bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessment of idiopathic rapid‐eye‐movement sleep behavior disorder by transcranial sonography, olfactory function test, and FP‐CIT‐SPECT
Authors: Unger Marcus M. , Möller Jens C. , Stiasny‐Kolster Karin , Mankel Katharina , Berg Daniela , Walter Uwe , Hoeffken Helmut , Mayer Geert , Oertel Wolfgang H.
Published: January 2008

Idiopathic rapid‐eye‐movement (REM) sleep behavior disorder (iRBD) has been suggested to be a risk factor for subsequent development of neurodegenerative disorders, especially Parkinson's disease (PD) and other α‐synucleinopathies. At present, it is not possible to predict whether or not an iRBD patient will eventually develop PD. Here, we report 5 iRBD patients who underwent a test battery comprising a neurological examination (including UPDRS rating), mini mental state examination testing, transcranial sonography, olfactory function testing, and presynaptic dopamine transporter imaging with FP‐CIT‐SPECT. Our preliminary data show the diverse pattern of individual combinations of pathological findings when a multimodal assessment approach is applied in this patient group. Large‐size longitudinal studies in iRBD patients are required to evaluate the usefulness of diagnostic tests to identify the subgroup of iRBD patients that is prone to develop PD. © 2007 Movement Disorder Society
Structure–function relationship of inhibitory Smads: Structural flexibility contributes to functional divergence
Authors: Hariharan Ramkumar , Pillai M. Radhakrishna
Published: January 2008

Smads are a small family of eukaryotic transcription regulators that play key roles in the transforming growth factor‐beta signaling cascade. Smad6 and Smad7, the inhibitory or I‐Smads, inhibit signaling downstream of TGF‐beta type I receptors, thereby acting as negative regulators of signaling mediated by TGF‐beta superfamily of ligands. Smad6 is known to specifically inhibit BMP type I receptor mediated signaling, while Smad7 is a more general inhibitor, able to block signaling mediated by a set of related TGF‐beta type I receptors, including type I receptors for BMP and TGF‐beta/Activin. In this study we have sought to understand the structural basis for this functional divergence of I‐Smads. We have created homology‐based models for the MH1 and MH2 domains of the two I‐Smads and have carried out detailed molecular dynamics (MD) simulations of these proteins in explicit solvent to investigate the flexibility of the domains. The molecular models show that the I‐Smads have lost many of the secondary structural elements found in the R‐Smads, giving rise to longer loops in the tertiary structure of Smad6 and Smad7. Detailed analysis of the structural models and the MD trajectories clearly reveal that compared to Smad6, Smad7 has a more flexible overall folding, marked by the presence of highly flexible amino acid residues in functionally important regions of the protein. Interestingly, three of these residues—Phe411, Lys401, and Cys406, map to L3 loop of Smad7 MH2 domain, which is a critical structural determinant in Smad–type I receptor interactions. The increased structural flexibility of Smad7, arising out of longer, more flexible loops in its MH2 domain, might enable Smad7 to interact with a set of related yet structurally diverse type I receptors. Taken together with experimental evidence published in recent literature that hint at structural factors underlying the generic nature of inhibition by Smad7, our results strongly suggest that structural flexibility could be a prime contributor to the functional differences between Smad6 and Smad7. Additionally, we have been able to use the Smad7 structural model to successfully rationalize the results of in vitro site‐specific mutagenesis experiments in published literature. This also provides biological validation for our model. Apart from this, analysis of the MH1 molcular model of Smad6 delineates a basic patch on the surface of the domain that might take part in nonspecific DNA binding by Smad6. This finding is consistent with earlier experimental data and is relevant since the characteristic beta‐hairpin DNA binding element of R‐Smads is completely absent in the I‐Smads. Finally, the molecular models described here can serve to guide future biochemical and genetic studies on I‐Smads. Proteins 2008. © 2008 Wiley‐Liss, Inc.
In silico study of the human rhodopsin and meta rhodopsin II/S‐arrestin complexes: Impact of single point mutations related to retina degenerative diseases
Authors: Mokarzel‐Falcón Leonardo , Padrón‐García Juan Alexander , Carrasco‐Velar Ramón , Berry Colin , Montero‐Cabrera Luis A.
Published: January 2008

We propose two models of the human S‐arrestin/rhodopsin complex in the inactive dark adapted rhodopsin and meta rhodopsin II form, obtained by homology modeling and knowledge based docking. First, a homology model for the human S‐arrestin was built and validated by molecular dynamics, showing an average root mean square deviation difference from the pattern behavior of 0.76 Å. Then, combining the human S‐arrestin model and the modeled structure of the two human rhodopsin forms, we propose two models of interaction for the human S‐arrestin/rhodopsin complex. The models involve two S‐arrestin regions related to the N domain (residues 68–78; 170–182) and a third constituent of the C domain (248–253), with the rhodopsin C terminus (330–348). Of the 22 single point mutations related to retinitis pigmentosa and congenital night blindness located in the cytoplasmatic portion of rhodopsin or in S‐arrestin, our models locate 16 in the interaction region and relate two others to possible dimer formation. Our calculations also predict that the light activated complex is more stable than the dark adapted rhodopsin and, therefore, of higher affinity to S‐arrestin. Proteins 2008. © 2008 Wiley‐Liss, Inc.
X‐ray crystal structure of the B component of Hemolysin BL from Bacillus cereus
Authors: Madegowda Mahendra , Eswaramoorthy Subramaniam , Burley Stephen K. , Swaminathan Subramanyam
Published: January 2008

