bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical investigations of flow over a sphere in the subcritical and supercritical regimes
Authors: Constantinescu George , Squires Kyle
Published: April 2004

The flow field around a sphere in an uniform flow has been analyzed numerically for conditions corresponding to the subcritical (laminar separation) and supercritical (turbulent separation) regimes spanning a wide range of Reynolds numbers (104–106). Particular attention has been devoted to assessing predictions of the pressure distribution, skin friction, and drag as well as to understanding the changes in the wake organization and vortex dynamics with the Reynolds number. The unsteady turbulent flow is computed using detached-eddy simulation, a hybrid approach that has Reynolds-averaged Navier–Stokes behavior near the wall and becomes a large eddy simulation in the regions away from solid surfaces. For both the subcritical and supercritical solutions, the agreement with experimental measurements for the mean drag and pressure distribution over the sphere is adequate; differences in skin friction exist due to the simplistic treatment of the attached boundary layers in the computations. Improved agreement in the skin-friction distribution is obtained for the supercritical flows in which boundary layer transition is fixed at the position observed in experiments conducted at the same Reynolds numbers. For the subcritical flows the Strouhal number, St, associated with the large-scale shedding is predicted at St∼0.195 along with a higher frequency component associated with the development of the Kelvin–Helmholtz instabilities in the detached shear layers. If in the subcritical regime the wake assumes a helical-like form due to the shedding of hairpin-like vortices at different azimuthal angles, in the supercritical regime the wake structure is characterized by “regular” shedding of hairpin-like vortices at approximately the same azimuthal angle and at a much higher frequency (St∼1.3) that is practically independent of the Reynolds number and not sensitive to the position of laminar-to-turbulent transition.
A comparative study of the turbulent Rayleigh–Taylor instability using high-resolution three-dimensional numerical simulations: The Alpha-Group collaboration
Authors: Dimonte Guy , Youngs D. L. , Dimits A. , Weber S. , Marinak M. , Wunsch S. , Garasi C. , Robinson A. , Andrews M. J. , Ramaprabhu P. , Calder A. C. , Fryxell B. , Biello J. , Dursi L. , MacNeice P. , Olson K. , Ricker P. , Rosner R. , Timmes F. , Tufo H. , Young Y.-N. , Zingale M.
Published: April 2004

The turbulent Rayleigh–Taylor instability is investigated in the limit of strong mode-coupling using a variety of high-resolution, multimode, three dimensional numerical simulations (NS). The perturbations are initialized with only short wavelength modes so that the self-similar evolution (i.e., bubble diameter Db∝amplitude hb) occurs solely by the nonlinear coupling (merger) of saturated modes. After an initial transient, it is found that hb∼αbAgt2, where A=Atwood number, g=acceleration, and t=time. The NS yield Db∼hb/3 in agreement with experiment but the simulation value αb∼0.025±0.003 is smaller than the experimental value αb∼0.057±0.008. By analyzing the dominant bubbles, it is found that the small value of αb can be attributed to a density dilution due to fine-scale mixing in our NS without interface reconstruction (IR) or an equivalent entrainment in our NS with IR. This may be characteristic of the mode coupling limit studied here and the associated αb may represent a lower bound that is insensitive to the initial amplitude. Larger values of αb can be obtained in the presence of additional long wavelength perturbations and this may be more characteristic of experiments. Here, the simulation data are also analyzed in terms of bubble dynamics, energy balance and the density fluctuation spectra.
Self-similar recoil of inviscid drops
Authors: Sierou Asimina , Lister John R.
Published: April 2004

After capillary pinchoff of a fluid thread or drop, the newly created drop tips recoil due to the large local curvature. Similarity solutions for the postpinchoff recoil of an axisymmetric inviscid fluid of density ρ1 and surface tension γ immersed in a surrounding fluid of density ρ2 are obtained over a range of the density ratio D=ρ2/ρ1. The far-field shape of the two new drops and the far-field dipole potentials are prescribed from known prepinching solutions [D. Leppinen and J. R. Lister, Phys. Fluids 15, 568 (2003)] and the positions and self-similar shape of the two recoiling tips are calculated. The momentum of the prepinching flow makes a significant difference to the recoiling shapes. Capillary waves are observed, in agreement with previous two-dimensional studies and analytical calculations, and the wave frequency is found to increase with D. The recoil of a single axisymmetric drop (with a conical far-field shape) under surface tension is also studied as a function of D and the far-field cone angle θ0. Capillary waves are again observed, and the results for small values of θ0 are shown to agree well with previous asymptotic predictions. The related problem of violent jet emission, following the formation of a near-conical structure with very high curvature at its tip, is also discussed and its similarity with the recoiling cone problem investigated.
Optimized sensor placement for urban flow measurement
Authors: Mokhasi Paritosh , Rempfer Dietmar
Published: April 2004

