bluuebunny/crossref_metadata_2025 huggingface dataset:
Roles of 14-3-3 and calmodulin binding in subcellular localization and function of the small G-protein Rem2
Authors: Béguin Pascal , Mahalakshmi Ramasubbu Narayanan , Nagashima Kazuaki , Cher Damian Hwee Kiat , Kuwamura Naomitsu , Yamada Yuichiro , Seino Yutaka , Hunziker Walter
Published: August 2005

kir/Gem, Rad, Rem and Rem2 comprise the RGK (Rad/Gem/kir) family of Ras-related small G-proteins. Two important functions of RGK proteins are the regulation of the VDCC (voltage-dependent Ca2+ channel) activity and cell-shape remodelling. RGK proteins interact with 14-3-3 and CaM (calmodulin), but their role on RGK protein function is poorly understood. In contrast with the other RGK family members, Rem2 has been reported to bind neither 14-3-3 nor induce membrane extensions. Furthermore, although Rem2 inhibits VDCC activity, it does not prevent cell-surface transport of Ca2+ channels as has been shown for kir/Gem. In the present study, we re-examined the functions of Rem2 and its interaction with 14-3-3 and CaM. We show that Rem2 in fact does interact with 14-3-3 and CaM and induces dendrite-like extensions in COS cells. 14-3-3, together with CaM, regulates the subcellular distribution of Rem2 between the cytoplasm and the nucleus. Rem2 also interacts with the β-subunits of VDCCs in a GTP-dependent fashion and inhibits Ca2+ channel activity by blocking the α-subunit expression at the cell surface. Thus Rem2 shares many previously unrecognized features with the other RGK family members.
An olive pollen protein with allergenic activity, Ole e 10, defines a novel family of carbohydrate-binding modules and is potentially implicated in pollen germination
Authors: Barral Patricia , Suárez Cinthya , Batanero Eva , Alfonso Carlos , Alché Juan de Dios , Rodríguez-García María Isabel , Villalba Mayte , Rivas Germán , Rodríguez Rosalía
Published: August 2005

CBMs (carbohydrate-binding modules) are the most common non-catalytic modules associated with enzymes active in plant cell-wall hydrolysis. They have been frequently identified by amino acid sequence alignments, but only a few have been experimentally established to have a carbohydrate-binding activity. A small olive pollen protein, Ole e 10 (10 kDa), has been described as a major inducer of type I allergy in humans. In the present study, the ability of Ole e 10 to bind several polysaccharides has been analysed by affinity gel electrophoresis, which demonstrated that the protein bound 1,3-β-glucans preferentially. Analytical ultracentrifugation studies confirmed binding to laminarin, at a protein/ligand ratio of 1:1. The interaction of Ole e 10 with laminarin induced a conformational change in the protein, as detected by CD and fluorescence analyses, and an increase of 3.6 °C in the thermal denaturation temperature of Ole e 10 in the presence of the glycan. These results, and the absence of alignment of the sequence of Ole e 10 with that of any classified CBM, indicate that this pollen protein defines a novel family of CBMs, which we propose to name CBM43. Immunolocalization of Ole e 10 in mature and germinating pollen by transmission electron microscopy and confocal laser scanning microscopy demonstrated the co-localization of Ole e 10 and callose (1,3-β-glucan) in the growing pollen tube, suggesting a role for this protein in the metabolism of carbohydrates and in pollen tube wall re-formation during germination.
The weakly bound He–HCCCN complex: High-resolution microwave spectra and intermolecular potential-energy surface
Authors: Topic Wendy C. , Jäger Wolfgang
Published: August 2005

Rotational spectra of the weakly bound He–HCCCN and He–DCCCN van der Waals complexes were observed using a pulsed-nozzle Fourier-transform microwave spectrometer in the 7–26-GHz frequency region. Nuclear quadrupole hyperfine structures due to the N14 and D nuclei (both with nuclear-spin quantum number I=1) were resolved and assigned. Both strong a and weaker b-type transitions were observed and the assigned transitions were used to fit the parameters of a distortable asymmetric rotor model. The dimers are floppy, near T-shaped complexes. Three intermolecular potential-energy surfaces were calculated using the coupled-cluster method with single and double excitations and noniterative inclusion of triple excitations. Bound-state rotational energy levels supported by these surfaces were determined. The quality of the potential-energy surfaces was assessed by comparing the experimental and calculated transition frequencies and also the corresponding spectroscopic parameters. Simple scaling of the surfaces improved both the transition frequencies and spectroscopic constants. Five other recently reported surfaces [O. Akin-Ojo, R. Bukowski, and K. Szalewicz, J. Chem. Phys. 119, 8379 (2003)], calculated using a variety of methods, and their agreement with spectroscopic properties of He–HCCCN are discussed.
Real-space Green’s tensors for stress and strain in crystals with cubic anisotropy
Authors: Faux David A. , Christmas Ursula M. E.
Published: August 2005

