bluuebunny/crossref_metadata_2025 huggingface dataset:
Operational interpretations of an extension of Fω with control operators
Authors: Harper Robert , Lillibridge Mark
Published: November 2008

We study the operational semantics of an extension of Girard's System Fω with two control operators: an abort operation that abandons the current control context, and a callcc operation that captures the current control context. Two classes of operational semantics are considered, each with a call-by-value and a call-by-name variant, differing in their treatment of polymorphic abstraction and instantiation. Under the standard semantics, polymorphic abstractions are values and polymorphic instantiation is a significant computation step; under the ML-like semantics evaluation proceeds beneath polymorphic abstractions and polymorphic instantiation is computationally insignificant. Compositional, type-preserving continuation-passing style (cps) transformation algorithms are given for the standard semantics, resulting in terms on which all four evaluation strategies coincide. This has as a corollary the soundness and termination of well-typed programs under the standard evaluation strategies. In contrast, such results are obtained for the call-by-value ML-like strategy only for a restricted sub-language in which constructor abstractions are limited to values. The ML-like call-by-name semantics is indistinguishable from the standard call-by-name semantics when attention is limited to complete programs.
Wavelets
Authors: DeVore Ronald A. , Lucier Bradley J.
Published: November 2008

The subject of ‘wavelets’ is expanding at such a tremendous rate that it is impossible to give, within these few pages, a complete introduction to all aspects of its theory. We hope, however, to allow the reader to become sufficiently acquainted with the subject to understand, in part, the enthusiasm of its proponents toward its potential application to various numerical problems. Furthermore, we hope that our exposition can guide the reader who wishes to make more serious excursions into the subject. Our viewpoint is biased by our experience in approximation theory and data compression; we warn the reader that there are other viewpoints that are either not represented here or discussed only briefly. For example, orthogonal wavelets were developed primarily in the context of signal processing, an application upon which we touch only indirectly. However, there are several good expositions (e.g. Daubechies (1990) and Rioul and Vetterli (1991)) of this application. A discussion of wavelet decompositions in the context of Littlewood-Paley theory can be found in the monograph of Frazieret al. (1991). We shall also not attempt to give a complete discussion of the history of wavelets. Historical accounts can be found in the book of Meyer (1990) and the introduction of the article of Daubechies (1990). We shall try to give sufficient historical commentary in the course of our presentation to provide some feeling for the subject's development.
Iterative solution of linear systems
Authors: Freund Roland W. , Golub Gene H. , Nachtigal Noël M.
Published: November 2008

Recent advances in the field of iterative methods for solving large linear systems are reviewed. The main focus is on developments in the area of conjugate gradient-type algorithms and Krylov subspace methods for nonHermitian matrices.
Interior methods for constrained optimization
Authors: Wright Margaret H.
Published: November 2008

Interior methods for optimization were widely used in the 1960s, primarily in the form of barrier methods. However, they were not seriously applied to linear programming because of the dominance of the simplex method. Barrier methods fell from favour during the 1970s for a variety of reasons, including their apparent inefficiency compared with the best available alternatives. In 1984, Karmarkar's announcement of a fast polynomial-time interior method for linear programming caused tremendous excitement in the field of optimization. A formal connection can be shown between his method and classical barrier methods, which have consequently undergone a renaissance in interest and popularity. Most papers published since 1984 have concentrated on issues of computational complexity in interior methods for linear programming. During the same period, implementations of interior methods have displayed great efficiency in solving many large linear programs of ever-increasing size. Interior methods have also been applied with notable success to nonlinear and combinatorial problems. This paper presents a self-contained survey of major themes in both classical material and recent developments related to the theory and practice of interior methods.
Parallel numerical linear algebra
Authors: Demmel James W. , Heath Michael T. , van der Vorst Henk A.
Published: November 2008

We survey general techniques and open problems in numerical linear algebra on parallel architectures. We first discuss basic principles of paralled processing, describing the costs of basic operations on parallel machines, including general principles for constructing efficient algorithms. We illustrate these principles using current architectures and software systems, and by showing how one would implement matrix multiplication. Then, we present direct and iterative algorithms for solving linear systems of equations, linear least squares problems, the symmetric eigenvalue problem, the nonsymmetric eigenvalue problem, and the singular value decomposition. We consider dense, band and sparse matrices.
Finite element solution of the Navier—Stokes equations
Authors: Fortin Michel
Published: November 2008

Viscous incompressible flows are of considerable interest for applications. Let us mention, for example, the design of hydraulic turbines or rheologically complex flows appearing in many processes involving plastics or molten metals. Their simulation raises a number of difficulties, some of which are likely to remain while others are now resolved. Among the latter are those related to incompressibility which are also present in the simulation of incompressible or nearly incompressible elastic materials. Among the still unresolved are those associated with high Reynolds numbers which are also met in compressible flows. They involve the formation of boundary layers and turbulence, an ever present phenomenon in fluid mechanics, implying that we have to simulate unsteady, highly unstable phenomena.
Wavelet and multiscale methods for operator equations
Authors: Dahmen Wolfgang
Published: November 2008

