bluuebunny/crossref_metadata_2025 huggingface dataset:
Interactions between magma and hydrothermal system in Oman ophiolite and in IODP Hole 1256D: Fossilization of a dynamic melt lens at fast spreading ridges
Authors: France Lydéric , Ildefonse Benoit , Koepke Juergen
Published: October 2009

The transition between the small melt lens observed on top of fast spreading ridge magma chambers and the overlying sheeted dike complex marks the interface between magma and the hydrothermal convective system. It is therefore critical to our understanding of fast spreading ridge accretion processes. We present maps of two areas of the Oman ophiolite where this transition zone is observed as continuous outcrops. Our observations, which include the base of the sheeted dike being crosscut by gabbros, are consistent with episodic dike injections in a steady state model but also suggest that the root of these dikes is commonly erased by vertical movements of the top of the melt lens. Dike assimilation is a possible mechanism for incorporating hydrated phases, which result from hydrothermal alteration, to the melt lens during upward migrations of its upper boundary. Upward migrations are also responsible for a granoblastic overprint of the root of the dikes that is also observed in the stoped diabase xenoliths. This granoblastic overprint attests to reheating of previously hydrothermally altered lithologies which can even trigger hydrous partial melting due to the lowering of the solidus of mafic lithologies by the presence of a water activity. Clinopyroxenes present in these granoblastic lithologies are typically low in Ti and Al content, thus strongly contrasting with corresponding magmatic clinopyroxene. This may attest to the recrystallization of clinopyroxenes after amphiboles under the peculiar conditions present at the root zone of the sheeted dike complex. Downward migrations of the top of the melt lens result in the crystallization of the isotropic gabbros at its roof, which represent the partly fossilized melt lens. Melt lens fossilization eventually occurs when magma supply is stopped or at the melt lens margins where the thermal conditions become cooler. Melt lens migration, recrystallization of hydrothermally altered sheeted dikes during reheating stages, and assimilation processes observed in the Oman ophiolite are consistent with the observations made in IODP Hole 1256D. We propose a general dynamic model in which the melt lens at fast spreading ridges undergoes upward and downward movements as a result of either eruption/replenishment stages or variations in the hydrothermal/magmatic fluxes.
Potential impact of global warming on North Pacific spring blooms projected by an eddy‐permitting 3‐D ocean ecosystem model
Authors: Hashioka Taketo , Sakamoto Takashi T. , Yamanaka Yasuhiro
Published: October 2009

Using an eddy‐permitting ecosystem model with a projected physical environment from a high‐resolution climate model, we explored the potential impact of global warming on spring blooms in the western North Pacific. We focused on statistically significant signals compared with natural variability. Considering 2xCO2 conditions, maximum biomass during the spring bloom is found to occur 10 to 20 days earlier due to strengthened stratification, and in the subarctic region, the bloom to decrease in magnitude relative to pre‐industrial simulation. However, in the northern part of the Kuroshio extension region where photosynthesis is not strongly limited by nutrients, the maximum biomass increases by 20 to 40% associated with rising temperatures, even though the annually averaged biomass slightly decreases. Our results reveal that even if global warming weakly affects annually averaged quantities, it could strongly affect certain species and biogeochemical processes which depend on seasonal events such as blooms.
How islands cause phytoplankton to bloom in their wakes
Authors: Hasegawa D. , Lewis M. R. , Gangopadhyay A.
Published: October 2009

The development of phytoplankton blooms in Von Kàrmàn vortex streets in island wakes has been investigated using a coupled bio‐physical model which evolves a geostrophically balanced flow past a relatively small (L = 10 km) oceanic island. Three major processes associated with the “island mass effect” are found to occur in series in our numerical experiment. First, increases in phytoplankton were observed in the lee due solely to passive advection from the deep maximum. Second, following the shedding of cyclonic eddies, upwelled nitrate enhances local primary production in the surface euphotic layer resulting in a phytoplankton bloom. The bloom peaks appeared about two weeks downstream from the island. Third, a weaker bloom is also found in the immediate lee of the island, associated with nutrient injection and longer residence time of upwelled water. The demonstrated detailed features of island mass effect are remarkably consonant with previously observed phenomena in the real ocean.
Generation of large‐scale gravity waves and neutral winds in the thermosphere from the dissipation of convectively generated gravity waves
Authors: Vadas Sharon L. , Liu Han‐li
Published: October 2009

We study the response of the thermosphere and ionosphere to the dissipation of gravity waves (GWs) excited by a deep convective plume on 1 October 2005 at 52.5°W, 15.0°S, and 2120 UT in Brazil. Those small‐ and medium‐scale GWs which reach the thermosphere dissipate at z ∼ 120–250 km in a direction opposite to the background wind ∼(1–2) density scale heights below. This localized momentum deposition creates horizontal thermospheric body forces that have large sizes and amplitudes and generates large‐scale secondary GWs and large‐scale traveling ionospheric disturbances (LSTIDs) that propagate globally away from the body force in all directions except that perpendicular to the force direction. For the convective plume at 2120 UT, the secondary GWs have horizontal wavelengths of λH ∼ 2100–2200 km, periods of τr ∼ 80 min, horizontal phase speeds of cH ∼ 480–510 m/s, density perturbations as large as ∣ρ′/∣ ∼ 3.6–5% at z = 400 km, relative [O] perturbations as large as ∼2–2.5% at z = 300 km, and total electron content perturbations as large as ∼8%. This transfer of momentum from local, relatively slow, small scales at the tropopause to global, fast, large scales in the thermosphere is independent of geomagnetic conditions. The various characteristics of these large‐scale waves may explain observations of LSTIDs at magnetically quiet times. We also find that this body force creates a localized “mean” horizontal wind in the direction of the body force. For the plume at 2120 UT, the wind is southward with an estimated maximum of vmax ∼ −400 m s−1 that is dissipated after ∼4 h. We also find that the induced body force direction varies throughout the day, depending on the winds in the lower thermosphere.
Spatial scaling of Arctic sea ice deformation
Authors: Stern H. L. , Lindsay R. W.
Published: October 2009

