bluuebunny/crossref_metadata_2025 huggingface dataset:
Probabilistic characterization of base flows in river basins: Roles of soil, vegetation, and geomorphology
Authors: Botter G. , Porporato A. , Daly E. , Rodriguez‐Iturbe I. , Rinaldo A.
Published: June 2007

In this paper we extend previous mathematical results on the probabilistic modeling of base flows driven by spatial and temporal fluctuations of soil moisture and affected by intermittent rainfall forcings and by heterogeneous transport, soil, and vegetation properties. Rainfall is modeled as a zero‐dimensional marked Poisson process with exponentially distributed intensity, and various descriptors of spatial heterogeneity are used. The master equation for the probability distribution (pdf) of the base flow (here epitomized by the mean daily flow rate in suitably sized catchments) and its moment‐generating function are derived by coupling soil moisture balances with a traveltime formulation of transport. Exact solutions for the flow moments are derived in the following cases: (1) two tributary areas in parallel, (2) the rigorous extension to N subbasins, and (3) a simplified geomorphic arrangement of subbasins. Base flow statistics obtained by naive spatial averages of heterogeneous properties exhibit the same mean of the exact solution but may significantly overestimate higher‐order moments. Relatively wet climate conditions seem to enhance the effects of the heterogeneity of soil, vegetation, transport, and geomorphic properties, particularly for low‐stage flow regimes. The probabilistic structure of the base flow is explicitly linked to relevant climatic and geomorphologic features in addition to the spatial distribution of soil and vegetation properties, with possible ecohydrological implications on long‐term water and nutrient mass balances in river basins.
Coupling between external and internal mass transfer during drying of a porous medium
Authors: Yiotis Andreas G. , Tsimpanogiannis Ioannis N. , Stubos Athanassios K. , Yortsos Yannis C.
Published: June 2007

We present a pore‐network model for drying processes in porous media that couples convective‐diffusive mass transfer over the external surface of a porous medium with mass transport mechanisms within the porous material, namely, the flow through liquid films that form at the pore walls and diffusion of the liquid vapors through the dry pores. We study the effects of the external boundary layer thickness, a film‐based capillary number, and the Peclet number of the purge gas that flows over the porous medium surface on the shape of the drying curves and the overall recovery times. We show that the drying rate remains practically constant, as long as the liquid films span across the entire pore network and provide hydraulic connectivity between the bulk liquid front and the product surface. This condition is satisfied when the drying process is controlled by the external mass transfer over the porous medium surface, rather than mass transport (through films and diffusion) within the porous material, e.g., for large values of the boundary layer thickness and small values of the film‐based capillary number. Our results explain previously reported experimental findings and provide a rigorous explanation of the experimentally reported constant‐rate period.
The Nitrone Disodium 2,4-Sulphophenyl-N-Tert-Butylnitrone is Without Cytoprotective Effect on Sodium Nitroprusside-Induced Cell Death in N1E-115 Neuroblastoma Cells in vitro
Authors: Hainsworth Atticus H , Bhuiyan Nasrin , Green A Richard
Published: June 2007

Disodium 2,4-sulphophenyl- N-tert-butylnitrone (NXY-059) is a novel free radical-trapping compound that is neuroprotective in both rodent and primate models of acute ischaemic stroke. Neuroprotection in vitro by NXY-059 has not been reported previously, and we have now investigated whether such an effect can be detected using a simple cell culture model of neurotoxicity. Neuron-like cells of the neuroblastoma-derived clonal cell line N1E-115 were exposed to the free radical-generating agent sodium nitroprusside (SNP), which produced a concentration-dependent reduction in mitochondrial complex II activity 24 h later (EC50 approximately 100 micromolar). Cell death induced by SNP (100 micromolar), assessed either by an increased proportion of apoptotic nuclear morphology or by mitochondrial complex II activity, was inhibited by a cocktail of known antioxidants (ascorbate, reduced glutathione, and dithiothreitol, all at 100 micromolar) but not by NXY-059 at a concentration known to be neuroprotective in vivo (300 micromolar). Disodium 2,4-sulphophenyl- N-tert-butylnitrone was also without effect on H2O2-mediated cytotoxicity. These results support recent data suggesting that in vivo NXY-059 probably acts at the neurovascular unit rather than at an intracellular site as a neuroprotective agent.
A blow-up problem of a class of axisymmetric Navier-Stokes equations with infinite energy
Authors: Ohkitani K.
Published: June 2007

We consider a class of axisymmetric Navier-Stokes equations that has geophysical applications. After reviewing stationary solutions studied by Donaldson-Sullivan (1960), we study nonstationary solutions. We compare behavior of this class of solution with that of the Fujita equation, a typical example of reaction-diffusion systems. We prove blowup for our system.
Electrochromic properties of WO3 nanowire films and mechanism responsible for the near infrared absorption
Authors: Chen Huanjun , Xu Ningsheng , Deng Shaozhi , Zhou Jun , Li Zhenglin , Ren Hao , Chen Jun , She Juncong
Published: June 2007