Real-space Green’s tensors are presented for the calculation of the stress or strain in infinite cubic crystals containing buried quantum wires or dots of arbitrary shape and composition, including the cubic anisotropy of elastic constants. The Green’s tensors are obtained as a polynomial series to second order in Δ, an expansion coefficient defined in terms of the elastic stiffnesses. The zeroth-order term in the series is the usual isotropic Green’s tensor. The results agree extremely well with the numerical, exact formulation of Pan and Yang [E. Pan and B. Yang, J. Appl. Phys. 90, 6190 (2001)] but compute considerably faster and are easier to implement. The present approach is used to determine the strain in the direction normal to the plane of a quantum well in different orientations. This constitutes a stringent test of the approximate Green’s tensor series and results are found to be in excellent agreement with standard solutions. The Green’s-function expansion for the hydrostatic strain is presented and found to be of a simple form for both dots and wires.
Infrared spectra of NH2NO, NH2NO+, and NNOH+ and of the N2⋯H2O complex trapped in solid neon
Authors: Jacox Marilyn E. , Thompson Warren E.
Published: August 2005

When a Ne:H2:N2O mixture is codeposited at 4.3 K with a beam of neon atoms that have been excited in a microwave discharge, NH2NO+ is stabilized in sufficient concentration for detection of five of its vibrational fundamentals. Their assignments are supported by isotopic substitution studies and by the results of unrestricted B3LYP/cc-pVTZ calculations. Electron recombination results in the stabilization of NH2NO, for which the previously reported argon-matrix assignments are confirmed and extended. The OH-stretching fundamental of NNOH+ also is present in the spectrum of the initial sample deposit, but because of proton sharing with the neon matrix is shifted 43.3cm−1 from the gas-phase band center. The OD-stretching fundamental of NNOD+ is identified for the first time in the present study. An absorption at 2311.1cm−1 is contributed by the NN-stretching vibration of a complex of N2, probably with an ionic species. On prolonged visible and near-ultraviolet irradiation of the deposit, absorptions of the binary N2⋯H2O complex become increasingly prominent.
Spatiotemporal clustering and temporal order in the excitable BZ reaction
Authors: Hastings Harold M. , Sobel Sabrina G. , Lemus Arely , Yuen Fiona , Peralta Catalina , Cammalleri Carolyn , Chabrel Johan , Chaterpaul Stephen , Frank Claudia , Hilaire Christian , Lang Daniel , Ravinovitch Daniel , Zaharakis Alex
Published: August 2005

The prototype experimental example of “spontaneous” pattern formation in an unstirred chemical medium is the oscillatory Belousov–Zhabotinsky (BZ) reaction: target patterns of outward-moving concentric rings are readily observed when the reaction is run in a thin layer in a Petri dish. In many experimental runs, new target centers appeared to form closer to pre-existing target centers than expected in a randomized model. Here we describe a simple direct test for the presence of temporal order in the spatiotemporal dynamics of target nucleation, and apply this test to detect significant temporal order in target formation in the ferroin-catalyzed BZ reaction. We also describe how mixing heterogeneity can generate temporal order, even in the absence of heterogeneous physical nucleating centers.
Franck-Condon analysis of the absorption and fluorescence spectra of all trans α,ω-diphenylpolyenes with one to seven polyene double bonds
Authors: Itoh Takao
Published: August 2005

Fluorescence and absorption spectra have been measured for all-trans α,ω-diphenylpolyenes with one to seven polyene double bonds in room-temperature solution, along with the fluorescence spectra of those with one to six polyene double bonds in n-alkane matrices at 77 K. All the spectral data were fitted by sums of Gaussians to treat the Franck-Condon envelopes of the measured spectra quantitatively. The Franck-Condon analyses of the spectra in the harmonic limit revealed that the displacements of the CC and C–C stretching vibrational modes in the 2 Ag state relative to those in the ground state, 1Ag1(S0), increase, while those in the 1Bu1 state show a slight decrease with the increase of the polyene chain length. It is also shown that the bandwidths of the absorption and fluorescence spectra exhibit a monotonic decrease with the increase of the chain length.
Experimental studies of the vapor phase nucleation of refractory compounds. VI. The condensation of sodium
Authors: Martínez Daniel M. , Ferguson Frank T. , Heist Richard H. , Nuth Joseph A.
Published: August 2005

In this paper we discuss the condensation of sodium vapor and the formation of a sodium aerosol as it occurs in a gas evaporation condensation chamber. A one-dimensional model describing the vapor transport to the vapor/aerosol interface was employed to determine the onset supersaturation, in which we assume the observed location of the interface is coincident with a nucleation rate maximum. We then present and discuss the resulting nucleation onset supersaturation data within the context of nucleation theory based on the liquid droplet model. Nucleation results appear to be consistent with a cesium vapor-to-liquid nucleation study performed in a thermal diffusion cloud chamber.
Guided ion-beam studies of the reactions of Con+ (n=2–20) with O2: Cobalt cluster-oxide and -dioxide bond energies
Authors: Liu Fuyi , Li Feng-Xia , Armentrout P. B.
Published: August 2005