Arctic sea ice deformation arises from spatial gradients in the ice velocity field. This deformation occurs across a wide range of spatial scales, from meters to thousands of kilometers. We analyze 7 years of sea ice deformation data from the RADARSAT Geophysical Processor System (RGPS) covering the western Arctic Ocean. We find that the mean deformation rate is related to the spatial scale over which it is measured according to a power law with exponent ∼−0.2, over a scale range from 10 to 1000 km (e.g., deformation rate doubles for a 30‐fold reduction in scale). Both the exponent and the deformation rate have distinct annual cycles. The exponent becomes more negative in summer as the ice pack weakens and internal stresses are not as readily transmitted over long distances. The deformation rate reaches a minimum in late winter when the ice pack is strongest. The deformation also exhibits considerable localization, in which the largest deformation rates are confined to smaller and smaller areas as the scale of measurement decreases. This supports a model for sea ice based on granular or fracture mechanics. The scaling exponent in the power law relationship tends to be larger in magnitude where the concentration of multiyear ice is low, consistent with a thinner and weaker ice pack. With decreasing multiyear ice in the Arctic and a thinning ice pack, an increase in the deformation rate has already been documented (from buoy data). However, the net effect of several deformation/thickness feedbacks is still uncertain.
Mars Climate Sounder limb profile retrieval of atmospheric temperature, pressure, and dust and water ice opacity
Authors: Kleinböhl Armin , Schofield John T. , Kass David M. , Abdou Wedad A. , Backus Charles R. , Sen Bhaswar , Shirley James H. , Lawson W. Gregory , Richardson Mark I. , Taylor Fredric W. , Teanby Nicholas A. , McCleese Daniel J.
Published: October 2009

The Mars Climate Sounder (MCS) onboard the Mars Reconnaissance Orbiter is the latest of a series of investigations devoted to improving the understanding of current Martian climate. MCS is a nine‐channel passive midinfrared and far‐infrared filter radiometer designed to measure thermal emission in limb and on‐planet geometries from which vertical profiles of atmospheric temperature, water vapor, dust, and condensates can be retrieved. Here we describe the algorithm that is used to retrieve atmospheric profiles from MCS limb measurements for delivery to the Planetary Data System. The algorithm is based on a modified Chahine method and uses a fast radiative transfer scheme based on the Curtis‐Godson approximation. It retrieves pressure and vertical profiles of atmospheric temperature, dust opacity, and water ice opacity. Water vapor retrievals involve a different approach and will be reported separately. Pressure can be retrieved to a precision of 1–2% and is used to establish the vertical coordinate. Temperature profiles are retrieved over a range from 5–10 to 80–90 km altitude with a typical altitude resolution of 4–6 km and a precision between 0.5 and 2 K over most of this altitude range. Dust and water ice opacity profiles also achieve vertical resolutions of about 5 km and typically have precisions of 10−4–10−5 km−1 at 463 cm−1 and 843 cm−1, respectively. Examples of temperature profiles as well as dust and water ice opacity profiles from the first year of the MCS mission are presented, and atmospheric features observed during periods employing different MCS operational modes are described. An intercomparison with historical temperature measurements from the Mars Global Surveyor mission shows good agreement.
Implementation of polarization agility in planar phased‐array antennas by means of interleaved subarrays
Authors: Simeoni Massimiliano , Lager Ioan E. , Coman Cristian I. , Roederer Antoine G.
Published: October 2009

A method for ensuring polarization agility in conjunction with beam steering in planar array antennas is proposed. It relies on interleaving two subarrays with orthogonal, linear polarizations that, together, can generate arbitrary polarization states: adjustable linear, elliptical, and left‐ or right‐handed circular. The complexity of the resulting system is comparable with that of standard, fully populated array antennas consisting of identical, linearly polarized elements. By dynamically controlling the amplitude and the phase of the signals fed to the subarrays, a stable polarization state can be maintained during beam steering. The concept is validated by numerically investigating an architecture obtained by interleaving nonuniform subarrays designed by means of a deterministic placement strategy. The effects of the mutual coupling between the different radiating elements are modeled and discussed.
Stone–Wales defects created by low energy recoils in single-walled silicon carbide nanotubes
Authors: Wang Zhiguo , Gao Fei , Li Jingbo , Zu Xiaotao , Weber William J.
Published: October 2009

