bluuebunny/crossref_metadata_2025 huggingface dataset:
Environmentally sustainable cities. Critical review and operational conditions
Authors: Bithas Kostas P. , Christofakis M.
Published: January 2006

The political objective calling for environmentally sustainable development has provided the canvas for lively dialogue amongst scientists and analysts. Be that as it may, what have been found wanting are operational conditions for the achievement of environmental sustainability within specific anthropogenic systems, with cities being cited as a prime example of such systems. Indeed, from a historical perspective, cities have always been based on the concentration of humans and man‐made elements, resulting in respective confinement of natural assets. As cities possess particular properties for their environmental basis, the general conditions governing sustainability require suitable modifications when applied to cities. In this context, the present paper examines the conditions for environmentally sustainable development in urban systems. The specific natural and socioeconomic characteristics of urban systems are systematically taken into account for defining environmentally sustainable development in cities. The paper proposes an operational framework for evaluating urban systems for their environmental performance. Urban systems, presenting specific characteristics necessary for creating welfare with high density, ask for particular conditions for their environmentally sustainable development. These conditions differ substantially from those defining sustainability in broader geographical systems. Copyright © 2006 John Wiley & Sons, Ltd and ERP Environment.
A discrete‐state discrete‐time model using indirect observation
Authors: Isaman Deanna J. M. , Herman William H. , Brown Morton B.
Published: January 2006

This research was motivated by a desire to model the progression of a chronic disease through various disease stages when data are not available to directly estimate all the transition parameters in the model. This is a common occurrence when time and expense make it infeasible to follow a single cohort to estimate all the transition parameters.

One difficulty of developing a model of chronic disease progression from such data is that the available studies often do not include the transitions of interest. For example, in our model of diabetic nephropathy, many clinical studies did not differentiate between patients without nephropathy and those who had microalbuminuria (a pre‐clinical stage of nephropathy). Another difficulty was a lack of data to directly estimate parameters of interest. We consider models which can accommodate such difficulties.

In this paper we consider the problem of estimating parameters of a discrete‐time Markov process when longitudinal data describing the entire process are not available. First, we present a likelihood approach to estimate parameters of a discrete‐time Markov model. Next, we use simulation to investigate the finite‐sample behaviour of our approach. Finally, we present two examples: a model of diabetic nephropathy and a model of cardiovascular disease in diabetes. Copyright © 2006 John Wiley & Sons, Ltd.
Assessing genetic effects in survival data by correlating martingale residuals with an application to age at onset of Huntington disease
Authors: Wintrebert Claire M. A. , Zwinderman Aeilko H. , Maat‐Kievit Anneke , Roos Raymund A. , van Houwelingen Hans C.
Published: January 2006

Genetic models for survival data are hard to formulate and hard to fit. For example, the popular gamma‐frailty model for sib‐pair data does not generalize easily to extended pedigrees and is not easy to fit.

In this paper we show how martingale residuals from a (marginal) Cox model can be employed to estimate the presence of a genetic effect and to estimate genetic correlations depending on the genetic distance (kinship).

The methodology is applied to age at onset of Huntington disease (HD) in carriers of the HD gene. The number of CAG repeats in the HD gene is a well‐known predictor for age at onset of the disease. However, there is an indication that other genes might be involved as well; leading to unexplained familial clustering.

Using our methodology, we found a clearly significant genetic association between the martingale residuals with correlations of about 0.6 for relatives that share 50 per cent of their genes (sib‐pairs and parent–child) and about 0.3 for relatives that share 25 per cent of their genes (grandparent–grandchild, uncle/aunt–niece/nephew). Copyright © 2006 John Wiley & Sons, Ltd.
Intraclass correlation coefficients and bootstrap methods of hierarchical binary outcomes
Authors: Ren Shiquan , Yang Shuqin , Lai Shenghan
Published: January 2006

Intraclass correlation coefficients are designed to assess consistency or conformity between two or more quantitative measurements. When multistage cluster sampling is implemented, no methods are readily available to estimate intraclass correlations of binomial‐distributed outcomes within a cluster. Because statistical distribution of the intraclass correlation coefficients could be complicated or unspecified, we propose using a bootstrap method to estimate the standard error and confidence interval within the framework of a multilevel generalized linear model. We compared the results derived from a parametric bootstrap method with those from a non‐parametric bootstrap method and found that the non‐parametric method is more robust. For non‐parametric bootstrap sampling, we showed that the effectiveness of sampling on the highest level is greater than that on lower levels; to illustrate the effectiveness, we analyse survey data in China and do simulation studies. Copyright © 2006 John Wiley & Sons, Ltd.
Bayesian semi‐parametric ROC analysis
Authors: Erkanli Alaattin , Sung Minje , Jane Costello E. , Angold Adrian
Published: January 2006

