bluuebunny/crossref_metadata_2025 huggingface dataset:
Instability of an oscillatory fluid layer with insoluble surfactants
Authors: GAO PENG , LU XI-YUN
Published: January 2008

The linear stability of an infinite fluid layer with a deformable free surface covered by an insoluble surfactant and bounded below by a horizontal rigid plate oscillating in its own plane is studied based on the Floquet theory. The differential system governing the stability problem for perturbations of arbitrary wavenumbers is solved numerically by a Chebyshev collocation method. Stability boundaries are obtained in a wide range of amplitude and frequency of the modulation as well as surfactant elasticity. Results show that the presence of the surfactant may significantly stabilize (destabilize) the flow by raising (lowering) the critical Reynolds number associated with the onset of instability. The effect of the surfactant plays a stabilizing role for small surfactant elasticity and a destabilizing one for relatively large surfactant elasticity. The destabilizing effect of the surfactant on the stability of flows with a zero-shear surface is found for the first time. The disturbance modes in the form of travelling waves may be induced by the surfactant and dominate the instability of the flow.
Modulational instabilities of surface plasmons on metallic plasma surfaces with nanoparticles
Authors: SHUKLA P. K. , STENFLO L.
Published: January 2008

The nonlinear coupling between high-frequency surface plasmons (SPs) and low-frequency ion oscillations on metallic plasma surfaces with charged nanoparticles is considered. It is shown that a finite-amplitude SP wave is modulationally unstable against the excitation of non-resonant ion oscillations. The growth rates and thresholds of the modulational instabilities are presented.
Nature and Nurture on Imperial China's Frontiers
Authors: PERDUE PETER C.
Published: January 2008

Ecologies of production and state classifications shaped Chinese imperial frontier policies. In Chinese classical debates about the effect of environment on human character, the dominant view held that all peoples could become civilised, but a dissenting view held that barbarians could never change their ways. Nomadic pastoralists likewise debated whether to adopt certain Han cultural practices or reject them. Chinese dynasties often accepted diversity, but at certain times tried to eliminate difference by persuasion or by force. Three cases illustrate these processes during the Qing period: the relationship between Manchus and Mongols, Qing policies towards aboriginal peoples and the settlement of Taiwan, and Qing policies towards southwestern mountain peoples. In each case, policies came out of the interaction of ethnic categorization, views on cultural transformation and frontier environments. When Qing rulers lost the ability to recognise such cultural distinctions, they lost a key to the endurance of the empire.
An Approximation by Lacunary Sequence of Vectors
Authors: DUBICKAS ARTŪRAS
Published: January 2008

Let $(t_k)_{k=0}^{\infty}$ be a sequence of real numbers satisfying $t_0 \ne 0$ and $|t_{k+1}| \geq (1+1/M) |t_{k}|$ for each k ≥ 0, where M ≥ 1 is a fixed number. We prove that, for any sequence of real numbers $(\xi_k)_{k=0}^{\infty}$, there is a real number ξ such that $\|t_k \xi-\xi_k\|>1/(80M \log(28M))$ for each k ≥ 0. Here, $\|x\|$ denotes the distance from $x \in \R$ to the nearest integer. This is a corollary derived from our main theorem, which is a more general matrix version of this statement with explicit constants.
CURRENCY AND CREDIT IN MEDIEVAL JAPAN
Authors: Sakurai Eiji
Published: January 2008

In contrast to the currency issued for use in ancient and early modern Japan, a feature of the currency of that country's medieval period was that the Japanese state did not mint its own coinage but rather imported the entirety of its supply of copper coins from China. An economy based on Chinese coins therefore lasted for 650 years, from the middle of the twelfth century, through the upheavals of the sixteenth century, down to the seventeenth century when the Tokugawa Bakufu once again minted coins. This article outlines the situation of currency and its specific features during this period, paying particular attention to the trend towards the use of credit, in such forms as bills of exchange and promissory notes. In addition, it points out that the medieval Japanese state had absolutely no motivation, either financially or geopolitically, to issue its own currency.
ASPECTS OF CHINESE LEGAL CULTURE – THE ARTICULATION OF WRITTEN LAW, STATE, AND SOCIETY: A REVIEW (PART TWO). PRIVATE LAW AND PRIVATE LAWYERS: A DISCUSSION ON THE “FIELDS” OF LAW
Authors: Bourgon Jérôme
Published: January 2008

The International Journal of Asian Studies has published four seminal articles by Japanese scholars of the history of Chinese law (2004–2007). In the first part of his review and analysis of the series (see IJAS 4:2, 2007), Jérôme Bourgon dealt in the main with the work of Shigeo Nakamura and Osamu Takamizawa. In the present part he concludes his discussion with an examination of the remaining articles, “The Nature of Social Agreements (yue) in the Legal Order of Ming and Qing China” by Hiroaki Terada and “Litigation Masters and the Litigation System of Ming and Qing China” by Susumu Fuma.
Numerical predictability experiments of cross‐shore sandbar migration
Authors: Ruessink B. G. , Kuriyama Y.
Published: January 2008