More than anything else, the increase of computing power seems to stimulate the greed for tackling ever larger problems involving large-scale numerical simulation. As a consequence, the need for understanding something like theintrinsic complexityof a problem occupies a more and more pivotal position. Moreover, computability often only becomes feasible if an algorithm can be found that isasymptotically optimal. This means that storage and the number of floating point operations needed to resolve the problem with desired accuracy remainproportionalto the problem size when the resolution of the discretization is refined. A significant reduction of complexity is indeed often possible, when the underlying problem admits a continuous model in terms of differential or integral equations. The physical phenomena behind such a model usually exhibit characteristic features over a wide range of scales. Accordingly, the most successful numerical schemes exploit in one way or another the interaction of different scales of discretization. A very prominent representative is themultigridmethodology; see, for instance, Hackbusch (1985) and Bramble (1993). In a way it has caused a breakthrough in numerical analysis since, in an important range of cases, it does indeed provide asymptotically optimal schemes. For closely related multilevel techniques and a unified treatment of several variants, such asmultiplicativeoradditive subspace correctionmethods, see Bramble, Pasciak and Xu (1990), Oswald (1994), Xu (1992), and Yserentant (1993). Although there remain many unresolved problems, multigrid or multilevel schemes in the classical framework of finite difference and finite element discretizations exhibit by now a comparatively clear profile. They are particularly powerful for elliptic and parabolic problems.
Complexity theory and numerical analysis
Authors: Smale Steve
Published: November 2008

Complexity theory of numerical analysis is the study of the number of arithmetic operations required to pass from the input to the output of a numerical problem.
Relative perturbation results for matrix eigenvalues and singular values
Authors: Ipsen Ilse C. F.
Published: November 2008

It used to be good enough to bound absolute of matrix eigenvalues and singular values. Not any more. Now it is fashionable to bound relative errors. We present a collection of relative perturbation results which have emerged during the past ten years.

No need to throw away all those absolute error bound, though. Deep down, the derivation of many relative bounds can be based on absolute bounds. This means that relative bounds are not always better. They may just be better sometimes – and exactly when depends on the perturbation.
Direct search algorithms for optimization calculations
Authors: Powell M. J. D.
Published: November 2008

Many different procedures have been proposed for optimization calculations when first derivatives are not available. Further, several researchers have contributed to the subject, including some who wish to prove convergence theorems, and some who wish to make any reduction in the least calculated value of the objective function. There is not even a key idea that can be used as a foundation of a review, except for the problem itself, which is the adjustment of variables so that a function becomes least, where each value of the function is returned by a subroutine for each trial vector of variables. Therefore the paper is a collection of essays on particular strategies and algorithms, in order to consider the advantages, limitations and theory of several techniques. The subjects addressed are line search methods, the restriction of vectors of variables to discrete grids, the use of geometric simplices, conjugate direction procedures, trust region algorithms that form linear or quadratic approximations to the objective function, and simulated annealing. We study the main features of the methods themselves, instead of providing a catalogue of references to published work, because an understanding of these features may be very helpful to future research.
Entwicklungen von Lesekompetenz und Lesemotivation Schereneffekte in der Sekundarstufe?
Authors: Retelsdorf Jan , Möller Jens
Published: November 2008

Zusammenfassung. In dieser Längsschnittstudie wurden die Entwicklungen von Lesekompetenz, Lesemotivation und Leseselbstkonzept am Anfang der Sekundarstufe untersucht. Insbesondere wurde dabei der Frage nach differenziellen Entwicklungen dieser Faktoren im mehrgliedrigen Schulsystem nachgegangen. Die Stichprobe umfasste N = 1409 Schüler aus 56 Gymnasien, Realschulen und Hauptschulen. Um schulformabhängige Entwicklungen zu untersuchen, wurden latente Differenzwertmodelle analysiert. Für die Lesekompetenz ergaben sich dabei etwa gleich große Leistungszuwächse für Schüler aller Schulformen, während die Lesemotivation der Gymnasiasten weniger rückläufig war als die von Schülern der anderen beiden Schulformen. Für das Leseselbstkonzept zeigte sich dagegen ein Aufholeffekt der Hauptschüler, während die Selbstkonzepte der Schüler der übrigen Schulformen stagnierten.
Perinatal Depression, Prevention Strategies, Personality, and the Importance of Therapy Acceptance
Authors: Garnier Salomé , De Tychey Claude , Lighezzolo Joelle , Claudon Philippe , Rebourg-Roesler Christine , Flach Isabelle
Published: November 2008

This comparative, short-term, longitudinal clinical study evaluated two depressed women during the perinatal period using multiple methodologies (interview, Rorschach, and measures of depression, coping, and quality of life). The results provide evidence for the interest and efficacy of a preventive therapeutic approach during this period. The study demonstrates that masochistic personality organization is a significant obstacle to patients’ acceptance of therapy and that a neurotic personality facilitates therapeutic acceptation. Possibilities for future research are discussed.
Seasonal distribution of ozone and its precursors over the tropical Indian region using regional chemistry‐transport model
Authors: Roy Sompriti , Beig Gufran , Jacob Daniela
Published: November 2008