This paper describes a semi‐parametric Bayesian approach for estimating receiver operating characteristic (ROC) curves based on mixtures of Dirichlet process priors (MDP). We address difficulties in modelling the underlying distribution of screening scores due to non‐normality that may lead to incorrect choices of diagnostic cut‐offs and unreliable estimates of prevalence of the disease. MDP is a robust tool for modelling non‐standard diagnostic distributions associated with imperfect classification of an underlying diseased population, for example, when a diagnostic test is not a gold standard. For posterior computations, we propose an efficient Gibbs sampling framework based on a finite‐dimensional approximation to MDP. We show, using both simulated and real data sets, that MDP modelling for ROC curve estimation closely parallels the frequentist kernel density estimation (KDE) approach. Copyright © 2006 John Wiley & Sons, Ltd.
Rapid Detection of Escherichia coli by Using Antibody‐Conjugated Silver Nanoshells
Authors: Kalele Suchita A. , Kundu Anita A. , Gosavi Suresh W. , Deobagkar Dileep N. , Deobagkar Deepti D. , Kulkarni Sulabha K.
Published: January 2006

Silver shells of 20 nm thickness have been deposited on silica particles of 200 nm diameter with narrow size distribution. Silver nanoshells dispersed in water exhibit a strong surface plasmon resonance band at 443 nm. This band was found to be very sensitive to rabbit immunoglobulin G antibodies, which were anchored on the nanoshells. These in turn could be utilized to detect the presence of small (≈5) to large numbers (≈109) of Escherichia coli in water. The protocol presented here proves to be a specific, rapid, reliable, and inexpensive method to detect E. coli.
pH‐Sensitive Dispersion and Debundling of Single‐Walled Carbon Nanotubes: Lysozyme as a Tool
Authors: Nepal Dhriti , Geckeler Kurt E.
Published: January 2006

Highly dispersed and debundled carbon nanotubes were prepared in an aqueous solution of lysozyme using a combination of ultrasonication and ultracentrifugation. The product is a pH‐sensitive dispersion, which remains in a highly dispersed state at pH<8 and pH>11, but in an aggregated state at pH 8–11. Photoluminescence measurements show that by changing the pH value, a reversible conversion of the highly dispersed state to the aggregated state (or vice versa) could be observed. Circular dichromism analysis confirmed that the secondary structure, as well as the majority of the tertiary structure, remains intact. Some lysozyme molecules were irreversibly bound to the nanotubes, which is possibly due to π–π or hydrophobic interactions. However, these interactions alone are not enough to produce fine dispersions of the nanotubes. Protonated amine interactions on the defect sites of the nanotubes play a vital role in the stabilization of the nanotubes below the isoelectric point and amine adsorption on the sidewalls of nanotubes occurs in cases where the pH value is higher than the isoelectric point.
Shape Control of II–VI Semiconductor Nanomaterials
Authors: Kumar Sandeep , Nann Thomas
Published: January 2006

Anisotropic II–VI semiconductor nanocrystals and nanoparticles have become important building blocks for (potential) nanotechnological applications. Even though a wide variety of differently shaped nanoparticles of this class can be prepared, the underlying mechanisms are mostly not fully understood. This Review article provides a brief overview of the currently studied shape‐evolution mechanisms and the most prominent synthesis methods for such particles, with an aim to provide a fundamental understanding on how different morphologies evolve, and to function as a tool to aid in the preparation of specific nanocrystals.
Regulation of two distinct alcohol oxidase promoters in the methylotrophic yeast Pichia methanolica
Authors: Nakagawa Tomoyuki , Inagaki Atsushi , Ito Takashi , Fujimura Shuki , Miyaji Tatsuro , Yurimoto Hiroya , Kato Nobuo , Sakai Yasuyoshi , Tomizuka Noboru
Published: January 2006

In this study, two Pichia methanolica alcohol oxidase (AOD) promoters, PMOD1 and PMOD2, were evaluated in a promoter assay system utilizing the acid phosphatase (AP) gene from Saccharomyces cerevisiae (ScPHO5) as a reporter. Heterologous gene expression driven by the PMOD1 and PMOD2 promoters was found to be strong and tightly regulated by carbon source at the transcriptional level. PMOD1 was induced not only by methanol but also by glycerol. PMOD2 was induced only by methanol, although it was not repressed on the addition of glycerol to a methanol medium, suggesting that PMOD2 is regulated in a manner distinct from that of other AOD‐gene promoters. On the other hand, methanol and oxygen level‐influenced gene expression mediated by PMOD1 and PMOD2. PMOD1 expression was optimal at low methanol concentrations, whereas PMOD2 was predominantly expressed at high methanol and high oxygen concentrations. Based on these results, both PMOD2 and PMOD1 should be useful tools for controlling heterologous gene expression in P. methanolica. In particular, it should be possible to differentially control the production phases of two heterologous proteins, using PMOD1 and PMOD2 in the same host cell and in the same flask. Copyright © 2006 John Wiley & Sons, Ltd.
Sediment biochemical and microbial variables for the evaluation of trophic status along the Italian and Albanian continental shelves
Authors: Vezzulli Luigi , Fabiano Mauro
Published: January 2006

