bluuebunny/crossref_metadata_2025 huggingface dataset:
Bifurcation of the East India Coastal Current east of Sri Lanka
Authors: Vinayachandran P. N. , Kagimoto T. , Masumoto Y. , Chauhan P. , Nayak S. R. , Yamagata T.
Published: August 2005

The East India Coastal Current (EICC) flows equatorward during October–December carrying low salinity water from the Bay of Bengal en route. Using results from a high resolution ocean general circulation model, satellite altimeter data, Argo float profiles and ocean color images we show that the EICC bifurcates east of Sri Lanka. One part continues along the coast of Sri Lanka but the major part of the EICC, called here as the East Sri Lanka Jet (ESLJ) flows eastward into the Bay of Bengal. As a result of this bifurcation, there is offshore transport of chlorophyll a rich low salinity water from the coast of Sri Lanka. Altimeter data from 1993–2004 show that the bifurcation occurred every year except during the Indian Ocean Dipole (IOD) years of 1994 and 1997. The bifurcation occurs when an anticyclonic eddy that propagates westward ahead of a downwelling Rossby wave front impinges on the Sri Lanka coast. This new finding suggests that the main route of the low salinity water from the Bay of Bengal into the southeastern Arabian Sea may not be along the coast around Sri Lanka but through the Winter Monsoon Current.
Epochs of phase coherence between El Niño/Southern Oscillation and Indian monsoon
Authors: Maraun D. , Kurths J.
Published: August 2005

We present a modern method used in nonlinear time series analysis to investigate the relation of two oscillating systems with respect to their phases, independently of their amplitudes. We study the difference of the phase dynamics between El Niño/Southern Oscillation (ENSO) and the Indian Monsoon on inter‐annual time scales. We identify distinct epochs, especially two intervals of phase coherence, 1886–1908 and 1964–1980, corroborating earlier findings from a new point of view. A significance test shows that the coherence is very unlikely to be the result of stochastic fluctuations. We also detect so far unknown periods of coupling which are invisible to linear methods. These findings suggest that the decreasing correlation during the last decades might be a typical epoch of the ENSO/Monsoon system having occurred repeatedly. The high time resolution of the method enables us to present an interpretation of how volcanic radiative forcing could cause the coupling.
Heavy ion abundances and spectra from the large solar energetic particle events of October–November 2003
Authors: Cohen C. M. S. , Stone E. C. , Mewaldt R. A. , Leske R. A. , Cummings A. C. , Mason G. M. , Desai M. I. , von Rosenvinge T. T. , Wiedenbeck M. E.
Published: August 2005

Observations from the Solar Isotope Spectrometer and the Ultra Low Energy Isotope Spectrometer on the ACE spacecraft during the extremely large events of October and November 2003 are combined to create heavy ion spectra over more than 3 decades in energy. The resulting spectra differed substantially in shape from event to event, as well as from element to element within a given event, resulting in energy‐dependent abundance ratios. Although the effects of strong local shock acceleration are apparent in the intensities of the 28 and 29 October events, these do not explain the order of magnitude differences between the event‐integrated abundances obtained at 0.64–0.91 MeV/nucleon and those at 12–60 MeV/nucleon. The higher‐energy abundances relative to the lower‐energy ones show trends with nuclear charge or charge‐to‐mass ratio that are similar for all the events and suggest that heavier ions are less efficiently accelerated to high energies. The position of the breaks in the energy spectra of O, Ne, Mg, Si, S, Ca, and Fe can be understood in terms of leakage from the shock region, if the mean free path is assumed to be a power law in rigidity. The resulting rigidity dependence is consistent with a source of wave turbulence in the vicinity of the shock when the ions are accelerated.
Quantum-instanton evaluation of the kinetic isotope effects
Authors: Vaníček Jiří , Miller William H. , Castillo Jesús F. , Javier Aoiz F.
Published: August 2005

A general quantum-mechanical method for computing kinetic isotope effects is presented. The method is based on the quantum-instanton approximation for the rate constant and on the path-integral Metropolis–Monte Carlo evaluation of the Boltzmann operator matrix elements. It computes the kinetic isotope effect directly, using a thermodynamic integration with respect to the mass of the isotope, thus avoiding the more computationally expensive process of computing the individual rate constants. The method should be more accurate than variational transition-state theories or the semiclassical instanton method since it does not assume a single tunneling path and does not use a semiclassical approximation of the Boltzmann operator. While the general Monte Carlo implementation makes the method accessible to systems with a large number of atoms, we present numerical results for the Eckart barrier and for the collinear and full three-dimensional isotope variants of the hydrogen exchange reaction H+H2→H2+H. In all seven test cases, for temperatures between 250 and 600 K, the error of the quantum instanton approximation for the kinetic isotope effects is less than ∼10%.
Structure of water nanoconfined between hydrophobic surfaces
Authors: Gordillo M. C. , Nagy G. , Martí J.
Published: August 2005

We report the results of a series of molecular-dynamics simulations of liquid water confined between two graphite plates with separations ranging from 7to15Å. Energies and free energies are provided, indicating also the corresponding stability density span of confined water phases. The structure of the different liquid layers is also discussed for all the considered systems. In particular, we studied atomic density profiles, two-dimensional radial distribution functions, hydrogen bonding, and angular orientations near the carbon plates.
Ultraviolet photodissociation dynamics of the SH radical
Authors: Zhou Weidong , Yuan Yan , Chen Shiping , Zhang Jingsong
Published: August 2005