W O 3 nanowire films were prepared by thermal evaporation. The electrochromic properties and relative near infrared absorption mechanism of the films in detail are investigated by electrochemistry, ultraviolet–visible–near infrared spectroscopy, x-ray diffraction spectroscopy, and some theoretical approaches. The studies indicate that WO3 nanowire films show excellent electrochromic properties, including a rapid response time (∼3s) and a large contrast ratio between the bleached and the colored states. These improvements are due to the loose structure of the films and the small diameter of a single nanowire. It is also shown that a lithium tungsten bronze structure appears when the film is colored, causing two broad absorption bands centering around 920 and 1800nm. A calculation including the Urbach effect, cation-polaron absorption and large polaron absorption was carried out to interpret the absorbance. A brief discussion of the discrepancy of the transmittance spectrum in the region λ>800nm between the nanowire film and other traditional films is presented in the end.
Broadband near-infrared emission from Tm3+∕Er3+ co-doped nanostructured glass ceramics
Authors: Chen Daqin , Wang Yuansheng , Bao Feng , Yu Yunlong
Published: June 2007

Transparent SiO2-Al2O3-NaF-YF3 glass ceramics co-doped with Er3+ and Tm3+ were prepared by melt quenching and subsequent heating. X-ray diffraction and transmission electron microscopy experiments revealed that β-YF3 nanocrystals incorporated with Er3+ and Tm3+ were precipitated homogeneously among the oxide glass matrix. An integrated broad near-infrared emission band in the wavelength region of 1300−1700 nm, consisting of Tm3+ emissions around 1472 nm (H34→F34) and 1626 nm (F34→H36), and Er3+ emission around 1543 nm (I413∕2→I415∕2), was obtained under 792 nm laser excitation. The full width at half maximum of this integrated band increased with the increasing of [Tm]/[Er] ratio, and it reached as large as 175 nm for the 0.1 mol% Er3+ and 0.8 mol% Tm3+ co-doped sample. The energy transfers between Er3+ and Tm3+ were proposed to play an important role in tailoring the emission bandwidth of the sample.
Effects of molecular interface modification in hybrid organic-inorganic photovoltaic cells
Authors: Goh Chiatzun , Scully Shawn R. , McGehee Michael D.
Published: June 2007

We have systematically investigated the effects of surface modification of titania (TiO2) in hybrid TiO2∕regioregular poly(3-hexylthiophene) (P3HT) photovoltaic cells. By employing a series of para-substituted benzoic acids with varying dipoles and a series of multiply substituted benzene carboxylic acids, the energy offset at the TiO2∕polymer interface and thus the open-circuit voltage of devices can be tuned systematically by 0.25 V. Transient photovoltage measurements showed that the recombination kinetics was dominated by charge carrier concentration in these devices and were closely associated with the dark current. The saturated photocurrent of TiO2∕P3HT devices exhibited more than a twofold enhancement when molecular modifiers with large electron affinity were employed. The ability of modifiers to accept charge from polymers, as revealed in photoluminescence quenching measurement with blends of polymers, was shown to be correlated with the enhancement in device photocurrent. A planar geometry photoluminescence quenching measurement showed that TiO2 substrates modified by these same molecules that accept charge quenched more excitons in regioregular P3HT than bare TiO2 surfaces. An exciton diffusion length in P3HT as large as 6.5−8.5 nm was extracted. By measuring the external quantum efficiency (EQE) of working devices, it was found that all of the excitons that were quenched were accountable as extracted photocurrent. EQE was effectively increased from 5% to 10%−14% with certain surface modifiers; consequently exciton harvesting was more than doubled. The use of ruthenium (II) sensitizing dyes with good exciton harvesting property coupled with suppression of the recombination kinetics improved the efficiency of optimized bilayer TiO2∕P3HT devices from 0.34% to 0.6% under AM 1.5 solar illuminations. The implication of this work is directly relevant to the design of nanostructured bulk heterojunction inorganic-organic cells, in which efficient exciton harvesting and control of the recombination kinetics are key to achieving high efficiency.
Finite element analysis of transmission of leaky Rayleigh waves at the extremity of a fluid-loaded thick plate
Authors: Lamkanfi Ebrahim , Declercq Nico F. , Van Paepegem Wim , Degrieck Joris
Published: June 2007

A numerical study based on finite element simulations reveals the experimentally indicated fact [N. F. Declercq et al., J. Appl. Phys. 96, 5836 (2004)] that leaky Rayleigh waves propagating along the horizontal surface of a thick fluid-loaded solid plate are transmitted around the corner of the solid plate. The mentioned experiments are based on the so-called Schoch effect, accompanied by the presence of a null strip in the reflected part of the beam, and phenomena occurring when the incident beam, generating the effect, approaches the edge of the solid plate. The referred experiments indicate that leaky Rayleigh waves are generated around the corner of the plate, but the experimental evidence is not fully conclusive whether the effect is caused merely by incident Rayleigh waves on the upper surface or by scattering effects when the incident beam interacts with the corner. The current study first confirms the reported experiments by means of the finite element method and then proofs that the assumption made in the referred paper about Rayleigh waves, being primarily stimulated by the edge of an incident bounded beam rather than the middle, is correct. Ultimately the model is applied to study leaky Rayleigh waves separately from the incident and reflected bounded beams. It is shown that the Rayleigh waves themselves are the physical origin of the transmission of Rayleigh waves rather than scattering effects caused by the incident bounded beam.
Downhill versus two-state protein folding in a statistical mechanical model
Authors: Bruscolini Pierpaolo , Pelizzola Alessandro , Zamparo Marco
Published: June 2007

