bluuebunny/crossref_metadata_2025 huggingface dataset:
First airborne gravity results over the Thwaites Glacier catchment, West Antarctica
Authors: Diehl Theresa M. , Holt John W. , Blankenship Donald D. , Young Duncan A. , Jordan Tom A. , Ferraccioli Fausto
Published: April 2008

Recent satellite observations of Thwaites Glacier in the Amundsen Sea Embayment, West Antarctica, have shown that the glacier is changing rapidly. The causes of its dynamic behavior are uncertain but are of concern because this glacier has the most negative mass balance of all Antarctic glaciers. To better understand Thwaites Glacier's subglacial setting, we conducted a multi‐instrumented aerogeophysical survey of its catchment and present here the first gravity results. We employed a new gravimeter, and it performed well despite extreme conditions and an unusual survey design. The unleveled free‐air gravity anomalies have a 2.3 mGal RMS error and a 9 km spatial resolution. Despite slightly higher than standard noise levels, the free‐air anomalies correlate well with radar‐derived subglacial topography. The new airborne gravity data assist in interpreting radar‐identified bedrock features and are an ideal basis for future studies of subglacial geology and its control on the dynamics of Thwaites Glacier.
Effects of micromilling on δ18O in biogenic aragonite
Authors: Foster L. C. , Andersson C. , Høie H. , Allison N. , Finch A. A. , Johansen T.
Published: April 2008

Extraction of small aliquots (μg‐mg) from aragonite samples such as corals, sclerosponges, bivalves, and otoliths is required for bulk oxygen isotope analyses. However, aragonite is a metastable polymorph of calcium carbonate that undergoes transformation to calcite, which is the more thermodynamically stable polymorph of CaCO3. This polymorph transformation occurs via heating and/or stress, and such conditions may occur during drilling. During this polymorph transition, exchange with atmospheric or organic C and O is possible. Therefore extracting aliquots during drilling without modification or contamination via isotope exchange is imperative for accurate isotopic analysis. Using a micromill, aliquots were taken from aragonite cod otoliths that had been grown in the laboratory under stable temperature conditions. X‐ray diffraction analysis showed that although 6% of the sample converts to calcite during drilling, there is no significant effect on δ18O.
Twentieth century Antarctic air temperature and snowfall simulations by IPCC climate models
Authors: Monaghan Andrew J. , Bromwich David H. , Schneider David P.
Published: April 2008

We compare new observationally‐based data sets of Antarctic near‐surface air temperature and snowfall accumulation with 20th century simulations from global climate models (GCMs) that support the Intergovernmental Panel on Climate Change Fourth Assessment Report. Annual Antarctic snowfall accumulation trends in the GCMs agree with observations during 1960–1999, and the sensitivity of snowfall accumulation to near‐surface air temperature fluctuations is approximately the same as observed, about 5% K−1. Thus if Antarctic temperatures rise as projected, snowfall increases may partially offset ice sheet mass loss by mitigating an additional 1 mm y−1 of global sea level rise by 2100. However, 20th century (1880–1999) annual Antarctic near‐surface air temperature trends in the GCMs are about 2.5‐to‐5 times larger‐than‐observed, possibly due to the radiative impact of unrealistic increases in water vapor. Resolving the relative contributions of dynamic and radiative forcing on Antarctic temperature variability in GCMs will lead to more robust 21st century projections.
Resonance in Hawaii waters from the 2006 Kuril Islands Tsunami
Authors: Munger Sophie , Cheung Kwok Fai
Published: April 2008

The 2006 Kuril Islands Tsunami, while not destructive to coastal properties, resulted in prolonged oscillations in Hawaii waters. This study examines the oscillation patterns and amplification through reconstruction of the tsunami using a nonlinear shallow‐water model. After validation with water‐level measurements, a Fast Fourier Transform of the computed surface elevation reveals profound oscillation modes at various periods around the Hawaiian Islands. The oscillation at the regional scale consists of standing waves across the island chain and resonance in interconnected channels, embayments, and shallow shelves. Resonance in embayments and standing edge waves dominate the oscillation in coastal waters. The results show strong correlation between bathymetric features and resonance oscillations and identify tsunami hazard areas for planning and emergency management.
Mapping of sea ice production for Antarctic coastal polynyas
Authors: Tamura Takeshi , Ohshima Kay I. , Nihashi Sohey
Published: April 2008

Active sea‐ice production in Antarctic coastal polynyas causes dense water formation, finally leading to Antarctic Bottom Water (AABW) formation. This study gives the first mapping of sea ice production in the Antarctic Ocean, based on heat‐flux calculation with ice thickness data derived from satellite data. The highest ice production occurs in the Ross Ice Shelf Polynya region. The ice production there decreased by ∼30% from the 1990s to the 2000s, which can be one candidate for causing the recent freshening of AABW. The Cape Darnley polynya in East Antarctica is found to be the second highest production area, suggesting a possible AABW formation area. According to our estimation, around 10% of Southern Ocean sea ice is produced in the major Antarctic coastal polynyas. The mapping provides surface heat‐ and salt‐flux conditions in the ice‐covered region, which have not been well understood.
Monsoon surges trigger oceanic eddy formation and propagation in the lee of the Philippine Islands
Authors: Pullen Julie , Doyle James D. , May Paul , Chavanne Cedric , Flament Pierre , Arnone Robert A.
Published: April 2008