The defect creation at low energy events was studied using density functional theory molecular dynamics simulations in silicon carbide nanotubes, and the displacement threshold energies determined exhibit a dependence on sizes, which decrease with decreasing diameter of the nanotubes. The Stone–Wales (SW) defect, which is a common defect configurations induced through irradiation in nanotubes, has also been investigated, and the formation energies of the SW defects increase with increasing diameter of the nanotubes. The mean threshold energies were found to be 23 and 18 eV for Si and C in armchair (5,5) nanotubes.
Performance improvement in transparent organic thin-film transistors with indium tin oxide/fullerene source/drain contact
Authors: Li Yu-Chang , Lin Yu-Ju , Wei Chia-Yu , Lin Zheng-Xian , Wen Ten-Chin , Chang Mei-Ying , Tsai Cheng-Liang , Wang Yeong-Her
Published: October 2009

With the use of fullerene (C60)/indium tin oxide (ITO) source/drain electrode, the performance of a transparent thin-film transistor could be enhanced dramatically. The drain current can be increased by a factor of more than 5. The improvements are attributed to the reduction of the injection barrier at the ITO/pentacene interface, which can be confirmed by the work function measured at the ITO/C60 and the contact resistance obtained by transmission line method. Meanwhile, the average transmittance in the visible region with a 3.5 nm C60 buffer layer for 65-nm-thick pentacene organic thin film transistors remains at 62.98%.
Room-temperature large refrigerant capacity of Gd6Co2Si3
Authors: Shen Jun , Wu Jian-Feng , Sun Ji-Rong
Published: October 2009

The magnetic properties and magnetocaloric effects of the Gd6Co2Si3 alloy are investigated. Gd6Co2Si3 undergoes a reversible second-order magnetic transition with a Curie temperature at room temperature (TC=295 K). A broad distribution of the magnetic entropy change ΔSm peak is observed, and the full width at half maximum of the ΔSm peak is found to be about 111 K under a magnetic field of 5 T. The large value of the refrigerant capacity (RC) is found to be comparable with those of pure Gd, which have maximal RC values for all the magnetocaloric materials reported previously. The maximal value of ΔSm is 6.3 J/kg K for a field change of 0–5 T. Excellent magnetocaloric properties, especially considerable values of RC, indicate the applicability of Gd6Co2Si3 for magnetic refrigeration in the room-temperature range.
Dielectric barrier discharge source for supersonic beams
Authors: Luria K. , Lavie N. , Even U.
Published: October 2009

We present a new excitation source for pulsed supersonic beams. The excitation is based on dielectric barrier discharge in the beam. It produces cold beams of metastable atoms, dissociated neutral atoms from molecular precursors, and both positive and negative ions with high efficiency and reliability.
Real time monitoring of the interaction of Si (100) with atomic hydrogen: The “H-insertion/Si-etching” kinetic model explaining Si surface modifications
Authors: Bianco Giuseppe V. , Losurdo Maria , Giangregorio Maria M. , Capezzuto Pio , Bruno Giovanni
Published: October 2009

The interaction of p- and n-type crystalline silicon [c-Si (100)], with atomic hydrogen produced by a remote radiofrequency (13.56 MHz) H2 plasma has been investigated in real time using in situ spectroscopic ellipsometry. The effects of substrate doping, temperature and time on the c-Si surface modifications are discussed. A thicker hydrogenated surface layer forms for n-type Si. This hydrogenated layer is subsequently etched by further exposure to hydrogen. A kinetic model based on the competition between hydrogen insertion and silicon etching is proposed to explain modifications of c-Si, and the rate constants of the hydrogen insertion and silicon etching processes are determined.
Searching for solvent cavities via electron photodetachment: The ultrafast charge-transfer-to-solvent dynamics of sodide in a series of ether solvents
Authors: Larsen Molly C. , Schwartz Benjamin J.
Published: October 2009

It was recently predicted by simulations and confirmed by neutron diffraction experiments that the structure of liquid tetrahydrofuran (THF) contains cavities. The cavities can be quite large and have a net positive electrostatic potential, so they can serve as pre-existing traps for excess electrons created via photodetachment from various solutes. In this paper, we use electron photodetachment via charge-transfer-to-solvent (CTTS) excitation of sodide (Na−) to probe for the presence of pre-existing cavities in a series of ether solvents: THF, diethyl ether, 1,2-dimethoxyethane (DME), and diglyme (DG). We find that electrons photodetached from sodide appear after a time delay with their equilibrium spectrum in all of these solvents, suggesting that the entire series of ethers contains pre-existing solvent cavities. We then use the variation in electron recombination dynamics with CTTS excitation wavelength to probe the nature of the cavities in the different ethers. We find that the cavities that form the deepest electron traps turn on at about the same energy in all four ether solvents investigated, but that the density of cavities is lower in DG and DME than in THF. We also examine the dynamics of the neutral sodium species that remains following CTTS photodetachment of an electron from sodide. We find that the reaction of the initially created gas-phase-like Na atom to form a (Na+,e−) tight-contact pair occurs at essentially the same rate in all four ether solvents, indicating that only local solvent motions and not bulk solvent rearrangements are what is responsible for driving the partial ejection of the remaining Na valence electron.
Thermal conductivity of graphene nanoribbons
Authors: Guo Zhixin , Zhang Dier , Gong Xin-Gao
Published: October 2009