The authors address the problem of downhill protein folding in the framework of a simple statistical mechanical model, which allows an exact solution for the equilibrium and a semianalytical treatment of the kinetics. Focusing on protein 1BBL, a candidate for downhill folding behavior, and comparing it to the WW domain of protein PIN1, a two-state folder of comparable size, the authors show that there are qualitative differences in both the equilibrium and kinetic properties of the two molecules. However, the barrierless scenario which would be expected if 1BBL were a true downhill folder is observed only at low enough temperature.
Pressure-induced spectral changes for the special-pair radical cation of the bacterial photosynthetic reaction center
Authors: Leiger Kristjan , Freiberg Arvi , Dahlbom Mats G. , Hush Noel S. , Reimers Jeffrey R.
Published: June 2007

The effect of pressure up to 6kbars on the near to mid infrared absorption spectrum (7500–14300cm−1 or 1333–700nm) of the oxidized reaction center of Rhodobacter sphaeroides is measured and interpreted using density-functional B3LYP, INDO, and PM5 calculations. Two weak electronic transition origins at ∼8010 and ∼10210cm−1 are unambiguously identified. The first transition is assigned to a Qy tripdoublet band that involves, in the localized description of the excitation, a triplet absorption on one of the bacteriochlorophyll molecules (PM) in the reaction center’s special pair intensified by the presence of a radical cation on the other (PL). While most chlorophyll transition energies decrease significantly with increasing pressure, the tripdoublet band is found to be almost pressure insensitive. This difference is attributed to the additional increase in the tripdoublet-band energy accompanying compression of the π-stacked special pair. The second band could either be the anticipated second Qy tripdoublet state, a Qx tripdoublet state, or a state involving excitation from a low-lying doubly occupied orbital to the half-occupied cationic orbital. A variety of absorption bands that are also resolved in the 8300–9600cm−1 region are assigned as vibrational structure associated with the first tripdoublet absorption. These sidebands are composites that are shown by the calculations to comprise many unresolved individual modes; while the calculated pressure sensitivity of each individual mode is small, the calculated pressure dependence of the combined sideband structure is qualitatively similar to the observed pressure dependence, preventing the positive identification of possible additional electronic transitions in this spectral region.
Robustness of a tailored hole target in laser-produced collimated proton beam generation
Authors: Nakamura M. , Kawata S. , Sonobe R. , Kong Q. , Miyazaki S. , Onuma N. , Kikuchi T.
Published: June 2007

A robustness of a thin-foil tailored hole target is demonstrated by particle simulations in laser-produced proton generation. The hole target has a hole at the target rear surface. When an intense short pulse laser illuminates the thin-foil target with the hole, transverse edge fields of an accelerated electron cloud and an ion cloud are shielded by a protuberant part of the hole so that the proton beam divergence is suppressed [Sonobe et al., Phys. Plasmas 12, 073104 (2005)]. This paper presents the robustness of the hole target against laser parameter changes in a laser spot size and in a laser pulse length against a contaminated proton source layer and against a laser alignment error. The 2.5-dimensional particle-in-cell simulations also show that a multiple-hole target is robust against a laser alignment error and a target positioning error. The multihole target may serve as a robust target for practical uses to produce a collimated proton beam.
Hydration dynamics of oriented DNA films investigated by time-domain terahertz spectroscopy
Authors: Kistner C. , André A. , Fischer T. , Thoma A. , Janke C. , Bartels A. , Gisler T. , Maret G. , Dekorsy T.
Published: June 2007

The B to A conformational transition of highly oriented DNA films due to a hydration change is observed with time-domain terahertz spectroscopy. Wet-spun films of calf thymus and salmon DNA are investigated for different film thicknesses and for different polarizations of the terahertz radiation relative to the DNA orientation. A clear polarization dependence is observed. Asynchronous optical sampling allows recording of terahertz absorption and background spectra in a few 10s, permitting the tracking of the dehydration dynamics on a time scale of minutes. The observation of a phase transition is corroborated by Raman spectroscopy.
16.5
μ
m
quantum cascade detector using miniband transport
Authors: Giorgetta Fabrizio R. , Baumann Esther , Graf Marcel , Ajili Lassaad , Hoyler Nicolas , Giovannini Marcella , Faist Jérôme , Hofstetter Daniel , Krötz Peter , Sonnabend Guido
Published: June 2007

The authors report on an InP based photovoltaic quantum cascade detector operating at 16.5μm and using miniband-based vertical transport. This concept allowed the construction of a longitudinal optical phonon extraction stair with two rungs without touching on a high device resistance. At 10K, they observed a responsivity of 1.72mA∕W and a Johnson noise limited detectivity of 2.2×109 Jones. Altogether, this design resulted in detection at temperatures of up to 90K with a lower bandwidth limit of 200MHz imposed by the measurement setup.
Dielectric charging in radio frequency microelectromechanical system capacitive switches: A study of material properties and device performance
Authors: Papaioannou G. , Papapolymerou J. , Pons P. , Plana R.
Published: June 2007

The paper analyze the direct relation between the dielectric polarization mechanisms and the radio frequency microelectromechanical system capacitive switches performance. The dielectric polarization mechanisms are investigated in metal-insulator-metal capacitors with the aid of the thermally stimulated depolarization current method. The performance of microelectromechanical system is studied through the temperature dependence of the bias for the minimum capacitance. The simultaneous assessment allows the discrimination of dipolar and space charge polarization that allows the prediction of the shift of capacitance minimum with temperature.
Computation of the free energy of solids
Authors: Almarza N. G.
Published: June 2007