Bacillus cereus Hemolysin BL enterotoxin, a ternary complex of three proteins, is the causative agent of food poisoning and requires all three components for virulence. The X‐ray structure of the binding domain of HBL suggests that it may form a pore similar to other soluble channel forming proteins. A putative pathway of pore formation is discussed. Proteins 2008; 71:534–540. Published 2007 Wiley‐Liss, Inc.
The failure of pronatalism in developed states ‘with cultural–ethnic hegemony’: the Israeli lesson
Authors: Winckler O.
Published: January 2008

During the past two decades, the ‘hot’ demographic issue in the developed states ‘with cultural–ethnic hegemony’ changed radically – from a focus on ‘global demographic pressure’, namely, the ‘Malthusian syndrome’ of rapid population growth in the developing countries, to the ethno‐religious composition of their own populations. The solution adopted by many of these countries to tackle the twin demographic challenges of population ageing and the changing dependency ratio was the implementation of pronatalist policies which aimed at reducing their dependence upon labour immigration. This article examines the efficiency of these pronatalist policies through the Israeli case. The core questions of the article are: Has the Israeli pronatalist policy achieved its basic aims? What influence did the Israeli natalist policy and the child allowance structure have on the fertility patterns of the Israeli‐Arabs? What can be learned from the Israeli experience regarding the efficiency of these pronatalist policies in developed states? The major lesson from the Israeli experience is that, to a large extent, these pronatalist polices failed. The fertility rate of the Jewish middle class, the Christian‐Arabs and the Druze steadily declined, while that of the Israeli‐Muslims, although lower since the 1960s, is still twice that of the Jewish middle class. One can find a similar situation in all of the developed states ‘with cultural–ethnic hegemony.’ Thus, the inescapable conclusion is that in democratic‐developed societies, in which women enjoy equity in every respect, fertility rates will eventually decline to below replacement‐level regardless of pronatalist financial benefits. Consequently, the process of the developed states ‘with cultural–ethnic hegemony’ becoming developed states ‘without cultural–ethnic hegemony’ is irreversible due to the constant need for massive labour immigration. In the case of Israel, at the dawn of the twenty‐first century, there are high fertility rates in only two communities – the Ultra‐Orthodox Jews and the Muslims – paradoxically the two ‘non‐Zionist’ communities. Copyright © 2008 John Wiley & Sons, Ltd.
Kinetics of Cinnamoyl Glycerol Formation
Authors: Holser Ronald A.
Published: January 2008

The esterifications of glycerol with cinnamic acid, 2‐methoxy cinnamic acid, and 4‐methoxy cinnamic acid were investigated in batch reactions. Conversions of over 50% were achieved for cinnamic acid and 4‐methoxy cinnamic acid within 8 h. After 24 h, conversions of over 80% were obtained for cinnamic acid and 4‐methoxy cinnamic acid. Conversions of 33 and 40% were observed for 2‐methoxy cinnamic acid after 8 and 24 h, respectively. These reactions were modeled by a system of sequential first‐order rate expressions. Kinetic parameters were estimated from experimental data fit to the model equations.
Tense over time: testing the Agreement/Tense Omission Model as an account of the pattern of tense-marking provision in early child English
Authors: PINE JULIAN M. , CONTI-RAMSDEN GINA , JOSEPH KATE L. , LIEVEN ELENA V. M. , SERRATRICE LUDOVICA
Published: January 2008

The Agreement/Tense Omission Model (ATOM) predicts that English-speaking children will show similar patterns of provision across different tense-marking morphemes (Rice, Wexler & Hershberger, 1998). The aim of the present study was to test this prediction by examining provision rates for third person singular present tense and first and third person singular forms of copula BE and auxiliary BE in longitudinal data from eleven English-speaking children between the ages of 1 ; 10 and 3 ; 0. The results show, first, that there were systematic differences in the provision rates of the different morphemes; second, that there were systematic differences in the rate at which all of the three morphemes were provided with pronominal and lexical subjects; and, third, that there were systematic differences in the rate at which copula BE and auxiliary BE were provided with the third person singular pronominal subjects It and He and the first person singular subject pronoun I. These results replicate those of Wilson (2003), while controlling for some possible objections to Wilson's analysis. They thus provide further evidence against the generativist view that children's rates of provision of different tense-marking morphemes are determined by a single underlying factor, and are consistent with the constructivist view that children's rates of provision reflect the gradual accumulation of knowledge about tense marking, with much of children's early knowledge being embedded in lexically specific constructions.
Atomic-Resolution STEM in the Aberration-Corrected JEOL JEM2200FS
Authors: Klie Robert F. , Johnson Craig , Zhu Yimei
Published: January 2008