Phytopigment concentrations (chlorophyll-a and phaeopigments), labile organic matter (proteins, carbohydrates and lipids), bacterial density and frequency of dividing cells were analysed in the sediments of a large coastal area covering the southern Adriatic continental shelf between Italy and Albania in order to describe the trophic status of coastal marine sediments. On average, sediments of the Italian coast displayed the highest phytopigment and biopolymeric carbon concentrations compared to sediments of the Albanian coast and indicated an increased nutritional status of this coastal ecosystem. Different trophic conditions were evidenced in terms of biopolymeric composition of sedimentary organic matter as an increase in protein and a decrease in the carbohydrate contributions to total biopolymeric carbon was observed moving from the Albanian to the Italian coast. Using a benthic approach for the evaluation of trophic status shallow Italian sediments (0–50 m) were mainly classified as eutrophic and were subjected to stronger anthropogenic disturbance. This was particularly evident in areas in front of city harbours (Brindisi and Barletta) that were classified as hypertrophic and displayed the highest biopolymeric carbon (BPC) concentrations and protein to carbohydrate ratio (PRT:CHO on average >1). In contrast Albanian sediments as well as deeper Italian stations (>50 m), resulted mainly in meso-oligotrophic and displayed lower BPC and PRT:CHO ratio (on average <1). The study of bacterial variables provided an improved approach for the conceptual definition of trophic state using benthic biochemical measures. An inverse relationship occurred between the nutritional contents and the bacterial density within meso-oligotrophic sediments. This may reflect an increase in ecosystem organization and complexity (i.e. increased abundance of the higher trophic levels) which may determine a reduction of the bacterial density at increasing trophic conditions. In contrast a positive correlation was found within eutrophic and hypertrophic sediments suggesting that at high organic matter concentrations the ecosystem is no longer capable of further organization.
Impact of hydrodynamic disturbance on the generation times of four species of marine naked amoebae
Authors: Cowie Phillip R. , Hannah Fiona
Published: January 2006

Four species of gymnamoebae isolated from a sandy shore were subjected to hydrodynamic disturbance within microcosms. Increasing the level of disturbance increased the generation times of all four isolates. Generation times of a small Platyamoeba sp. and a limax amoeba were least affected by increasing disturbance. The greatest increase in generation times was observed in populations of two large (>15 μm) Mayorella sp. and Vannella sp. This study shows that hydrodynamic disturbance may be an important community structuring force within natural marine amoebae communities.
Egg size and clutch size in three species of Nihonotrypaea (Decapoda: Thalassinidea: Callianassidae) from western Kyushu, Japan
Authors: Kubo K. , Shimoda K. , Tamaki A.
Published: January 2006

Three species of the callianassid genus Nihonotrypaea occur in the Ariake Sound estuarine system, southern Japan; they consist of two tidal-flat species (N. harmandi; N. japonica) and one boulder-beach species (N. petalura), with maximum population densities of 1440, 343, and 12 ind m−2, respectively. Nihonotrypaea harmandi and N. petalura are distributed along the coastline from the outermost part of the sound to the open sea, while N. japonica occurs in the middle part of the sound. Nihonotrypaea japonica has an extended reproductive period from late winter to autumn, while those of the other species are from late spring or summer to autumn. Interspecific comparisons were made for recently laid egg size (as volume) and clutch size (as number of eggs per female). Only in N. japonica was a seasonal egg size variation observed, being significantly larger in winter to spring (mean=0.106 mm3) than in summer (0.080 mm3). By contrast, clutch size was significantly smaller in winter to spring, resulting in nearly the same clutch volume per female (product of the mean egg volume and clutch size) between the seasons. Among the three species, the egg size was ordered as N. japonica (overall mean volume through the seasons=0.092 mm3)>>N. petalura (0.057 mm3)>N. harmandi (0.054 mm3). The clutch size was ordered as N. harmandi>N. petalura≈N. japonica. The clutch volume was ordered as N. japonica≈N. harmandi>N. petalura. The smallest clutch volume value for N. petalura female showed an opposite trend to the relative size of the major cheliped found in a previous study.
Direct observations of protandrous sex change in the patellid limpet Patella vulgata
Authors: Le Quesne W.J.F. , Hawkins S.J.
Published: January 2006

Direct observations of sex change were made on Patella vulgata, which has long been considered a protandrous hermaphrodite based on indirect methods. Thirty per cent of the male limpets that were marked during the spawning season in 2003 were female when they were re-examined during the spawning season in 2004. This confirms that protandry does occur within the superfamily Patellidae.
Description of Merluccius tasmanicus sp. nov. and redescription of Merluccius australis (Pisces: Merlucciidae)
Authors: Matallanas J. , Lloris D.
Published: January 2006

A new hake species, Merluccius tasmanicus sp. nov., is described from New Zealand waters and another species, Merluccius australis is redescribed. Merluccius tasmanicus sp. nov. differs from all other congeneric species in the following combination of characters: upper profile of the head slowly concave; lateral line slowly concave in the caudal region; body depth 4.9–5.9 times in standard length (SL); orbital diameter 6.1–7.1 times in head length, 2.1–2.2 times in snout length and 1.6–1.9 times in interorbital width; second dorsal fin rays, 42–43; anal fin rays, 42–44; lateral line scales ∼164. Merluccius australis is redescribed to clarify the identity of this species. Merluccius australis differs from all other congeneric species in the following combination of characters: upper profile of the head straight; lateral line straight in the caudal region; body depth 6.6–7.1 times in SL; orbital diameter 4.5–5.4 times in head length, 1.2–1.7 times in snout length and 1.0–1.3 times in interorbital width; second dorsal fin rays, 40–43; anal fin rays, 40–43; lateral line scales, more than 155. Merluccius tasmanicus sp. nov. is found in New Zealand and Patagonian waters and occasionally in Japanese waters; Merluccius australis is reported in both New Zealand and Patagonian waters.
The language teacher's development
Authors: Mann Steve
Published: January 2006