The kinetic-energy dependence for the reactions of Con+ (n=2–20) with O2 is measured as a function of kinetic energy over a range of 0to10eV in a guided ion-beam tandem mass spectrometer. A variety of Com+, ComO+, and ComO2+ (m⩽n) product ions is observed, with the dioxide cluster ions dominating the products for all larger clusters. Reaction efficiencies of Con+ cations with O2 are near unity for all but the dimer. Bond dissociation energies for both cobalt cluster oxides and dioxides are derived from threshold analysis of the energy dependence of the endothermic reactions using several different methods. These values show little dependence on cluster size for clusters larger than three atoms. The trends in this thermochemistry and the stabilities of oxygenated cobalt clusters are discussed. The bond energies of Con+–O for larger clusters are found to be very close to the value for desorption of atomic oxygen from bulk-phase cobalt. Rate constants for O2 chemisorption on the cationic clusters are compared with results from previous work on cationic, anionic, and neutral cobalt clusters.
Kinetic theory for identical, frictional, nearly elastic disks
Authors: Yoon David K. , Jenkins James T.
Published: August 2005

We develop kinetic theory for slightly frictional and nearly elastic disks. The tangential interaction is modeled by two parameters: a Coulomb friction coefficient and a tangential restitution coefficient. Assuming Maxwellian velocity distribution functions for both translational and rotational velocities, we derive exact expressions for the rates of dissipation of translational and rotational fluctuation energies per unit area. Setting the rotational dissipation rate to zero, as in a steady, homogeneous shearing flow, we find the ratio of the rotational temperature to the translational. In the case of small friction, this is used to determine an effective coefficient of normal restitution. In this way, the effects of small friction can be incorporated into the theory, thereby dispensing with the need to separately consider the complete balances for the momentum and the energy of the rotational motion.
Prediction of silicon oxynitride plasma etching using a generalized regression neural network
Authors: Kim Byungwhan , Lee Byung Teak
Published: August 2005

A prediction model of silicon oxynitride (SiON) etching was constructed using a neural network. Model prediction performance was improved by means of genetic algorithm. The etching was conducted in a C2F6 inductively coupled plasma. A 24 full factorial experiment was employed to systematically characterize parameter effects on SiON etching. The process parameters include radio frequency source power, bias power, pressure, and C2F6 flow rate. To test the appropriateness of the trained model, additional 16 experiments were conducted. For comparison, four types of statistical regression models were built. Compared to the best regression model, the optimized neural network model demonstrated an improvement of about 52%. The optimized model was used to infer etch mechanisms as a function of parameters. The pressure effect was noticeably large only as relatively large ion bombardment was maintained in the process chamber. Ion-bombardment-activated polymer deposition played the most significant role in interpreting the complex effect of bias power or C2F6 flow rate. Moreover, [CF2] was expected to be the predominant precursor to polymer deposition.
Natural convection near an isothermal wall far downstream from a source
Authors: Kurdyumov Vadim N.
Published: August 2005

Steady, two-dimensional, free convection flows near an isothermal wall are considered downstream from a heat source at large Grashof numbers for cases when the temperature of the wall is maintained the same as that of the fluid far from the wall. The analyses are given for two cases: (A) for a vertical wall and (B) for a horizontal wall, when the thermal plume spreads along the wall horizontally. The study is based on the Boussinesq boundary layer equations. The solutions have been found in the self-similar form of the second kind. The asymptotic solutions for very large and small Prandtl numbers in the case of the vertical wall, and for very large Prandtl numbers in the case of the horizontal wall are presented. It was found that in the case of the horizontal wall the self-similar solution does not exist in the specific low Prandtl-number regime, σ<0.04218.
Hydrogen-induced recovery of photoluminescence from annealed a-Si:H∕a-SiO2 multilayers
Authors: Rui Yunjun , Chen Deyuan , Xu Jun , Zhang Yongjun , Yang Ling , Mei Jiaxin , Ma Zhongyuan , Cen Zhanhong , Li Wei , Xu Ling , Huang Xinfan , Chen Kunji
Published: August 2005

a - Si : H ∕ Si O 2 multilayers prepared by plasma-enhanced chemical-vapor deposition exhibit a luminescence band around 760nm, which is quenched after a dehydrogenation process. Subsequent hydrogen plasma annealing (HPA) treatments are carried out, and the luminescence is then recovered. The effects of HPA are investigated as functions of hydrogen annealing time and temperature. Fourier transform infrared spectroscopy and Raman-scattering spectroscopy are used to study the change of the microstructures and bonding configurations due to the HPA treatments. It is indicated that the atomic hydrogen cannot only diffuse into the film to reduce the density of nonradiative recombination centers but can also relax the film network and improve the microstructure order of the a-Si:H sublayers. All these factors are believed to contribute to the recovery of the luminescence signals of the a-Si:H∕SiO2 multilayers.
Identification of soft phonon modes in Ge–Sb–Te using electron diffraction
Authors: Naito Muneyuki , Ishimaru Manabu , Hirotsu Yoshihiko , Takashima Masaki
Published: August 2005

The atomistic structure of crystalline Ge–Sb–Te thin film for phase-change optical recording was investigated using transmission electron microscopy and nanobeam electron diffraction. Nonradial diffuse streaks were observed in electron diffraction patterns obtained from laser-induced crystalline phases of Ge–Sb–Te thin films. The intensities of the diffuse streaks were pronounced in particular directions in this alloy. The diffuse streaks were due to low-frequency transverse lattice waves that occur along directions perpendicular to the near neighbor zigzag atomic chains.
Optical-absorption intensities and intermanifold emission cross sections of trivalent erbium ions in calcium fluorophosphate
Authors: Sardar Dhiraj K. , Coeckelenbergh Cody H. , Yow Raylon M. , Gruber John B. , Allik Toomas H.
Published: August 2005

