bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved method for rosin and fatty acids in tall oil
Authors: Balder E. E. , Crowell E. P.
Published: June 2007

An analytical procedure is presented for determination of the rosin and fatty acid contents of tall oil products. Rosin acids are determined by titration after selective esterification of the fatty acids at room temperature with anhydrous methanolic hydrochloric acid reagent. The fatty acid content is calculated by difference from acid number and rosin acid determinations. The method presented has smaller sample requirements, shorter analysis time, greater selectivity, and improved precision above 15% rosin acid compared to standard procedures. The standard deviations for the determination of percent rosin and fatty acids have been found to be 0.30 and 0.34, respectively, over the entire concentration range. The reaction mechanism of acid catalyzed esterification is discussed with respect to the reaction rates and selectivity. The esterification variables which were investigated include catalyst concentration, sample size, reaction time, selectivity, and effect of water.
Effect of some isothiocyanates on the hydrogenation of canola oil
Authors: Abraham V. , deMan J. M.
Published: June 2007

Sulfur compounds were added to refined and bleached canola oil before hydrogenation in the form of allyl, heptyl and 2‐phenethyl isothiocyanates, and the effects on hydrogenation rate, solid fat content and percentagetrans fatty acids were determined. The poisoning effect was most pronounced with allyl isothiocyanate and least with phenethyl isothiocyanate. As the amount of added sulfur increased, the hydrogenation rate decreased. Of the three isothiocyanates used, allyl isothiocyanate caused formation of larger amounts oftrans isomers. An increased sulfur level in the oil resulted in increased solid fat content andtrans isomer level. Allyl isothiocyanate also caused formation of larger amounts of solid fat than other isothiocyanates at all levels of sulfur addition.
Determination of oil in sunflowerseeds
Authors: Kochhar S. P. , Rossell J. B.
Published: June 2007

Oil content measurement in sunflowerseeds on an “as is” basis by current official methods is often associated with poor reproducibility. This study shows that the main factor contributing to this poor agreement is the particle size to which seeds are ground. This invariably influences the homogeneity of the bulk ground sample from which subsequent subsamples are taken. It is therefore suggested that oil content determinations on sunflowerseeds should be carried out on seed samples that have been evenly and finely ground, to a particle size not greater than 2.0 mm, in a mechanical mill such as the Ultra‐Centrifugal mill. Other factors investigated were seed composition (free husk, empty husk, crude fiber and seed meats) and structural differences in the seeds by light microscopy.
Evaluation of physicochemical changes in cooking oil during heating
Authors: Yoon Suk Hoo , Kim Sun Ki , Kim Kil Hwan , Kwon Tai Wan , Teah Yau Kun
Published: June 2007

Rice bran oil and double fractionated palm olein (DF palm olein) were heated at 180 C for 50 hr to measure lipid deterioration in the oils. Free fatty acid content of both oils increased during heating; however, iodine value and smoke point decreased. Solid fat contents of both oils were unaffected by heating time. Cloud point of rice bran oil was much lower than that of palm olein. Color of oils changed gradually to dark brown from light yellow with increased heating time. Absolute content of polyunsaturated fatty acid, such as linoleic acid, reduced more than that of monounsaturated fatty acid, such as oleic acid, in both oils. In both oils, iodine value correlated very well with linoleic acid content, with correlation coefficient higher than 0.96.
A convenient method for preparation of monofluorocarboxylic acids
Authors: Watanabe S. , Fujita T. , Sakamoto M. , Endo H. , Kitazume T.
Published: June 2007

Monofluoro esters were prepared by the reaction of hydroxy esters with N,N‐diethyl‐1,1,2,3,3,3‐hexafluoro propylamine (PPDA). Saponification of these monofluoroesters with enzyme (lipase MY) was attempted to give their corresponding monofluorocarboxylic acids in moderate yields.
Autoxidation of ethyl eicosapentaenoate and docosahexaenoate
Authors: Cho Soon‐Yeong , Miyashita Kazuo , Miyazawa Teruo , Fujimoto Kenshiro , Kaneda Takashi
Published: June 2007

The extent of oxidation of ethyl esters of eicosapentaenoic (EPA) and docosahexaenoic acids (DHA) was compared quantitatively with that of ethyl linoleate (Lo) and ethyl linolenate (Ln) by oxygen uptake and formation of conjugated diene, hydroperoxide and secondary oxidation products. EPA and DHA esters were oxidized rapidly even at 5 C in the dark after an induction period of 3–4 days, while the induction periods of Ln and Lo esters were 20 days and more than 60 days, respectively. Oxygen uptake of EPA and DHA esters after the induction period was 5.2 and 8.5 times faster than that of ethyl Ln, respectively. Hydroperoxides of EPA and DHA esters are much less stable than those of ethyl Lo. The peroxide value is not necessarily a good indication of oxidation in these polyenoic acids because a considerable amount of secondary products is formed at the early stage of oxidation. Polymers were found to be major secondary products in these polyenoic esters.
A methyl docosahexaenoate: Its isolation and characterization
Authors: Hammond Earl G. , Lundberg W. O.
Published: June 2007

A methyl docosahexaenoate has been prepared from hog brain phosphatides and its purity established. From its physical and chemical characteristics as well as other considerations, the double bonds, all of which are in thecis configuration, have been tentatively assigned to positions 4, 7, 10, 13, 16, and 19 in the carbon chain.
Catalysis of fat hydrolysis by an acid regenerated cation exchange resin
Authors: Sutton William J. L. , Moore Harold E.
Published: June 2007

An acid regenerated cation exchange resin (Dowex‐50, 200–400 mesh) is an effective catalyst for tallow splitting. The optimum level of catalyst was approximately 3% of the weight of fat. A two‐stage operation for 12 hr. at 100°C. gave fatty acid yields which ranged from 96% to 100% (calculated as % oleic acid).