We have investigated the thermal conductivity of graphene nanoribbons (GNRs) with different edge shapes as a function of length, width, and strain using nonequilibrium molecular dynamics method. The initial GNR for the functional variations has dimensions of 2×11 nm2. Strong length dependence of thermal conductivity is obtained, indicating high thermal conductivities of GNRs, which is consistent with the experimental results for graphene. A tensile/compressive uniaxial strain can remarkably decrease the thermal conductivity of GNR.
Closed-form evaluation of integrals appearing in positronium decay
Authors: Amdeberhan Tewodros , Moll Victor H. , Straub Armin
Published: October 2009

A theoretical prediction for the total width of the positronium decay in quantum electrodynamics has been given by Kniehl et al. [“Irrational constants in positronium decays,” Nucl. Phys. B (Proc. Suppl.) 184, 14 (2008), arXiv:hep-ph/0811.0306] in the form of an expansion in Sommerfeld’s fine-structure constant. The coefficients of this expansion are given in the form of two-dimensional definite integrals, with an integrand involving the polylogarithm function. We provide here an analytic expression for the one-loop contribution to this problem.
Dynamic properties of cluster glass in La0.25Ca0.75MnO3 nanoparticles
Authors: Huang X. H. , Ding J. F. , Jiang Z. L. , Yin Y. W. , Yu Q. X. , Li X. G.
Published: October 2009

The dynamic magnetic properties of cluster glass in La0.25Ca0.75MnO3 nanoparticles with average particle size range from 40 to 1000 nm have been investigated by measuring the frequency and dc magnetic field (H) dependencies of the ac susceptibility. The frequency-dependent Tf, the freezing temperature of the ferromagnetic clusters determined by the peak in the real part of the ac susceptibility χ′ versus T curve with H=0, is fit to a power law. The relaxation time constant τ0 decreases as the particle size increases from 40 to 350 nm, which indicates the decrease in the size of the clusters at the surface of the nanoparticle. The relationship between H and Tf(H) deviates from the De Almeida–Thouless-type phase boundary at relatively high fields for the samples with size range from 40 to 350 nm. Moreover, for the samples with particle sizes of 40 and 100 nm, τ0 increases with increasing H, which indicates the increasing cluster size and may be ascribed to the competition between the influence of H and the local anisotropy field in the shell spins. All these results may give rise to a new insight into the behaviors of the cluster glass state in the nanosized antiferromagnetic charge-ordered perovskite manganites.
Glass-forming ability enhanced by proper additions of oxygen in a Fe-based bulk metallic glass
Authors: Li H. X. , Gao J. E. , Jiao Z. B. , Wu Y. , Lu Z. P.
Published: October 2009

Effects of oxygen on glass formation in the Fe73Mo3.0C7.0Si3.3B5.0P8.7 bulk metallic glass were studied in detail. Surprisingly, it was found that a critical level of oxygen is effective in enhancing the glass-forming ability of the current Fe-based bulk metallic glass due to the facts that (i) oxygen can increase the crystallization resistance via suppressing the precipitation of the competitive primary phase and (ii) oxygen can stabilize the glass-forming liquid as manifested by the decrease in the liquidus temperature. However, excess oxygen additions will destabilize the liquid and induce the formation of more stable oxygen-containing crystalline phase, thus deteriorating the glass-forming ability.
Nonlinear dielectric effect of dipolar fluids
Authors: Szalai I. , Nagy S. , Dietrich S.
Published: October 2009

The nonlinear dielectric effect for dipolar fluids is studied within the framework of the mean spherical approximation (MSA) of hard core dipolar Yukawa fluids. Based on earlier results for the electric field dependence of the polarization our analytical results show so-called normal saturation effects, which are in good agreement with corresponding NVT ensemble Monte Carlo (MC) simulation data. The linear and the nonlinear dielectric permittivities obtained from MC simulations are determined from the fluctuations of the total dipole moment of the system in the absence of an applied electric field. We compare the MSA based theoretical results with the corresponding Langevin and Debye–Weiss behaviors and with actual experimental data.
The self-energy beyond GW: Local and nonlocal vertex corrections
Authors: Romaniello P. , Guyot S. , Reining L.
Published: October 2009

It is commonly accepted that the GW approximation for the electron self-energy is successful for the description of the band structure of weakly to moderately correlated systems, whereas it will fail for strongly correlated materials. In the present work, we discuss two important aspects of this approximation: first, the “self-screening error,” which is due to an incorrect treatment of induced exchange, and second, the atomic limit, in which, instead, correlation is directly responsible for the observed problem. Using the example of the removal of a particle from a box, we show that the self-screening error stems from the use of test charge-test charge screening and that it can be corrected by a two-point vertex contribution to the self-energy derived from time-dependent density functional theory (TDDFT). We explain why the addition of a particle, instead, requires the use of a different approximate vertex. This illustrates why the general vertex function, valid both for valence and conduction states, must be a three-point function. Moreover, we show that also the bad performance of GW in the atomic limit is due to the neglect of the vertex in the self-energy; in that case, the TDDFT-derived vertex correction is not sufficient in order to remove the error even qualitatively. We discuss the effects of the self-screening error as well as the atomic limit using GW for the exactly solvable two-site Hubbard model.
Origin of reduction in phonon thermal conductivity of microporous solids
Authors: Hopkins Patrick E. , Rakich Peter T. , Olsson Roy H. , El-kady Ihab F. , Phinney Leslie M.
Published: October 2009