An off‐line regional chemistry‐transport model (REMO‐CTM) has been applied for the first time to the Indian geographical region to simulate the distribution of ozone and its precursors at the boundary level. The model accounts for the winds from ECMWF as lateral boundaries and latest emission inventories of the ozone precursors for the year 2003. An attempt has been made to validate the model with meteorological parameters like precipitation data and wind fields available from observations, satellite data for CO, and that of surface ozone observations over different parts of India. Model results reproduce the precipitation pattern reasonably well. The qualitative agreement of model and ozone data is also found to be reasonable. Present results are also compared with the global chemistry transport model. The seasonal distribution of ozone and its precursors over the Indian region indicates a differential pattern driven by the spatial synoptic weather condition and local emissions. The continental tropical convergence zone (CTCZ) and long‐range/regional transport also play an important role, especially over the Indo‐Gangetic plains where the ozone, CO, and NOx concentrations are found to be higher as compared to other parts of India.
The Far‐infrared Earth
Authors: Harries J. , Carli B. , Rizzi R. , Serio C. , Mlynczak M. , Palchetti L. , Maestri T. , Brindley H. , Masiello G.
Published: November 2008

The paper presents a review of the far‐infrared (FIR) properties of the Earth's atmosphere and their role in climate. These properties have been relatively poorly understood, and it is one of the purposes of this review to demonstrate that in recent years we have made great strides in improving this understanding. Seen from space, the Earth is a cool object, with an effective emitting temperature of about 255 K. This contrasts with a global mean surface temperature of ∼288 K and is due primarily to strong absorption of outgoing longwave energy by water vapor, carbon dioxide, and clouds (especially ice). A large fraction of this absorption occurs in the FIR, and so the Earth is effectively a FIR planet. The FIR is important in a number of key climate processes, for example, the water vapor and cloud feedbacks (especially ice clouds). The FIR is also a spectral region which can be used to remotely sense and retrieve atmospheric composition in the presence of ice clouds. Recent developments in instrumentation have allowed progress in each of these areas, which are described, and proposals for a spaceborne FIR instrument are being formulated. It is timely to review the FIR properties of the clear and cloudy atmosphere, the role of FIR processes in climate, and its use in observing our planet from space.
Sampling design for compliance monitoring of surface water quality: A case study in a Polder area
Authors: Brus D. J. , Knotters M.
Published: November 2008

International agreements such as the EU Water Framework Directive (WFD) ask for efficient sampling methods for monitoring natural resources. In this paper a general methodology for designing efficient, statistically sound monitoring schemes is described. An important decision is the choice between a design‐based and a model‐based method, implying the choice between probability (random) sampling and purposive sampling. For mapping purposes, model‐based methods are more appropriate, whereas to obtain valid results for the universe as a whole, such as in testing water quality standards against legal standards, we generally prefer a design‐based method. Four basic sampling patterns in space‐time universe are described: static, synchronous, static‐synchronous, and rotational. A case study is carried out for monitoring the quality of surface water at two farms in western Netherlands, wherein a synchronous sampling design is applied, with stratified simple random sampling in both space and time. To reduce laboratory costs the aliquots taken at the locations of a given sampling round are bulked to form a composite. To test the spatiotemporal mean N‐total concentration during the summer half‐year against the MAR standard with a power of 80% at a concentration 15% below the MAR standard and with a confidence of 95%, six to nine sampling rounds are needed with 50 to 75 locations per sampling round. For P‐total the required number of sampling rounds differs strongly between the two farms, but is for both farms much larger than for N‐total.
Genesis and shape of natural solution cavities within salt deposits
Authors: Gechter Daniel , Huggenberger Peter , Ackerer Philippe , Waber H. Niklaus
Published: November 2008

Since the genesis and shape of natural deep‐seated cavities within a salt body are insufficiently understood, the current study tries to shed some light on this topic. To this end, freshwater was pumped slowly through a horizontal borehole in rock salt cores. Owing to fast halite dissolution kinetics, high solubility, and slow inflow rate, halite dissolution took place only in the inflow of the rock salt cylinder. The shape of the created cavities is an approximately symmetrical half cone with a horizontal base facing upward. A conceptual model is presented that is inspired by the experimental results and based on theoretical hydraulic‐geochemical considerations, as well as on field observations. It proposes that triangular prism or conically shaped cavities develop within salt under confined conditions, where aggressive water flows upward along a fracture/conduit from an insoluble aquifer into the soluble stratum. Such cavity enlargements may cause land subsidence and structure collapse.
Detection and attribution of Atlantic salinity changes
Authors: Stott Peter A. , Sutton Rowan T. , Smith Doug M.
Published: November 2008

An analysis of observed and modeled oceanic salinity changes shows that significant changes of salinity, which are predicted in the World's oceans as a result of human influence, are beginning to emerge. A significant increase in salinity has been observed in recent decades in the 20N–50N latitude band of the Atlantic ocean, although changes at sub‐polar latitudes of the Atlantic, and in other ocean basins, are not found to be significant compared to modeled internal variability. An optimal detection analysis of spatial patterns of salinity trends detects a human influence on the observed salinity increases in the Atlantic ocean. These results indicate the growing potential for using observations to constrain important properties of the climate system's response to anthropogenic forcing.
Preoperative Assessment of the Peripheral Vascular Disease Patient for Free Tissue Transfers
Authors: Colen Lawrence , Musson Anne
Published: November 2008