Ultraviolet (UV) photodissociation dynamics of jet-cooled SH radical (in XΠ3∕22, ν″=0–2) is studied in the photolysis wavelength region of 216–232nm using high-n Rydberg atom time-of-flight technique. In this wavelength region, anisotropy β parameter of the H-atom product is ∼−1, and spin-orbit branching fractions of the S(PJ3) product are close to S(P23):S(P13):S(P03)=0.51:0.36:0.13. The UV photolysis of SH is via a direct dissociation and is initiated on the repulsive Σ−2 potential-energy curve in the Franck-Condon region after the perpendicular transition Σ−2-XΠ2. The S(PJ3) product fine-structure state distribution approaches that in the sudden limit dissociation on the single repulsive Σ−2 state, but it is also affected by the nonadiabatic couplings among the repulsive Σ−4, Σ−2, and Π4 states, which redistribute the photodissociation flux from the initially excited Σ−2 state to the Σ−4 and Π4 states. The bond dissociation energy D0(S–H)=29245±25cm−1 is obtained.
Ultrasound generated by a femtosecond and a picosecond laser pulse near the ablation threshold
Authors: Hébert H. , Vidal F. , Martin F. , Kieffer J.-C. , Nadeau A. , Johnston T. W. , Blouin A. , Moreau A. , Monchalin J.-P.
Published: August 2005

We have investigated high-frequency ultrasound generated by single laser pulses in thin (50μm) aluminum foils as a function of the laser fluence. Laser-pulse durations of 80fs and 270ps were used to compare the ultrasound generated in two very different regimes: thermoelastic and ablation. The measured rear-surface displacement induced by the ultrasound pulse is similar after 50-μm propagation through the foils for the two laser-pulse durations in the fluence range of 0.1–0.7J∕cm2. For fluences greater than the ablation threshold (0.25 and 0.63J∕cm2 for the 80-fs and 270-ps pulses, respectively), the ultrasound amplitude generated by the 270-ps laser pulse is increased significantly due to absorption of laser energy by the ablating plasma. This is not observed for the 80-fs laser pulse since ablation is produced well after the laser-pulse irradiation of the target. The measured surface displacement as a function of laser fluence is compared to the calculations of a one-dimensional fluid code for both laser-pulse durations. The model calculations agree in many ways with the experimental results, but some discrepancies are observed.
Influence of insulating layer thickness and interface structure on the electronic structure and magnetic properties of Ni3Fe∕Al2O3∕Ni3Fe magnetic tunnel junction
Authors: Zhou Yuan , Bi Xiaofang
Published: August 2005

Several models of the Ni3Fe∕Al2O3∕Ni3Fe magnetic tunnel junction have been established for investigating the electronic structure and magnetic property with various insulating layer thicknesses and interface structures. The discrete variational method in the framework of density-functional theory and the local-spin-density approximation has been employed in the calculations. The spin polarization of the ferromagnetic layer shows a maximum value as the insulating layer thickness increases. The change of magnetic moment is similar to that of the spin polarization. In addition, it has been found that the Al layer structure at the ferromagnetic/insulating interface influences the spin polarization to a great extent. The charge transfer between the Ni3Fe layer and the Al layer at the interface was also calculated. The tunnel magnetoresistance ratio of the junction was estimated on the basis of Julliere’s theory [M. Julliere, Phys. Lett. 54, 225 (1975)] and shows a monotonous increase with the insulating layer thickness in the range of 0.3–1.0 nm, which is in good agreement with the reported experimental results.
Structure and spectroscopic properties of C–Ni and CNx–Ni nanocomposite films
Authors: Kovács Gy. J. , Koós A. , Bertoni G. , Sáfrán G. , Geszti O. , Serin V. , Colliex C. , Radnóczi G.
Published: August 2005

Magnetron-sputtered carbon-nickel and carbon-nitride-nickel thin films were investigated by high-resolution transmission electron microscopy (HRTEM), energy dispersive x-ray spectroscopy, electron-energy-loss spectroscopy (EELS), and scanning tunneling microscopy∕spectroscopy (STM∕STS) to clarify the relationship between the structure and the spectroscopic properties. The films were deposited in argon or nitrogen plasma at temperatures from 25to800°C. The microstructures can be described as a nanocomposite, built from Ni or Ni3C nanocrystals in a carbon∕CNx matrix. The nanocomposite shows columnar structure up to 200°C deposition temperature, and above this temperature gradually changes to globular morphology. The C∕CNx matrix also grows thicker as the deposition temperature increases. The matrix is amorphous at high nitrogen content and low deposition temperature and it is ordered into 3–5 layer thick graphitic shells around the Ni3C or Ni crystallites at higher temperatures. The surface roughness of the nanocomposite ranges between 0.7 and 2.3nm, increasing with increasing deposition temperature. EELS measurements confirm the expected chemical interaction between nickel and carbon. EELS suggests that the nitrogen is incorporated only into the matrix in CNx–Ni samples, mainly with sp1 bonds for deposition temperature below 500°C. STS investigations show that the conductivity increases with increasing deposition temperature. A conductivity gap of 1–2V exists in the nanocomposite films. A structural model based on the HRTEM investigation is given that can describe the spectroscopic properties and their behavior with the deposition temperature.
Transport studies of isolated molecular wires in self-assembled monolayer devices
Authors: Burtman V. , Ndobe A. S. , Vardeny Z. V.
Published: August 2005

