bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-avoiding walks subject to boundary constraints
Authors: Wall Frederick T. , Seitz William A. , Chin John C. , Mandel Frederic
Published: February 2003

A statistical study is carried out for self-avoiding walks on infintely long square lattice strips, two and three lines wide. The two-layer problem is solved completely and the three-layer problem asymptotically. In each instance, the mean square end-to-end separation of a walk is found, as expected, to be asymptotically proportional to the square of the number of steps for long walks; in other words, 〈x2〉=an2, where 〈x2〉 is the mean square x component of net distance traversed and n is the number of steps (assumed to be large). For the two-layer problem, a=0.5236, and for the three-layer problem, a=0.3899.
Thermodynamics of the MSA for simple fluids
Authors: Ho/ye J. S. , Stell G.
Published: February 2003

An analytic study is made of the thermodynamic properties of the mean spherical approximation for a simple fluid and simple fluid mixtures. It immediately suggests several improved approximations.
Calculations of magnetic susceptibility of polyatomic molecules
Authors: Lazzeretti Paolo , Zanasi Riccardo , Cadioli Beniamino
Published: February 2003

The magnetic susceptibility of H2O, NH3, and CH4 molecules has been evaluated within the framework of coupled and uncoupled Hartree–Fock perturbation theories for the Fock–Dirac density matrix, employing several basis sets of gaugeless Gaussian functions. The results provided by the largest basis sets are in good agreement with experiment as well as with other ab initio calculations. Quantities necessary to assess the degree of gauge independence of the susceptibility and to evaluate this property for an arbitrary gauge origin are also reported. The reliability of the uncoupled approach suggested here is systematically analyzed by investigating the upper bounds to the error affecting the geometric approximation to the paramagnetic susceptibility. The results demonstrate the practicality of the simple and inexpensive uncoupled scheme with respect to the cumbersome coupled method.
Isostructural phase transitions due to core collapse. III. A model for solid mixtures
Authors: Kincaid J. M. , Stell G.
Published: February 2003

Our earlier development of a statistical mechanical theory of isostructural phase transitions due to core collapse [J. Chem. Phys. 65, 2161, 2172 (1976)] is extended to the treatment of solid mixtures exhibiting isostructural transitions. Since mixtures in which two solid phases coexist are typically in states of mechanical but not material equilibrium, we consider the theory for states of mechanical equilibrium only, as well as the theory for coexisting phases in true stable thermodynamic equilibrium. Using an extremely simple Hamiltonian model we find good qualitative agreement between the results of a first-order perturbation theory and the recent experimental results for Ce1−xThx mixtures. In particular, the theory accounts for the experimentally observed decrease in critical temperature with increasing x and for the dependence of the observed resistivity–temperature isobars upon x.
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o study of perturbations between the X 1Σ+g and b 3Σ−g states of the C2 molecule
Authors: Langhoff S. R. , Sink M. L. , Pritchard R. H. , Kern C. W. , Strickler S. J. , Boyd Mark J.
Published: February 2003

We report ab initio calculations of the energies and wavefunctions for the X 1Σ+g and b 3Σ−g states of C2 at several levels of accuracy. The best calculations, using a double-zeta basis of Gaussian-lobe functions and including dσ and dπ functions and extensive CI, give good agreement with experimental potential curves. These wavefunctions are used to compute spin–orbit coupling between the two states. The results agree well with the matrix elements obtained from the perturbations observed by Ballik and Ramsay. Some implications of our results for the theory of intersystem crossing are discussed.
High resolution 13C NMR in solids: 13C local fields of CH, CH2, and CH3
Authors: Rybaczewski E. F. , Neff B. L. , Waugh J. S. , Sherfinski J. S.
Published: February 2003

A method for measuring proton positions in solids via two-dimensional Fourier transform NMR is described. This method is applied to single crystals containing CH, CH2, and CH3 groups.
The vibrational spectrum and lattice dynamics of polycrystalline ammonium hydrosulfide
Authors: Bragin J. , Diem M. , Guthals D. , Chang S.
Published: February 2003

The infrared spectra of NH4HS and ND4DS have been recorded from 200 to 4000 cm−1 at liquid nitrogen temperatures, and the Raman spectra of these substances have been recorded from 0 to 4000 cm−1 over the temperature range 83–390°K. No evidence of a second solid phase was obtained. Internal and external fundamentals were assigned, in detail, based on selection rules, isotopic frequency shifts, and analogy with other structurally similar salts. Barriers to anion and cation reorientation of 3.8 and 1.9 kcal/mole, respectively, have been calculated from librational assignments. The implications of the infrared spectrum of NH4HS for the possible spectroscopic detection of this substance in the atmosphere of the planet Jupiter are discussed.
Electrical conductivity and charge compensation in Nb doped TiO2 rutile
Authors: Baumard J. F. , Tani E.
Published: February 2003

The electrical conductivity of rutile doped with 0.04–3 at.% niobium is reported as a function of oxygen pressure in the temperature range 1273–1623 K. The charge compensation is discussed in terms of a point defect model, under the assumption of a substitutional incorporation of niobium into the titanium rutile sublattice. Two kinds of charge compensation occur according to the temperature and the oxygen pressure, via an electronic or a lattice defect, in a Ti1−yNbyO2 or a Ti1−yNbyO2+y/2 solid solution, respectively. In the overstoichiometric range of the oxide, the data, when applied to undoped rutile, allow some conclusions about the atomic or electronic transport properties, both in the high and low temperature regimes.
Matrix photodissociation and photoionization of carbon tetrahalides with noble gas resonance radiation
Authors: Prochaska Frank T. , Andrews Lester
Published: February 2003