We report on the performance of our aberration-corrected JEOL-JEM2200FS electron microscope. This high-resolution field-mission TEM/STEM is equipped with a Schottky field-emission gun operated at 200 kV, a CEOS probe corrector, and an in-column energy filter. We focus on the performance of the probe corrector and show that the Si [110] dumbbell structure can be routinely resolved in STEM mode with the power spectrum indicating a probe size of ~1 Å. Ronchigram analysis suggests that the constant phase area is extended from 15 mrad to 35 mrad after corrector tuning. We also report the performance of our newly installed JEOL-JEM2200MCO, an upgraded version of the JEM2200FS, equipped with two CEOS aberration correctors (and a monochromator), one for the probe-forming lens and the other for the postspecimen objective lens. Based on Young's fringe analysis of Au particles on amorphous Ge, initial results show that the information limit in TEM mode with the aberration correction (Cs= −3.8 μm) is ~0.12 nm. Materials research applications using these two instruments are described including atomic-column-resolved Z-contrast imaging and electron energy-loss spectroscopy of oxide hetero-interfaces and strain mapping of a SrTiO3tilt-grain boundary. The requirements for a high-precision TEM laboratory to house an aberration-corrected microscope are also discussed.
Improving predictions of summer climate change in the United States
Authors: Hall A. , Qu X. , Neelin J. D.
Published: January 2008

Across vast, agriculturally intensive regions of the United States, the spread in predictions of summer temperature and soil moisture under global warming is curiously elevated in current climate models. Some models show modest warming of 2–3C° and little drying or slight moistening by the 22nd century, while at the other extreme are simulations with warming as large as 7–8C° and 20–40% reductions in soil moisture. We show this region of large spread arises from differences in simulations of snow albedo feedback. During winter and early spring, models with strong snow albedo feedback exhibit large reductions in snowpack and hence water storage. This water deficit persists in summer soil moisture, with reduced evapotranspiration yielding warmer temperatures. Comparison of simulated feedback strength to observations of the feedback from the current climate's seasonal cycle suggests the inter‐model differences are excessive. At the same time, the multi‐model mean feedback strength agrees reasonably well with the observed value. We estimate that if the next generation of models were brought into line with observations of snow albedo feedback, the unusually wide divergence in simulations of summer warming and drying over the US would shrink by roughly one third to one half.
Density functional study of the interaction between small Au clusters, Aun (n=1–7) and the rutile TiO2 surface. II. Adsorption on a partially reduced surface
Authors: Chrétien Steeve , Metiu Horia
Published: January 2008

We use density functional theory to examine the electronic structure of small Aun (n=1–7) clusters, supported on a rutile TiO2(110) surface having oxygen vacancies on the surface (a partially reduced surface). Except for the monomer, the binding energy of all Au clusters to the partially reduced surface is larger by ∼0.25eV than the binding energy to a stoichiometric surface. The bonding site and the orientation of the cluster are controlled by the shape of the highest occupied molecular orbitals (HOMOs) of the free cluster (free cluster means a gas-phase cluster with the same geometry as the supported one). The bond is strong when the lobes of the HOMOs overlap with those of the high-energy states of the clean oxide surface (i.e., with no gold) that have lobes on the bridging and the in-plane oxygen atoms. In other words, the cluster takes a shape and a location that optimizes the contact of its HOMOs with the oxygen atoms. Fivefold coordinated Ti atoms located at a defect site (5c-Ti*) participate in the binding only when a protruding lobe of the singly occupied molecular orbital (for odd n) or the lowest unoccupied molecular orbital (for even n) of the free Aun cluster points toward a 5c-Ti* atom. The oxygen vacancy influences the binding energy of the clusters (except for Au1) only when they are in direct contact with the defect. The desorption energy and the total charge on clusters that are close to, but do not overlap with, the vacancy differ little from the values they have when the cluster is adsorbed on a stoichiometric surface. The behavior of Au1 is rather remarkable. The atom prefers to bind directly to the vacancy site with a binding energy of 1.81eV. However, it also makes a strong bond (1.21eV) with any 5c-Ti atom even if that atom is far from the vacancy site. In contrast, the binding of a Au monomer to the 5c-Ti atom of a surface without vacancies is weak (0.45eV). The presence of the vacancy activates the 5c-Ti atoms by populating states at the bottom of the conduction band. These states are delocalized and have lobes protruding out of the surface at the location of the 5c-Ti atoms. It is the overlap of these lobes with the highest orbital of the Au atom that is the major reason for the bonding to the 5c-Ti atom, no matter how far the latter is from the vacancy. The energy for breaking an adsorbed cluster into two adsorbed fragments is smaller than the kinetic energy of the mass-selected clusters deposited on the surface in experiments. However, this is not sufficient for breaking the cluster upon impact with the surface, since only a fraction of the available energy will go into the reaction coordinate for breakup.
White light emission from single layer poly (n-vinylcarbazole) polymeric light-emitting devices by mixing singlet and triplet excimer emissions
Authors: Qian Lei , Bera Debasis , Holloway Paul H.
Published: January 2008

White light electroluminescence (EL) was obtained by mixing emission from singlet and triplet excimers from a single poly (n-vinylcarbazole) (PVK) spin cast layer after irradiation of the solution with UV light. With increased UV light irradiation, the intensity from the triplet excimer (red-630nm) of PVK increased compared with that of the singlet excimer (blue-460nm) due to an increased population of both adjacent benzene rings being aligned with one another (fully overlapping) versus only one of the adjacent benzene rings being aligned (partially overlapping). The emission color changed from blue to white with increased UV irradiation time while the EL brightness and current density decreased and the turn-on voltage increased.
Photochemical processes in doped argon-neon core-shell clusters: The effect of cage size on the dissociation of molecular oxygen
Authors: Laarmann T. , Wabnitz H. , von Haeften K. , Möller T.
Published: January 2008