The Dowex‐50 catalyst was easily recovered after each operation, regenerated with 100 ml. of 4N. hydrochloric acid, and used again in the next operation with no appreciable decrease in catalytic activity.

The original resin can be used in continued efficient tallow splitting operations if the residual resin is regenerated after each complete operation and additional fresh resin is added to make up mechanical loss.
Photoactivation and color formation in antioxidant treated lard
Authors: Dugan {jrJr.} L. R. , Marx Lotte
Published: June 2007

A study has been made of factors causing blue colors in antioxidant treated lards.

The formation of blue‐colored lards or of blue‐black sludges in lard storage tanks is due to reaction of propyl gallate in the antioxidant with iron contamination in the lard.

The solubility of the antioxidant mixture in lard is not a factor in the formation of blue‐colored lard.

A new cause of blue‐colored lard has been discovered. This is a photoactivated blue color resulting from irradiation of antioxidant treated lard. The blue color was developed in lard treated with BHA, propyl gallate, and citric acid only when lecithin was present and the lard was contaminated with iron. The state of oxidation of the lard did not contribute to these colors.
Molecular mechanism of edema formation in nephrotic syndrome: therapeutic implications
Authors: Doucet Alain , Favre Guillaume , Deschênes Georges
Published: June 2007

Sodium retention and edema are common features of nephrotic syndrome that are classically attributed to hypovolemia and activation of the renin–angiotensin–aldosterone system. However, numbers of clinical and experimental findings argue against this underfill theory. In this review we analyze data from the literature in both nephrotic patients and experimental models of nephrotic syndrome that converge to demonstrate that sodium retention is not related to the renin–angiotensin–aldosterone status and that fluid leakage from capillary to the interstitium does not result from an imbalance of Starling forces, but from changes of the intrinsic properties of the capillary endothelial filtration barrier. We also discuss how most recent findings on the cellular and molecular mechanisms of sodium retention has allowed the development of an efficient treatment of edema in nephrotic patients.
Generation of ENU‐Induced Mouse Mutants with Hypocholesterolemia: Novel Tools for Dissecting Plasma Lipoprotein Homeostasis
Authors: Aigner Bernhard , Rathkolb Birgit , Mohr Manuela , Klempt Martina , Hrabé de Angelis Martin , Wolf Eckhard
Published: June 2007

Pathologic plasma lipoprotein cholesterol levels play a key role in the development and pathogenesis of human atherosclerotic cardiovascular diseases. Plasma cholesterol homeostasis is regulated by genetic predispositions and environmental factors. Animal models showing aberrant plasma cholesterol levels are used for the identification and analysis of novel causative genes. Here, we searched for inherited hypocholesterolemia phenotypes in randomly mutant mice which may contribute to the detection of disease protective alleles. In the Munich ENU mouse mutagenesis project, clinical chemistry blood analysis was carried out on more than 15,500 G1 offspring and 230 G3 pedigrees of chemically mutagenized inbred C3H mice to detect dominant and recessive mutations leading to a decreased plasma total cholesterol level. We identified 66 animals consistently showing hypocholesterolemia. Transmission of the altered phenotype to the subsequent generations led to the successful establishment of 14 independent hypocholesterolemic lines. Line‐specific differences were detected by clinical chemistry analysis of plasma HDL cholesterol, LDL cholesterol and triglycerides. Thus, we successfully established a novel panel of ENU‐derived mutant mouse lines for their use in the identification of alleles selectively influencing the plasma cholesterol homeostasis. Such findings may be subsequently used for humans and other species.
Tony Blair’s Vietnam: The Iraq War and the ‘special relationship’ in historical perspective
Authors: DANCHEV ALEX
Published: June 2007

This article examines Tony Blair’s policy and posture on Iraq through the prism of the special relationship in which he was reared. At the same time, it examines his policy and posture on the special relationship through the prism of Iraq. In this context it proposes a Vietnam analogy of a kind, with reference to Blair’s white-hot predecessor Harold Wilson: a curious affinity of fate – disenchantment, disgrace, and moral ruination.
Reconstructing Iraq: merging discourses of security and development
Authors: SOVACOOL BENJAMIN , HALFON SAUL
Published: June 2007

This article argues that reconstruction is an emerging discourse of international politics that merges security and development discourses in powerful and troubling ways. We focus on Iraq as a site for articulating and institutionalising a particular version of reconstruction, uncovering five narratives that constitute Iraqi reconstruction discourse. We conclude by suggesting that reconstruction repackages security and development into a singular, technical, and bureaucratic worldview. This view obscures working and reliable solutions to poverty and instability by treating development as a central justification for war, and war as a promising way to develop a state and society.
Beyond Strauss, lies, and the war in Iraq: Hannah Arendt’s critique of neoconservatism
Authors: OWENS PATRICIA
Published: June 2007