Experiments have shown that the coaxial orifice discharge tube is an effective windowless resonance lamp for argon and neon photolysis of matrix-isolated molecules. Argon resonance photoionization of CCl4 produced CCl+3 at 1037 cm−1, which photolyzed with intense visible light. Discharged noble gas mixtures produced increased yields of CCl3 and CCl2 and new bands sensitive to near-infrared photolysis, which are assigned to the weakly-bound species CCl+3–Cl, CCl2–Cl+2, and Cl+3. Krypton resonance photoionization of CBr4 gave CBr+3 at 874 cm−1, which also decreased with intense mercury arc photolysis.
Paramagnetic Gd(IO3)3. Crystal structure of the transition metal iodates. IV
Authors: Liminga R. , Abrahams S. C. , Bernstein J. L.
Published: February 2003

Gd(IO3)3, type I, crystallizes in the monoclinic system with space group P21/a and four formulas in the unit cell. The lattice constants, at 297 °K, are a=13.4365(9), b=8.5226(5), c=7.1356(5) Å and β=99.717(7) ° for λCuKα1=1.540598 Å. A total of 5012 independent reflections were measured on a CAD-4 diffractometer, using Nb-filtered MoKα radiation. The crystal structure was solved using a combination of Patterson and Fourier series, and was refined by the method of least squares. The final agreement factor R is 0.033. The iodate ions form a three-dimensional network based on shared oxygen atoms, with the Gd3+ ion located within a distorted dodecahedron of oxygen atoms. The three independent IO−3 ions form triangular pyramids, with three short I–O bonds of average length 1.803 Å and average O–I–O angle of 98.7°. Each I atom has three additional oxygen neighbors at distances in the range 2.741–3.194 Å that complete its distorted octahedron. Gd(IO3)3, type I is the archetype for an isostructural family of of rare-earth iodates extending from Ce to Lu. By contrast, no more than five (including Pm) rare-earth ions are represented in any of the other five known types of anhydrous rare-earth iodates. Small variations from monotonic in the lattice constants of type I anhydrous iodates are found, as predicted by the ’’tetrad’’ effect.
Adsorption and geometry: the boundary layer approximation
Authors: Philip J. R.
Published: February 2003

The unitary approach to capillary condensation and adsorption uses the ’’boundary layer approximation’’ that the adsorptive potential depends only on the normal distance of the liquid–vapor interface from the solid. This paper develops a critique of this approximation through calculations for various relevant configurations of the solid. The distance dependence of the intermolecular potential, h (ρ), may be inferred from the variation of adsorptive potential F with ν, the film thickness on a single infinite plate, since h (ρ) =π1/2(d/dν)(dF/dν2) ‖ν=ρ. Exact solutions of the adsorptive field are found for h an inverse power law, with special attention to the powers −6 and −4. The configurations investigated are (a) parallel plates, (b) tubes, (c) cylinders, (d) spherical cavities, (e) spheres, (f) wedge-shaped pores, and (g) edges. The results are apparently all new, except for a special case of (a). For numerical examples of capillary condensation and adsorption, it is found that the unitary approach, using F (ν), leads to an error in the total potential of −8% for parallel plates and −12% for tubes. For these and other simple configurations, replacement of F (ν) by the appropriate potential function F0(ν) makes the unitary approach exact.
Quantum mechanical second virial coefficient of a gas with square-well plus hard-core potential
Authors: Sinha S. K. , Singh Y.
Published: February 2003

The quantum mechanical second virial coefficient of a gas with square-well plus hard-core potential is evaluated at low and high temperatures. The low temperature result is given in a series in the ascending powers of (a/λ), and the first four coefficients are given. The direct part of the second virial coefficient at high temperature is given in a series in the ascending powers of (λ/a), and the first three coefficients are given. Our result for the first coefficient in the high temperature series is in agreement with the result of previous workers.
Double resonance interferometry: Relaxation times for dipolar forbidden transitions and off-resonance effects in an AX spin system
Authors: Stoll M. E. , Vega A. J. , Vaughan R. W.
Published: February 2003

Experimental and theoretical results of a nuclear magnetic double resonance interferometric study of a model AX spin system are presented. Measurements of the characteristic relaxation times of off-diagonal density matrix elements corresponding to magnetic-dipole-forbidden transitions are presented, and the use of such relaxation time constants to obtain information including cross correlations of the fluctuating fields at the A and X nuclear sites is discussed. Off-resonance effects produce large changes in the spectra, and exploitation of these effects to indirectly measure the precise resonance frequency of a spin with a small magnetogyric ratio is discussed.
Piezoelectric langbeinite-type K2Cd2(SO4)3: Room temperature crystal structure and ferroelastic transformation
Authors: Abrahams S. C. , Bernstein J. L.
Published: February 2003