In this paper, we discuss a novel approach to the description of atmospheric flows in urban geometries. Our technique is based on the method of proper orthogonal decomposition (POD). We devise a method that enables us to compute the time-varying coefficients of a Karhunen–Loève expansion of the urban flow field using knowledge of instantaneous velocity data taken at a minimum number of locations simultaneously. Using the POD basis functions and these velocity data, we solve a set of linear equations which gives us an estimate of the exact expansion coefficients. This method allows us to compute estimates for all coefficients thereby enabling us to reconstruct a close approximation to the flow field which is optimal in a certain sense. A quantitative comparison of the approximate coefficients with the coefficients of an exact Karhunen–Loève expansion shows that the method works very well. Our method provides a practical approach to reconstructing the flow field using a minimum amount of information.
Organic plastic laser in holographic materials by photopolymerization
Authors: Dorkenoo Kokou D. , Crégut Olivier , Fort Alain
Published: April 2004

We demonstrate how to excite a laser mode in a thin film of organic holographic material. By initiating a photopolymerization process with visible light, we generate a distributed feedback laser in such films. The technique fulfills two important aims. First, the construction of a tunable laser with the help of an interferometric system and, second, the fabrication of a corrugated surface without the help of any etching or photolithography process. In short, we demonstrate a full laser action in a plastic medium doped with rhodamine 6G, which acts as a lasing dye. Usually, a major problem with such lasers is the aging of the dye. In the approach we develop, this problem can be overcome by periodically cleaning the gain region and refilling it with fresh dye molecules.
Fingering instabilities of exothermic reaction-diffusion fronts in porous media
Authors: Kalliadasis S. , Yang J. , De Wit A.
Published: April 2004

We consider the density fingering of exothermic autocatalytic fronts in vertically oriented Hele-Shaw cells with chemical reactions whose solutal and thermal contributions to density changes have opposite signs. Using the Darcy–Boussinesq equations we examine the influence of the competition between solutal and thermal density changes on the linear stability of traveling fronts and the fully nonlinear dynamics. Ascending fronts are characterized by standard Rayleigh–Taylor fingering dispersion curves and in the nonlinear stage of the instability they feature thermal plumes. Descending fronts on the other hand behave strikingly differently as they can feature for some values of the parameters Turing-type dispersion curves and stationary patterns with fingers of constant amplitude and wavelength.
Characteristic scales and drag reduction evaluation in turbulent channel flow of nonconstant viscosity viscoelastic fluids
Authors: Housiadas Kostas D. , Beris Antony N.
Published: April 2004

The polymer-induced drag reduction in turbulent viscoelastic channel flow is customarily investigated from first principles through direct numerical simulations. In contrast to Newtonian fluid mechanics, in viscoelastic fluid mechanics there are more parameters and those are typically referenced under standard, zero shear-rate conditions. For a nonconstant viscosity non-Newtonian fluid it is necessary to correlate the effective wall viscosity to the parameters of the model. This correlation can only be evaluated a posteriori based on the wall statistics. It is used here to relate the computational to the wall units. Furthermore, the relationship between the effective wall properties and the corresponding steady shear values is elucidated. Moreover, an accurate and robust procedure for evaluating the overall drag reduction is presented.
Rotating plasma discharges of high-pressure molecular vapor using circularly polarized microwaves
Authors: Kim Jin Joong , Ko Jung Tae , Won Dong Ho , Kim Jeong Won , Kim S. S. , Chang Hong-Young
Published: April 2004

We report an experimental demonstration of rotating plasma discharges of diatomic molecular vapor at pressures of a few hundred kPa, i.e., above atmospheric pressure, using circularly polarized microwaves at 2.45 GHz with no external magnetic fields. The active zone of discharges is observed to rotate at frequency of the order of 0.1–20 Hz, which is equivalent to a linear speed of a few cm/s, depending upon the power level, with the same rotation as that of applied circularly polarized microwave fields, regardless of their helicity. The lethargic rotation of the plasma discharges is explained on the basis of ponderomotive force including absorption of the intrinsic angular momentum of the circularly polarized microwaves.
Flow characteristics of liquids in microtubes driven by a high pressure
Authors: Cui Hai-hang , Silber-Li Zhan-hua , Zhu Shan-nong
Published: April 2004

The flow characteristics of liquids in microtubes driven by a high pressure ranging from 1 MPa to 30 MPa are studied in this paper. The diameter of the microtube is from 3 μm to 10 μm and liquids composed of simple small molecules are chosen as the working fluids. The Reynolds number ranges from 0.1 to 24. The behavior of isopropanol and carbon tetrachloride under high pressure is found different from the prediction from conventional Hagen–Poiseuille (HP) equation. The normalized friction coefficient C* increases significantly with the pressure. From an analysis of the microtube deformation, liquid compressibility, viscous heating and wall slip, it may be seen that the viscosity at high pressure plays an important role here. An exponential function of viscosity vs pressure is introduced into the HP equation to counteract the difference between experimental and theoretical values. However, this difference is not so marked for di-water.
Numerical simulations of flow and heat transfer past a circular cylinder with a periodic array of fins
Authors: Lee Dong Hyuk , Ha Man Yeong , Balachandar S. , Lee Sangsan
Published: April 2004

