bluuebunny/crossref_metadata_2025 huggingface dataset:
Angular dependence of Gaussian‐Lobe orbitals. III. Polyhedric lobe edifices
Authors: Le Rouzo H. , Silvi B.
Published: December 2004

An analysis is presented that shows how the angular symmetry defects of lobe orbitals constructed from a polyhedric edifice can be accurately evaluated, and how these lobe orbitals can be related to harmonic Gaussian functions, the exponents being tranferred by a scale factor procedure.
Back donation in Ni(CO)4: Comments on papers by K. H. Johnson and by K. H. Johnson and U. Wahlgren
Authors: Larsson S. , Braga M.
Published: December 2004

It is shown that multiple scattering Xα calculations on Ni(CO)4 predict a strong back‐donation effect contrary to what is stated in previous papers on the subject.
Electrophilic superdelocalizability and carcinogenesis by polycyclic aromatic hydrocarbons—Pullman theory
Authors: Memory J. D.
Published: December 2004

A correlation is shown between carcinogenic potency and K‐region electrophilic superdelocalizability for a variety of aromatic compounds.
Atomic dipole approximation and energies of interactions between purine and pyrimidine bases. I. Electrostatic interactions of adenine with uracil, thymine, thiouracils, dihydrouracil, and 5‐fluorouracil
Authors: Geller M. , Jaworski A. , Pohorille A.
Published: December 2004

The atomic dipole approximation has been employed to calculate the energies of electrostatic interaction between adenine and various pyrimidine derivatives. Minima of the interaction energy for various planar configurations were determined. Inclusion of the “monopole–dipole” and “dipole–dipole” terms in the multipole expansion improves considerably the agreement with experimental data. The effect of sulfur substitution has been investigated in detail. Formation of NH…︁S hydrogen bonds is less favorable than of NH…︁O bonds, due largely to the lower atomic dipole of the sulfur atom resulting from the shift of the π‐electron charge toward the neighboring carbon. The results are relevant to the interactions of thiouracils in nucleic acids.
Theoretical studies of hemoproteins. I. Mathematical description of the allosteric effect
Authors: Kikuchi Takeshi , Nishimoto Kichisuke
Published: December 2004

A new theoretical approach to the cooperativity of an enzyme has been proposed. When we applied the present theory to the allosteric effect of hemoglobin, we obtained a so‐called Koshland–Nemethy–Filmer formula. Our theory suggested that the sigmoid curve becomes sharper when the affinity of the first oxygen molecule of the hemoglobin is smaller.
Valence photoelectron spectrum of CoO. Ab initio calculations of energies and relative intensities within a limited CI framework
Authors: Wahlgren Ulf , Johansen Helge
Published: December 2004

The valence spectrum of CoO has been calculated using the CoO610− cluster, stabilized by an electrostatic field, as a model of bulk CoO. The wave functions were generated using basis sets of better than double‐zeta quality. SCF wave functions were obtained for the ground state and for the first ionized state of the cluster. Limited CI calculations were performed using these orbital sets. The lowest states of the ion correspond to the main lines in the spectrum, while higher states can give rise to high‐energy satellites to the main lines. The relative intensities of these satellites were estimated in the case of high‐energy incident photons.
Spin‐Free configuration‐interaction study of molecules using single‐parameter alternat molecular orbitals
Authors: Sarma C. R. , Dinesha K. V.
Published: December 2004

A procedure is outlined for a programmable spin‐free configuration‐interaction (CI) study in molecules using single‐parameter alternant molecular orbitals for generating various configurations. The configurations were chosen to form bases for the irreducible representation {2N/2–2, 12S} of the general linear group GL(n). Using a transformation to biorthogonal space the CI matrix elements of a spin‐free Hamiltonian were generated. The procedure has been used to obtain the π‐electron energies for the 3,1Ag and 3,1Bu states of cis‐ and trans‐butadiene.
Modification of virtual orbitals
Authors: Beebe Nelson H. F.
Published: December 2004

The utility of modifying the virtual orbitals of the Fock operator by introducition of an additional potential is discussed. A particularly convenient form for computational implementations is obtained, and improved methods for the practical solution of the secular problem are recommended.
Hydrophobic “pocket” on photosynthesizing membrane near photosystem II
Authors: Yasnikov A. A. , Volkova N. V. , Kanivets N. P. , Mushketik L. S. , Vasilenok L. I. , Kukhar' V. P. , Pavlenko A. F.
Published: December 2004

Studies concerning the effect of 2‐alkyl pyridine N‐oxides with different substituents on electron transfer, phosphorylation, and light‐dependent proton transport in photosynthesizing membranes of chloroplasts were conducted. It is determined that 2‐alkyl pyridine N‐oxides with short alkyl chains stimulate the Hill reaction and light‐dependent proton transport inside chloroplasts. Compounds having alkyl residues with 6‐10 carbon atoms in the chain inhibit electron transport, ADP phosphorylation, and reduction of ferrocyanide in thylakoids. A conclusion is drawn on the presence of the hydrophobic “pocket,” which is of importance for organization of the electron‐transport chain of chloroplasts, near photosystem II.
Intensities of spin‐forbidden transitions in molecular oxygen and selective heavy‐atom effects
Authors: Minaev B. F.
Published: December 2004