We present a procedure to compute the absolute free energy of solid phases by Monte Carlo simulation. The method is based on the so-called “Einstein-crystal” method of Frenkel and Ladd [J. Chem. Phys. 81, 3188 (1984)]. The new technique is more general and simplifies the calculation for systems with hard core interactions. In addition, the reference Einstein crystal is built up to fulfill translational invariance, which seems to reduce the system size dependence of the results.
Variation of thin film edge magnetic properties with patterning process conditions in Ni80Fe20 stripes
Authors: Maranville Brian B. , McMichael Robert D. , Abraham David W.
Published: June 2007

The authors report the effect of etch depth on the magnetic properties of thin film edges in magnetic nanostructures. In transversely magnetized stripes of 20-nm-thick Ni80Fe20, they use ferromagnetic resonance spectroscopy to measure the edge saturation field and effective out-of-plane stiffness field of the trapped-spin-wave edge mode as a function of ion etch depth. With increasing etching depth, the edge surface angle changes from 47° to 80°, and the field required to saturate the edge magnetization perpendicular to the stripe axis nearly doubles. This trend is largely confirmed by micromagnetic modeling of the edge geometry.
Thermoelectric properties and electronic structure of Zintl compound BaZn2Sb2
Authors: Wang Xiao-Jun , Tang Mei-Bo , Zhao Jing-Tai , Chen Hao-Hong , Yang Xin-Xin
Published: June 2007

Polycrystalline sample of the title compound was prepared and its thermoelectric properties from 2to675K were investigated. This Zintl compound shows rather low thermal conductivity, 1.6Wm−1K−1, at room temperature. The value of its thermoelectric figure of merit ZT reaches 0.31 at 675K. Its electronic structure, calculated by ab initio methods, suggests that the electrical transport are mainly ascribe to [Zn2Sb2] framework for p-type BaZn2Sb2. The heat capacity curve at low temperature was fitted lineally to obtain Debye temperature (about 208K). It provides the authors with a host lattice for modification and optimization the thermoelectric properties through substitution and/or doping.
Enhancement of quantum efficiency of organic light emitting devices by doping magnetic nanoparticles
Authors: Sun Cheng-Jun , Wu Yue , Xu Zhihua , Hu Bin , Bai Jianmin , Wang Jian-Ping , Shen Jian
Published: June 2007

Magnetic nanoparticles of CoFe are used as dopants to enhance the quantum efficiency of electroluminance in a single layer organic light emitting device (OLED). The enhancement of quantum efficiency increases with both increasing density of CoFe nanoparticles and external magnetic field. For a given OLED with 0.1wt% doping, the enhancement of the quantum efficiency reaches ∼27% and ∼32% without and with a magnetic field, respectively. The origin of these improvements could be attributed to the simultaneous increases of the portion of excitons among total charge carriers and the fraction of singlets among the total excitons
Long range diffusion noise in platinum microwires with metallic adhesion layers
Authors: Moktadir Z. , van Honschoten J. W. , Elwenspoek M.
Published: June 2007

Voltage fluctuations of platinum wires hosted by silicon nitride beams were investigated. The authors considered four variants of the wires: three with an adhesion layer and one without an adhesion layer. They found that the presence of an adhesion layer changes the nature of the power spectrum which is 1∕f for wires with no adhesion layers and 1∕f3∕2 for wires with an adhesion layer. They attribute the value of the exponent α=3∕2 found in wires with adhesion layers to the long range diffusion of oxygen atoms along the interface between the adhesion layer and the platinum layer.
Intra- and intertube tunneling transport in ropes of single-walled carbon nanotubes
Authors: Seemann K. M. , Ebbecke J. , Hörner A. L. , Wixforth A.
Published: June 2007

The authors report on intra- and intertube tunneling induced current oscillations in an individual rope of single-walled carbon nanotubes. Defects within single tubes and tube-tube contacts provide tunneling barriers of different transparencies and heights, respectively, and the formation of quantum dots in between. As a function of the bias voltage, the authors observe a transition from an intratube to an intertube tunneling dominated transport. The samples were fabricated on prepatterned silicon substrates employing surface acoustic wave induced streaming leading to an alignment of the ropes with respect to the contacts.
Continuous field-flow separation of particle populations in a dielectrophoretic chip with three dimensional electrodes
Authors: Iliescu Ciprian , Tresset Guillaume , Xu Guolin
Published: June 2007

This letter presents a dielectrophoretic (DEP) separation method of particles under continuous flow. The method consists of flowing two particle populations through a microfluidic channel, in which the vertical walls are the electrodes of the DEP device. The irregular shape of the electrodes generates both electric field and fluid velocity gradients. As a result, the particles that exhibit negative DEP can be trapped in the fluidic dead zones, while the particles that experience positive DEP are concentrated in the regions with high velocity and collected at the outlet. The device was tested with dead and living yeast cells.
Inhibition of spinal microglial cathepsin S for the reversal of neuropathic pain
Authors: Clark Anna K. , Yip Ping K. , Grist John , Gentry Clive , Staniland Amelia A. , Marchand Fabien , Dehvari Maliheh , Wotherspoon Glen , Winter Janet , Ullah Jakir , Bevan Stuart , Malcangio Marzia
Published: June 2007