Porous structures have strong tunable size effects due to increased surface area. Size effects on phonon thermal conductivity have been observed in porous materials with periodic voids on the order of microns. This letter explores the origin of this size effect on phonon thermal conductivity observed in periodic microporous membranes. Pore-edge boundary scattering of low frequency phonons explains the temperature trends in the thermal conductivity; further reduction in thermal conductivity is explained by the porosity.
n
-type β-FeSi2/intrinsic-Si/p-type Si heterojunction photodiodes for near-infrared light detection at room temperature
Authors: Shaban Mahmoud , Izumi Shota , Nomoto Keita , Yoshitake Tsuyoshi
Published: October 2009

n -Type β-FeSi2/intrinsic-Si/p-type Si heterojunctions, prepared by facing-targets direct-current sputtering, were evaluated as near-infrared photodetectors. The built-in potential was estimated to be approximately 1 V from capacitance-voltage characteristics. Diodes with a junction area of 0.03 mm2 exhibited a junction capacitance of 4.4 pF at zero bias. At room temperature, the devices exhibited responsivity of 140 mA/W and external quantum efficiency of 13% at a bias voltage of −5 V. The detectivity at zero bias was estimated to be 2.8×109 cm√Hz/W at the wavelength of 1.31 μm. These results indicate their high application potential as near-infrared photodiodes integrated with Si.
Stretching induced Hall current and conductance anisotropy in graphene
Authors: Wright A. R. , Zhang C.
Published: October 2009

We evaluate the effect of stretching on the optical conductance of graphene. It is found that the low energy (Dirac regime) isotropy that leads to the “universal conductance” is lost. More significantly, due to the loss of C3 symmetry, a nonzero Hall conductance emerges for stretching along chiral directions, reaching a maximum at a stretching angle of 45°, and being as high as σ0=e2/4ℏ at van Hove singular point for bond angle changes of about 2°. Our results indicate that the optical properties of graphene can be tuned by a weak mechanical deformation.
Saturation magnetization in supersaturated solid solution of Co–Cu alloy
Authors: Yuasa Motohiro , Kajikawa Kota , Hakamada Masataka , Mabuchi Mamoru
Published: October 2009

The magnetovolume effect has been investigated using a supersaturated solid solution of a Co–19 at. %Cu alloy processed by electrodeposition. The enhanced saturation magnetization of the Co–Cu alloy was attributed to both metastable fcc Co and lattice expansion. The density functional theory using the CASTEP code revealed that an enhanced magnetic moment due to the magnetovolume effect is obtained in fcc Co, but not in hcp Co.
Number sensitive detection and direct imaging of dipolar coupled magnetic nanoparticles by tunnel magnetoresistive sensors
Authors: Albon C. , Weddemann A. , Auge A. , Meißner D. , Rott K. , Jutzi P. , Hütten A.
Published: October 2009

The suitability of magnetic tunnel junctions for the detection of magnetic nanoparticles is related to their scalability onto the nanoscale size regime without a significant loss of sensitivity. Elliptically shaped MgO based tunnel magnetoresistance sensors are used to provide a sharp detection of 14 nm Co nanoparticles. The measured signal is related to the degree of coverage of the sensor area by a nanoparticle layer. Moreover, the nanoparticles magnetostatic interaction on the sensor surface is clearly distinguished by the presence of a coercitive field in the detected signal. Experimentally obtained results are compared to theoretical models.
Influence of dc-bias on phase stability in Mn-doped Na0.5Bi0.5TiO3-5.6 at. %BaTiO3 single crystals
Authors: Ge Wenwei , Cao Hu , Li Jiefang , Viehland D. , Zhang Qinhui , Luo Haosu
Published: October 2009

Mn-doped Na0.5Bi0.5TiO3-5.6 at. %BaTiO3 (Mn:NBT-5.6%BT) single crystals were grown by a top-seeded solution growth method. Tetragonal and rhombohedral phases were found to coexist in the as-grown condition. The dielectric and structural properties were studied as a function of temperature under dc electrical bias. An induced phase stability change from rhombohedral to tetragonal phases occurred under an electric-field applied along the ⟨001⟩ direction.
Placing Power in the Creative City: Governmentalities and Subjectivities in Liberty Village, Toronto
Authors: Catungal John Paul , Leslie Deborah
Published: October 2009

In this paper we analyze the making of Liberty Village as a creative hub in inner-city Toronto. We focus on the role of property developers and the Liberty Village Business Improvement Association in fostering the area's internal economic geography. Drawing on the literature on governmentality, we dissect how the production of a place identity requires both the production of new subjectivities and the exclusion of alternative actors and understandings of organization within the district.
A spatially structured tagging model to estimate movement and fishing mortality rates for the blue shark (Prionace glauca) in the North Atlantic Ocean
Authors: Aires-da-Silva Alexandre M. , Maunder Mark N. , Gallucci Vincent F. , Kohler Nancy E. , Hoey John J.
Published: October 2009

