bluuebunny/crossref_metadata_2025 huggingface dataset:
Rationalizing and functionalizing stannaspherene: Very stable stannaspherene “alloys”
Authors: Zdetsis Aristides D.
Published: December 2009

It is illustrated here by ab initio calculations based on density functional theory and other high level methods that the high stability of the icosahedral Sn122− dianion known as stannaspherene, reflects stability toward ionization rather than cohesion. This could be also connected with novel fluxional rearrangements and paths of Sn121− leading eventually to Sn122− involving charge transfer. In view of the very similar structural and electronic properties with the corresponding isovalent borane (B12H12)2−, it is demonstrated that stannaspherene can be further rationalized and functionalized on the basis of an isolobal analogy between group 14 clusters and isovalent boranes, carboranes, and bisboranes. Such analogy is of the same nature with analogous isolobal and isovalent similarities between silicon, hydrogenated silicon-carbon clusters and deltahedral boranes and carboranes, which the present author, scoptically and synoptically, has described as the “boron connection.” It is predicted and verified theoretically: First, that the isovalent Bi2Sn10 and Sb2Sn10 clusters, considered as the microscopic analogs of tin-bismuth alloys, are very stable (more stable than stannaspherene itself) very symmetric and isolobal to Sn122−; and second, that embedded clusters of the form M@Sn122−, M@Bi2Sn10, M=Pt,Pd are very stable and highly symmetrical (Ih and D5d respectively) with large highest occupied-lowest unoccupied molecular orbital gaps and very large embedding energies of the order of 5–6 eV. It is furthermore predicted that Pt@Sn122− and Pt@Bi2Sn10 can be synthesized in view of their higher stability compared to Pt@Pb122− which has already been synthesized. The marginal energy difference of 0.03 eV between the meta- and the para-isomer of Bi2Sn10 indicates a fluxional behavior with respect to Bi–Sn interchange which should be related with the Sn121− fluxionality leading eventually to Sn122−. This rearrangement is also associated with a strange aromatic behavior. The same type of Bi–Sn fluxionality is also encountered in higher energy structures. Due to the “inert pair effect” in tin, the validity of the isolobal analogy is much stronger and fully valid compared to isovalent species based on germanium or silicon, such as Ge122−, Bi2Ge10, and Ge10C2H2 and Si122−, Bi2Si10, and Si10C2H2. The present ideas are in full agreement with available experiments and suggest even further functionalization of stannaspherene, analogous to metaloboranes, metalocarboranes, and stannaboranes with several potential applications.
Capillary torque in a liquid bridge between two angled filaments
Authors: Bedarkar Amol , Wu Xiang-Fa
Published: December 2009

Capillary torque is induced when a liquid bridge forms between two angle-positioned filaments. This paper aims to study the dependency of such capillary torque upon the filament orientation angle, filament spacing, contact angle, and liquid volume through detailed numerical simulation using a surface finite element scheme. Numerical results show that for hydrophilic liquid with contact angle below 90° and at given liquid volume as well as filament spacing, the surface energy of the system grows nonlinearly with increasing filament orientation angle from 0° (parallel filaments) to 90° (cross-positioned filaments). Accordingly, the capillary torque induced by the distorted liquid bridge increases from a torque-free state at 0° to the peak value and then decreases to the second torque-free state at 90°. At fixed filament orientation angle, the capillary torque grows with the liquid volume while decreases rapidly with increasing either contact angle or filament spacing. The peak value of capillary torque depends upon both the geometries and wetting property of the liquid bridge-filament system. A family of characteristic curves in terms of capillary torque with the filament orientation angle is determined at varying volume of liquid bridge, filament spacing ratio, and contact angle. The results and concepts developed in work are applicable for the study of wetting and spreading of liquids in fiber networks, microfluidics-based microstructural assembly, biological cell operation, etc.
Impact of the electroforming process on the device stability of epitaxial Fe-doped SrTiO3 resistive switching cells
Authors: Menke T. , Dittmann R. , Meuffels P. , Szot K. , Waser R.
Published: December 2009

In this work, the results of our detailed investigations on the electroforming procedure in Pt/SrTi0.99Fe0.01O3/SrTi0.99Nb0.01O3 [Pt/STO(Fe)/Nb:STO] metal-insulator-metal (MIM)-devices and its impact on the performance of resistive switching memory devices are presented. Questions about the exact location of the modifications triggered by the electroforming procedure within the investigated MIM-devices will be addressed. From a technological point of view, the thermal stability of formed devices becomes important. An increase in the device resistances during retention measurements has been observed indicating the presence of internal redistribution effects. These may result from an oxygen vacancy gradient induced by the forming process. However, these internal relaxation effects will not end up in the unformed state. Annealing experiments under defined atmospheric conditions allowed distinguishing between internal and external rediffusion effects. We found that SrTiO3 starts to interact with the surrounding atmosphere at moderate temperatures. The occurring external reoxidation effect set the device back to its initial (unformed) state. As a result, the investigated MIM-structures can no longer be regarded as closed systems and presented the large implication on the retention of such devices. The experimental findings are supported by calculations of the penetration depth of oxygen ions/vacancies in SrTiO3.
Convergence of the nonisentropic Euler–Maxwell equations to compressible Euler–Poisson equations
Authors: Yang Jianwei , Wang Shu
Published: December 2009