A spectroscopic analysis is performed on trivalent erbium ions, Er3+, doped into calcium fluorophosphate (FAP) to assess this material for its potential as a near-infrared laser host. The Judd-Ofelt model is applied to the orientation-averaged, room-temperature absorption intensities of Er3+ in FAP to obtain the phenomenological intensity parameters: Ω2=5.86×10−20cm2, Ω4=0.38×10−20cm2, and Ω6=0.88×10−20cm2. The intensity parameters are used to determine the radiative decay rates (emission probabilities), radiative lifetimes, and branching ratios of the Er3+ transitions from the upper multiplet manifolds to the corresponding lower-lying multiplet manifolds LJ2S+1 of Er3+ in FAP. Using the radiative decay rates for Er3+ transitions between the corresponding excited states and the lower-lying states, the radiative lifetimes of eight excited states are determined in this host. The room temperature fluorescence lifetime and the radiative lifetime of the Er3+I13∕24→I15∕24(1.53μm) transition are reported and the quantum efficiency is determined to be 69% for 1.0wt%Er3+:FAP. In addition, the orientationally resolved emission cross sections for the S3∕24→I15∕24 and I13∕24→I15∕24 transitions are presented.
Optimal probes for withdrawal of uncontaminated fluid samples
Authors: Sherwood J. D.
Published: August 2005

Withdrawal of fluid by a composite probe pushed against the face z=0 of a porous half-space z>0 is modeled assuming incompressible Darcy flow. The probe is circular, of radius a, with an inner sampling section of radius αa and a concentric outer guard probe αa<rβa is saturated with fluid 2; the two fluids have the same viscosity. It is assumed that the interface between the two fluids is sharp and remains so as it moves through the rock. The pressure in the probe is lower than that of the pore fluid in the rock, so that the fluid interface is convected with the fluids towards the probe. This idealized axisymmetric problem is solved numerically, and it is shown that an analysis based on far-field spherical flow towards a point sink is a good approximation when the nondimensional depth of fluid 1 is large, i.e., β⪢1. The inner sampling probe eventually produces pure fluid 2, and this technique has been proposed for sampling pore fluids in rock surrounding an oil well [A. Hrametz, C. Gardner, M. Wais, and M. Proett, U.S. Patent No. 6,301,959 B1 (16 October 2001)]. Fluid 1 is drilling fluid filtrate, which has displaced the original pore fluid (fluid 2), a pure sample of which is required. The time required to collect an uncontaminated sample of original pore fluid can be minimized by a suitable choice of the probe geometry α [J. Sherwood, J. Fitzgerald and B. Hill, U.S. Patent No. 6,719,049 B2 (13 April 2004)]. It is shown that the optimal choice of α depends on the depth of filtrate invasion β and the volume of sample required.
Rectifying characteristics of WSi0.8–GaN Schottky barrier diodes with a GaN cap layer grown at low temperature
Authors: Sheu J. K. , Lee M. L. , Lai W. C. , Tseng H. C. , Chi G. C.
Published: August 2005

Undoped GaN/low-temperature (LT) GaN∕WSi0.8 and undoped GaN∕WSi0.8 Schottky barrier contacts were prepared. Introducing the LT GaN on top of the conventional structures markedly reduced the leakage current and increased the barrier height. The measured barrier heights of the LT GaN-caped samples and the conventional samples were around 1 and 0.55eV, respectively. The thermal stability of the Schottky barrier contacts was also studied and the barrier height was shown to be very stable even when the annealing temperature was increased to 950°C for 1h.
Ballistic hole transport in a quantum wire
Authors: Pfeiffer L. N. , de Picciotto R. , West K. W. , Baldwin K. W. , Quay C. H. L.
Published: August 2005

We report ballistic hole conduction in 2μm long GaAs quantum wires of nominal cross-section 15 nm by 15 nm. In each of eight test wires, we observe several quantized conduction steps of approximate height 0.77e2∕h. The wires were fabricated using the cleaved edge overgrowth molecular-beam epitaxy process, and the modulation-doped acceptors were incorporated using a carbon filament as the source of atomic carbon.
Solid-state current amplifier based on impact ionization
Authors: Lee Hong-Wei , Hawkins Aaron R.
Published: August 2005

The operation principle, fabrication, and measurement results for a stand-alone amplifier based on impact ionization are reported. The device was built in silicon using standard microelectronic processes. Testing was performed by connecting the device to both silicon and indium-gallium-arsenide photodiodes to demonstrate its compatibility with arbitrary current sources. Preamplified leakage currents of less than 1nA were measured along with current gains greater than 100.
Germanium hut nanostressors on freestanding thin silicon membranes
Authors: Evans P. G. , Tinberg D. S. , Roberts M. M. , Lagally M. G. , Xiao Y. , Lai B. , Cai Z.
Published: August 2005