Two winter monsoon surge events (northerly and easterly) of January 2005 are captured in a one‐way coupled atmosphere (8 km resolution) and ocean (3 km resolution) simulation of the Philippines region. Intensified wind jets and wakes in the lee of Mindoro and Luzon Islands induce the generation and migration of a pair of counter‐rotating oceanic eddies in the model, with propagation direction related to the orientation of the winds during each of the surges. Features shared by the eddies include size (100–200 km), depth (∼300 m) and propagation speed (0.1–0.15 m s−1 for cyclones). Mean wintertime model wind stress positive (negative) curl coincides with the climatological cyclone (anticyclone) distribution from a prior 8‐year altimetry‐based census of eddies in the southeast quadrant of the South China Sea during the winter monsoon. Moreover, the simulation results agree with contemporaneous satellite and historical in situ data characterizing regional oceanic eddy and atmospheric surface jet properties.
Fingerprinting particle origins according to their size distribution at a UK rural site
Authors: Charron Aurélie , Birmili Wolfram , Harrison Roy M.
Published: April 2008

This paper presents an examination of the source signature or origin signature represented by particle number size distributions and modal diameters measured at a rural receptor site in southern England which receives air from a range of polluted and less polluted origins. At this site, particle number size distributions (11–450 nm) with smaller modal diameters (<50 nm) are measured in clean maritime air masses, while particle number size distributions with larger modal diameters (>50 nm) correspond to anthropogenic emissions from local or more remote activities and long range transport. Nucleation mode and aged‐nucleation mode particles (mainly from 18 to 33 nm) were mostly new particles from nucleation. Accumulation mode particles (90–120 nm) were associated with aged polluted air masses, two thirds of which arrived from continental Europe. Aitken mode particles had different origins with different signatures. Some of them corresponded to local vehicular emissions and in this case the distributions are typically bimodal. Particle number size distributions with the smallest Aitken modal diameters (around 44 nm) corresponded to background particles in westerly maritime air masses; possibly new particles formed upwind. Particle number size distributions with the largest Aitken modal diameters (around 67 nm) were transported from anthropogenic sources that are thought to be mainly within the UK.
Magnetic fabric of sheared till: A strain indicator for evaluating the bed deformation model of glacier flow
Authors: Hooyer Thomas S. , Iverson Neal R. , Lagroix France , Thomason Jason F.
Published: April 2008

Wet‐based portions of ice sheets may move primarily by shearing their till beds, resulting in high sediment fluxes and the development of subglacial landforms. This model of glacier movement, which requires high bed shear strains, can be tested using till microstructural characteristics that evolve during till deformation. Here we examine the development of magnetic fabric using a ring shear device to deform two Wisconsin‐age basal tills to shear strains as high as 70. Hysteresis experiments and the dependence of magnetic susceptibility of these tills on temperature demonstrate that anisotropy of magnetic susceptibility (AMS) develops during shear due to the rotation of primarily magnetite particles that are silt sized or smaller. At moderate shear strains (∼6–25), principal axes of maximum magnetic susceptibility develop a strong fabric (S1 eignevalues of 0.83–0.96), without further strengthening at higher strains. During deformation, directions of maximum susceptibility cluster strongly in the direction of shear and plunge “up‐glacier,” consistent with the behavior of pebbles and sand particles studied in earlier experiments. In contrast, the magnitude of AMS does not vary systematically with strain and is small relative to its variability among samples; this is because most magnetite grains are contained as inclusions in larger particles and hence do not align during shear. Although processes other than pervasive bed deformation may result in strong flow parallel fabrics, AMS fabrics provide a rapid and objective means of identifying basal tills that have not been sheared sufficiently to be compatible with the bed deformation model.
Experimental study of bedrock erosion by granular flows
Authors: Hsu Leslie , Dietrich William E. , Sklar Leonard S.
Published: April 2008

Field studies suggest that bedrock incision by granular flows may be the primary process cutting valleys in steep, unglaciated landscapes. An expression has been proposed for debris flow incision into bedrock which posits that erosion rate depends on stresses due to granular interactions at the snout of debris flows. Here, we explore this idea by conducting laboratory experiments to test the hypothesis that bedrock erosion is related to grain collisional stresses which scale with shear rate and particle size. We placed granular material in a 56‐cm‐diameter rotating drum to explore the relationship between erosion of a synthetic bedrock sample and variables such as grain size, shear rate, water content, and bed strength. Grain collisional stresses are estimated as the inertial stress using the product of the squares of particle size and vertical shear rate. Our uniform granular material consisted of 1‐mm sand and quartzite river gravel with means of 4, 6, or 10 mm. In 67 experimental runs, the eroded depth of the bed sample varied with inertial stresses in the granular flow to a power less than 1.0 and inversely with the bed strength. The flows tended to slip on smooth boundaries, resulting in higher erosion rates than no‐slip cases. We found that lateral wall resistance generated shear across the channel, producing two cells whose widths depended on wall roughness. While the hypothesized inertial stress dependency is supported with these data, wear mechanics needs to account for grain dynamics specifically at the snout and possibly to include lateral shear effects.
Rapid exhumation and mountain building in the Western Alps: Petrology and 40Ar/39Ar geochronology of detritus from Tertiary basins of southeastern France
Authors: Morag Navot , Avigad Dov , Harlavan Yehudit , McWilliams Michael O. , Michard André
Published: April 2008