Large numbers of blue sharks are caught as bycatch, and have even become the target species in pelagic longline fisheries in the North Atlantic Ocean. The status of the stock is ambiguous due to the limitations of the fishery-dependent data. This study presents a spatially structured tagging model to estimate blue shark movement and fishing mortality rates in the North Atlantic Ocean. The model uses the blue shark tag-recovery data collected by the United States National Marine Fisheries Service Cooperative Shark Tagging Program (1965–2004). Four major geographical regions (two on each side of the ocean) are assumed. The blue shark fishing mortality rates (F) were found to be heterogeneous across the four regions. While the estimates of F obtained for the western North Atlantic Ocean were historically lower than 0.1 year–1, the F estimates over the most recent decade (1990s) in the eastern side of the ocean are rapidly approaching 0.2 year–1. Because of the particular life-history of the blue shark, these results suggest careful monitoring of the fishery as the juvenile and pregnant female segments of the stock are highly vulnerable to exploitation in the eastern North Atlantic Ocean.
Short-lived dissolved nitrate pulses in a shallow Western Australian coastal lagoon
Authors: Lourey M. J. , Kirkman H.
Published: October 2009

The source of nutrients that sustains abundant benthic primary productivity on Western Australian coastal reef systems is unknown, but it is possible that cycling between organic matter production and remineralisation contributes and may be enhanced by variations in the magnitude of physical forcing. We have used a 5-year nitrate dataset collected at weekly, daily and hourly temporal scales to investigate dynamics and supply mechanisms in Marmion Lagoon, Perth, Western Australia. Nitrate concentrations were variable over short time scales (hours) and formed pulses of elevated nutrient concentrations. On average, nitrate concentrations were highest during the high energy winter period (June to August) and scant wave data (June to August 1984) suggest a general correlation between wave activity and nitrate concentration. While it was not possible to definitively link variations in nitrate to wave forcing, increased energy may have promoted carbon recycling and nitrate release (possibly through abrasion of macroalgae, resuspension of detrital material or enhanced pore water exchange). Rapid uptake suggests that the nitrate pulses observed here may help sustain primary productivity in this shallow high energy environment. High temporal (hourly) variability suggests future surveys must sample at a frequency adequate to isolate long-term temporal trends from short-term background variations.
Site-specific modification of Alzheimer's peptides by cholesterol oxidation products enhances aggregation energetics and neurotoxicity
Authors: Usui Kenji , Hulleman John D. , Paulsson Johan F. , Siegel Sarah J. , Powers Evan T. , Kelly Jeffery W.
Published: October 2009

Accumulation of amyloid β-peptide (Aβ) and tau aggregates, possibly linked to age-associated deficiencies in protein homeostasis, appear to cause Alzheimer's disease. Schiff-base formation between Aβ and the aldehyde-bearing cholesterol oxidation product 3-β-hydroxy-5-oxo-5,6-
seco
cholestan-6-al is known to increase Aβ amyloidogenicity. Here, we synthesized Aβ variants site-specifically modified with the cholesterol aldehyde at Asp-1, Lys-16, or Lys-28, rather than studying mixtures. These distinct modifications have a similar effect on the thermodynamic propensity for aggregation, enabling aggregation at low concentrations. In contrast, the modification site differentially influences the aggregation kinetics; Lys-16-modified Aβ formed amorphous aggregates fastest and at the lowest concentration (within 2 h at a concentration of 20 nM), followed by the Lys-28 and Asp-1 conjugates. Also, the aggregates resulting from Aβ Lys-16 cholesterol aldehyde conjugation were more toxic to primary rat cortical neurons than treatment with unmodified Aβ under identical conditions and at the same concentration. Our results show that Aβ modification by cholesterol derivatives, especially at Lys-16, renders it kinetically and thermodynamically competent to form neurotoxic aggregates at concentrations approaching the physiologic concentration of Aβ.
Peripatetic health-care workers as potential superspreaders
Authors: Temime Laura , Opatowski Lulla , Pannet Yohan , Brun-Buisson Christian , Boëlle Pierre Yves , Guillemot Didier
Published: October 2009

Many nosocomial outbreaks exhibit “superspreading events” in which cross-transmission occurs via a single individual to a large number of patients. We investigated how heterogeneity in Health-Care Worker (HCW) behaviors, especially compliance to hand hygiene, may cause superspreading events. In particular, we compared the superspreading potential of peripatetic (noncohorted) HCWs with that of other HCWs. We developed an agent-based model for hand transmission of a pathogen in a hospital ward. Three HCW profiles were allowed: 2 assigned profiles, one with frequent contacts with a limited number of patients, another with fewer contacts but with more patients; and one peripatetic profile, with a single daily contact with all patients. We used data from the literature on common nosocomial pathogens (
Staphylococcus aureus
,
Enterococci
). The average number of patients colonized over 1 month increases with noncompliance to hand hygiene. Importantly, we show that this increase depends on the profile of noncompliant HCWs; for instance, it remains low for a single noncompliant assigned HCW but can be quite large for a single noncompliant peripatetic HCW. Outbreaks with this single fully noncompliant peripatetic HCW (representing only 4.5% of the staff) are similar to those predicted when all HCWs are noncompliant following 23% of patient contacts. Noncompliant peripatetic HCWs may play a disproportionate role in disseminating pathogens in a hospital ward. Their unique profile makes them potential superspreaders. This suggests that average compliance to hygiene may not be a good indicator of nosocomial risk in real life health care settings with several HCW profiles.
Atomic substitution reveals the structural basis for substrate adenine recognition and removal by adenine DNA glycosylase
Authors: Lee Seongmin , Verdine Gregory L.
Published: October 2009