The caging effect of the host environment on photochemical reactions of molecular oxygen is investigated using monochromatic synchrotron radiation and spectrally resolved fluorescence. Oxygen doped clusters are formed by coexpansion of argon and oxygen, by pickup of molecular oxygen or by multiple pickup of argon and oxygen by neon clusters. Sequential pickup provides radially ordered core-shell structures in which a central oxygen molecule is surrounded by argon layers of variable thickness inside large neon clusters. Pure argon and core-shell argon-neon clusters excited with ∼12eV monochromatic synchrotron radiation show strong fluorescence in the vacuum ultraviolet (vuv) spectral range. When the clusters are doped with O2, fluorescence in the visible (vis) spectral range is observed and the vuv radiation is found to be quenched. Energy-resolved vis fluorescence spectra show the 2Σ+1→1Σ+1(ArO(S1)→ArO(D1)) transition from argon oxide as well as the vibrational progression AΔu′3(ν′=0)→XΣg−3(ν″) of O2 indicating that molecular oxygen dissociates and occasionally recombines depending on the experimental conditions. Both the emission from ArO and O2 as well the vuv quenching by oxygen are found to depend on the excitation energy, providing evidence that the energy transfer from the photoexcited cluster to the embedded oxygen proceeds via the O2+ ground state. The O2+ decays via dissociative recombination and either reacts with Ar resulting in electronically excited ArO or it recombines to O2 within the Ar cage. Variation of the Ar layer thickness in O2–Ar–Ne core-shell clusters shows that a stable cage is formed by two solvation layers.
Two-body correlations among particles confined to a spherical surface: Packing effects
Authors: Viveros-Méndez P. X. , Méndez-Alcaraz J. M. , González-Mozuelos P.
Published: January 2008

The two-point correlation functions among particles confined to move within a spherical two-dimensional space are studied here using Monte Carlo simulations in the canonical ensemble and the corresponding liquid theory concepts. This work takes a simple model system with soft-sphere interactions among the particles lying on the spherical surface. We focus this study on the ordering induced by the particle packing and the restrictions imposed by the system topology. The corresponding grand canonical results are obtained from the canonical Monte Carlo data using the standard statistical mechanics formulas. These grand canonical ensemble results show that as the strength of the interactions increases, the system transits between liquidlike states and crystal-like states as the average number of particles on the spherical surface matches certain specific values. The crystal-like states correspond to sharp minima in the plot of the standard deviation in the number of particles on the spherical surface versus the average value of this number. We also test the validity of the integral equation approaches for this kind of closed but boundless systems: It is found that the Percus-Yevick approximation overestimates the correlations for this system in a liquid state, whereas the hypernetted-chain approximation underestimates these correlations.
Complete phase behavior of the symmetrical colloidal electrolyte
Authors: Caballero José B. , Noya Eva G. , Vega Carlos
Published: January 2008

We computed the complete phase diagram of the symmetrical colloidal electrolyte by means of Monte Carlo simulations. Thermodynamic integration, together with the Einstein-crystal method, and Gibbs-Duhem integration were used to calculate the equilibrium phase behavior. The system was modeled via the linear screening theory, where the electrostatic interactions are screened by the presence of salt in the medium, characterized by the inverse Debye length, κ (in this work κσ=6). Our results show that at high temperature, the hard-sphere picture is recovered, i.e., the liquid crystallizes into a fcc crystal that does not exhibit charge ordering. In the low temperature region, the liquid freezes into a CsCl structure because charge correlations enhance the pairing between oppositely charged colloids, making the liquid-gas transition metastable with respect to crystallization. Upon increasing density, the CsCl solid transforms into a CuAu-like crystal and this one, in turn, transforms into a tetragonal ordered crystal near close packing. Finally, we have studied the ordered-disordered transitions finding three triple points where the phases in coexistence are liquid–CsCl–disordered fcc, CsCl–CuAu–disordered fcc, and CuAu–tetragonal–disordered fcc.
Dynamical phases of the Hindmarsh-Rose neuronal model: Studies of the transition from bursting to spiking chaos
Authors: Innocenti Giacomo , Morelli Alice , Genesio Roberto , Torcini Alessandro
Published: January 2008

The dynamical phases of the Hindmarsh-Rose neuronal model are analyzed in detail by varying the external current I. For increasing current values, the model exhibits a peculiar cascade of nonchaotic and chaotic period-adding bifurcations leading the system from the silent regime to a chaotic state dominated by bursting events. At higher I-values, this phase is substituted by a regime of continuous chaotic spiking and finally via an inverse period doubling cascade the system returns to silence. The analysis is focused on the transition between the two chaotic phases displayed by the model: one dominated by spiking dynamics and the other by bursts. At the transition an abrupt shrinking of the attractor size associated with a sharp peak in the maximal Lyapunov exponent is observable. However, the transition appears to be continuous and smoothed out over a finite current interval, where bursts and spikes coexist. The beginning of the transition (from the bursting side) is signaled from a structural modification in the interspike interval return map. This change in the map shape is associated with the disappearance of the family of solutions responsible for the onset of the bursting chaos. The successive passage from bursting to spiking chaos is associated with a progressive pruning of unstable long-lasting bursts.
Thermal activation of ferroelectric switching
Authors: Chong K. B. , Guiu F. , Reece M. J.
Published: January 2008