This paper is concerned with the convergence of the time-dependent and nonisentropic Euler–Maxwell equations to compressible Euler–Poisson equations in a torus via the nonrelativistic limit. By using the method of formal asymptotic expansions, we analyze the nonrelativistic limit for periodic problems with the prepared initial data. It is shown that the small parameter problem has unique solutions existing in the finite time interval where the corresponding limit problems have smooth solutions. Furthermore, the convergence of solutions is rigorously justified.
Understanding of nanoscale periodic stripes on fracture surface of metallic glasses
Authors: Wang Y. T. , Xi X. K. , Wang G. , Xia X. X. , Wang W. H.
Published: December 2009

We report the observation of nanoscale striped periodic pattern with similar distinctive characteristics independent of loading conditions on the fracture surface of various bulk metallic glasses. We demonstrate that the periodic stripes are formed by the orderly assembly of nanoscale regular dimples. The similarities between our observed striped pattern and various unequilibrium systems such as oscillating granular and colloidal suspensions systems are found. By drawing an analogy between glassy and granular materials, we propose a model that can capture and simulate the characteristics of the observed corrugations. Our results would provide insight into the origin of fracture surface roughening in brittle materials.
High-efficiency turquoise-blue electrophosphorescence from a Pt(II)-pyridyltriazolate complex in a phosphine oxide host
Authors: Bhansali Unnat S. , Polikarpov Evgueni , Swensen James S. , Chen Wei-Hsuan , Jia Huiping , Gaspar Daniel J. , Gnade Bruce E. , Padmaperuma Asanga B. , Omary Mohammad A.
Published: December 2009

We demonstrate high-efficiency turquoise-blue electrophosphorescence from bis[3,5-bis(2-pyridyl)-1,2,4-triazolato]platinum(II) [Pt(ptp)2] doped in 4-(diphenylphosphoryl)-N,N-diphenylaniline(HM-A1). Organic light-emitting diodes (OLEDs) with 5% Pt(ptp)2:HM-A1 attain peak power efficiency of 61.2 lm/W, versus 40.8 lm/W for analogous devices employing the standard turquoise-blue phosphor bis[(4,6-difluorophenyl)-pyridinato-N,C2′](picolinato)iridium(III) (FIrpic). Devices with x% Pt(ptp)2:HM-A1 exhibit blue emission maxima (λmax∼480 nm) with monotonic increase in excimer/monomer intensity ratio at higher doping levels within 1%–10%, causing color shift toward green and less charge balance. This work represents a significant step toward optimizing future white OLEDs from the same phosphor via combination of low-doped and higher-doped or neat films.
Ab initio potential energy surfaces for NH(Σ3−)–NH(Σ3−) with analytical long range
Authors: Janssen Liesbeth M. C. , Groenenboom Gerrit C. , van der Avoird Ad , Żuchowski Piotr S. , Podeszwa Rafał
Published: December 2009

We present four-dimensional ab initio potential energy surfaces for the three different spin states of the NH(Σ3−)–NH(Σ3−) complex. The potentials are partially based on the work of Dhont et al. [J. Chem. Phys. 123, 184302 (2005)]. The surface for the quintet state is obtained at the RCCSD(T)/augmented correlation-consistent polarized valence triple-zeta (aug-cc-pVTZ) level of theory and the energy differences with the singlet and triplet states are calculated at the complete active space with nth-order perturbation theory/aug-cc-pVTZ (n=2,3) level of theory. The ab initio potentials are fitted to coupled spherical harmonics in the angular coordinates, and the long range is further expanded as a power series in 1/R. The RCCSD(T) potential is corrected for a size-consistency error of about 0.5×10−6 Eh prior to fitting. The long-range coefficients obtained from the fit are found to be in good agreement with first and second-order perturbation theory calculations.
Characteristics of terahertz radiation emitted from the intrinsic Josephson junctions in high-Tc superconductor Bi2Sr2CaCu2O8+δ
Authors: Minami H. , Kakeya I. , Yamaguchi H. , Yamamoto T. , Kadowaki K.
Published: December 2009

Characteristic features of terahertz radiation emitted from a rectangular mesa comprised stacked intrinsic Josephson junctions in the layered high-Tc superconductor Bi2Sr2CaCu2O8+δ are reported. The emission with the total power of ∼5 μW at 0.63 THz shows a characteristic spatial distribution reflecting the rectangular shape. The stability of the emission was measured for at least 20 min. and the power fluctuation was found to be less than 4%. Furthermore, the radiation is highly polarized linearly with a ratio of 50:1. All features, including the spectral purity narrower than 4 GHz at full width at half maximum, promise a stable, coherent, and continuous terahertz source for various applications.
Heavy atom nitroxyl radicals. IV. Experimental and theoretical studies of the F2P=S free radical in the gas phase
Authors: Yang Jie , Clouthier Dennis J. , Tarroni Riccardo
Published: December 2009

