bluuebunny/crossref_metadata_2025_split huggingface dataset:
Possible incorporation of the purine–purine mispairs in the DNA helix and the interpretation of the transversion‐type point mutations
Authors: Kothekar V. , Bolis G. , Rein Robert 
Published: December 2004

AbstractThe stereochemical and energetic compatibility of incorporation of the non‐Watson–Crick hydrogen bonded purine–purine base pairs of normal tautomers in the helical structure of B‐DNA is studied here. The hydrogen bonding positions of the possible “mispairs” of the bases GA, GG, and AA are optimized first in the base plane by translational and rotational movement along the hydrogen bonds and then introduced at an appropriate position in the DNA structure. The optimum backbone geometries which can accommodate the “mispairs” are obtained by force field computations. The stereochemical and energetic aspects of the various mispairs are discussed in light of their possible incorporation in DNA and as mutational intermediates for the “transversion”‐type point mutations.
Molecular electrotatic potential of a triple stranded helix: Poly(dT)·poly(dA)·poly(dT)
Authors: Corbin Sylvie , Lavery Richard , Pullman Bernard 
Published: December 2004

AbstractThe molecular electrostatic potential of the triple helix poly(dT)·tpoly(dA)·poly(dT) is calculated, and the results are examined in relation to those obtained for its component double and single helical parts. For the double helix presenting the standard Watson–Crick hydrogen bonds, the deepest potentials are formed on the side of the major groove, a situation similar to that observed in the A‐DNA duplex. For the double helix presenting Hoogsteen‐type hydrogen bonds the deepest potentials lie in the major groove, on the side of the pyrimidine strand. In the triple helix the deepest potentials are located in the major groove in a narrow zone over the thymine bases of the Watson–Crick pair.
Evaluation of GTO molecular integrals
Authors: Harris Frank E. 
Published: December 2004

AbstractMethods for evaluating the function Fm(t) occurring in molecular integrals over Gaussian‐type orbitals are reviewed and extended. Formulas based on Bessel function and continued‐fraction expansions are analyzed. The recommended evaluation procedures, embodied in a portable computer program, involve Padé approximations for various argument intervals and use recursion in m. The program is economical in storage requirements and faster than those in current use.
Cluster Xα approach to magnetic interactions and phase transitions in solids
Authors: Gubanov V. A. , Liechtenstein A. I. , Postnikov A. V. 
Published: December 2004

AbstractA magnetic transition state model is developed for the description of magnetic interactions and magnetic phase transitions in solids. The model is based on the one‐electron Xα molecular orbital calculations of clusters embedded in crystal lattice and allows quantitative investigations of magnetic interactions in d and f metals, their alloys, and compounds. The energies of local spin excitations and magnetic transition temperatures are calculated for a series of systems with the electronic states localized to a different extent. The effects of covalent bonding are introduced directly into magnetic parameters calculations and appear to be of crucial importance. Magnetic properties of some disordered alloys are considered basing on the results of Xα cluster calculations performed. In the low concentration limit, the local moment existence problem is being discussed. The dependence of magnetic properties upon concentration is considered. The results of calculations allow to give the reasonable interpretation of the experimental data available and show good possibilities of the cluster model in the description of magnetic effects in solids.
Use of VN−1 potentials in Green's function calculations
Authors: Winkler Peter 
Published: December 2004

AbstractAn analysis of the leading effects of a propagator approach to the calculation of resonance energies is presented. By comparison with ΔSCF results, a simple approximation formula has been developed which contains the main features of the VN−1 potential option and the diagonal Tamm–Dancoff approximation. This result is expected to be a useful guide for further refinements of the many‐body aspects of the theory.
Responses to light in individual growth and reproduction of two Acer species and the long‐term consequences
Authors: Uraguchi Aya , Kubo Takuya 
Published: December 2004

AbstractDespite widespread interest in plant responses to light, few studies have addressed the lifetime consequences of the responses. We have addressed this issue by studying Acer mono and Acer amoenum trees in a cool temperate forest in northern Japan. By analyzing field data, it was detected that growth and flowering rates increased with light availability for each species. A stochastic individual‐based model consisting of growth, flowering, and survival processes was used to estimate lifetime reproductive outputs under three treatments of light conditions. These analyses indicated that A. mono had high variation in lifetime reproductive output under different light conditions, and that the variation was mainly caused by the growth response and not by the flowering response. In contrast, A. amoenum showed stable lifetime reproductive outputs across all light conditions. Our results demonstrated that responses detected by data analyses do not always lead to changes in lifetime reproductive output. This result highlights the importance of lifetime integration for the evaluation of the long‐term impact of performance responses. These results also revealed some of the ways in which individuals of the two Acer species may contribute to overall population regulation.
Characterization of an Aedes aegypti bacterial artificial chromosome (BAC) library and chromosomal assignment of BAC clones for physical mapping quantitative trait loci that influence Plasmodium susceptibility
Authors: Jiménez L. V. , Kang B.‐K. , DeBruyn B. , Lovin D. D. , Severson D. W. 
Published: December 2004