Intensities of a1Δg←X 3∑g− and b 1∑g+ ← X 3∑g− transitions in molecular oxygen have been calculated on the basis of the INDO method taking into account spin‐orbit coupling by perturbation theory. The transitions are magnetic dipole in nature. The first of them (a − X) steals its intensity from 3Πg‐3∑g− and 1Πg‐1Δg transitions, which are determined by the orbital angular‐momentum operator. This source is not the principal one for the intensity of the second (b‐X) transition. Its intensity is stolen principally from microwave transitions between spin sublevels of the ground 3∑g− state. The last source explains the large difference in intensities of the a‐X and b‐X transitions. Calculated oscillator strengths are in a good agreement with experiment. The same integrals that determine the intensity also determine the parameters of the spin Hamiltonian for the ground 3∑g− state. These parameters are in a good agreement with experiment also, showing the validity of the whole calculation. In a condensed phase the investigated transitions are enhanced by intermolecular exchange interaction. It is known that an external heavy atom (EHA) enhances the b‐X transition of oxygen in solution, but does not influence the a‐X transition. In the collision complex O2‐EHA, which has a geometry without inversion symmetry, the microwave transitions between spin sublevels of the “3∑g−” state obtain electric‐dipole moments, which are stolen from the charge‐transfer transition. This mechanism explains the selective effect of EHA.
Notes on hydrogenic Gaussian lobe functions
Authors: Hoor Marten J. Ten
Published: December 2004

The Gaussian lobe representation of 2p and 3dxy functions of a one‐electron atom has been reconsidered. Contrary to earlier results, it has been found that the minimum energy associated with the simplest case of these functions is reached when the expansion centers coincide with the nucleus. This also seems to be true for representations with larger expansion lengths. Under similar conditions, Whitten's octahedral representation of the 2p function gives a better energy value than Poshusta's tetrahedral one.
Ab initio calculation of ESCA satellite intensities for a copper–chlorine complex
Authors: Larsson S. , de Mello P. Corrêa , Hehenberger M.
Published: December 2004

Ab initio SCF calculations carried out on the planar cluster CuCl42− suggest that the strong satellites at the high‐binding energy side of inner‐shell ESCA lines of Cu are due to charge relaxations in the σ‐bonding orbitals which mix with Cu 3d. The satellite state with the largest intensity may be described as a one‐electron excitation Cu 3d → Cl 3p.
SCF Theory of multiplet states
Authors: Carbó R. , Domingo Ll. , Gregori J.
Published: December 2004

The SCF theory of multiplet monodeterminantal states is described from a comprehensive viewpoint. In this context, the formalism and derived theorems are developed, as well as the description of a SCF closed‐shell‐like structure, namely the hypermultiplet. Numerical applications are discussed taking as a model the H2O molecule and its first positive ion. Wave functions of double ζ‐quality, with computed molecular properties of 16 states are given.
Electron correlation effects in SCF+CI wave functions—Fermi and coulomb correlation holes in HCN
Authors: Cooper Ian L. , Pounder Christopher N. M.
Published: December 2004

The Coulomb correlation hole distribution function has been computed with respect to various reference centers in the HCN molecule, using standard SCF+CI type wave functions. The extent to which statistical correlation between unlike‐spin electrons is introduced into an SCF wave function through the inclusion of configuration interaction has been assessed by an examination of the range and depth of such holes, and compared with the behavior of analogous Fermi distribution functions. Our results show that the range of Fermi correlation is consistently longer than that of the corresponding Coulomb correlation.
Theoretical study of some Van der Waals molecules
Authors: Kołos W. , Corongiu G. , Clementi E.
Published: December 2004

The Van der Waals molecules Ar · HF, Ar · H2O, and Ar · HCl have been analyzed with potential surfaces obtained by SCF energies corrected for the basis set superposition error and by including dispersion forces. The computed properties for these Van der Waals molecules are in good agreement with recent experimental observations.
Normal‐mode vibrational frequencies and thermodynamic properties of uracil and 4‐hydroxyuracil
Authors: Shibata Masayuki , Zielinski Theresa Julia , Rein Robert
Published: December 2004

Normal‐mode vibrational frequencies were obtained for uracil and 4‐hydroxyuracil with the MINDO/3 SCF method. MINDO/3 vibrational frequencies and the moments of inertia for STO‐3G optimized geometries yielded a ΔS for U ⇄ U* of 1.06 e.u./mol by standard statistical thermodynamic equations. ΔG is then 6.29 kcal/mol in the gas phase for U ⇄ U*. The reaction field continuum model of solvent effect lowers ΔG to 5.3 kcal/mol in aqueous solution. The tautomeric equilibrium constant in solution is then 1.3 × 10−4, in good agreement with experimental values.
Regression analysis of enzyme reaction. O‐methylation of catechol derivatives by catechol‐O‐methyltransferase
Authors: Shinagawa Yasuko , Shinagawa Yoshiya
Published: December 2004

The electronic structures of catechol derivatives, 3,4‐dihydroxy‐1‐substituted benzenes, including epinephrine and norepinephrine, were calculated by means of the CNDO/2 and the MINDO/3 methods. Correlation between the maximum velocities divided by the molecular weight, as between the inverse of Michaelis–Menten constants in the O‐methylation reaction catalyzed by catechol‐O‐methyltransferase and the electronic indices calculated on the basis of the frontier electron theory was found. The correlation coefficient between the observed maximum velocities divided by the molecular weight and the calculated ones was 0.873. The regression analysis showed that the Coulombic forces at the C3 and C4 positions and the electron acceptable indices at C6 and meta‐O positions represented the best correlation with the biological activities (Vmax and Km). The electronic indices of the catechol moieties represent the rate‐limiting factor of the O‐methylation reaction.
Application of lie algebra to ligand‐field theory
Authors: Au‐Chin Tang , Chia‐Chung Sun , Bei‐Foo Li
Published: December 2004