The difluorothiophosphoryl (F2PS) free radical has been produced in a supersonic discharge jet from a precursor mixture of F3PS and high pressure argon and detected by laser-induced fluorescence and single vibronic level emission spectroscopy. With the aid of high level ab initio predictions of the properties of the ground and first two excited doublet states, the observed band system has been positively identified as B̃2A′-X̃2A′. The electronic transition involves promotion of an electron from the π to the π∗ orbital with concomitant increases in the out-of-plane angle and PS bond length on excitation. The observed vibrational structure, Franck–Condon profile, rotational band contours, T0 energy, and ground and excited state vibrational frequencies are all in accord with expectations based on our theoretical predictions.
Shock-induced melting of (100)-oriented nitromethane: Energy partitioning and vibrational mode heating
Authors: Dawes Richard , Siavosh-Haghighi Ali , Sewell Thomas D. , Thompson Donald L.
Published: December 2009

A study of the structural relaxation of nitromethane subsequent to shock loading normal to the (100) crystal plane performed using molecular dynamics and a nonreactive potential was reported recently [J. Chem. Phys. 131, 064503 (2009)]. Starting from initial temperatures of T0=50 and 200 K, shocks were simulated using impact velocities Up ranging from 0.5 to 3.0 km s−1; clear evidence of melting was obtained for shocks initiated with impacts of 2.0 km s−1 and higher. Here, we report the results of analyses of those simulation data using a method based on the Eckart frame normal-mode analysis that allows partitioning of the kinetic energy among the molecular degrees of freedom. A description of the energy transfer is obtained in terms of average translational and rotational kinetic energies in addition to the rates of individual vibrational mode heating. Generally, at early times postshock a large superheating of the translational and rotational degrees of freedom (corresponding to phonon modes of the crystal) is observed. The lowest frequency vibrations (gateway modes) are rapidly excited and also exhibit superheating. Excitation of the remaining vibrational modes occurs more slowly. A rapid, early excitation of the symmetric C–H stretch mode was observed for the shock conditions T0=50 K and Up=2.0 km s−1 due to a combination of favorable alignment of molecular orientation with the shock direction and frequency matching between the vibration and shock velocity.
Intermolecular momentum transfer in poly(perfluorosulfonic acid) membrane hydrated by aqueous solution of methanol: A molecular dynamics simulation study
Authors: Shao Changle , Yan Liuming , Ji Xiaobo , Zhu Suhua
Published: December 2009

Intermolecular momentum transfer in methanol-water mixture solvated poly(perfluoro-sulfonic acid) membrane is studied in terms of center of mass velocity cross-correlation functions between molecular mass centers in their first coordination shells based on molecular dynamics simulations. Moreover, the center of mass velocity cross-correlation functions are also decomposed into longitudinal and transversal contributions. The fastest momentum transfer is observed between hydronium cation and water molecule due to the strong hydrogen bond interaction. The center of mass velocity cross-correlation functions reach peak value in about 36 fs, corresponding to a single collision with a neighboring molecule. For the momentum transfer between the water molecule and methanol molecule, the peaking time is 70 fs or about twice of that between hydronium cation and water molecule. Oscillation of the center of mass velocity cross-correlation functions between hydronium cation and water molecule is also observed due to the cage effect in their equilibrium positions.
Origin of inverse tunneling magnetoresistance in a symmetric junction revealed by delaminating the buried electronic interface
Authors: Yang J. Joshua , Xiang Hua , Ji Chengxiang , Stickle William F. , Stewart Duncan R. , Ohlberg Douglas A. A. , Williams R. Stanley , Chang Y. Austin
Published: December 2009

Electrical properties of modern electronic devices are usually controlled by the physical and chemical structure of one or more buried material interfaces. Accessing these buried interfaces by energetic ion milling can destroy this structural information. We report a delamination technique that exposes pristine buried interfaces for x-ray photoemission spectroscopy. We use this technique to show that unusual inverse tunneling magnetoresistance in a nominally symmetric (Co,Fe)/AlOx/(Co,Fe) magnetic tunnel junction devices is attributable to subtle over-oxidation of the lower AlOx/CoFe interface. Ion-milling investigation of the same samples misleads by chemically reducing the signature Fe oxide species during milling.
Dielectric elastomers of interpenetrating networks
Authors: Suo Zhigang , Zhu Jian
Published: December 2009

Recent experiments have shown that a voltage can induce a large deformation in an elastomer of interpenetrating networks. To understand the observation, this paper describes a model of interpenetrating networks of long and short chains. As the voltage ramps up, the elastomer may undergo snap-through instability. The network with long chains fills the space and keeps elastomer complaint at small to modest deformation. The network with short chains acts as a safety net that restrains the elastomer from thinning excessively.
Tunneling spectroscopy and magnon excitation in Co2FeAl/MgO/Co–Fe magnetic tunnel junctions
Authors: Ebke Daniel , Drewello Volker , Schäfers Markus , Reiss Günter , Thomas Andy
Published: December 2009