Langbeinite-type dipotassium dicadmium trisulfate K2Cd2(SO4)3 is piezoelectric at room temperature and can be ferroelastically reoriented at higher temperatures. Crystallizing in space group P212121 with four formulas in the unit cell, the lattice constants at 298.2 °K are a=10.2082(2), b=10.2837(3), c=10.1661(1) Å for CuKα1=1.540562 Å. The integrated intensities of 13 525 structure factors, within a complete sphere of reflection of radius (sinϑ)/λ=1.20 Å−1, were measured on a CAD-4 diffractometer with Nb-filtered MoKα radiation. The crystal structure was solved by use of Patterson and Fourier series, and refined by the method of least squares based on 3554 symmetry-independent Fmeas. The final agreement factor R=0.023 and the δR normal probability plot is slightly nonlinear. All atomic positions are within 0.8 Å of those reported in the archetype cubic mineral langbeinite K2Mg2(SO4)3 following a simple transformation. The S–O distances in the three independent SO2−4 tetrahedra range from 1.460(3) to 1.484(3) Å, with an average value of 1.470(8) Å. The two independent Cd2+ ions occupy irregular six-coordinated polyhedra with average Cd–O distances of 2.278 Å. One of the independent K+ ions has eight and the other ten nearest-neighbor O atoms less than 3.25 Å distant, with respective average K–O distances of 2.954 and 2.956 Å. Application of 5 MNm−2 normal to (010), followed by heating to 435 °K and then cooling to room temperature still under applied stress, results in reorientation from abc to bca. The largest displacement required for room temperature ferroelastic reorientation is 1.19 Å for an oxygen atom.
Low temperature vibrational spectroscopy. I. Hexachlorotellurates
Authors: Berg Rolf W. , Poulsen Finn W. , Bjerrum Niels J.
Published: February 2003

Far infrared and Raman spectra of six hexachlorotellurate (IV) salts have been obtained at ∼100 K for the first time. In the rubidium, cesium, ammonium, and tetramethylammonium salts the Raman active T2g cation lattice translatory mode was found. In the monoclinic K2[TeCl6] a number of low frequency lattice modes were observed and interpreted in terms of a phase transition near 165 K, similar to transitions in other K2[MX6] salts. The cubic tetramethylammonium hexachlorotellurate salt undergoes a phase transition of supposed first order at a temperature near 110 K, corresponding to transitions known in analogous uranium and tin compounds. Possible reasons for the transitions are discussed. In the low temperature phases the ν4 and ν6 bendings of [TeCl6]2− have been identified with bands near ∼130 and ∼110 cm−1. No evidence seemed to favor any stereochemical distortion due to the lone pair of electrons present in hexachlorotellurates.
A study of the reaction O−3+CO2?CO−3+O2 and its implication on the thermochemistry of CO3 and O3 and their negative ions
Authors: Dotan I. , Davidson J. A. , Streit G. E. , Albritton D. L. , Fehsenfeld F. C.
Published: February 2003

The reaction O−3+CO2?CO−3+O2 has been examined in the forward and reverse directions in a variable-temperature flowing afterglow from 200 to 600 K and in a flow-drift tube at mean relative kinetic energies from 0.04 to 1 eV. The forward direction is clearly established as the exothermic direction. Furthermore, collisional dissociation of CO−3 and O−3 ions in the flow-drift tube at high E/N to form O− shows that CO−3 is the more stable ion. All of this implies that D (CO2+O−) ≳D (O2+O−). Kinetic-equilibrium studies at the higher temperatures show that the reverse rate constant is less than 6×10−15 cm3 s−1 below 600 K. When this is combined with the estimated entropy change of the reaction one obtains the quantitative lower limit D (CO2+O−) −D (O2+O−) ?0.58 eV. The reaction OH−+O3→O−3+OH is found to be fast, thereby establishing lower limits for the electron affinity of O3 and the O− bond dissociation energy of O−3. When taken with the above limit for the relative CO−3 and O−3 bond dissociation energy one obtains lower limits for the electron affinity of CO3 and the O− bond dissociation energy of CO−3. The latter lower limit does not overlap an upper limit for D (CO2+O−) obtained from recent photodissociation studies. The relation of this discrepancy to the electron affinity of O3 is discussed.
Energy transfer between electronically excited argon and nitrogen: A kinetic model for the 3371 and the 3577 Å laser emissions
Authors: Puech Vincent , Collier Franck , Cottin Patrice
Published: February 2003

Laser action of an argon–nitrogen mixture excited by an electron beam has been studied. We report laser action at 3577 Å, but also at 3371 Å. In previous kinetic models laser emission at 3371 Å was forbidden. In this paper we present a new kinetic model based on a total transfer reaction between Ar (4s) and N2(C 3Πu). The main feature of our model is to permit laser action at 3371 Å only if the excitation time is short enough. The experiments performed with a small electron gun possessing the required characteristics (risetime=1 ns FWHM=10 ns) permitted us to observe laser emissions at 3371 and 3577 Å. For strong cavity coupling the emission is more powerful on the 3371 line than on the 3577 Å line. The same experiments made with an electron gun of a larger energy and a longer excitation pulse exhibits only a laser emission at 3577 Å, in agreement with theoretical computations.
Absorption spectra of matrix-isolated alkaline earth metal diatomic molecules
Authors: Miller John C. , Ault Bruce S. , Andrews Lester
Published: February 2003

Mg, Ca, and Sr atoms were codeposited with argon and krypton at 10 K for optical absorption investigation of the van der Waals diatomic molecules. Very strong and weak structured absorptions were observed for Mg2 at 367 and 444 nm, respectively. An unstructured 507 nm and a strong structured 648 nm absorption were found for Ca2, and a strong structured 710 nm absorption was observed for Sr2. Intermediate absorptions with intermediate spacings were observed for CaMg, SrMg, and SrCa in mixed-metal experiments. The strong absorptions are assigned to 1Σ+u(1S+1P) ←1Σ+g(1S+1S) transitions.
Observation of orbiting resonances in the scattering of He+Ne
Authors: Grace R. S. , Johnson Dean L. , Skofronick J. G.
Published: February 2003