A recent major conceptual advance has been the recognition of the importance of immune system–neuronal interactions in the modulation of brain function, one example of which is spinal pain processing in neuropathic states. Here, we report that in peripheral nerve-injured rats, the lysosomal cysteine protease cathepsin S (CatS) is critical for the maintenance of neuropathic pain and spinal microglia activation. After injury, CatS was exclusively expressed by activated microglia in the ipsilateral dorsal horn, where expression peaked at day 7, remaining high on day 14. Intrathecal delivery of an irreversible CatS inhibitor, morpholinurea-leucine-homophenylalanine-vinyl phenyl sulfone (LHVS), was antihyperalgesic and antiallodynic in neuropathic rats and attenuated spinal microglia activation. Consistent with a pronociceptive role of endogenous CatS, spinal intrathecal delivery of rat recombinant CatS (rrCatS) induced hyperalgesia and allodynia in naïve rats and activated p38 mitogen-activated protein kinase (MAPK) in spinal cord microglia. A bioinformatics approach revealed that the transmembrane chemokine fractalkine (FKN) is a potential substrate for CatS cleavage. We show that rrCatS incubation reduced the levels of cell-associated FKN in cultured sensory neurons and that a neutralizing antibody against FKN prevented both FKN- and CatS-induced allodynia, hyperalgesia, and p38 MAPK activation. Furthermore, rrCatS induced allodynia in wild-type but not CX3CR1-knockout mice. We suggest that under conditions of increased nociception, microglial CatS is responsible for the liberation of neuronal FKN, which stimulates p38 MAPK phosphorylation in microglia, thereby activating neurons via the release of pronociceptive mediators.
Rapid bulk endocytosis and its kinetics of fission pore closure at a central synapse
Authors: Wu Wei , Wu Ling-Gang
Published: June 2007

Upon exocytosis, fused vesicles must be retrieved for recycling. One route of retrieval is to generate endosome-like structures, from which small vesicles bud off. Endosome-like structures are widely thought to be generated slowly (≈1 min) from the plasma membrane, a process called bulk endocytosis. Although the concept of bulk endocytosis seems established, the kinetic evidence showing the instant of the bulk membrane fission at synapses is still missing. The present work provides this missing piece of evidence at a calyx-type synapse. We used the capacitance measurement technique, which offers a high time resolution (≈1 ms) to resolve the fission process. The instant of bulk membrane fission was reflected as a brief downward capacitance shift (DCS) of ≈20–500 fF (mean = 123 fF) with 10–90% decay time of ≈30–500 ms. At least 8.6–11.0% of exocytosed vesicles were retrieved by DCSs. During a DCS, the decrease in the fission pore conductance was detected, from which we found that the fission pore diameter decreased at ≈39 nm/s. This provided the measurement of the rate of fission during bulk endocytosis at synapses. The DCS frequency peaked (≈0.021 Hz) in <10 s after stimulation and decayed with a half time <20 s, indicating that the time course of bulk endocytosis is much faster than previously estimated with low time-resolution techniques. Our results also suggest that bulk endocytosis was composed of two kinetically different steps: the DCS that reflected the fission process and the time between stimulation and the DCS, during which membrane invagination led to the fission pore formation.
Differential homing mechanisms regulate regionalized effector CD8αβ
+
T cell accumulation within the small intestine
Authors: Stenstad Hanna , Svensson Marcus , Cucak Helena , Kotarsky Knut , Agace William W.
Published: June 2007

The CC chemokine receptor (CCR)9 is expressed on the majority of small intestinal, but few colonic, T cells, whereas its ligand CCL25 is constitutively expressed by small intestinal epithelial cells. As such, CCR9/CCL25 have been proposed to play a central role in regulating small intestinal but not colonic immune responses and thus to organize regionalized immunity within the intestinal mucosa. Here, we demonstrate that CCL25 is expressed at reduced levels by epithelial cells in the distal compared with proximal small intestine, which correlated with less efficient CCR9-dependent effector CD8αβ
+
T cell entry into the ileal epithelium.
In vitro
-generated α
4
β
7
+
effector CD8αβ
+
T cell entry into the lamina propria was less dependent on CCR9 than entry into the epithelium along the entire length of the small intestine and in particular in the ileum. CCR9-independent α
4
β
7
+
effector CD8αβ
+
T cell entry was pertussis toxin-sensitive, suggesting a role for additional Gα
I
-linked G protein-coupled receptors. Finally,
in vivo
-primed effector CD8αβ
+
T cells displayed regionalized differences in their entry to the small intestinal epithelium with enhanced CCR9-independent entry to the ileum. These results highlight a hitherto underappreciated compartmentalization of immune responses within the small intestine and have direct implications for targeting strategies aimed at regulating T cell localization to the small intestinal mucosa.
Synthetic ecosystems based on airborne inter- and intrakingdom communication
Authors: Weber Wilfried , Daoud-El Baba Marie , Fussenegger Martin
Published: June 2007

Intercellular communication within an organism, between populations, or across species and kingdoms forms the basis of many ecosystems in which organisms coexist through symbiotic, parasitic, or predator–prey relationships. Using multistep airborne communication and signal transduction, we present synthetic ecosystems within a mammalian cell population, in mice, or across species and kingdoms. Inter- and intrakingdom communication was enabled by using sender cells that produce volatile aldehydes, small vitamin-derived molecules, or antibiotics that diffuse, by gas or liquid phase, to receiver cells and induce the expression of specific target genes. Intercellular and cross-kingdom communication was shown to enable quorum sensing between and among mammalian cells, bacteria, yeast, and plants, resulting in precise spatiotemporal control of IFN-β production. Interconnection of bacterial, yeast, and mammalian cell signaling enabled the construction of multistep signal transduction and processing networks as well as the design of synthetic ecosystems that mimic fundamental coexistence patterns in nature, including symbiosis, parasitism, and oscillating predator–prey interactions.
Alternating electric fields arrest cell proliferation in animal tumor models and human brain tumors
Authors: Kirson Eilon D. , Dbalý Vladimír , Tovaryš František , Vymazal Josef , Soustiel Jean F. , Itzhaki Aviran , Mordechovich Daniel , Steinberg-Shapira Shirley , Gurvich Zoya , Schneiderman Rosa , Wasserman Yoram , Salzberg Marc , Ryffel Bernhard , Goldsher Dorit , Dekel Erez , Palti Yoram
Published: June 2007