By applying the theory of thermally activated nucleation to the switching of ferroelectric domains, a method is developed to experimentally obtain the value of both the activation enthalpy, ΔH, and activation volume, V*, for the thermally activated process involved in ferroelectric switching. The method was applied to the switching of a soft lead zirconate titanate and values of ΔH=(0.16±0.02) eV and V*=(1.62±0.16)×10−25 m3 were obtained at the coercive field. These values imply that the energy, ΔU, required for the formation of switching nuclei is mainly supplied by the work done by the electric field. A comparison of these values with those obtained from theoretical considerations suggests that the switching is achieved by the sideways expansion of nuclei formed at the domain boundaries in the form of low amplitude and long wavelength fluctuations of the domain walls.
Mediation of long-range attraction selectively between negatively charged colloids on surfaces by solvation
Authors: Kung William , Olvera de la Cruz Monica
Published: January 2008

We propose a mean-field analytical model to account for the observed asymmetry in the ability to form long-range attraction by the negatively charged colloidal particles and not their equivalently charged positive counterpart. We conjecture that this asymmetry is due to solvation effects, and we phenomenologically capture its physics by considering the relative strength of this water-induced short-range repulsion between the different charge species. We then apply our model to the colloidal system of negatively charged disks that are neutralized by a sea of counterions and strongly absorbed to an interface in a compressible binary system. We demonstrate the resulting coexistence between a dilute isotropic ionic phase and a condensed hexagonal lattice phase as a function of density and interaction strength.
Gyrokinetic theory and simulation of angular momentum transport
Authors: Waltz R. E. , Staebler G. M. , Candy J. , Hinton F. L.
Published: January 2008

A gyrokinetic theory of turbulent toroidal angular momentum transport as well as modifications to neoclassical poloidal rotation from turbulence is formulated starting from the fundamental six-dimensional kinetic equation. The gyro-Bohm scaled transport is evaluated from toroidal delta-f gyrokinetic simulations using the GYRO code [Candy and Waltz, J. Comput. Phys. 186, 545 (2003)]. The simulations recover two pinch mechanisms in the radial transport of toroidal angular momentum: The slab geometry E×B shear pinch [Dominguez and Staebler, Phys. Fluids B 5, 387 (1993)] and the toroidal geometry “Coriolis” pinch [Peeters, Angioni, and Strintzi, Phys. Rev. Lett. 98, 265003 (2007)]. The pinches allow the steady state null stress (or angular momentum transport flow) condition required to understand intrinsic (or spontaneous) toroidal rotation in heated tokamak without an internal source of torque [Staebler, Kinsey, and Waltz, Bull. Am. Phys. Soc. 46, 221 (2001)]. A predicted turbulent shift in the neoclassical poloidal rotation [Staebler, Phys. Plasmas 11, 1064 (2004)] appears to be small at the finite relative gyroradius (rho-star) of current experiments.
Far-wake characteristics of two-dimensional flow past a normal flat plate
Authors: Saha Arun K.
Published: January 2008

Direct numerical simulation of flow past a normal flat plate having an aspect ratio of 0.125 has been carried out at Reynolds number range of 30–175. The unsteady far-wake observed at low Reynolds number becomes steady for 75⩽Re⩽140. The steady far-wake undergoes a transition at Re=145 with large scale unsteadiness observed in the far-wake. The frequency of the large scale vortex structures, also called secondary vortex structures, is lower than that of the near-wake. At Re=150, the low frequency far-wake vortex street undulates at another frequency, which increases with increasing Reynolds number, resulting in a tertiary vortex pattern. The transitions are found to have no significant effect on the mean integral parameters such as the drag coefficient and the Strouhal number.
A model for two-dimensional bursty turbulence in magnetized plasmas
Authors: Servidio Sergio , Primavera Leonardo , Carbone Vincenzo , Noullez Alain , Rypdal Kristoffer
Published: January 2008

The nonlinear dynamics of two-dimensional electrostatic interchange modes in a magnetized plasma is investigated through a simple model that replaces the instability mechanism due to magnetic field curvature by an external source of vorticity and mass. Simulations in a cylindrical domain, with a spatially localized and randomized source at the center of the domain, reveal the eruption of mushroom-shaped bursts that propagate radially and are absorbed by the boundaries. Burst sizes and the interburst waiting times exhibit power-law statistics, which indicates long-range interburst correlations, similar to what has been found in sandpile models for avalanching systems. It is shown from the simulations that the dynamics can be characterized by a Yaglom relation for the third-order mixed moment involving the particle number density as a passive scalar and the E×B drift velocity, and hence that the burst phenomenology can be described within the framework of turbulence theory. Statistical features are qualitatively in agreement with experiments of intermittent transport at the edge of plasma devices, and suggest that essential features such as transport can be described by this simple model of bursty turbulence.
Piezoresponse imaging of lead zirconate titanate microfibers and numerical analysis of its electric field distribution
Authors: Wang Yu , Santiago-Avilés Jorge
Published: January 2008

Piezoresponse imaging technique was transplanted from thin film to probe polarization domains and local properties in single electrospun lead zirconate titanate microfibers. The corresponding electric field distribution was numerically analyzed. The biased conic tip is found to produce a field that peaks on its apex and decreases rapidly toward the bottom metal electrode. A strong field exists only in a thin surface region and cannot pole the affected domain even with its magnitude of 108V∕m on the fiber surface.
Effect of carbon addition on the glass-forming ability of mechanically alloyed Fe-based alloys
Authors: Sharma Satyajeet , Suryanarayana C.
Published: January 2008