We have fabricated a variety of isolated molecule diodes based on self-assembled monolayers (SAMs) of solid-state mixture (SSM) of molecular wires [1,4-methane benzene dithiol (Me-BDT)], and molecular insulator spacers [penthane 1-thiol (PT)] with different concentration ratios r of wires∕spacers, which were sandwiched between two gold (Au) electrodes. We introduce two specialized methods borrowed from surface science to (i) confirm the connectivity between the Me-BDT molecules with the upper Au electrode, and (ii) count the number of isolated molecular wires in the devices. The electrical transport properties of the SSM SAM diodes were studied at different temperatures via the conductance and differential conductance spectra. We found that a potential barrier caused by the spatial connectivity gap between the PT molecules and the upper Au electrode dominates the transport properties of the pure PT SAM diode (r=0). The transport properties of SSM diodes with r values in the range 10−8<r<10−4 are dominated by the conductance of the isolated Me-BDT molecules in the device. We found that the temperature dependence of the SSM diodes is much weaker than that of the pure PT device, indicating the importance of the Me-BDT simultaneous bonding to the two Au electrodes that facilitates electrical transport. From the differential conductance spectra we also found that the energy difference between the Au electrode Fermi level and the Me-BDT highest occupied molecular-orbital (or lowest unoccupied molecular-orbital) level is ∼1.5eV; where it is ∼2.5eV for the PT molecule. The weak temperature-dependent transport that we obtained for the SSM diodes reflects the weak temperature dependence of Δ. In addition, our measurements reveal that the conductance of SSM diodes scales linearly with r, showing that the charge transport in these devices is dominated by the sum of the isolated Me-BDT molecular conductance in the device. Based on this finding, and the measured number of the Me-BDT molecules in the device we obtained the “single molecule resistance,” RM. We measured RM=6×109Ω for isolated Me-BDT molecules, which is consistent with previous measurements using other transport measuring techniques. A simple model for calculating RM, where the transport is governed by electron tunneling through the Me-BDT molecule using the WKB approximation, is in good agreement with the experimental data, thus validating the procedures used for our measurements.
Optimized flexoelectric response in a chiral liquid-crystal phase device
Authors: Broughton B. J. , Clarke M. J. , Blatch A. E. , Coles H. J.
Published: August 2005

In this paper, a device type is presented in which the conventional geometry for the flexoelectro-optic effect is rotated, utilizing planar-aligned short-pitch chiral nematic and in-plane electric fields. The cell is optically neutral at zero applied field due to having its helix axis lie in the direction of light propagation, and at optical communication wavelengths (1550nm) polarization rotation is insignificant due to the helical pitch of the material being shorter than the illuminating wavelength. An electric field, applied in the plane of the cell, has been found to induce a birefringence via a combination of dielectric helix unwinding and flexoelectric deformation of the director helix. The magnitude of the birefringence and direction of the induced optic axis in the plane of the cell are dependent on the amplitude and direction of the applied electric field, providing potential for use in a fast endlessly rotatable polarization controller. Herein, the chiral nematic materials utilized in the cell are bimesogenic liquid crystals designed to optimize the contribution from the flexoelectro-optic effect, and eliminate dielectric helix unwinding. The materials are also polymer network stabilized to preserve the texture against degradation in the applied fields. The results presented show a progression from a combined dielectric and flexoelectrically induced birefringence of 0.016 at field strengths up to 6.8V∕μm, to a purely flexoelectric-induced birefringence of 0.0135, sufficient for a quarter wave plate in a 29-μm-thick cell. Response times are of the order of hundreds of microseconds for both reaction to an applied field and relaxation upon removal.
Microheterogeneity and field-cooling effects on Pb[(Zn1∕3Nb2∕3)0.955Ti0.045]O3 single crystals probed by micro-Brillouin scattering
Authors: Kim Do Han , Ko Jae-Hyeon , Feng C. D. , Kojima Seiji
Published: August 2005

Microheterogeneity and field-cooling effects were investigated on Pb[(Zn1∕3Nb2∕3)0.955Ti0.045]O3 (PZN-4.5%PT) single crystals by using a high-resolution micro-Brillouin scattering. The temperature dependence of Brillouin shift showed a typical relaxor behavior with marked softening on approaching the diffuse phase transition, but also revealed a clear microareal variation in a rhombohedral phase below 150°C which means a heterogeneity exists over a length scale of at least a few microns in PZN-4.5%PT. These two features seem to correlate with the coexistence of both micronsized domains and irregular nanosized domains, recently confirmed by high-resolution domain studies. This complex domain structure may make each microdomain represent different relaxor behaviors due to its own polar nanoregions and their dynamics. When the crystal was cooled under the electric field along the [001] direction from a cubic phase, two field-induced changes were observed in the Brillouin shift at around 143°C and 106°C. This observation is in good agreement with the dielectric measurements, meaning a medium-range ordered phase exists between short-range ordered and long-range order phases.
Tuning stimulated emission of organic thin films by molecular reorientation
Authors: Lin Hao-Wu , Lin Chun-Liang , Wu Chung-Chih , Chao Teng-Chih , Wong Ken-Tsung
Published: August 2005