Experimental total cross section measurements for the He+Ne atom pairs are presented over the relative velocity range of 88 to 1200 m/sec. One orbiting resonance is observed at 160 m/sec. The data around 100 m/sec are consistent with the existence of another resonance at 88 m/sec. A comparison of experimental results to calculated cross sections gives the best fit for the HFD potential. This fit suggest that the lowest velocity resonance is from an l=3 partial wave, while the higher velocity resonance is from an l=4 partial wave.
On the possible role of a mixed valence–Rydberg state in the fluorescence of indoles
Authors: Lami Hans
Published: February 2003

Murrell’s localized orbital model is applied to indole, considered as composed of three fragments: benzene, ethylene, and a ≳NH group. In addition to the usual locally excited and charge-transfer states, locally excited 3s and 3pπ Rydberg states of the ≳NH group have been introduced and the mixed valence–Rydberg (3dπ) character of the locally excited state of the ethylene fragment considered. The model predicts a pure Rydberg 3s←1A transition at 46 kK, polarized perpendicular to the molecular plane, which may explain the disappearance, in condensed media, of a shoulder (at 42.4 kK) present in the vapor phase absorption spectrum of indole. The 3dπ orbital confers a long range character to the 1La excited state. Experiment unambiguously shows that ’’exciplex’’ formation of indoles with polar solvents occurs only if the emission originates from this state. Change, in polar media, from the Franck–Condon to a solvated Rydberg state, is therefore postulated.
NMR study of proton transfer interactions in the system pyridine +HCl (0%–95%)
Authors: Shuppert J. W. , Angell C. A.
Published: February 2003

Pyridinium chloride, which has proven useful in a number of molten salt studies where it serves as a strong chloride donor Lewis base, is freely soluble in both excess acid and excess base. To probe the proton transfer interactions involved, proton NMR studies have been performed on pyridine+HCl solutions in the composition range 0%–95% HCl at temperatures ranging from −100°C to 200°C. This system is rich in examples of the way in which competing hydrogen bonding interactions can affect the magnetic environment of the involved protons. The most obvious of these is the increased magnetic shielding that develops in the vicinity of the N–H+ proton of the pyridinium cation as excess HCl competes for the Cl− ions, initially to form HCl2− anion and later to form more extended HCl⋅⋅⋅HCl−2 aggregates. As excess pyridine is added to PyHCl a shift in the opposite direction occurs, due either to the formation of symmetrical [Py–H–Py]+ species, to the repression of PyHCl autodissociation, or to a combination of both effects as expressed by (PyHCl)2 dimer formation. Less obvious but equally interesting is the deshielding of the proton in the HCl2− anion of the PyH+–HCl2− melt which accompanies addition of pyridine. This results from a competition between Py with Cl− for the HCl proton and a consequent tendency to produce the [PyH⋅⋅⋅Cl⋅⋅⋅HPy]+ species implied by the stoichiometry of certain crystalline compounds. Finally the ring protons themselves reflect the competition of excess HCl for the Cl− of PyHCl and the consequent shifts in ring electron density which accompany the inward movement of the N–H+ proton. The trends are such as to bring the observed ring proton chemical shifts relative to pyridine into better accord with theoretical predictions for the isolated PyH+ cation. The trend is continued when excess HCl is replaced by the stronger Lewis acids ZnCl2 and AlCl3 and in the case of excess AlCl3, agreement with theory is almost quantitive except for the α proton shifts. For the latter, the observed shifts are not even qualitatively correct.
Optical spectrum of Cr3+ in octahedral fluoride lattices: Refinements on an open-shell SCF MO calculation
Authors: Pueyo L. , Richardson J. W.
Published: February 2003

The six lower electronic transitions observed in octahedral fluoride compounds containing Cr3+ are calculated in the framework of an open-shell SCF MO methodology. An initial, isolated-cluster description is presented and compared with a more elaborate representation which includes the external lattice potential, a cluster correlation energy correction, and spin-orbit and configuration interactions. When these refinements are included, the six transition energies observed in K2NaCrF6 are computed with a mean deviation of 0.6 kK, a sixth of the initial value. The theoretical equilibrium distance is only 0.014 Å removed from experiment. CI and cluster correlation energies play a competitive role in locating the t3 doublets; the calculation places t3−2T1g above t3−2Eg and below t2e−4T2g. Due to the variation of spin-orbit interaction with distance, these levels change in character so rapidly that a more realistic procedure than the usual Franck–Condon approximation has been employed in the calculation of the transition intensity pattern via the magnetic dipole mechanism. Surprisingly, the equilibrium distance of 1Γ7−4T2g is computed only 0.01 Å greater than that of the ground state, but this small separation still allows at least one vibrational overtone to have observable intensity. Some of our results may be related to cubic oxide compounds and in this context quantitative discussions are presented about the doublet-quartet mixing, the structure of the 4A2g→2T2g broad band, and the Stokes shift observed in the emission spectra of those crystals.
Biphasic Estradiol-induced AKT Phosphorylation Is Modulated by PTEN via MAP Kinase in HepG2 Cells
Authors: Marino Maria , Acconcia Filippo , Trentalance Anna
Published: February 2003

