bluuebunny/crossref_metadata_2025 huggingface dataset:
Defect equilibria in fluorite structure crystals
Authors: Tallant D. R. , Moore D. S. , Wright J. C.
Published: February 2003

The defect distribution of charge compensated sites in Er3+:CaF2 crystals has been measured by laser spectroscopy over a concentration range from 10−4 to 1.0 mol %. The measurements show the transition from the low concentration region, where the site distribution is described by simple pairing of Er3+ and fluoride interstitial ions to a high concentration region dominated by clustering of the simple pairs. The simple pairs undergo a decrease in the absolute concentration in this region in direct conflict with all equilibrium models of solid state defect equilibria. A model is proposed which describes the measured site distribution and also explains the anomalous behavior observed in many other experiments. The model describes the distribution by requiring the cation equilibria to be frozen at a high temperature and the fluoride equilibria at a low temperature, in agreement with the temperature dependence of their mobilities. The excess fluoride interstitial ions are then ’’gettered’’ by the clustered pairs forcing dissociation of the simple pairs.
Absolute rate constants for the reaction of O3(P) atoms with allene, 1,3-butadiene, and vinyl methyl ether over the temperature range 297–439 °K
Authors: Atkinson R. , Pitts J. N.
Published: February 2003

Absolute rate constants for the reaction of O(3P) atoms with allene, 1,3-butadiene, and vinyl methyl ether have been determined over the temperature range 297–439 °K using a flash photolysis–NO2 chemiluminescence technique. The Arrhenius expressions obtained were k2(allene) =2.04×10−11 e−(1755±200)/RT cm3 molecule−1 sec−1, k2(1,3-butadiene) =2.26×10−11 e−(105±200)/RT cm3 molecule−1 sec−1, k2(vinyl methyl ether) =6.32×10−12 e(75±200)/RT cm3 molecule−1 sec−1, with room temperature rate constants of (1.07±0.11) ×10−12 cm3 molecule−1 sec−1, (1.94±0.19) ×10−11 cm3 molecule−1 sec−1 and (7.14±0.71) ×10−12 cm3 molecule−1 sec−1 for allene, 1,3-butadiene, and vinyl methyl ether, respectively.
The nonexponential character of the Zeeman relaxation of reorienting methyl groups in solids
Authors: Wind R. A. , Emid S. , Pourquié J. F. J. M. , Smidt J.
Published: February 2003

If the rapid reorientations of methyl groups in solids are the dominant relaxation mechanisms, it is theoretically found that the Zeeman system is dynamically coupled to the so-called rotational polarization system, resulting in a nonexponential Zeeman relaxation. Though this result has been confirmed experimentally, in many samples within measuring error an exponential Zeeman relaxation has been observed. In order to decide whether or not this is contradictory to the theory the degree of nonexponentiality has been further investigated in this paper. It is shown that the nonexponential character depends stronly on the following parameters: (i) the way in which the spin system is prepared for the observation of the Zeeman relaxation, (ii) the number of protons not belonging to the methyl groups, (iii) the relaxation due to the intermethyl dipolar interactions, and (iv) the temperature. It is found that under specific conditions the observed relaxation can become almost exponential. The corresponding time constant, however, can differ considerably from that predicted by the usual spin temperature theory. Therefore, the interpretation of the experiments with this theory can lead to incorrect values of the different parameters characterizing the relaxation process. The various results have been illustrated with experiments on polycrystalline samples of 2,6-dimethylphenol, methylcyanide, 2-methylpiperazine, and 1,4-dimethoxy-2,6-dimethylbenzene.
Correlations at a fluid surface
Authors: Sullivan D. E. , Stell G.
Published: February 2003

A new formalism is developed for the statistical mechanical description of fluid surfaces that enables the interfacial density profile and the density profile in the vicinity of a wall to be treated in a parallel fashion. The work facilitates a direct comparison between interfacial and wall-fluid phenomena and immediately suggests a new approximation procedure for computing the interfacial density. As an illustrative example, the approach is applied to a fluid of sticky spheres, treated in the bulk according to the Percus–Yevick approximation. The results are of sufficient analytic simplicity in our approximation to permit a closed-form representation of the density profile in the vicinity of a smooth hard wall, and an interfacial profile given by a simple quadrature over an analytic function.
Resonance line shapes in the Rydberg spectra of large molecules
Authors: Druger S. D.
Published: February 2003

The theory of line shapes in absorption to nearly degenerate states of large molecules is re-examined by relaxing the assumptions of the Bixon–Jortner model. The use of a single interaction strength to describe the coupling of a given sparse state to all members of the quasicontinuum of dissipative states is shown to produce an absorption intensity that vanishes at an energy determined independently of the assumed zero-order quasicontinuum level spacings. A more general theory is developed. The variation in coupling strength to nearby quasicontinuum states is shown to yield an absorption intensity that fails to vanish near resonance, and sometimes to suppress the characteristic features of the antiresonance line shape expected on the basis of simpler models, thus accounting for the scarcity of observable antiresonances and for some features of the naphthalene absorption spectrum. A new interference effect, involving the coalescence of neighboring absorption peaks into a single narrowed peak, is demonstrated.
Coupling-strength incoherence and the absorption line shape of an isolated resonance in a large molecule
Authors: Druger S. D.
Published: February 2003