The heteroepitaxial growth of Ge on thin Si membranes can lead to significant bending under self-assembled Ge hut nanostructures. Undercut silicon-on-insulator mesas approximate a Si freestanding membrane and serve as a crystalline substrate for the growth of Ge huts. Synchrotron x-ray microdiffraction shows a local curvature on the lateral scale of the size of the hut and an overall bending of the freestanding region. In comparison with conventional mechanically rigid substrates, the freestanding film can bend significantly. We have found a local radius of curvature of 6μm beneath huts on 30-nm-thick Si membranes.
Pooled association genome scanning: Validation and use to identify addiction vulnerability loci in two samples
Authors: Liu Qing-Rong , Drgon Tomas , Walther Donna , Johnson Catherine , Poleskaya Oxanna , Hess Judith , Uhl George R.
Published: August 2005

Association genome scanning is of increasing interest for identifying the chromosomal regions that contain gene variants that contribute to vulnerability to complex disorders, including addictions. To improve the power and feasibility of this approach, we have validated “10k” microarray-based allelic frequency assessments in pooled DNA samples and have used this approach to seek allelic frequency differences between heavy polysubstance abusers and well characterized control individuals. Thirty-eight loci contain SNPs that display robust allele frequency differences between abusers and controls in both European- and African-American samples. These loci identify an alcohol/acetaldehyde dehydrogenase gene cluster and genes implicated in cellular signaling, gene regulation, development, “cell adhesion,” and Mendelian disorders. The results converge with previous linkage and association results for addictions. Pooled association genome scanning provides a useful tool for elucidating molecular genetic underpinnings of complex disorders and identifies both previously understood and previously unanticipated mechanisms for addiction vulnerability.
NKG2D-independent suppression of T cell proliferation by H60 and MICA
Authors: Kriegeskorte Anja K. , Gebhardt Friedemann E. , Porcellini Simona , Schiemann Matthias , Stemberger Christian , Franz Tobias J. , Huster Katharina M. , Carayannopoulos Leon N. , Yokoyama Wayne M. , Colonna Marco , Siccardi Antonio G. , Bauer Stefan , Busch Dirk H.
Published: August 2005

The activating receptor NKG2D recognizes a wide range of different ligands, some of which are primarily expressed in “stressed” tissues or on tumor cells. Until now, similar stimulatory effects on natural killer and CD8+T cells have been described for all NKG2D ligands, and the NKG2D receptor/ligand system has therefore been interpreted as a sensor system involved in tumor immune surveillance and activation of immune responses. We show here that the NKG2D ligands H60 and MIC class 1 chain-related protein A (MICA) can also mediate strong suppressive effects on T cell proliferation. Responsiveness to H60- and MICA-mediated suppression requires IL-10 and involves a receptor other than NKG2D. These findings might provide explanations for the observation that strongin vivoNKG2D ligand expression, such as that on tumor cells, sometimes fails to support effective immune responses and links this observation to a distinct subgroup of NKG2D ligands.
CD1d ligation on human monocytes directly signals rapid NF-κB activation and production of bioactive IL-12
Authors: Yue Simon C. , Shaulov Angela , Wang Ruojie , Balk Steven P. , Exley Mark A.
Published: August 2005

Natural killer T cells (NKT cells) expressing a semiinvariant CD1d-reactive T cell receptor (invariant NKT, iNKT) can be rapidly activated by monocytes or immature dendritic cells (iDCs) bearing a CD1d-presented glycolipid antigen and can in turn stimulate these myeloid cells to mature and produce IL-12. Previous studies have shown that iNKT-produced IFNγ and CD40 ligand contribute to this dendritic cell maturation. This study demonstrates that CD1d ligation alone, in the absence of iNKT, could rapidly (within 24 h) stimulate production of bioactive IL-12p70 by CD1d+human peripheral blood monocytes as well as iDCs. IFNγ alone had no effect, but it markedly enhanced CD1d-stimulated IL-12 production. Monocyte differentiation, as assessed by CD40 and CD1a up-regulation, was also accelerated by CD1d stimulation, consistent with this representing a physiological response. CD1d ligation on the human monocytic cell line THP-1 similarly specifically stimulated IL-12 production. Biochemical studies showed that IL-12 release correlated with rapid phosphorylation of IκB, a critical step in NF-κB activation. Selective NF-κB inhibition blocked this CD1d-stimulated IL-12 production. Finally, CD1d ligation could also enhance IL-12 production in the presence of suboptimal LPS or CD40 stimulation. These findings demonstrate an innate immune signaling function for CD1d and provide a mechanism for the rapid activation of monocytes and iDCs by CD1d-reactive T cells.
Fractal intermediates in the self-assembly of silicatein filaments
Authors: Murr Meredith M. , Morse Daniel E.
Published: August 2005

Silicateins are proteins with catalytic, structure-directing activity that are responsible for silica biosynthesis in certain sponges; they are the constituents of macroscopic protein filaments that are found occluded within the silica needles made by
Tethya aurantia
. Self-assembly of the silicatein monomers and oligomers is shown to form fibrous structures by a mechanism that is fundamentally different from any previously described filament-assembly process. This assembly proceeds through the formation of diffusion-limited, fractally patterned aggregates on the path to filament formation. The driving force for this self-assembly is suggested to be entropic, mediated by the interaction of hydrophobic patches on the surfaces of the silicatein subunits that are not found on highly homologous congeners that do not form filaments. Our results are consistent with a model in which silicatein monomers associate into oligomers that are stabilized by intermolecular disulfide bonds. These oligomeric units assemble into a fractal network that subsequently condenses and organizes into a filamentous structure. These results represent a potentially general mechanism for protein fiber self-assembly.
The metabolic basis of whole-organism RNA and phosphorus content
Authors: Gillooly James F. , Allen Andrew P. , Brown James H. , Elser James J. , del Rio Carlos Martinez , Savage Van M. , West Geoffrey B. , Woodruff William H. , Woods H. Arthur
Published: August 2005