What are we to make of the neoconservative challenge to traditional international thought? Should we content ourselves, as many have done, to return to classical realism in response? Rather than offer another realist assessment of neoconservative foreign policy this article turns to Hannah Arendt. In a very different language, Arendt articulated a critique of the dangers of moralism in the political realm that avoids realist cynicism. She is also better placed to challenge the neoconservative vision of international affairs, ideological conviction, and their relationship to democratic society. Reading Arendt against Leo Strauss suggests that the fundamental problem with neoconservative ideology concerns its understanding of the place of philosophy in the public realm, the relationship between political thought and practice, ideas and action. She suggests why neoconservatives may be experts at selling wars but seem less adept at winning them.
Towards a consequentialist evaluation of security: bringing together the Copenhagen and the Welsh Schools of security studies
Authors: FLOYD RITA
Published: June 2007

This article constitutes an attempted bridge-building between the so-called ‘Copenhagen School’ and the so-called ‘Welsh School’ of security studies. The thesis of communality rests upon an evaluative bifurcation of the concept of securitisation into positive and negative securitisation. In tandem with this lies a bifurcation of the concept of desecuritisation into positive and negative desecuritisation. The two positive concepts are believed to be of equal value, with both trumping over the two negative concepts.

This evaluative strategy of securitisation/desecuritisation, it is hoped will combine the optimistic perception of security by ‘Welsh School’ critical security theorists, with the more pessimistic perception of security associated with the Copenhagen School – particularly with that of Ole Wæver, the originator of securitisation theory. Such a strategy is seen as advantageous for three reasons. First, it is believed that the more unified these critical theories are, the stronger a challenge they can offer to the mainstream of security studies; second, the more united the academy the more adoptable are its theories for policymakers (EU or otherwise) and third the strategy proposed here paves the way for a more evaluative engagement with security on the part of the analyst, allowing for normative – but denying infinite – conceptualisations of security.

In order to show that there are differences between the utility of securitisation and desecuritisation, this article demonstrates the distinctions by way of illustrative examples, all of which are taken from the environmental security sector. By means of this practical application, the article will show that neither securitisation nor desecuritisation are, in and of themselves positive or negative. It is rather the case that the outcome of a securitisation/desecuritisation is always issue dependent – something reflected here in the suggested two-tier structure of securitisation.
Quantitative morphology of rocks at the Mars Pathfinder landing site
Authors: Yingst R. Aileen , Haldemann A. F. C. , Biedermann Kimberly L. , Monhead Aimee M.
Published: June 2007

We adapt and test a standard terrestrial technique of assessing morphology quantitatively for use with sites on Mars based on two‐dimensional equations and particle outlines, whereby images of particles obtained remotely may yield dimensionless, numerical shape and roundness values consistent with previous knowledge of the lithology and sedimentary transport history. Our test site was the particle‐rich Rock Garden at the Mars Pathfinder landing site, a location where the primary geologic processes and lithology have been determined by other means. A total of 575 particles were assessed in terms of size, sphericity, elongation, and roundness; qualitative roundness was determined for 460 particles. Particles are mostly pebble‐ to cobble‐sized and have an average sphericity of 0.75, elongation of 0.63, and relative roundness of 0.083; 69% of particles are subangular or subrounded. Particle sphericity is unimodal, with a size‐sphericity profile matching trends for terrestrial populations of similar lithology and elongations nearly identical to those for particles at Vikings 1 and 2. This matches the predictions for a site with the single overall lithology implied from other analyses. Roundness data indicate one or possibly two particle populations, representing the primary processes that likely affected particle roundness most strongly: impact and catastrophic flooding. Finally, we tested a hypothesis suggesting that darker, smaller, more angular particles comprise a population transported through impact cratering, while larger, less dark, more rounded particles are associated with catastrophic flood transport. The opposite result is seen: larger particles throughout the Rock Garden are more angular than smaller ones.
Modeling storm surge flooding of an urban area with particular reference to modeling uncertainties: A case study of Canvey Island, United Kingdom
Authors: Brown James D. , Spencer Tom , Moeller Iris
Published: June 2007

A coupled storm surge and overland flow model is used to simulate extreme coastal flooding of Canvey Island, a dense urban area located at the mouth of the Thames Estuary, U.K. The flood model is based on a shock‐capturing numerical scheme and resolves the terrain and buildings of the study area with high‐resolution topographic data. Repeat simulation is used to propagate uncertainties in model inputs and parameters through to uncertainties in model outputs, and the main sources of uncertainties are described. The greatest uncertainties originate from the forcing inputs to the flood model, including coastal water levels and sea defense failures, rather than its internal boundaries, such as the model terrain and bottom friction. This is consistent with studies in rural and semideveloped floodplains and reflects a combination of high sensitivity to, and uncertainty in, the forcing inputs. However, other numerical and physical variables introduce significant uncertainties, of which many are specific to, or altered by, the urban floodplain. In particular, model predictions are sensitive to the spatial resolution (Δs) of the numerical grid. This includes the effects of Δs on boundary features (walls, hedges, etc.), which are described in the bed friction coefficient, and on the representation of buildings, which are described in the model terrain. Finally, model predictions are integrated across multiple combinations of breach width and location to explore the “relative” hazards (i.e., spatial and temporal variations in hazard) associated with the floodplain geography.
Interplay between faults and lava flows in construction of the upper oceanic crust: The East Pacific Rise crest 9°25′–9°58′N
Authors: Escartín J. , Soule S. A. , Fornari D. J. , Tivey M. A. , Schouten H. , Perfit M. R.
Published: June 2007