A generalization of the Fano line shape formula is obtained for a single sparse state coupled to a quasicontinuum of discrete states that carry oscillator strength. The qualitative effects of coupling strength incoherence on the observed line shape are examined. The Rydberg–valence antiresonance line shape is examined in terms of this model, and early treatments of the antiresonance are shown inadequate as a consequence of their assumption that the Fano line shape parameters are energy independent.
Electron spin resonance of Cu2+ in strontium acetate hemihydrate
Authors: Krishnan V. G.
Published: February 2003

Electron spin resonance (ESR) studies have been made on Cu2+ ion incorporated into the single crystals of strontium acetate hemihydrate. Only a single set of Cu2+ hyperfine lines are observed at all orientations of the magnetic field. From the inconsistency observed between the symmetry of the ESR spectra and the unit cell it is concluded that the Cu2+ ion enters the lattice interstitially.
Dipole moment derivatives and infrared intensities. III. Transferable polar tensors for fluorinated methanes
Authors: Newton James H. , Levine Robert A. , Person Willis B.
Published: February 2003

The atomic polar tensors for H and F atoms derived from the experimental values for the integrated infrared molar absorption coefficients for the fundamental vibrations of CH3F are used to predict the intensities of the fundamental vibrations of CF4, CF3H, and CH2F2. These predictions are compared with the values found by experimental measurements. In general, the agreement is quite good (the predicted values agree with the experimental values within a factor of 2, and often are much better), encouraging further investigation of these parameters for prediction of infrared intensities.
Sector rules for rotatory strength of low symmetry chromophores: Lactones, lactams, and peptides
Authors: Ong Edith C. , Cusachs L. Chopin , Weigang Oscar E.
Published: February 2003

A sector rule is developed for optically active lactones and lactams through the application of perturbation theory. The sign and qualitative magnitude of the 220 nm circular dichroism can be predicted by observing the placement of polarizable nonpolar substituents about the chromophore group. The perturbation treatment shows the effect on a sector rule of adding electric dipole allowedness to the zero-order electric quadrupole allowedness of the carboxylate ion chromophore from which the lactone or lactam derives. The observed difference in sign of circular dichroism between similar lactams and lactones has significant implications for the theoretical assignment of the long wavelength n–π* transition(s) in peptides. The peptide (lactam) transition is concluded to resemble most nearly the 1A2←1A1(n–π*) transition of the carboxylate ion. A transition resembling 1B1←1A1(n–π*) in carboxylate ion is expected at only slightly shorter wavelengths. A reversed order in wavelength is expected for the corresponding transitions in lactones.
Decomposition theory of chemical reactions
Authors: Rabitz Suzanne , Rabitz Herschel
Published: February 2003

The coupled channel formulation is utilized to variationally derive approximate closed-form expressions for reactive transition matrices. In conjunction with this effort it is shown that the effect of differing choices of possible channel coupling arrays becomes important when incomplete channel basis sets are used. Generalized techniques are employed to derive the necessary variational principles. The inherent coupling of the Green’s functions in the resulting expression for the transition matrix makes inclusion of continuum states in the basis sets less crucial. The practical viability of this formulation as a computational scheme for chemical systems is discussed.
Evaluation of the strain derivatives of electronic polarizabilities and dielectric constants of alkaline earth fluorides
Authors: Sharma J. C. , Sharma H. P. , Shanker Jai
Published: February 2003

A method recently developed for explaining the photoelastic behavior of alkali halides has been applied to evaluate the strain derivatives of electronic polarizabilities and dielectric constants of alkaline earth fluorides. The calculated values of the strain derivative of electronic polarizabilities present a reasonable agreement with experimental data. Values of the strain derivative of the electronic dielectric constants for CaF2, SrF2, and BaF2 calculated in the present study within the framework of Clausius–Mossotti theory are in agreement with the corresponding experimental values. The sensitivity of the results on the electronic polarizabilities of ions has been discussed.
EPR studies of VO2+ in single crystals of ZnSO4⋅7H2O and certain polycrystalline sulfates
Authors: Viswanath A. Kasi
Published: February 2003

EPR studies of vanadyl doped ZnSO4⋅7H2O are reported. Vanadyl is found to have fixed orientations in the lattice and there are two magnetically inequivalent complexes in the lattice. The angular variation of the spectra is studied in the crystallographic ab, bc, and ac planes. The principal values of g and A and the direction cosines which the principal axes make with the crystallographic axes are found. Vanadium enters the lattice substitutionally in the place of Zn2+ and gets bonded to five water molecules of the lattice to form a stable [VO(H2O)5]2+ complex. The results obtained from the EPR studies of the polycrystalline samples of vanadyl doped Mg(NH4)2(SO4)2 ⋅6H2O, K2SO4, and 3CdSO4⋅8H2O are also reported. The spectra are analyzed using a spin-Hamiltonian corresponding to tetragonal symmetry. In the optical absorption spectrum of vanadyl doped ZnSO4⋅7H2O two bands are observed in the visible region which are attributed to d–d transitions. The EPR results in conjunction with the optical results give the spin orbit coupling constant of vanadium. A semiempirical molecular orbital approach is used and the bonding parameters are estimated. The data reported in the literature for VO2+ doped crystals are taken and the bonding parameters are calculated. The EPR results are correlated with the bonding parameters. The observed changes in g and A are correlated to the ligand properties. The anisotropy in g is correlated to the ligand field strength. The isotropic contact term is related to the bonding coefficient β2. The deviations in β22 values from the expected values are explained by considering the delocalization of the unpaired electron on to the ligand orbitals. β12 value is found to indicate the delocalization in the σ system. A plot of κ against β12 gives a straight line.
Crossed molecular beam study of the endoergic reaction Hg+I2→HgI+I from threshold to 2.6 eV (c.m.)
Authors: Mayer T. M. , Wilcomb B. E. , Bernstein R. B.
Published: February 2003