Magnetic tunnel junctions with the Heusler compound Co2FeAl as the soft electrode are prepared. Pinned Co–Fe is used as the hard reference electrode. The junctions show a high tunnel magnetoresistance ratio of 273% at 13 K. The electronic transport characteristics are investigated by tunneling spectroscopy—dI/dV and d2I/dV2 are discussed. In the parallel magnetic state the tunneling spectra are asymmetric with respect to the bias voltage, with a pronounced bias-independent region. In the antiparallel state the dependence on bias voltage is much stronger and the curves are symmetric. The findings can be explained with a gap in the minority density of states of Co2FeAl.
Fermi-level depinning and hole injection induced two-dimensional electron related radiative emissions from a forward biased Ni/Au-AlGaN/GaN Schottky diode
Authors: Li B. K. , Wang M. J. , Chen K. J. , Wang J. N.
Published: December 2009

Electroluminescence (EL) from a forward biased Ni/Au-AlGaN/GaN Schottky diode was observed and studied. According to the EL spectra, which were dominated by the GaN near band edge emissions, holes were injected into the GaN layer. It was found that the turn-on voltage of the EL emission coincided with the second turn-on voltage that indicates the appearance of a second conduction channel in the diode’s forward current-voltage characteristics. This coincidence implied that the second conduction channel originated from the hole injection. A model based on the Fermi-level depinning caused by the current induced interface states ionization is proposed to explain the hole injection process and the observed EL characteristics.
Controlling the composition of a confined fluid by an electric field
Authors: Brunet C. , Malherbe J. G. , Amokrane S.
Published: December 2009

Starting from a generic model of a pore/bulk mixture equilibrium, we propose a novel method for modulating the composition of the confined fluid without having to modify the bulk state. To achieve this, two basic mechanisms—sensitivity of the pore filling to the bulk thermodynamic state and electric field effect—are combined. We show by Monte Carlo simulation that the composition can be controlled both in a continuous and in a jumpwise way. Near the bulk demixing instability, we demonstrate a field induced population inversion in the pore. The conditions for the realization of this method should be best met with colloids, but being based on robust and generic mechanisms, it should also be applicable to some molecular fluids.
Perception of Parallelepipeds: Perkins's Law
Authors: Li Yunfeng
Published: December 2009

Two experiments were carried out to study the perception of parallelepipeds. In the first, the subjects were shown images of parallelepipeds and were asked to judge the 3-D orientations of the faces of the parallelepipeds, as well as the shapes of the faces. These two types of judgments were found to be inconsistent. Specifically, the parallelepipeds reconstructed from judgments of 3-D orientations of the faces were systematically different from the parallelepipeds reconstructed from judgments of the shape of the faces. In the second experiment, the subjects were asked to choose which reconstruction was closer to their percept. In most trials the subjects chose the 3-D parallelepiped reconstructed from judgments of the shapes of the faces. These results suggest that the percept of the shape of a 3-D object is not based on the judgments of the 3-D orientations of the object's surfaces. Instead, the 3-D shape percept is based on simplicity constraints. A new computational model is presented, which generalizes Perkins's law (Perkins 1972). Instead of orthogonality, the new model uses mirror-symmetry and planarity constraints, in conjunction with maximum 3-D compactness and minimum surface-area constraints. The parallelepipeds recovered by the model are very close to the parallelepipeds perceived by the subjects.
The Fabrication and Progress of Core-Shell Composite Materials
Authors: Cao Shunsheng , Chen Juanrong , Hu Jie
Published: December 2009

Core-shell materials, in which a layer or multilayer of inorganic or organic material surrounds an inorganic or organic particle core, have been investigated both as a means to improve the stability and surface chemistry of the core particle and as a way of accessing unique physical and chemical properties that are not possible from one material alone. As a result, the fabrication of core-shell particles is attracting a great deal of interest because of their unique properties and potential applicability in catalysis, semiconductors, drug delivery, enzyme immobilization, molecular recognition, chemical sensing, etc. As evidenced by the literature described and discussed in this review, a basic understanding of the mechanism and recent progress in production methods have enabled the fabrication of core-shell particles with unique and tailored properties for various applications in materials science.
Synthesis and Single Chain Fluorescence of a Sulfonated Conjugated Polymer
Authors: Gómez Daniel E. , Tan Tina A. T. , White Jonathan M. , Bell Toby D. M. , Ghiggino Kenneth P.
Published: December 2009

A water-soluble sulfonated conjugated phenylene vinylene polymer (Alt-Co-DPS-PPV) has been prepared by a Horner–Emmons reaction involving the condensation of a disulfonyl aryl bisphosphonate and terephthaldehyde. The photoluminescence from single chains of the polymer dispersed in a poly(vinyl alcohol) film at room temperature has been studied by confocal imaging techniques. Fluorescence intensity trajectories from Alt-Co-DPS-PPV single chains exhibit intermittencies or ‘blinking’ on both short (sub-millisecond) and long (seconds) time scales. The short time-scale intensity fluctuation data has been successfully analyzed using a simple model involving excursions from the fluorescent excited singlet state of the polymer chromophore to a non-emitting triplet state. It is found that the triplet state lifetime is molecule dependent and can be perturbed by the presence of the added heavy atom, iodide. These single chain fluorescence studies provide an insight into the distribution of excited state behaviours that make up the bulk polymer photochemical properties.
Microwave-Induced Molecular Rearrangements. Flash Thermolysis in the Gas-Phase and in Solution: Synthesis of Quinolones and Naphthyridones
Authors: Lecoq Delphine , Chalmers Benjamin A. , Veedu Rakesh N. , Kvaskoff David , Bernhardt Paul V. , Wentrup Curt
Published: December 2009