In this letter, employing the spectroscopic ellipsometry, we study the phenomena of molecular reorientation in amorphous thin films of a ter(9,9-diarylfluorene) compound T3 upon annealing around or above its glass transition temperature. Molecular reorientation results in changes in the in-plane optical constants, which in turn could alter the waveguiding characteristics of a thin-film slab waveguide. Employing such properties, we demonstrate continuous tuning of the wavelength of amplified spontaneous emission of a T3 slab waveguide within one sample. Such an approach has the particular advantage of permitting facile tuning of stimulated emission after device fabrication.
Evaluation of different extractants for the estimation of bioavailable selenium in seleniferous soils of Northwest India
Authors: Dhillon K. S. , Rani Neeraj , Dhillon S. K.
Published: August 2005

Efficacy of various extractants—AB-DTPA, 0.5 m Na2CO3, 0.25 m KCl, 0.1 m KH2PO4, hot water, and isotopically exchangeable selenium (Se)—was studied for estimating bioavailable Se in 15 naturally occurring alkaline seleniferous soils in north-western India. Total Se concentration in these soils varied from 0.6 to 3.1 µg/g. Amount of Se extracted as isotopically exchangeable was the greatest, and that extracted with 0.5 m Na2CO3 was the smallest. When grown in the seleniferous soils, raya (Brassica juncea) accumulated (μg Se/g dry matter) 1.5–86.6, wheat (Triticum aestivum L.) 0.7–58.3, maize (Zea mays L.) 1.7–8.6, and rice (Oryza sativa L.) 1.5–4.6. Raya, wheat, and maize plants absorbed Se more than the maximum permissible level for animal consumption (5 μg Se/g dry matter) in 9, 8, and 4 experimental soils, respectively. Selenium concentration of maize was significantly correlated with the amount of Se extracted by 0.25 m KCl (r = 0.646,P < 0.01), 0.1 m KH2PO4 (r = 0.498,P < 0.10), and with total Se concentration (r = 0.628,P < 0.05) of the soils; Se concentration in rice was correlated with AB-DTPA extractable Se (r = 0.443,P < 0.10). Highly significant relationships between hot water soluble Se and concentration of Se in raya (r = 0.705,P < 0.01), wheat (r = 0.696,P < 0.01), maize (r = 0.698,P < 0.01), and rice (r = 0.559,P < 0.05) suggest that it can reliably quantify bioavailable Se in seleniferous soils of north-western India. Hot water soluble Se was positively correlated with electrical conductivity (r = 0.514,P < 0.05), total Se concentration (r = 0.710,P < 0.01), and KCl-extractable Se (r = 0.712,P < 0.01) of the soils.
Role of root inputs from a dinitrogen-fixing tree in soil carbon and nitrogen sequestration in a tropical agroforestry system
Authors: Sierra Jorge , Nygren Pekka
Published: August 2005

Agroforestry is often mentioned as a suitable technology for land rehabilitation in the tropics and for mitigation of climate change because this land-use favours nutrient recycling and C sequestration. The aim of this work was to estimate soil C sequestration in a 12-year-old tropical silvopastoral system composed of a legume tree (Gliricidia sepium) and a C4 fodder grass (Dichanthium aristatum), and to link it with tree root biomass and N status in the soil. The site was under cut-and-carry management, i.e. tree pruning residues and cut grass were removed from the field and fed to stabled animals elsewhere. Thus, main sources for tree C and N inputs were root activity and turnover. Organic C derived from the trees and tree root biomass were determined based on natural 13C abundance. For the 0–0.2 m soil layer, the biomass of tree roots ≤2 mm diameter was 2.4 Mg/ha when the trees were pruned every 6 months (SS6), and 0.6 Mg/ha when pruned every 2 months (SS2). Both C (R2 = 0.39, P < 0.05) and N (R2 = 0.82, P < 0.05) sequestration were correlated with tree root biomass. The trees and grass contributed 18 and 8 Mg C/ha to soil, respectively, over the 12-year experiment in SS6. The net increase of 2.5 Mg N/ha in soil, originating from the trees, contributed to the net soil C sequestration. In SS2, trees contributed 16 Mg C/ha to soil over 12 years, but grass-derived C was reduced by 2 Mg C/ha because of the small amount of grass litter. The increase of 1.7 Mg N/ha in soil, derived from the trees, was not large enough to avoid C loss in this plot. Differences in soil C and N sequestration between plots were due to differences in system management, which affected the amount and the C/N ratio of inputs and outputs.
Laboratory calibrations of water content reflectometers and their in-situ verification
Authors: Stenger Roland , Barkle Greg , Burgess Craig
Published: August 2005

Like time domain reflectometers, cheaper CS615 water content reflectometers (WCRs) also measure dielectric properties of the soil to determine its volumetric water content (VWC), but are more affected by environmental factors. Quadratic equations described the laboratory data from 12 horizons of 4 soils of vastly differing properties slightly better than linear equations. Root mean squared errors (RMSE) averaged over the 3 horizons increased slightly in the order Gley (av. 1.0%), Pumice (av. 1.3%), Recent (av. 1.6%), and Allophanic soil (av. 1.9%). Using the manufacturer’s standard calibration resulted in significantly higher RMSE (av. 6.2–25.3%) and mean errors (av. –5.5% to +21.5%), with the VWC of the 2 soils of volcanic origin being underestimated. An atypical dielectric response of water stored in volcanic soils has been attributed to their low bulk density, high porosity, and large specific surface area. The in-situ verification was hampered by the variability observed between the data from duplicate WCRs. Measuring the inter-sensor variability in air and water indicated that this could account for a significant part of this variability, while small-scale variation of VWC in-situ was also observed. Nevertheless, the laboratory calibrations were usually better, or at least similarly suited, to describe the in-situ data than the manufacturer’s calibrations.
Sustainable harvest regimes for magpie geese (Anseranas semipalmata) under spatial and temporal heterogeneity
Authors: Brook Barry W. , Whitehead Peter J.
Published: August 2005