The endoergic reaction Hg+I2→HgI+I−1.15 eV has been studied by the crossed molecular beam technique over a range of average relative translational energy, ?tr, from 0.9 to 2.6 eV (c.m.). A supersonic seeded beam of Hg in H2, of variable Hg velocity, is crossed by a thermal beam of I2. In-plane angular distributions of the HgI product are measured as a function of ?tr, with an electron bombardment (EB) ionizer, mass filter detector. Center-of-mass (c.m.) product angular and recoil velocity distributions are deduced from the laboratory angular distributions by an iterative fitting procedure. The HgI angular distributions are bimodal, characteristic of a long-lived complex mechanism. The products’ recoil energy distribution is peaked at abnormally high E′tr. The average value, ?′tr, increases monotonically with ?tr. Reaction proceeds essentially at the thermodynamic threshold (i.e., with no intrinsic activation barrier), and the post-threshold excitation function is found to be of the form σR(Etr) ∝ (E−E0)s/Etr, where 1<s<2 and E0=1.15 eV. The reaction cross section σR(?tr) rises to a broad maximum at about 2 eV with a moderate decline at higher energies. A statistical–dynamical model of the reaction is developed which involves an orientation–averaged barrier (∼0.7 eV) to the formation of a long-lived complex, presumably IHgI, followed by decay of the complex, either to products or to reactants. The shape of the cross section function in the threshold region, the branching ratio for the decay of the complex, and the product translational energy distributions are strongly correlated with the existence of this barrier to complex formation. The decline in σR(?tr) at high energy is due to collision-induced dissociation of I2, and/or dissociation of product HgI molecules formed with internal excitation above 0.39 eV (the dissociation limit of HgI), both processes with a threshold of 1.54 eV. The statistical–dynamical calculations account for the main qualitative features of the reaction with a minimum number of assumptions. However, the present results are not entirely unequivocal because of a possible systematic experimental bias associated with decreased EB detection efficiency of internally excited HgI molecules.
Vibrational relaxation of water vapor
Authors: Finzi Jack , Hovis Floyd E. , Panfilov Victor N. , Hess Peter , Moore C. Bradley
Published: February 2003

The method of laser-excited vibrational fluorescence is used to measure the vibrational relaxation rates of H2 18O in collisions with H2 18O, Ar, N2, and O2. Pumping of various vibration–rotation lines of the ν1 and ν3 stretching levels with a tunable infrared laser leads to the same measured rate constants. In pure H2 18O the stretching levels are found to relax together with a rate constant of 2.2×10−11 cm3 molecule−1 sec−1, the bend overtone relaxes with a rate constant of 9.1×10−11 cm3 molecule−1 sec−1, and the bend fundamental relaxes with a rate constant between 5×10−11 and 9×10−11 cm3 molecule−1 sec−1. Relative intensity measurements show that the dominant relaxation pathway is V→V transfer from the stretching vibrations to the v2=2 bending level followed by stepwise V→T, R relaxation to v2=1 and then v2=0.
Lifetimes of the x 1Σ−g and y 1Πg states of N2
Authors: Hummer Charles R. , Burns Donal J.
Published: February 2003

The lifetimes of the x 1Σ−g and y 1Πg states have been measured by monitoring emissions from the Fifth Positive system and Kaplan’s Second system in N2. The x 1Σ−g state is found to have a lifetime of 23.1±1.1 nsec, while that of the y 1Πg is 19.9±0.4 nsec.
Metastable states of small rare gas crystallites
Authors: Etters R. D. , Danilowicz R. , Kaelberer J.
Published: February 2003

Metastable states of rare gas crystallites containing N atoms are investigated for N=5,6,7, and 8. In particular, the stability, structures, structural transformation, and binding energy versus temperature are determined using a Monte Carlo method. The square pyramid isomer for N=5 is found to be unstable at any finite temperature. The other metastable isomers are all found to make spontaneous transitions to the ground state if the temperature is greater than about one half that of meltings. Comparisons with previous work are also made.
Recovery of the long range potential in BeAr+ by potential inversion methods
Authors: Goble James H. , Hartman Dennis C. , Winn John S.
Published: February 2003

The results of the potential inversion methods of Dunham, Simons, Parr, and Finlan, Thakkar, Huffaker, and the Padé approximate technique are presented for the X 2Σ+ state of BeAr+. The method of Thakker is shown to yield reasonable behavior at long range, leading to an ion-induced dipole interaction. A simple model potential is shown to provide a good description of the bonding in both the ground state and the A 2Πr state. The effective nuclear charge of Be+ is found to be 1.29 in the X state and 1.88 in the A state. Integration of the various potentials to determine the vibrational eigenvalues shows the superiority of the Thakkar and Huffaker methods and shows the three parameter model potential to be a very good representation of the true potential.
Anisotropic density fluctuations in argon at different densities: Far infrared measurements and molecular dynamic calculations
Authors: Frenkel D. , van der Elsken J.
Published: February 2003