Ligand‐field theory is treated in a systematic and unified way by means of Lie algebra.
V‐Coupling coefficients from SO(3) to the octahedral group
Authors: Au‐Chin Tang , Ching‐Yu Cho , Chia‐Chung Sun
Published: December 2004

The properties of V‐coupling coefficients from SO(3) to the octahedral group are discussed and, for the purpose of practical use in ligand field theory, the numerical values from j = 1/2 to j = 12 1/2 have been worked out through an Elliott‐503 computer. The values for j ≤ 4 1/2 are listed.
LCAO‐MO treatment for deep levels produced by ion implantation of oxygen in gallium arsenide
Authors: Ruo‐Zhuang Liu , Wen‐Lin Feng
Published: December 2004

The ion implantation of oxygen in either n or p‐type gallium arsenide results in the formation of a semi‐insulating layer that is thermally stable. There still is no reasonable explanation for this phenomenon (except one of us has made a preliminary investigation

See Ref. 1.

). In this paper, we simulate the crystal of GaAs by a molecular cluster. As is well known the molecular‐cluster model has a shortcoming in introducing “surface states” owing to the dangling of atomic bonds on the surfaces.

See Ref. 2.

In order to suppress this effect, the dangling bonds were saturated with hydrogen atoms as proposed by Larkins.

See Ref. 3.

Therefore, in this paper the perfect crystal of GaAs was simulated by a cluster of atoms with a composition Ga4As13H36 (which corresponds to a pseudocluster Ga13As13). In the authors' opinion, this kind of treatment may cause minor changes in the positions of a few energy levels, but the general energy diagram pattern will reflect the main features of the real crystal. The electronic states of the entire system are then computed by an LCAO‐MO technique (extended‐Hückel theory). The substitutional oxygen OAs, the arsenic vacancy VAs, and the OAsVAs complex are treated similarly. The results of the calculation show that the substitutional oxygen (OAs) forms deep donor levels in the forbidden gap. The arsenic vacancy also forms donor levels in the forbidden gap. On the other hand, the OAsVAs complex forms deep acceptor levels in the forbidden gap. Thus we have given a reasonable model for the mechanism of the formation of an insulating layer produced by oxygen ion implantation in GaAs.
Microscopic theory of the average band gap of semiconductors
Authors: Van Doren V. E. , Van Camp P. E. , Devreese J. T.
Published: December 2004

In Phillips' spectroscopic theory of semiconductors, the covalency and ionicity are derived empirically from the average band gap between the highest valence and lowest conduction bands. In this paper an explicit expression for the average band gap is derived based on a continued fraction representation of the polarizability matrix. Results of a calculation for six covalent and polar semiconductors, using the pseudopotential model, are presented and compare favorably with experimental values.
N2 Laser‐excited luminescence of antiferromagnetically coupled trinuclear chromium(III) complexes
Authors: Morita Makoto , Kato Yoshiaki
Published: December 2004

Exchange interaction parameters in several trinuclear chromium(III) complexes [Cr3O(R‐COO)6(H2O)3]X·nH2O (R = CH3, C2H5) are determined in the study of luminescence, time‐resolved luminescence (TRS), and decay time measurements over the temperature range 4–100°K. The presence of four inequivalent trinuclear clusters and a luminescence anomaly at 25 and 55°K are observed in the basic chromium(III) acetate prisms. Magnetic anomalies reported earlier should be attributed to the distortion and disordering of the hydrogen‐bonded channels in crystals at low temperatures.
Synchrotron radiation spectroscopy of quasi‐one‐dimensional materials
Authors: Mitani T. , Suga S. , Tokura Y. , Koyama K. , Nakada I. , Koda T.
Published: December 2004

The optical reflectivity spectra of quasi‐one‐dimensional polymers (SN)x, trans‐(CH)x, and polydiacetylene are investigated in an energy range from 1 to 25 eV by use of synchrotron radiation. Observed structures associated with π‐electron states are interpreted in terms of the quasi‐one‐dimensional one‐electron bands calculated by the LCAO‐type model.
Variational functions of the padé type—application to the ground state of the helium atom
Authors: Jolly P. , Saxena R. P. , Srivastava P. K. , Sane K. V.
Published: December 2004

It is shown that trial functions involving Padé approximants yield satisfactory results for the ground state of the helium atom. In particular, the five‐parameter form reproduces the best variational function of the type Ψ = e–zsϕ(u) obtained numerically, to a remarkable extent.
Multipole polarizabilities and shielding factors of the hydrogen atom from the hydrodynamic analogy to quantum mechanics. III
Authors: Shukla G. C. , Issa M. R. , Narayan M. S.
Published: December 2004

Variational iterative solutions for multipole polarizabilities of the H atom have been carried out. The resulting numerical values of the Cauchy coefficients are in harmony with our recent work. The large frequency expansion of the multipole polarizabilities of the H atom is also calculated. The first term in such expansions, the multipole oscillator strength sum rule, is in harmony with earlier work.
Experimental designs for finding stationary points and for computing force constant matrix
Authors: Sana M.
Published: December 2004