We reported previously in HepG2 cells that estradiol induces cell cycle progression throughout the G1–S transition by the parallel stimulation of both PKC-α and ERK signaling molecules. The analysis of the cyclin D1gene expression showed that only the MAP kinase pathway was involved. Here, the presence of rapid/nongenomic, estradiol-regulated, PI3K/AKT signal transduction pathway, its modulation by the levels of the tumor suppressor PTEN, its cross-talk with the ERK pathway, and its involvement in DNA synthesis and cyclin D1gene promoter activity have all been studied in HepG2 cells. 17β-Estradiol induced the rapid and biphasic phosphorylation of AKT. These phosphorylations were independent of each other, being the first wave of activation independent of the estrogen receptor (ER), whereas the second was dependent on ER. Both activations were dependent on PI3K activity; furthermore, the ERK pathway modulated AKT phosphorylation by acting on the PTEN levels. The results showed that the PI3K pathway, as well as ER, were strongly involved in both G1–S progression and cyclin D1promoter activity by acting on its proximal region (-254 base pairs). These data indicate that in HepG2 cells, different rapid/nongenomic estradiol-induced signal transduction pathways modulate the multiple steps of G1–S phase transition.
Basolateral Cycling Mediated by a Lumenal Domain Targeting Determinant
Authors: Puthenveedu Manojkumar A. , Bruns Jennifer R. , Weisz Ora A. , Linstedt Adam D.
Published: February 2003

All identified basolateral sorting signals of integral membrane proteins are cytoplasmically disposed, suggesting that basolateral targeting is mediated exclusively by direct interaction with vesicle coat components. Here, we report that GPP130, a cis-Golgi protein that undergoes endosome-to-Golgi retrieval using the late endosome-bypass pathway in nonpolarized cells, cycles via the basolateral membrane in polarized MDCK cells. Significantly, the membrane-proximal lumenal domain of GPP130, which mediates GPP130 localization and trafficking in nonpolarized cells, was both necessary and sufficient for basolateral cycling in MDCK cells. The use of lumenal determinants for both basolateral cycling and endosome-to-Golgi retrieval suggests that a novel receptor-mediated mechanism operates at both the trans-Golgi network and distal sites to sort GPP130 along the late-endosome-bypass retrieval pathway in polarized cells.
Receptor-mediated Regulation of PI3Ks Confines PI(3,4,5)P3to the Leading Edge of Chemotaxing Cells
Authors: Huang Yi Elaine , Iijima Miho , Parent Carole A. , Funamoto Satoru , Firtel Richard A. , Devreotes Peter
Published: February 2003

Recent studies have demonstrated that PH domains specific for PI(3,4,5)P3accumulate at the leading edge of a number of migrating cells and that PI3Ks and PTEN associate with the membrane at the front and back, respectively, of chemotaxing Dictyostelium discoideum cells. However, the dependence of chemoattractant induced changes in PI(3,4,5)P3on PI3K and PTEN activities have not been defined. We find that bulk PI(3,4,5)P3levels increase transiently upon chemoattractant stimulation, and the changes are greater and more prolonged in pten–cells. PI3K activation increases within 5 s of chemoattractant addition and then declines to a low level of activity identically in wild-type and pten–cells. Reconstitution of the PI3K activation profile can be achieved by mixing membranes from stimulated pi3k1–/pi3k2–cells with cytosolic PI3Ks from unstimulated cells. These studies show that significant control of chemotaxis occurs upstream of the PI3Ks and that regulation of the PI3Ks and PTEN cooperate to shape the temporal and spatial localization of PI(3,4,5)P3.
Towards a computational model for −1 eukaryotic frameshifting sites
Authors: Bekaert Michaël , Bidou Laure , Denise Alain , Duchateau-Nguyen Guillemette , Forest Jean-Paul , Froidevaux Christine , Hatin Isabelle , Rousset Jean-Pierre , Termier Michel
Published: February 2003

Motivation: Unconventional decoding events are now well acknowledged, but not yet well formalized. In this study, we present a bioinformatics analysis of eukaryotic −1 frameshifting, in order to model this event.

Results: A consensus model has already been established for −1 frameshifting sites. Our purpose here is to provide new constraints which make the model more precise. We show how a machine learning approach can be used to refine the current model. We identify new properties that may be involved in frameshifting. Each of the properties found was experimentally validated. Initially, we identify features of the overall model that are to be simultaneously satisfied. We then focus on the following two components: the spacer and the slippery sequence. As a main result, we point out that the identity of the primary structure of the so-called spacer is of great importance.

Availability: Sequences of the oligonucleotides in the functional tests are available at http://www.igmors.u-psud.fr/rousset/bioinformatics/

Contact: bekaert@igmors.u-psud.frjpforest@lri.frchris@lri.fr

* To whom correspondence should be addressed.
MELINA: motif extraction from
promoter regions of potentially co-regulated genes
Authors: Poluliakh Natalia , Takagi Toshihisa , Nakai Kenta
Published: February 2003

Summary: ‘Melina’ assists users to compare the results of four public softwares for DNA motif extraction in order to both confirm the reliability of each finding and avoid missing important motifs. It is also useful to optimize the sensitivity of software with a series of different parameter settings.

Availability: Melina is available at http://www.hgc.ims.u-tokyo.ac.jp/Melina/

Contact: knakai@ims.u-tokyo.ac.jp

* To whom correspondence should be addressed.
AltAVisT: Comparing alternative multiple sequence alignments
Authors: Morgenstern Burkhard , Goel Sachin , Sczyrba Alexander , Dress Andreas
Published: February 2003

Summary: We introduce a WWW-based tool that is able to compare two alternative multiple alignments of a given sequence set. Regions where both alignments coincide are color-coded to visualize the local agreement between the two alignments and to identify those regions that can be considered to be reliably aligned.