Understanding the storage, flux, and turnover of nutrients in organisms is important for quantifying contributions of biota to biogeochemical cycles. Here we present a model that predicts the storage of phosphorus-rich RNA and whole-body phosphorus content in eukaryotes based on the mass- and temperature-dependence of ATP production in mitochondria. Data from a broad assortment of eukaryotes support the model's two main predictions. First, whole-body RNA concentration is proportional to mitochondrial density and consequently scales with body mass to the -1/4 power. Second, whole-body phosphorus content declines with increasing body mass in eukaryotic unicells but approaches a relatively constant value in large multicellular animals because the fraction of phosphorus in RNA decreases relative to the fraction in other pools. Extension of the model shows that differences in the flux of RNA-associated phosphorus are due to the size dependencies of metabolic rate and RNA concentration. Thus, the model explicitly links two biological currencies at the individual level: energy in the form of ATP and materials in the form of phosphorus, both of which are critical to the functioning of ecosystems. The model provides a framework for linking attributes of individuals to the storage and flux of phosphorus in ecosystems.
A Novel Degron-mediated Degradation of the RTG Pathway Regulator, Mks1p, by SCFGrr1
Authors: Liu Zhengchang , Spírek Mário , Thornton Janet , Butow Ronald A.
Published: August 2005

Yeast cells respond to mitochondrial dysfunction by altering the expression of a subset of nuclear genes, a process known as retrograde signaling (RS). RS terminates with two transcription factors, Rtg1p and Rtg3p. One positive regulator, Rtg2p, and four negative regulators, Lst8p, Mks1p, and the redundant 14-3-3 proteins, Bmh1p and Bmh2p, control RS upstream of Rtg1/3p. Mks1p is negatively regulated by binding to Rtg2p and positively regulated when bound to Bmh1/2p. Here we report that Grr1p, a component of the SCFGrr1 E3 ubiquitin ligase, modulates RS by affecting Mks1p levels. Grr1p polyubiquitinates Mks1p not bound to either Rtg2p or to Bmh1/2p, targeting it for degradation. An acidic domain region of Mks1p constitutes the portable Mks1p degron sequence. We have isolated dominant mutations in Grr1p leading to increased Mks1p degradation. These mutations result in a gain of positive charge on the concave surface of the leucine rich repeat (LRR) domain of Grr1p, the proposed substrate binding site. We propose that Mks1p is a central player of RS and is acted upon by multiple regulators of the pathway.
Managing Market, Hierarchy, and Network: The Jiuda Salt Industries, Ltd., 1917–1937
Authors: Bun Kwan Man
Published: August 2005

As China underwent industrialization during the Republican period, how did companies deal with the problems of expansion, competition, and relationship with the state? Using the concept of network capitalism, this article demythologizes the “enigma” of Chinese network by analyzing the experience of the Jiuda Salt Industries, Ltd. Fan Xudong, the company’s founder, deftly managed his network portfolio for information and other resources. Kith and kin as shareholders, interlocking directorates, and cross-shareholding, as well as hierarchical management and cartels, were utilized to raise capital and manage local markets. Market, hierarchy, and network thus constitute three complementary organization principles in explaining Jiuda’s success.
Vertical Integration, Business Diversification, and Firm Architecture: The Case of the China Egg Produce Company in Shanghai, 1923–1950
Authors: Chang Ning Jennifer
Published: August 2005

This article is a case study of a Chinese indigenous firm in the refrigerated egg-packing industry during the interwar period. I argue that the China Egg Produce Company (CEPC) was quick to grasp Western management in terms of vertical integration and business diversification. In addition, this firm took advantage of embedded social relations and social networks to construct a strong “internal architecture.” As a result, CEPC not only rivaled some six to eight British and American enterprises, but also took the lead in persuading them to form an international cartel during the 1930s. The data presented in this case study shows the surprising vitality and adaptability of Chinese businesses and suggests that China was in the process of developing a modern business system prior to the chaotic events of the late 1940s.
Myth and Reality in Chinese Financial Cliques in 1936
Authors: Sheehan Brett
Published: August 2005

Much of current scholarly work argues that China and Chinese communities are distinguished by a culturally specific and unique pattern of networking based on personal relations (guanxi), but there is little agreement about whether such personal relations produce discrete factions or more disbursed, weblike connections. The literature on banking networks is similarly unclear, and most discussion has focused on regional groups, such as a clique made up of natives from Zhejiang and Jiangsu provinces, or shared professional values among bankers. None of these approaches adequately describes actual connections, and this case study provides a new and empirically broad approach that applies tools of network analysis to interlocking bank directorships in 1936. This analysis shows the existence of twenty-four isolated banks; three very small, discrete, and regionally based groups; and one huge, diffuse, and weblike bank network that included virtually all Chinese bank assets and extended to most of China’s economically developed regions.
Regressive evolution of an eye pigment gene in independently evolved eyeless subterranean diving beetles
Authors: Leys Remko , Cooper Steven J.B , Strecker Ulrike , Wilkens Horst
Published: August 2005