Tertiary convergence, high‐pressure−low‐temperature (HP‐LT) metamorphism and subsequent exhumation in the internal Western Alps were concurrent with detrital deposition in foreland basins at the external periphery of the orogen. In the present work we have probed the geochronology and chemistry of white mica grains and metamorphic pebbles from the foreland basins of SE France in order to gain additional perspective on exhumation rates and mountain building processes in the internal domain of the Tertiary orogen. Our data indicate that throughout the Tertiary these basins were mainly fed from a relatively low pressure source, dominated by Si‐poor micas yielding pre‐Alpine 40Ar/39Ar ages. Small amounts of detritus composed of high‐pressure minerals and pebbles are first detected in early Oligocene (∼30−32 Ma) strata of the Barrême basin. The 40Ar/39Ar geochronology of phengites from garnet‐blueschist pebbles from these strata yielded 34 ± 3 Ma ages indicating rapid ascent and exposure of HP‐LT rocks in the internal part of the orogen shortly after metamorphism. To explain the preponderance of pre‐Alpine micas alongside the rare presence of Alpine HP‐LT detritus we suggest that the general architecture of the Western Alps, whereby inner HP‐LT metamorphic units are cut off from the SE France basins by a low‐grade lid of Brianconnais back thrusts, was rapidly built in the early Oligocene and did not change significantly since then.
Use of groundwater lifetime expectancy for the performance assessment of a deep geologic radioactive waste repository: 2. Application to a Canadian Shield environment
Authors: Park Y.‐J. , Cornaton F. J. , Normani S. D. , Sykes J. F. , Sudicky E. A.
Published: April 2008

F. J. Cornaton et al. (2008) introduced the concept of lifetime expectancy as a performance measure of the safety of subsurface repositories, on the basis of the travel time for contaminants released at a certain point in the subsurface to reach the biosphere or compliance area. The methodologies are applied to a hypothetical but realistic Canadian Shield crystalline rock environment, which is considered to be one of the most geologically stable areas on Earth. In an approximately 10 × 10 × 1.5 km3 hypothetical study area, up to 1000 major and intermediate fracture zones are generated from surface lineament analyses and subsurface surveys. In the study area, mean and probability density of lifetime expectancy are analyzed with realistic geologic and hydrologic shield settings in order to demonstrate the applicability of the theory and the numerical model for optimally locating a deep subsurface repository for the safe storage of spent nuclear fuel. The results demonstrate that, in general, groundwater lifetime expectancy increases with depth and it is greatest inside major matrix blocks. Various sources and aspects of uncertainty are considered, specifically geometric and hydraulic parameters of permeable fracture zones. Sensitivity analyses indicate that the existence and location of permeable fracture zones and the relationship between fracture zone permeability and depth from ground surface are the most significant factors for lifetime expectancy distribution in such a crystalline rock environment. As a consequence, it is successfully demonstrated that the concept of lifetime expectancy can be applied to siting and performance assessment studies for deep geologic repositories in crystalline fractured rock settings.
Advection, dispersion, and filtration of fine particles within emergent vegetation of the Florida Everglades
Authors: Huang Yong H. , Saiers James E. , Harvey Judson W. , Noe Gregory B. , Mylon Steven
Published: April 2008

The movement of particulate matter within wetland surface waters affects nutrient cycling, contaminant mobility, and the evolution of the wetland landscape. Despite the importance of particle transport in influencing wetland form and function, there are few data sets that illuminate, in a quantitative way, the transport behavior of particulate matter within surface waters containing emergent vegetation. We report observations from experiments on the transport of 1 μm latex microspheres at a wetland field site located in Water Conservation Area 3A of the Florida Everglades. The experiments involved line source injections of particles inside two 4.8‐m‐long surface water flumes constructed within a transition zone between an Eleocharis slough and Cladium jamaicense ridge and within a Cladium jamaicense ridge. We compared the measurements of particle transport to calculations of two‐dimensional advection‐dispersion model that accounted for a linear increase in water velocities with elevation above the ground surface. The results of this analysis revealed that particle spreading by longitudinal and vertical dispersion was substantially greater in the ridge than within the transition zone and that particle capture by aquatic vegetation lowered surface water particle concentrations and, at least for the timescale of our experiments, could be represented as an irreversible, first‐order kinetics process. We found generally good agreement between our field‐based estimates of particle dispersion and water velocity and estimates determined from published theory, suggesting that the advective‐dispersive transport of particulate matter within complex wetland environments can be approximated on the basis of measurable properties of the flow and aquatic vegetation.
Recent changes in subsurface temperature and salinity in the Canary region
Authors: Benítez‐Barrios V. M. , Hernández‐Guerra A. , Vélez‐Belchí P. , Machín F. , Fraile‐Nuez E.
Published: April 2008

Based on hydrographic sections carried out during the last decade in the Canary region at 29° 10′N, we show that there has been a statistically significant rise in temperature and salinity on isobars between 1500 and 2300 db. The maximum increase, found at 1600 db, is occurring at a rate of 0.29°C and 0.047 per decade. Isobaric change decomposition into changes on neutral surfaces and changes due to the vertical displacement of the isoneutrals was performed. Results reveal that the lower part of North Atlantic Central Water (NACW) cooled and freshened on neutral surfaces, suggesting changes in the freshwater fluxes at the outcropping region. However, the signal in deep waters (1500–2300 db) was principally due to a downward displacement of the isoneutrals, although water mass modification is observed in the range of Mediterranean Water (MW) influence.
Fast processes in liquid metal foams investigated by high-speed synchrotron x-ray microradioscopy
Authors: García-Moreno F. , Rack A. , Helfen L. , Baumbach T. , Zabler S. , Babcsán N. , Banhart J. , Martin T. , Ponchut C. , Di Michiel M.
Published: April 2008