Three-dimensional, time-dependent solutions of flow and heat transfer past a circular cylinder with a periodic array of circular fins is obtained using an accurate and efficient spectral multidomain methodology. A Fourier expansion with a corresponding uniform grid is used along the circumferential direction. A spectral multidomain method with Chebyshev collocation is used along the r–z plane to handle the periodic array of circular fins attached to the surface of the cylinder. At a Reynolds number of 300 based on the cylinder diameter, results for the finned cylinder are compared with those of a smooth cylinder in order to see the effects of the presence of the fin array on flow and heat transfer. Detailed structure of fluid flow and temperature fields are obtained as a function of time to investigate how the fin array changes heat transfer mechanism related to the vortical structure in the wake region.
Influence of the density gradient on the duration of Si-Kα pulses generated by a double femtosecond-laser pulse
Authors: Pisani F. , Andiel U. , Eidmann K. , Witte K. , Uschmann I. , Morak A. , Förster E. , Sauerbrey R.
Published: April 2004

We have studied the duration of Si-Kα x-ray pulses generated by two subsequent femtosecond-laser pulses (λ=395 nm, pulse duration=180 fs) separated by 20 ps, which were focused on a glass target to intensities of a few 1017 W/cm2. A toroidally bent crystal was used to image the Si-Kα pulses emitted by the target on the cathode of an ultrafast streak camera. While the duration of the first Kα pulse is 1.1 ps, the duration of the second Kα pulse is considerably longer by ≈0.7 ps. This effect is attributed to the preplasma created by the first laser pulse and seen by the second one.
Improvement of second-harmonic generation in quantum-cascade lasers with true phase matching
Authors: Malis Oana , Belyanin Alexey , Gmachl Claire , Sivco Deborah L. , Peabody Milton L. , Sergent A. Michael , Cho Alfred Y.
Published: April 2004

About a 100-fold improvement of the second-harmonic generation in a quantum-cascade laser with integrated optical nonlinearity was obtained by including phase-matching considerations in the design of the deep-etched ridge waveguide. The waveguide layer structure was optimized to minimize the phase mismatch of the zero-order mode of the fundamental light with the second-order transverse mode of the second-harmonic light. Exact phase matching is made possible by the faster decrease of the modal refractive index of the fundamental light with decreasing ridge width relative to the refractive index of the second-harmonic light. Up to 240 μW of the second-harmonic power and a nonlinear power conversion efficiency of up to 36 mW/W2 were achieved.
Onset of temporal aperiodicity in high Prandtl number liquid bridge under terrestrial conditions
Authors: Melnikov D. E. , Shevtsova V. M. , Legros J. C.
Published: April 2004

The paper presents a three-dimensional numerical study of the bifurcations and onset of chaotic regime for the thermoconvective oscillatory flow in cylindrical liquid bridge. Three-dimensional Navier–Stokes equations in Boussinesq approximation are solved numerically by finite volume method. Silicone oil 1cSt, with rather large Prandtl number, Pr=18.8, is chosen as test liquid. The simulations are done at normal gravity conditions and unit aspect ratio. The dependence of viscosity of the fluid upon temperature allows us to be close to the real phenomenon. Both spatial and temporal changes occurring in the system are analyzed. The results are compared to the experimental data. A following sequence of well-defined dynamic regimes was detected when temperature difference between the supporting disks is increasing: steady, periodic, quasiperiodic, periodic, and chaotic. The observed succession of bifurcations on the way to chaos is similar to the one coming from experiments. Except for these dynamic bifurcations the system exhibits numerous transitions in spatial organization of the flow. Two-dimensional steady-state flow undergoes standing wave (SW) with azimuthal wave number m=1 as a result of supercritical Hopf bifurcation. Moving above the critical point the following succession of flow states has been numerically found: SW(m=1)→TW (m=1)→SW(m=1+2)→TW(m=1+2). The transition to chaos occurs while the flow pattern represents a traveling wave (TW) with a mixed mode m=1+2, while the m=2 is dominant. Particular attention is paid to the analysis of special properties of the flow: entropy, net azimuthal flow, frequency skips, splitting of maxima, and related phenomena.
Effects of clinorotation and positive dielectrophoresis on suspensions of heavy particles
Authors: Markarian Nikolai , Yeksel Mike , Khusid Boris , Kumar Anil , Tin Padetha
Published: April 2004

Experiments in both microgravity (aboard the NASA research aircraft KC-135) and ground-based environments were conducted in a clinostat (a channel slowly rotated around its horizontal axis to simulate “weightlessness”) in which a dilute suspension of heavy, positively polarized spheres was exposed to a high-gradient strong ac electric field. While dielectrophoresis is shown to provide a powerful method for the manipulation and concentration of particles in clinostats, we find that clinorotation does not simulate the zero gravity morphology of the aggregation pattern due to an unexpectedly pronounced effect of a relatively weak, rotating gravity. This effect imposes certain limitations on the use of ground-based tests for predicting the operation of electrotechnologies for the control and manipulation of suspensions in microgravity.
Time dependent β-convection in rapidly rotating spherical shells
Authors: Morin V. , Dormy E.
Published: April 2004