Regressive evolution, the reduction or total loss of non-functional characters, is a fairly common evolutionary phenomenon in subterranean taxa. However, the genetic basis of regressive evolution is not well understood. Here we investigate the molecular evolution of the eye pigment genecinnabarin several independently evolved lineages of subterranean water beetles using maximum likelihood analyses. We found that in eyeless lineagescinnabarhas an increased rate of sequence evolution, as well as mutations leading to frame shifts and stop codons, indicative of pseudogenes. These results are consistent with the hypothesis that regressive evolution of eyes proceeds by random mutations, in the absence of selection, that ultimately lead to the loss of gene function in protein-coding genes specific to the eye pathway.
A grid-enabled lightweight computational steering client: a .NET PDA implementation
Authors: Kalawsky R.S , Nee S.P , Holmes I , Coveney P.V
Published: August 2005

The grid has been developed to support large-scale computer simulations in a diverse range of scientific and engineering fields. Consequently, the increasing availability of powerful distributed computing resources is changing how scientists undertake large-scale modelling/simulation. Instead of being limited to local computing resources, scientists are now able to make use of supercomputing facilities around the world. These grid resources comprise specialized distributed three-dimensional visualization environments through to massive computational systems. The scientist usually accesses these resources from reasonably high-end desktop computers. Even though most modern desktop computers are provided with reasonably powerful three-dimensional graphical hardware, not all scientific applications require high-end three-dimensional visualization because the data of interest is essentially numerical or two-dimensional graphical data. For these applications, a much simpler two-dimensional graphical displays can be used. Since large jobs can take many hours to complete the scientist needs access to a technology that will allow them to still monitor and control their job while away from their desks. This paper describes an effective method of monitoring and controlling a set of chained computer simulations by means of a lightweight steering client based on a small personal digital assistant (PDA). The concept of using a PDA to steer a series of computational jobs across a supercomputing resource may seem strange at first but when scientists realize they can use these devices to connect to their computation wherever there is a wireless network (or cellular phone network) the concept becomes very compelling. Apart from providing a much needed easy-to-use interface, the PDA-based steering client has the benefit of freeing the scientist from the desktop. It is during this monitoring stage that the hand-held PDA client is of particular value as it gives the application scientist greater freedom to leave his or her desk but still communicate with their simulation, with the proviso that they remain within the range of a wireless network.
Physical and computational scaling issues in lattice Boltzmann simulations of binary fluid mixtures
Authors: Cates M.E , Desplat J.-C , Stansell P , Wagner A.J , Stratford K , Adhikari R , Pagonabarraga I
Published: August 2005

We describe some scaling issues that arise when using lattice Boltzmann (LB) methods to simulate binary fluid mixtures—both in the presence and absence of colloidal particles. Two types of scaling problem arise: physical and computational. Physical scaling concerns how to relate simulation parameters to those of the real world. To do this effectively requires careful physics, because (in common with other methods) LB cannot fully resolve the hierarchy of length, energy and time-scales that arise in typical flows of complex fluids. Care is needed in deciding what physics to resolve and what to leave unresolved, particularly when colloidal particles are present in one or both of two fluid phases. This influences steering of simulation parameters such as fluid viscosity and interfacial tension. When the physics is anisotropic (for example, in systems under shear) careful adaptation of the geometry of the simulation box may be needed; an example of this, relating to our study of the effect of colloidal particles on the Rayleigh–Plateau instability of a fluid cylinder, is described. The second and closely related set of scaling issues are computational in nature: how do you scale-up simulations to very large lattice sizes? The problem is acute for systems undergoing shear flow. Here one requires a set of blockwise co-moving frames to the fluid, each connected to the next by a Lees–Edwards like boundary condition. These matching planes lead to small numerical errors whose cumulative effects can become severe; strategies for minimizing such effects are discussed.
Computational steering in Monte Carlo simulations of thin film polystyrene
Authors: Mason Daniel R , Sutton Adrian P
Published: August 2005

High molecular weight polymer systems show very long relaxation times, of the order of milliseconds or more. This time-scale proves practically inaccessible for atomic-scale dynamical simulation such as molecular dynamics. Even with a Monte Carlo (MC) simulation, the generation of statistically independent configurations is non-trivial. Many moves have been proposed to enhance the efficiency of MC simulation of polymers. Each is described by a proposal density

(

x

′;

x

): the probability of selecting the trial state

x

′ given that the system is in the current state

x

. This proposal density must be parametrized for a particular chain length, chemistry and temperature. Choosing the correct set of parameters can greatly increase the rate at which the system explores its configuration space. Computational steering (CS) provides a new methodology for a systematic search to optimize the proposal densities for individual moves, and to combine groups of moves to greatly improve the equilibration of a model polymer system. We show that monitoring the correlation time of the system is an ideal single parameter for characterizing the efficiency of a proposal density function, and that this is best evaluated by a distributed network of replicas of the system, with the operator making decisions based on the averages generated over these replicas. We have developed an MC code for simulating an anisotropic atomistic bead model which implements the CS paradigm. We report simulations of thin film polystyrene.
Interaction Effect between Phosphorus and Zinc on their Availability in Soil in Relation to their Contents in Stevia (Stevia rebaudiana)
Authors: Das Kuntal , Dang Raman , Shivananda T. N. , Sur Pintu
Published: August 2005