This paper provides a commentary on recent contributions to the subject of teacher development and growth, focusing particularly on our understanding of some of the processes and tools that have been identified as instrumental and supportive in teacher development. Implicit in the notions of ‘reflective practice’, ‘exploratory teaching’, and ‘practitioner inquiry’ is the view that teachers develop by studying their own practice, collecting data and using reflective processes as the basis for evaluation and change. Such processes have a reflexive relationship with the construction of teacher knowledge and beliefs. Collaborative and co-operative processes can help sustain individual reflection and development.
Nonlinear evolution of the MHD Kelvin‐Helmholtz instability in a compressible plasma
Authors: Lai S. H. , Lyu L. H.
Published: January 2006

Kelvin‐Helmholtz (K‐H) instability at a magnetohydrodynamic (MHD) tangential discontinuity (TD) is studied by means of two‐dimensional MHD simulation. The TD is of finite thickness with both magnetic shear and velocity shear across the TD. Our simulation results indicate that the nonlinear evolution of MHD surface waves at the TD depends on the fast‐mode Mach numbers of the plasma flows on two sides of the TD in the surface wave rest frame. When the fast‐mode Mach numbers on both sides of the TD are less than 1, the K‐H instability can grow into vortices or kink‐type surface waves, depending on the orientation of the ambient magnetic field and the plasma beta. When the fast‐mode Mach number on either side of the TD is greater than 1, nonlinear fast‐mode plane waves are developed from the ridges of the surface waves and extended distance from the TD. A theoretical model based on the fast magnetosonic Mach cone formation is proposed to explain the formation of these nonlinear plane waves. The Mach angle of the fast magnetosonic Mach cone as a function of Mach number, orientation of ambient magnetic field, and plasma beta is derived. The flaring angles of these nonlinear plane waves measured from our simulation results are in good agreement with the Mach angles predicted by the theoretical model. Applications of our results to the Earth's magnetopause and to the solar wind are also discussed.
Main and interactive effects of warming, clipping, and doubled precipitation on soil CO2 efflux in a grassland ecosystem
Authors: Zhou Xuhui , Sherry Rebecca A. , An Yuan , Wallace Linda L. , Luo Yiqi
Published: January 2006

We conducted two experiments, one long term with a 2°C increase (Experiment 1) and one short term with a 4.4°C increase (Experiment 2), to investigate main and interactive effects of warming, clipping, and doubled precipitation on soil CO2 efflux and its temperature sensitivity in a U.S. tallgrass prairie. On average, warming increased soil CO2 efflux by 13.0% (p < 0.01) in Experiment 1, by 22.9% (p < 0.0001) in Experiment 2, and by 26.6% (p < 0.0001) in the transient study of Experiment 2. Doubled precipitation resulted in an increase of 9.0% (p < 0.05) in soil CO2 efflux in Experiment 2. Yearly clipping did not significantly affect soil CO2 efflux (p = 0.66) in Experiment 1, while clipping decreased soil CO2 efflux by 16.1% (p < 0.05) in the transient study. Temperature sensitivity of soil CO2 efflux significantly decreased from an apparent Q10 value of 2.51 in unwarmed plots to 2.02 in warmed plots without extra precipitation and from 2.57 to 2.23 with doubled precipitation in Experiment 2. No significant interactive effects among the experimental factors were statistically found on soil CO2 efflux or their temperature sensitivities except for the warming × clipping interaction (p < 0.05) in the transient study. Our observed minor interactive effects relative to main ones suggest that results from single‐factor experiments are useful in informing us of potential responses of soil CO2 efflux to multifactor global change, at least in our ecosystem.
Comparison of 14CO2, CO, and SF6 as tracers for recently added fossil fuel CO2 in the atmosphere and implications for biological CO2 exchange
Authors: Turnbull J. C. , Miller J. B. , Lehman S. J. , Tans P. P. , Sparks R. J. , Southon J.
Published: January 2006

We use the nearly ideal tracer 14CO2 to estimate the fossil fuel CO2 enhancement in boundary layer air at two sites in New England and Colorado. Improved Δ14C measurement precision of 1.6–2.6‰ provides fossil fuel CO2 detection capability of 0.8–1.5 ppm. Using the indirect tracers CO and SF6, we obtain two additional independent estimates of the fossil fuel CO2 component, and we assess the biases in these methods with respect to the 14CO2‐based estimates. The SF6‐based estimates vary considerably from the 14CO2‐based estimates, and are at times implausibly large. The CO‐based estimates are less variable, but show seasonally coherent biases with respect to the 14CO2 method.
What is the effect of cloud inhomogeneities on actinic fluxes and chemical species concentrations?
Authors: Bouet Christel , Szczap Frédéric , Leriche Maud , Benassi Albert
Published: January 2006