The distribution of faults and fault characteristics along the East Pacific Rise (EPR) crest between 9°25′N and 9°58′N were studied using high‐resolution side‐scan sonar data and near‐bottom bathymetric profiles. The resulting analysis shows important variations in the density of deformational features and tectonic strain estimates at young seafloor relative to older, sediment‐covered seafloor of the same spreading age. We estimate that the expression of tectonic deformation and associated strain on “old” seafloor is ∼5 times greater than that on “young” seafloor, owing to the frequent fault burial by recent lava flows. Thus the unseen, volcanically overprinted tectonic deformation may contribute from 30% to 100% of the ∼300 m of subsidence required to fully build up the extrusive pile (Layer 2A). Many longer lava flows (greater than ∼1 km) dam against inward facing fault scarps. This limits their length at distances of 1–2 km, which are coincident with where the extrusive layer acquires its full thickness. More than 2% of plate separation at the EPR is accommodated by brittle deformation, which consists mainly of inward facing faults (∼70%). Faulting at the EPR crest occurs within the narrow, ∼4 km wide upper crust that behaves as a brittle lid overlying the axial magma chamber. Deformation at greater distances off axis (up to 40 km) is accommodated by flexure of the lithosphere due to thermal subsidence, resulting in ∼50% inward facing faults accommodating ∼50% of the strain. On the basis of observed burial of faults by lava flows and damming of flows by fault scarps, we find that the development of Layer 2A is strongly controlled by low‐relief growth faults that form at the ridge crest and its upper flanks. In turn, those faults have a profound impact on how lava flows are distributed along and across the ridge crest.
Rise and emplacement of magma during horizontal shortening of the brittle crust: Insights from experimental modeling
Authors: Galland Olivier , Cobbold Peter R. , de Bremond d’Ars Jean , Hallot Erwan
Published: June 2007

Magmatic activity tends to concentrate at plate margins. At divergent margins, extensional tectonics provide steep conduits for magma to reach the surface. At rapidly convergent margins, such as the Andes, one might imagine that horizontal compression prevents the rise of magma. Nevertheless, volcanoes are also common. In order to study the mechanisms by which magma rises in a compressional context, we resorted to laboratory experiments, in which a brittle crust was shortened, while magma was intruding. Our model materials were (1) cohesive fine‐grained silica powder, representing brittle crust, and (2) molten low‐viscosity vegetable oil, representing magma. In general, horizontal shortening and injection were coeval but independent processes. Thrust faults accommodated the shortening, while overpressured oil formed hydraulic fractures. In those experiments where there was no shortening, injection resulted in a saucer‐shaped intrusive body. In the other experiments, where there was shortening, oil formed a basal sill, before rising along thrust faults. Once in place, the sill lubricated the base of the model, so that arcuate thrusts formed at the leading edge of a plateau. Uplift of the plateau promoted further intrusion of oil at depth. In general, the pattern of deformation and intrusion depended on the kinematic ratio R between rates of shortening and injection. The lengths of the basal sill and plateau increased with decreasing R. On the basis of these results, we have reexamined two natural examples of magmatic complexes, which were emplaced in compressional tectonic settings, Tromen volcano in Argentina and the Boulder Batholith of Montana.
A laboratory study of longitudinal waves in surfactant films in a water wave tank
Authors: Liu Xinan , Duncan James H. , Korenowski Gerald M. , Kelly Joseph S.
Published: June 2007

The dynamics of longitudinal surface waves in surfactant films in a large wave tank (14.8 m long, 1.2 m wide, and 1.0 m deep) were studied experimentally. Three soluble surfactants (Triton X‐100, sodium dodecyl sulfate, and hemicyanine) were added to the tank water in separated experiments; however, other naturally occurring surfactants were present as well. Since it is exceedingly difficult to control surfactants in large water tanks, these mixed surfactant conditions are probably typical of laboratory‐scale experiments on the effects of surfactants on gravity‐capillary wave phenomena. In the present experiments, longitudinal waves were generated with a Teflon bar that barely touched the water surface and oscillated horizontally in a direction perpendicular to its length. The longitudinal waves were measured with a technique that is based on the phase shift of capillary waves that were generated mechanically with a propagation direction perpendicular to that of the longitudinal waves. The wave number (αL), the phase speed, and the damping coefficient (βL) of the longitudinal waves were obtained for wave frequencies ranging from 0.2 to 1.5 Hz in the various surfactant films. The experimental data agree well with the theoretical dispersion relationship of longitudinal waves, and the fitting of this equation to the experimental data yielded the equilibrium surface elasticity, the surface viscosity, and the surface‐to‐bulk diffusion parameter. For nearly all experimental conditions, βL/αL was greater than 0.414, its value based on theory with the surface viscosity set to zero. It was found that the longitudinal wave dispersion curves intersect the capillary‐gravity wave dispersion curves at frequencies ranging from 2.53 to 3.55 Hz. This intersection point is known to be the frequency of the maximum damping of capillary‐gravity waves.
Statistical modeling of total ozone: Selection of appropriate explanatory variables
Authors: Mäder Jörg A. , Staehelin Johannes , Brunner Dominik , Stahel Werner A. , Wohltmann Ingo , Peter Thomas
Published: June 2007