Availability: http://bibiserv.techfak.uni-bielefeld.de/altavist/

Contact: burkhard@TechFak.Uni-Bielefeld.DE

* To whom correspondence should be addressed.
Multitasking in Replication Is Common among Geminiviruses
Authors: Preiss Werner , Jeske Holger
Published: February 2003

Geminiviruses package single-stranded circular DNA and replicate via double-stranded DNA intermediates. During the past decade, increasing evidence has led to the general acceptance that their replication follows a rolling-circle replication mechanism like bacteriophages with single-stranded DNA. In a recent study, we showed that this is also true forAbutilon mosaic geminivirus(AbMV), but that this particular virus may also use a recombination-dependent replication (RDR) route in analogy to T4 phages. Because AbMV is a special case, since it has been propagated on ornamental plants for more than a hundred years, it was interesting to determine whether RDR is common among other geminiviruses. We analyzed geminiviruses from different genera and geographic origins by using BND cellulose chromatography in combination with an improved high resolution two-dimensional gel electrophoresis, and we conclude that multitasking in replication is widespread, at least forAfrican cassava mosaic,Beet curly top,Tomato golden mosaic, andTomato yellow leaf curl virus.
Origin and Evolution of Japanese Encephalitis Virus in Southeast Asia
Authors: Solomon Tom , Ni Haolin , Beasley David W. C. , Ekkelenkamp Miquel , Cardosa Mary Jane , Barrett Alan D. T.
Published: February 2003

Since it emerged in Japan in the 1870s, Japanese encephalitis has spread across Asia and has become the most important cause of epidemic encephalitis worldwide. Four genotypes of Japanese encephalitis virus (JEV) are presently recognized (representatives of genotypes I to III have been fully sequenced), but its origin is not known. We have determined the complete nucleotide and amino acid sequence of a genotype IV Indonesian isolate (JKT6468) which represents the oldest lineage, compared it with other fully sequenced genomes, and examined the geographical distribution of all known isolates. JKT6468 was the least similar, with nucleotide divergence ranging from 17.4 to 19.6% and amino acid divergence ranging from 4.7 to 6.5%. It included an unusual series of amino acids at the carboxy terminus of the core protein unlike that seen in other JEV strains. Three signature amino acids in the envelope protein (including E327 Leu→Thr/Ser on the exposed lateral surface of the putative receptor binding domain) distinguished genotype IV strains from more recent genotypes. Analysis of all 290 JEV isolates for which sequence data are available showed that the Indonesia-Malaysia region has all genotypes of JEV circulating, whereas only more recent genotypes circulate in other areas (
P
< 0.0001). These results suggest that JEV originated from its ancestral virus in the Indonesia-Malaysia region and evolved there into the different genotypes which then spread across Asia. Our data, together with recent evidence on the origins of other emerging viruses, including dengue virus and Nipah virus, imply that tropical southeast Asia may be an important zone for emerging pathogens.
Tat-Neutralizing Antibodies in Vaccinated Macaques
Authors: Tikhonov Ilia , Ruckwardt Tracy J. , Hatfield Glen S. , Pauza C. David
Published: February 2003

The human immunodeficiency virus Tat protein is essential for virus replication and is a candidate vaccine antigen. Macaques immunized with Tat or chemically modified Tat toxoid having the same clade B sequence developed strong antibody responses. We compared these antisera for their abilities to recognize diverse Tat sequences. An overlapping peptide array covering three clade B and two clade C Tat sequences was constructed to help identify reactive linear epitopes. Sera from Tat-immunized macaques were broadly cross-reactive with clade B and clade C sequences but recognized a clade B-specific epitope in the basic domain. Sera from Tat toxoid-immunized macaques had a more restricted pattern of recognition, reacting mainly with clade B and with only one clade B basic domain sequence, which included the rare amino acids RPPQ at positions 57 to 60. Monoclonal antibodies against the amino terminus or the domain RPPQ sequence blocked Tat uptake into T cells and neutralized Tat in a cell-based transactivation assay. Macaques immunized with Tat or Tat toxoid proteins varied in their responses to minor epitopes, but all developed a strong response to the amino terminus, and antisera were capable of neutralizing Tat in a transactivation assay.
Association of Polymorphisms of the Apolipoprotein(a) Gene With Lipoprotein(a) Levels and Myocardial Infarction
Authors: Holmer Stephan R. , Hengstenberg Christian , Kraft Hans-Georg , Mayer Björn , Pöll Melanie , Kürzinger Susanne , Fischer Marcus , Löwel Hannelore , Klein Gernot , Riegger Günter A.J. , Schunkert Heribert
Published: February 2003

Background—

Serum lipoprotein(a) [Lp(a)] concentration is largely determined by variability at the apolipoprotein(a) gene locus. Most prominent effects relate to polymorphisms in the promoter (a pentanucleotide [PN] repeat) and coding regions (a kringle IV [K4] repeat), the latter of which also affects Lp(a) particle size. The impact of these polymorphisms on cardiovascular risk is poorly understood.

Methods and Results—

We studied both polymorphisms and Lp(a) levels in 834 registry-based myocardial infarction (MI) patients (38% women) and 1548 population-based controls. Lp(a) concentrations were inversely related with the numbers of K4 and PN repeats. However, the effect of the PN polymorphism was restricted to subjects producing small Lp(a) particles (≤8 PN 66.1 mg/dL versus >8 PN 8.7 mg/dL;
P
<0.0001). The odds to present with MI were elevated in individuals producing small Lp(a) particles (≤22 K4 repeats; OR 1.47 for men and 1.69 for women;
P
<
0.002) and in women with ≤8 PN repeats (OR 1.46,
P
=0.009). Interestingly, in women, the frequent haplotype with ≤8 PN and ≤22 K4 repeats, which is related to high levels of small Lp(a) particles, resulted in an elevated OR for MI (1.79;
P
=0.01) independently of Lp(a) serum concentration.