We use an experimental design method for computing a local quadratic form which is adequate to find stationary points and to evaluate the force constant matrix on a k‐dimensional potential energy hypersurface. Two types of designs are particularly discussed: the composite and the Doehiert's plane. We give examples for illustrating the methodology. Some thermodynamical properties are deduced from our results. Such a method may be used with every type of theoretical calculations (SCF or CI) and with any program without modification.
A scaled “one‐electron Hamiltonian” model for open‐shell LCAO–MO–SCF calculations
Authors: Bhattacharyya Sankar Prasad
Published: December 2004

An approximate technique of generating orthonormality‐constrained one‐electron orbitals for the description of open‐shell systems is suggested. The “off‐diagonal Lagrangian‐multiplier problem” is circumvented by using a common potential for both the closed‐ and open‐shell electrons. This common potential is generated by a scaling of the usual exchange potential of Hartree–Fock theory. The problem of choosing an appropriate scaling parameter (μ) is considered from both variational and perturbative points of view. The relationship of the present method with some other approximate open‐shell theories is explored. The numerical results of computations carried out at the semiempirical MO level are presented in order to bring to light the dependence of computed molecular properties on the magnitude of the scaling parameter.
n‐Local energies as accuracy measures on approximate wave functions
Authors: Grelland Hans H.
Published: December 2004

A class of multilocal functions called n‐local energies, which can serve as accuracy criteria on approximate wave functions, are defined. Their interpretation is discussed and their multilocal form is shown to be a result of the holistic character of the quantum description. The analogy with the reduced local energy of Thomas, Javor, and Rothstein is demonstrated. The explicit formula for the simplest n‐local energy capable of measuring the deviation from the exact solutions of the Schrödinger equation is obtained in the one‐determinantal case.
Molecular calculations with the nonempirical ab initioMODPOT, VRDDO, and MODPOT/VRDDO procedures. XII. Carcinogenic 3‐methylcholanthrene and its metabolites using a MERGE technique
Authors: Hariharan P. C. , Popkie Herbert E. , Kaufman Joyce J.
Published: December 2004

Ab initio MODPOT/VRDDO/MERGE calculations were carried out on carcinogenic 3‐methylcholanthrene (3‐MCA) and its metabolites. The results for 3‐MCA were compared to our earlier similar calculations for carcinogenic benzo(a)pyrene (BP). Both compounds 3‐MCA and BP are carcinogenic and are metabolically activated by similar mechanisms but in different positions. Both the calculated wave functions for 3‐MCA and BP and the electrostatic molecular potential contour maps generated from these wave functions correctly reflect the similarity of mechanisms of metabolic activation and the differences in position. Our calculated results both for BP and for 3‐MCA reflect accurately their experimentally observed behavior. Thus this combination of theoretical techniques can be used with confidence to describe the behavior of the polycyclic aromatic hydrocarbons (PAH's) and their metabolites. The ab initio MODPOT/VRDDO method incorporates two very desirable options into our fast ab initio Gaussian programs: MODPOT–ab initio effective core model potentials—and a charge‐conserving integral prescreening approximation which we named VRDDO (variable retention of diatomic differential overlap). For orbital energies and population analysis the MODPOT/VRDDO results agree to essentially three decimal places with completely ab initio calculations using the same valence atomic basis set. For this series of very closely related congeners our recent MERGE technique which allows reuse of integrals from a common skeletal fragment was used. The ab initio MODPOT/VRDDO/MERGE calculations were carried out for 3‐MCA, 3‐MCA oxides, 3‐MCA dihydrodiols, and 3‐MCA dihydrodiolepoxides. The metabolites investigated were 3‐MCA 9,10‐oxide; 3‐MCA 7,8‐oxide; 3‐MCA 9,10‐dihydrodiol [trans(axial, axial); trans(equatorial, equatorial); cis(axial, equatorial); cis(equatorial, axial)]; and 3‐MCA 9,10‐dihydrodiol–7,8‐epoxide [for both conformations A and B of the dihydrodiol and for all stereoisomers of the dihydrodiolepoxides relative to below and above the plane: ααα, and ααβ αβα αββ βαα βαβ ββα and βββ (most stable)]. Calculations were also carried out for opening of the C7OC8 epoxide ring both towards C7 and C8 for the most stable isomer Aβββ (above the ring). Opening the epoxide ring between C7 and O leads to a more stable intermediate than opening the epoxide ring between C8 and O. Again, however, as with opening the epoxide ring in BP 7,8‐dihydrodiol–9,10‐epoxide there is no buildup of positive charge on C7 in the 3‐MCA metabolites as postulated by some cancer researchers, but rather the C7 becomes slightly more negative. Nor is there a buildup of negative charge on the O atom, but rather it becomes slightly more positive. As the epoxide ring is opened further than 90° for the OC7C8 or OC8C7 angles, there appears to be a possible mixing of configurations that is being investigated further.
Explicitly correlated configuration interaction studies using spherical Gaussians. I. Theoretical considerations
Authors: Karunakaran K. M. , Christoffersen Ralph E.
Published: December 2004

The formalism for a configuration interaction approach is presented, in which explicit introduction of interelectronic coordinates into individual configurations is accomplished through the use of spherical Gaussian correlation factors. Formulas for all required matrix elements over these configurations are derived, and a computationally convenient algorithm to evaluate the matrix elements is presented. In addition, analysis of the form of the correlation factor shows that both angular and radial correlation can be obtained using spherical Gaussian correlation factors.
Computations of intermolecular interactions: Expansion of a charge‐transfer energy contribution in the framework of an additive procedure. Applications to hydrogen‐bonded systems
Authors: Gresh N. , Claverie P. , Pullman A.
Published: December 2004