A set of 44 potential explanatory variables is used for statistical modeling of monthly mean total ozone values of 158 ground‐based stations. A stepwise elimination process leads to zonally optimized multiple regression models, which account for approximately 78% of the variance in total ozone in the tropics, 85% south of 60°S and more than 90% in the three remaining zones while only retaining six explanatory variables in the model. In all regions the dynamics appear to dominate ozone variability, which is primarily described by a proxy specifically designed to describe the effects of short‐term isentropic excursions at different altitude levels and the compression/expansion of air connected to convergence/divergence. The influence of equivalent effective stratospheric chlorine (EESC) is also important in all regions, indicating the significant effects of anthropogenic emissions of ozone depleting substances (ODS). In addition to the dynamics and EESC, the influence of volcanic eruptions, represented by the integrated surface area density of stratospheric aerosols (SAD), has the largest impact on total ozone in northern regions. The results of the analysis are less clear in the Southern Hemisphere where only a few long‐enough ozone time series are available.
Changes in the variability of North Pacific Oscillation around 1975/1976 and its relationship with East Asian winter climate
Authors: Wang Lin , Chen Wen , Huang Ronghui
Published: June 2007

The variability of North Pacific Oscillation (NPO) and the associated atmospheric circulation in the boreal winter are studied with the HadSLP2, the National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR), and the ECMWF 40‐year reanalysis (ERA‐40) data. The results show that the variability of NPO is not stationary with a typical period around 3 years during 1957–1975 and shifting to around 5–6 years after that. Linear correlation and regression analysis indicates that in the winters before 1975 the geopotential height field related to the NPO is characterized by a barotropic north‐south dipole around the Pacific sector, which is the traditional NPO mode. In this subperiod, the El Niño/Southern Oscillation (ENSO) has a dominant influence on the NPO. There is anomalous stationary wave propagation associated with the NPO from the subtropical‐central Pacific to the northern Pacific. And the NPO has no significant relations to the East Asian climate. In the winters after 1975, however, the atmospheric circulation related to the NPO exhibits a circum‐global wave train pattern over the extratropical regions in the Northern Hemisphere. Particularly, the northward wave activity propagation is enhanced over the extratropics of East Asia. The remote forcing from the tropical eastern Pacific sea surface temperature anomalies becomes small. Hence the NPO has a close relationship with the circulation over East Asia during this period.
Interannual variability of the Gulf of Alaska eddy field
Authors: Ladd Carol
Published: June 2007

Regions of high eddy kinetic energy (EKE) in the Gulf of Alaska (GOA), calculated from altimetry data, denote formation regions and translation pathways for eddies. High EKE is observed along the shelf break in winter and spring with lower values in summer and autumn. Three regions of high EKE are examined in detail. In the eastern GOA, particularly high EKE occurred in 1998. In the northwestern GOA, eddies were observed quasi‐annually between 1999 and 2004, but were less frequent prior to that time (or in 2005 and 2006). Eddies northeast of Kodiak Island have been implicated in high offshelf chlorophyll concentrations observed from ocean color satellites. Correlations between EKE and chlorophyll concentration are significant there suggesting that EKE may be valuable for predicting phytoplankton blooms in this region.
Orientation of the reconnection X‐line
Authors: Swisdak M. , Drake J. F.
Published: June 2007

We propose a criterion for identifying the orientation of the X‐line when two regions of plasma with arbitrary densities, temperatures, and magnetic fields undergo reconnection. The X‐line points in the direction that maximizes the (suitably‐defined) Alfvén speed characterizing the reconnection outflow. For many situations a good approximation is that the X‐line bisects the angle formed by the magnetic fields.
Electron energy loss spectra of finite carbon nanotubes
Authors: Chen R. B. , Chang C. P. , Lee C. H. , Lin M. F.
Published: June 2007

The sp3 tight-binding model and the gradient approximation are, respectively, used to calculate electronic states and the loss function of finite carbon nanotubes. The study results show that the loss spectra of finite carbon nanotubes are strongly dependent on the nanotube geometric structure (length, radius, and chiral angle) and the magnetic flux. The prominent peaks at ω<4γ0 (γ0 is the nearest-neighbor overlap integral) mainly result from the π states, while the peaks at ω>4γ0 result from the π+σ states. For ω<4γ0, most loss spectra contain four peaks in the different finite carbon nanotubes (CNTs) systems. The peak energy versus length graph is a monotonous curve for zigzag nanotubes, while the one for armchair nanotubes is oscillatory. Prominent peak energies are almost independent of length for sufficiently long CNTs. These results illustrate the quasi-zero-dimensional character. Moreover, finite armchair CNTs reveal dominating π and π+σ plasmon peaks at ∼2γ0≈6 eV and ∼6.5γ0≈18 eV, respectively. Yet, for finite zigzag CNTs plasmon peaks exist at ∼2.15γ0 and ∼6.6γ0, due to special localized states at the outermost zigzag positions. The predicted loss spectra and the plasmon frequencies could be verified by electron energy loss spectra.
Space charge effects on the active region of a planar organic photodetector
Authors: Agostinelli T. , Caironi M. , Natali D. , Sampietro M. , Biagioni P. , Finazzi M. , Duò L.
Published: June 2007