We developed a population model of magpie geese in the Northern Territory that considered spatial and temporal variation and related sources of uncertainty, building on previous analyses of the plausible rates of increase for this species. The model was used to explore realistic limits to recreational and indigenous harvest and to examine productive, yet risk-averse, management regimes for long-term sustainability. Harvest strategies based on a proportional off-take provided similar yields to a fixed quota system, but resulted in a reduced risk of substantial population decline. Moreover, higher harvests could be supported in model systems that incorporated dispersal phenomena consistent with patterns suggested by the observed distributional and abundance patterns. However, irrespective of harvest strategy and spatial structure, off-take at the levels implied in previously published analyses are clearly unsustainable. These results illustrate the desirability of matching the design of management systems to the heterogeneity of population processes. Management regimes that fail to take account of spatial and temporal heterogeneity could damage the interests of important stakeholder groups and potentially imperil the future viability of the species. However, the costs of disaggregated management systems may be substantial and benefits of investment in them need to be clearly demonstrated. Gaining better appreciation of spatial variation in harvests should be given high priority.
Which mosaic? A landscape ecological approach for evaluating interactions between fire regimes, habitat and animals
Authors: Bradstock R. A. , Bedward M. , Gill A. M. , Cohn J. S.
Published: August 2005

The link between ‘fire mosaics’ and persistence of animal species is part of a prominent ecological/land management paradigm. This paradigm deals largely with the effects of fire on animals on the basis of individual events. The universality of the paradigm can be questioned on a variety of grounds, a major deficiency being the inability to deal with quantitative effects of recurrent fire (the fire regime). A conceptual model of fire-related habitat elements is proposed for exploration of a continuum of species/habitat/landscape/fire regime combinations. This approach predicts that the dependence of species on fire-mediated habitat heterogeneity will be highly variable and strongly context-dependent. A spatially explicit simulation model was used to examine the persistence of malleefowl (Leipoa ocellata) in a specific landscape/habitat context where dependence on fire-mosaics should be high. Results suggest that persistence of L. ocellata populations will be dependent on intervention using small patchy fires but that there is an optimum rate of intervention. Results were sensitive to spatial pattern of prescribed fire, landscape type (topography) and probability of wildfire. Underlying effects of the fire-interval distribution (the ‘invisible’ mosaic) on plant species and habitat account for these results. A management emphasis on species/landscape context and awareness of the ‘invisible’ mosaic is advocated.
Landscapes, ecology and wildlife management in highly modified environments - an Australian perspective
Authors: Hobbs Richard J.
Published: August 2005

Landscapes in southern Australia have been extensively modified by a variety of human activities, predominantly agriculture and urban development. Over much of the area, native vegetation has been replaced with agriculture or buildings and infrastructure. A continuum exists from areas that remain largely intact, but are modified in some way (e.g. forests managed for timber production), to areas where the remaining native vegetation is fragmented to varying degrees. Habitat management will vary across this continuum, depending on the degree of habitat loss and isolation. In areas outside the main zones of agricultural and urban development, the process of habitat loss and fragmentation is less in evidence. Here, instead, the landscapes remain apparently structurally intact, in that the native vegetation is not actually removed. However, these landscapes have also, in many cases, been significantly modified, particularly by pastoralism and related activities, to the extent that their value as habitat is impaired. Declining habitat value in northern landscapes may lead to the same types of functional fragmentation as found in the south. An examination of the differences and similarities between southern and northern landscapes can highlight what can be learned from the southern experience which may be of value in savanna landscapes. In both cases, the importance of considering impacts in relation to species-specific responses needs to be emphasised.
Circuit topology and the evolution of robustness in two-gene circadian oscillators
Authors: Wagner Andreas
Published: August 2005

Many parameters driving the behavior of biochemical circuits vary extensively and are thus not fine-tuned. Therefore, the topology of such circuits (the who-interacts-with-whom) is key to understanding their central properties. I here explore several hundred different topologies of a simple biochemical model of circadian oscillations to ask two questions: Do different circuits differ dramatically in their robustness to parameter change? If so, can a process of gradual molecular evolution find highly robust topologies when starting from less robust topologies? I find that the distribution of robustness among different circuit topologies is highly skewed: Most show low robustness, whereas very few topologies are highly robust. To address the second evolutionary question, I define a topology graph, each of whose nodes corresponds to one circuit topology that shows circadian oscillations. Two nodes in this graph are connected if they differ by only one regulatory interaction within the circuit. For the circadian oscillator I study, most topologies are connected in this graph, making evolutionary transitions from low to high robustness easy. A similar approach has been used to study the evolution of robustness in biological macromolecules, with similar results. This suggests that the same principles govern the evolution of robustness on different levels of biological organization. The regulatory interlocking of several oscillating gene products in biological circadian oscillators may exist because it provides robustness.
Single-nucleotide polymorphism detection with “wire-like” DNA probes that display quasi “on–off” digital action
Authors: Inouye Masahiko , Ikeda Reona , Takase Masayoshi , Tsuri Takashi , Chiba Junya
Published: August 2005