A procedure is given to derive an explicit charge‐transfer contribution from the Murrell–Randic–Williams formula, and to implement it in the framework of an additive procedure for the computation of intermolecular interaction energies, as a sum of electrostatic, repulsion, polarization, dispersion, and charge‐transfer terms. Comparisons are performed between the radial and angular dependence of this term in model hydrogen‐bonded systems, and that of the charge‐transfer term resulting from SCF supermolecule computations. The evolution of the derived term can be matched very satisfactorily to that of an SCF counterpart when the counterpoise correction is taken into account. The underlying features governing the radial and angular evolution of the counterpoise and charge transfer terms are underlined.
Electronic state representations at molecular potential pseudocrossings
Authors: Olson John A. , Micha David A.
Published: December 2004

A diabatic representation is introduced to describe electronic states around adiabatic pseudocrossings, as an alternative to presently available representations. A transformation from the adiabatic to the new diabatic representation is chosen to assure well behaved diabatic potentials for arbitrary momentum coupling strengths. Parameters of the transformation are determined by minimizing momentum couplings in the pseudocrossing region. The problem of two electronic states in one relative position variable is treated in detail and is studied with a numerical model. A comparison of results of our procedure and of other available ones is given. The present developments also provide a criterion for neglecting momentum couplings based on their strength and on the range of collision energies.
Some remarks on multiconfiguration time‐dependent Hartree–Fock theory
Authors: McWeeny R.
Published: December 2004

Recent progress in multiconfiguration time‐dependent Hartree–Fock (MC–TDHF) theory is reviewed. The generality of a formalism first put forward by Moccia [Int. J. Quantum Chemistry 8, 293 (1974)] is emphasized, and illustrative applications are discussed. A calculation of the frequency‐dependent electric‐dipole polarizability of the helium atom shows that even with a modest amount of CI, it is possible to achieve an accuracy comparable to that obtained by use of Hylleraas‐type wave functions.
Mechanistic studies of oxene reactions with organic substrates: Reaction paths on MNDO enthalpy surfaces—models for cytochrome P450 oxidations
Authors: Pudzianowski Andrew T. , Loew Gilda H.
Published: December 2004

In a systematic study, the characteristics of triplet oxene models for alkane, alkene, chloroalkane, and aryl oxidations by the cytochrome P450s have been examined using the semiempirical molecular orbital method MNDO and the formalism of statistical mechanics. Specific model substrates chosen were: methane, ethylene, propene, carbon tetrachloride, chloroform, and toluene. It was found that transition state geometries and activation entropies were reliably predicted, but that an empirical factor was necessary to correct overestimation of activation enthalpies. It was determined that both hydroxylations and epoxidation initiated by a O(3P) atom are nonconcerted; and that oxidations of CCl bonds (halosylations) occur by a two‐step mechanism similar to hydroxylation. It is shown that the radical mechanisms derived from these studies are consistent with a range of observed properties of cytochrome P450 reactions and provide reasonable explanations for secondary deuterium isotope effects and substituent effects in cytochrome P450 epoxidation of styrenes, suicide inactivation of a P450 enzyme by ethylene, and the characteristics of aerobic CCl4 and CHCl3 metabolism. A triplet oxene mechanism for the initial steps of aromatic epoxidation and hydroxylation is also discussed.
Identification of genes down‐regulated during melanoma progression: a cDNA array study
Authors: Baldi Alfonso , Battista Tullio , De Luca Antonio , Santini Daniele , Rossiello Luigi , Baldi Feliciano , Natali Pier Giorgio , Lombardi Daniela , Picardo Mauro , Felsani Armando , Paggi Marco G.
Published: December 2004

Abstract: In order to identify genes relevant for melanoma development, we carried out cDNA array experiments employing an in vitro model of human melanoma progression, consisting of two cell lines: one, LP, derived from a primary melanoma and the other, LM, from its metastatic supraclavicular lymph node. Basic cDNA array data identified 26 genes as down‐regulated in the LM cell line. Northern blot analysis confirmed an effective transcriptional down‐regulation for five out of 13 genes analyzed. The products of these five genes belong to different functional protein types, such as transcription and translation regulators (Edg‐2, eIF‐3 p110, and RNPL/RBM3), extracellular communicators (PRSS11) and members of the major histocompatibility complex (β2‐microglobulin). Some previously described differences in expression patterns, such as loss of HLA I, were confirmed by our array data. In addition, we identified and validated for the first time the reduced expression level of several genes during melanoma progression. In particular, reduced Edg‐2 gene product expression was also confirmed in a group of 50 primary melanomas and unrelated metastases. In conclusion, comparative hybridization by means of cDNA arrays assisted in identifying a series of novel progression‐associated changes in gene expression, confirming, at the same time, a number of previously described results.
Identification, distribution and expression of osteoadherin during tooth formation
Authors: Petersson Ulrika , Hultenby Kjell , Wendel Mikael
Published: December 2004