Planar organic photodetectors represent a simple, cheap, and versatile alternative to devices built in sandwich configuration. The nonuniform electric field distribution in these structures has significant consequences on the extent of the device active region, because photogeneration of free carriers in organic semiconductors is a field-assisted phenomenon. By means of microscopy mapping of the photocurrent in a poly(p-phenylene vinylene) based planar device, we show that due to the deep trapping of photogenerated electrons leading to negative space charge accumulation, exciton dissociation occurs only close to the positively biased electrode. The effect of large leakage currents in defining the device active region is also analyzed and discussed.
Real time in situ ellipsometric and gravimetric monitoring for electrochemistry experiments
Authors: Broch Laurent , Johann Luc , Stein Nicolas , Zimmer Alexandre , Beck Raphaël
Published: June 2007

This work describes a new system using real time spectroscopic ellipsometer with simultaneous electrochemical and electrochemical quartz crystal microbalance (EQCM) measurements. This method is particularly adapted to characterize electrolyte/electrode interfaces during electrochemical and chemical processes in liquid medium. The ellipsometer, based on a rotating compensator Horiba Jobin-Yvon ellipsometer, has been adapted to acquire Ψ-Δ spectra every 25ms on a spectral range fixed from 400to800nm. Measurements with short sampling times are only achievable with a fixed analyzer position (A=45°). Therefore the ellipsometer calibration is extremely important for high precision measurements and we propose a spectroscopic calibration (i.e., determination of the azimuth of elements according to the wavelength) on the whole spectral range. A homemade EQCM was developed to detect mass variations attached to the electrode. This additional instrument provides further information useful for ellipsometric data modeling of complex electrochemical systems. The EQCM measures frequency variations of piezoelectric quartz crystal oscillator working at 5MHz. These frequency variations are linked to mass variations of electrode surface with a precision of 20ngcm−2 every 160ms. Data acquisition has been developed in order to simultaneously record spectroscopic ellipsometry, EQCM, and electrochemical measurements by a single computer. Finally the electrodeposition of bismuth telluride film was monitored by this new in situ experimental setup and the density of electroplated layers was extracted from the optical thickness and EQCM mass.
Development of a parallel-plate avalanche counter to perform conversion electron Mössbauer spectroscopy at low temperatures
Authors: Mantovan Roberto , Fanciulli Marco
Published: June 2007

We describe an experimental setup based on a sealed parallel-plate avalanche counter, which allows conversion electron Mössbauer spectroscopy at temperatures down to 120K. A study of the counting gas performances is carried out in order to find out the appropriate operating conditions. The detector can work in a wide range of pressures and voltages at room and low temperatures, for both iron- and tin-based Mössbauer transitions. An estimation of the gas gain is obtained by using a simple approach, which considers the avalanche gas process in parallel-plate geometry. The gas gain as a function of the filling pressure shows a maximum at room temperature and a monotonic increase at low temperature. The experimental setup has been tested with the determination of the Debye temperature of β-Sn, SnO2, and ε-FeSi.
Ferroelectric and pyroelectric properties of highly (110)-oriented Pb(Zr0.40Ti0.60)O3 thin films grown on Pt∕LaNiO3∕SiO2∕Si substrates
Authors: Guo Yiping , Akai Daisuke , Swada Kzauaki , Ishida Makoto
Published: June 2007

Pb ( Zr 0.4 Ti 0.6 ) O 3 thin films with a thickness of 500nm were spin coated on (110) preferred Pt bottom electrodes using a sol-gel method, in which the (110) preferred Pt bottom electrode was developed by using a (100)-oriented conductive oxide electrode LaNiO3 film as an adhesion layer on a SiO2∕Si substrate. X-ray diffraction analysis and field emission scanning electron microscopy show that the as-grown Pb(Zr0.4Ti0.6)O3 films are highly (110)-oriented with a columnar structure. It indicates that the (110) preferred Pt bottom electrode is effective for growing highly (110)-oriented Pb(Zr0.4Ti0.6)O3 films. The as-grown Pb(Zr0.4Ti0.6)O3 films show excellent dielectric and ferroelectric properties with dielectric constant ε33T∕ε0=1620, loss tangent tanδ=2.1%, spontaneous polarization 2Ps=158μC∕cm2, and remnant polarization 2Pr=92μC∕cm2. Excellent pyroelectric properties are also detected in the (110)-oriented films. At room temperature, the pyroelectric coefficient and the figure of merit for detectivity can reach up to 7.8×10−4Cm−2K−1 and 1.79×10−5Pa−0.5, respectively.
Effective thickness and dielectric constant of interfacial layers of Pt∕Bi3.15Nd0.85Ti3O12∕SrRuO3 capacitors
Authors: Yang H. , Suvorova N. A. , Jain M. , Kang B. S. , Li Y. , Hawley M. E. , Dowden P. C. , DePaula R. F. , Jia Q. X. , Lu C. J.
Published: June 2007

Epitaxial c-axis-oriented Bi3.15Nd0.85Ti3O12 (BNT) thin films with thickness ranging from 150to350nm were deposited on conductive SrRuO3 (SRO) on (001) SrTiO3 substrates by pulsed laser deposition. The top Pt electrode was deposited by sputtering to construct a capacitor Pt/BNT/SRO. The authors have evaluated the effective thickness (ti) and dielectric constant (εi) of interfacial layers at the Pt/BNT and BNT/SRO interfaces based on the optical refractive index of the BNT layer and the capacitance frequency as well as the current-voltage characteristics of the capacitors. Using a series capacitor model, they have found that the dielectric constant of bulk BNT and the ti∕εi ratio are 586 and 1.46nm, respectively. Knowing the optical dielectric constant (εopt) and the product of εoptti of BNT thin films, the authors have estimated that the effective thickness and dielectric constant of the interfacial layers are 20.1nm and 13.7, respectively.
Highly sensitive sensors for alkali metal ions based on complementary-metal-oxide-semiconductor-compatible silicon nanowires
Authors: Zhang Guo-Jun , Agarwal Ajay , Buddharaju Kavitha D. , Singh Navab , Gao Zhiqiang
Published: June 2007