Adenine DNA glycosylase catalyzes the glycolytic removal of adenine from the promutagenic A·oxoG base pair in DNA. The general features of DNA recognition by an adenine DNA glycosylase,
Bacillus stearothermophilus
MutY, have previously been revealed via the X-ray structure of a catalytically inactive mutant protein bound to an A:oxoG-containing DNA duplex. Although the structure revealed the substrate adenine to be, as expected, extruded from the DNA helix and inserted into an extrahelical active site pocket on the enzyme, the substrate adenine engaged in no direct contacts with active site residues. This feature was paradoxical, because other glycosylases have been observed to engage their substrates primarily through direct contacts. The lack of direct contacts in the case of MutY suggested that either MutY uses a distinctive logic for substrate recognition or that the X-ray structure had captured a noncatalytically competent state in lesion recognition. To gain further insight into this issue, we crystallized wild-type MutY bound to DNA containing a catalytically inactive analog of 2′-deoxyadenosine in which a single 2′-H atom was replaced by fluorine. The structure of this fluorinated lesion-recognition complex (FLRC) reveals the substrate adenine buried more deeply into the active site pocket than in the prior structure and now engaged in multiple direct hydrogen bonding and hydrophobic interactions. This structure appears to capture the catalytically competent state of adenine DNA glycosylases, and it suggests a catalytic mechanism for this class of enzymes, one in which general acid-catalyzed protonation of the nucleobase promotes glycosidic bond cleavage.
Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging
Authors: van Mameren Joost , Gross Peter , Farge Geraldine , Hooijman Pleuni , Modesti Mauro , Falkenberg Maria , Wuite Gijs J. L. , Peterman Erwin J. G.
Published: October 2009

Single-molecule manipulation studies have revealed that double-stranded DNA undergoes a structural transition when subjected to tension. At forces that depend on the attachment geometry of the DNA (65 pN or 110 pN), it elongates ≈1.7-fold and its elastic properties change dramatically. The nature of this overstretched DNA has been under debate. In one model, the DNA cooperatively unwinds, while base pairing remains intact. In a competing model, the hydrogen bonds between base pairs break and two single DNA strands are formed, comparable to thermal DNA melting. Here, we resolve the structural basis of DNA overstretching using a combination of fluorescence microscopy, optical tweezers, and microfluidics. In DNA molecules undergoing the transition, we visualize double- and single-stranded segments using specific fluorescent labels. Our data directly demonstrate that overstretching comprises a gradual conversion from double-stranded to single-stranded DNA, irrespective of the attachment geometry. We found that these conversions favorably initiate from nicks or free DNA ends. These discontinuities in the phosphodiester backbone serve as energetically favorable nucleation points for melting. When both DNA strands are intact and no nicks or free ends are present, the overstretching force increases from 65 to 110 pN and melting initiates throughout the molecule, comparable to thermal melting. These results provide unique insights in the thermodynamics of DNA and DNA-protein interactions.
Nanoparticle-based bio-barcode assay redefines “undetectable” PSA and biochemical recurrence after radical prostatectomy
Authors: Thaxton C. Shad , Elghanian Robert , Thomas Audrey D. , Stoeva Savka I. , Lee Jae-Seung , Smith Norm D. , Schaeffer Anthony J. , Klocker Helmut , Horninger Wolfgang , Bartsch Georg , Mirkin Chad A.
Published: October 2009

We report the development of a previously undescribed gold nanoparticle bio-barcode assay probe for the detection of prostate specific antigen (PSA) at 330 fg/mL, automation of the assay, and the results of a clinical pilot study designed to assess the ability of the assay to detect PSA in the serum of 18 men who have undergone radical prostatectomy for prostate cancer. Due to a lack of sensitivity, available PSA immunoassays are often not capable of detecting PSA in the serum of men after radical prostatectomy. This new bio-barcode PSA assay is ≈300 times more sensitive than commercial immunoassays. Significantly, with the barcode assay, every patient in this cohort had a measurable serum PSA level after radical prostatectomy. Patients were separated into categories based on PSA levels as a function of time. One group of patients showed low levels of PSA with no significant increase with time and did not recur. Others showed, at some point postprostatectomy, rising PSA levels. The majority recurred. Therefore, this new ultrasensitive assay points to significant possible outcomes: (
i
) The ability to tell patients, who have undetectable PSA levels with conventional assays, but detectable and nonrising levels with the barcode assay, that their cancer will not recur. (
ii
) The ability to assign recurrence earlier because of the ability to measure increasing levels of PSA before conventional tools can make such assignments. (
iii
) The ability to use PSA levels that are not detectable with conventional assays to follow the response of patients to adjuvant or salvage therapies.
Reciprocal regulation of Wnt and Gpr177/mouse Wntless is required for embryonic axis formation
Authors: Fu Jiang , Jiang Ming , Mirando Anthony J. , Yu Hsiao-Man Ivy , Hsu Wei
Published: October 2009