Rupture of an individual film in an evolving liquid metal foam is investigated by means of high-speed x-ray radioscopy using white synchrotron radiation. At a frame rate of 5000frames∕s, the rupture event is spread over three to four images. The images show that the remnants of the rupturing film are pulled into the surrounding plateau borders in 600±100μs which conforms well with a liquid movement governed by inertia and not by viscosity. Within one order of magnitude, the viscosity of the liquid involved must be similar to the viscosity of pure liquid aluminium.
Electrical hysteresis of the Ti0.25Al0.75Ox dielectric films after high-temperature treatment
Authors: Shi Lei , Xia Yidong , Yin Kuibo , Liu Zhiguo
Published: April 2008

The primary goal of this work is to investigate the electrical hysteresis of dielectric pseudobinary Ti0.25Al0.75Ox films after high-temperature treatment. The Ti0.25Al0.75Ox films show electrical hysteresis in the C-V measurements after high-temperature treatment. The C-V curves shifting to positive flatband voltage indicate the existence of negative fixed charges in the films. By virtue of high-resolution transmission electron microscopy, it is deduced that the films include several nanosized crystals regions, which are attributed to the hexagonal unreacted Al2O3 and orthorhombic solid state reaction product TiAl2O5 after high-temperature treatment. While the annealing treatment is up to 900°C, the preferable crystal direction is the direction perpendicular to the c axis in the orthorhombic TiAl2O5 lattice.
Energy transfer from semiconductor nanocrystal monolayers to metal surfaces revealed by time-resolved photoluminescence spectroscopy
Authors: Ueda Akihiro , Tayagaki Takeshi , Kanemitsu Yoshihiko
Published: April 2008

We studied photoluminescence (PL) and energy transfer dynamics in CdSe nanocrystal (NC) assembled monolayers on Au surfaces. The close-packed CdSe NC monolayers were fabricated using the Langmuir–Blodgett method on spin-coated inert polymer films on rough-surface Au substrates. The PL intensity and PL decay time were dependent on the distance between the CdSe NCs and Au surfaces. These observations indicate that the metal-semiconductor distance and the luminescence-energy dependences of the energy transfer rate can be understood in terms of the Coulomb interaction between excitons in NCs and plasmons on the Au surfaces.
Multiferroic Pb(Fe0.66W0.33)0.80Ti0.20O3 thin films: A room-temperature relaxor ferroelectric and weak ferromagnetic
Authors: Kumar Ashok , Rivera I. , Katiyar R. S. , Scott J. F.
Published: April 2008

We report the synthesis of single-phase Pb(Fe0.66W0.33)0.80Ti0.20O3 thin films by chemical solution deposition techniques on Pt∕Ti∕SiO2∕Si(100) substrates. At room temperature it showed relaxor behavior up to 50kHz frequency and almost linear dielectric constant for higher frequency. The dielectric diffusivity (γ=1.89) calculated from modified Curie-Weiss laws and nonlinear Vogel-Fulcher fitting implies relaxor characteristics of the films. Capacitance variation as function of applied field showed perfect “butterfly loops” for frequency (>10kHZ) at room temperature and for a full range of experimental frequencies near the freezing temperature (∼240K). Magnetization versus applied magnetic field displayed weak ferromagnetic properties.
Photoluminescence from highly excited AlN epitaxial layers
Authors: Yamada Yoichi , Choi Kihyun , Shin Seungho , Murotani Hideaki , Taguchi Tsunemasa , Okada Narihito , Amano Hiroshi
Published: April 2008

Excitonic optical properties of AlN epitaxial layers have been studied by means of photoluminescence and optical reflectance spectroscopies. The binding energy of free excitons was estimated to be 57meV on the basis of the energy separation between the n=1 ground and n=2 excited states. In addition, the luminescence line due to radiative recombination of biexcitons was observed under high density excitation. The energy separation between free-exciton luminescence and biexciton luminescence was 19meV, which corresponded to the binding energy of biexcitons. Therefore, the ratio of the biexciton binding energy to the exciton binding energy was approximately 0.33.
Unified retention model for localized charge trapping nonvolatile memory device
Authors: Shapira Asia , Shur Yael , Shacham-Diamand Yosi , Shappir Assaf , Eitan Boaz
Published: April 2008

Retention after cycling in an NROM nonvolatile memory cell is investigated. Electrical characterizations combined with two-dimensional simulations were employed. By combining subthreshold current characterizations with gate-induced drain leakage measurements, the retention loss mechanisms are quantified and differentiated. A unified retention model for the NROM technology is proposed, incorporating both lateral charge transport in the nitride layer and hot carrier-induced interface-states formation. The fabrication conditions in the various studies reported in the literature and the resultant impact on interface-states formation are most likely the cause of the formally nonresolved debate regarding the origin of retention loss in NROM technology.
Effect of chain length on low temperature gold-gold bonding by self-assembled monolayers
Authors: Ang X. F. , Chen Z. , Wong C. C. , Wei J.
Published: April 2008