We have recently shown that low intensity, intermediate frequency, electric fields inhibit by an anti-microtubule mechanism of action, cancerous cell growth
in vitro
. Using implanted electrodes, these fields were also shown to inhibit the growth of dermal tumors in mice. The present study extends these findings to additional cell lines [human breast carcinoma; MDA-MB-231, and human non-small-cell lung carcinoma (H1299)] and to animal tumor models (intradermal B16F1 melanoma and intracranial F-98 glioma) using external insulated electrodes. These findings led to the initiation of a pilot clinical trial of the effects of TTFields in 10 patients with recurrent glioblastoma (GBM). Median time to disease progression in these patients was 26.1 weeks and median overall survival was 62.2 weeks. These time to disease progression and OS values are more than double the reported medians of historical control patients. No device-related serious adverse events were seen after >70 months of cumulative treatment in all of the patients. The only device-related side effect seen was a mild to moderate contact dermatitis beneath the field delivering electrodes. We conclude that TTFields are a safe and effective new treatment modality which effectively slows down tumor growth
in vitro
,
in vivo
and, as demonstrated here, in human cancer patients.
Structural and thermodynamic characterization of a cytoplasmic dynein light chain–intermediate chain complex
Authors: Williams John C. , Roulhac Petra L. , Roy Anindya G. , Vallee Richard B. , Fitzgerald Michael C. , Hendrickson Wayne A.
Published: June 2007

Cytoplasmic dynein is a microtubule-based motor protein complex that plays important roles in a wide range of fundamental cellular processes, including vesicular transport, mitosis, and cell migration. A single major form of cytoplasmic dynein associates with membranous organelles, mitotic kinetochores, the mitotic and migratory cell cortex, centrosomes, and mRNA complexes. The ability of cytoplasmic dynein to recognize such diverse forms of cargo is thought to be associated with its several accessory subunits, which reside at the base of the molecule. The dynein light chains (LCs) LC8 and TcTex1 form a subcomplex with dynein intermediate chains, and they also interact with numerous protein and ribonucleoprotein partners. This observation has led to the hypothesis that these subunits serve to tether cargo to the dynein motor. Here, we present the structure and a thermodynamic analysis of a complex of LC8 and TcTex1 associated with their intermediate chain scaffold. The intermediate chains effectively block the major putative cargo binding sites within the light chains. These data suggest that, in the dynein complex, the LCs do not bind cargo, in apparent disagreement with a role for LCs in dynein cargo binding interactions.
Robust coding of flow-field parameters by axo-axonal gap junctions between fly visual interneurons
Authors: Cuntz Hermann , Haag Juergen , Forstner Friedrich , Segev Idan , Borst Alexander
Published: June 2007

Complex flight maneuvers require a sophisticated system to exploit the optic flow resulting from moving images of the environment projected onto the retina. In the fly's visual course control center, the lobula plate, 10 so-called vertical system (VS) cells are thought to match, with their complex receptive fields, the optic flow resulting from rotation around different body axes. However, signals of single VS cells are unreliable indicators of such optic flow parameters in the context of their noisy, texture-dependent input from local motion measurements. Here we propose an alternative encoding scheme based on network simulations of biophysically realistic compartmental models of VS cells. The simulations incorporate recent data about the highly selective connectivity between VS cells consisting of an electrical axo-axonal coupling between adjacent cells and a reciprocal inhibition between the most distant cells. We find that this particular wiring performs a linear interpolation between the output signals of VS cells, leading to a robust representation of the axis of rotation even in the presence of textureless patches of the visual surround.
Poleward Tubulin Flux in Spindles: Regulation and Function in Mitotic Cells
Authors: Buster Daniel W. , Zhang Dong , Sharp David J.
Published: June 2007

The poleward flux of tubulin subunits through spindle microtubules is a striking and conserved phenomenon whose function and molecular components remain poorly understood. To screen for novel components of the flux machinery, we utilized RNA interference to deplete regulators of microtubule dynamics, individually and in various combinations, from S2 cells and examined the resulting impact on flux rate. This led to the identification of two previously unknown flux inhibitors, KLP59C and KLP67A, and a flux promoter, Mini-spindles. Furthermore, we find that flux rate is regulated by functional antagonism among microtubule stabilizers and destabilizers specifically at plus ends. Finally, by examining mitosis on spindles in which flux has been up- or down-regulated or restored after the codepletion of antagonistic flux regulators, we show that flux is an integral contributor to anaphase A but is not responsible for chromosome congression, interkinetochore tension, or the establishment of normal spindle length during prometaphase/metaphase.
Classification of small molecules by two- and three-dimensional decomposition kernels
Authors: Ceroni Alessio , Costa Fabrizio , Frasconi Paolo
Published: June 2007

Motivation: Several kernel-based methods have been recently introduced for the classification of small molecules. Most available kernels on molecules are based on 2D representations obtained from chemical structures, but far less work has focused so far on the definition of effective kernels that can also exploit 3D information.