3- and 4-Pyridyliminopropadienones were prepared by flash vacuum thermolysis of Meldrum’s acid derivatives and characterized by low temperature IR spectroscopy. They react with dimethylamine to afford 1,5-, 1,6-, and 1,7-naphthyridones. The same naphthyridones are also obtained by microwave irradiation of the Meldrum’s acid derivatives. Quinolones were obtained by microwave irradiation of phenylaminomethylene-Meldrum’s acids and 1-phenylpyrrole-2,3-diones.
Crop performance as affected by three opening configurations for no-till seeder in annual double cropping regions of northern China
Authors: Yao Zonglu , Li Hongwen , Gao Huanwen , Wang Xiaoyan , He Jin
Published: December 2009

The furrow opening configuration used by no-till seeders can have a major effect on crop emergence in conservation tillage systems. This is particularly important in annual double-cropping regions (winter wheat and summer maize) of northern China where large volumes of residue remain on the soil surface after maize harvesting. This problem has been investigated using 3 different opening configurations for no-till wheat seeding near Beijing in 2004–05 and 2005–06, and assessing performance in terms of soil disturbance, residue cover index, soil cone index, fuel consumption, winter wheat emergence, plant growth, and subsequent yield.
In this cropping system, the single-disc opening configuration significantly decreased mean soil disturbance and increased residue cover index compared with the combined strip-chop and strip-till opening configurations, but winter wheat emergence was 6–9% less, probably due to greater levels of residue cover and greater seed zone soil cone index. Winter wheat growth after seeding in combined strip-chop and strip-till seeded plots was faster than that in single-disc seeded plots and mean yield was greater. The most suitable furrow opening configuration in heavy residue cover conditions appeared to be the strip-chop one, which can provide similar crop performance with marginally better fuel economy than the strip-till opening configuration. These results should be seen as preliminary, but they are still valuable for the design and selection of no-till wheat seeders for double cropping in this region of China.
Effects of time-controlled grazing on runoff and sediment loss
Authors: Sanjari Gholamreza , Yu Bofu , Ghadiri Hossein , Ciesiolka Cyril A. A. , Rose Calvin W.
Published: December 2009

The time-controlled rotational grazing (TC grazing) has become popular in Australia and elsewhere in the world to provide graziers and ranchers with improved productivity over traditional practices. However, this grazing system, which involves short periods of intensive grazing, has raised concerns about sustainability and environmental impacts on water and soil resources, and ecosystem health generally. A runoff experiment at the catchment scale was established on the grazing property ‘Currajong’ in the south-east region of Queensland, Australia, to investigate the effects of continuous and TC grazing on runoff and sediment generation from 2001 to 2006.
Sediment loss was reduced significantly under TC grazing compared with continuous grazing irrespective of the size of runoff events. This effect was more pronounced in the catchments with soils of gentler slopes and greater depths. The reduction in soil erosion was achieved despite the fact that the increase in ground cover under TC grazing had little effect on runoff coefficient or runoff depth. Decrease in runoff in relation to the increase in surface cover only occurred for small events, whereas for large rainfall events, runoff generated irrespective of the level of ground cover.
This study showed that ground cover is a key driver in reducing sediment concentration, resulting in a significantly lower sediment loss under TC grazing. In the study area a minimum of 70% of surface cover as a threshold appeared to be needed to efficiently protect the soil surface from erosive forces of rain and runoff and to control soil erosion. The results also indicate that TC grazing has a superior capability to produce and maintain a higher level of ground cover (up to 90%) than continuous grazing (up to 65%). The long rest periods in TC grazing are seen as the major contributor to soil and pasture recovery after intensive defoliations by grazing animals, leading to an increase in above-ground organic material and thus surface cover over time.
Chromogranin B P413L variant as risk factor and modifier of disease onset for amyotrophic lateral sclerosis
Authors: Gros-Louis Francois , Andersen Peter M. , Dupre Nicolas , Urushitani Makoto , Dion Patrick , Souchon Frederique , D'Amour Monique , Camu William , Meininger Vincent , Bouchard Jean-Pierre , Rouleau Guy A. , Julien Jean-Pierre
Published: December 2009

Recently, chromogranins were reported to interact specifically with mutant forms of superoxide dismutase that are linked to amyotrophic lateral sclerosis (ALS). This interaction led us to analyze the frequencies of sequence variants of the
CHGB
gene in ALS patients and matched controls from three different countries. Of particular interest was the finding of the P413L
CHGB
variant present in 10% of ALS patients (
n
= 705) as compared to 4.5% in controls (
n
= 751), conferring a 2.2-fold greater relative risk to develop the disease (
P
< 0.0001). This effect was mainly contributed by the samples of French origin that yielded a frequency of the P413L variation at 17% in ALS (
n
= 289) and 5% in controls (
n
= 448), conferring a 3.3-fold greater risk to develop ALS. Furthermore, the P413L
CHGB
variant is associated with an earlier age of onset by almost a decade in both sporadic ALS and familial ALS cases. Genetic variation influencing age of onset in ALS had not previously been reported. Expression of fusion CHGB-EGFP constructs in SHSY-5Y cells revealed that the P413L variation can cause defective sorting of CHGB into secretory granules. The finding that
CHGB
may act as a susceptibility gene and modifier of onset in ALS is consistent with the emerging view that dysfunction of the secretory pathway may contribute to increased vulnerability of motor neurons.
Plant extinctions and introductions lead to phylogenetic and taxonomic homogenization of the European flora
Authors: Winter Marten , Schweiger Oliver , Klotz Stefan , Nentwig Wolfgang , Andriopoulos Pavlos , Arianoutsou Margarita , Basnou Corina , Delipetrou Pinelopi , Didžiulis Viktoras , Hejda Martin , Hulme Philip E. , Lambdon Philip W. , Pergl Jan , Pyšek Petr , Roy David B. , Kühn Ingolf
Published: December 2009