Surf zone sandbars, common features along the world's sandy coastlines, continuously change their position in response to time‐variable offshore wave conditions. Process‐based predictions of cross‐shore sandbar migration, relevant to the understanding of autonomous and artificially altered evolution of beaches, are intrinsically imprecise because of uncertainty in the model equations and, potentially, the sensitive dependence on the initial bathymetry. However, the magnitude of the resulting predictability limit and its dominant source are unknown. Here we show that cross‐shore sandbar migration on the time scale of years is deterministically forced rather than deterministically chaotic, and that the unpredictability of sandbar migration results primarily from model inadequacy during major wave events. Because the unpredictability of sandbar migration is related to the stochastic nature of the forcing, the predictability limit is not a fixed value but depends on the timing of the wave event. We anticipate that detailed experiments to understand nearshore evolution from the underlying first principles will eventually pay off by extending the range of plausible simulated behavior and, consequently, will increase our ability to understand and predict how coasts may respond to changing climate.
Did Tsunami‐Launched Gravity Waves Trigger Ionospheric Turbulence over Arecibo?
Authors: Lee M. C. , Pradipta R. , Burke W. J. , Labno A. , Burton L. M. , Cohen J. A. , Dorfman S. E. , Coster A. J. , Sulzer M. P. , Kuo S. P.
Published: January 2008

We report on measurements of ionospheric plasma dynamics conducted at the Arecibo Observatory between 20:00 and 24:00 local time (LT) on December 25 and 26, 2004 using the 430 MHz incoherent scatter radar (ISR). For interpretive purposes these measurements are supported by data from two nearby ionosondes and Global Positioning System (GPS) satellites. The ISR detected different ionospheric behaviors during the vertical‐transmission periods on the consecutive, magnetically quiet nights. On the night of December 25 the ionosphere descended smoothly and spread F signatures faded. For about two hours on the following evening the bottomside ionosphere rose by ∼50 km, inducing plasma irregularities and intense spread F. Alternating cycles of bottom‐side plasma rising and falling persisted through the remainder of the experiments. We postulate that this sinusoidal behavior is a response to gravity waves propagating above Puerto Rico. Nearly simultaneous data from two nearby stations show that GPS signals were modified by variations in total electron content (TEC) indicating the presence of traveling ionospheric disturbances (TIDs). The December 26 experiments were conducted about a day after an MW = 9.2 earthquake launched tsunami waves first across the Indian, then into the Atlantic and Pacific Oceans. We suggest that coupling at the tsunami sea‐air interface launched gravity waves that propagated for great distances beneath the mesopause. GPS data recorded TEC variation in Asia, Europe, and the Caribbean, suggesting that TIDs were induced on a global scale at the wake of tsunami‐launched gravity waves. Energy from imperfectly ducted gravity waves leaked into the ionosphere, partially over Puerto Rico. The wind‐velocity field of these gravity waves caused local ionospheric plasma to rise, seeding bottomside irregularities via the generalized Rayleigh‐Taylor instability.
Quantifying transient mantle convective uplift: An example from the Faroe‐Shetland basin
Authors: Champion M. E. Shaw , White N. J. , Jones S. M. , Lovell J. P. B.
Published: January 2008

The Icelandic mantle plume generated maximum uplift in early Paleogene times. The Faroe‐Shetland basin, which fringes the North Atlantic margin of Europe, was close to the center of early Paleogene Icelandic plume activity. Three‐dimensional seismic reflection data from the Faroe‐Shetland basin reveal sedimentary geometries that allow a phase of transient uplift to be accurately reconstructed and quantified. Close to the Paleocene/Eocene boundary (circa 56 Ma), rapid uplift resulted in fluvial incision into marine sediments. This unconformity was buried by nonmarine sediments, recording the decay of transient uplift. Relief on the unconformity was ∼550 m, constraining the minimum amount of surface uplift. Some 60 m of this uplift can be attributed to the isostatic response to erosional unloading. Tectonic uplift of over 490 m peaked and decayed within 3 Ma. Rates of water‐loaded tectonic subsidence following peak uplift are several times greater than maximum expected postrift subsidence rates. The amplitude and duration of this transient effect is best explained by a mantle convective phenomenon. We suggest that a region of hot plume material flowed laterally beneath the lithosphere, producing transient uplift which decayed when plume material was advected farther away. Our analysis suggests that under certain circumstances, stratigraphic records can yield valuable quantitative information about aspects of mantle convective circulation.
Antibody diversification by somatic mutation: from Burnet onwards
Authors: Neuberger Michael S
Published: January 2008

The clonal selection theory proposed by Burnet required a genetic process, for which there was then no precedent, which randomizes the region of the gene(s) responsible for the specification of γ‐globulin molecules. Work over the subsequent half‐century substantiated Burnet's speculation, revealing two distinct novel genetic processes. During early development (when Burnet first thought the randomization took place) programmed gene segment rearrangement catalysed by the RAG1/RAG2 recombinase generates a substantial diversity of immunoglobulin molecules (the primary repertoire). Somatic hypermutation (triggered by the activation‐induced deaminase (AID) DNA deaminase) then occurs following antigen encounter in man and mouse, yielding a secondary repertoire. This hypermutation allows both limitless diversification as well as maturation of the antibody response by a process of somatic evolution akin to that envisioned by Burnet in later formulations of the clonal selection theory. AID‐triggered antigen receptor diversification probably arose earlier in evolution than RAG‐mediated repertoire generation. Here I trace our insights into the molecular mechanism antibody somatic mutation from when it was first proposed through to our current understanding of how it is triggered by targeted deamination of deoxycytidine residues in immunoglobulin gene DNA.
On the interpretation of continuous wave electron spin resonance spectra of tempo-palmitate in 5-cyanobiphenyl
Authors: Zerbetto Mirco , Polimeno Antonino , Cimino Paola , Barone Vincenzo
Published: January 2008