From measurements of the pure rotational lines of a linear probe molecule dissolved in a simple fluid one can deduce the power spectra of the anisotropic density fluctuations of l=1 and l=2 symmetry of the fluid. The power spectra thus obtained for argon at various densities are compared with the results of molecular dynamics calculations and with the approximate power spectra which can be calculated starting from neutron-scattering data. The density dependence of the high frequency components of the l=1 power spectrum and of the zero frequency component of the l=2 power spectrum give a strong characteristic of the dense fluid.
An electron-gas study of the bonding, structure, and octahedral ligand-field splitting in transition-metal halides
Authors: Clugston Michael J. , Gordon Roy G.
Published: February 2003

We present a discussion of the structure and the ligand-field splitting parameter 10Dq for some d1 titanium (III) halides. Our approach is based on an ionic model allowing for the inclusion both of electrostatic and of non-Coulombic repulsive contributions. The point-Coulombic forces are treated exactly using the Madelung constant for each specific crystal. Only the metal–ligand and ligand–ligand short-range repulsions are taken to be of importance, and are calculated using the electron-gas model. Our results show that for the chloride the model is poor and hence that covalency is essential for understanding the heavier halides. For the fluoride systems, however, we obtain values for the bond distances, and the lattice energy for the trifluoride, which are accurate within five per cent of experiment. As previous approaches have shown, we find the negative sign for 10Dq when only the purely electrostatic interaction is included. We show in addition that overlap repulsion provides the major part of the balance which corrects the ordering of the eg and t2g states. We conclude that for fluorides at least the ionic model is an excellent starting-point for an understanding of their properties.
H(2s) and H(2p) branching ratio in the photodissociation of H2 near threshold
Authors: Mentall J. E. , Guyon P. M.
Published: February 2003

The excitation spectrum for producing Lyman-α fluorescence by photodissociating H2 has been obtained with 0.12 Å bandwidth in the dissociation threshold region. At 839 Å, the peak in the fluorescence cross section, one observes Lyman-α emission from several continuums and from the J=1 and J=2 predissociated rotational levels of the D 1Π+u(v′=3) state. At this wavelength the branching ratio σ (2s)/[σ (2s)+σ (2p)] was obtained using a quenching field method. It was determined that 57% of the excited atoms are produced in the metastable 2 2S1/2 state. From a study of the fluorescence signal versus pressure a cross section of 0.9×10−14 cm2 was derived from the chemi-ionization reaction H2+H(2s) →H+3+e−.
Raman study of the ferroelectric phase transition in PbHPO4 and PbHAsO4
Authors: Lavren?i? B. B. , Petzelt J.
Published: February 2003

The Raman spectra of PbHPO4 and PbHAsO in the para- and ferroelectric phases and also PbDAsO4 (room temperature only) have been measured. Mode assignment of most predicted modes has been made. Weak underdamped soft modes have been observed below 100 cm−1 in the ferroelectric phase of both hydrogen compounds which confirms the role of the proton tunnelling in the double minimum potential. PbDAsO4 seems not to be isomorphous to PbHAsO4 at room temperature.
Monopole effects on electronic excitation interactions between large molecules. I. Application to energy transfer in chlorophylls
Authors: Chang Jane C.
Published: February 2003

The transition monopole theory of electronic excitation interaction is described and applied to the theory of resonance transfer for chlorophyll molecules. It is then compared with analogous results based on transition dipole theory. The correction to the Förster theory of resonance transfer is evaluated in various geometries for the case of short range transfer. The enhancement or reduction factor for the transfer rate in various chlorophylls is of the order of two to one tenth for the range that we are interested in, i.e., 12–30 Å, and anisotropy of the transfer rate is greatly increased. A possible enhancement of the transfer rates in the case of forbidden transitions in porphin is discussed.
Ezrin Regulates E-Cadherin-dependent Adherens Junction Assembly through Rac1 Activation
Authors: Pujuguet Philippe , Del Maestro Laurence , Gautreau Alexis , Louvard Daniel , Arpin Monique
Published: February 2003

Ezrin, a membrane cytoskeleton linker, is involved in cellular functions, including epithelial cell morphogenesis and adhesion. A mutant form of ezrin, ezrin T567D, maintains the protein in an open conformation, which when expressed in Madin-Darby canine kidney cells causes extensive formation of lamellipodia and altered cell-cell contacts at low cell density. Furthermore, these cells do not form tubules when grown in a collagen type I matrix. While measuring the activity of Rho family GTPases, we found that Rac1, but not RhoA or Cdc 42, is activated in ezrin T567D-expressing cells, compared with cells expressing wild-type ezrin. Together with Rac1 activation, we observed an accumulation of E-cadherin in intracellular compartments and a concomitant decrease in the level of E-cadherin present at the plasma membrane. This effect could be reversed with a dominant negative form of Rac1, N17Rac1. We show that after a calcium switch, the delivery of E-cadherin from an internalized pool to the plasma membrane is greatly delayed in ezrin T567D-producing cells. In confluent cells, ezrin T567D production decreases the rate of E-cadherin internalization. Our results identify a new role for ezrin in cell adhesion through the activation of the GTPase Rac1 and the trafficking of E-cadherin to the plasma membrane.
Spindle Formation inAspergillusIs Coupled to Tubulin Movement into the Nucleus
Authors: Ovechkina Yulia , Maddox Paul , Oakley C. Elizabeth , Xiang Xin , Osmani Stephen A. , Salmon Edward D. , Oakley Berl R.
Published: February 2003

