bluuebunny/crossref_metadata_2025 huggingface dataset:
Collision-energy-resolved Penning ionization electron spectroscopy of bromomethanes (CH3Br, CH2Br2, and CHBr3) by collision with He*(23S) metastable atoms
Authors: Kishimoto Naoki , Matsumura Eiichi , Ohno Koichi , Deleuze Michael S.
Published: July 2004

Ionization of bromomethanes (CH3Br, CH2Br2, and CHBr3) upon collision with metastable He*(2 3S) atoms has been studied by means of collision-energy-resolved Penning ionization electron spectroscopy. Lone-pair (nBr) orbitals of Br4p characters have larger ionization cross sections than σC-Br orbitals. The collision-energy dependence of the partial ionization cross sections shows that the interaction potential between the molecule and the He*(2 3S) atom is highly anisotropic around CH3Br or CH2Br2, while isotropic attractive interactions are found for CHBr3. Bands observed at electron energies of ∼2 eV in the He*(2 3S) Penning ionization electron spectra (PIES) of CH2Br2 and CHBr3 have no counterpart in ultraviolet (He I) photoionization spectra and theoretical (third-order algebraic diagrammatic construction) one-electron and shake-up ionization spectra. Energy analysis of the processes involved demonstrates that these bands and further bands overlapping with σC-Br or πCH2 levels are related to autoionization of dissociating (He+-Br−) pairs. Similarly, a band at an electron energy of ∼1 eV in the He*(2 3S) PIES spectra of CH3Br has been ascribed to autoionizing Br** atoms released by dissociation of (unidentified) excited states of the target molecule. A further autoionization (S) band can be discerned at ∼1 eV below the lone-pair nBr bands in the He*(2 3S) PIES spectrum of CHBr3. This band has been ascribed to the decay of autoionizing Rydberg states of the target molecule (M**) into vibrationally excited states of the molecular ion. It was found that for this transition, the interaction potential that prevails in the entrance channel is merely attractive.
A cellular automaton for the modeling of oscillations in a surface reaction
Authors: Lemos M. C. , Jiménez-Morales F.
Published: July 2004

The reaction of CO and O over a catalytic surface is studied with a cellular automata (CA) model. We extend the CA model proposed by Mai and von Niessen [Phys. Rev. A 44 R6165 (1991)] taking into account the variation of the temperature of the catalyst with the aim of analyzing the existence of oscillations in this reaction. The rate constants for different processes which govern the reaction are chosen in the Arrhenius form. Quasiperiodic, aperiodic, O-poisoned, and CO-poisoned regimes are observed depending on the temperature relaxation parameter. The results from the CA model presented are in agreement with several oscillatory behaviors which the catalyzed oxidation of CO exhibits.
Phase behavior and critical properties of size-asymmetric, primitive-model electrolytes
Authors: Qin Yuan , Prausnitz John M.
Published: July 2004

The theory of J. Jiang et al. [J. Chem. Phys. 116, 7977 (2002)] for size-symmetric electrolytes is extended to size-asymmetric electrolytes. When compared to molecular-simulation results, this extension gives the correct trend of critical properties with size asymmetry.
Theory of aging in structural glasses
Authors: Lubchenko Vassiliy , Wolynes Peter G.
Published: July 2004

The random first-order transition theory of the dynamics of supercooled liquids is extended to treat aging phenomena in nonequilibrium structural glasses. A reformulation of the idea of “entropic droplets” in terms of libraries of local energy landscapes is introduced which treats in a uniform way the supercooled liquid (reproducing earlier results) and glassy regimes. The resulting microscopic theory of aging makes contact with the Nayaranaswamy-Moynihan-Tool nonlinear relaxation formalism and the Hodge-Scherer extrapolation of the Adam-Gibbs formula, but deviations from both approaches are predicted and shown to be consistent with experiment. The nonlinearity of glassy relaxation is shown to quantitatively correlate with liquid fragility. The residual non-Arrhenius temperature dependence of relaxation observed in quenched glasses is explained. The broadening of relaxation spectra in the nonequilibrium glass with decreasing temperature is quantitatively predicted. The theory leads to the prediction of spatially fluctuating fictive temperatures in the long-aged glassy state, which have non-Gaussian statistics. This can give rise to “ultraslow” relaxations in systems after deep quenches.
The quasi-independent curvilinear coordinate approximation for geometry optimization
Authors: Németh Károly , Challacombe Matt
Published: July 2004

This paper presents an efficient alternative to well established algorithms for molecular geometry optimization. This approach exploits the approximate decoupling of molecular energetics in a curvilinear internal coordinate system, allowing separation of the 3N-dimensional optimization problem into an O(N) set of quasi-independent one-dimensional problems. Each uncoupled optimization is developed by a weighted least squares fit of energy gradients in the internal coordinate system followed by extrapolation. In construction of the weights, only an implicit dependence on topologically connected internal coordinates is present. This new approach is competitive with the best internal coordinate geometry optimization algorithms in the literature and works well for large biological problems with complicated hydrogen bond networks and ligand binding motifs.
Linear-scaling formation of Kohn-Sham Hamiltonian: Application to the calculation of excitation energies and polarizabilities of large molecular systems
Authors: Watson Mark A. , Sałek Paweł , Macak Peter , Helgaker Trygve
Published: July 2004