Lower extremity reconstruction or salvage in patients with severe peripheral vascular disease is a unique challenge, requiring knowledge of the vascular anatomy, including the location of intraluminal irregularities and stenoses. In a retrospective study that includes four case reports, the authors describe the impressive ability of the Duplex imaging system, to assist in the proper selection of recipient vessels and of those areas within the vessels most suitable for anastomoses.
Exploring chemical space with discrete, gradient, and hybrid optimization methods
Authors: Balamurugan D. , Yang Weitao , Beratan David N.
Published: November 2008

Discrete, gradient, and hybrid optimization methods are applied to the challenge of discovering molecules with optimized properties. The cost and performance of the approaches were studied using a tight-binding model to maximize the static first electronic hyperpolarizability of molecules. Our analysis shows that discrete branch and bound methods provide robust strategies for inverse chemical design involving diverse chemical structures. Based on the linear combination of atomic potentials, a hybrid discrete-gradient optimization strategy significantly improves the performance of the gradient methods. The hybrid method performs better than dead-end elimination and competes with branch and bound and genetic algorithms. The branch and bound methods for these model Hamiltonians are more cost effective than genetic algorithms for moderate-sized molecular optimization.
Translational diffusion of water and its dependence on temperature in charged and uncharged clays: A neutron scattering study
Authors: González Sánchez Fátima , Jurányi Fanni , Gimmi Thomas , Van Loon Luc , Unruh Tobias , Diamond Larryn W.
Published: November 2008

The water diffusion in four different, highly compacted clays [montmorillonite in the Na- and Ca-forms, illite in the Na- and Ca-forms, kaolinite, and pyrophyllite (bulk dry density ρb=1.85±0.05g∕cm3)] was studied at the atomic level by means of quasielastic neutron scattering. The experiments were performed on two time-of-flight spectrometers and at three different energy resolutions [FOCUS at SINQ, PSI (3.65 and 5.75Å), and TOFTOF at FRM II (10Å)] for reliable data analysis and at temperatures between 27 and 95°C. Two different jump diffusion models were used to describe the translational motion. Both models describe the data equally well and give the following ranking of diffusion coefficients: Na-montmorillonite⩽Ca-montmorillonite<Ca-illite<Na-illite<water⩽pyrophyllite⩽kaolinite. Uncharged clays had slightly larger diffusion coefficients than that of bulk water due to their hydrophobic surfaces. The time between jumps, τt, follows the sequence: Ca-montmorillonite⩾Na-montmorillonite>Ca-illite>Na-illite⩾kaolinite>pyrophyllite⩾water, in both jump diffusion models. For clays with a permanent layer charge (montmorillonite and illite) a reduction in the water content by a factor of 2 resulted in a decrease in the self-diffusion coefficients and an increase in the time between jumps as compared to the full saturation. The uncharged clay kaolinite exhibited no change in the water mobility between the two hydration states. The rotational relaxation time of water was affected by the charged clay surfaces, especially in the case of montmorillonite; the uncharged clays presented a waterlike behavior. The activation energies for translational diffusion were calculated from the Arrhenius law, which adequately describes the systems in the studied temperature range. Na- and Ca-montmorillonite (∼11–12kJ∕mol), Na-illite (∼13kJ∕mol), kaolinite and pyrophyllite (∼14kJ∕mol), and Ca-illite (∼15kJ∕mol) all had lower activation energies than bulk water (∼17kJ∕mol in this study). This may originate from the reduced number and strength of the H-bonds between water and the clay surfaces, or ions, as compared to those in bulk water. Our comparative study suggests that the compensating cations in swelling clays have only a minor effect on the water diffusion rates at these high densities, whereas these cations influence the water motion in non-swelling clays.
New techniques for high-temperature melting measurements in volatile refractory materials via laser surface heating
Authors: Manara D. , Sheindlin M. , Heinz W. , Ronchi C.
Published: November 2008

An original technique for the measurement of high-temperature phase transitions was implemented based on a laser-heating method, enabling chemically unstable, refractory materials to be melted under controlled conditions. This technique includes two independent but correlated methods: In the first, fast multichannel pyrometry is employed to measure thermograms and spectral emissivity; in the second, a low-power probe laser beam is used for the detection of reflectivity changes induced by phase transitions on the sample surface. The experiments are carried out under medium (≈102 kPa) or high (≈102 MPa) inert-gas pressures in order to kinetically suppress evaporation in volatile or chemically instable samples. Two models for the simulation of the laser-heating pulses are as well introduced. Some results are presented about the successful application of this technique to the study of the melting behavior of oxides such as UO2+x, ZrO2, and their mixed oxides. The method can be extended to a broad class of refractory materials.
Electronic structures of SiC nanoribbons
Authors: Sun Lian , Li Yafei , Li Zhenyu , Li Qunxiang , Zhou Zhen , Chen Zhongfang , Yang Jinlong , Hou J. G.
Published: November 2008