A quasi-geostrophic, or β, model of nonlinear thermal convection in rapidly rotating spherical fluid shells is investigated. We study time dependent instabilities for a range of Rayleigh number and Ekman number with a Prandtl number set to the unity. Above the onset of convection, increasing the Rayleigh number for a given Ekman number, we reproduce the sequence of bifurcations described by Busse [Phys. Fluids 14, 1301 (2002)] for the three-dimensional case: A first transition results in vacillating flow; a second transition gives rise to chaotic oscillations in time and localized convection in space; then a third leads to quasi-periodic relaxation oscillations. This study shows that the quasigeostrophic model encompasses the desired bifurcation sequence. It allows the investigation of a range of Ekman numbers unavailable to three-dimensional models with present computing resources. Decreasing the Ekman number, we unexpectedly found that all three transitions occur for marginally supercritical Rayleigh number. The range of Rayleigh number for which the amplitude of convection is steady vanishes in the asymptotic limit of small Ekman numbers. This effect could significantly alter the nature of the instability characterizing the onset of convection in particular whether it is a supercritical or subcritical bifurcation.
Spiral exchange interaction in diluted magnetic semiconductor junction
Authors: Sun Shih-Jye , Cheng Song-Shien , Lin Hsiu-Hau
Published: April 2004

We studied the exchange interactions mediated by polarized itinerant carriers in diluted magnetic semiconductor (DMS) junction. In contrast to the ordinary Ruderman–Kittel–Kasuya–Yosida oscillations, the induced moment possesses an interesting spiral motion, accompanied by angular oscillations. The spiral motion remains robust in the entire T<Tc regime while the oscillatory motion gets enhanced as T→Tc. To explore the phenomena, it is proposed that a ferromagnet/DMS/ferromagnet junction would bring out interesting spin-dependent transport properties and possible applications in spintronics.
Impact of spin blocking on the energy relaxation of electrons in quantum-dot lasers
Authors: Cao C. , Deppe D. G.
Published: April 2004

The impact of the electron spin relaxation time on the electron distribution in quantum-dot lasers is analyzed. The results show that a relatively long spin relaxation time (∼300 ps) can create a nonequilibrium carrier distribution in quantum-dot lasers. It is shown that a mechanism we call “spin blocking” increases emission from the quantum-dot excited states and can lead to excited state lasing in quantum-dot lasers.
Survival of native plants of Hawkesbury Sandstone communities with additional nutrients: effect of plant age and habitat
Authors: Thomson V. P. , Leishman M. R.
Published: April 2004

Australian soils are naturally low in nutrient concentrations, particularly nitrogen (N) and phosphorus (P). Native plants are well adapted to low-nutrient soils, and can be adversely affected when exposed to higher concentrations of nutrients. The Hawkesbury Sandstone soils in northern Sydney are naturally low in nutrients, but often receive additional nutrient input from urban stormwater run-off. Increases in soil nutrients in urban bushland are associated with the presence of exotic species, and the decline in the diversity of native species. This study tested the hypothesis that high concentrations of nutrients, in particular P, in the disturbed soils of urban bushland, reduce survival of native plants. We examined the survival of native species under five different nutrient concentrations that are typical of nutrient-enriched urban bushland soil, in two glasshouse experiments. The experiments examined both survival of seedlings and survival of 6-month-old plants. We used native species that are adapted to both nutrient-poor and nutrient-rich soils. In general, the survival of native plants decreased with increasing nutrient concentrations. At soil total-P concentrations >200 mg kg–1, most plants died. Seedlings were more sensitive to added nutrients than the 6-month-old plants. Species that were from higher-nutrient soil had consistently higher survival than species from low-nutrient soils, under the nutrient addition treatments. These results suggest that at high soil nutrient concentrations typical of stormwater-affected urban bushland, native plant species of low-nutrient soils will be unable to survive. If ecological restoration works are to be done in such areas, replanting with more mature plants from naturally high-nutrient habitats is likely to be the most successful. However, restoration of these areas may have limited success and they are likely to remain dominated by exotic plant species.
Physical and functional association of RNA polymerase II and the proteasome
Authors: Gillette Thomas G. , Gonzalez Fernando , Delahodde Agnes , Johnston Stephen Albert , Kodadek Thomas
Published: April 2004

Recent studies from a number of laboratories have revealed a surprising number of connections between RNA polymerase II transcription and the ubiquitin/proteasome pathway. We now find yet another intersection of these pathways by showing that the 26S proteasome associates with regions of the
GAL1
,
GAL10
, and
HSP82
genes, including the 3′ ends, in a transcription-dependent fashion. The appearance of the proteasome on these inducible genes correlates with both the accumulation of transcripts and the buildup of RNA polymerase II complexes in the same region. Furthermore, the 26S proteasome and RNA polymerase II coimmunoprecipitate, and inhibition of 26S proteolytic activity leads to increased read through of a transcription termination site. We suggest that the proteasome is generally recruited to the DNA at sites of stalled RNA polymerase and may act to resolve these complexes.
Illegitimate WNT signaling promotes proliferation of multiple myeloma cells
Authors: Derksen Patrick W. B. , Tjin Esther , Meijer Helen P. , Klok Melanie D. , Mac Gillavry Harold D. , van Oers Marinus H. J. , Lokhorst Henk M. , Bloem Andries C. , Clevers Hans , Nusse Roel , van der Neut Ronald , Spaargaren Marcel , Pals Steven T.
Published: April 2004