Osteoadherin (OSAD) is a keratan sulfate‐containing proteoglycan, belonging to the small leucine‐rich proteoglycan (SLRP) family. In bone OSAD has been localized in primary spongiosa within the bovine fetal rib growth plate. Moreover, in situ hybridization has shown expression of OSAD in osteoblasts close to the cartilage and bone border in the growth plate of rat femur. mRNA expression has also detected OSAD in mature osteoblasts on the surface of bone trabeculae. We have identified OSAD in extracts of bovine dentin, and the identity was verified by N‐terminal sequencing. Western blot analysis detected two bands in bovine bone and dentin at 85 kDa and 60 kDa. Northern blot analysis of RNA samples from 5‐d‐old‐rat tooth and femur showed a 1.9‐kb transcript for OSAD in both tissues. OSAD was located to the mineralized dentin matrix, cementum and surrounding alveolar bone by immunohistochemistry, and in situ hybridization showed OSAD to be highly expressed during early crown formation in the entire odontoblast cell layer, in the area of Hertwig's epithelial root sheath, in the cells of the newly formed mantle dentin, and in the odontoblasts at the fissures. Ultrastructural studies indicated that OSAD might be associated with collagen fibrils. Thus, OSAD may play an important role during tooth development and biomineralization of dentin.
Building effective strategies for the management of endodontic pain
Authors: Keiser Karl , Hargreaves Kenneth M.
Published: December 2004

Recent advances in the understanding of pain physiology and pharmacology have provided dental practitioners with more reliable information upon which clinical decisions in the treatment of endodontic pain can be based. This article provides practical treatment strategies based upon current scientific evidence and uses information presented in the prior articles of this issue of Endodontic Topics to make treatment recommendations for given patient scenarios.
Effect of photoperiod on development and growth in a pentatomid bug, Dolycoris baccarum
Authors: Nakamura Keiji
Published: December 2004

The effect of photoperiod on nymphal development, growth and adult size was examined in a pentatomid bug, Dolycoris baccarum, collected in Osaka (a warm temperate region) and Hokkaido (a subfrigid region), Japan. When insects were reared from eggs at 25°C, the developmental period was long and adult size was large under photoperiods close to the critical photoperiod for the induction of adult diapause. Adults of the Hokkaido population were larger than those of the Osaka population. There was no significant correlation between developmental period and adult size. Insects also showed variation in their growth rate: growth rate was low under photoperiods a little longer than the critical photoperiod for the induction of diapause. The ecological significance of variation in development and growth is discussed.
Measures of hippocampal volumes, diffusion and 1H MRS metabolic abnormalities in temporal lobe epilepsy provide partially complementary information
Authors: Düzel E. , Kaufmann J. , Guderian S. , Szentkuti A. , Schott B. , Bodammer N. , Hopf M. , Kanowski M. , Tempelmann C. , Heinze H. J.
Published: December 2004

We assessed whether interictal measures of hippocampal volume, hippocampal diffusion and metabolic abnormalities yield correlated or complementary information about hippocampal pathology in patients with temporal lobe epilepsy (TLE). Volumes, apparent diffusion coefficients (ADC) and ratios of N‐acetyl‐aspartate (NAA) to Creatine/Phosphocreatine (Cr) and Choline (Cho) were measured from each hippocampus during one magnetic resonance imaging (MRI) session in patients with TLE. Structural MRI showed unilateral hippocampal sclerosis (HS) in 13 patients and was normal in the remaining nine patients. Pearson's correlation (two‐tailed) between ADC values and NAA/(Cr + Cho) ratios was significant (P = 0.04, r = −0.45) for the hippocampus ipsilateral to the epileptogenic zone as determined on the basis of interictal and ictal scalp EEG recordings. This finding was driven by a very high correlation between the two measures in the presence of HS (P < 0.001, r = −0.96). Furthermore, ipsilateral ADC values but not NAA/(Cr + Cho) ratios were correlated with disease duration (P = 0.001, r = 0.67). Hippocampal volumes did not correlate with either ADC values, NAA/(Cr + Cho) ratios or disease duration. These data suggest that hippocampal volumes, NAA/(Cr + Cho) ratios and ADC values capture partially complementary aspects of hippocampal pathology.
Transient postictal urinary retention: presentation of three cases
Authors: Vander T. , Ifergane G.
Published: December 2004

A transient focal neurologic deficit after epileptic event is a well‐known phenomenon. We report for the first time in English literature, three cases of transient urinary retention after seizures. The possible pathophysiologic mechanisms are discussed.
Distribution of human CD30 gene promoter microsatellite alleles in healthy and human immunodeficiency virus‐1 infected populations
Authors: McIntyre M. Q. , Price P. , Franchina M. , French M. A. , Abraham L. J.
Published: December 2004

The human CD30 gene, found on chromosome 1; 1p36, contains a microsatellite of the type [(CCAT)2−12CCACTTATGCAT]n within the promoter. As the microsatellite has been shown to be both polymorphic and involved in the transcriptional regulation of this gene, it is of potential interest with respect to interindividual differences in CD30 expression. Here we describe a method for determining length variation of this repeat region and determine the frequency and distribution of alleles of the CD30 microsatellite within the Western Australian population. As soluble CD30 levels are predictive for disease associated with human immunodeficiency virus (HIV)‐1 infection, we also determined allele frequencies in an HIV+ cohort.
Structural and functional characteristics of a dominant‐negative isoform of porcine MHC class II transactivator
Authors: Quinn G. , Bower R. , Dos‐Santos Cruz G. , Giovino M. , Xu Y. , Patience C. , Schuurman H.‐J.
Published: December 2004