Electronic structures of SiC nanoribbons have been studied by spin-polarized first-principles calculations. The armchair nanoribbons are nonmagnetic semiconductors, while the zigzag nanoribbons are magnetic metals. The spin polarization in the zigzag SiC nanoribbons is originated from the unpaired electrons localized on the ribbon edges. Interestingly, the zigzag nanoribbons narrower than ∼4 nm present half-metallic behavior. Without the aid of external field or chemical modification, the metal-free half-metallicity predicted for narrow SiC zigzag nanoribbons opens a facile way for nanomaterial-based spintronics applications.
Self-doped lanthanum manganites as a phase-separated system: Transformation of magnetic, resonance, and transport properties with doping and hydrostatic compression
Authors: Doroshev V. D. , Borodin V. A. , Kamenev V. I. , Mazur A. S. , Tarasenko T. N. , Tovstolytkin A. I. , Trukhanov S. V.
Published: November 2008

The magnetic, resonance, and electric properties of LaxMnO3+δ (0.815≤x≤1.0) polycrystalline samples have been studied in the temperature range of 77–370 K and at high pressures of up to 11.5 kbar. It is shown that the increase in the La/Mn ratio gives rise to a change in the low temperature magnetic state from ferromagnetic to cluster spin glass, as well as to a drastic transformation of electric properties. A peculiar double-peaked shape is characteristic of the resistivity versus temperature curves for the intermediate range of x values. Within this range, the application of high pressures drastically changes both the value of resistivity and the character of its temperature dependence. It is shown that the approach, which regards the state of LaxMnO3+δ polycrystals as a mixture of interpenetrating paramagnetic insulating and ferromagnetic metallic phases, is able to successfully describe the peculiarities of the temperature dependence of total resistivity, as well as the features of its transformation under hydrostatic compression. It is demonstrated that the formation of a low temperature resistance peak is a result of a wide-temperature-region coexistence of the phases, which exhibits opposite trends in the temperature dependences of resistivity. The conclusion is made that not only does hydrostatic compression result in drastic changes in the relative volume fractions of the coexisting phases, but it also affects the intrinsic parameters of each of the phases.
Biofunctionalization, cytotoxicity, and cell uptake of lanthanide doped hydrophobically ligated NaYF4 upconversion nanophosphors
Authors: Shan Jingning , Chen Jianbo , Meng Juan , Collins Josh , Soboyejo Wole , Friedberg Joseph S. , Ju Yiguang
Published: November 2008

Surface biofunctionalization of the hydrophobic lanthanide ion doped hexagonal phase NaYF4:Yb,Er upconversion nanophosphors (UCNPs) was achieved by introducing amino and carboxyl groups, respectively. Amino groups were added by using the 3-aminopropyltrimethoxysilane reaction after a thin layer of SiO2 coating. The carboxyl groups on surface were added directly by coating modified amphiphilic polyacrylic acid polymer. Experimental studies of cytotoxicity and cell uptake of UCNPs were conducted. The cytotoxicity analysis of the functionalized UCNPs was conducted by methylthiazol tetrazolium assays. Cell uptake was accomplished by incubating the UCNPs with human osteosarcoma cells and proved by transmission electron microscopy. The results showed that the functionalized UCNPs had very low toxicity compared with the control group, while UCNPs taken into the cells indicated that they had very high biocompatibility. The imaging of UCNPs, which were incubated with AB12 mouse mesothelioma cells and excited by 1 W 980 nm light, showed individual particles with visible light emission. These results exhibited promising applications of functionalized UCNPs in cell imaging and photodynamic therapy.
Atomic structure and glass forming ability of Cu46Zr46Al8 bulk metallic glass
Authors: Wang X. D. , Jiang Q. K. , Cao Q. P. , Bednarcik J. , Franz H. , Jiang J. Z.
Published: November 2008

By using a combination of state-of-the-art experimental and computational methods, the high glass forming ability (GFA) of Cu46Zr46Al8 alloy is studied from the view of its atomic packing. Three-dimensional atomic configuration is well established. It is found that Al atoms almost homogeneously distribute around Cu and Zr atoms without segregation, causing the local environment around Cu and Zr atoms in Cu46Zr46Al8 bulk metallic glass different from that of the major competing phase of Cu10Zr7. Furthermore, the addition of Al not only increases the amount of icosahedronlike clusters but also makes them more homogeneous distribution, which can enhance the GFA by increasing the structural incompatibility with the competing crystalline phases.
Enhancement of exchange bias and ferromagnetic resonance frequency by using multilayer antidot arrays
Authors: Phuoc Nguyen N. , Lim S. L. , Xu F. , Ma Y. G. , Ong C. K.
Published: November 2008

A systematic investigation of the dependences of the exchange bias and the ferromagnetic resonance frequency on the pore size of the antidot arrays fabricated by depositing Permalloy-FeMn multilayer thin films onto self-organized porous anodic aluminum oxide membranes was carried out. The magnetic and microwave properties of the antidot arrays with different pore sizes ranging from 30 to 80 nm are characterized and compared with that of the continuous thin films. It was found that the exchange bias field and the ferromagnetic resonance frequency are increased with the increase of the pore size, which may tentatively be interpreted in the framework of the random field model. It was also found that by using the antidot arrays in the best condition (the FeNi thickness is 20 nm and the pore size is 80 nm), one can enhance the exchange bias field from 65 to 135 Oe and the ferromagnetic resonance frequency from 3.1 to 4.1 GHz accordingly.
An improved active region concept for highly efficient GaSb-based optically in-well pumped vertical-external-cavity surface-emitting lasers
Authors: Schulz Nicola , Rösener Benno , Moser Rüdiger , Rattunde Marcel , Manz Christian , Köhler Klaus , Wagner Joachim
Published: November 2008