Highly sensitive sensors for alkali metal ions based on complementary-metal-oxide- semiconductor-compatible silicon nanowires (SiNWs) with crown ethers covalently immobilized on their surface are presented. A densely packed organic monolayer terminated with amine groups is introduced to the SiNW surface via hydrosilylation. Amine-modified crown ethers, acting as sensing elements, are then immobilized onto the SiNWs through a cross-linking reaction with the monolayer. The crown ether–functionalized SiNWs recognize Na+ and K+ according to their complexation ability to the crown ethers. The SiNW sensors are highly selective and capable of achieving an ultralow detection limit down to 50nM, over three orders of magnitude lower than that of conventional crown ether–based ion-selective electrodes.
Acute stress increases interstitial fluid amyloid-β via corticotropin-releasing factor and neuronal activity
Authors: Kang Jae-Eun , Cirrito John R. , Dong Hongxin , Csernansky John G. , Holtzman David M.
Published: June 2007

Aggregation of the amyloid-β (Aβ) peptide in the extracellular space of the brain is critical in the pathogenesis of Alzheimer's disease. Aβ is produced by neurons and released into the brain interstitial fluid (ISF), a process regulated by synaptic activity. To determine whether behavioral stressors can regulate ISF Aβ levels, we assessed the effects of chronic and acute stress paradigms in amyloid precursor protein transgenic mice. Isolation stress over 3 months increased Aβ levels by 84%. Similarly, acute restraint stress increased Aβ levels over hours. Exogenous corticotropin-releasing factor (CRF) but not corticosterone mimicked the effects of acute restraint stress. Inhibition of endogenous CRF receptors or neuronal activity blocked the effects of acute stress on Aβ. Thus, behavioral stressors can rapidly increase ISF Aβ through neuronal activity in a CRF-dependent manner, and the results suggest a mechanism by which behavioral stress may affect Alzheimer's disease pathogenesis.
Involvement of host cellular multivesicular body functions in hepatitis B virus budding
Authors: Watanabe Tokiko , Sorensen Ericka M. , Naito Akira , Schott Meghan , Kim Seungtaek , Ahlquist Paul
Published: June 2007

Hepatitis B virus (HBV) is a major human pathogen that chronically infects ≈350 million people, causing liver disease and liver cancer. HBV virions bud into an endoplasmic reticulum (ER)-associated intracellular compartment, but the mechanisms of HBV assembly, budding, and release remain poorly understood. Budding of retroviruses and some other enveloped RNA viruses from plasma membranes requires host functions involved in protein sorting into late endosomal multivesicular bodies (MVBs). To determine whether budding of DNA-containing HBV virions at intracellular membranes also involves MVB functions, we used immunofluorescence to show that, in human hepatoma cells, HBV envelope protein colocalizes with MVB proteins AIP1/ALIX and VPS4B. We also found that a dominant negative (DN) AIP1 mutant inhibited production and/or release of enveloped virions without significant effects on intracellular nucleocapsid formation, whereas DN VPS4B inhibited both nucleocapsid production and budding. By contrast, DN AIP1 and VPS4 had no effect on the efficiency of release of enveloped, nucleocapsid-lacking HBV subviral particles, which are produced in vast excess over virions, and dramatically increased the release of unenveloped, naked nucleocapsids by an apparently nonlytic route. Thus, host MVB functions are required for efficient budding and release of enveloped HBV virions and may be a valuable target for HBV control. Moreover, HBV enveloped virions, enveloped subviral particles, and unenveloped nucleocapsids are all released by distinct pathways with separate host factor requirements.
Parkin-mediated Monoubiquitination of the PDZ Protein PICK1 Regulates the Activity of Acid-sensing Ion Channels
Authors: Joch Monica , Ase Ariel R. , Chen Carol X.-Q. , MacDonald Penny A. , Kontogiannea Maria , Corera Amadou T. , Brice Alexis , Séguéla Philippe , Fon Edward A.
Published: June 2007

Mutations in the parkin gene result in an autosomal recessive juvenile-onset form of Parkinson's disease. As an E3 ubiquitin-ligase, parkin promotes the attachment of ubiquitin onto specific substrate proteins. Defects in the ubiquitination of parkin substrates are therefore believed to lead to neurodegeneration in Parkinson's disease. Here, we identify the PSD-95/Discs-large/Zona Occludens-1 (PDZ) protein PICK1 as a novel parkin substrate. We find that parkin binds PICK1 via a PDZ-mediated interaction, which predominantly promotes PICK1 monoubiquitination rather than polyubiquitination. Consistent with monoubiquitination and recent work implicating parkin in proteasome-independent pathways, parkin does not promote PICK1 degradation. However, parkin regulates the effects of PICK1 on one of its other PDZ partners, the acid-sensing ion channel (ASIC). Overexpression of wild-type, but not PDZ binding– or E3 ubiquitin-ligase–defective parkin abolishes the previously described, protein kinase C-induced, PICK1-dependent potentiation of ASIC2a currents in non-neuronal cells. Conversely, the loss of parkin in hippocampal neurons from parkin knockout mice unmasks prominent potentiation of native ASIC currents, which is normally suppressed by endogenous parkin in wild-type neurons. Given that ASIC channels contribute to excitotoxicity, our work provides a mechanism explaining how defects in parkin-mediated PICK1 monoubiquitination could enhance ASIC activity and thereby promote neurodegeneration in Parkinson's disease.
A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments
Authors: Zhou Yiyong , Cras-Méneur Corentin , Ohsugi Mitsuru , Stormo Gary D. , Permutt M. Alan.
Published: June 2007

