating protein carrier and evaluated immunogenicity of the conjugate in two animal species. We used a differential immunoassay to demonstrate induction of high levels of carbohydrate-specific antibodies; however, these antibodies showed poor recognition of recombinant gp160 and failed to neutralize a panel of viral isolates in entry-based neutralization assays. To ascertain whether antibodies produced during natural infection could recognize the mimetics, we screened a panel of HIV-1-positive and -negative sera for binding to gp120 and the synthetic antigens. We present evidence from both direct and competitive binding assays that no significant recognition of the glycopeptides was observed, although certain sera did contain antibodies that could compete with 2G12 for binding to recombinant gp120.
Aptamer-based endocytosis of a lysosomal enzyme
Authors: Chen Chi-hong B. , Dellamaggiore Kenneth R. , Ouellette Christopher P. , Sedano Cecilia D. , Lizadjohry Meikana , Chernis George A. , Gonzales Michelle , Baltasar Francis E. , Fan Audrey L. , Myerowitz Rachel , Neufeld Elizabeth F.
Published: October 2008

Enzyme replacement therapy for lysosomal storage diseases is currently based on endocytosis of lysosomal enzymes via the mannose or mannose 6-phosphate receptors. We are developing a technology for endocytosis of lysosomal enzymes that depends on generic, chemically conjugated reagents. These reagents are aptamers (single-stranded nucleic acid molecules) selected to bind to the extracellular domain of the mouse transferrin receptor. After selection, an RNA aptamer and a DNA aptamer were modified with biotin and linked to dye-labeled streptavidin for detection by confocal microscopy. Aptamer–streptavidin conjugates showed saturable uptake into mouse fibroblasts (Ltk−cells), which could be inhibited by an excess of free aptamer but not by tRNA, calf thymus DNA, or transferrin. The RNA aptamer–streptavidin conjugate was mouse-specific, as human cells (293T) did not take it up unless first transfected with the mouse transferrin receptor. Some streptavidin separated from the recycling pathway of transferrin and colocalized with lysosomes. After characterization in the model system, the DNA aptamer was conjugated to a lysosomal enzyme, α-l-iduronidase, from which mannose 6-phosphate had been removed. The aptamer had been modified by attachment of terminal glycerol for oxidation by periodate and reaction of the resulting aldehyde with amino groups on the protein. Dephospho-α-l-iduronidase-aptamer conjugate was taken up in saturable manner by α-l-iduronidase-deficient mouse fibroblasts, with half-maximal uptake estimated as 1.6 nM. Endocytosed enzyme–aptamer conjugate corrected glycosaminoglycan accumulation, indicating that it reached lysosomes and was functional in those organelles. Both uptake and correction were inhibited by unconjugated aptamer, confirming the role of the aptamer in receptor-mediated endocytosis.
Late onset muscle plasticity in the whisker pad of enucleated rats
Authors: Toscano-Márquez Brenda , Martínez-Martínez Eduardo , Manjarrez Elías , Martínez Lourdes , Mendoza-Torreblanca Julieta , Gutiérrez-Ospina Gabriel
Published: October 2008

Blindness leads to a major reorganization of neural pathways associated with touch. Because incoming somatosensory information influences motor output, it is plausible that motor plasticity occurs in the blind. In this work, we evaluated this issue at the peripheral level in enucleated rats. Whisker muscles in enucleated rats 160 days of age or older showed increased cytochrome oxidase activity, capillary density, motor plate size, and amplitude of evoked field potentials as compared with their control counterparts. Such differences were not observed at ages 10 and 60 days, the capillary density was the exception being greater in the enucleated rat at the latter age. Interestingly, there was a trend to increased neurotrophin-3 concentrations in the whisker pads of enucleated rats throughout postnatal development. Our results show that neonatal enucleation leads to late onset plasticity of the whisker's motor system.
CD40L+ CD4+ memory T cells migrate in a CD62P-dependent fashion into reactive lymph nodes and license dendritic cells for T cell priming
Authors: Martín-Fontecha Alfonso , Baumjohann Dirk , Guarda Greta , Reboldi Andrea , Hons Miroslav , Lanzavecchia Antonio , Sallusto Federica
Published: October 2008

There is growing evidence that the maturation state of dendritic cells (DCs) is a critical parameter determining the balance between tolerance and immunity. We report that mouse CD4+ effector memory T (TEM) cells, but not naive or central memory T cells, constitutively expressed CD40L at levels sufficient to induce DC maturation in vitro and in vivo in the absence of antigenic stimulation. CD4+ TEM cells were excluded from resting lymph nodes but migrated in a CD62P-dependent fashion into reactive lymph nodes that were induced to express CD62P, in a transient or sustained fashion, on high endothelial venules. Trafficking of CD4+ TEM cells into chronic reactive lymph nodes maintained resident DCs in a mature state and promoted naive T cell responses and experimental autoimmune encephalomyelitis (EAE) to antigens administered in the absence of adjuvants. Antibodies to CD62P, which blocked CD4+ TEM cell migration into reactive lymph nodes, inhibited DC maturation, T cell priming, and induction of EAE. These results show that TEM cells can behave as endogenous adjuvants and suggest a mechanistic link between lymphocyte traffic in lymph nodes and induction of autoimmunity.
Macaques vaccinated with live-attenuated SIV control replication of heterologous virus
Authors: Reynolds Matthew R. , Weiler Andrea M. , Weisgrau Kim L. , Piaskowski Shari M. , Furlott Jessica R. , Weinfurter Jason T. , Kaizu Masahiko , Soma Taeko , León Enrique J. , MacNair Caitlin , Leaman Dan P. , Zwick Michael B. , Gostick Emma , Musani Solomon K. , Price David A. , Friedrich Thomas C. , Rakasz Eva G. , Wilson Nancy A. , McDermott Adrian B. , Boyle Rosanne , Allison David B. , Burton Dennis R. , Koff Wayne C. , Watkins David I.
Published: October 2008