Electron spin resonance (ESR) measurements are highly informative on the dynamic behavior of molecules, which is of fundamental importance to understand their stability, biological functions and activities, and catalytic action. The wealth of dynamic information which can be extracted from a continuous wave electron spin resonance (cw-ESR) spectrum can be inferred by a basic theoretical approach defined within the stochastic Liouville equation formalism, i.e., the direct inclusion of motional dynamics in the form of stochastic (Fokker-Planck/diffusive) operators in the super Hamiltonian Ĥ governing the time evolution of the system. Modeling requires the characterization of magnetic parameters (e.g., hyperfine and Zeeman tensors) and the calculation of ESR observables in terms of spectral densities. The magnetic observables can be pursued by the employment of density functional theory which is apt, provided that hybrid functionals are employed, for the accurate computation of structural properties of molecular systems. Recently, an ab initio integrated computational approach to the in silico interpretation of cw-ESR spectra of multilabeled systems in isotropic fluids has been discussed. In this work we present the extension to the case of nematic liquid crystalline environments by performing simulations of the ESR spectra of the prototypical nitroxide probe 4-(hexadecanoyloxy)-2,2,6,6-tetramethylpiperidine-1-oxy in isotropic and nematic phases of 5-cyanobiphenyl. We first discuss the basic ingredients of the integrated approach, i.e., (1) determination of geometric and local magnetic parameters by quantum-mechanical calculations, taking into account the solvent and, when needed, the vibrational averaging contributions; (2) numerical solution of a stochastic Liouville equation in the presence of diffusive rotational dynamics, based on (3) parameterization of diffusion rotational tensor provided by a hydrodynamic model. Next we present simulated spectra with minimal resorting to fitting procedures, proving that the combination of sensitive ESR spectroscopy and sophisticated modeling can be highly helpful in providing three-dimensional structural and dynamic information on molecular systems in anisotropic environments.
Model for reversible nanoparticle assembly in a polymer matrix
Authors: Rahedi Andrew J. , Douglas Jack F. , Starr Francis W.
Published: January 2008

The clustering of nanoparticles (NPs) in solutions and polymer melts depends sensitively on the strength and directionality of the NP interactions involved, as well as the molecular geometry and interactions of the dispersing fluids. Since clustering can strongly influence the properties of polymer-NP materials, we aim to better elucidate the mechanism of reversible self-assembly of highly symmetric NPs into clusters under equilibrium conditions. Our results are based on molecular dynamics simulations of icosahedral NP with a long-ranged interaction intended to mimic the polymer-mediated interactions of a polymer-melt matrix. To distinguish effects of polymer-mediated interactions from bare NP interactions, we compare the NP assembly in our coarse-grained model to the case where the NP interactions are purely short ranged. For the “control” case of NPs with short-ranged interactions and no polymer matrix, we find that the particles exhibit ordinary phase separation. By incorporating physically plausible long-ranged interactions, we suppress phase separation and qualitatively reproduce the thermally reversible cluster formation found previously in computations for NPs with short-ranged interactions in an explicit polymer-melt matrix. We further characterize the assembly process by evaluating the cluster properties and the location of the self-assembly transition. Our findings are consistent with a theoretical model for equilibrium clustering when the particle association is subject to a constraint. In particular, the density dependence of the average cluster mass exhibits a linear concentration dependence, in contrast to the square root dependence found in freely associating systems. The coarse-grained model we use to simulate NP in a polymer matrix shares many features of potentials used to model colloidal systems. The model should be practically valuable for exploring factors that control the dispersion of NP in polymer matrices where explicit simulation of the polymer matrix is too time consuming.
Stabilization of resonance states by an asymptotic Coulomb potential
Authors: Adamson S. , Kharlampidi D. , Dementiev A.
Published: January 2008

The capability of using stabilization method with the asymptotic Coulomb potential for accurate resonance state parameter calculations is investigated for the one-dimensional model problem with a single open channel. It is shown that the replacement of the potential box conditions by the quantization with asymptotic Coulomb potential does not yield the significant errors in energy and width of resonances if the additional mathematical conditions are correctly taken into account. Analytical results are confirmed by the numerical calculations.
The OH− anion acting as an acid
Authors: Huang Lulu , Massa Lou , Bernal Ivan , Karle Jerome
Published: January 2008