An improved active region concept for GaSb-based optically pumped vertical-external-cavity surface-emitting lasers (VECSELs) is presented. The concept is based on GaxIn1−xAsySb1−y quantum wells embedded between AlAsySb1−y barrier layers designed for optical in-well pumping. Advantages of this concept are a high modal gain, the suppression of thermal leakage currents, and an improved thermal conductivity of the active region compared to a conventional GaInAsSb/AlGaAsSb active region design. An in-well pumped VECSEL emitting at 2.24 μm has been realized according to this concept, yielding at a heatsink temperature of 20 °C in continuous-wave operation a power slope efficiency of more than 32% and an absorption of the 1.96 μm pump light of more than 50% without pump recycling.
Magnetization logarithmic susceptibility, damping parameter, and dynamics symmetry extraction
Authors: Wang Xiaobin , Zhu Wenzhong , Xi Haiwen , Gao Zheng , Dimitrov Dimitar
Published: November 2008

Magnetization logarithmic susceptibility is obtained for thermal assisted magnetization reversals under periodic driving forces. Using examples of magnetic elements excited by periodic spin torque currents, we demonstrate both theoretically and experimentally that frequency dependence of magnetization logarithmic susceptibility can be used to extract magnetization dynamics symmetry information and damping parameters for large amplitude nonlinear magnetization reversal.
Setting the chaperonin timer: A two-stroke, two-speed, protein machine
Authors: Grason John P. , Gresham Jennifer S. , Lorimer George H.
Published: November 2008

In a study of the timing mechanism of the chaperonin nanomachine we show that the hemicycle time (HCT) is determined by the mean residence time (MRT) of GroES on the
cis
ring of GroEL. In turn, this is governed by allosteric interactions within the
trans
ring of GroEL. Ligands that enhance the R (relaxed) state (residual ADP, the product of the previous hemicycle, and K
+
) extend the MRT and the HCT, whereas ligands that enhance the T (taut) state (unfolded substrate protein, SP) decrease the MRT and the HCT. In the absence of SP, the chaperonin machine idles in the resting state, but in the presence of SP it operates close to the speed limit, set by the rate of ATP hydrolysis by the
cis
ring. Thus, the conformational states of the
trans
ring largely control the speed of the complete chaperonin cycle.
Setting the chaperonin timer: The effects of K
+
and substrate protein on ATP hydrolysis
Authors: Grason John P. , Gresham Jennifer S. , Widjaja Lusiana , Wehri Sarah C. , Lorimer George H.
Published: November 2008

The effects of potassium ion on the nested allostery of GroEL are due to increases in the affinity for nucleotide. Both positive allosteric transitions, TT-TR and TR-RR, occur at lower [ATP] as [K
+
] is increased. Negative cooperativity in the double-ringed system is also due to an increase in the affinity of the
trans
ring for the product ADP as [K
+
] is increased. Consequently, (
i
) rates of ATP hydrolysis are inversely proportional to [K
+
] and (
ii
) the residence time of GroES bound to the
cis
ring is prolonged and the hemicycle time extended. Substrate protein suppresses negative cooperativity by decreasing the affinity of the
trans
ring for ADP, reducing the hemicycle time to a constant minimum. The
trans
ring thus serves as a variable timer. ATP added to the asymmetric GroEL-GroES resting-state complex lacking
trans
ring ADP is hydrolyzed in the newly formed
cis
ring with a presteady-state burst of ≈6 mol of Pi per mole of 14-mer. No burst is observed when the
trans
ring contains ADP. The amplitude and kinetics of ATP hydrolysis in the
cis
ring are independent of the presence or absence of encapsulated substrate protein and independent of K
+
at concentrations where there are profound effects on the linear steady-state rate. The hydrolysis of ATP by the
cis
ring constitutes a second, nonvariable timer of the chaperonin cycle.
Anthropogenic impacts to large lakes in China: the Tai Hu example
Authors: Dokulil M. , Chen W. , Cai Q.
Published: November 2008

The objective of this study is to summarise limnological effects of cultural eutrophication in some Chinese lakes. Detailed data are shown for Lake Tai Hu as an example for a very large shallow lake affected by anthropogenic impacts. Urban and industrial waste water discharged to the lake result in high nutrient concentrations, large algal blooms dominated by cyanobacteria, mainly species of Microcystis and strong horizontal gradients. Algal growth in this lake is mainly ligh and/or phosphorus limited. This situation is typical for most of the lakes included in this review although some of the large deep lakes seem to be nitrogen deficient. In some cases toxicological effects may be the reason for observed discrepancies. Lakes are of vital importance for populations in China as drinking water and nutritional resources. To prevent water shortage because of conflicting usage, anticipation, control and management of water pollution is urgently needed. Moreover, efforts must be taken to rehabilitate deteriorated freshwater ecosystems.
Application of exergy and specific exergy as ecological indicators of coastal areas
Authors: Jørgensen S.E.
Published: November 2008