The purpose of the present paper is to evaluate the bias introduced by the commonly used homogeneous plane‐parallel cloud hypothesis in the computation of actinic fluxes, photolysis coefficients, and main tropospheric species concentrations. Accordingly, these quantities obtained for an inhomogeneous cloud field generated with a stochastic model are compared to their homogeneous plane‐parallel equivalent. Results show that neglecting cloud inhomogeneities has a significant impact on actinic flux. For instance, the bias introduced by the homogeneous plane‐parallel cloud hypothesis can reach more than 100% below the cloud leading to a comparable bias in photolysis coefficients and, in turn, creating an enhancement of the oxidizing capacity of the system.
Reassessing the role of stochastic forcing in the 1997–1998 El Niño
Authors: Vecchi G. A. , Wittenberg A. T. , Rosati A.
Published: January 2006

We explore the extent to which stochastic atmospheric variability was fundamental to development of extreme sea surface temperature anomalies (SSTAs) during the 1997–8 El Niño. The observed western equatorial Pacific westerly zonal stress anomalies (τax), which appeared between Nov. 1996 and May 1997 as a series of episodic bursts, were largely reproducible by an atmospheric general circulation model (AGCM) ensemble forced with observed SST. Retrospective forecasts using a hybrid coupled model (HCM) indicate that coupling only the part of τax linearly related to large‐scale tropical Pacific SSTA is insufficient to capture the observed 1997 warming; but, accounting in the HCM for all the τax that was connected to SST, recovers most of the strong SSTA warming. The AGCM‐estimated range of stochastic τax forcing induces substantial dispersion in the forecasts, but does not obscure the large‐scale warming in most HCM ensemble members.
Undersaturation of inert gases at the ocean surface: A thermal pumping mechanism
Authors: McNeil Craig L.
Published: January 2006

A diurnal ‘thermal pumping’ mechanism is proposed to explain why undersaturation of inert gases may develop at the sea surface during extended periods of low wind speed and net warming. A simple two‐layer model of the upper ocean with parameterized air‐sea gas exchange is used to explain the process. The model predicts maximum undersaturations of 0.25% for Ne, 0.75% for N2, 0.88% for Ar, and 1.12% for Kr for an assumed diurnal warming signal of 2°C, a gas transfer rate appropriate to a wind speed of 4 ms−1, and the simplifying assumption of no net warming over the day. The model results depend on the air‐sea gas transfer rate and the details of the upper ocean heating and mixing cycle. Observations of N2 undersaturation from the tropical Atlantic provide supporting experimental evidence.
Impact of lunar cycle on the precipitation in India
Authors: Roy Shouraseni Sen
Published: January 2006

Scientists for different regions of the world have indicated the impact of lunar cycle on different climatic parameters including precipitation. In the present study the impact of the lunar cycle on the precipitation in India has been analyzed. Daily precipitation records were assembled for 129 stations spread across the subcontinent for the time period 1910 to 2000. The results of the study indicate a general tendency towards the increased occurrences of precipitation a few days after the full moon in the interiors. The west coast of India showed tendency towards higher precipitation amounts in the ascending phase of the lunar cycle.
Vertical partition of ocean heat transport in isothermal coordinates
Authors: Saenko Oleg A. , Merryfield William J.
Published: January 2006

The meridional overturning circulation (MOC), associated with deep water formation in the North Atlantic, is thought to play an important part in the transport of heat by the climate system. According to observational estimates, and simple scaling arguments, the transport of heat by the MOC is ∼1 PW. However, in one recent modeling study (Boccaletti et al., 2005), this estimate is reduced to 0.4 PW. Using a model with higher resolution, the issue of heat transport partitioning between the circulation in the upper ocean and that due to the flows in the deep ocean is revisited here. It is found that, out of about 3 PW of heat entering the low‐latitude ocean through the surface, approximately 65% is transported poleward by the directly wind‐driven circulations in the upper ocean. However, 0.85 ± 0.35 PW of the peak northward heat transport at 15–20°N, can be associated with the MOC. In the Southern Hemisphere, the net effect of the deep flows on the heat transport is weaker, so that the corresponding maximum at 15–20°S is essentially due to the flows in the upper ocean.
Galactic cosmic ray modulation during the last five solar cycles
Authors: Sabbah I. , Rybanský M.
Published: January 2006

Neutron monitor counts observed at Climax have been used to study galactic cosmic ray modulation during the time interval 1953–2001. This interval covers five solar cycles including four‐field reversal. Cosmic ray intensity (CRI) is better correlated (r = 0.93) to the solar coronal hole area (CHA) than to solar activity represent by the sunspot number (R). The heliospheric current sheet (HCS) tilt angle, Ψ, tracks CRI very well by several solar rotations a head. CRI is anticorrelated to the magnitude of the interplanetary magnetic field (B) as well as to the product of B and solar wind speed (BV). It lags CHA by 3–6 solar rotaion during A < 0. This is the time needed by solar wind to reach ∼25–50 AU where modulation starts. The values of the cross correlation function between CRI and each of the parameters: CHA, R, and BV are higher for A < 0 than for A > 0. CRI lags B by 4 solar rotations and the product BV by 2 solar rotations during A < 0. The solar wind speed is the most effective parameter responsible for the flat CRI time profile during 1972–1978. Galactic cosmic rays (GCRs) particles react mainly to the heliospheric condition near HCS. They drift more slowly during A < 0 than during A > 0.
Low‐frequency wave characteristics in the upstream and downstream regime of the terrestrial bow shock
Authors: Narita Y. , Glassmeier K.‐H. , Fornaçon K.‐H. , Richter I. , Schäfer S. , Motschmann U. , Dandouras I. , Rème H. , Georgescu E.
Published: January 2006