The effect of carbon addition on the glass-forming ability (GFA) of mechanically alloyed Fe-based Fe42M28Zr10B20 (M=Ni, Al, or Ge) amorphous alloy systems was investigated. It was shown that when B was partially replaced by 10at.% C in the Fe–Ni–Zr–B and Fe–Al–Zr–B alloy systems, the GFA of the systems had increased significantly, as determined by the reduced milling time required for amorphization. However, when carbon was added to the Fe–Ge–Zr–B alloy system, the GFA was decreased drastically and no amorphization was observed. The role of carbon on the GFA of alloy systems has been discussed from the thermodynamic and kinetic points of view.
Nanoscale heat transfer in a thin aluminum film and femtosecond time-resolved electron diffraction
Authors: Tang Jau
Published: January 2008

We examined nanoscale heat transfer and structural dynamics by analyzing ultrafast electron diffraction data of a laser-heated aluminum film. The excellent agreement between model calculations with experimental data allows us to elucidate the mechanism of dynamic expansion/contraction involving acoustic wave propagation from the stressed bulk atoms and the more well-understood mechanism of linear thermal expansion.
Observation of laser-induced surface waves on flat silicon surface
Authors: Tomita Takuro , Fukumori Yasuhiro , Kinoshita Keita , Matsuo Shigeki , Hashimoto Shuichi
Published: January 2008

We found that irradiation by a single femtosecond laser pulse produced a surface wave structure on a (100) silicon surface. The surface wave structure bearing a concentric shape was produced only in the edge regions in the direction of the electric field from the center. The increase in the number of irradiating pulses allowed the concentric structure gradually to align perpendicularly to the laser beam’s electric field. The period of the surface wave structure was nearly equal to the wavelength of the irradiating laser pulse. In this accord, we propose that this structure is a precursor of ripple formation.
Type-II InGaN-GaNAs quantum wells for lasers applications
Authors: Arif Ronald A , Zhao Hongping , Tansu Nelson
Published: January 2008

We present a visible III-nitride gain medium based on type-II InGaN-GaNAs quantum well (QW), employing thin dilute-As (∼3%) GaNAs layer. The utilization of GaNAs layer shifts the hole confinement to the center of the type-II QW, which significantly reduces the charge separation effect. The optical gain and spontaneous recombination rate of the type-II InGaN-GaNAs QW are analyzed and compared with those of conventional InGaN QW emitting in the blue regime (λ∼450nm), using six-band k.p formalism for energy dispersion of the III-nitride wurtzite semiconductor. The use of type-II QW leads to significant improvement in the optical gain and spontaneous recombination rate.
Hysteretic ac loss of polygonally arranged superconducting strips carrying ac transport current
Authors: Mawatari Yasunori , Kajikawa Kazuhiro
Published: January 2008

The hysteretic ac loss of a current-carrying conductor in which multiple superconducting strips are polygonally arranged around a cylindrical former is theoretically investigated as a model of superconducting cables. Using the critical state model, we analytically derive the ac loss Qn of a total of n strips. The normalized loss Qn∕Q1 is determined by the number of strips n and the ratio of the strip width 2w to the diameter 2R of the cylindrical former. When n⪢1 and w∕R⪡1, the behavior of Qn is similar to that of an infinite array of coplanar strips.
X-shaped third harmonic generated by ultrashort infrared pulse filamentation in air
Authors: Xu Han , Xiong Hui , Li Ruxin , Cheng Ya , Xu Zhizhan , Chin See Leang
Published: January 2008

The authors report the measurement of the angularly resolved spectrum of the third harmonic generated in a femtosecond filament in air and its evolution with increasing pump power. Pumped by a focused infrared ultrashort pulse with a carrier wavelength of 1270nm, a pulse duration of ∼20fs, and pulse energy up to 487μJ, the generated third harmonic is composed of an on-axis emission and a conical ring emission. When the pump power is sufficiently high, angularly resolved spectra with significant X-like feature could be observed, indicating the formation of nonlinear X wave at third harmonic.
Tuning lipid mixtures to induce or suppress domain formation across leaflets of unsupported asymmetric bilayers
Authors: Collins Marcus D. , Keller Sarah L.
Published: January 2008

Plasma membranes of cells are asymmetric in both lipid and protein composition. The mechanism by which proteins on both sides of the membrane colocalize during signaling events is unknown but may be due to the induction of inner leaflet domains by the outer leaflet. Here we show that liquid domains form in asymmetric Montal–Mueller planar bilayers in which one leaflet's composition would phase-separate in a symmetric bilayer and the other's would not. Equally important, by tuning the lipid composition of the second leaflet, we are able to suppress domains in the first leaflet. When domains are present in asymmetric membranes, each leaflet contains regions of three distinct lipid compositions, implying strong interleaflet interactions. Our results show that mechanisms of domain induction between the outer and inner leaflets of cell plasma membranes do not necessarily require the participation of membrane proteins. Based on these findings, we suggest mechanisms by which cells could actively regulate protein function by modulating local lipid composition or interleaflet interactions.
Methane oxidation at 55°C and pH 2 by a thermoacidophilic bacterium belonging to the
Verrucomicrobia
phylum
Authors: Islam Tajul , Jensen Sigmund , Reigstad Laila Johanne , Larsen Øivind , Birkeland Nils-Kåre
Published: January 2008