Exergy and specific exergy have been found together with nine other ecological attributes for 12 coastal ecosystems. The correlation of the 11 attributes was examined, and the extent to which exergy and specific exergy can be applied as indicators to assess ecosystem health was discussed. The two concepts cover a range of important properties of ecosystems, but other indicators are also required to provide a sufficiently comprehensive assessment of ecosystem health.
Application of the hydraulic biotope concept to the classification of instream habitats
Authors: Wadeson R.A. , Rowntree K.M.
Published: November 2008

A simple matrix developed by a small group of ecologists, geomorphologists and an hydraulic engineer at a workshop in February 1995 was proposed as a standardised classification tool for the recognition of hydraulic biotopes, instream flow environments recognised on the basis of surface flow type and substrate class. Research was carried out in the Buffalo River, South Africa, to test the validity of this classification with respect to measurable hydraulic attributes. Hydraulic biotopes were classified at a number of sites representing a range of stream morphologies, channel scale and discharge. The hydraulic attributes at each sampling point were measured. Using simple measures of flow depth, velocity and bed roughness, hydraulic indices were calculated to describe both the near bed conditions (shear velocity and ‘roughness’ Reynolds number) and the mean flow in the water column (Froude number and Reynolds number). Results indicate that hydraulic biotope classes can be considered as significantly different in terms of flow hydraulics. Hydraulic characteristics appear to be consistent within classes across different spatial scales. An assessment of the influence of discharge showed that differences are recognised in the classes of the lower energy environments (pool and run) but despite considerable within class variability, no significant differences were observed across discharges in the higher energy environments. The hydraulic biotope classification and associated hydraulic biotope matrix shows good potential as a standardised method for classifying instream environments over a range of channel scales and discharges.
The relation between macroinvertebrate assemblages in the Rhine–Meuse delta (The Netherlands) and sediment quality
Authors: Reinhold-Dudok van Heel H.C. , den Besten P.J.
Published: November 2008

Data from ecological and ecotoxicological research were analysed together in order to gain more insight into the biological effects caused by sediment pollution in the delta of the rivers Rhine and Meuse. Information from the following three sources was integrated: surveys of the macroinvertebrate assemblages, chemical analyses in sediment and bioassays. On the basis of cluster analysis and multivariate analysis of a dataset consisting of macrofauna samples from 283 sampling points, it was concluded that the most important factors determining species composition are: presence of solid substrates, depth, current velocity, erosion caused by wind or shipping, and grain size distribution and organic matter content of the sediment. In order to evaluate the role of sediment toxicity in more detail, subsets of the dataset were formed that corresponded with more homogenous clusters of sampling points with regard to sediment characteristics. The degree of sediment toxicity was based on the effects observed in three bioassays with whole sediment or sediment pore water. Further multivariate statistical analysis was performed for four sediment types. Direct linear gradient analysis indicated that for the sediment types fine sand, sandy silt and silt, sediment toxicity can explain part of the variation in species composition. Sediment toxicity was positively correlated with the levels of heavy metals, mineral oil, hexachlorobenzene and/or endrin. It is concluded that the approach followed in this study can contribute to our understanding of the influence of chemical pollution on macroinvertebrate communities.
On the transformation from healthy to degraded aquatic ecosystems
Authors: Rapport David J.
Published: November 2008

Aquatic ecosystems that have become degraded under stress show similarities both in the signs of pathology and in the mechanisms that promote degradation. A review of the transformations in several aquatic systems, including the Laurentian Great Lakes (Canada/US), the Baltic Sea (Finland) and Lake Chapala (Mexico) reveals signs of ‘ecosystem distress’, including alterations in primary and secondary productivity, nutrient cycling, species diversity and biotic composition. A shift from a predominantly vertical to horizontal nutrient spiraling characterizes all three aquatic ecosystems, as does a reduction in the abundance of the larger (high-valued) fish stocks. Once the health of robust systems begins to decline, mechanisms are called into play that tend to perpetuate the ecosystem breakdown. The process may be difficult to reverse, even when sources of initial stress are removed.
Extending causality in the Great Lakes basin ecosystem
Authors: Vallentyne J.R.
Published: November 2008

Michael Gilbertson (Gilbertson, M., 1997. Can. J. Fish. Aquat. Sci. 54, 483–495) has asserted that the adoption of an ecosystem approach to problem-solving in the Great Lakes Water Quality Agreement (GLWQA) of 1978 has undermined the ability of Canada and the United States to grapple effectively with transboundary water pollution. In opposition to this, arguments are presented to suggest that Gilbertson errs in: (1) identifying pollution as the main focus of the GLWQA of 1978; (2) failing to demonstrate that the rise of the ecosystem approach to management caused a reduction of progress in eliminating persistent toxic substances; (3) failing to realize through extended chains of causality that the ecosystem approach and forensic approach to transboundary problem-solving are complementary. The texts and discussions leading up to the signing of the GLWQAs of 1972 and 1978 make it clear that the ecosystem approach to transboundary problem-solving is essential to achieving the purpose of the Great Lakes Water Quality Agreement of 1978 both in regard to the “integrity” clause and the elimination of persistent toxic substances and other pollutants.
A novel signaling pathway impact analysis
Authors: Tarca Adi Laurentiu , Draghici Sorin , Khatri Purvesh , Hassan Sonia S. , Mittal Pooja , Kim Jung-sun , Kim Chong Jai , Kusanovic Juan Pedro , Romero Roberto
Published: November 2008