The unrestrained growth of tumor cells is generally attributed to mutations in essential growth control genes, but tumor cells are also influenced by signals from the environment. In multiple myeloma (MM), the factors and signals coming from the bone marrow microenvironment are possibly even essential for the growth of the tumor cells. As targets for intervention, these signals may be equally important as mutated oncogenes. Given their oncogenic potential, WNT signals form a class of paracrine growth factors that could act to influence MM cell growth. In this paper, we report that MM cells have hallmarks of active WNT signaling, whereas the cells have not undergone detectable mutations in WNT signaling genes such asadenomatous polyposis coliand β-catenin(CTNNB1). We show that the malignant MM plasma cells overexpress β-catenin, including its N-terminally unphosphorylated form, suggesting active β-catenin/T cell factor-mediated transcription. Further accumulation and nuclear localization of β-catenin, and/or increased cell proliferation, was achieved by stimulation of WNT signaling with either Wnt3a, LiCl, or the constitutively active S33Y mutant of β-catenin. In contrast, by blocking WNT signaling by dominant-negative T cell factor, we can interfere with the growth of MM cells. We therefore suggest that MM cells are dependent on an active WNT signal, which may have important implications for the management of this incurable form of cancer.
Epoxidation of unfunctionalized olefins by Mn(salen) catalyst using organic peracids as oxygen source: A theoretical study
Authors: Khavrutskii Ilja V. , Musaev Djamaladdin G. , Morokuma Keiji
Published: April 2004

The mechanism and origin of asymmetric induction in the Mn
III
(salen)-catalyzed epoxidation by peracetic acid have been elucidated by the density functional [Becke three-parameter hybrid functional combined with Lee–Yang–Parr correlation functional (B3LYP)] method in two different regimes: with and without an axial ligand. The acylperoxo complexes of Mn
II,III,IV
in
cisON cisNO
and
trans
geometrical configurations cannot compete with the catalyst-free Prilezhaev epoxidation. Instead, oxo species perform epoxidation following the O—O bond cleavage in the acylperoxo complexes. The epoxidation may proceed in a concerted and/or radical-mediated stepwise manner. The actual mechanism of the epoxidation depends on the electronic and oxidation state of the oxo species and the nature of the axial ligand. The olefin can approach the reactive MnO fragment of both
cis
and
trans
-
l
-isomers of the plain oxo species along multiple distinct directions: native approaches. The native approaches are used to rationalize the inversion of the absolute configuration of the product epoxide due to the axial ligand.
Suppression of caspase-8- and -10-associated RING proteins results in sensitization to death ligands and inhibition of tumor cell growth
Authors: McDonald E. Robert , El-Deiry Wafik S.
Published: April 2004

The destruction of cellular targets during apoptosis is carried out by caspases, which are negatively regulated by the inhibitor of apoptosis proteins (IAP); however, death effector domain (DED) caspases of the extrinsic pathway are refractory to the IAP family. We have isolated a family of apoptotic inhibitors [caspases-8- and -10-associated RING proteins (CARPs)] that bind to and negatively regulate DED caspases. When overexpressed, CARPs, via an IAP-like RING domain, can contribute to the ubiquitin-mediated proteolysis of DED caspases. Furthermore, CARPs are rapidly cleaved during apoptosis. However, in tumors and tumor cell lines, they are overexpressed, and their silencing leads to restoration of efficient apoptosis via enhanced activation of DED caspases. Long-term inhibition of CARP expression results in suppression of cancer cell growth, highlighting their importance in tumor cell survival.
Enantioselective Diels–Alder reactions catalyzed by hydrogen bonding
Authors: Thadani Avinash N. , Stankovic Ana R. , Rawal Viresh H.
Published: April 2004

Like molecules of life (e.g., proteins and DNA), many pharmaceutical drugs are also asymmetric (chiral); they are not superimposable on their mirror images. One mirror image form (enantiomer) of a drug can have desirable activity, the other not. Consequently, the development of methods for the selective synthesis of one enantiomer is of great scientific and economic importance. We report here that a simple, commercially available chiral alcohol, α,α,α′,α′-tetraaryl-1,3-dioxolane-4,5-dimethanol (TADDOL), catalyzes the
all
-carbon Diels–Alder reactions of aminosiloxydienes and substituted acroleins to afford the products in good yields and high enantioselectivities (up to 92% enantiomeric excess). It is remarkable that the reactions are promoted by hydrogen bonding, the ubiquitous “glue” that helps to keep water molecules together and holds up the 3D structures of proteins. Hydrogen bond catalysis is little used in chemical synthesis, wherein most reactions are promoted by complexes of Lewis acidic metal salts coordinated to chiral ligands. As it does for enzymes, hydrogen bonding not only organizes TADDOL into a well defined conformation, but, functioning as a Brønsted acid catalyst, it also activates the dienophile toward reaction with the diene. The gross structure of the TADDOL has been found to have a profound influence on both the rate and the enantioselectivity of the cycloadditions. These structure–function effects are rationalized by evaluating the conformation adopted by the TADDOLs in the crystal state. It is suggested that π,π-stacking plays an central role in the overall catalytic cycle, in particular, the enantioselective step.
Dissecting the pathological effects of human Aβ40 and Aβ42 in
Drosophila
: A potential model for Alzheimer's disease
Authors: Iijima Koichi , Liu Hsin-Ping , Chiang Ann-Shyn , Hearn Stephen A. , Konsolaki Mary , Zhong Yi
Published: April 2004