In many important organisms, including many algae and most fungi, the nuclear envelope does not disassemble during mitosis. This fact raises the possibility that mitotic onset and/or exit might be regulated, in part, by movement of important mitotic proteins into and out of the nucleoplasm. We have used two methods to determine whether tubulin levels in the nucleoplasm are regulated in the fungus Aspergillus nidulans. First, we have used benomyl to disassemble microtubules and create a pool of free tubulin that can be readily observed by immunofluorescence. We find that tubulin is substantially excluded from interphase nuclei, but is present in mitotic nuclei. Second, we have observed a green fluorescent protein/α-tubulin fusion in living cells by time-lapse spinning-disk confocal microscopy. We find that tubulin is excluded from interphase nuclei, enters the nucleus seconds before the mitotic spindle begins to form, and is removed from the nucleoplasm during the M-to-G1transition. Our data indicate that regulation of intranuclear tubulin levels plays an important, perhaps essential, role in the control of mitotic spindle formation in A. nidulans. They suggest that regulation of protein movement into the nucleoplasm may be important for regulating mitotic onset in organisms with intranuclear mitosis.
Constriction and Dnm1p Recruitment Are Distinct Processes in Mitochondrial Fission
Authors: Legesse-Miller Aster , Massol Ramiro H. , Kirchhausen Tom
Published: February 2003

Mitochondria undergo cycles of fusion and fission crucial for organelle homeostasis. Fission is regulated partially by recruitment of the large GTPase Dnm1p to the outer mitochondrial membrane. Using three-dimensional time-lapse fluorescence imaging of Saccharomyces cerevisiae cells, we found that Dnm1p-EGFP appears and disappears at “hot spots” along mitochondrial tubes. It forms patches that convert rapidly into different shapes regardless of whether mitochondrial fission ensues or not. Moreover, the thickness of the mitochondrial matrix displays frequent temporal fluctuations apparently unrelated to fission or to recruitment of Dnm1p-EGFP. These results suggest that mitochondrial fission requires coordination of at least two distinct processes.
Discovering well-ordered folding patterns in nucleotide sequences
Authors: Le Shu-Yun , Chen Jih-H. , Konings Danielle , Maizel Jacob V.
Published: February 2003

Motivation: Growing evidence demonstrates that local well-ordered structures are closely correlated with cis-acting elements in the post-transcriptional regulation of gene expression. The prediction of a well-ordered folding sequence (WFS) in genomic sequences is very helpful in the determination of local RNA elements with structure-dependent functions in mRNAs.

Results: In this study, the quality of local WFS is assessed by the energy difference (Ediff) between the free energies of the global minimal structure folded in the segment and its corresponding optimal restrained structure (ORS). The ORS is an optimal structure under the condition in which none of the base-pairs in the global minimal structure is allowed to form. Those WFSs in HIV-1 mRNA, various ferritin mRNAs and genomic sequences containing let-7 RNA gene were searched by a novel method, ed_scan. Our results indicate that the detected WFSs are coincident with known Rev response element in HIV-1 mRNA, iron-responsive elements in ferritin mRNAs and small let-7 RNAs in Caenorhabditis elegans, Caenorhabditis briggsae and Drosophila melanogaster genomic sequences. Statistical significance of the WFS is addressed by a quantitative measure Zscre that is a z-score of Ediff and extensive random simulations. We suggest that WFSs with high statistical significance have structural roles involving their sequence information.

Availability: The source code of ed_scan is available via anonymous ftp as ftp://ftp.ncifcrf.gov/pub/users/shuyun/scan/ed_scan.tar.

Contact: shuyun@orleans.ncifcrf.gov

* To whom correspondence should be addressed.
FORRepeats: detects repeats on entire chromosomes and between genomes
Authors: Lefebvre A. , Lecroq T. , Dauchel H. , Alexandre J.
Published: February 2003

Motivation: As more and more whole genomes are available, there is a need for new methods to compare large sequences and transfer biological knowledge from annotated genomes to related new ones. BLAST is not suitable to compare multimegabase DNA sequences. MegaBLAST is designed to compare closely related large sequences. Some tools to detect repeats in large sequences have already been developed such as MUMmer or REPuter. They also have time or space restrictions. Moreover, in terms of applications, REPuter only computes repeats and MUMmer works better with related genomes.

Results: We present a heuristic method, named FORRepeats, which is based on a novel data structure called factor oracle. In the first step it detects exact repeats in large sequences. Then, in the second step, it computes approximate repeats and performs pairwise comparison. We compared its computational characteristics with BLAST and REPuter. Results demonstrate that it is fast and space economical. We show FORRepeats ability to perform intra-genomic comparison and to detect repeated DNA sequences in the complete genome of the model plant Arabidopsis thaliana.