In the crystalline state, the OH− anion is shown to be capable of acting as a base or as an acid with respect to waters of crystallization to which it is linked by hydrogen bonds. We examined the OH− anion in three crystalline samples and studied its behavior using quantum mechanics. Four quantum mechanical approximations were employed (HF, B3LYP, SVWN, and MP2) to obtain the relative stability of isomers of the H3O2− molecule in the three crystals considered. In one crystal state (LICQIX), the H3O2− anion corresponds to a geometry in which OH− acts as an acid, but not so as a free molecule. The free anion H3O2− has two qualitatively different structures. In one structure, the hydrogen bond is long, while in the other structure, the hydrogen bond is shorter and the hydrogen atom lies at an equal distance between donor and acceptor oxygen atoms.
Growth of resistive instabilities in E×B plasma discharge simulations
Authors: Fernandez E. , Scharfe M. K. , Thomas C. A. , Gascon N. , Cappelli M. A.
Published: January 2008

Two-dimensional hybrid numerical simulations of E×B discharges used in Hall thruster propulsion point to the presence of strong fluctuations attributable to resistive instabilities in the frequency range of f≈0.1–10MHz and the wavenumber range of λ−1≈10–500m−1. Analytical analyses confirm that these resistive modes are of the convective type, become increasingly unstable at low electron mobility, and are particularly intense at high voltage. The simulations, which model cross-field electron flow via an experimentally measured mobility, exhibit large fluctuation power in a region corresponding to a strong electron transport barrier. The analysis gives an electron mobility (μe) -dependent growth rate (γ) scaling as γ∼μe−1∕2. The predicted phase velocity of these waves is close to the ion velocity, somewhat lower than that seen in the simulations. Including the electron pressure contribution lowers the growth rate at high frequencies, and introduces a phase velocity that is shifted by ± the ion acoustic speed for the stable and unstable branch, respectively. Surprisingly, the phase velocity of the strong disturbances at high frequency seen in the simulations is found to be in agreement with that of the initially stable branch. Finite ionization/particle wall recombination does not change the overall conclusions at high frequencies. However, at lower f or larger λ, the growth rate of the instability is dominated by the ionization rate, and the disturbances are better described as “ionization” instabilities. The transition/competition between ionization, electron pressure, and resistive behavior gives rise to a “quiescent frequency band” where the growth rate is found to be small, consistent with what is seen in the numerical experiments. While simple linear analysis captures much of the observed simulation behavior, comparison with limited experimental data at low frequency suggests that other effects, in particular azimuthal dynamics, are very important, and further motivate extending the hybrid simulation models to three dimensions.
Thermodiffusion in nanofluids under different gravity conditions
Authors: Savino Raffaele , Paterna Diego
Published: January 2008

A convective transport model is developed to study the role of thermal diffusion, or the Ludwig–Soret effect, in nanofluid systems with temperature gradients. The study deals with a fluid suspension of nanoparticles enclosed between two differentially heated horizontal, relatively closely spaced plates (Bénard configuration). An order-of-magnitude analysis is performed to identify the relevant parameters of the problem. Three-dimensional simulations are performed taking into account different conditions, including normal or microgravity conditions, gravity orientation, and positive or negative Soret effect. Different modes of convective instabilities are shown to be present in the system, which are associated with the gravity force and the density differences induced by concentration gradients. The characteristic flow patterns and instability developments are in agreement with the experimental findings obtained by independent investigators on colloidal suspensions. The onset of instabilities, their characteristic time scales, and flow patterns corresponding with different geometrical configurations, gravity levels, and gravity orientation are shown.
Dependence of high order harmonics intensity on laser focal spot position in preformed plasma plumes
Authors: Singhal H. , Ganeev R. , Naik P. A. , Arora V. , Chakravarty U. , Gupta P. D.
Published: January 2008

The dependence of the high-order harmonic intensity on the laser focal spot position in laser produced plasma plumes is experimentally studied. High order harmonics up to the 59th order (λ∼13.5 nm) were generated by focusing 48 fs laser pulses from a Ti:sapphire laser system in silver plasma plume produced using 300 ps uncompressed laser radiation as the prepulse. The intensity of harmonics nearly vanished when the best focus was located in the plume center, whereas it peaked on either side with unequal intensity. The focal spot position corresponding to the peak harmonic intensity moved away from the plume center for higher order harmonics. The results are explained in terms of the variation of phase mismatch between the driving laser beam and harmonics radiation produced, relativistic drift of electrons, and defocusing effect due to radial ionization gradient in the plasma for different focal spot positions.
Transport of parallel momentum by collisionless drift wave turbulence
Authors: Diamond P. H. , McDevitt C. J. , Gürcan Ö. D. , Hahm T. S. , Naulin V.
Published: January 2008

This paper presents a novel, unified approach to the theory of turbulent transport of parallel momentum by collisionless drift waves. The physics of resonant and nonresonant off-diagonal contributions to the momentum flux is emphasized, and collisionless momentum exchange between waves and particles is accounted for. Two related momentum conservation theorems are derived. These relate the resonant particle momentum flux, the wave momentum flux, and the refractive force. A perturbative calculation, in the spirit of Chapman–Enskog theory, is used to obtain the wave momentum flux, which contributes significantly to the residual stress. A general equation for mean k∥ (⟨k∥⟩) is derived and used to develop a generalized theory of symmetry breaking. The resonant particle momentum flux is calculated, and pinch and residual stress effects are identified. The implications of the theory for intrinsic rotation and momentum transport bifurcations are discussed.
Influence of (Ni81Fe19)100−xCrx seed layer on structure and magnetic properties of NiFe/PtMn bilayers
Authors: An Yukai , Liu Jiwen , Ma Yongchang
Published: January 2008