We present calculations of excitation energies and polarizabilities in large molecular systems at the local-density and generalized-gradient approximation levels of density-functional theory (DFT). Our results are obtained using a linear-scaling DFT implementation in the program system DALTON for the formation of the Kohn-Sham Hamiltonian. For the Coulomb contribution, we introduce a modification of the fast multipole method to calculations over Gaussian charge distributions. It affords a simpler implementation than the original continuous fast multipole method by partitioning the electrostatic Coulomb interactions into “classical” and “nonclassical” terms which are explicitly evaluated by linear-scaling multipole techniques and a modified two-electron integral code, respectively. As an illustration of the code, we have studied the singlet and triplet excitation energies as well as the static and dynamic polarizabilities of polyethylenes, polyenes, polyynes, and graphite sheets with an emphasis on the trends observed with system size.
Insights into the structures, energetics, and vibrations of aqua-rubidium(I) complexes: Ab Initio study
Authors: Park Jungwon , Kołaski Maciej , Lee Han Myoung , Kim Kwang S.
Published: July 2004

We have carried out ab initio and density functional theory calculations of hydrated rubidium cations. The calculations involve a detailed evaluation of the structures, thermodynamic properties, and IR spectra of several plausible conformers of Rb+(H2O)n=1–8 clusters. An extensive search was made to find out the most stable conformers. Since the water-water interactions are important in hydrated Rb+ complexes, we investigated the vibrational frequency shifts of the OH stretching modes depending on the number of water molecules and the presence/absence of outer-shell water molecules. The predicted harmonic and anharmonic vibrational frequencies of the aqua-Rb+ clusters reflect the H-bonding signature, and would be used in experimental identification of the hydrated structures of Rb+ cation.
Single molecule photon emission statistics for non-Markovian blinking models
Authors: Zheng Yujun , Brown Frank L. H.
Published: July 2004

The statistics of photon emission from a single molecule under continuous wave excitation are considered. In particular, we study stochastic model systems where photon emission rates evolve in time with non-Markovian dynamics. Our calculations are based on the recently introduced generalized optical Bloch equation (GBE) formalism, but with numerical complications beyond those seen in previous Markovian stochastic models. A spectral representation is introduced to facilitate the numerical solution of the GBE equations for these more challenging cases.
Characterization of heteronuclear decoupling through proton spin dynamics in solid-state nuclear magnetic resonance spectroscopy
Authors: De Paëpe Gaël , Eléna Bénédicte , Emsley Lyndon
Published: July 2004

The work presented here aims at understanding the performance of phase modulated heteronuclear decoupling sequences such as Cosine Modulation or Two Pulse Phase Modulation. To that end we provide an analytical description of the intrinsic behavior of Cosine Modulation decoupling with respect to radio-frequency-inhomogeneity and the proton–proton dipolar coupling network. We discover through a Modulation Frame average Hamiltonian analysis that best decoupling is obtained under conditions where the heteronuclear interactions are removed but notably where homonuclear couplings are recoupled at a homonuclear Rotary Resonance (HORROR) condition in the Modulation Frame. These conclusions are supported by extensive experimental investigations, and notably through the introduction of proton nutation experiments to characterize spin dynamics in solids under decoupling conditions. The theoretical framework presented in this paper allows the prediction of the optimum parameters for a given set of experimental conditions.
Predissociation and autoionization of triplet Rydberg states in molecular hydrogen
Authors: Dinu Laura , Picard Yan J. , van der Zande Wim J.
Published: July 2004

We present single-photon spectroscopy in molecular hydrogen starting from the metastable c3Πu− state to a number of triplet nd-Rydberg states (v=0–4, n=12–20). Using fast beam spectroscopy both the autoionization channel and the predissociation channel are quantified, field free, as well as with small electric fields. Coupling with the i3Πg state is assumed to be responsible for field-free predissociation of the v=0 Rydberg levels. The stronger observed predissociation channel of the v=1 Rydberg levels is due to the nonadiabatic interaction with the h3Σg+ state in combination with l mixing due to an external electric field. No direct evidence is found for possible electric field induced predissociation of the gerade Rydberg states by low lying ungerade states. The competition between autoionization and predissociation is discussed in terms of possible consequences for dissociative recombination involving low energy electron collisions with the H2+ molecular ion.
Kinetic temperature effects on 4He dimers in jets
Authors: Kariotis R. , Bruch L. W. , Kornilov O.
Published: July 2004

The formation of dimers in a free jet cryogenic expansion of 4He gas has been studied by measuring mole fractions as a function of source temperature and pressure using diffraction from a nanostructured transmission grating. The data sets are limited to low source pressures for which dimers and trimers are the only appreciable cluster populations in the beam. The final cluster mole fractions are corrected for residual gas attenuation in the source chamber by an extrapolation over several residual gas pressures. A set of rate equations used to model the cluster formation in a free jet expansion has been extended to include the departure of the ambient translational temperature from the isentropic-equilibrium values as the density decreases with increasing distance. The effect of collisions in restoring the equilibrium temperature is treated with a relaxation time approximation. There are distinct distance ranges where the dimer and trimer mole fractions and the ambient temperature near their asymptotic values. The present modeling reproduces the apparent threshold observed at low source pressures for the survival of dimers in the asymptotic beam. Except for these low source pressures, there are only small changes relative to results based on the isentropic temperature.
A mean field analysis of the static dielectric behavior of linear lower alcohols
Authors: Pieruccini M. , Saija F.
Published: July 2004