Availability: see contact

Contact: arnaud.lefebvre@univ-rouen.fr

* To whom correspondence should be addressed.
‘Hybrid Protein Model’ for optimally defining 3D protein structure fragments
Authors: de Brevern A.G. , Hazout S.
Published: February 2003

Motivation: Our aim is to develop a process that automatically defines a repertory of contiguous 3D protein structure fragments and can be used in homology modeling. We present here improvements to the method we introduced previously: the ‘hybrid protein model’ (de Brevern and Hazout, Theor. Chem. Acc., 106, 36–47, (2001)) The hybrid protein learns a non-redundant databank encoded in a structural alphabet composed of 16 Protein Blocks (PBs; de Brevern et al., Proteins, 41, 271–287, (2000)). Every local fold is learned by looking for the most similar pattern present in the hybrid protein and modifying it slightly. Finally each position corresponds to a cluster of similar 3D local folds.

Results: In this paper, we describe improvements to our method for building an optimal hybrid protein: (i) ‘baby training,’ which is defined as the introduction of large structure fragments and the progressive reduction in the size of training fragments; and (ii) the deletion of the redundant parts of the hybrid protein. This repertory of contiguous 3D protein structure fragments should be a useful tool for molecular modeling

Contact: debrevern@urbb.jussieu.fr

* To whom correspondence should be addressed.
SimiTri—visualizing similarity relationships for groups of
sequences
Authors: Parkinson John , Blaxter Mark
Published: February 2003

Global sequence comparisons between large datasets, such as those arising from genome projects, can be problematic to display and analyze. We have developed SimiTri, a Java/Perl-based application, which allows simultaneous display and analysis of relative similarity relationships of the dataset of interest to three different databases. We illustrate its utility in identifying Caenorhabditis elegans genes that have distinct patterns of phylogenetic affinity suggestive of horizontal gene transfer. SimiTri is freely downloadable from http://www.nematodes.org/SimiTri/ and the source code is freely available from the authors.

Contact: john.parkinson@ed.ac.uk

* To whom correspondence should be addressed.
KnowledgeEditor: a new tool for interactive modeling and analyzing
biological pathways based on microarray data
Authors: Toyoda Tetsuro , Konagaya Akihiko
Published: February 2003

Summary: KnowledgeEditor is a graphical workbench for biological experts to model biomolecular network graphs. The modeled network data are represented by SRML, and can be published via the internet with the help of plug-in module ‘GSCope’. KnowledgeEditor helps us to model and analyze biological pathways based on microarray data. It is possible to analyze the drawn networks by simulating up–down regulatory cascade in molecular interactions.

Availability: KnowledgeEditor is available at http://gscope.gsc.riken.go.jp/

Contact: bioinfo@gsc.riken.go.jp

* To whom correspondence should be addressed.
PCMA: fast and accurate multiple sequence alignment based on profile consistency
Authors: Pei Jimin , Sadreyev Ruslan , Grishin Nick V.
Published: February 2003

Summary: PCMA (profile consistency multiple sequence alignment) is a progressive multiple sequence alignment program that combines two different alignment strategies. Highly similar sequences are aligned in a fast way as in ClustalW, forming pre-aligned groups. The T-Coffee strategy is applied to align the relatively divergent groups based on profile–profile comparison and consistency. The scoring function for local alignments of pre-aligned groups is based on a novel profile–profile comparison method that is a generalization of the PSI-BLAST approach to profile–sequence comparison. PCMA balances speed and accuracy in a flexible way and is suitable for aligning large numbers of sequences.

Availability: PCMA is freely available for non-commercial use. Pre-compiled versions for several platforms can be downloaded from ftp://iole.swmed.edu/pub/PCMA/

Contact: jpei@mednet.swmed.edugrishin@chop.swmed.edu

* To whom correspondence should be addressed.
cMap: the comparative genetic map viewer
Authors: Fang Z. , Polacco M. , Chen S. , Schroeder S. , Hancock D. , Sanchez H. , Coe E.
Published: February 2003

Summary: cMap, a www comparative genetic map graphical utility, has a search capability and provides comparison of two genetic maps within or between species with dynamic links to data resources and text lists of the shared loci, running in a relational database environment. Currently, maps from three species (maize ‘Zea mays L.’, rice‘ Oryza sativa L.’, and sorghum ‘Sorghum bicolor L.’), representing over 13 800 distinct loci, are available for comparison at http://www.agron.missouri.edu/cMapDB/cMap.html

Availability: cMap source code is available without cost on request for non-commercial use.

Contact: fangz@missouri.edu

* To whom correspondence should be addressed.

† Current address: Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611, USA
Application possibilities of new AW/EP additive types in watermiscible metalworking fluids
Authors: Pedišić Lj. , Šarić M. , Bielen S.
Published: February 2003

Metalworking fluids are applied in metal working operations in order to decrease tribological effects and increase economy. Primarily they are used for cooling the tools and the workpieces and also for lubricating the cutting edges. The components of metalworking fluids responsible for decrease in friction are AW/EP additives. To comply with the very strong European legislation for human and environmental protection, important compounds for metalworking fluids formulation are reduced. Based on this, chlorinated paraffin, a widely used AW/EP additive, should be replaced with less harmful compounds. The application possibility of new types of AW/EP additives as chlorinated paraffin replacements is investigated in this paper. These additives are synthetic esters of carboxylic fatty acids, phosphoric and dithiophosphoric acid derivatives. Watermiscible metalworking fluids formulations are prepared with the new types of additives and examined at laboratory test machines–EP‐Four ball, Wear‐Four ball machine and Reichert balance machine.
Research on materials of piston and cylinder of water hydraulic pump
Authors: Huayong Yang , Jian Yang , Hua Zhou
Published: February 2003