Members of the Wnt family are secreted glycoproteins that trigger cellular signals essential for proper development of organisms. Cellular signaling induced by Wnt proteins is involved in diverse developmental processes and human diseases. Previous studies have generated an enormous wealth of knowledge on the events in signal-receiving cells. However, relatively little is known about the making of Wnt in signal-producing cells. Here, we describe that
Gpr177
, the mouse orthologue of
Drosophila Wls
, is expressed during formation of embryonic axes. Embryos with deficient Gpr177 exhibit defects in establishment of the body axis, a phenotype highly reminiscent to the loss of Wnt3. Although many different mammalian Wnt proteins are required for a wide range of developmental processes, the Wnt3 ablation exhibits the earliest developmental abnormality. This suggests that the Gpr177-mediated Wnt production cannot be substituted. As a direct target of Wnt,
Gpr177
is activated by β-catenin and LEF/TCF-dependent transcription. This activation alters the cellular distributions of Gpr177 which binds to Wnt proteins and assists their sorting and secretion in a feedback regulatory mechanism. Our findings demonstrate that the loss of Gpr177 affects Wnt production in the signal-producing cells, leading to alterations of Wnt signaling in the signal-receiving cells. A reciprocal regulation of Wnt and Gpr177 is essential for the patterning of the anterior-posterior axis during mammalian development.
An essential role for RPE-derived soluble VEGF in the maintenance of the choriocapillaris
Authors: Saint-Geniez Magali , Kurihara Tomoki , Sekiyama Eiichi , Maldonado Angel E. , D'Amore Patricia A.
Published: October 2009

Clinical and experimental observations indicate a role for VEGF secreted by the retinal pigment epithelium (RPE) in the maintenance of the choriocapillaris (CC). VEGF in mice is produced as three isoforms, VEGF120, VEGF164, and VEGF188, that differ in their ability to bind heparan sulfate proteoglycan. RPE normally produces the more soluble isoforms, VEGF120 and VEGF164, but virtually no VEGF188, reflecting the fact that molecules secreted by the RPE must diffuse across Bruch's membrane (BrM) to reach the choriocapillaris. To determine the role of RPE-derived soluble VEGF on the choriocapillaris survival, we used mice that produce only VEGF188. VEGF188/188 mice exhibited normal choriocapillaris development. However, beginning at 7 months of age, we observed a progressive degeneration characterized by choriocapillaris atrophy, RPE and BrM abnormalities, culminating in areas of RPE loss and dramatic choroidal remodeling. Increased photoreceptor apoptosis in aged VEGF188/188 mice led to a decline in visual acuity as detected by electroretinogram (ERG). These changes are reminiscent of geographic atrophy (GA) and point to a role for RPE-derived VEGF in the maintenance of the choriocapillaris.
Recent changes in a remote Arctic lake are unique within the past 200,000 years
Authors: Axford Yarrow , Briner Jason P. , Cooke Colin A. , Francis Donna R. , Michelutti Neal , Miller Gifford H. , Smol John P. , Thomas Elizabeth K. , Wilson Cheryl R. , Wolfe Alexander P.
Published: October 2009

The Arctic is currently undergoing dramatic environmental transformations, but it remains largely unknown how these changes compare with long-term natural variability. Here we present a lake sediment sequence from the Canadian Arctic that records warm periods of the past 200,000 years, including the 20th century. This record provides a perspective on recent changes in the Arctic and predates by approximately 80,000 years the oldest stratigraphically intact ice core recovered from the Greenland Ice Sheet. The early Holocene and the warmest part of the Last Interglacial (Marine Isotope Stage or MIS 5e) were the only periods of the past 200,000 years with summer temperatures comparable to or exceeding today's at this site. Paleoecological and geochemical data indicate that the past three interglacial periods were characterized by similar trajectories in temperature, lake biology, and lakewater pH, all of which tracked orbitally-driven solar insolation. In recent decades, however, the study site has deviated from this recurring natural pattern and has entered an environmental regime that is unique within the past 200 millennia.
Experimental determination of the evolvability of a transcription factor
Authors: Maerkl Sebastian J. , Quake Stephen R.
Published: October 2009

Sequence-specific binding of a transcription factor to DNA is the central event in any transcriptional regulatory network. However, relatively little is known about the evolutionary plasticity of transcription factors. For example, the exact functional consequence of an amino acid substitution on the DNA-binding specificity of most transcription factors is currently not predictable. Furthermore, although the major structural families of transcription factors have been identified, the detailed DNA-binding repertoires within most families have not been characterized. We studied the sequence recognition code and evolvability of the basic helix–loop–helix transcription factor family by creating all possible 95 single-point mutations of five DNA-contacting residues of Max, a human helix–loop–helix transcription factor and measured the detailed DNA-binding repertoire of each mutant. Our results show that the sequence-specific repertoire of Max accessible through single-point mutations is extremely limited, and we are able to predict 92% of the naturally occurring diversity at these positions. All naturally occurring basic regions were also found to be accessible through functional intermediates. Finally, we observed a set of amino acids that are functional in vitro but are not found to be used naturally, indicating that functionality alone is not sufficient for selection.