Conclusions—

The K4 and PN repeat polymorphisms largely explain the high variability of serum Lp(a) levels. A haplotype with ≤8 PN and ≤22 K4 repeats is characterized by high concentrations of small Lp(a) particles. Our observation that this haplotype was associated with MI independently of Lp(a) serum levels may suggest that Lp(a) particle size in addition to its concentration may modulate MI risk in women.
Effect of Epicardial or Biventricular Pacing to Prolong QT Interval and Increase Transmural Dispersion of Repolarization
Authors: Medina-Ravell Victor A. , Lankipalli Ramarao S. , Yan Gan-Xin , Antzelevitch Charles , Medina-Malpica Napoleon A. , Medina-Malpica Otto A. , Droogan Christopher , Kowey Peter R.
Published: February 2003

Background—

The present study examined pacing site–dependent changes in QT interval and transmural dispersion of repolarization (TDR) and their potential role in the development of torsade de pointes (TdP).

Methods and Results—

In humans, the QT interval, JT interval, and TDR were measured in 29 patients with heart failure during right ventricular endocardial pacing (RVEndoP), biventricular pacing (BiVP), and left ventricular epicardial pacing (LVEpiP). In animal experiments, pacing site–dependent changes in ventricular repolarization were examined with a rabbit left ventricular wedge preparation in which action potentials from endocardium and epicardium could be simultaneously recorded with a transmural ECG. In humans, LVEpiP and BiVP led to significant QT and JT prolongation. LVEpiP also enhanced TDR. Frequent R-on-T extrasystoles generated by BiVP and LVEpiP but completely inhibited by RVEndoP occurred in 4 patients, of whom 1 developed multiple episodes of nonsustained polymorphic ventricular tachycardia and another suffered incessant TdP. In rabbit experiments, switching from endocardial to epicardial pacing produced a net increase in QT interval and TDR by 17±5 and 22±5 ms, respectively (n=6,
P
<0.01), without parallel increases in ventricular transmembrane action potential durations. Epicardial pacing facilitated transmural propagation of early afterdepolarization, leading to the development of R-on-T extrasystoles and TdP in the presence of action potential duration–prolonging agents.

Conclusions—

LVEpiP and BiVP increase QT, JT, and TDR by altering the transmural sequence of activation of the intrinsically heterogeneous ventricular myocardium. Our data suggest that the resultant exaggeration of arrhythmic substrates can lead to the development of TdP in a subset of patients.
Mitochondrial ferritin expression in erythroid cells from patients with sideroblastic anemia
Authors: Cazzola Mario , Invernizzi Rosangela , Bergamaschi Gaetano , Levi Sonia , Corsi Barbara , Travaglino Erica , Rolandi Valeria , Biasiotto Giorgio , Drysdale Jim , Arosio Paolo
Published: February 2003

The sideroblastic anemias are characterized by ring sideroblasts, that is, red cell precursors with mitochondrial iron accumulation. We therefore studied the expression of mitochondrial ferritin (MtF) in these conditions. Erythroid cells from 13 patients with refractory anemia with ring sideroblasts (RARS) and 3 patients with X-linked sideroblastic anemia (XLSA) were analyzed for the distribution of cytoplasmic H ferritin (HF) and MtF using immunocytochemical methods. We also studied 11 healthy controls, 5 patients with refractory anemia without ring sideroblasts (RA), and 7 patients with RA with excess of blasts (RAEB). About one fourth of normal immature red cells, mostly proerythroblasts and basophilic erythroblasts, showed diffuse cytoplasmic positivity for HF, but very few were positive for MtF (0%-10%). Similar patterns were found in anemic patients without ring sideroblasts. In contrast, many erythroblasts from patients with sideroblastic anemia (82%-90% in XLSA and 36%-84% in RARS) were positive for MtF, which regularly appeared as granules ringing the nucleus. Double immunocytochemical staining confirmed the different cellular distribution of HF and MtF. There was a highly significant relationship between the percentage of MtF+ erythroblasts and that of ring sideroblasts (SpearmanR = 0.90; P < .0001). Reverse transcription-polymerase chain reaction studies demonstrated the presence of MtF mRNA in circulating reticulocytes of 2 patients with XLSA but not in controls. These findings suggest that most of the iron deposited in perinuclear mitochondria of ring sideroblasts is present in the form of MtF and that this latter might be a specific marker of sideroblastic anemia.
The human herpes virus 8–encoded viral FLICE inhibitory protein protects against growth factor withdrawal–induced apoptosis via NF-κB activation
Authors: Sun Qinmiao , Matta Hittu , Chaudhary Preet M.
Published: February 2003