Results: We introduce new ideas for building kernels on small molecules that can effectively use and combine 2D and 3D information. We tested these kernels in conjunction with support vector machines for binary classification on the 60 NCI cancer screening datasets as well as on the NCI HIV data set. Our results show that 3D information leveraged by these kernels can consistently improve prediction accuracy in all datasets.

Availability: An implementation of the small molecule classifier is available from http://www.dsi.unifi.it/neural/src/3DDK

Contact:  costa@dsi.unifi.it
Proteolytic cleavage of glycoprotein B is dispensable for in vitro replication, but required for syncytium formation of pseudorabies virus
Authors: Okazaki Katsunori
Published: June 2007

Glycoprotein B (gB) is the most conserved glycoprotein among herpesviruses and it plays important roles in virus infectivity. In most herpesviruses, including pseudorabies virus (PRV), gB is cleaved by a cellular protease into two disulfide-linked subunits. In the present study, I found that the PRV gB generated in human colon carcinoma LoVo cells, which lack the ubiquitous protease furin, remained in the uncleaved form and the virus replicated in these cells without cell fusion. The uncleaved gB was converted into its subunits after furin digestion. The virus also replicated in Madin–Darby bovine kidney cells without cell fusion in the presence of a furin inhibitor, whereas distinct syncytia were formed in the absence of the inhibitor. LoVo cells constitutively expressing furin showed cell fusion when they were infected with the virus. Penetration kinetics assays revealed that the virus carrying uncleaved gB penetrated the cells at the same rate as the virus carrying cleaved gB. These results indicate that PRV gB is cleaved by furin and that the cleavage is dispensable for virus replication in vitro. Furthermore, gB cleavage is involved in syncytium formation but not in penetration kinetics, suggesting that different mechanisms operate between cell–cell fusion and virus–cell fusion by PRV.
Molecular epidemiology of vesicular stomatitis New Jersey virus from the 2004–2005 US outbreak indicates a common origin with Mexican strains
Authors: Rainwater-Lovett Kaitlin , Pauszek Steven J. , Kelley William N. , Rodriguez Luis L.
Published: June 2007

Vesicular stomatitis (VS) outbreaks of unknown origin occur at 8–10-year intervals in the south-western USA with the most recent outbreak beginning in 2004. A previous study has suggested that strains causing US outbreaks are closely related to strains causing outbreaks in Mexico [Rodriguez (2002) Virus Res
85, 211–219]. This study determined the phylogenetic relationships among 116 vesicular stomatitis New Jersey virus (VSNJV) strains obtained from the 2004 outbreak and from endemic areas in Mexico. All 69 US viruses showed little sequence divergence (≤1.3 %), regardless of their location or time of collection, and clustered with 11 Mexican viruses into a genetic lineage not previously present in the USA. Furthermore, viruses with identical phosphoprotein hypervariable region sequences to those causing the US outbreaks in 1995–1997 and 2004–2005 were found circulating in Mexico between 2002 and 2004. Molecular adaptation analysis provided evidence for positive selection in the phosphoprotein and glycoprotein genes during a south-to-north migration among 69 US viruses collected between the spring and autumn of 2004 and 2005. Phylogenetic data, temporal–spatial distribution and the finding of viral strains identical to those causing major outbreaks in the USA circulating in Mexico demonstrated that VS outbreaks in the south-western USA are the result of the introduction of viral strains from endemic areas in Mexico.
Genetic divergence of Chikungunya viruses in India (1963–2006) with special reference to the 2005–2006 explosive epidemic
Authors: Arankalle Vidya A. , Shrivastava Shubham , Cherian Sarah , Gunjikar Rashmi S. , Walimbe Atul M. , Jadhav Santosh M. , Sudeep A. B. , Mishra Akhilesh C.
Published: June 2007

Re-emergence of Chikungunya (CHIK), caused by CHIK virus, was recorded in India during 2005–2006 after a gap of 32 years, causing 1.3 million cases in 13 states. Several islands of the Indian Ocean reported similar outbreaks in the same period. These outbreaks were attributed to the African genotype of CHIK virus. To examine relatedness of the Indian isolates (IND-06) with Reunion Island isolates (RU), full-genome sequences of five CHIK virus isolates representative of different Indian states were determined. In addition, an isolate obtained from mosquitoes in the year 2000 (Yawat-2000), identified as being of the African genotype, and two older strains isolated in 1963 and 1973 (of the Asian genotype), were sequenced. The IND-06 isolates shared 99.9 % nucleotide identity with RU isolates, confirming involvement of the same strain in these outbreaks. The IND-06 isolates shared 98.2 % identity with the Yawat-2000 isolate. Of two crucial substitutions reported for RU isolates in the E1 region, M269V was noted in the Yawat-2000 and IND-06 isolates, whereas D284E was seen only in the IND-06 isolates. The A226V shift observed with the progression of the epidemic in Reunion Island, probably associated with adaptation to the mosquito vector, was absent in all of the Indian isolates. Three unique substitutions were noted in the IND-06 isolates: two (T128K and T376M) in the Nsp1 region and one (P23S) in the capsid protein. The two Asian strains showed 99.4 % nucleotide identity to each other, indicating relative stability of the virus. No evidence of recombination of the Asian and African genotypes, or of positive selection was observed. The results may help in understanding the association, if any, of the unique mutations with the explosive nature of the CHIK outbreak.
Hepatitis C virus internal ribosome entry site initiates protein synthesis at the authentic initiation codon in yeast
Authors: Masek Tomas , Vopalensky Vaclav , Horvath Ondrej , Vortelova Lucie , Feketova Zuzana , Pospisek Martin
Published: June 2007