Human activities have altered the composition of biotas through two fundamental processes: native extinctions and alien introductions. Both processes affect the taxonomic (i.e., species identity) and phylogenetic (i.e., species evolutionary history) structure of species assemblages. However, it is not known what the relative magnitude of these effects is at large spatial scales. Here we analyze the large-scale effects of plant extinctions and introductions on taxonomic and phylogenetic diversity of floras across Europe, using data from 23 regions. Considering both native losses and alien additions in concert reveals that plant invasions since AD 1500 exceeded extinctions, resulting in (i) increased taxonomic diversity (i.e., species richness) but decreased phylogenetic diversity within European regions, and (ii) increased taxonomic and phylogenetic similarity among European regions. Those extinct species were phylogenetically and taxonomically unique and typical of individual regions, and extinctions usually were not continent-wide and therefore led to differentiation. By contrast, because introduced alien species tended to be closely related to native species, the floristic differentiation due to species extinction was lessened by taxonomic and phylogenetic homogenization effects. This was especially due to species that are alien to a region but native to other parts of Europe. As a result, floras of many European regions have partly lost and will continue to lose their uniqueness. The results suggest that biodiversity needs to be assessed in terms of both species taxonomic and phylogenetic identity, but the latter is rarely used as a metric of the biodiversity dynamics.
A nitric oxide/cysteine interaction mediates the activation of soluble guanylate cyclase
Authors: Fernhoff Nathaniel B. , Derbyshire Emily R. , Marletta Michael A.
Published: December 2009

Nitric oxide (NO) regulates a number of essential physiological processes by activating soluble guanylate cyclase (sGC) to produce the second messenger cGMP. The mechanism of NO sensing was previously thought to result exclusively from NO binding to the sGC heme; however, recent studies indicate that heme-bound NO only partially activates sGC and additional NO is involved in the mechanism of maximal NO activation. Furthermore, thiol oxidation of sGC cysteines results in the loss of enzyme activity. Herein the role of cysteines in NO-stimulated sGC activity investigated. We find that the thiol modifying reagent methyl methanethiosulfonate specifically inhibits NO activation of sGC by blocking a non-heme site, which defines a role for sGC cysteine(s) in mediating NO binding. The nature of the NO/cysteine interaction was probed by examining the effects of redox active reagents on NO-stimulated activity. These results show that NO binding to, and dissociation from, the critical cysteine(s) does not involve a change in the thiol redox state. Evidence is provided for non-heme NO in the physiological activation of sGC in context of a primary cell culture of human umbilical vein endothelial cells. These findings have relevance to diseases involving the NO/cGMP signaling pathway.
Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms
Authors: Boyer Mickaël , Yutin Natalya , Pagnier Isabelle , Barrassi Lina , Fournous Ghislain , Espinosa Leon , Robert Catherine , Azza Saïd , Sun Siyang , Rossmann Michael G. , Suzan-Monti Marie , La Scola Bernard , Koonin Eugene V. , Raoult Didier
Published: December 2009

Giant viruses such as Mimivirus isolated from amoeba found in aquatic habitats show biological sophistication comparable to that of simple cellular life forms and seem to evolve by similar mechanisms, including extensive gene duplication and horizontal gene transfer (HGT), possibly in part through a viral parasite, the virophage. We report here the isolation of “Marseille” virus, a previously uncharacterized giant virus of amoeba. The virions of Marseillevirus encompass a 368-kb genome, a minimum of 49 proteins, and some messenger RNAs. Phylogenetic analysis of core genes indicates that Marseillevirus is the prototype of a family of nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes. The genome repertoire of the virus is composed of typical NCLDV core genes and genes apparently obtained from eukaryotic hosts and their parasites or symbionts, both bacterial and viral. We propose that amoebae are “melting pots” of microbial evolution where diverse forms emerge, including giant viruses with complex gene repertoires of various origins.
Loss of MeCP2 in aminergic neurons causes cell-autonomous defects in neurotransmitter synthesis and specific behavioral abnormalities
Authors: Samaco Rodney C. , Mandel-Brehm Caleigh , Chao Hsiao-Tuan , Ward Christopher S. , Fyffe-Maricich Sharyl L. , Ren Jun , Hyland Keith , Thaller Christina , Maricich Stephen M. , Humphreys Peter , Greer John J. , Percy Alan , Glaze Daniel G. , Zoghbi Huda Y. , Neul Jeffrey L.
Published: December 2009