The MHC class II transactivator, CIITA, is critical for MHC class II gene expression in all species studied to date. We isolated an interferon (IFN)‐γ‐inducible isoform of porcine CIITA (pCIITA′) encoding a protein of 566 amino acids (aa) with significant homology to human CIITA (hCIITA). Analysis indicated that pCIITA′ lacks the entire GTP‐binding domain that is important for nuclear translocation and activation of target genes by hCIITA. In pCIITA′ this region is replaced by a 14‐aa motif with homology to several signalling peptide sequences. Expression of pCIITA′ in porcine (ST‐IOWA) and human (HeLa) cell lines resulted in suppression of IFN‐γ‐stimulated MHC class II gene expression, at the protein and mRNA levels. We also identified two IFN‐γ‐inducible variants of hCIITA, hCIITAlo and hCIITA′ from Hela cells, both exhibiting dominant‐negative suppression of MHC class II gene expression. Interestingly, hCIITA′ encodes a predicted protein of 546 aa with a strikingly similar organization to pCIITA′ including the 14‐aa GTP‐binding domain‐replacement motif in which 10 out of 14 amino acids are identical to the pig sequence. Expression of hCIITA′ and hCIITAlo sequences in Hela cells suppressed IFN‐γ‐induced MHC class II gene expression. hCIITAlo, a predicted 303‐aa protein with deleted GTP‐binding and carboxy‐terminal domain, displayed a more subtle suppression of IFN‐γ‐induced MHC class II expression. These in vitro data indicate that there may be a role in vivo for isoforms of CIITA that can suppress full‐length CIITA‐mediated MHC class II gene expression. Both humans and now, potentially, pigs are candidate donors for organ and tissue allografts and xenografts, respectively. Regulation of MHC class II gene expression by manipulation of CIITA isoform expression in humans and pigs may provide a useful strategy for attenuation of T‐cell‐mediated cellular rejection.
Sequences and diversity of 17 new Ovar‐DRB1 alleles from three breeds of sheep
Authors: Konnai S. , Nagaoka Y. , Takeshima S. , Onuma M. , Aida Y.
Published: December 2004

To investigate the genetic diversity of the sheep MHC (Ovar) class II DRB1 locus, we amplified exon 2 of Ovar‐DRB1 alleles by polymerase chain reaction (PCR) and determined the nucleotide sequences of both resultant strands after cloning. In our study of a total of 97 sheep of three breeds, namely, Suffolk, Cheviot and Corriedale, we identified 18 previously published alleles and 17 new alleles. These alleles were 83.4 to 94.1% identical at the nucleotide level and 71.4 to 90.9% identical at the amino acid level to Ovar‐DRB1*0101. We identified six new alleles in Cheviot sheep and 11 new alleles in Suffolk sheep. Furthermore, we identified 15, 6 and 1 allele in Suffolk, Cheviot and Corriedale sheep, respectively, that have only been found in these breeds to date. Analysis of the frequencies of the various Ovar‐DRB1 alleles in each breed indicated that Ovar‐DRB1*0702 was the most frequent allele in Suffolk sheep (23.9%), Ovar‐DRB1*0203 was the most frequent allele in Cheviot sheep (27.5%) and Ovar‐DRB1*0201 was the most frequent allele in Corriedale sheep (25.0%). A comparative analysis of the positions of polymorphic residues in the first extracellular domain of the DRB genes of sheep, humans and mice revealed an extraordinary similarity amongst the positions of polymorphic residues that are associated with the antigen recognition site (ARS). Moreover, the extent of polymorphism seems to be similar in sheep, humans and mice.
Experimental in situ transformation of vermiculites to study the weathering impact of tree species on the soil
Authors: Augusto L. , Ranger J. , Turpault M. ‐P. , Bonnaud P.
Published: December 2004

Weathering of soil minerals under forest seems to depend on the species present. To study the influence of tree species we placed unweathered vermiculites in the soil and assessed the impact in terms of saturation index of earth‐alkaline cations and cation exchange capacity in 64 forest stands, dominated by different species and growing side by side at 20 sites on acidic soils. The vermiculites were of two types, one with a large charge and the other with a small charge. Minerals were maintained in the soil for 1 and 3 years.

The minerals placed in the topsoil and in soils with low buffering capacity were more acidified and weathered than those deeper in the soil and in less acid conditions. The vermiculites were transformed into hydroxylated interlayered vermiculites, and the formation of hydroxides in the interlayer space decreased the vermiculites' cation exchange capacities. The high‐charge vermiculite had a greater affinity for aluminium than the low‐charge variety. The effect of tree species was significant but small compared with factors such as soil type, depth and duration of incubation. Nevertheless, we can rank the acidifying and weathering caused by the trees in the following order: Picea abies, Abies alba > Pinus sylvestris, Pseudotsuga menziesii > Quercus spp., Fagus sylvatica. This in situ experimental approach enabled us to study potential trends in pedogenesis in few years.
Mobilization of aluminium, iron and silicon by Picea abies and ectomycorrhizas in a forest soil
Authors: Van Hees P. A. W. , Jones D. L. , Jentschke G. , Godbold D. L.
Published: December 2004