Hepatitis C virus (HCV) is an important pathogen causing both acute and chronic infections in humans. The HCV polyprotein is synthesized by cap-independent translation initiation after ribosome binding to the highly structured internal ribosome entry site (IRES). The HCV IRES has been shown to have a low requirement for translation initiation factors and the ability to bind directly to the 40S ribosomal subunit. A novel yeast bicistronic reporter system, suitable for sensitive and accurate analysis of IRES activity, has been developed. It employs signal amplification based on the Gal4p transcription factor-mediated activation of a variety of secondary reporter genes. The system has a broad dynamic range and, depending on the nature of the particular secondary reporter, can be used both for precise measurements of IRES activity and for selection and screening for novel IRES variants and IREStrans-acting factors. By using this novel bicistronic system, it was shown that the HCV IRES is functional in yeast cells. Mutational analysis of the IRES loop IV and the adjacent region revealed that, in yeast, as in mammalian cells, translation initiates preferentially at the authentic342AUG codon and that disruption of the HCV IRES loop IV abrogates its function, whilst minor positional changes or substitutions of the initiation codon within loop IV are largely tolerated. These findings bring more general insights to translation initiation, but also open the door for utilization of yeast and its sophisticated genetics for searching for new antiviral drugs and HCV IREStrans-acting proteins.
Increased PrP mRNA expression in lymphoid follicles of the ileal Peyer's patch of sheep experimentally exposed to the scrapie agent
Authors: Austbø Lars , Espenes Arild , Olsaker Ingrid , Press Charles McL. , Skretting Grethe
Published: June 2007

To understand the functional role of cellular prion protein (PrPC) in the initiation and maintenance of prion disease within the host, it is important to obtain a more detailed understanding of PrPC transcription in tissues during the development of disease. Using an experimental model with oral infection, we examined the effect of scrapie and the accumulation of the scrapie related form of the prion protein (PrPSc) on the expression level of PrP mRNA in the ileal Peyer's patch of sheep. In the early phase of infection, prior to PrPSc accumulation, no effect on the PrP expression was detected. However, it was found that lambs with PrP genotypes associated with high susceptibility for scrapie generally had higher PrP mRNA levels than lambs with less susceptible genotypes. Further, in highly susceptible VRQ/VRQ sheep at a stage of disease with high accumulation of PrPSc, real-time RT-PCR and microdissection were used to investigate levels of PrP mRNA in four different tissue compartments. An increased level of PrP mRNA was found in lymphoid follicles of infected sheep compared with controls, indicating upregulation of PrP expression in the follicles to compensate for the loss of PrPC converted to PrPSc, or that PrPSc accumulation directly or indirectly influences the PrP expression. Still, the PrP expression level in the follicles was low compared with the other compartments investigated, suggesting that although increased PrP expression could contribute to PrPSc accumulation, other factors are also important in the processes leading to accumulation of PrPSc in the follicles.
Complete genome and phylogenetic position of bovine papillomavirus type 7
Authors: Ogawa Tomoko , Tomita Yoshimi , Okada Mineyuki , Shirasawa Hiroshi
Published: June 2007

Six bovine papillomavirus (BPV) types and 16 putative BPV types have been reported previously. Here, the complete genome sequence of BAPV6, a novel putative BPV type isolated from cattle in Japan, was determined by using multiple-primed rolling-circle amplification. The genome consisted of 7412 bp (G+C content of 46 mol%) that encoded five early (E1, E2, E4, E6 and E7) and two late (L1 and L2) genes, but did not encode the E5 gene. The E6 protein contained a non-consensus CxxC(x)33CxxC and a consensus CxxC(x)29CxxC zinc-binding domain, and the E7 protein lacked the LxCxE motif. The nucleotide sequence of the L1 open reading frame (ORF) was related most closely (57–58 %) to the L1 ORF of member(s) of the genera Betapapillomavirus, Gammapapillomavirus and Pipapillomavirus. Phylogenetic analysis based on the complete L1 ORF suggests that BAPV6 should be classified in a novel genus in the family Papillomaviridae as BPV-7.
Susceptibility of cancer cells to herpes simplex virus-dependent apoptosis
Authors: Nguyen Marie L. , Kraft Rachel M. , Blaho John A.
Published: June 2007

Apoptosis has recently been associated with herpes simplex virus 1 (HSV-1) latency and disease severity. There is an intricate balance between pro- and anti-apoptotic processes during HSV-1 infection. When anti-apoptotic pathways are suppressed, this balance is upset and the cells die by apoptosis, referred to here as HSV-1-dependent apoptosis (HDAP). It has been observed previously that HeLa cancer cells exhibit an enhanced sensitivity to HDAP. Here, a series of specific patient-derived cancer cells was utilized to investigate the cell-type specificity of HDAP. The results showed that a human mammary tumour cell line was sensitive to HDAP, whilst syngeneic normal cells were resistant. Furthermore, low-passage-number primary human mammary epithelial cells were resistant to HDAP. When the susceptibility of human colon, brain, breast and cervical cancer cells was assessed, the only cells insensitive to HDAP were those resistant to all environmental stimuli tested. This implies that the HDAP resistance was probably due to mutations in the cellular apoptotic machinery. Thus, the susceptibility of cancer cells to HDAP requires that they possess a functional ability to undergo programmed cell death.