Rett syndrome (RTT) is characterized by specific motor, cognitive, and behavioral deficits. Because several of these abnormalities occur in other disease states associated with alterations in aminergic neurotransmitters, we investigated the contribution of such alterations to RTT pathogenesis. We found that both individuals with RTT and
Mecp2
-null mice have lower-than-normal levels of aminergic metabolites and content. Deleting
Mecp2
from either TH-positive dopaminergic and noradrenergic neurons or PET1-positive serotonergic neurons in mice decreased corresponding neurotransmitter concentration and specific phenotypes, likely through MeCP2 regulation of rate-limiting enzymes involved in aminergic neurotransmitter production. These data support a cell-autonomous, MeCP2-dependent mechanism for the regulation of aminergic neurotransmitter synthesis contributing to unique behavioral phenotypes.
David Zeisberger’s Description of Delaware Morphology (1827)
Authors: Swiggers Pierre
Published: December 2009

This article proposes an analysis of the linguistic work of the Moravian missionary David Zeisberger (1721–1808), and more particularly of his grammar of the Delaware language (= [Lenni-]Lenape), which was published in 1827 in an English translation by Peter S. Du Ponceau (1760–1844), on the basis of the author’s German manuscript. A life-sketch and a short presentation of Zeisberger’s missionary work are intended to place the Delaware grammar in the context of his scholarly output, thus allowing the reader to adequately appreciate the practical orientation of the work. The analysis of the grammar, which is essentially a description of Delaware verb morphology, focuses on the parts-of-speech model, and on the treatment of the various word classes, with special attention being paid to the verb. The article offers a detailed study of the organization of the verb paradigms, of the division into conjugations and into ‘forms’ (positive, negative, etc.), and of the description of verbal ‘transitions’. The practical and analytical outlook of Zeisberger is confirmed by the lexicographically oriented treatment of the undeclinable parts of speech: the adverb, the preposition, the conjunction and the interjection. The conclusion insists on the fact that Zeisberger’s grammar was an important source for 19th-century linguists interested in language typology and more particularly in the structure of polysynthetic languages.
Translating Non-Denominational Concepts in Describing a Religious System
Authors: Pharo Lars Kirkhusmo
Published: December 2009

In an earlier article (Pharo 2007), the author investigated how Spanish ethnographer-missionaries and missionary-linguists of the Colonial period translated the concept of ‘religion’ into various indigenous Mesoamerican languages. In the present article, he concedes that “assorted Mesoamerican notions may well together, as a family of concepts, be subordinated to the abstract superior concept of ‘religion’. Other relevant modern Spanish concepts like ‘sagrado’, ‘creencia’, ‘ritual’ and ‘costumbre’ etc. can thus be studied in the dictionaries.” In particular ‘costumbre’ (“custom”, “habit”) proves to be a central word among present-day Mesoamericans, not only to circumscribe their own religious practice, but also to designate ‘religion’ as well. As a result, the author, this time, analyses Spanish concepts associated with religion – but not exclusively with Christianity, i.e., neutral religious notions are the object of the analysis – translated into Nahuatl and Yucatec as recorded in colonial period dictionaries. The general hypothesis is that the dictionaries, in particular theVocabulario(1555 and 1571) by the Franciscan Alonso de Molina (1514–1585), constituted a pedagogical strategy of transculturation at this early stage of the mission, not a radical linguistic attempt at acculturation, in order to transmit the unfamiliar Christian notions (such as conversion) to the natives of Mesoamerica.
Portuguese and Other European Missionaries in Africa
Authors: Levi Joseph Abraham
Published: December 2009

This study looks at some of the works produced by Catholic missionaries in Africa from the pre-dawn of the Modern Era (Fall of Constantinople, 1453), in particular the Fall of Ceuta (1415), to the Berlin Conference (1884–1885). Particular emphasis will be placed on the linguistic production of a few Franciscan, Augustinian, Capuchin, Dominican, and/or Jesuit clerics, working under the aegis of the Portuguese Crown, who – with the invaluable help of native assistants, usually members of the clergy or closely affiliated with the Church – compiled the first grammars, word lists, glossaries, and dictionaries of the indigenous languages with which they worked and interacted on a daily basis. Their endeavour, though meritorious and not always free from preconceived ideas of the ‘other’, paved the way for future studies in the field.
Emotion Modelling Towards Affective Pathogenesis
Authors: Bas James Le
Published: December 2009

Objective: There is a need in psychiatry for models that integrate pathological states with normal systems. The interaction of arousal and emotion is the focus of an exploration of affective pathogenesis.

Method: Given that the explicit causes of affective disorder remain nascent, methods of linking emotion and disorder are evaluated.

Results: A network model of emotional families is presented, in which emotions exist as quantal gradients. Morbid emotional states are seen as the activation of distal emotion sites. The phenomenology of affective disorders is described with reference to this model. Recourse is made to non-linear dynamic theory.