The static dielectric responses of methanol, ethanol, and 1-propanol up to 1-hexanol are discussed in terms of a stiff-chain lattice model for the alcohol clusters. An analytical expression for the Kirkwood correlation factor gK is derived in terms of the canonical partition function associated to the configurational statistics of any of the dimers building up a chain. This allows for the estimate of the dipole moment μ0 of an alcohol molecule in the liquid phase from the temperature dependence of the dielectric constant. All alcohol species appear to be characterized by a dipole moment larger than in the vapor phase. The Kirkwood correlation factor is found to be an increasing function of the alkyl tail length.
The McCormack model for gas mixtures: Heat transfer in a plane channel
Authors: Garcia R. D. M. , Siewert C. E.
Published: July 2004

An analytical version of the discrete-ordinates method (the ADO method) is used to establish a concise and particularly accurate solution to the heat-transfer problem in a plane channel for a binary gas mixture described by the McCormack kinetic model. The solution yields for the general (specular-diffuse) case of Maxwell boundary conditions for each of the two species, the density and temperature profiles for both types of particles, as well as the overall heat flow associated with each of the two species of gas particles. Numerical results are reported for two binary mixtures (Ne–Ar and He–Xe). The algorithm is considered especially easy to use, and the developed (FORTRAN) code requires typically less than a second on a 2.2 GHz Pentium 4 machine to compute all quantities of interest.
The effect of the cation substitution on the structural and vibrational properties of Cs2NaGaxSc1−xF6 solid solution
Authors: Doriguetto A. C. , Boschi T. M. , Pizani P. S. , Mascarenhas Y. P. , Ellena J.
Published: July 2004

Raman scattering and x-ray diffration were used to characterize the structural and vibrational properties of the Cs2NaGaxSc1−xF6 solid solutions, for x ranging from 0.0 to 1.0. The Raman spectra, taken at room and low temperature, allow us to follow the phase evolution in detail and indicate the breaking of the local symmetry since low Ga concentration levels. Five compositions were studied by x-ray diffraction: x=0.0, 0.2, 0.5, 0.8, and 1.0. A cubic space group, Fm3̄m, was found to x=0.0 and x=0.2 and a trigonal one was found to x=0.5, 0.8, and 1.0. Details of both phases are presented and the correlation between x-ray diffraction and Raman scattering is discussed.
Infrared spectra of seeded hydrogen clusters: (paraH2)N–OCS, (orthoH2)N–OCS, and (HD)N–OCS, N=2–7
Authors: Tang J. , McKellar A. R. W.
Published: July 2004

Infrared spectra of hydrogen–carbonyl sulfide clusters containing paraH2, orthoH2, or HD have been studied in the 2060 cm−1 region of the C–O stretching vibration. The clusters were formed in pulsed supersonic jet expansions and probed using a tunable infrared diode laser spectrometer. Simple symmetric rotor type spectra were observed and assigned for clusters containing up to N=7 hydrogen molecules. There was no resolved K structure, and Q-branch features were present for orthoH2 and HD but absent for paraH2. These characteristics can be rationalized in terms of near symmetric rotor structures, very low effective rotational temperatures (0.15 to 0.6 K), and nuclear spin statistics. The observed vibrational shifts were compared with those from recent observations on the same clusters embedded in helium nanodroplets. The observed rotational constants for the paraH2 clusters are in good agreement with a recent quantum Monte Carlo simulation. Some mixed clusters were also observed, such as HD–HD–He–OCS and paraH2–orthoH2–OCS.
Assessment of recently developed exchange-correlation functionals for the description of torsion potentials in π-conjugated molecules
Authors: Sancho-Garcı́a Juan Carlos , Cornil Jérôme
Published: July 2004

Newly developed exchange-correlation functionals in density functional theory (DFT) have been applied to describe conjugation effects in organic molecules. The performance of the various approaches is assessed through the calculation of torsion energy profiles and their critical comparison with available experimental data. Our results indicate that the OPTX-B95 exchange-correlation functional as well as its corresponding hybrid versions perform better than the well-established BLYP or B3LYP schemes when dealing with π-conjugated molecules. In contrast, the recently introduced VSXC functional is not as reliable as other DFT methods for the systems examined here.
Global periodic attractor for strongly damped wave equations with time-periodic driving force
Authors: Li Hongyan , Zhou Shengfan , Yin Fuqi
Published: July 2004

In this paper, we consider the existence of a global periodic attractor for a strongly damped nonlinear wave equation with time-periodic driving force under homogeneous Dirichlet boundary condition. It is proved that in certain parameter region, for arbitrary time-periodic driving force, the system has a unique periodic solution attracting any bounded set exponentially. This implies that the system behaves exactly as a one-dimensional system. We mention, in particular, that the obtained result can be used to prove the existence of global periodic attractor of the usual damped and driven wave equations.
Energy momentum, wave velocities and characteristic shocks in Euler’s variational equations with application to the Born–Infeld theory
Authors: Boillat Guy , Ruggeri Tommaso
Published: July 2004