The tensile strength of thermocompression gold joints formed with prior surface coatings of alkanethiol self-assembled monolayers (SAMs) depends on the chain length (n) of the SAM. Enhancement of bond strength is most significant at n=6 while no improvement can be achieved using octadecanethiol (n=18). These contrasting behaviors can be interpreted as a consequence of two dominant roles of alkanethiols that govern the bonding phenomenon, namely, the passivation of gold surfaces and the ease of mechanical and/or thermal displacement.
Theoretical and experimental depth-resolved cathodoluminescence microanalysis of excitonic emission from ZnO epilayers
Authors: Ye J. D. , Zhao H. , Liu W. , Gu S. L. , Zhang R. , Zheng Y. D. , Tan S. T. , Sun X. W. , Lo G. Q. , Teo K. L.
Published: April 2008

In this letter, the excitonic emissions from ZnO epilayers were studied by depth-resolved cathodoluminescence (CL) microanalysis. An excellent agreement between the redshift of the experimental depth-resolved CL emission and theoretically simulated values was observed, which clearly identified its origin to be the strong internal absorption in ZnO epilayer. Moreover, the rigorous Monte Carlo simulated CL generation profiles with the correction of self-absorption exhibit the reasonable correspondence with the measured CL intensities. The intensity discrepancies for low and high excitation cases have been interpreted by the occurrence of the excess carrier nonradiative recombination on the surface space charge layer and the exciton nonradiative quenching processing by defects or structural disorders near the interface of ZnO and sapphire.
Preparation and characterization of thermoconductive polymer nanocomposite with branched alumina nanofiber
Authors: Shimazaki Yuzuru , Hojo Fusao , Takezawa Yoshitaka
Published: April 2008

A highly thermoconductive resin with branched filler is reported. The filler was fabricated by calcination of aluminium isopropoxide adsorbed onto paper filter (cellulose fibers). Scanning electron microscopy and x-ray diffraction measurement demonstrated that the filler consists of α-alumina nanofiber with a branched structure. The thermal conductivity of the filler-resin nanocomposite was two to five times larger than that predicted by the well-known Bruggeman equation, which postulates the composite with spherical filler in the matrix. The branched shape of the α-alumina nanofiber increased the probability of formation of phonon paths with lower thermal resistance, leading to the high thermal conductivity of the nanocomposite.
First-principles calculations of structural, electronic and magnetic properties of SeNiO3
Authors: Cao Y. L. , Cai M. Q. , Yang G. W.
Published: April 2008

First-principles calculations on the structural, electronic, and magnetic properties of the distorted perovskite SeNiO3 show that the G-type antiferromagnetic structure with the insulating ground state that has about 3.77eV band gap is more stable than other possible configurations. The hybridizations of Se–O and Ni–O cause the spin magnetic moment to reduce to 1.86μB in comparison with 2μB of the Ni2+3d8 configuration. The similarity between the orbital-resolved densities of Ni 3d states is attributed to the unusual structure of SeNiO3 and the covalent bond of the Ni–O.
Band alignments and defect levels in Si–HfO2 gate stacks: Oxygen vacancy and Fermi-level pinning
Authors: Broqvist Peter , Alkauskas Audrius , Pasquarello Alfredo
Published: April 2008

The determination of band alignments and defect levels is demonstrated for the technologically relevant Si–SiO2–HfO2 gate stack. The proposed scheme, which combines first-principles molecular dynamics for model generation and hybrid density functionals for electronic-structure calculations, yields band offsets in close agreement with experiment. Charge transition and pinning levels associated with oxygen vacancies are aligned with respect to the silicon band edges. The vacancies are shown to preferentially reside in the amorphous transition layer, consistent with experimental observations of Fermi-level pinning.
Trends in the hydrology of the western US bear the imprint of manmade climate change
Authors: Levi Barbara Goss
Published: April 2008

Water managers may no longer be safe in assuming that resources will remain within their historical range of uncertainty.
Interferometry data challenge prevailing view of wave propagation in the cochlea
Authors: Wilson Mark
Published: April 2008

Nonlinear amplification of sound in the inner ear generates distortion that leaks out through the eardrum. But how those waves travel backward along the cochlear spiral remains unsettled.
Cosmic sound waves rule
Authors: Eisenstein Daniel J. , Bennett Charles L.
Published: April 2008

In the microwave background and the distribution of galaxies, relic imprints of primordial sound waves have contributed to an extraordinarily detailed history of the cosmos. And they provide yardsticks for resolving a great mystery.
Chemistry on the computer
Authors: Head-Gordon Martin , Artacho Emilio
Published: April 2008

Although exact descriptions of the quantum mechanics of molecules are computationally intractable, chemists and physicists have devised approximations that are efficient enough to be practical and accurate enough to be useful.
Final Bush R&D budget again boosts physical sciences; takes parting shot at earmarks
Authors: Kramer David
Published: April 2008

For the third year, President Bush’s American Competitiveness Initiative proposes big increases for NSF, the Department of Energy, and NIST. Funding for most other agencies would rise modestly.
Crystal structure and functional analysis of tetracenomycin ARO/CYC: Implications for cyclization specificity of aromatic polyketides
Authors: Ames Brian Douglas , Korman Tyler Paz , Zhang Wenjun , Smith Peter , Vu Thanh , Tang Yi , Tsai Shiou-Chuan
Published: April 2008