Motivation: Currently most of the methods for identifying differentially expressed genes fall into the category of so called single-gene-analysis, performing hypothesis testing on a gene-by-gene basis. In a single-gene-analysis approach, estimating the variability of each gene is required to determine whether a gene is differentially expressed or not. Poor accuracy of variability estimation makes it difficult to identify genes with small fold-changes unless a very large number of replicate experiments are performed.

Results: We propose a method that can avoid the difficult task of estimating variability for each gene, while reliably identifying a group of differentially expressed genes with low false discovery rates, even when the fold-changes are very small. In this article, a new characterization of differentially expressed genes is established based on a theorem about the distribution of ranks of genes sorted by (log) ratios within each array. This characterization of differentially expressed genes based on rank is an example of all-gene-analysis instead of single gene analysis. We apply the method to a cDNA microarray dataset and many low fold-changed genes (as low as 1.3 fold-changes) are reliably identified without carrying out hypothesis testing on a gene-by-gene basis. The false discovery rate is estimated in two different ways reflecting the variability from all the genes without the complications related to multiple hypothesis testing. We also provide some comparisons between our approach and single-gene-analysis based methods.

Contact:  yyzhou@netra.wustl.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Alvira: comparative genomics of viral strains
Authors: Enault François , Fremez Romain , Baranowski Eric , Faraut Thomas
Published: June 2007

Motivation: The Alvira tool is a general purpose multiple sequence alignment viewer with a special emphasis on the comparative analysis of viral genomes. This new tool has been devised specifically to address the problem of the simultaneous analysis of a large number of viral strains. The multiple alignment is embedded in a graph that can be explored at different levels of resolution.

Availability: The Alvira software is available at: http://bioinfo.genopole-toulouse.prd.fr/Alvira

Contact:  fenault@toulouse.inra.fr

Supplementary information: A tutorial is available at Alvira's homepage.
PrPCWD in rectal lymphoid tissue of deer (Odocoileus spp.)
Authors: Wolfe Lisa L. , Spraker Terry R. , González Lorenzo , Dagleish Mark P. , Sirochman Tracey M. , Brown Jeremy C. , Jeffrey Martin , Miller Michael W.
Published: June 2007

The utility of rectal lymphoid tissue sampling for the diagnosis of chronic wasting disease (CWD) infections in mule deer (Odocoileus hemionus) and white-tailed deer (Odocoileus virginianus) was evaluated. CWD-associated prion protein (PrPCWD) deposits were observed in the rectal mucosa from 19 orally inoculated mule deer by 381 days post-inoculation (p.i.); similarly, 45 out of 50 naturally infected mule deer had PrPCWD in their rectal mucosa. In orally inoculated white-tailed deer, the presence of glycine (G) or serine (S) at codon 96 of the native PrP (denoted 96GG, 96GS or 96SS) appeared to influence the temporal patterns of PrPCWD deposition: nine out of 11 infected 96GG individuals had PrPCWD in their rectal mucosa by 342 days p.i., whereas only three out of seven infected 96GS individuals had PrPCWD in their rectal mucosa by 381 days p.i. and none of three 96SS individuals had PrPCWD in their rectal mucosa by 751 days p.i. These findings support further evaluation of rectal mucosa sampling in CWD surveillance.
Genital warts in Burmeister's porpoises: characterization of Phocoena spinipinnis papillomavirus type 1 (PsPV-1) and evidence for a second, distantly related PsPV
Authors: Van Bressem Marie-Françoise , Cassonnet Patricia , Rector Annabel , Desaintes Christian , Van Waerebeek Koen , Alfaro-Shigueto Joanna , Van Ranst Marc , Orth Gérard
Published: June 2007

We identified sequences from two distantly related papillomaviruses in genital warts from two Burmeister's porpoises, including a PV antigen-positive specimen, and characterized Phocoena spinipinnis papillomavirus type 1 (PsPV-1). The PsPV-1 genome comprises 7879 nt and presents unusual features. It lacks an E7, an E8 and a bona fide E5 open reading frame (ORF) and has a large E6 ORF. PsPV-1 L1 ORF showed the highest percentage of nucleotide identity (54–55 %) with human papillomavirus type 5, bovine papillomavirus type 3 (BPV-3) and Tursiops truncatus papillomavirus type 2 (TtPV-2). This warrants the classification of PsPV-1 as the prototype of the genus Omikronpapillomavirus. PsPV-1 clustered with TtPV-2 in the E6 and E1E2 phylogenetic trees and with TtPV-2 and BPV-3 in the L2L1 tree. This supports the hypothesis that PV evolution may not be monophyletic across all genes.