We consider the Euler’s variational equations deriving from a general Lagrangian L(∂αqr,qs). Under the assumption of convexity of energy, we write down some inequalities for the energy-momentum tensor including Hawking–Ellis energy conditions. We show that there exists the same number of positive and negative wave velocities and no velocity can change sign. Finally, we study the structure of the characteristic shocks with particular attention to the generalized Born–Infeld Lagrangian describing the electron with spin.
‘Free’ Food, the Local Production of Worth, and the Circuit of Decommodification: A Value Theory of the Surplus
Authors: Henderson George
Published: July 2004

“The wealth of those societies in which the capitalist mode of production prevails, presents itself as an ‘immense accumulation of commodities’, its unit being a single commodity. Our investigation must therefore begin with the analysis of a commodity” [Marx, 1967 Capital, Volume 1 first paragraph (International Publishers, New York)]. As Marx moves beyond the first paragraph of Capital, he famously argues that value makes the commodity a ‘hieroglyphic’. But his own opening is also a sort of hieroglyphic: it rings true for bourgeois economy as it does for his critique of that economy, but for entirely different reasons. The purpose of Capital is to obliterate this apparent corroboration, yet a hieroglyphic quality is maintained throughout, as Marx subjects his own successive claims to iterative, immanent critique. This chain cannot be said to be indefinite for Marx, but neither is it complete. Here, I hark back to Marx's opening gambit to ask: in capitalist society, what else accumulates besides commodities proper? The paper proceeds iteratively, offering a series of revised opening claims that mimic yet spiral away from Marx's original. I argue specifically that, although devaluation (decommodification) inheres in the production and circulation of value, it has its own accumulation logic. The example is of food banking. I explore this activity as simultaneously material, representational, and political, and examine the constitutive force of each of these modalities. I treat food banking, therefore, as a form of commodity afterlife, through which devaluation becomes (imperfectly) a positivity.
Crystal structure of pyrogallol–phloroglucinol transhydroxylase, an Mo enzyme capable of intermolecular hydroxyl transfer between phenols
Authors: Messerschmidt Albrecht , Niessen Holger , Abt Dietmar , Einsle Oliver , Schink Bernhard , Kroneck Peter M. H.
Published: July 2004

The Mo enzyme transhydroxylase from the anaerobic microorganism
Pelobacter acidigallici
catalyzes the conversion of pyrogallol to phloroglucinol. Such trihydroxybenzenes and their derivatives represent important building blocks of plant polymers. None of the transferred hydroxyl groups originates from water during transhydroxylation; instead a cosubstrate, such as 1,2,3,5-tetrahydroxybenzene, is used in a reaction without apparent electron transfer. Here, we report on the crystal structure of the enzyme in the reduced Mo(IV) state, which we solved by single anomalous-diffraction technique. It represents the largest structure (1,149 amino acid residues per molecule, 12 independent molecules per unit cell), which has been solved so far by single anomalous-diffraction technique. Tranhydroxylase is a heterodimer, with the active Mo–molybdopterin guanine dinucleotide (MGD)
2
site in the α-subunit, and three [4Fe—4S] centers in the β-subunit. The latter subunit carries a seven-stranded, mainly antiparallel β-barrel domain. We propose a scheme for the transhydroxylation reaction based on 3D structures of complexes of the enzyme with various polyphenols serving either as substrate or inhibitor.
Tubular precipitation and redox gradients on a bubbling template
Authors: Stone David A. , Goldstein Raymond E.
Published: July 2004

Tubular structures created by precipitation abound in nature, from chimneys at hydrothermal vents to soda straws in caves. Their formation is controlled by chemical gradients within which precipitation occurs, defining a surface that templates the growing structure. We report a self-organized periodic templating mechanism producing tubular structures electrochemically in iron-ammonium-sulfate solutions; iron oxides precipitate on the surface of bubbles that linger at the tube rim and then detach, leaving behind a ring of material. The acid–base and redox gradients spontaneously generated by diffusion of ammonia from the bubble into solution organize radial compositional layering within the tube wall, a mechanism studied on a larger scale by complex Liesegang patterns of iron oxides formed as ammonia diffuses through a gel containing FeSO
4
. When magnetite forms within the wall, a tube may grow curved in an external magnetic field. Connections with free-boundary problems in speleothem formation are emphasized.
Malnutrition is an independent factor associated with nosocomial infections
Authors: Schneider Stéphane M. , Veyres Patricia , Pivot Xavier , Soummer Anne-Marie , Jambou Patrick , Filippi Jérôme , van Obberghen Emmanuel , Hébuterne Xavier
Published: July 2004