Polyketides are a class of natural products with highly diverse chemical structures and pharmaceutical activities. Polyketide cyclization, promoted by the aromatase/cyclase (ARO/CYC), helps diversify aromatic polyketides. How the ARO/CYC promotes highly specific cyclization is not well understood because of the lack of a first-ring ARO/CYC structure. The 1.9 Å crystal structure of Tcm ARO/CYC reveals that the enzyme belongs to the Bet v1-like superfamily (or STAR domain family) with a helix–grip fold, and contains a highly conserved interior pocket. Docking, mutagenesis, and an
in vivo
assay show that the size, shape, and composition of the pocket are important to orient and specifically fold the polyketide chain for C9-C14 first-ring and C7-C16 second-ring cyclizations. Two pocket residues, R69 and Y35, were found to be essential for promoting first- and second-ring cyclization specificity. Different pocket residue mutations affected the polyketide product distribution. A mechanism is proposed based on the structure-mutation-docking results. These results strongly suggest that the regiospecific cyclizations of the first two rings and subsequent aromatizations take place in the interior pocket. The chemical insights gleaned from this work pave the foundation toward defining the molecular rules for the ARO/CYC cyclization specificity, whose rational control will be important for future endeavors in the engineered biosynthesis of novel anticancer and antibiotic aromatic polyketides.
ASPicDB: A database resource for alternative splicing analysis
Authors: Castrignanò T. , D’Antonio M. , Anselmo A. , Carrabino D. , D’Onorio De Meo A. , D’Erchia A. M. , Licciulli F. , Mangiulli M. , Mignone F. , Pavesi G. , Picardi E. , Riva A. , Rizzi R. , Bonizzoni P. , Pesole G.
Published: April 2008

Motivation: Alternative splicing has recently emerged as a key mechanism responsible for the expansion of transcriptome and proteome complexity in human and other organisms. Although several online resources devoted to alternative splicing analysis are available they may suffer from limitations related both to the computational methodologies adopted and to the extent of the annotations they provide that prevent the full exploitation of the available data. Furthermore, current resources provide limited query and download facilities.

Results: ASPicDB is a database designed to provide access to reliable annotations of the alternative splicing pattern of human genes and to the functional annotation of predicted splicing isoforms. Splice-site detection and full-length transcript modeling have been carried out by a genome-wide application of the ASPic algorithm, based on the multiple alignments of gene-related transcripts (typically a Unigene cluster) to the genomic sequence, a strategy that greatly improves prediction accuracy compared to methods based on independent and progressive alignments.

Enhanced query and download facilities for annotations and sequences allow users to select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation.

ASPicDB, which is regularly updated on a monthly basis, also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST sequences and their library source annotation.

Availability:  www.caspur.it/ASPicDB

Contact:  graziano.pesole@biologia.uniba.it

Supplementary information: Supplementary data are available at Bioinformatics online.
GeneTrack—a genomic data processing and visualization framework
Authors: Albert Istvan , Wachi Shinichiro , Jiang Cizhong , Pugh B. Franklin
Published: April 2008

Motivation: High-throughput ‘ChIP-chip’ and ‘ChIP-seq’ methodologies generate sufficiently large data sets that analysis poses significant informatics challenges, particularly for research groups with modest computational support. To address this challenge, we devised a software platform for storing, analyzing and visualizing high resolution genome-wide binding data. GeneTrack automates several steps of a typical data processing pipeline, including smoothing and peak detection, and facilitates dissemination of the results via the web. Our software is freely available via the Google Project Hosting environment at http://genetrack.googlecode.com

Contact:  iual@psu.edu
‘De nouveaux rythmes’: The Free Verse of Laforgue's ‘Solo de Lune’
Authors: Holmes Anne
Published: April 2008

This article considers Laforgue's ‘Solo de lune’ in the light of the Symbolists' claim that their free verse was inspired by music. After referring to the views of two contemporary poets on the subject (that Laforgue's free verse was psychologically rather than musically determined) and outlining Laforgue's position with regard to music and his counter-claim, his practice is examined in two areas: first, ‘Solo de lune’'s double narrative and consequently contrapuntal structure, alternating free verse with an approximate ‘quatrain populaire’; second, the use of other musical features which work against the random nature of free verse (parallelism, modulation, innovative phonetic repetition). The article argues that Laforgue's musical aspirations influence both the structure and the detail of the text. Finally, Laforgue's interest in connecting the three art forms — music, Impressionist painting, and liberated verse — and his awareness of a parallel modernity, are briefly illustrated.
La Filiation inversée: Annie Ernaux et le ‘corps glorieux’
Authors: Fort Pierre-Louis
Published: April 2008

Cet article s'intéresse à façon dont la filiation est remise en perspective dans l'œuvre d'Annie Ernaux. Plus précisément centré sur
Une femme
, le texte que l'auteur a consacré à sa mère disparue, il montre comment la filiation s'y trouve inversée, la fille devenant la mère de sa propre mère. L'analyse étudie ainsi cette redistribution des rôles et en dégage les enjeux. Elle insiste sur l'omniprésence corporelle de la mère dans le récit avant de montrer, au moyen d'une lecture précise du texte (que soutient une interrogation du paratexte et une lecture attentive de la Bible) par quels processus Ernaux parvient à créer le ‘corps glorieux’ de sa mère.
La Jouissance de la vérité ou le plaisir tragique selon le Chancelier d'Aguesseau
Authors: Brillaud Jérôme
Published: April 2008