Accumulation of amyloid-β (Aβ) peptides in the brain has been suggested to be the primary event in sequential progression of Alzheimer's disease (AD). Here, we use
Drosophila
to examine whether expression of either the human Aβ40 or Aβ42 peptide in the
Drosophila
brain can induce pathological phenotypes resembling AD. The expression of Aβ42 led to the formation of diffused amyloid deposits, age-dependent learning defects, and extensive neurodegeneration. In contrast, expression of Aβ40 caused only age-dependent learning defects but did not lead to the formation of amyloid deposits or neurodegeneration. These results strongly suggest that accumulation of Aβ42 in the brain is sufficient to cause behavioral deficits and neurodegeneration. Moreover,
Drosophila
may serve as a model for facilitating the understanding of molecular mechanisms underlying Aβ toxicity and the discovery of novel therapeutic targets for AD.
Insight into molecular core clock mechanism of embryonic and early postnatal rat suprachiasmatic nucleus
Authors: Sládek Martin , Sumová Alena , Kováčiková Zuzana , Bendová Zdenka , Laurinová Kristýna , Illnerová Helena
Published: April 2004

Rhythmicity of the rat suprachiasmatic nucleus (SCN), a site of the circadian clock, develops prenatally. A molecular clockwork responsible for the rhythmicity consists of clock genes and their negative and positive transcriptional–translational feedback loops. The aim of the present study was to discover the development of the clockwork during ontogenesis. Daily profiles of
Per1
,
Per2
,
Cry1
,
Bmal1
, and
Clock
mRNA in the SCN of fetuses at the embryonic day (E)19 and of newborn rats at the postnatal day (P)3 and P10 were assessed by the
in situ
hybridization method. In addition, daily profiles of PER1, PER2, and CRY1 proteins at E19 were assessed by immunohistochemistry. As early as at E19, all the studied clock genes were already expressed in the SCN. However, no SCN rhythm in their expression was detected;
Per1
,
Cry1
, and
Clock
mRNA levels were low, whereas
Bmal1
mRNA levels were high and
Per2
mRNA levels were medium. Moreover, no rhythms of PER1, PER2, and CRY1 were detectable, as no immunoreactive cells were present at E19. At P3, rhythms in
Per1
,
Per2
,
Cry1
, and
Bmal1
, but not in
Clock
mRNA, were expressed in the SCN. The rhythm matured gradually; at P10, the amplitude of
Per1
,
Per2
, and
Bmal1
mRNA rhythms was more pronounced than at P3. Altogether, the data show a gradual development of both the positive and negative elements of the molecular clockwork, from no detectable rhythmicity at E19 to highly developed rhythms at P10.
The T-Stem Determines the Cytosolic or Mitochondrial Localization of Trypanosomal tRNAsMet
Authors: Crausaz Esseiva Anne , Maréchal-Drouard Laurence , Cosset Anne , Schneider André
Published: April 2004

The mitochondrion of Trypanosoma brucei lacks tRNA genes. Organellar translation therefore depends on import of cytosolic, nucleus-encoded tRNAs. Except for the cytosol-specific initiator tRNAMet, all trypanosomal tRNAs function in both the cytosol and the mitochondrion. The initiator tRNAMetis closely related to the imported elongator tRNAMet. Thus, the distinct localization of the two tRNAsMetmust be specified by the 26 nucleotides, which differ between the two molecules. Using transgenic T. brucei cell lines and subsequent cell fractionation, we show that the T-stem is both required and sufficient to specify the localization of the tRNAsMet. Furthermore, it was shown that the tRNAMetT-stem localization determinants are also functional in the context of two other tRNAs. In vivo analysis of the modified nucleotides found in the initiator tRNAMetindicates that the T-stem localization determinants do not require modified nucleotides. In contrast, import of native tRNAsMetinto isolated mitochondria suggests that nucleotide modifications might be involved in regulating the extent of import of elongator tRNAMet.
F2CS: FSSP to CATH and SCOP prediction server
Authors: Getz Gad , Starovolsky Alina , Domany Eytan
Published: April 2004

Summary: The F2CS server provides access to the software, F2CS2.00, which implements an automated prediction method of SCOP and CATH classifications of proteins, based on their FSSP Z-scores.

Availability: Free at http://www.weizmann.ac.il/physics/complex/compphys/f2cs/

Supplementary information: The site contains links to additional figures and tables.
Ligand Depot: a data warehouse for ligands bound to macromolecules
Authors: Feng Zukang , Chen Li , Maddula Himabindu , Akcan Ozgur , Oughtred Rose , Berman Helen M. , Westbrook John
Published: April 2004

Summary: Ligand Depot is an integrated data resource for finding information about small molecules bound to proteins and nucleic acids. The initial release (version 1.0, November, 2003) focuses on providing chemical and structural information for small molecules found as part of the structures deposited in the Protein Data Bank. Ligand Depot accepts keyword-based queries and also provides a graphical interface for performing chemical substructure searches. A wide variety of web resources that contain information on small molecules may also be accessed through Ligand Depot.