Influence of (Ni81Fe19)100−xCrx seed layer on structure and magnetic properties of NiFe/PtMn bilayers was systemically investigated by magnetic measurements and x-ray diffraction. The results indicated that the pinning field Hex of NiFe/PtMn bilayers has a strong correlation with the Cr content of (Ni81Fe19)100−xCrx seed layer, which can effectively influence grain size, crystal texture, and L10 ordering phase transformation of PtMn. When the Cr content is 40%, PtMn shows strong (111) texture and large grain size, but the L10 ordering phase transformation is weak after annealing, which resulting in a low pinning field Hex. When the Cr content is 34% and 50%, PtMn has weak (111) texture and small grain size, but these are in favor of the L10 ordering phase transformation after annealing, resulting in a high pinning field Hex.
Electrical characteristics of layered palladium alkanethiolates by conducting atomic force microscopy
Authors: John Neena Susan , Pati S. K. , Kulkarni G. U.
Published: January 2008

Current-voltage measurements on individual Pd(II) alkanethiolate nanostructures of varying bilayer thicknesses (hexyl to hexadecyl) employing conducting atomic force microscopy have shown the presence of a low current region near zero bias, the width of which increases with the bilayer thickness. The resistance in this region varies exponentially with the bilayer thickness with a low decay parameter value of 0.2±0.04Å−1 indicating a long-range nonresonant tunneling through the alkyl chains. The changeover from low current to high current with increasing bias is accompanied by a negative differential resistance feature, which arises due to Pd–S charge transfer.
Electrical conductivity of thermoresponsive shape-memory polymer with embedded micron sized Ni powder chains
Authors: Leng J. S. , Lan X. , Liu Y. J. , Du S. Y. , Huang W. M. , Liu N. , Phee S. J. , Yuan Q.
Published: January 2008

The electrical resistivity of a thermoresponsive polyurethane shape-memory polymer (SMP) filled with micron sized Ni powders is investigated in this letter. We show that, by forming conductive Ni chains under a weak static magnetic field (0.03T), the electrical conductivity of the SMP composite in the chain direction can be improved significantly, which makes it more suitable for Joule heat induced shape recovery. In addition, Ni chains reinforce the SMP significantly but their influence on the glass transition temperature is about the same as that of the randomly distributed Ni powders.
Climate forcing from the transport sectors
Authors: Fuglestvedt Jan , Berntsen Terje , Myhre Gunnar , Rypdal Kristin , Skeie Ragnhild Bieltvedt
Published: January 2008

Although the transport sector is responsible for a large and growing share of global emissions affecting climate, its overall contribution has not been quantified. We provide a comprehensive analysis of radiative forcing from the road transport, shipping, aviation, and rail subsectors, using both past- and forward-looking perspectives. We find that, since preindustrial times, transport has contributed ≈15% and 31% of the total man-made CO
2
and O
3
forcing, respectively. A forward-looking perspective shows that the current emissions from transport are responsible for ≈16% of the integrated net forcing over 100 years from all current man-made emissions. The dominating contributor to positive forcing (warming) is CO
2
, followed by tropospheric O
3
. By subsector, road transport is the largest contributor to warming. The transport sector also exerts cooling through reduced methane lifetime and atmospheric aerosol effects. Shipping causes net cooling, except on future time scales of several centuries. Much of the forcing from transport comes from emissions not covered by the Kyoto Protocol.
Net energy of cellulosic ethanol from switchgrass
Authors: Schmer M. R. , Vogel K. P. , Mitchell R. B. , Perrin R. K.
Published: January 2008

Perennial herbaceous plants such as switchgrass (
Panicum virgatum
L.) are being evaluated as cellulosic bioenergy crops. Two major concerns have been the net energy efficiency and economic feasibility of switchgrass and similar crops. All previous energy analyses have been based on data from research plots (<5 m
2
) and estimated inputs. We managed switchgrass as a biomass energy crop in field trials of 3–9 ha (1 ha = 10,000 m
2
) on marginal cropland on 10 farms across a wide precipitation and temperature gradient in the midcontinental U.S. to determine net energy and economic costs based on known farm inputs and harvested yields. In this report, we summarize the agricultural energy input costs, biomass yield, estimated ethanol output, greenhouse gas emissions, and net energy results. Annual biomass yields of established fields averaged 5.2 -11.1 Mg·ha
−1
with a resulting average estimated net energy yield (NEY) of 60 GJ·ha
−1
·y
−1
. Switchgrass produced 540% more renewable than nonrenewable energy consumed. Switchgrass monocultures managed for high yield produced 93% more biomass yield and an equivalent estimated NEY than previous estimates from human-made prairies that received low agricultural inputs. Estimated average greenhouse gas (GHG) emissions from cellulosic ethanol derived from switchgrass were 94% lower than estimated GHG from gasoline. This is a baseline study that represents the genetic material and agronomic technology available for switchgrass production in 2000 and 2001, when the fields were planted. Improved genetics and agronomics may further enhance energy sustainability and biofuel yield of switchgrass.
Signaling networks assembled by oncogenic EGFR and c-Met
Authors: Guo Ailan , Villén Judit , Kornhauser Jon , Lee Kimberly A. , Stokes Matthew P. , Rikova Klarisa , Possemato Anthony , Nardone Julie , Innocenti Gregory , Wetzel Randall , Wang Yi , MacNeill Joan , Mitchell Jeffrey , Gygi Steven P. , Rush John , Polakiewicz Roberto D. , Comb Michael J.
Published: January 2008