In this paper, experiments were carried out to study the friction and wear performance for the materials of the piston and cylinder in a water hydraulic axial piston pump. The matching of a 940 stainless steel circle with a F102 engineering plastics block and a 940 stainless steel circle with an Al2O3 ceramic block were also studied. The wearing capacities were calculated by theoretical formulae based on the grinding crack widths. When pure water is used as hydraulic transmission medium, it is better to use ceramic with engineering plastics as matching materials for the piston and cylinder of water hydraulic axial piston pump. The experimental results have provided a theoretical basis for selecting the matching materials of the piston and cylinder.
Contact resistance of metal‐coated polymer particles used in anisotropically conductive adhesives
Authors: Määttänen Jarmo
Published: February 2003

The increasing demand for fine pitch interconnections has led to a growth of interest in anisotropically conductive adhesives (ACAs) as an alternative to solder joints in high density applications. The understanding of the conduction mechanisms for ACAs is of vital importance when choosing the right adhesive for a specific application. In the conductivity model, a formula has been created that can be used to estimate how the degree of deformation of the particles effects the resistance, especially in the case of soft metal‐coated polymer particles. Using this model, it is possible to estimate the total contact resistance. Some comparisons are made with real measurements for gold and indium‐tin‐oxide (ITO) surfaces, using gold‐coated polymer particles and gold bumped chips. For gold surfaces, the measurements have shown reasonably good correlation with the model. In the case of the ITO surface, the interface resistances seem to be the major part of the total resistance.
Reducing bonding cycle time of adhesive flip chip process
Authors: Seppälä Anne , Aalto Kati , Ristolainen Eero
Published: February 2003

Flip chip assembly using anisotropic conductive adhesives offers an interesting alternative for making high‐density interconnections. The use of conventional organic printed circuit boards makes this technique even more attractive. However, a low‐cost adhesive flip chip bonding process will require a reduced bonding cycle time or the use of multi‐head joining equipment. Adhesive flip chip bonding is characterized by a long bonding cycle time due to the relatively long curing time of adhesives and the need for simultaneous application of pressure during the curing process. In soldered flip chip techniques, the bonding time per assembly is shorter, because all the chips on the substrate can be soldered in a reflow oven at the same time. In this study, the minimum pre‐curing time needed to make a reliable adhesive joint was determined using one commercial anisotropic conductive adhesive film used on FR‐4 substrates. The results are promising, since bonding time reduction from 40 s to 10 s does not reduce the joint reliability.
Human Papillomavirus Type 31 E5 Protein Supports Cell Cycle Progression and Activates Late Viral Functions upon Epithelial Differentiation
Authors: Fehrmann Frauke , Klumpp David J. , Laimins Laimonis A.
Published: February 2003

The function of the E5 protein of human papillomaviruses (HPV) is not well characterized, and controversies exist about its role in the viral life cycle. To determine the function of E5 within the life cycle of HPV type 31 (HPV31) we first constructed HPV31 mutant genomes that contained an altered AUG initiation codon or stop codons in E5. Cell lines were established which harbored transfected wild-type or E5 mutant HPV31 genomes. These cell lines all maintained episomal copies of HPV31 and revealed similar phenotypes with respect to growth rate, early gene expression, and viral copy number in undifferentiated monolayer cultures. Following epithelial differentiation, genome amplification and differentiation-dependent late gene expression were observed in mutant cell lines, but at a rate significantly reduced from that observed in cells containing the wild-type genomes. Organotypic raft cultures indicated that E5 does not effect the expression of differentiation markers but does reduce expression of late viral proteins. Western analysis and immunofluorescence staining for cyclins during epithelial differentiation revealed a decreased expression of cyclin A and B in E5 mutant cells compared to HPV wild-type cells. Using a replating assay, a significant reduction in colony-forming ability was detected in the absence of E5 expression when cells containing wild-type or E5 mutant HPV genomes were allowed to proliferate following 24 h in suspension-induced differentiation. This suggests that HPV E5 modifies the differentiation-induced cell cycle exit and supports the ability of HPV31-positive keratinocytes to retain proliferative competence. In these studies, E5 was found to have little effect on the levels of the epidermal growth factor receptor (EGFR) or on its phosphorylation status. This indicates that EGFR is not a target of E5 action. Our results propose a role for high risk HPV E5 in modulation of late viral functions through activation of proliferative capacity in differentiated cells. We suspect that the primary target of E5 is a membrane protein or receptor that then acts to alter the levels or activities of cell cycle regulators.
Neutralization of Human Immunodeficiency Virus Type 1 by sCD4-17b, a Single-Chain Chimeric Protein, Based on Sequential Interaction of gp120 with CD4 and Coreceptor
Authors: Dey Barna , Del Castillo Christie S. , Berger Edward A.
Published: February 2003