Availability: Ligand Depot is available at http://ligand-depot.rutgers.edu/. Version 1.0 supports multiple operating systems including Windows, Unix, Linux and the Macintosh operating system. The current drawing tool works in Internet Explorer, Netscape and Mozilla on Windows, Unix and Linux.
A reflection on theory building and the development of management knowledge
Authors: Trim Peter R.J. , Lee Yang‐Im
Published: April 2004

The process of management research involves various complexities and can sometimes be viewed as highly time consuming. Good research can and does provide a momentum for further research to be undertaken and this means that a researcher may have to think “outside the box” in order to achieve new insights. A researcher may also need to adopt a rather “risky” research strategy that encapsulates the critical theory approach, if they are to achieve something unique. However daunting this appears, it should be appreciated that the processes of globalization and interconnectivity allow various methodological approaches to be used vis‐à‐vis the collection, analysis and interpretation of data. In order that new models, concepts and theories can be produced, it is necessary for researchers to engage in theory building, and to try out methods such as the grounded theory approach.
Legal and privacy issues surrounding customer databases and e‐merchant bankruptcies: reflections on Toysmart.com
Authors: Kelly Eileen P. , Erickson G. Scott
Published: April 2004

From a consumer perspective, the issue of personal, informational privacy is of growing concern as our society becomes more and more digitized. For businesses however, detailed customer information is a valuable and lucrative commodity. The latter is particularly true for online businesses with few tangible assets. In order to allay consumer privacy fears, some online businesses post privacy policies promising not to divulge customer information. Yet, when an online business files for bankruptcy, creditors will demand that the customer database be sold with other assets. This article examines the legal and privacy issues surrounding customer databases that arise when an online business files for bankruptcy
International CALIBER – 2004
Authors: Vijayakumar J.K. , Patel Yatrik
Published: April 2004

Reports on INFLIBNET’s annual convention International CALIBER – 2004 that was held at Jamia Millia Islamia, a central university in New Delhi on 11‐13 February. States that the theme of the convention was “Road Map to New Generation of libraries using emerging technologies” and papers were presented which emphasized the importance of the architecture of information for libraries and the need for a globalized information environment. The concluding session of the convention proposed that CALIBER – 2004 was an excellent opportunity for librarians and students to interact with experts in the field and that it would boost the ongoing initiatives for a library information system in agriculture libraries.
Of budgets and boycotts: the battle over open access publishing
Authors: Medeiros Norm
Published: April 2004

This article recounts the history of electronic journals, and the evolution of library processes to manage them. The article reviews recent controversies regarding the future of electronic publishing, and describes one important and innovative electronic publisher, the Public Library of Science.
OCLC’s Office of Research: the value of research to an organization and to a profession
Authors: Ward Diane Marie
Published: April 2004

Presents a survey of the OCLC Office of Research (OR) with emphasis on two projects (Web Characterization Project and Economics of Digital Preservation), and their impact on the library and information science community. The OR is characterized as a model of an informatics organization that recognizes the needs of its library constituents and delivers new technological products as a result of ongoing research projects.
The second demographic transition, new household forms and the urban population of France during the 1990s
Authors: Ogden Philip E , Hall Ray
Published: April 2004

European household structures and their geography have been transformed in recent decades as a response to the interplay of demographic events and changing lifestyles. The formation of new households generally outstrips the rate of population increase, as more numerous and smaller households result from changing patterns of marriage, child‐bearing, divorce and longevity. This paper tests some of the underlying hypotheses of the ‘second demographic transition’ using data from the most recent (1999) French population census. It provides an analysis of changing national household structures over the last quarter of the twentieth century and highlights the importance of smaller households, with particular emphasis on the rise of living alone. Trends identified in earlier work have intensified during the 1990s. In discussing the geography of new household forms, the paper focuses particularly on the evolution of major central cities and argues for more explicit links between their distinctive population and household structures and wider socio‐economic change.
Conceptual framework for the persistence of flood‐initiated geomorphological features
Authors: Calver Ann , Anderson Malcolm G
Published: April 2004

The paper is concerned with the degree to which geomorphological features formed by a large magnitude river flood may be expected to persist in the landscape. Fluvial and hillslope features formed in association with a particularly rare flood, on Exmoor in southwest England, are analysed after a post‐event period of 50 years. New recurrence interval analyses and field assessments are combined with earlier data. The concept of static and dynamic aspects of landscape persistence is suggested, and the relative persistence potential of flood‐initiated features is indicated in relation to the recurrence interval of formative events.
An improved approach for predicting the distribution of rare and endangered species from occurrence and pseudo‐absence data
Authors: Engler Robin , Guisan Antoine , Rechsteiner Luca
Published: April 2004

Few examples of habitat‐modelling studies of rare and endangered species exist in the literature, although from a conservation perspective predicting their distribution would prove particularly useful. Paucity of data and lack of valid absences are the probable reasons for this shortcoming. Analytic solutions to accommodate the lack of absence include the ecological niche factor analysis (ENFA) and the use of generalized linear models (GLM) with simulated pseudo‐absences.

In this study we tested a new approach to generating pseudo‐absences, based on a preliminary ENFA habitat suitability (HS) map, for the endangered species Eryngium alpinum. This method of generating pseudo‐absences was compared with two others: (i) use of a GLM with pseudo‐absences generated totally at random, and (ii) use of an ENFA only.