Establishing a reliable genotyping protocol is a critical matter in postsequence genetics. In this article, we describe a highly sensitive electrochemical detection of complementary DNAs (up to 43-mer) based on hole transport with molecular-scale, “wire-like” DNA probes. The presence of a single-base mismatch in the DNA duplexes caused a dramatic decrease in the electrochemical response. We applied this method to detect all of the possible transition and transversion SNPs and achieved “on–off”-type discrimination of fully complementary DNAs from their SNPs. Furthermore, naturally occurring polymorphisms, “hot spots” from the
p53
gene, could clearly be distinguished from wild type by using our methodology.
Carbon nanotubes as multifunctional biological transporters and near-infrared agents for selective cancer cell destruction
Authors: Kam Nadine Wong Shi , O'Connell Michael , Wisdom Jeffrey A. , Dai Hongjie
Published: August 2005

Biological systems are known to be highly transparent to 700- to 1,100-nm near-infrared (NIR) light. It is shown here that the strong optical absorbance of single-walled carbon nanotubes (SWNTs) in this special spectral window, an intrinsic property of SWNTs, can be used for optical stimulation of nanotubes inside living cells to afford multifunctional nanotube biological transporters. For oligonucleotides transported inside living cells by nanotubes, the oligos can translocate into cell nucleus upon endosomal rupture triggered by NIR laser pulses. Continuous NIR radiation can cause cell death because of excessive local heating of SWNTin vitro. Selective cancer cell destruction can be achieved by functionalization of SWNT with a folate moiety, selective internalization of SWNTs inside cells labeled with folate receptor tumor markers, and NIR-triggered cell death, without harming receptor-free normal cells. Thus, the transporting capabilities of carbon nanotubes combined with suitable functionalization chemistry and their intrinsic optical properties can lead to new classes of novel nanomaterials for drug delivery and cancer therapy.
In situ
measurement of solute transport in the bone lacunar-canalicular system
Authors: Wang Liyun , Wang Yilin , Han Yuefeng , Henderson Scott C. , Majeska Robert J. , Weinbaum Sheldon , Schaffler Mitchell B.
Published: August 2005

Solute transport through the bone lacunar-canalicular system is believed to be essential for osteocyte survival and function but has proved difficult to measure. We report an approach that permits direct measurement of real-time solute movement in intact bones. By using fluorescence recovery after photobleaching, the movement of a vitally injected fluorescent dye (sodium fluorescein) among individual osteocytic lacunae was visualized
in situ
beneath the periosteal surface of mouse cortical bone at depths up to 50 μm with laser scanning confocal microscopy. Transport was analyzed by using a two-compartment mathematical model of solute diffusion that accounted for the characteristic anatomical features of the lacunar-canalicular system. The diffusion coefficient of fluorescein (376 Da) was determined to be 3.3 ± 0.6 × 10
-6
cm
2
/sec, which is 62% of its diffusion coefficient in water and is similar to diffusion coefficients measured for comparably sized molecules in cartilage. The diffusion of fluorescein in bone is also consistent with the presence of an osteocyte pericellular matrix whose structure resembles that proposed for the endothelial glycocalyx [Squire, J. M., Chew, M., Nneji, G., Neal, C., Barry, J. & Michel, C. (2001)
J. Struct. Biol.
136, 239–255]. To our knowledge, this is the first instance where the dynamics of molecular movement has been measured directly in the bone lacunar-canalicular system. This
in situ
imaging approach should also facilitate the analysis of convection-based transport mechanisms in bones of living animals.
Three-dimensional structure of the quorum-quenching
N
-acyl homoserine lactone hydrolase from
Bacillus thuringiensis
Authors: Liu Dali , Lepore Bryan W. , Petsko Gregory A. , Thomas Pei W. , Stone Everett M. , Fast Walter , Ringe Dagmar
Published: August 2005

The three-dimensional structure of the
N
-acyl-
l
-homoserine lactone hydrolase (AHL lactonase) from
Bacillus thuringiensis
has been determined, by using single-wavelength anomalous dispersion (SAD) phasing, to 1.6-Å resolution. AHLs are produced by many Gram-negative bacteria as signaling molecules used in quorum-sensing pathways that indirectly sense cell density and regulate communal behavior. Because of their importance in pathogenicity, quorum-sensing pathways have been suggested as potential targets for the development of novel therapeutics. Quorum-sensing can be disrupted by enzymes evolved to degrade these lactones, such as AHL lactonases. These enzymes are members of the metallo-β-lactamase superfamily and contain two zinc ions in their active sites. The zinc ions are coordinated to a number of ligands, including a single oxygen of a bridging carboxylate and a bridging water/hydroxide ion, thought to be the nucleophile that hydrolyzes the AHLs to ring-opened products, which can no longer act as quorum signals.
Establishment of NOD-Pdcd1-/-mice as an efficient animal model of type I diabetes
Authors: Wang Jian , Yoshida Taku , Nakaki Fumio , Hiai Hiroshi , Okazaki Taku , Honjo Tasuku
Published: August 2005