The aim of the present prospective study was to determine if malnutrition, measured using a simple validated score, is an independent risk factor for nosocomial infections (NI) in non-selected hospital in-patients. Between 29 and 31 May 2001, a survey on the prevalence of NI was conducted on all 1637 in-patients (61 (sd 25) years old) in a French university hospital as part of a national survey. Actual and usual body weights were recorded in all in-patients, and serum albumin levels were measured on all blood samples taken during the week before the study. Nutritional status was evaluated by using the nutritional risk index (NRI). Albumin values were obtained in 1084 patients, and complete weight information was obtained in 911. Therefore, NRI was calculated in 630 patients (61 (sd 20) years old): 427 (67·8%) were malnourished. NI prevalence was 8·7%: 4·4% in non-malnourished patients, 7·6% in moderately malnourished patients and 14·6% in severely malnourished patients. In univariate analysis, the odds ratios for NI were 1·46 (95% CI 1·2, 2·1) in moderately malnourished patients and 4·8 (95% CI 4·6, 6·4) in severely malnourished patients. In multivariate analysis, age, immunodeficiency and NRI class influenced NI risk. Vascular and urinary catheters, and surgical intervention, were the extrinsic factors associated with NI, with odds ratios ranging from 2·0 (95% CI 1·8, 2·6) for vascular catheters to 10·8 (95% CI 8·8, 12·6) for association of the three factors. In conclusion, in non-selected hospitalized patients, malnutrition assessed with a simple and objective marker is an independent risk factor for NI. An early screening for malnutrition may therefore be helpful to reduce the high prevalence of NI.
Adaptation of lipid metabolism, tissue composition and flesh quality in gilthead sea bream (Sparus aurata) to the replacement of dietary fish oil by linseed and soyabean oils
Authors: Menoyo D. , Izquierdo M. S. , Robaina L. , Ginés R. , Lopez-Bote C. J. , Bautista J. M.
Published: July 2004

Linseed (LO) and soyabean (SO) oils were evaluated as fish-oil (FO) substitutes in the diets of marketable-sized gilthead sea bream (Sparus aurata). Practical diets were designed factorially with the lipid added as follows (%): FO 100, LO 60+FO 40, LO 80+FO 20, SO 60+FO 40, SO 80+FO 20. The effects of experimental diets on growth, fatty acids patterns in liver and muscle, flesh quality variables and activities of selected enzymes involved in lipid synthesis and catabolism were determined at the end of a 7-month trial. Fatty acid composition of liver and muscle generally reflected the fatty acid composition of the diets. Then−3 PUFA levels were significantly reduced by the inclusion of vegetable oils. This tendency was more pronounced for EPA than for docosahexaenoic acid. Then−3:n−6 fatty acid ratio reached the lowest values in fish fed the SO diets; this was associated with a higher liver lipid deposition. No differences were found in fillet texture and pH. However, under conditions of forced peroxidation, muscles from fish fed the SO diets had lower peroxidation levels. Vegetable oil substitution decreased lipogenesis in liver and this effect was greatest at the highest substitution level. In contrast, muscle β-oxidation enzymes had increased activities with vegetable oil substitution. Thus, the lower hepatic lipogenesis was correlated with an increased lipid utilisation in muscle. It is concluded that growth and lipid metabolism were affected by experimental diets.
Effect of dietary cholesterol with or without saturated fat on plasma lipoprotein cholesterol levels in the laboratory opossum (Monodelphis domestica) model for diet-induced hyperlipidaemia
Authors: Kushwaha Rampratap S. , VandeBerg Jane F. , VandeBerg John L.
Published: July 2004

Laboratory opossums (Monodelphis domestica) show extreme genetic variability in their responsiveness to dietary lipids; a great proportion of the genetic variability in responsiveness is due to a single major gene. To determine whether the major gene for dietary response detected by genetic analysis in opossums is responsive to dietary cholesterol or dietary saturated fat, or a combination of both, we used males and females of susceptible and resistant lines of laboratory opossums that were 5 to 7 months old. The animals were challenged with three different experimental diets (high-cholesterol diets with or without high saturated fat from lard or coconut oil) and plasma lipoproteins were measured. Plasma and VLDL+LDL-cholesterol concentrations increased several-fold when the animals were fed the diet containing elevated cholesterol (P>0·001) or elevated cholesterol and fat (P>0·001) and differed between the two lines when they were fed high-cholesterol diets with or without fat (P>0·001). Plasma HDL-cholesterol concentrations were higher (P>0·05) in animals of the resistant line than in the susceptible line when they were fed the basal diet (550 (sem 30)v. 440 (sem 20) mg/l) and when they were fed the low-cholesterol and high-fat diet (600 (sem 30)v. 490 (sem 30) mg/l). Dietary coconut oil and lard had similar effects on plasma lipoprotein cholesterol concentrations in the susceptible line of opossums. A reduction in dietary cholesterol by 50% with either the lard or coconut oil blunted the plasma cholesterol response. The results from the present studies suggest that the major gene for dietary response previously detected by genetic analysis in laboratory opossums affects the response to dietary cholesterol but not to saturated fat.
Olive oil and its main phenolic micronutrient (oleuropein) prevent inflammation-induced bone loss in the ovariectomised rat
Authors: Puel C. , Quintin A. , Agalias A. , Mathey J. , Obled C. , Mazur A. , Davicco M. J. , Lebecque P. , Skaltsounis A. L. , Coxam V.
Published: July 2004