Collisionless shocks in space are accompanied by the low‐frequency waves of the magnetic field both upstream and downstream of the shock. However, characteristics of these waves in the plasma rest frame are poorly understood, since spatial scale such as wavelength is hardly determined using single or at best two spacecraft observations. Taking advantage of multipoint measurements of the Cluster spacecraft, we present a statistical study to reveal the rest frame properties of the waves in the terrestrial bow shock environment such as frequencies, wave numbers, phase velocities, propagation directions, polarization and transport ratios for the quasi‐parallel and the quasi‐perpendicular shock regimes and in the upstream region, the outer, the middle, and the inner magnetosheath. We find that the quasi‐parallel shock upstream waves (or the foreshock waves) exhibit properties of the fast mode wave excited by the ion beam instability. Upstream of the quasi‐perpendicular shock the waves also exhibit similar properties to the foreshock waves, but the wave mode identification needs further investigations. In the magnetosheath the waves exhibit properties which are persistent from the outer to the inner magnetosheath. They can be interpreted as the mirror mode coupled to the plasma inhomogeneity or as the slow mode. We also find an organization in the wave propagation pattern that the upstream waves propagate toward upstream, while the magnetosheath waves propagate toward the flank region and toward the magnetopause. It is concluded that wave properties are different between the upstream and the downstream regions, but they are similar between the quasi‐parallel and the quasi‐perpendicular shock regimes, suggesting that the upstream waves are not transmitted to the downstream region across the shock and that the downstream waves do not depend on the shock angle (between the upstream magnetic field and the shock normal direction).
Long‐term persistence and multifractality of precipitation and river runoff records
Authors: Kantelhardt Jan W. , Koscielny‐Bunde Eva , Rybski Diego , Braun Peter , Bunde Armin , Havlin Shlomo
Published: January 2006

We discuss and compare the multifractal temporal scaling properties of precipitation and river discharge records on large timescales. To detect long‐term correlations and multifractal behavior in the presence of trends, we apply recently developed methods (detrended fluctuation analysis (DFA) and multifractal DFA) that can systematically detect nonstationarities and overcome trends in the data at all timescales. We find that above some crossover time that usually is several weeks, the daily runoffs are characterized by an asymptotic scaling exponent that indicates a slow power law decay of the runoff autocorrelation function and varies from river to river in a wide range. Below the crossovers, pronounced short‐term correlations occur. In contrast, most of the precipitation series show scaling behavior corresponding to a rapid decay of the autocorrelation function. For the multifractal characterization of the data we determine the generalized Hurst exponents and fit them by three operational models. While the fits based on the universal multifractal model describe well the scaling behavior of the positive moments in nearly all runoff and precipitation records, positive as well as negative moments are consistent with two‐parameter fits from a modified version of the multiplicative cascade model for all runoff records and most of the precipitation records. For some precipitation records with weak multifractality, however, a simple bifractal characterization gives the best fit of the data.
Uncertainty in a chemistry‐transport model due to physical parameterizations and numerical approximations: An ensemble approach applied to ozone modeling
Authors: Mallet Vivien , Sportisse Bruno
Published: January 2006

This paper estimates the uncertainty in the outputs of a chemistry‐transport model due to physical parameterizations and numerical approximations. An ensemble of 20 simulations is generated from a reference simulation in which one key parameterization (chemical mechanism, dry deposition parameterization, turbulent closure, etc.) or one numerical approximation (grid size, splitting method, etc.) is changed at a time. Intercomparisons of the simulations and comparisons with observations allow us to assess the impact of each parameterization and numerical approximation and the robustness of the model. An ensemble of 16 simulations is also generated with multiple changes in the reference simulation in order to estimate the overall uncertainty. The case study is a four‐month simulation of ozone concentrations over Europe in 2001 performed using the modeling system Polyphemus. It is shown that there is a high uncertainty due to the physical parameterizations (notably the turbulence closure and the chemical mechanism). The low robustness suggests that ensemble approaches are necessary in most applications.
Physically based parameterization of cirrus cloud formation for use in global atmospheric models
Authors: Kärcher B. , Hendricks J. , Lohmann U.
Published: January 2006

Motivated by the need to study the climatic impact of aerosol‐related cirrus cloud changes, a physically based parameterization scheme of ice initiation and initial growth of ice crystals in young cirrus clouds has been developed. The scheme tracks the number density and size of nucleated ice crystals as a function of vertical wind speed, temperature, ice saturation ratio, aerosol number size distributions, and preexisting cloud ice, allowing for competition between heterogeneous ice nuclei and liquid aerosol particles during freezing. Predictions of the parameterization are compared with numerical parcel simulations of ice nucleation and growth from atmospheric aerosols, with a special focus on explaining the indirect effects of ice nuclei on the properties of young cirrus clouds. The uncertainties of the parameterization are discussed and its implementation in a general circulation model is briefly outlined. This new scheme establishes a flexible framework for a comprehensive assessment of indirect aerosol effects on and properties of cirrus clouds in global climate, chemistry transport, and weather forecast models.
Bed load bias: Comparison of measurements obtained using two (76 and 152 mm) Helley‐Smith samplers in a gravel bed river
Authors: Vericat Damia , Church Michael , Batalla Ramon J.
Published: January 2006