Methanotrophic bacteria constitute a ubiquitous group of microorganisms playing an important role in the biogeochemical carbon cycle and in control of global warming through natural reduction of methane emission. These bacteria share the unique ability of using methane as a sole carbon and energy source and have been found in a great variety of habitats. Phylogenetically, known methanotrophs constitute a rather limited group and have so far only been affiliated with the
Proteobacteria
. Here, we report the isolation and initial characterization of a nonproteobacterial obligately methanotrophic bacterium. The isolate, designated Kam1, was recovered from an acidic hot spring in Kamchatka, Russia, and is more thermoacidophilic than any other known methanotroph, with optimal growth at ≈55°C and pH 3.5. Kam1 is only distantly related to all previously known methanotrophs and belongs to the
Verrucomicrobia
lineage of evolution. Genes for methane monooxygenases, essential for initiation of methane oxidation, could not be detected by using standard primers in PCR amplification and Southern blot analysis, suggesting the presence of a different methane oxidation enzyme. Kam1 also lacks the well developed intracellular membrane systems typical for other methanotrophs. The isolate represents a previously unrecognized biological methane sink, and, due to its unusual phylogenetic affiliation, it will shed important light on the origin, evolution, and diversity of biological methane oxidation and on the adaptation of this process to extreme habitats. Furthermore, Kam1 will add to our knowledge of the metabolic traits and biogeochemical roles of the widespread but poorly understood
Verrucomicrobia
phylum.
Origins of barriers and barrierless folding in BBL
Authors: Cho Samuel S. , Weinkam Patrick , Wolynes Peter G.
Published: January 2008

In contrast to classical chemical phenomenology, theory suggests that proteins may undergo downhill folding without an activation barrier under certain thermodynamic conditions. Recently, the BBL protein was proposed to fold by such a downhill scenario, but discrepancies between experimental results found in different groups argue against this. After briefly reviewing the major experimental studies of the BBL folding mechanism, we show that simulations of both coarse-grained and atomistic models can reconcile the seemingly conflicting observations.
Disruption of the RIIβ subunit of PKA reverses the obesity syndrome of agouti lethal yellow mice
Authors: Czyzyk Traci A. , Sikorski Maria A. , Yang Linghai , McKnight G. Stanley
Published: January 2008

Agouti lethal yellow (A
y
) mice express agouti ectopically because of a genetic rearrangement at the agouti locus. The agouti peptide is a potent antagonist of the melanocortin 4 receptor (MC4R) expressed in neurons, and this leads to hyperphagia, hypoactivity, and increased fat mass. The MC4R signals through Gs and is thought to stimulate the production of cAMP and activation of downstream cAMP effector molecules such as PKA. Disruption of the RIIβ regulatory subunit gene of PKA results in release of the active catalytic subunit and an increase in basal PKA activity in cells where RIIβ is highly expressed. Because RIIβ is expressed in neurons including those in the hypothalamic nuclei where MC4R is prominent we tested the possibility that the RIIβ knockout might rescue the body weight phenotypes of the A
y
mice. Disruption of the RIIβ PKA regulatory subunit gene in mice leads to a 50% reduction in white adipose tissue and resistance to diet-induced obesity and hyperglycemia. The RIIβ mutation rescued the elevated body weight, hyperphagia, and obesity of A
y
mice. Partial rescue of the A
y
phenotypes was even observed on an RIIβ heterozygote background. These results suggest that the RIIβ gene mutation alters adiposity and locomotor activity by modifying PKA signaling pathways downstream of the agouti antagonism of MC4R in the hypothalamus.
The TLR3 signaling complex forms by cooperative receptor dimerization
Authors: Leonard Joshua N. , Ghirlando Rodolfo , Askins Janine , Bell Jessica K. , Margulies David H. , Davies David R. , Segal David M.
Published: January 2008

Toll-like receptors (TLRs) initiate immune responses by recognizing pathogen-associated molecules, but the molecular basis for recognition is poorly understood. In particular, it is unclear how receptor-ligand interactions lead to the initiation of downstream signaling. Here, we describe the mechanism by which TLR3 recognizes its ligand, double-stranded RNA (dsRNA), and forms an active signaling complex. We show that dsRNA binds saturably, specifically, and reversibly to a defined ligand-binding site (or sites) on the TLR3 ectodomain (TLR3ecd). Binding affinities increase with both buffer acidity and ligand size. Purified TLR3ecd protein is exclusively monomeric in solution, but through a highly cooperative process, it forms dimers when bound to dsRNA, and multiple TLR3ecd dimers bind to long dsRNA strands. The smallest dsRNA oligonucleotides that form stable complexes with TLR3ecd (40–50 bp) each bind one TLR3ecd dimer, and these are also the smallest oligonucleotides that efficiently activate TLR3 in cells. We conclude that TLR3 assembles on dsRNA as stable dimers and that the minimal signaling unit is one TLR3 dimer.
Role of Insulin Receptor and Balance in Insulin Receptor Isoforms A and B in Regulation of Apoptosis in Simian Virus 40-immortalized Neonatal Hepatocytes
Authors: Nevado Carmen , Benito Manuel , Valverde Angela M.
Published: January 2008