A greenhouse experiment was conducted at the Indian Institute of Horticultural Research (IIHR), Bangalore to study the interaction effect between phosphorus and zinc on their availability in soil in relation to their contents in stevia (Stevia rebaudiana). The results show that the amount of available P and Zn content in soil has been found to increase initially and, thereafter, the amount of the same decreased with the progress of plant growth up to 60 days irrespective of treatments. The amount of P and Zn in soils showed an increase with their separate applications either as soil or foliar spray while that of the same value significantly decreased both in soils and plants due to their combined applications, suggesting a mutual antagonistic effect between Zn and P affecting each other's availability in soil and content in the stevia plant.
A Reassessment of the SIDS Back to Sleep Campaign
Authors: Pelligra Ralph , Doman Glen , Leisman Gerry
Published: August 2005

The Back to Sleep Campaign was initiated in 1994 to implement the American Academy of Pediatrics' (AAP) recommendation that infants be placed in the nonprone sleeping position to reduce the risk of the Sudden Infant Death Syndrome (SIDS). This paper offers a challenge to the Back to Sleep Campaign (BTSC) from two perspectives: (1) the questionable validity of SIDS mortality and risk statistics, and (2) the BTSC as human experimentation rather than as confirmed preventive therapy.

The principal argument that initiated the BTSC and that continues to justify its existence is the observed parallel declines in the number of infants placed in the prone sleeping position and the number of reported SIDS deaths. We are compelled to challenge both the implied causal relationship between these observations and the SIDS mortality statistics themselves.
Suicide in New Zealand
Authors: Shahtahmasebi Said
Published: August 2005

This paper explores and questions some of the notions associated with suicide including mental illness. On average, about two-thirds of suicide cases do not come into contact with mental health services, therefore, we have no objective assessment of their mental status or their life events. One method of improving our objective understanding of suicide would be to use data mining techniques in order to build life event histories on all deaths due to suicide. Although such an exercise would require major funding, partial case histories became publicly available from a coroner's inquest on cases of suicide during a period of three months in Christchurch, New Zealand. The case histories were accompanied by a newspaper article reporting comments from some of the families involved. A straightforward contextual analysis of this information suggests that (i) only five cases had contact with mental health services, in two of the cases this was due to a previous suicide attempt and in the other three it was due to drug and alcohol dependency; (ii) mental illness as the cause of suicide is fixed in the public mindset, (iii) this in turn makes psychological autopsy type studies that seek information from families and friends questionable; (iv) proportionally more females attempt, but more men tend to complete suicide; and (v) not only is the mental health-suicide relationship tenuous, but suicide also appears to be a process outcome. It is hoped that this will stimulate debate and the collaboration of international experts regardless of their school of thought.
Subcutaneous Leiomyosarcoma of the Frenulum
Authors: Mendis D. , Bott S. R. J. , Davies J. H.
Published: August 2005

Leiomyosarcomas of the penis are rare, with only 29 reported cases to date. We record the case of a patient who presented with a 2-year history of a seemingly indolent penile skin lesion. On histopathology of the local resection, a diagnosis of subcutaneous leiomyosarcoma was made. Specifically, leiomyosarcoma of the penile frenulum has not been clearly reported previously. The patient underwent a further excision to ensure an adequate resection margin and has had no disease recurrence at subsequent follow-up. Our case was of a lesion that, although clinically benign, was malignant and this possibility should be borne in mind when assessing patients.
Changes in basal cell mitosis and transepidermal water loss in skin cultures treated with vitamins C and E
Authors: Parish W. E. , Read J. , Paterson S. E.
Published: August 2005

Abstract:  Three variants of the living skin equivalent cultures were compared in order to determine the most suitable to grow human differentiated epidermis to test beneficial properties of nutrients. Criteria of culture quality were mitotic index and transepidermal water loss (TEWL) assayed by means of a ServoMed Evaporimeter EP‐2TM (ServoMed, Kinna, Sweden). Standards were donor skin mean mitotic index 11.1% and TEWL of living subjects mean 6.4 g/m2/h. Cultures (i) in 5% serum, 10 ng/ml of epidermal growth factor (EGF) at 37°C and 95% relative humidity (RH); mitotic index on day 14, 19.2%, but on day 21, 1.8% and TEWL 9.5 g/m2/h on day 18. (ii) In 1% serum, no EGF, 33°C and 95% RH, mitotic index on day 21, 9.1% and TEWL, 9.5% on day 18. (iii) Culture in same medium, 33°C and 60% RH, mitotic index on day 28, 9.5% and TEWL 6.1 g/m2/h on day 18 as in vivo. Incubation in 60% RH was achieved using a novel chamber and dishes exposing only the corneum, sealing the medium. Vitamins C and E were used as model test nutrients. Culture conditions were 1% serum, no EGF at 33°C and 95% RH. Vitamin C at 142 and 284 µM increased the mitotic index after 10‐ and 15‐day treatment, but at 586 µM it was weakly toxic. Vitamin E at 20 and 40 µM did not. Both vitamins reduced TEWL providing functional data in support of previous reports on barrier properties. These are functional biomarkers of skin benefit relevant to skin in vivo.