We designed a novel single-chain chimeric protein, designated sCD4-17b, for neutralization of human immunodeficiency virus type 1 (HIV-1). The recombinant protein contains domains 1 and 2 of soluble CD4 (sCD4), connected via a flexible polypeptide linker to a single-chain variable region construct of 17b, a human monoclonal antibody that targets a conserved CD4-induced epitope on gp120 overlapping the coreceptor binding region. We hypothesized that the sCD4 moiety would bind gp120 and expose the 17b epitope; the 17b moiety would then bind, thereby blocking coreceptor interaction and neutralizing infection. The sCD4-17b protein, expressed by a recombinant vaccinia virus, potently neutralized a prototypic R5 clade B primary isolate, with a 50% inhibitory concentration of 3.2 nM (0.16 μg/ml) and >95% neutralization at 32 nM (1.6 μg/ml). The individual components (sCD4 and 17b, singly or in combination) had minimal effects at these concentrations, demonstrating that the activity of sCD4-17b reflected the ability of a single chimeric molecule to bind gp120 simultaneously via two independent moieties. sCD4-17b was highly potent compared to the previously characterized broadly cross-reactive neutralizing monoclonal antibodies IgGb12, 2G12, and 2F5. Multiple primary isolates were neutralized, including two previously described as antibody resistant. Neutralization occurred for both R5 and X4 strains and was not restricted to clade B. However, several primary isolates were insensitive over the concentration range tested, despite the known presence of binding sites for both CD4 and 17b. sCD4-17b has potential utility for passive immunization against HIV-1 in several contexts, including maternal transmission, postexposure prophylaxis, and sexual transmission (topical microbicide).
Mutation of Host
dnaJ
Homolog Inhibits Brome Mosaic Virus Negative-Strand RNA Synthesis
Authors: Tomita Yuriko , Mizuno Tomomitsu , Díez Juana , Naito Satoshi , Ahlquist Paul , Ishikawa Masayuki
Published: February 2003

The replication of positive-strand RNA viruses involves not only viral proteins but also multiple cellular proteins and intracellular membranes. In both plant cells and the yeast
Saccharomyces cerevisiae
, brome mosaic virus (BMV), a member of the alphavirus-like superfamily, replicates its RNA in endoplasmic reticulum (ER)-associated complexes containing viral 1a and 2a proteins. Prior to negative-strand RNA synthesis, 1a localizes to ER membranes and recruits both positive-strand BMV RNA templates and the polymerase-like 2a protein to ER membranes. Here, we show that BMV RNA replication in
S. cerevisiae
is markedly inhibited by a mutation in the host
YDJ1
gene, which encodes a chaperone Ydj1p related to
Escherichia coli
DnaJ. In the
ydj1
mutant, negative-strand RNA accumulation was inhibited even though 1a protein associated with membranes and the positive-strand RNA3 replication template and 2a protein were recruited to membranes as in wild-type cells. In addition, we found that in
ydj1
mutant cells but not wild-type cells, a fraction of 2a protein accumulated in a membrane-free but insoluble, rapidly sedimenting form. These and other results show that Ydj1p is involved in forming BMV replication complexes active in negative-strand RNA synthesis and suggest that a chaperone system involving Ydj1p participates in 2a protein folding or assembly into the active replication complex.
Inhibition of Adaptive Vγ2Vδ2+T-Cell Responses during Active Mycobacterial Coinfection of Simian Immunodeficiency Virus SIVmac-Infected Monkeys
Authors: Zhou Dejiang , Lai Xiaomin , Shen Yun , Sehgal Prabhat , Shen Ling , Simon Meredith , Qiu Liyou , Huang Dan , Du George Z. , Wang Qifan , Letvin Norman L. , Chen Zheng W.
Published: February 2003

Adaptive immune responses of γδ T cells during active mycobacterial coinfection of human immunodeficiency virus-infected humans have not been studied. Macaques infected with the simian immunodeficiency virus (SIV) SIVmac were employed to determine the extent to which a coincident AIDS virus infection might compromise immune responses of mycobacterium-specific Vγ2Vδ2+T cells during active mycobacterial infection. Control SIVmac-negative macaques developed primary and recall expansions of phosphoantigen-specific Vγ2Vδ2+T cells afterMycobacterium bovisBCG infection and BCG reinfection, respectively. In contrast, SIVmac-infected macaques did not exhibit sound primary and recall expansions of Vγ2Vδ2+T cells in the blood and pulmonary alveoli following BCG infection and reinfection. The absence of adaptive Vγ2Vδ2+T-cell responses was associated with profound CD4+T-cell deficiency and subsequent development of SIVmac-related tuberculosis-like disease in the coinfected monkeys. Consistently, Vγ2Vδ2+T cells from coinfected monkeys displayed a reduced capacity to expand in vitro following stimulation with phosphoantigen. The reduced ability of Vγ2Vδ2+peripheral blood lymphocytes (PBL) to expand could be restored to some extent by coculture of these cells with CD4+T cells purified from PBL of SIV-negative monkeys. Furthermore, naïve monkeys inoculated simultaneously with SIVmac and BCG were unable to sustain expansion of Vγ2Vδ2+T cells at the time that the coinfected monkeys developed lymphoid depletion and a fatal tuberculosis-like disease. Nevertheless, no deletion in Vδ2 T-cell receptor repertoire was identified in SIVmac-BCG-coinfected macaques, implicating an SIVmac-induced down-regulation rather than a clonal exhaustion of these cells. Thus, an SIVmac-induced compromise of the adaptive Vγ2Vδ2+T-cell responses may contribute to the immunopathogenesis of the SIV-related tuberculosis-like disease in macaques.