We assess how the size of the Helley‐Smith (HS) bed load sampler nozzle affects the accuracy of bed load sampling. Semitheoretical considerations show that the larger grains resident on the streambed can influence the sample either by blocking the sampler entrance or by causing the sampler to rest in a “perched” position. Probabilities for interference can be derived from the distribution of grain sizes but they do not capture the actual complexity of the influence of the bed on sampler performance. We therefore make an empirical comparison of sediment trapped by HS samplers with 76‐ and 152‐mm intakes during floods in the gravel bed lower Ebro River. Most bed load rates appeared higher when sampled with the HS152. The largest clasts collected by the HS76 also tend to be smaller than those obtained with the HS152 at the same flow. Analyzing paired bed load samples, we find the probability of a bed load sample collected with the HS152 to be biased is around 43% in the conditions of the present study, whereas 65% of samples were biased when obtained with the HS76. The analysis emphasizes the influence of bed material texture over sampler performance and demonstrates that the use of samplers with intake size much larger than bed grain size (i.e., ∼5D) will increase the accuracy of bed load grain size distributions and the precision of annual load estimates in gravel bed rivers.
Analytical solution to seepage problem from a soil channel with a curvilinear bottom
Authors: Chahar Bhagu R.
Published: January 2006

An exact analytical solution for the quantity of seepage from a semicircular channel is not available because of difficulties in the conformal mapping. In the present study an inverse method has been used to obtain an exact solution for seepage from a curved channel whose boundary maps along a circle onto the hodograph plane. The solution involves inverse hodograph and Schwarz‐Christoffel transformation. The solution also includes a set of parametric equations for the shape of the channel perimeter and loci of phreatic lines. The channel shape is an approximate semiellipse with the top width as the major axis and twice the water depth as the minor axis and vice versa. The average of the corresponding ellipse and parabola gives nearly the exact shape of the channel. Also, this channel is non‐self‐intersecting and is feasible from a very deep channel to a very wide channel, unlike Kozeny's trochoid shape, which is self‐intersecting for a top width to depth ratio less than 1.14. Its seepage function is a linear combination of seepage functions for a slit and a strip. However, this channel allows more seepage loss than a trochoid channel. A special case of the resulting channel is an approximate semicircular section.
Maintenance of plastid RNA editing activities independently of their target sites
Authors: Tillich Michael , Poltnigg Peter , Kushnir Sergei , Schmitz‐Linneweber Christian
Published: January 2006

RNA editing in plant organelles is mediated by site‐specific, nuclear‐encoded factors. Previous data suggested that the maintenance of these factors depends on the presence of their rapidly evolving cognate sites. The surprising ability of allotetraploid Nicotiana tabacum (tobacco) to edit a foreign site in the chloroplast ndhA messenger RNA was thought to be inherited from its diploid male ancestor, Nicotiana tomentosiformis. Here, we show that the same ndhA editing activity is also present in Nicotiana sylvestris, which is the female diploid progenitor of tobacco and which lacks the ndhA site. Hence, heterologous editing is not simply a result of tobacco's allopolyploid genome organization. Analyses of other editing sites after sexual or somatic transfer between land plants showed that heterologous editing occurs at a surprisingly high frequency. This suggests that the corresponding editing activities are conserved despite the absence of their target sites, potentially because they serve other functions in the plant cell.
Ca2+ shuttling between endoplasmic reticulum and mitochondria underlying Ca2+ oscillations
Authors: Ishii Kiyoaki , Hirose Kenzo , Iino Masamitsu
Published: January 2006

Although many cell functions are regulated by Ca2+ oscillations induced by a cyclic release of Ca2+ from intracellular Ca2+ stores, the pacemaker mechanism of Ca2+ oscillations remains to be explained. Using green fluorescent protein‐based Ca2+ indicators that are targeted to intracellular Ca2+ stores, the endoplasmic reticulum (ER) and mitochondria, we found that Ca2+ shuttles between the ER and mitochondria in phase with Ca2+ oscillations. Following agonist stimulation, Ca2+ release from the ER generated the first Ca2+ oscillation and loaded mitochondria with Ca2+. Before the second Ca2+ oscillation, Ca2+ release from the mitochondria by means of the Na+/Ca2+ exchanger caused a gradual increase in cytoplasmic Ca2+ concentration, inducing a regenerative ER Ca2+ release, which generated the peak of Ca2+ oscillation and partially reloaded the mitochondria. This sequence of events was repeated until mitochondrial Ca2+ was depleted. Thus, Ca2+ shuttling between the ER and mitochondria may have a pacemaker role in the generation of Ca2+ oscillations.
Tudor, MBT and chromo domains gauge the degree of lysine methylation
Authors: Kim Jeesun , Daniel Jeremy , Espejo Alexsandra , Lake Aimee , Krishna Murli , Xia Li , Zhang Yi , Bedford Mark T
Published: January 2006