Mice deficient in programmed cell death 1 (PD-1,Pdcd1), an immunoinhibitory receptor belonging to the CD28/cytotoxic T lymphocyte-associated antigen-4 family, spontaneously develop lupus-like autoimmune disease and autoimmune dilated cardiomyopathy on C57BL/6 and BALB/c backgrounds, respectively. However, how PD-1 deficiency induces different forms of autoimmune diseases on these two strains was unknown. Here, we report that PD-1 deficiency specifically accelerates the onset and frequency of type I diabetes in NOD (nonobese diabetic) mice, with strong T helper 1 polarization of T cells infiltrating into islets. These results suggest that PD-1 deficiency accelerates autoimmune predisposition of the background strain, leading to the induction of different forms of autoimmune diseases depending on the genetic background of the strain. Using NOD-Pdcd1-/-mice as an efficient animal model of type I diabetes, we screened diabetes-susceptible loci by genetic linkage analysis. The diabetic incidence of NOD-Pdcd1-/-mice was controlled by five genetic loci, including three known recessive loci [Idd(insulin-dependent diabetes)1,Idd17, andIdd20] and two previously unidentified dominant loci [Iddp(Iddunder PD-1 deficiency)1andIddp2].
Interactions of WASp, myosin-I, and verprolin with Arp2/3 complex during actin patch assembly in fission yeast
Authors: Sirotkin Vladimir , Beltzner Christopher C. , Marchand Jean-Baptiste , Pollard Thomas D.
Published: August 2005

Yeast actin patches are dynamic structures that form at the sites of cell growth and are thought to play a role in endocytosis. We used biochemical analysis and live cell imaging to investigate actin patch assembly in fission yeast Schizosaccharomyces pombe. Patch assembly proceeds via two parallel pathways: one dependent on WASp Wsp1p and verprolin Vrp1p converges with another dependent on class 1 myosin Myo1p to activate the actin-related protein 2/3 (Arp2/3) complex. Wsp1p activates Arp2/3 complex via a conventional mechanism, resulting in branched filaments. Myo1p is a weaker Arp2/3 complex activator that makes unstable branches and is enhanced by verprolin. During patch assembly in vivo, Wsp1p and Vrp1p arrive first independent of Myo1p. Arp2/3 complex associates with nascent activator patches over 6–9 s while remaining stationary. After reaching a maximum concentration, Arp2/3 complex patches move centripetally as activator proteins dissociate. Genetic dependencies of patch formation suggest that patch formation involves cross talk between Myo1p and Wsp1p/Vrp1p pathways.
Transcytosis of NgCAM in epithelial cells reflects differential signal recognition on the endocytic and secretory pathways
Authors: Anderson Eric , Maday Sandra , Sfakianos Jeff , Hull Michael , Winckler Bettina , Sheff David , Fölsch Heike , Mellman Ira
Published: August 2005

NgCAM is a cell adhesion molecule that is largely axonal in neurons and apical in epithelia. In Madin-Darby canine kidney cells, NgCAM is targeted to the apical surface by transcytosis, being first inserted into the basolateral domain from which it is internalized and transported to the apical domain. Initial basolateral transport is mediated by a sequence motif (Y33RSL) decoded by the AP-1B clathrin adaptor complex. This motif is a substrate in vitro for tyrosine phosphorylation by p60src, a modification that disrupts NgCAM's ability to interact with clathrin adaptors. Based on the behavior of various NgCAM mutants, it appears that after arrival at the basolateral surface, the AP-1B interaction site is silenced by phosphorylation of Tyr33. This slows endocytosis and inhibits basolateral recycling from endosomes, resulting in NgCAM transcytosis due to a cryptic apical targeting signal in its extracellular domain. Thus, transcytosis of NgCAM and perhaps other membrane proteins may reflect the spatial regulation of recognition by adaptors such as AP-1B.
IgG marker of optic-spinal multiple sclerosis binds to the aquaporin-4 water channel
Authors: Lennon Vanda A. , Kryzer Thomas J. , Pittock Sean J. , Verkman A.S. , Hinson Shannon R.
Published: August 2005

Neuromyelitis optica (NMO) is an inflammatory demyelinating disease that selectively affects optic nerves and spinal cord. It is considered a severe variant of multiple sclerosis (MS), and frequently is misdiagnosed as MS, but prognosis and optimal treatments differ. A serum immunoglobulin G autoantibody (NMO-IgG) serves as a specific marker for NMO. Here we show that NMO-IgG binds selectively to the aquaporin-4 water channel, a component of the dystroglycan protein complex located in astrocytic foot processes at the blood-brain barrier. NMO may represent the first example of a novel class of autoimmune channelopathy.
Characterization of the early stages of thymic NKT cell development
Authors: Benlagha Kamel , Wei Datsen G. , Veiga Joel , Teyton Luc , Bendelac Albert
Published: August 2005

Upon reaching the mature heat stable antigen (HSA)low thymic developmental stage, CD1d-restricted Vα14-Jα18 thymocytes undergo a well-characterized sequence of expansion and differentiation steps that lead to the peripheral interleukin-4/interferon-γ–producing NKT phenotype. However, their more immature HSAhigh precursors have remained elusive, and it has been difficult to determine unambiguously whether NKT cells originate from a CD4+CD8+ double-positive (DP) stage, and when the CD4+ and CD4−CD8− double-negative (DN) NKT subsets are formed. Here, we have used a CD1d tetramer-based enrichment strategy to physically identify HSAhigh precursors in thymuses of newborn mice, including an elusive DPlow stage and a CD4+ stage, which were present at a frequency of ∼10−6. These HSAhigh DP and CD4+ stages appeared to be nondividing, and already exhibited the same Vβ8 bias that characterizes mature NKT cells. This implied that the massive expansion of NKT cells is separated temporally from positive selection, but faithfully amplifies the selected TCR repertoire. Furthermore, we found that, unlike the DN γδ T cells, the DN NKT cells did not originate from a pTα-independent pathway bypassing the DP stage, but instead were produced during a short window of time from the conversion of a fraction of HSAlow NK1.1neg CD4 cells. These findings identify the HSAhigh CD4+ stage as a potential branchpoint between NKT and conventional T lineages and between the CD4 and DN NKT sublineages.
Regulation of TCR δ and α repertoires by local and long-distance control of variable gene segment chromatin structure
Authors: Hawwari Abbas , Krangel Michael S.
Published: August 2005