Weathering of soil minerals is a key determinant of ground and surface water quality and is also important in pedogenic and rhizosphere processes. The relative importance of biotic and abiotic studies in mineral weathering, however, is poorly understood. We investigated the impact of Picea abies seedlings, an ectomycorrhizal fungus and humic acid on the solubilization of aluminium (Al), iron (Fe) and silicon (Si) in an E horizon forest soil over 10 months. Elemental budgets were constructed based upon losses in drainage water, accumulation in plants and changes in the pools of exchangeable ions. Plants and mycorrhizas or both had a significant effect on the total amounts of Al, Fe and Si mobilized from the soil. Significantly larger amounts of Al and Fe were recovered in plants than those lost in drainage water, whereas the opposite trend was true for Si. The continual addition of dissolved organic matter to the soil in the form of humic acid had an effect only on mobilization of Fe, which increased due to larger plant uptake and an increase in the exchangeable pool. The mobilization of Fe and Si were positively correlated with hyphal length, soil respiration and concentrations of oxalate in the soil solution, and mobilization of Al was strongly correlated with plant weight. Scanning electron microscopy revealed that most fungal hyphae were associated with mineral surfaces with little occupation of cracks and micropores within mineral grains. Evidently ectomycorrhizas have important impacts on mineral dissolution and the chemistry of forest soils.
Role of aggregate surface and core fraction in the sequestration of carbon from dung in a temperate grassland soil
Authors: Bol R. , Amelung W. , Friedrich C.
Published: December 2004

The sequestration of dung carbon in soil depends on the location and rate at which it is immobilized in soil aggregates. Here C4 dung (δ13C = −16.1‰) or C3 dung (δ13C = −26.8‰) were applied to a temperate permanent pasture C3 soil (δ13C = −27.9‰). Triplicate samples were taken from C3 and C4 dung remaining at the surface, and in the 0–1 and 1–5 cm soil layers in the unamended control and under the C3 and C4 dung patches after 7, 14, 29, 42 and 70 days after the application of the dung. Macroaggregates (≥ 4 mm) at the lower depth (1–5 cm) were mechanically fractionated into surface and core fractions by a combination of shock freezing followed by wet sieving.

Neither overall nor differential carbon isotope fractionation occurred in the dung remaining at the surface. The incorporation of C4 dung significantly increased the δ13C content of the 0–1 cm layer of the C3 soil. Dung C sequestration did not exceed 10% for the 0–1 cm layer and was only 20% for the whole soil (0–30 cm) during the 7‐day experiment. Only 32–66% of the C from dung in the 1–5 cm layer was sequestered in the aggregates; the major proportion was initially preferentially attached to their surfaces, but incorporated into aggregates within the following 14 days. The majority of dung, however, soon resided between the aggregates, pointing to the important role of the inter‐aggregate fraction in short‐term C dynamics of dung in this pasture soil.
Scour and fill patterns in a New Zealand stream and potential implications for invertebrate refugia
Authors: Matthaei C.H.ristoph D. , Peacock Kathi A. , Townsend Colin R.
Published: December 2004

1. The hyporheic zone has long been regarded as a potential refugium for lotic invertebrates during disturbance. However, there have been few attempts to quantify the stability of this habitat during high flow events. In a New Zealand stream with an unstable bed, the present authors monitored spatial patterns of scour and fill in a riffle in a wide flood plain and at two sites in a constrained reach: a pool‐riffle with bedrock outcrops and a plane‐bed (a bedform characterized by long stretches of planar stream bed).

2. At each 20‐m site, 100 scour chains were installed in a systematic grid with about 1 m between chains. Scour was measured by comparing the length of chain exposed before and after a high flow event, whereas filling depth was equivalent to the thickness of the sediment deposited on top of the chains during the event. For each chain, the present authors noted dominant particle size and degree of packing of the surrounding bed, water depth and presence or absence of large stones upstream. Chains were re‐located after four smaller spates, one intermediate event and one large flood.

3. Most events caused a complex mosaic of bed patches which experienced scour, fill or remained undisturbed. These patterns, which were mostly site‐ and event‐specific, were often significantly influenced by the longitudinal or lateral position of the chains in the spatial grids.

4. The cumulative effect of the six high flow events differed substantially between sites. The first site experienced predominantly scour, the second both scour and fill, and the third almost exclusively fill. These differences were partly explained by channel geomorphology. The bedrock outcrops at the constrained pool‐riffle site forced the flow at high discharge, causing deep scour in these areas, whereas a backwater effect at the third site reduced near‐bottom shear stress during larger events and led to sediment deposition.

5. Except for a single event at the second site, scour affected mainly the uppermost 10–15 cm of the stream bed. Therefore, almost the entire hyporheic zone below this depth would have been available as refugium for invertebrates, in addition to the often consider‐able number of bed patches which remained undisturbed during the six high flow events.

6. Fill without earlier scour during the same high flow event was common at all sites. Most previous studies have assumed that lotic invertebrates are mainly affected by scour during high flow events, but the consequences of sediment deposition may be just as far reaching.
Consequences of defoliation on phenological interaction between Epirrita autumnata and its host plant, Mountain Birch
Authors: KAITANIEMI P. , RUOHOMÄKI K. , HAUKIOJA E.
Published: December 2004

1. Defoliation‐induced changes in the budbreak phenology of Mountain Birches (Betula pubescens ssp. tortuosa (Ledeb.) Nyman), and their effects on herbivore performance, were investigated during an outbreak of the spring‐feeding geometrid, Epirrita autumnata (Bkh.).

2. Total defoliation (followed by refoliation) by E. autumnata larvae was required to achieve significant delaying of budbreak of Mountain Birch one year after damage.

3. Delayed budbreak has potentially deleterious effects on herbivore performance. However, E. autumnata larvae show phenotypic responses that increase the synchrony between larvae and leaves: high larval density, a prerequisite for severe defoliation, delays egg hatch in the following year.

4. Late hatching larvae performed as well on birches with delayed budbreak due to the previous year’s total defoliation as did early hatching larvae on birches with earlier budbreak.