The present study was designed to evaluate the effect of olive oil and its main polyphenol (oleuropein) in ovariectomised rats with or without inflammation. Rats (6 months old) were ovariectomised or sham-operated as control. Ovariectomised rats were separated into three groups receiving different diets for 3 months: a control diet with 25 g peanut oil and 25 g rapeseed oil/kg (OVX), the control diet with 50 g olive oil/kg or the control diet with 0·15 g oleuropein/kg. The sham-operated group was given the same control diet as OVX. Inflammation was induced 3 weeks before the end of the experiment by subcutaneous injections of talc (magnesium silicate) in one-half of each group. The sucess of ovariectomy was verified at necropsy by the atrophy of uterine horns. Inflammation, oleuropein or olive oil intakes did not have any uterotrophic activity, as they had had no effect on uterus weight. The plasma concentration of α-1-acid glycoprotein (an indicator of inflammation) was increased in OVX rats with inflammation. With regard to bone variables, osteopenia in OVX was exacerbated by inflammation, as shown by a decrease in metaphyseal and total femoral mineral density. Both oleuropein and olive oil prevented this bone loss in OVX rats with inflammation. At necropsy, oleuropein and olive oil consumption had had no effect on plasma osteocalcin concentrations (marker of bone formation) or on urinary deoxypyridinoline excretion (marker of bone resorption). In conclusion, oleuropein and olive-oil feeding can prevent inflammation-induced osteopenia in OVX rats.
Ultrastructural Demonstration of Mercury Granules in the Placenta of Metallothionein-Null Pregnant Mice after Exposure to Mercury Vapor
Authors: Shimada Akinori , Yamamoto Emi , Morita Takehito , Yoshida Minoru , Suzuki Junko S. , Satoh Masahiko , Tohyama Chiharu
Published: July 2004

The placenta plays an important role in the regulation of maternal to fetal transfer of toxic substances, including nonessential metals. Metallothioneins (MTs), which are known to have protective effects against heavy metal toxicity, exist in the placenta, but the exact localization of placental MTs (both MT-I and MT-III) and their physiological role in the placenta exposed to mercury are unclear. The present study was performed to examine the localization of MTs and mercury granules in the placenta of mice exposed to mercury vapor. On gestational day 16, MT-I & II-null and wild-type mice were exposed to mercury vapor at 4.9 to 5.9 mg/m3 for 2 hours. At 24 and 48 hours after exposure, the placentas were examined for mercury distribution (autometallography), MT immunoreactivity, and MT mRNA expression (in situ hybridization). No histological changes were observed in the placentas of either MT-null or wild-type mice. Mercury deposition was demonstrated along the boundary between the junctional zone and the labyrinth zone, as well as in the yolk sac, maternal decidual cells, and labyrinth trophoblasts of both MT-null and wild-type mice. MT-I & -II immunoreactivity, which was confined to wild-type mice, was demonstrated in the yolk sac and decidual cells; mercury was also shown in both structures, suggesting that mercury granules were bound to MTs. MT-III mRNA expression was observed in the yolk sac, decidual cells, and spongiotrophoblasts in both MT-null and wild-type mice. There was, however, no evidence of MT at the boundary between the junctional and labyrinth zones, where substantial mercury deposits were demonstrated. These results suggest that placental MTs and the other unknown molecules may be related to the barrier to the placental transfer of mercury.
MedlineR: an open source library in R for Medline literature data mining
Authors: Lin Simon M. , McConnell Patrick , Johnson Kimberly F. , Shoemaker Jennifer
Published: July 2004

Summary: We describe an open source library written in the R programming language for Medline literature data mining. This MedlineR library includes programs to query Medline through the NCBI PubMed database; to construct the co-occurrence matrix; and to visualize the network topology of query terms. The open source nature of this library allows users to extend it freely in the statistical programming language of R. To demonstrate its utility, we have built an application to analyze term-association by using only 10 lines of code. We provide MedlineR as a library foundation for bioinformaticians and statisticians to build more sophisticated literature data mining applications.

Availability: The library is available from http://dbsr.duke.edu/pub/MedlineR.
DIVAA: analysis of amino acid diversity in multiple aligned protein sequences
Authors: Rodi Diane J. , Mandava Suneeta , Makowski Lee
Published: July 2004

Motivation: Multiple alignments of proteins are an effective way of identifying conserved amino acids that provide clues to functional relationships among proteins. Quantitation of the abundances of amino acids found at each position in a sequence motif can provide a basis for understanding the structural and functional constraints at each point. Distribution of information across a motif has been used previously, but the non-intuitive nature of the analysis has limited its impact.

Results: Here, we introduce a quantitative measure of amino acid sequence diversity (DIVAA) that has a simple, intuitive meaning. Diversity, as a measure of sequence conservation or variation, is inextricably linked to the probability of selecting identical pairs from a distribution. We demonstrate its utility through the analysis of four populations: ATP-binding P-loops, hypervariable domains of kappa light chains, signal sequences, and the N- and C- termini of proteins. DIVAA provides a simple means to generate hypotheses concerning the contribution of individual residues to the functional and evolutionary relationships among proteins.

Availability: Access to DIVAA software is available at RELIC (http://relic.bio.anl.gov)
Exploring protein fold space by secondary structure prediction using data distribution method on Grid platform
Authors: Lee Soojin , Cho Min-Kyu , Jung Jin-Won , Kim Jai-Hoon , Lee Weontae
Published: July 2004

Motivation: Since the newly developed Grid platform has been considered as a powerful tool to share resources in the Internet environment, it is of interest to demonstrate an efficient methodology to process massive biological data on the Grid environments at a low cost. This paper presents an efficient and economical method based on a Grid platform to predict secondary structures of all proteins in a given organism, which normally requires a long computation time through sequential execution, by means of processing a large amount of protein sequence data simultaneously. From the prediction results, a genome scale protein fold space can be pursued.

