bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractAb 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

AbstractThe 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

AbstractA 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

AbstractA 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

AbstractRecent 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

AbstractIn 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.
Effect of photoperiod on development and growth in a pentatomid bug, Dolycoris baccarum
Authors: Nakamura Keiji 
Published: December 2004

AbstractThe 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.
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

SummaryThe 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

SummaryThe 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

SummaryTo 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

SummaryWeathering 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

SummaryWeathering 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

SummaryThe 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.
Habitat quality ranking depends on habitat‐independent environmental factors: a model and results from Callosobruchus maculatus
Authors: KAWECKI T. J. 
Published: December 2004

1. Survival and reproduction in different habitats of a heterogeneous environment are affected by intrinsic habitat properties as well as by habitat‐independent extrinsic factors. It is argued that the ranking of habitats according to quality may depend on extrinsic environmental factors that act with the same intensity in all habitats. This can happen if, across habitats, high reproductive success in the absence of extrinsic mortality is coupled with late reproduction. 2. In a model of a semelparous organism with overlapping generations that uses two habitats, the effect of different patterns of extrinsic mortality on habitat quality are analysed, as measured by the reproductive value of an egg, which estimates its expected contribution to the future gene pool. 3. Measurements of fitness components in Callosobruchus maculatus (F.) (Coleoptera: Bruchidae) on four host species demonstrate that, across hosts, long development can be associated with high reproductive success in the absence of extrinsic mortality. As a result, the quality ranking of three out of the four hosts would be different in a stable population regulated by intraspecific competition and egg parasitoids than in a growing population or a stable population regulated by age‐independent larval mortality. 4. It is suggested that habitat‐independent mortality may play a role in the evolution of ecological niches.