A major question regarding the sensitivity of solid tumors to targeted kinase inhibitors is why some tumors respond and others do not. The observation that many tumors express EGF receptor (EGFR), yet only a small subset with EGFR-activating mutations respond clinically to EGFR inhibitors (EGFRIs), suggests that responsive tumors uniquely depend on EGFR signaling for their survival. The nature of this dependence is not understood. Here, we investigate dependence on EGFR signaling by comparing non-small-cell lung cancer cell lines driven by EGFR-activating mutations and genomic amplifications using a global proteomic analysis of phospho-tyrosine signaling. We identify an extensive receptor tyrosine kinase signaling network established in cells expressing mutated and activated EGFR or expressing amplified c-Met. We show that in drug sensitive cells the targeted tyrosine kinase drives other RTKs and an extensive network of downstream signaling that collapse with drug treatment. Comparison of the signaling networks in EGFR and c-Met-dependent cells identify a “core network” of ≈50 proteins that participate in pathways mediating drug response.
Interactions between the direct and indirect effects of predators determine life history evolution in a killifish
Authors: Walsh Matthew R. , Reznick David N.
Published: January 2008

The ecological impacts of the indirect effects of predators are well established, but the evolutionary consequences are unknown. Predators often decrease prey density, which indirectly increases the resources available to surviving prey. This ecological effect could provide a link to evolution because it is generally assumed that resource availability influences life history evolution. Yet, predictions from theory that consider food availability are inconsistent, and evidence for an important role of resources in shaping life history evolution is absent. We compared life history traits in a Trinidadian killifish,
Rivulus hartii
, from fish communities that differ in predation intensity; predators are associated with lower population density and faster growth rates. To determine whether the indirect effects of predators influence evolutionary change, we reared second-generation-born fish under two food levels that approximated natural differences in resources between communities.
Rivulus
from sites with predators are younger and smaller at maturity. They have increased reproductive investment and produce many small eggs and smaller hatchlings. Such divergence is predicted as a direct effect of predation. We also found significant interactions between predator community and food level for age and size at maturity, fecundity, and egg size. These interactions, whereby the differences between communities were more pronounced at high-food levels, argue that evolution in
Rivulus
has been influenced by the indirect effects of predators mediated through resource availability.
Rivulus
from sites with predators better exploit the higher resources in those habitats. Therefore, both direct and indirect effects of predators have evolutionary consequences.
Addressing the health benefits and risks, involving vitamin D or skin cancer, of increased sun exposure
Authors: Moan Johan , Porojnicu Alina Carmen , Dahlback Arne , Setlow Richard B.
Published: January 2008

Solar radiation is the main cause of skin cancers. However, it also is a main source of vitamin D for humans. Because the optimal status of vitamin D protects against internal cancers and a number of other diseases, a controversy exists: Will increased sun exposure lead to net health benefits or risks? We calculated the relative yield of vitamin D photosynthesis as a function of latitude with a radiative transfer model and cylinder geometry for the human skin surface. The annual yield of vitamin D is 3.4 and 4.8 times larger below the equator than in the U.K. and Scandinavia, respectively. In populations with similar skin types, there are clear latitude gradients of all major forms of skin cancer, indicating a north–south gradient in real sun exposure. Surprisingly, the incidence rates of major internal cancers also increase from north to south. However, the survival prognosis also improves significantly from north to south. Reasons for these findings are discussed in view of the role of vitamin D. In Norway, melanoma rates increased by a factor of 6 from 1960 to 1990, while the prognosis improved in the same period. After 1990, melanoma rates have remained constant or even decreased in age groups <50 years, whereas the prognosis has not improved further. These data, together with those for internal cancers and the beneficial effects of an optimal vitamin D status, indicate that increased sun exposure may lead to improved cancer prognosis and, possibly, give more positive than adverse health effects.
Human CMV infection induces 5-lipoxygenase expression and leukotriene B4 production in vascular smooth muscle cells
Authors: Qiu Hong , Strååt Klas , Rahbar Afsar , Wan Min , Söderberg-Nauclér Cecilia , Haeggström Jesper Z.
Published: January 2008