Results: Using the improved Grid platform, the secondary structure prediction on genomic scale and protein topology derived from the new scoring scheme for four different model proteomes was presented. This protein fold space was compared with structures from the Protein Data Bank, database and it showed similarly aligned distribution. Therefore, the fold space approach based on this new scoring scheme could be a guideline for predicting a folding family in a given organism.
Primer Design and Marker Clustering for Multiplex SNP-IT Primer Extension Genotyping Assay using Statistical Modeling
Authors: Yuryev Anton , Huang Jianping , Scott Kathryn E. , Kuebler Jennifer , Donaldson Miriam , Phillips Michael S. , Pohl Mark , Boyce-Jacino Michael T.
Published: July 2004

Motivation: The optimization of the primer design is critical for the development of high-throughput SNP genotyping methods. Recently developed statistical models of the SNP-IT primer extension genotyping reaction allow further improvement of primer quality for the assay.

Results: Here we describe how the statistical models can be used to improve primer design for the assay. We also show how to optimize clustering of the SNP markers into multiplex panels using statistical model for multiplex SNP-IT. The primer set failure probability calculated by a model is used as a minimization function for both primer selection and primers clustering. Three clustering algorithms for the multiplex genotyping SNP-IT assay are described and their relative performance is evaluated. We also describe the approaches to improve the speed of primer design and clustering calculations when using the statistical models. Our clustering decreases the average failure probability of the marker set by 7–25%. The experimental marker failure rate in the multiplex reaction was reduced dramatically and success rate can be achieved as high as 96%.

Availability: The primer design using statistical models is freely available from www.autoprimer.com
The ‘subsequent artificial neural network’ (SANN) approach might bring more classificatory power to ANN-based DNA microarray analyses
Authors: Linder Roland , Dew Dawn , Sudhoff Holger , Theegarten Dirk , Remberger Klaus , Pöppl Siegfried J. , Wagner Mathias
Published: July 2004

Motivation: Human decisions often proceed in two steps. Initially those most preferred are chosen followed by a subsequent choice of these preferences. Applying one artificial neural network (ANN), a classification is limited to the preselection process. The final categorization is only possible by a subsequent ANN that distinguishes the pre-chosen classes. Existing strategies using coupled ANNs are discussed and a new approach particularly suited for multiclass classification problems is introduced (‘Subsequent ANN’, SANN).

Results: Evaluating a simulated data base comprising 3 classes, classification results of SANN were obviously superior to those achieved by ANN. To evaluate a real-world data base the microarray benchmark GCM (14 classes) was chosen. The ANN results reached 72%, comparable to previous results. Using SANN, up to 81% of the tumors were correctly classified.

Availability: Programs used in this work and numerical results are available upon request.
NMRb: a web-site repository for raw NMR datasets
Authors: Pons J. L. , Malliavin T. E. , Tramesel D. , Delsuc M. A.
Published: July 2004

Summary: The development of NMR in structural proteomics requires the availability of automatic structure determination methods. Many researchers are commonly confronted with the lack of raw datasets during the validation step of such methods. In order to increase test possibilities, the NMRb web-site offers a database of NMR raw datasets, ordered by spectral characteristics.

Availability: NMRb is available from: http://nmrb.cbs.cnrs.fr

Supplementary information: General organization of NMRb figure, relational model organization, and XML structure files are available from http://nmrb.cbs.cnrs.fr/nmrb-doc.html
Discovering patterns to extract protein–protein interactions from full texts
Authors: Huang Minlie , Zhu Xiaoyan , Hao Yu , Payan Donald G. , Qu Kunbin , Li Ming
Published: July 2004

Motivation: Although there are several databases storing protein–protein interactions, most such data still exist only in the scientific literature. They are scattered in scientific literature written in natural languages, defying data mining efforts. Much time and labor have to be spent on extracting protein pathways from literature. Our aim is to develop a robust and powerful methodology to mine protein–protein interactions from biomedical texts.

Results: We present a novel and robust approach for extracting protein–protein interactions from literature. Our method uses a dynamic programming algorithm to compute distinguishing patterns by aligning relevant sentences and key verbs that describe protein interactions. A matching algorithm is designed to extract the interactions between proteins. Equipped only with a dictionary of protein names, our system achieves a recall rate of 80.0% and precision rate of 80.5%.

Availability: The program is available on request from the authors.
Occipital Condyle Fractures
Authors: Tuli Sagun , Tator Charles H. , Fehlings Michael G. , Mackay Margot
Published: July 2004

OBJECTIVE:

Occipital condyle fractures (OCFs) are infrequently recognized. Three recent cases of OCF in our center prompted a review of the incidence, clinical presentation, diagnosis, and treatment of this entity.

METHODS:

A retrospective review of medical records and radiographic results was performed for 93 of 316 consecutive patients who were victims of trauma, who presented at the Toronto Hospital during a 13-month period, and who had undergone computed tomography of the occiput.