Motivation: Gene expression class comparison studies may identify hundreds or thousands of genes as differentially expressed (DE) between sample groups. Gaining biological insight from the result of such experiments can be approached, for instance, by identifying the signaling pathways impacted by the observed changes. Most of the existing pathway analysis methods focus on either the number of DE genes observed in a given pathway (enrichment analysis methods), or on the correlation between the pathway genes and the class of the samples (functional class scoring methods). Both approaches treat the pathways as simple sets of genes, disregarding the complex gene interactions that these pathways are built to describe.

Results: We describe a novel signaling pathway impact analysis (SPIA) that combines the evidence obtained from the classical enrichment analysis with a novel type of evidence, which measures the actual perturbation on a given pathway under a given condition. A bootstrap procedure is used to assess the significance of the observed total pathway perturbation. Using simulations we show that the evidence derived from perturbations is independent of the pathway enrichment evidence. This allows us to calculate a global pathway significance P-value, which combines the enrichment and perturbation P-values. We illustrate the capabilities of the novel method on four real datasets. The results obtained on these data show that SPIA has better specificity and more sensitivity than several widely used pathway analysis methods.

Availability: SPIA was implemented as an R package available at http://vortex.cs.wayne.edu/ontoexpress/

Contact:  sorin@wayne.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bitter sweeteners: tetrazole derivatives of arylsulfonylalcanoids – synthesis, structure and comparative study
Authors: Kalinowska-Tłuścik Justyna , Jarzembek Krystyna , Śliwiński Jan , Oleksyn Barbara J. , Kozik Violetta , Polański Jarosław
Published: November 2008

Within a research project aimed at the design of new sweeteners, the tetrazole moiety was introduced to arylsulfonylalkanoic acids (ASA) as a bioisostere of the carboxyl group. The crystal structures of four newly synthesized tetrazole derivatives and one intermediate product of the reaction were determined in order to explain the bitter taste of these compounds. Three chiral compounds crystallize as racemic mixtures in centrosymmetric space groups of the monoclinic system, whereas the non-chiral compound, with a higher dipole moment, crystallizes in the polar space group Cc. Intermolecular N—H...N hydrogen bonds between tetrazole moieties were observed in all four structures and are compared with the analogous interactions observed in tetrazole derivatives deposited in the Cambridge Structural Database (CSD). Specifically, the typical N1—H...N4 as well as N1—H...N3 interactions, which are less abundant in the CSD, are described. The formation of the latter interaction type can be hypothetically explained by an asymmetry of π-electron distribution in the tetrazole rings caused by the crystalline environment. Important features of the crystal architecture are the chains of molecules linked by N—H...N bonds. A possible reason for the lack of a sweet taste of the tetrazoles investigated may be the improper position of the tetrazole H atom, and the mutual orientation of the proton donor and acceptor in their molecules. This orientation does not allow the tetrazoles to interact with the sweet-taste receptor in a way similar to that of ASA. The bitter taste of the investigated compounds needs further study.
Modular crystals as modulated structures: the case of the lillianite homologous series
Authors: Elcoro Luis , Perez-Mato J. M. , Friese Karen , Petříček Václav , Balić-Žunić Tonči , Olsen Lars Arnskov
Published: November 2008

The use of the superspace formalism is extended to the description and refinement of the homologous series of modular structures with two symmetry-related modules with different orientations. The lillianite homologous series has been taken as a study case. Starting from a commensurate modulated composite description with two basic subsystems corresponding to the two different modules, it is shown how a more efficient description can be achieved using so-called zigzag modulation functions. These linear zigzag modulations, newly implemented in the program JANA2006, have very large fixed amplitudes and introduce in the starting model the two orientations of the underlying module sublattices. We show that a composite approach with this type of function, which treats the cations and anions as two separate subsystems forming a misfit compound, is the most appropriate and robust method for the refinements.
Structures of mono-unsaturated triacylglycerols. V. The β′1-2, β′-3 and β2-3 polymorphs of 1,3-dilauroyl-2-oleoylglycerol (LaOLa) from synchrotron and laboratory powder diffraction data
Authors: van Mechelen Jan B. , Goubitz Kees , Pop Mihaela , Peschar Rene , Schenk Henk
Published: November 2008

The crystal structures of the \beta ^{\prime}_1-2, the β′-3 and the β2-3 polymorphs of 1,3-dilauroyl-2-oleoylglycerol have been solved from powder diffraction data. The packing of the β2-3 polymorph is similar to that of other cis mono-unsaturated triacylglycerols. Both the β′ polymorphs are crystallized in a novel type of packing in which one of the saturated lauroyl chains is packed side-by-side with part of the unsaturated oleoyl chain.