We have investigated the unique role of the insulin receptor (IR) and the balance of its isoforms A and B in the regulation of apoptosis in simian virus 40 (SV40)-immortalized neonatal hepatocytes. Immortalized hepatocytes lacking (HIR KO) or expressing the entire IR (HIR LoxP), and cells expressing either IRA (HIR RecA) or IRB (HIR RecB) have been generated. IR deficiency in hepatocytes increases sensitivity to the withdrawal of growth factors, because these cells display an increase in reactive oxygen species, a decrease in Bcl-xL, a rapid accumulation of nuclear Foxo1, and up-regulation of Bim. These events resulted in acceleration of caspase-3 activation, DNA laddering, and cell death. The single expression of either IRA or IRB produced a stronger apoptotic phenotype. In these cells, protein complexes containing IRA or IRB and Fas/Fas-associating protein with death domain activated caspase-8, and, ultimately, caspase-3. In hepatocytes expressing IRA, Bid cleavage and cytochrome C release were increased whereas direct activation of caspase-3 by caspase-8 and a more rapid apoptotic process occurred in hepatocytes expressing IRB. Conversely, coexpression of IRA and IRB in IR-deficient hepatocytes rescued from apoptosis. Our results suggest that balance alteration of IRA and IRB may serve as a ligand-independent apoptotic trigger in hepatocytes, which may regulate liver development.
Axin and GSK3-β control Smad3 protein stability and modulate TGF-β signaling
Authors: Guo Xing , Ramirez Alejandro , Waddell David S. , Li Zhizhong , Liu Xuedong , Wang Xiao-Fan
Published: January 2008

The broad range of biological responses elicited by transforming growth factor-β (TGF-β) in various types of tissues and cells is mainly determined by the expression level and activity of the effector proteins Smad2 and Smad3. It is not fully understood how the baseline properties of Smad3 are regulated, although this molecule is in complex with many other proteins at the steady state. Here we show that nonactivated Smad3, but not Smad2, undergoes proteasome-dependent degradation due to the concerted action of the scaffolding protein Axin and its associated kinase, glycogen synthase kinase 3-β (GSK3-β). Smad3 physically interacts with Axin and GSK3-β only in the absence of TGF-β. Reduction in the expression or activity of Axin/GSK3-β leads to increased Smad3 stability and transcriptional activity without affecting TGF-β receptors or Smad2, whereas overexpression of these proteins promotes Smad3 basal degradation and desensitizes cells to TGF-β. Mechanistically, Axin facilitates GSK3-β-mediated phosphorylation of Smad3 at Thr66, which triggers Smad3 ubiquitination and degradation. Thr66 mutants of Smad3 show altered protein stability and hence transcriptional activity. These results indicate that the steady-state stability of Smad3 is an important determinant of cellular sensitivity to TGF-β, and suggest a new function of the Axin/GSK3-β complex in modulating critical TGF-β/Smad3-regulated processes during development and tumor progression.
APC/C-Cdh1-mediated degradation of the Polo kinase Cdc5 promotes the return of Cdc14 into the nucleolus
Authors: Visintin Clara , Tomson Brett N. , Rahal Rami , Paulson Jennifer , Cohen Michael , Taunton Jack , Amon Angelika , Visintin Rosella
Published: January 2008

In the budding yeastSaccharomyces cerevisiae, the protein phosphatase Cdc14 triggers exit from mitosis by promoting the inactivation of cyclin-dependent kinases (CDKs). Cdc14’s activity is controlled by Cfi1/Net1, which holds and inhibits the phosphatase in the nucleolus from G1 until metaphase. During anaphase, two regulatory networks, the Cdc14 Early Anaphase Release (FEAR) network and the Mitotic Exit Network (MEN), promote the dissociation of Cdc14 from its inhibitor, allowing the phosphatase to reach its targets throughout the cell. The molecular circuits that trigger the return of Cdc14 into the nucleolus after the completion of exit from mitosis are not known. Here we show that activation of a ubiquitin ligase known as the Anaphase-Promoting Complex or Cyclosome (APC/C) bound to the specificity factor Cdh1 triggers the degradation of the Polo kinase Cdc5, a key factor in releasing Cdc14 from its inhibitor in the nucleolus.
Evolutionary and geological events across the Precambrian–Cambrian boundary
Authors: BRASIER M. D.
Published: January 2008

Over the last decade, palaeontologists around the world have been striving to understand one of the most remarkable episodes in the fossil record: the explosive evolution of skeletal fossils around the Precambrian–Cambrian boundary. When examined in the field, the close association of geological and biological events is apparent. An important succession in this respect is the classic Precambrian and Cambrian area of Charnwood–Nuneaton in the English Midlands. Here it can be seen that the boundary also spans a time of major tectonic and oceanographic changes. Could these have contributed to the ‘Cambrian evolutionary explosion’?
Geological traces of Saxon churches in the London Basin
Authors: POTTER JOHN F.
Published: January 2008

A comprehensive examination of the building materials of London Basin churches suggests that many more may reveal evidence of an Anglo‐Saxon origin than has previously been accepted.
The geological photographs of the BAAS
Authors: MCKENNA GRAHAM
Published: January 2008

Several thousand geological photographs collected by the British Association for the Advancement of Science (BAAS), some dating back well over 120 years, have recently been deposited with the national geological records held by the British Geological Survey at Keyworth.
The Rock of Gibraltar
Authors: ROSE EDWARD P. F. , ROSENBAUM M. S.
Published: January 2008

Most people have heard of the Rock of Gibraltar, yet few know anything of its geology. Recent studies now interpret the Rock as a partly overturned mass of Jurassic limestone, thrust into position during continent‐continent collision by about 15–20 million years ago, and shaped largely by shoreline processes active during Pleistocene tectonic uplift. The Rock's geology has implications for currently developing interpretations of the geological evolution of the western Mediterranean region and for the fast‐growing development of Gibraltar's urban environment.