The influence of two different spatial resolutions (i.e. grain) was also assessed for tackling the dilemma of quality (grain) vs. quantity (number of occurrences). Each combination of the three above‐mentioned methods with the two grains generated a distinct HS map.

Four evaluation measures were used for comparing these HS maps: total deviance explained, best kappa, Gini coefficient and minimal predicted area (MPA). The last is a new evaluation criterion proposed in this study.

Results showed that (i) GLM models using ENFA‐weighted pseudo‐absence provide better results, except for the MPA value, and that (ii) quality (spatial resolution and locational accuracy) of the data appears to be more important than quantity (number of occurrences). Furthermore, the proposed MPA value is suggested as a useful measure of model evaluation when used to complement classical statistical measures.

Synthesis and applications. We suggest that the use of ENFA‐weighted pseudo‐absence is a possible way to enhance the quality of GLM‐based potential distribution maps and that data quality (i.e. spatial resolution) prevails over quantity (i.e. number of data). Increased accuracy of potential distribution maps could help to define better suitable areas for species protection and reintroduction.
Impacts of stream acidification on litter breakdown: implications for assessing ecosystem functioning
Authors: Dangles Olivier , Gessner Mark O. , Guerold François , Chauvet Eric
Published: April 2004

Scientific understanding of acidification in aquatic ecosystems relies on effective assessment, which at present is mostly limited to chemical and sometimes structural biological variables. Effects on ecosystem functioning are, in contrast, largely neglected. Litter breakdown is a potentially useful, highly integrative and crucial process that could enhance such assessment programmes.

Breakdown rates of beechFagus sylvaticaleaves were determined in 25 woodland headwater streams along an acidification gradient in the Vosges Mountains, France. Additional data relating to micro‐organisms (microbial respiration, fungal biomass and degree of conditioning measured as leaf palatability) and macroinvertebrates (shredder diversity, abundance and biomass) associated with decomposing leaves were collected to elucidate the mechanisms underlying leaf breakdown.

Breakdown rates varied more than 20‐fold between the most acidified and circumneutral sites (k = 0·0002–0·0055 day−1). Stream water alkalinity and total Al concentration together accounted for 88% of the variation in litter breakdown rates among streams. Microbial factors associated with decaying leaves, particularly microbial respiration, declined with increasing stream acidity and were significantly related to Ca2+and total Al concentrations.

Total abundance, biomass and richness of leaf‐shredding invertebrates associated with decomposing leaves were not related to stream acidity. However, the abundance and biomass of the amphipodGammarus fossarum, an acid‐sensitive and particularly efficient leaf‐shredder, showed a strong positive relationship with leaf breakdown rate.Gammarusabundance and microbial respiration together accounted for 85% of the variation in litter breakdown rates among streams.

Synthesis and applications. These results indicate that leaf‐litter breakdown responds strongly to stream acidification, with both microbial decomposers and invertebrate detritivores markedly affected. Measuring leaf breakdown rate may be developed into a simple, powerful and low‐cost tool for assessing a critical component of ecosystem functioning. We advocate further investigation of this approach for the routine biomonitoring of freshwaters affected by, or recovering from, other anthropogenic stresses.
Long‐term effects of burning slash on plant communities and arbuscular mycorrhizae in a semi‐arid woodland
Authors: Haskins Kristin E. , Gehring Catherine A.
Published: April 2004

Burning of slash (woody debris) piles resulting from the harvest of fuel wood is a common management technique designed to reduce fire risk and increase establishment of understorey vegetation in many semi‐arid woodlands. However, the consequences of slash burning on plant communities and their below‐ground fungal mutualists are poorly understood.

We examined how the burning of slash piles affected understorey plant communities and arbuscular mycorrhizal (AM) fungi in a pinyon–juniper woodland in northern Arizona, USA, 5 years after harvesting. We analysed plant communities and AM inoculum potential along 16 transects in: (i) burned slash pile sites; (ii) interspaces between burned slash piles; (iii) non‐burned canopy sites; and (iv) non‐burned interspaces. We quantified AM colonization of dominant native and exotic plants in burned and non‐burned areas.

Burned areas had significantly fewer understorey plant species than non‐burned areas, and exotic species were four times more abundant at burned slash sites than at other sites.

Exotic plants from burned and non‐burned areas exhibited levels of AM colonization that were 50% greater than native plants. Bioassay and field‐collected plants exhibited similar levels of AM colonization and there were no significant treatment differences.

The total biomass of bioassay plants grown in soil from burned slash sites averaged 19% greater than plant biomass from other sites, and had 27% more phosphorus in their shoot tissue; however, tissue nitrogen contents were similar.

Synthesis and applications. These results suggest that either fire did not reduce AM inoculum potential, or that AM fungal populations recovered in the 5 years after the slash was burned. Changes in understorey plant communities and increases in exotic species with burning could result from other soil changes (e.g. species of AM fungi present), reduction of native species in the seed bank or greater dispersal ability of exotic plants compared with native plant species. We suggest that burning slash piles as a management tool in pinyon–juniper woodlands can result in plant communities that are persistently dominated by exotic species. Management approaches that utilize fuel wood harvest alone or that incorporate seeding of native plants may achieve the desired results.