Le Chancelier d'Aguesseau, architecte du code civil, était aussi homme de lettres. En réponse à un discours de facture aristotélicienne sur la tragédie prononcé par Valincour, il compose des remarques sur la nature du plaisir tragique qui se situent en marge des théories contemporaines. Nous nous proposons ainsi d'étudier les
Remarques
sur la tragédie de d'Aguesseau en regard des textes de Fontenelle et de Dubos qui abordent également la question du plaisir tragique. L'originalité du texte de d'Aguesseau se situe dans une nouvelle conception du plaisir tragique entendu comme un accès à la vérité signifiée lors de l'émotion produite par la tragédie. La mise en échec momentanée du jugement lors de l'émotion esthétique autorise le surgissement d'une vérité morale provisionnelle. Le plaisir tragique, selon l'hypothèse de d'Aguesseau, consisterait en une ‘jouissance de la vérité’ ressentie lors de la représentation des tragédies.
School-based indicators of tuna population status
Authors: Dell James T. , Hobday Alistair J.
Published: April 2008

Dell, J. T. and Hobday, A. J. 2008. School-based indicators of tuna population status. – ICES Journal of Marine Science, 65: 612–622. Theory and limited observation suggest that fish schools consist of more individuals of similar size when populations are large than when they are small. The hypothesis that population size might be indicated by school structure is tested for southern bluefin tuna (SBT), a commercially important large pelagic species, which has undergone an estimated 60% reduction in juvenile biomass since 1960. Fish size data are used to determine whether there have been changes in schooling behaviour that can be used as simple indicators of abundance. During tagging studies, juvenile SBT are removed sequentially from a school, measured, tagged, and released. These sequential size measurements are used here to describe school composition from different years in two locations using simple school metrics (including mean fish size, variance in size, and mean difference in size between sequential fish). Trends were significant in most metrics over the 40-year period analysed, and were inversely related to independent estimates of population size. Simple school metrics are cost-efficient and easily interpreted by stakeholders. Monitoring population trends in near real time through school composition metrics may indicate further decline or recovery of SBT and, therefore, assist future management of tuna and other schooling species.
Post-Transcriptional Gene Silencing in the Root System of the Actinorhizal Tree Allocasuarina verticillata
Authors: Gherbi Hassen , Nambiar-Veetil Mathish , Zhong Chonglu , Félix Jessy , Autran Daphné , Girardin Raphaël , Vaissayre Virginie , Auguy Florence , Bogusz Didier , Franche Claudine
Published: April 2008

In recent years, RNA interference has been exploited as a tool for investigating gene function in plants. We tested the potential of double-stranded RNA interference technology for silencing a transgene in the actinorhizal tree Allocasuarina verticillata. The approach was undertaken using stably transformed shoots expressing the β-glucuronidase (GUS) gene under the control of the constitutive promoter 35S; the shoots were further transformed with the Agrobacterium rhizogenes A4RS containing hairpin RNA (hpRNA) directed toward the GUS gene, and driven by the 35S promoter. The silencing and control vectors contained the reporter gene of the green fluorescent protein (GFP), thus allowing a screening of GUS-silenced composite plantlets for autofluorescence. With this rapid procedure, histochemical data established that the reporter gene was strongly silenced in both fluorescent roots and actinorhizal nodules. Fluorometric data further established that the level of GUS silencing was usually greater than 90% in the hairy roots containing the hairpin GUS sequences. We found that the silencing process of the reporter gene did not spread to the aerial part of the composite A. verticillata plants. Real-time quantitative polymerase chain reaction showed that GUS mRNAs were substantially reduced in roots and, thereby, confirmed the knock-down of the GUS transgene in the GFP+ hairy roots. The approach described here will provide a versatile tool for the rapid assessment of symbiotically related host genes in actinorhizal plants of the Casuarinaceae family.
api, A Novel Medicago truncatula Symbiotic Mutant Impaired in Nodule Primordium Invasion
Authors: Teillet Alice , Garcia Joseph , de Billy Françoise , Gherardi Michèle , Huguet Thierry , Barker David G. , de Carvalho-Niebel Fernanda , Journet Etienne-Pascal
Published: April 2008

Genetic approaches have proved to be extremely useful in dissecting the complex nitrogen-fixing Rhizobium–legume endosymbiotic association. Here we describe a novel Medicago truncatula mutant called api, whose primary phenotype is the blockage of rhizobial infection just prior to nodule primordium invasion, leading to the formation of large infection pockets within the cortex of noninvaded root outgrowths. The mutant api originally was identified as a double symbiotic mutant associated with a new allele (nip-3) of the NIP/LATD gene, following the screening of an ethylmethane sulphonate–mutagenized population. Detailed characterization of the segregating single api mutant showed that rhizobial infection is also defective at the earlier stage of infection thread (IT) initiation in root hairs, as well as later during IT growth in the small percentage of nodules which overcome the primordium invasion block. Neither modulating ethylene biosynthesis (with L-α-(2-aminoethoxyvinylglycine or 1-aminocyclopropane-1-carboxylic acid) nor reducing ethylene sensitivity in a skl genetic background alters the basic api phenotype, suggesting that API function is not closely linked to ethylene metabolism or signaling. Genetic mapping places the API gene on the upper arm of the M. truncatula linkage group 4, and epistasis analyses show that API functions downstream of BIT1/ERN1 and LIN and upstream of NIP/LATD and the DNF genes.
Citrate Uptake into Pectobacterium atrosepticum Is Critical for Bacterial Virulence
Authors: Urbany Claude , Neuhaus H. Ekkehard
Published: April 2008