An effective AIDS vaccine will need to protect against globally diverse isolates of HIV. To address this issue in macaques, we administered a live-attenuated simian immunodeficiency virus (SIV) vaccine and challenged with a highly pathogenic heterologous isolate. Vaccinees reduced viral replication by ∼2 logs between weeks 2–32 (P ≤ 0.049) postchallenge. Remarkably, vaccinees expressing MHC-I (MHC class I) alleles previously associated with viral control completely suppressed acute phase replication of the challenge virus, implicating CD8+ T cells in this control. Furthermore, transient depletion of peripheral CD8+ lymphocytes in four vaccinees during the chronic phase resulted in an increase in virus replication. In two of these animals, the recrudescent virus population contained only the vaccine strain and not the challenge virus. Alarmingly, however, we found evidence of recombinant viruses emerging in some of the vaccinated animals. This finding argues strongly against an attenuated virus vaccine as a solution to the AIDS epidemic. On a more positive note, our results suggest that MHC-I–restricted CD8+ T cells contribute to the protection induced by the live-attenuated SIV vaccine and demonstrate that vaccine-induced CD8+ T cell responses can control replication of heterologous challenge viruses.
Strategies to Prevent Central Line–Associated Bloodstream Infections in Acute Care Hospitals
Authors: Marschall Jonas , Mermel Leonard A. , Classen David , Arias Kathleen M. , Podgorny Kelly , Anderson Deverick J. , Burstin Helen , Calfee David P. , Coffin Susan E. , Dubberke Erik R. , Fraser Victoria , Gerding Dale N. , Griffin Frances A. , Gross Peter , Kaye Keith S. , Klompas Michael , Lo Evelyn , Nicolle Lindsay , Pegues David A. , Perl Trish M. , Saint Sanjay , Salgado Cassandra D. , Weinstein Robert A. , Wise Robert , Yokoe Deborah S.
Published: October 2008

Previously published guidelines are available that provide comprehensive recommendations for detecting and preventing healthcare-associated infections. The intent of this document is to highlight practical recommendations in a concise format designed to assist acute care hospitals in implementing and prioritizing their central line–associated bloodstream infection (CLABSI) prevention efforts. Refer to the Society for Healthcare Epidemiology of America/Infectious Diseases Society of America “Compendium of Strategies to Prevent Healthcare-Associated Infections” Executive Summary and Introduction and accompanying editorial for additional discussion.

1. Patients at risk for CLABSIs in acute care facilities

a. Intensive care unit (ICU) population: The risk of CLABSI in ICU patients is high. Reasons for this include the frequent insertion of multiple catheters, the use of specific types of catheters that are almost exclusively inserted in ICU patients and associated with substantial risk (eg, arterial catheters), and the fact that catheters are frequently placed in emergency circumstances, repeatedly accessed each day, and often needed for extended periods.

b. Non-ICU population: Although the primary focus of attention over the past 2 decades has been the ICU setting, recent data suggest that the greatest numbers of patients with central lines are in hospital units outside the ICU, where there is a substantial risk of CLABSI.

2. Outcomes associated with hospital-acquired CLABSI

a. Increased length of hospital stay

b. Increased cost; the non-inflation-adjusted attributable cost of CLABSIs has been found to vary from $3,700 to $29,000 per episode
Strategies to Prevent Ventilator-Associated Pneumonia in Acute Care Hospitals
Authors: Coffin Susan E. , Klompas Michael , Classen David , Arias Kathleen M. , Podgorny Kelly , Anderson Deverick J. , Burstin Helen , Calfee David P. , Dubberke Erik R. , Fraser Victoria , Gerding Dale N. , Griffin Frances A. , Gross Peter , Kaye Keith S. , Lo Evelyn , Marschall Jonas , Mermel Leonard A. , Nicolle Lindsay , Pegues David A. , Perl Trish M. , Saint Sanjay , Salgado Cassandra D. , Weinstein Robert A. , Wise Robert , Yokoe Deborah S.
Published: October 2008

Previously published guidelines are available that provide comprehensive recommendations for detecting and preventing healthcare-associated infections. The intent of this document is to highlight practical recommendations in a concise format designed to assist acute care hospitals in implementing and prioritizing their ventilator-associated pneumonia (VAP) prevention efforts. Refer to the Society for Healthcare Epidemiology of America/Infectious Diseases Society of America “Compendium of Strategies to Prevent Healthcare-Associated Infections” Executive Summary and Introduction and accompanying editorial for additional discussion.

1. Occurrence of VAP in acute care facilities.

a. VAP is one of the most common infections acquired by adults and children in intensive care units (ICUs).

i. In early studies, it was reported that 10%-20% of patients undergoing ventilation developed VAP. More-recent publications report rates of VAP that range from 1 to 4 cases per 1,000 ventilator-days, but rates may exceed 10 cases per 1,000 ventilator-days in some neonatal and surgical patient populations. The results of recent quality improvement initiatives, however, suggest that many cases of VAP might be prevented by careful attention to the process of care.

2. Outcomes associated with VAP

a. VAP is a cause of significant patient morbidity and mortality, increased utilization of healthcare resources, and excess cost.

i. The mortality attributable to VAP may exceed 10%.

ii. Patients with VAP require prolonged periods of mechanical ventilation, extended hospitalizations, excess use of antimicrobial medications, and increased direct medical costs.