Leukotrienes (LTs) are powerful proinflammatory lipid mediators that may play a central role in cardiovascular diseases, including arteriosclerosis, myocardial infarction, and stroke. Owing to restricted expression of 5-lipoxygenase (5-LO), the enzyme required for their synthesis, LTs are almost exclusively produced by myeloid cells. Here, we report that human cytomegalovirus (HCMV) infection of human vascular smooth muscle cells (SMCs) increases 5-LO mRNA levels by up to 170-fold in a dose- and time-dependent manner. Infected cells expressed 5-LO protein, as shown by immunohistochemistry, enabling them to synthesize bioactive LTB4. HCMV-infected vascular SMCs expressing 5-LO protein were readily detected in tissue samples from CMV-infected patients with inflammatory bowel disease or AIDS. Thus, pathogen-induced LT production in HCMV-infected tissues may contribute to local inflammation, consistent with the ability of HCMV to control cellular and immunological functions. HCMV-induced LT biosynthesis in SMCs offers a molecular mechanism to explain HCMV-induced pathogenesis in inflammatory diseases.
FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments
Authors: Nagarajan Niranjan , Keich Uri
Published: January 2008

Summary: As was shown in Nagarajan et al. (2005), commonly used approximations for assessing the significance of multiple alignments can be be very inaccurate. To address this, we present here the FAST package, an open-source collection of programs and libraries for efficiently and reliably computing the significance of ungapped local alignments. We also describe other potential applications in Bioinformatics where these programs can be adapted for significance testing.

Availability: The FAST package includes C++ implementations of various algorithms that can be used as stand-alone programs or as a library of subroutines. The package and a web-server for some of the programs are available at www.cs.cornell.edu/~keich/FAST

Contact:  keich@cs.cornell.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Expectation and experiences of childbirth in primiparae with caesarean section
Authors: Wiklund I , Edman G , Ryding E‐L , Andolf E
Published: January 2008

Objective  The aim of this study was to examine the expectations and experiences in women undergoing a caesarean section on maternal request and compare these with women undergoing caesarean section with breech presentation as the indication and women who intended to have vaginal delivery acting as a control group. A second aim was to study whether assisted delivery and emergency caesarean section in the control group affected the birth experience.

Design  A prospective group‐comparison cohort study.

Setting  Danderyd Hospital, Stockholm, Sweden.

Sample  First‐time mothers (n= 496) were recruited to the study in week 37–39 of gestation and follow up was carried out 3 months after delivery. Comparisons were made between ‘caesarean section on maternal request’, ‘caesarean section due to breech presentation’ and ‘controls planning a vaginal delivery’.

Methods  The instrument used was the Wijma Delivery Expectancy/Experience Questionnaire (W‐DEQ).

Main outcome measures  Expectations prior to delivery and experiences at 3 months after birth.

Results  Mothers requesting a caesarean section had more negative expectations of a vaginal delivery (P < 0.001) and 43.4% in this group showed a clinically significant fear of delivery. Mothers in the two groups expecting a vaginal delivery, but having an emergency caesarean section or an assisted vaginal delivery had more negative experiences of childbirth (P < 0.001).

Conclusions  Women requesting caesarean section did not always suffer from clinically significant fear of childbirth. The finding that women subjected to complicated deliveries had a negative birth experience emphasises the importance of postnatal support.
Use of a decision aid for prenatal testing of fetal abnormalities to improve women’s informed decision making: a cluster randomised controlled trial [ISRCTN22532458]
Authors: Nagle C , Gunn J , Bell R , Lewis S , Meiser B , Metcalfe S , Ukoumunne OC , Halliday J
Published: January 2008

Objective  To evaluate the effectiveness of a decision aid for prenatal testing of fetal abnormalities compared with a pamphlet in supporting women’s decision making.

Design  A cluster randomised controlled trial.

Setting  Primary health care.

Population  Women in early pregnancy consulting a GP.

Methods  GPs were randomised to provide women with either a decision aid or a pamphlet. The decision aid was a 24‐page booklet designed using the Ottowa Decision Framework. The pamphlet was an existing resource available in the trial setting.

Main outcome measures  Validated scales were used to measure the primary outcomes, informed choice and decisional conflict, and the secondary outcomes, anxiety, depression, attitudes to the pregnancy/fetus and acceptability of the resource. Outcomes were measured at 14 weeks of gestation from questionnaires that women completed and returned by post.

Findings  Women in the intervention group were more likely to make an informed decision 76% (126/165) than those in the control group 65% (107/165) (adjusted OR 2.08; 95% CI 1.14–3.81). A greater proportion of women in the intervention group 88% (147/167) had a ‘good’ level of knowledge than those in the control group 72% (123/171) (adjusted OR 3.43; 95% CI 1.79–6.58). Mean (SD) decisional conflict scores were low in both groups, decision aid 1.71 (0.49), pamphlet 1.65 (0.55) (adjusted mean difference 0.10; 95% CI −0.02 to 0.22). There was no strong evidence of differences between the trial arms in the measures of psychological or acceptability outcomes.

Conclusion  A tailored prenatal testing decision aid plays an important role in improving women’s knowledge of first and second trimester screening tests and assisting them to make decisions about screening and diagnostic tests that are consistent with their values.
Selective single blastocyst transfer reduces the multiple pregnancy rate and increases pregnancy rates: a pre‐ and postintervention study
Authors: Khalaf Y , El‐Toukhy T , Coomarasamy A , Kamal A , Bolton V , Braude P
Published: January 2008

Objective  To examine the clinical pregnancy rate (CPR) and multiple pregnancy rate (MPR) in a large in vitro fertilisation (IVF) programme before and after the introduction of single blastocyst transfer (SBT) strategy in a selected group of women.