The post‐translational modification of histones regulates many cellular processes, including transcription, replication and DNA repair. A large number of combinations of post‐translational modifications are possible. This cipher is referred to as the histone code. Many of the enzymes that lay down this code have been identified. However, so far, few code‐reading proteins have been identified. Here, we describe a protein‐array approach for identifying methyl‐specific interacting proteins. We found that not only chromo domains but also tudor and MBT domains bind to methylated peptides from the amino‐terminal tails of histones H3 and H4. Binding specificity observed on the protein‐domain microarray was corroborated using peptide pull‐downs, surface plasma resonance and far western blotting. Thus, our studies expose tudor and MBT domains as new classes of methyl‐lysine‐binding protein modules, and also demonstrates that protein‐domain microarrays are powerful tools for the identification of new domain types that recognize histone modifications.
Coherent control of pump-probe signals of helical structures by adaptive pulse polarizations
Authors: Voronine Dmitri , Abramavicius Darius , Mukamel Shaul
Published: January 2006

The simplification of the pump-probe spectrum of excitons by pure-phase-polarization pulse shaping is investigated by a simulation study. The state of light is manipulated by varying the phases of two perpendicular polarization components of the pump, holding its total spectral and temporal intensity profiles fixed. Genetic and iterative Fourier transform algorithms are used to search for pulse phase functions that optimize the ratio of the signal at two frequencies. New features are extracted from the congested pump-probe spectrum of a helical pentamer by selecting a combination of Liouville space pathways. Tensor components which dominate the optimized spectra are identified.
Spectroscopic analysis of small organic molecules: A comprehensive near-edge x-ray-absorption fine-structure study of C6-ring-containing molecules
Authors: Kolczewski C. , Püttner R. , Martins M. , Schlachter A. S. , Snell G. , Sant’Anna M. M. , Hermann K. , Kaindl G.
Published: January 2006

We report high-resolution C 1s near-edge x-ray-absorption fine-structure (NEXAFS) spectra of the C6-ring-containing molecules benzene (C6H6), 1,3- and 1,4-cyclohexadiene (C6H8), cyclohexene (C6H10), cyclohexane (C6H12), styrene (C8H8), and ethylbenzene (C8H10) which allow us to examine the gradual development of delocalization of the corresponding π electron systems. Due to the high experimental resolution, vibrational progressions can be partly resolved in the spectra. The experimental spectra are compared with theoretical NEXAFS spectra obtained from density-functional theory calculations where electronic final-state relaxation is accounted for. The comparison yields very good agreement between theoretical spectra and experimental results. In all cases, the spectra can be described by excitations to π*- and σ*-type final-state orbitals with valence character, while final-state orbitals of Rydberg character make only minor contributions. The lowest C 1s→1π* excitation energy is found to agree in the (experimental and theoretical) spectra of all molecules except for 1,3-cyclohexadiene (C6H8) where an energy smaller by about 0.6 eV is obtained. The theoretical analysis can explain this result by different binding properties of this molecule compared to the others.
A systematic multireference perturbation-theory study of the low-lying states of SiC3
Authors: Rintelman Jamie M. , Gordon Mark S. , Fletcher Graham D. , Ivanic Joseph
Published: January 2006

The three known lowest-energy isomers of SiC3, two cyclic singlets (2s and 3s) and a linear triplet (1t), have been reinvestigated using multireference second-order perturbation theory (MRPT2). The dependence of the relative energies of the isomers upon the quality of the basis sets and the sizes of the reference active spaces is explored. When using a complete-active-space self-consistent-field reference wave function with 12 electrons in 11 orbitals [CASSCF (12, 11)] together with basis sets that increase in size up to the correlation-consistent polarized core-valence quadruple zeta basis set (cc-pCVQZ), the MRPT2 method consistently predicts the linear triplet to be the most stable isomer. A new parallel direct determinant MRPT2 code has been used to systematically explore reference spaces that vary in size from CASSCF (8,8) to full optimized reaction space [FORS or CASSCF (16,16)] with the cc-pCVQZ basis. It is found that the relative energies of the isomers change substantially as the active space is increased. At the best level of theory, MRPT2 with a full valence FORS reference, the 2s isomer is predicted to be more stable than 3s and 1t by 4.7 and 2.2kcal∕mol, respectively.
Moving embedded lattice solitons
Authors: Malomed B. A. , Fujioka J. , Espinosa-Cerón A. , Rodríguez R. F. , González S.
Published: January 2006

It was recently proved that solitons embedded in the spectrum of linear waves may exist in discrete systems, and explicit solutions for isolated unstable embedded lattice solitons (ELS) of a differential-difference version of a higher-order nonlinear Schrödinger equation were found [González-Pérez-Sandi, Fujioka, and Malomed, Physica D 197, 86 (2004)]. The discovery of these ELS gives rise to relevant questions such as the following: (1) Are there continuous families of ELS? (2) Can ELS be stable? (3) Is it possible for ELS to move along the lattice? (4) How do ELS interact? The present work addresses these questions by showing that a novel equation (a discrete version of a complex modified Korteweg–de Vries equation that includes next-nearest-neighbor couplings) has a two-parameter continuous family of exact ELS. These solitons can move with arbitrary velocities across the lattice, and the numerical simulations demonstrate that these ELS are completely stable. Moreover, the numerical tests show that these ELS are robust enough to withstand collisions, and the result of a collision is only a shift in the positions of the solitons. The model may apply to the description of a Bose-Einstein condensate with dipole-dipole interactions between the atoms, trapped in a deep optical-lattice potential.