RESULTS:

A review of the literature regarding OCF revealed that cranial nerve deficits occurred in 31% of the patients with OCFs; of those, the deficits were delayed in 38%. Three new cases of OCF, with neck pain but without cranial nerve deficits, have been reported. The cervical spine x-rays revealed nothing abnormal in 96% of the reported cases. In our retrospective review, asymptomatic OCF was revealed by computed tomography for 1 of the 93 patients.

CONCLUSION:

OCF is a diagnostic challenge. We suggest that computed tomographic scans of 0-C2 be obtained in the following circumstances: presence of lower cranial nerve deficits, associated head injury or basal cranial fracture, or persistent severe neck pain despite normal radiographic results. We propose a new classification system for the management and treatment of OCF based on the stability of the 0-C1-C2 joint complex reflected by the presence of displacement of the condyle, computed tomographic or radiographic evidence of 0-C1-C2 instability, and magnetic resonance evidence of ligamentous injury. OCFs are divided into the following types: Type 1 (stable), undisplaced fracture; Type 2A (stable), displaced fracture with no ligamentous instability; and Type 2B (unstable), displaced fracture with ligamentous instability.
Long-term Tumor Control and Functional Outcome in Patients with Cavernous Sinus Meningiomas Treated by Radiotherapy with or without Previous Surgery: Is There an Alternative to Aggressive Tumor Removal?
Authors: Dufour Henry , Muracciole Xavier , Métellus Philippe , Régis Jean , Chinot Olivier , Grisoli François
Published: July 2004

OBJECTIVE

We report the long-term follow-up of 31 patients with cavernous sinus meningiomas who were treated either with surgery and radiotherapy (RT) or with RT alone. This retrospective review was undertaken to compare long-term efficacy and morbidity of RT with or without previous surgery versus complete, aggressive surgical removal.

METHODS

Between 1980 and 1997, we performed a retrospective study of 31 patients harboring cavernous sinus meningiomas. The patient group comprised 25 women and 6 men. Patients were divided into two therapeutic categories: patients treated with surgery and RT (Group I, 17 patients) and patients treated with RT alone (Group II, 14 patients). Twenty-five patients (14 in Group I and 11 in Group II) were treated for primary tumors, and 6 patients (3 in Group I and 3 in Group II) were treated for recurrent disease. All three patients who were treated by RT alone at the time of recurrent disease had had previous surgery as initial treatment. Tumor control, treatment morbidity, and functional outcomes were evaluated for all patients. Twenty-eight patients were alive at the time of analysis, with a median follow-up period of 6.1 years.

RESULTS

The progression-free survival rate was 92.8% at 10-year follow-up. Only two patients exhibited tumor progression after initial treatment. One of the patients who experienced tumor regrowth 4 years after surgery and RT benefited from additional conventional external beam radiation, and this patient exhibited no evidence of tumor progression at the last follow-up examination 6 years later. Two patients experienced cranial nerve impairment after surgery, and no patients developed late radiation toxicity. Follow-up status as measured by the Karnofsky Performance Scale deteriorated in 7% of patients and was the same or improved in 93% of patients.

CONCLUSION

The results of combined surgery and RT or RT alone indicated a high rate of tumor control and a low risk of complications. Complete aggressive surgical removal of cavernous sinus meningiomas is associated with an increased incidence of morbidity and mortality and does not demonstrate a better rate of tumor control. Conventional external beam radiation seems to be an efficient and safe initial or adjuvant treatment of these lesions, and these findings should serve as a basis for evaluating new alternatives such as radiosurgery or stereotactic RT.
Effect of Carotid Endarterectomy on Chronic Ocular Ischemic Syndrome Due to Internal Carotid Artery Stenosis
Authors: Kawaguchi Shoichiro , Okuno Shuzo , Sakaki Toshisuke , Nishikawa Norikiyo
Published: July 2004

OBJECTIVE

We evaluated the effect of carotid endarterectomy on chronic ocular ischemic syndrome due to internal carotid artery stenosis by use of data obtained from ophthalmic artery color Doppler flow imaging.

METHODS

We examined 11 patients with ocular ischemic syndrome due to internal carotid artery stenosis (>70% stenosis) who were being treated by carotid endarterectomy. Ophthalmic artery color Doppler flow imaging indicated ophthalmic artery flow direction and peak systolic flow velocity and was performed before and at 1 week, 1 month, and 3 months after surgery.

RESULTS

We assessed the ophthalmic arteries of 11 patients via color Doppler flow imaging. Before undergoing carotid endarterectomy, five patients showed reversed ophthalmic artery flow. In the other six patients who experienced antegrade ophthalmic artery flow, the average peak systolic flow velocity was 0.09 ± 0.05 m/s (mean ± standard deviation). Preoperative reversed flow resolved in each patient 1 week after undergoing surgery. All patients showed antegrade ophthalmic artery flow. The average peak systolic flow velocity in the patients who had preoperative antegrade flow rose significantly, to 0.21 ± 0.14 m/s (P < 0.05). There was no significant change as compared with findings at 1 week after surgery. During the follow-up period (mean, 32.4 mo), no patients complained of recurrent visual symptoms. At the end of the study period, visual acuity had improved in five patients and had not worsened in the other six patients.

CONCLUSION

Carotid endarterectomy was effective for improving or preventing the progress of chronic ocular ischemia caused by internal carotid artery stenosis.