To analyze whether metabolite import into Pectobacterium atrosepticum cells affects bacterial virulence, we investigated the function of a carrier which exhibits significant structural homology to characterized carboxylic-acid transport proteins. The corresponding gene, ECA3984, previously annotated as coding for a Na+/sulphate carrier, in fact encodes a highly specific citrate transporter (Cit1) which is energized by the proton-motive force. Expression of the cit1 gene is stimulated by the presence of citrate in the growth medium and is substantial during growth of P. atrosepticum on potato tuber tissue. Infection of tuber tissue with P. atrosepticum leads to reduced citrate levels. P. atrosepticum insertion mutants, lacking the functional Cit1 protein, did not grow in medium containing citrate as the sole carbon source, showed a substantially reduced ability to macerate potato tuber tissue, and did not provoke reduced citrate levels in the plant tissue upon infection. We propose that citrate uptake into P. atrosepticum is critical for full bacterial virulence.
Two Xanthomonas Extracellular Polygalacturonases, PghAxc and PghBxc, Are Regulated by Type III Secretion Regulators HrpX and HrpG and Are Required for Virulence
Authors: Wang Lifeng , Rong Wei , He Chaozu
Published: April 2008

Xanthomonas campestris pv. campestris, the causal agent of black rot disease, produces a suite of extracellular cell-wall degrading enzymes (CWDE) that are involved in bacterial virulence. Polygalacturonase (PG) is an important CWDE and functions to degrade the pectic layers of plant cell walls. Although previous studies have documented the virulence functions of PG in Erwinia and Ralstonia species, the regulation of PG genes still needs to be elucidated. In this study, we identified two novel PG genes (pghAxc and pghBxc) encoding functional PG from X. campestris pv. campestris 8004. The expressions of these two PG genes are regulated by the type III secretion regulators HrpX and HrpG and the global regulator Clp. These PG genes could be efficiently induced in planta and were required for the full virulence of X. campestris pv. campestris to Arabidopsis. In addition, these PG were confirmed to be secreted via the type II secretion system in an Xps-dependent manner.
Oxalic Acid Is an Elicitor of Plant Programmed Cell Death during Sclerotinia sclerotiorum Disease Development
Authors: Kim Kyoung Su , Min Ji-Young , Dickman Martin B.
Published: April 2008

Accumulating evidence supports the idea that necrotrophic plant pathogens interact with their hosts by controlling cell death. Sclerotinia sclerotiorum is a necrotrophic ascomycete fungus with a broad host range (>400 species). Previously, we established that oxalic acid (OA) is an important pathogenicity determinant of this fungus. In this report, we describe a mechanism by which oxalate contributes to the pathogenic success of this fungus; namely, that OA induces a programmed cell death (PCD) response in plant tissue that is required for disease development. This response exhibits features associated with mammalian apoptosis, including DNA laddering and TUNEL reactive cells. Fungal mutants deficient in OA production are nonpathogenic, and apoptotic-like characteristics are not observed following plant inoculation. The induction of PCD by OA is independent of the pH-reducing abilities of this organic acid, which is required for sclerotial development. Moreover, oxalate also induces increased reactive oxygen species (ROS) levels in the plant, which correlate to PCD. When ROS induction is inhibited, apoptotic-like cell death induced by OA does not occur. Taken together, we show that Sclerotinia spp.-secreted OA is an elicitor of PCD in plants and is responsible for induction of apoptotic-like features in the plant during disease development. This PCD is essential for fungal pathogenicity and involves ROS. Thus, OA appears to function by triggering in the plant pathways responsible for PCD. Further, OA secretion by Sclerotinia spp. is not directly toxic but, more subtly, may function as a signaling molecule.
Evidence for Transcriptional and Post-Translational Regulation of Sucrose Synthase in Pea Nodules by the Cellular Redox State
Authors: Marino Daniel , Hohnjec Natalija , Küster Helge , Moran Jose F. , González Esther M. , Arrese-Igor Cesar
Published: April 2008

Nitrogen fixation (NF) in legume nodules is very sensitive to environmental constraints. Nodule sucrose synthase (SS; EC 2.4.1.13) has been suggested to play a crucial role in those circumstances because its downregulation leads to an impaired glycolytic carbon flux and, therefore, a depletion of carbon substrates for bacteroids. In the present study, the likelihood of SS being regulated by oxidative signaling has been addressed by the in vivo supply of paraquat (PQ) to nodulated pea plants and the in vitro effects of oxidizing and reducing agents on nodule SS. PQ produced cellular redox imbalance leading to an inhibition of NF. This was preceded by the downregulation of SS gene expression, protein content, and activity. In vitro, oxidizing agents were able to inhibit SS activity and this inhibition was completely reversed by the addition of dithiothreitol. The overall results are consistent with a regulation model of nodule SS exerted by the cellular redox state at both the transcriptional and post-translational levels. The importance of such mechanisms for the regulation of NF in response to environmental stresses are discussed.