Conclusions: Metaphoric emotion models have face validity and may prove a useful heuristic.
Academics of the Future? A Survey of Final Year Medical Students
Authors: Galletly Cherrie , Chur-Hansen Anna , Air Tracy , Chapman Ian
Published: December 2009

Objective: The aim of this study was to survey final year medical students at an Australian medical school about their views and experiences regarding academic medicine

Methods: A four page questionnaire was developed and administered to each group of final (6th) year medical students upon completion of their psychiatry rotation

Results: For 82% clinical teaching would probably or definitely be part of their future careers, while 63% expected that they would undertake formal teaching. Thirty-three percent of students anticipated limited or no involvement in research. While 26% of students expected that they would undertake a higher degree, only 13% were interested in pursuing an academic career

Conclusions: The dearth of academics in medicine and in psychiatry in particular is of considerable concern. This study provides some possible avenues for further exploration to address this professional challenge
Bound states of the Dirac equation with some physical potentials by the Nikiforov–Uvarov method
Authors: Setare Mohammad R , Haidari S
Published: December 2009

Exact analytical solutions for the s-wave Dirac equation with the reflectionless-type, Rosen–Morse and Manning–Rosen potentials are obtained, under the condition of spin symmetry. We obtained bound state energy eigenvalues and corresponding spinor wave function in the framework of the Nikiforov–Uvarov (NU) method.
PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches
Authors: Watson-Haigh Nathan S. , Kadarmideen Haja N. , Reverter Antonio
Published: December 2009

Summary: We make the PCIT algorithm, used for detecting meaningful gene–gene associations in co-expression networks, available as an R package. Automatic detection of a suitable parallel environment is used such that scripts are portable between parallel and non-parallel environments with no modification of the script.

Availability and implementation: Source code and binaries freely available (under GPL-3) for download via CRAN at http://cran.r-project.org/package=PCIT, implemented in R and supported on Linux and MS Windows.

Contact:  nathan.watson-haigh@csiro.au
On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics
Authors: Pham Thang V. , Piersma Sander R. , Warmoes Marc , Jimenez Connie R.
Published: December 2009

Motivation: Spectral count data generated from label-free tandem mass spectrometry-based proteomic experiments can be used to quantify protein's abundances reliably. Comparing spectral count data from different sample groups such as control and disease is an essential step in statistical analysis for the determination of altered protein level and biomarker discovery. The Fisher's exact test, the G-test, the t-test and the local-pooled-error technique (LPE) are commonly used for differential analysis of spectral count data. However, our initial experiments in two cancer studies show that the current methods are unable to declare at 95% confidence level a number of protein markers that have been judged to be differential on the basis of the biology of the disease and the spectral count numbers. A shortcoming of these tests is that they do not take into account within- and between-sample variations together. Hence, our aim is to improve upon existing techniques by incorporating both the within- and between-sample variations.

Result: We propose to use the beta-binomial distribution to test the significance of differential protein abundances expressed in spectral counts in label-free mass spectrometry-based proteomics. The beta-binomial test naturally normalizes for total sample count. Experimental results show that the beta-binomial test performs favorably in comparison with other methods on several datasets in terms of both true detection rate and false positive rate. In addition, it can be applied for experiments with one or more replicates, and for multiple condition comparisons. Finally, we have implemented a software package for parameter estimation of two beta-binomial models and the associated statistical tests.

Availability and implementation: A software package implemented in R is freely available for download at http://www.oncoproteomics.nl/.

Contact:  t.pham@vumc.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
A novel method for accurate one-dimensional protein structure prediction based on fragment matching
Authors: Zhou Tuping , Shu Nanjiang , Hovmöller Sven
Published: December 2009

Motivation: The precise prediction of one-dimensional (1D) protein structure as represented by the protein secondary structure and 1D string of discrete state of dihedral angles (i.e. Shape Strings) is a prerequisite for the successful prediction of three-dimensional (3D) structure as well as protein–protein interaction. We have developed a novel 1D structure prediction method, called Frag1D, based on a straightforward fragment matching algorithm and demonstrated its success in the prediction of three sets of 1D structural alphabets, i.e. the classical three-state secondary structure, three- and eight-state Shape Strings.

Results: By exploiting the vast protein sequence and protein structure data available, we have brought secondary-structure prediction closer to the expected theoretical limit. When tested by a leave-one-out cross validation on a non-redundant set of PDB cutting at 30% sequence identity containing 5860 protein chains, the overall per-residue accuracy for secondary-structure prediction, i.e. Q3 is 82.9%. The overall per-residue accuracy for three- and eight-state Shape Strings are 85.1 and 71.5%, respectively. We have also benchmarked our program with the latest version of PSIPRED for secondary structure prediction and our program predicted 0.3% better in Q3 when tested on 2241 chains with the same training set. For Shape Strings, we compared our method with a recently published method with the same dataset and definition as used by that method. Our program predicted at 2.2% better in accuracy for three-state Shape Strings. By quantitatively investigating the effect of data base size on 1D structure prediction we show that the accuracy increases by ∼1% with every doubling of the database size.

Availability: The program is available for download at http://www.fos.su.se/∼nanjiang/Frag1D/download. Supplementary data are available at http://www.fos.su.se/∼nanjiang/Frag1D/supplement/suppl.html

Contact:  svenh@struc.su.se

Supplementary information:  Supplementary data are available at Bioinformatics online.