Murine Tcrd and Tcra gene segments reside in a single genetic locus and undergo recombination in CD4−CD8− (double negative [DN]) and CD4+CD8+ (double positive [DP]) thymocytes, respectively. TcraTcrd locus variable gene segments are subject to complex regulation. Only a small subset of ∼100 variable gene segments contributes substantially to the adult TCRδ repertoire. Moreover, although most contribute to the TCRα repertoire, variable gene segments that are Jα proximal are preferentially used during primary Tcra recombination. We investigate the role of local chromatin accessibility in determining the developmental pattern of TcraTcrd locus variable gene segment recombination. We find variable gene segments to be heterogeneous with respect to acetylation of histones H3 and H4. Those that dominate the adult TCRδ repertoire are hyperacetylated in DN thymocytes, independent of their position in the locus. Moreover, proximal variable gene segments show dramatic increases in histone acetylation and germline transcription in DP thymocytes, a result of super long-distance regulation by the Tcra enhancer. Our results imply that differences in chromatin accessibility contribute to biases in TcraTcrd locus variable gene segment recombination in DN and DP thymocytes and extend the distance over which the Tcra enhancer can regulate chromatin structure to a remarkable 525 kb.
Disc Arthroplasty in the Management of the Painful Lumbar Motion Segment
Authors: German John W. , Foley Kevin T.
Published: August 2005

Study Design.

A review of the published literature regarding lumbar arthroplasty.

Objective.

To describe the current state of lumbar total disc replacement and, in particular, the recent clinical results of the Charité and ProDisc trials.

Summary of Background Data.

Lumbar fusion remains the surgical procedure of choice for patients with chronic low back pain unresponsive to nonsurgical management. Lumbar fusion is a strictly palliative procedure with suboptimal clinical results obtained by a significant proportion of patients. Adjacent segment disease is thought to limit the long-term clinical results with up to 20% of patients requiring secondary surgical interventions within the decade following a “successful” lumbar fusion. Total disc replacement has been developed as a potential means to improve the long-term outcome of these patients.

Methods.

Literature review of total lumbar disc replacement.

Results.

The surgical decision-making process, a description of current lumbar disc arthroplasty devices, and early clinical results are described.

Conclusion.

In appropriately chosen patients, lumbar disc arthroplasty provided clinical results similar to those obtained with interbody fusion at 2 years. The long-term results with respect to the effect of these devices on adjacent segment degeneration are not known, as the incidence of adjacent segment degeneration is not an endpoint of the current trials.
Nucleus Pulposus Replacement
Authors: Di Martino Alberto , Vaccaro Alexander R. , Lee Joon Yung , Denaro Vincenzo , Lim Moe R.
Published: August 2005

Study Design.

A critical review of available and emerging nucleus pulposus replacement implants.

Objectives.

To review the biomechanics, design, and clinical data of currently available and developing nucleus pulposus replacement technologies.

Summary of Background Data.

The interest in minimally invasive treatment of degenerative disc disease has grown as the technology for intervertebral motion-sparing devices continues to improve. Replacement of nucleus pulposus without anular obliteration represents a tempting alternative to spinal fusion procedures. The aim in nucleus pulposus replacement is to slow adjacent level degeneration, restore normal loads to the diseased level, and restore segmental spinal biomechanics.

Methods.

A literature review of currently available biomaterials, biomechanics, and available preclinical and clinical data on nucleus pulposus replacement implants.

Results.

New synthetic biomaterials have recently been developed to closely mimic native biomechanics during compressive loading cycles of the intervertebral disc. This, in conjunction with improved understanding of global spine biomechanics, has allowed the development of novel nucleus replacement implants. These implants are currently at different stages of preclinical and clinical investigations.

Conclusions.

Although some of the newly designed prosthesis have shown some promising results in preclinical studies, rigorous short- and long-term clinical evaluations will be critical in evaluating their true efficacy.
Dynamic Stabilization in the Surgical Management of Painful Lumbar Spinal Disorders
Authors: Nockels Russ P.
Published: August 2005

Study Design.

A literature review.

Objective.

To evaluate the mechanisms of action and effectiveness of posterior dynamic stabilization devices in the management of painful spinal disorders.

Summary of Background Data.

Dynamic stabilization may provide pain relief by altering the transmission of abnormal loads across the degenerated disc space.

Methods.

A Medline search was conducted.

Results.

Articles supporting abnormal load transmission across the disc space and clinical reviews of currently available posterior dynamic systems were included.

Conclusions.

Posterior dynamic stabilization systems may provide benefit comparable to fusion techniques, but without the elimination of movement. Further study is required to determine optimal design and clinical indications.