Design  A 3‐year pre‐ and postintervention study.

Setting  A tertiary reproductive medicine and assisted conception unit in a London teaching hospital.

Population  Two thousand four hundred and fifty‐one fresh IVF cycles performed between July 2004 and June 2007 at the Assisted Conception Unit at Guy’s and St Thomas’ Hospital NHS Foundation Trust were included in the study.

Methods  In January 2006, we implemented a multidisciplinary intervention involving the introduction of a selective day 5 SBT service together with an educational programme on the risks of multiple pregnancy and potential advantages of blastocyst transfer aimed at couples at high risk of multiple pregnancy.

Main outcome measures  The CPR per cycle started and MPR per clinical pregnancy achieved.

Results  A statistically significant increase in the CPR from 27% (324/1198) to 32% (395/1253) (risk difference [RD] 5%, risk ratio [RR] 1.17, 95% CI 1.03–1.32, P= 0.015) and reduction in the MPR per clinical pregnancy from 32% (103/272) to 17% (69/395) (RD 15%, RR 0.46, 95% CI 0.35–0.60, P < 0.001) were observed after introduction of the SBT service.

Conclusion  Selective SBT in women with good prognosis can reduce the MPR after IVF while maintaining the overall success rate of the IVF programme.
The effect of early versus delayed postcaesarean feeding on women’s satisfaction: a randomised controlled trial
Authors: Izbizky GH , Minig L , Sebastiani MA , Otaño L
Published: January 2008

Objective  To evaluate the effect of early versus delayed feeding after caesarean section on the woman’s satisfaction.

Design  Randomised, controlled trial.

Setting  Tertiary care hospital.

Population  Healthy pregnant women were enrolled for the study during antenatal care visits.

Methods  Uncomplicated singleton pregnancies undergoing a planned or intrapartum caesarean section performed under regional anaesthesia were randomly assigned to either (1) a ‘delayed feeding’ group who started oral fluids 4 hours after surgery with diet introduced at 24 hours; or (2) an ‘early feeding’ group who were offered a regular diet within the first 8 hours.

Main outcome measures  Primary outcome was the woman’s satisfaction measured with a visual analogue scale (VAS) before their hospital discharge. The secondary outcomes were: pain, anorexia, abdominal distension, persistent nausea and/or vomiting, time to the first bowel movement and passage of flatus.

Results  Two hundred women were recruited, with 103 randomised to delayed feeding and 97 to early feeding. The woman’s satisfaction (mean VAS ± SD) was similar in both groups; 73 ± 17 mm in the delayed feeding group and 77 ± 13 mm in the early feeding group (P= 0.12). A statistically significant difference was observed in mean postoperative pain: 29 ± 13 mm in the delayed feeding group versus 24 ± 11 mm in the early feeding group (P= 0.008). No other significant differences in postoperative variables were recorded, and there were no major postoperative complications observed in either group.

Conclusion  Early feeding after uncomplicated caesarean in low‐risk women is equivalent in terms of the woman’s satisfaction and the reduced perceived pain.
The impact of psychological abuse by an intimate partner on the mental health of pregnant women
Authors: Tiwari A , Chan KL , Fong D , Leung WC , Brownridge DA , Lam H , Wong B , Lam CM , Chau F , Chan A , Cheung KB , Ho PC
Published: January 2008

Objective  The objective of this first population‐based study in Hong Kong was to assess the impact of psychological abuse by an intimate partner on the mental health of pregnant women.

Design  Survey.

Setting  Antenatal clinics in seven public hospitals in Hong Kong.

Population  Three thousand two hundred and forty‐five pregnant women.

Methods  The Abuse Assessment Screen (AAS) and demographic questionnaires were administered face‐to‐face at 32–36 weeks of gestation. At 1 week postpartum, the AAS, Edinburgh Postnatal Depression Scale and SF‐12 Health Survey were administered by telephone.

Main outcome measures  Intimate partner violence, postnatal depression and health‐related quality of life.

Results  Two hundred and ninety six (9.1%) of the participants reported abuse by an intimate partner in the past year. Of those abused, 216 (73%) reported psychological abuse only and 80 (27%) reported physical and/or sexual abuse. Forty six (57.5%) in the physical and/or sexual abuse group also reported psychological abuse. Women in the psychological abuse only group had a higher risk of postnatal depression compared with nonabused women (adjusted OR: 1.84, 95% CI: 1.12–3.02). They were also at a higher risk of thinking about harming themselves (adjusted OR: 3.50, 95% CI: 1.49–8.20) and had significantly poorer mental health‐related quality of life (P < 0.001). The higher risks of postnatal depression and thinking of harming themselves were not observed in the physical and/or sexual abuse group although significantly poorer mental health‐related quality of life (P < 0.001) was observed.

Conclusions  Psychological abuse by an intimate partner against pregnant women has a negative impact on their mental health postdelivery. Furthermore, psychological abuse in the absence of physical and/or sexual abuse can have a detrimental effect on the mental health of abused women. The findings underscore the importance of screening pregnant women for abuse by an intimate partner and the need for developing, implementing and evaluating interventions to address psychological abuse.