The human herpes virus 8 (HHV8)–encoded viral FLICE (Fas-associating protein with death domain–like interleukin-1–converting enzyme) inhibitory protein (vFLIP) is believed to protect cells against death receptor–mediated apoptosis. In the present study we demonstrate that expression of HHV8 vFLIP in a growth factor–dependent TF-1 leukemia cell line protects against growth factor withdrawal–induced apoptosis. Unlike vector-expressing cells, those expressing HHV8 vFLIP maintain their mitochondrial membrane potential upon withdrawal from growth factor and also exhibit a block in the activation of caspases. The protective effect of HHV8 vFLIP is associated with its ability to activate the nuclear factor–κ B (NF-κB) pathway and is missing in the vFLIP encoded by equine herpes virus 2 that lacks this activity. Inhibition of the NF-κB pathway by IκB superrepressor, lactacystin, MG132, arsenic trioxide, and phenylarsine oxide reverse the protection against growth factor withdrawal–induced apoptosis conferred by HHV8 vFLIP. HHV8 vFLIP up-regulates the expression of Bcl-xL, an antiapoptotic member of the Bcl2 family, which is a known target of the NF-κB pathway. Collectively, the above results suggest that HHV8 vFLIP–induced NF-κB activation may contribute to cellular transformation seen in association with HHV8 infection by preventing the apoptosis of cells destined to die because of growth factor deprivation.
CCR4 versus CCR10 in human cutaneous TH lymphocyte trafficking
Authors: Soler Dulce , Humphreys Tricia L. , Spinola Stanley M. , Campbell James J.
Published: February 2003

The chemokine receptors (CCRs) CCR4 and CCR10, and the cutaneous lymphocyte antigen (CLA), have each been proposed as critical mediators of skin-specific TH lymphocyte homing in mice and humans. CLA initiates skin homing by mediating E-selectin–dependent tethering and rolling within cutaneous venules, but the specific roles of CCR4 and CCR10 are unclear. We have generated an antihuman CCR10 monoclonal antibody (mAb; 1B5) to illuminate the individual contributions of these molecules. This mAb allows us to compare CCR10, CCR4, and CLA expression within human THpopulations. The mAb 1B5 recognizes functional CCR10 expression, as chemotactic responsiveness to cutaneous T-cell–attracting chemokine (CTACK)/CCL27 (a CCR10 ligand) parallels the staining of TH subsets. We find CCR10 expressed by only a minority (approximately 30%) of blood-borne, skin-homing (CLA+/CCR4+) TH cells. However, essentially all members of the relatively small “effector” (CLA+/CCR4+/CD27−/CCR7−) skin-homing TH population express CCR10. Most skin-infiltrating lymphocytes in allergic delayed-type hypersensitivity (DTH) and bacterial chancroid skin lesions express both CCR4 and CLA, but only about 10% express CCR10. This suggests for the 2 models of TH skin homing studied here that CCR10+ TH cells have no advantage over other CLA+/CCR4+ TH cells in homing to cutaneous sites. We conclude that the skin-homing THcompartment is itself divided into distinct subpopulations, the smaller of which expresses both CCR4 and CCR10, and the larger of which expresses only CCR4. Thus, CCR10 is unlikely to be necessary for cutaneous homing of TH cells in the models studied here. CCR10 may instead play a role in the movement of specialized “effector” cutaneous TH cells to and/or within epidermal microenvironments.
Persistence of malignant hematopoietic progenitors in chronic myelogenous leukemia patients in complete cytogenetic remission following imatinib mesylate treatment
Authors: Bhatia Ravi , Holtz Melissa , Niu Ning , Gray Rachel , Snyder David S. , Sawyers Charles L. , Arber Daniel A. , Slovak Marilyn L. , Forman Stephen J.
Published: February 2003

The BCR/ABL tyrosine kinase inhibitor imatinib mesylate (Gleevec, STI571; Novartis, Basel, Switzerland) has shown remarkable efficacy in the treatment of chronic myelogenous leukemia (CML), with a high proportion of patients achieving complete cytogenetic responses (CCRs). However, it is not clear whether remissions will be durable and whether imatinib mesylate can eliminate the malignant primitive progenitors in which the disease arises. We investigated whether residual BCR/ABL+ hematopoietic progenitors were present in patients who achieved CCRs with imatinib mesylate treatment. CD34+ progenitor cells were selected from bone marrow mononuclear cells (MNCs) and analyzed for the presence of the BCR/ABL fusion gene by fluorescence in situ hybridization (FISH). CD34+ cells were also plated in committed progenitor (colony-forming cell, or CFC) and primitive progenitor (long-term bone marrow culture-initiating cell, or LTCIC) cultures and resulting colonies analyzed for the presence of BCR/ABL+ cells by FISH. Using these assays, residual BCR/ABL+ progenitors were detected in all patients studied. Quantitative reverse transcriptase–polymerase chain reaction (RT-PCR) analysis demonstrated increased levels of BCR/ABL mRNA in CD34+ cells compared with total MNCs. Evaluation of samples collected at different time points demonstrated persistence of BCR/ABL+ progenitors despite continued treatment with imatinib mesylate. Our results indicate that inhibition of BCR/ABL tyrosine kinase activity by imatinib mesylate does not eliminate malignant primitive progenitors in CML patients. Patients in CCR with imatinib mesylate treatment need to be followed carefully to assess for risk of relapse.
Optimal harvesting policies for a generalized Gordon–Schaefer model in randomly varying environment
Authors: Shah M. A. , Sharma Usha
Published: February 2003

A non‐linear stochastic model has been proposed and analized for fish harvesting. The model encompasses Gordon–Schaefer model and Pella–Tomlinson model that have been used in the study of extensive data on baleen whales, harp seals and Gulf of St. Lawrence cod. It has been established that the harvesting of those species is more profitable in terms of biomass for which data supports α>2, as compared to that for which α⩽2, where α is general index in the model:

Copyright © 2003 John Wiley & Sons, Ltd.