AbstractPrevious studies have confirmed a genetic basis for susceptibility of mosquitoes to Plasmodium parasites. Here we describe our efforts to characterize a bacterial artificial chromosome genomic library for the yellow fever mosquito, Aedes aegypti, and to identify BAC clones containing genetic markers that define quantitative trait loci (QTL) for Plasmodium gallinaceum susceptibility. This library (NDL) was prepared from the Ae. aegypti Liverpool strain and consists of 50 304 clones arrayed in 384‐well microplates. We used PCR analysis with oligonucleotide primer pairs specific to 106 genetic markers (as sequence‐tagged sites or STS) to screen the NDL library. Each STS identified between one and thirteen independent clones with an average of 3.3 clones. The average insert size was 122 kb and therefore the NDL library provides approximately 7.87‐fold genome coverage. The availability of the NDL library should greatly facilitate physical mapping efforts, including positional cloning of QTL for traits of interest such as Plasmodium susceptibility and for whole genome sequence determination and assembly.
Three new species of Sarcophaga Meigen found during ecological studies on flesh flies (Diptera: Sarcophagidae) in Thailand
Authors: Pape Thomas , Bänziger Hans 
Published: December 2004

AbstractThree new species of Sarcophaga Meigen, 1826 are described from Thailand: Sarcophaga (Sarcosolomonia) circa sp. nov., S. (Mehria) lanna sp. nov. and S. (Rosellea) suthep sp. nov.
Identification of novel single nucleotide polymorphisms within the NOTCH4 gene and determination of association with MHC alleles
Authors: Tazi‐Ahnini R. , Timms J. M. , Cox A. , Wilson A. G. 
Published: December 2004

SummaryMapping of disease susceptibility loci within the MHC has been partly hampered by the high degree of polymorphism of the HLA genes and the high level of linkage disequilibrium (LD) between markers within the MHC region. It is therefore important to identify new markers and determine the level of LD between HLA alleles and non‐HLA genes. The NOTCH4 gene lies at the centromeric end of the MHC class III region, approximately 335 kb telomeric of the DRB1 locus. The encoded protein is an oncogene that is important in regulating vascular development and remodelling. A recent report has linked polymorphisms within NOTCH4 with risk of developing schizophrenia. We have investigated if coding polymorphisms exist within this gene and have identified three single nucleotide polymorphisms; a synonomous T to C transition at +1297 (HGBASE accession number SNP000064386), a synonomous A to G transition at +3061 (SNP000064387) and an A to G transition at +3063 which results in a replacement of glycine with aspartic acid at amino acid 279 (SNP000064388). The allele frequencies of +1297T, +3061A and +3063G were 0.65, 0.66 and 0.66, respectively. Linkage disequilibrium was detected both between these markers and with MHC alleles. These findings can be used in the fine mapping of disease susceptibility alleles within the MHC.
An evaluation of Com‐B27, a fluorescein‐conjugated mouse anti‐HLA‐B27 reagent
Authors: Coates E. , Rees T. J. , Darke C. 
Published: December 2004

SummaryWe evaluated the HLA‐B27 typing reagent Com‐B27, which is claimed to show minimal cross‐reactivity with HLA‐B7, for use in flow cytometry‐based typing. This combination reagent consists of the fluorescein‐conjugated HLA‐B27 mouse monoclonal antibody ABC‐m3 and a non‐conjugated HLA‐B7 monoclonal antibody that is claimed to block the reactivity of ABC‐m3 to B7 without affecting its reactivity to B27. It reacted well with B27 (B*2702, B*2705) and B2708 [mean median channel fluorescence intensity (MCFI) 8.40] and weakly with B7 (including cells from homozygous B*07 donors), B42/B73 and B22/B37/B44 reference cells (mean MCFI 2.05, 3.09 and 1.10, respectively). It showed a uniform discrimination between B7 and B27/B2708 with no ‘overlap’ in MCFI values, which was seen with the standard ABC‐m3 antibody. There was complete agreement when our standard three‐antibody‐based B27/B2708 flow cytometry assay and the Com‐B27 reagent alone were used to independently assign B27/B2708 status to 651 random patients. Thus, the Com‐B27 reagent provided improved discrimination between B7 and B27/B2708 over the ABC‐m3 antibody, and its B27/B2708 assignments were comparable with our standard flow cytometry assay. However, for consistently reliable B27/B2708 typing we continue to recommend the use of a minimum of two B27 reagents in a protocol that includes DNA‐based testing of ‘equivocal’ B27/B2708 assignments.
Genetic susceptibility to carrageenan‐induced innate inflammatory response in inbred strains of rats
Authors: Joe B. , Garrett M. R. , Dene H. , Remmers E. F. , Meng H. 
Published: December 2004

SummaryRat models are useful for the genetic dissection of the biology of innate immunity. Inbred rat strains were evaluated for carrageenan‐induced innate inflammatory responses. Results indicated that the genetic control of innate immune responses is polygenic and influenced by gender, and may not necessarily be consistent with the genetics of experimental arthritis. The newly identified susceptible strains, in order of decreasing susceptibility, include Dahl salt‐sensitive (S), Dahl salt‐resistant (R), Milan normotensive strain (MNS) and Wistar Kyoto (WKY) rats. Similarly, the newly identified relatively resistant strains, in decreasing order of resistance, include DA rats, spontaneously hypertensive rats (SHRs) and Brown Norway (BN) rats. Linkage analyses using combinations of these susceptible and resistant strains are proposed.
A linkage analysis of the CTLA4 gene region in Finnish patients with type 1 diabetes
Authors: Turpeinen H. , Laine A. P. , Hermann R. , Simell O. , Veijola R. , Knip M. , Ilonen J. 
Published: December 2004

SummaryThe cytotoxic T‐lymphocyte antigen 4 (CTLA4) region on 2q33 has been shown to be linked to, and associated with, type 1 diabetes (T1D) and suggested to be one of the loci contributing to diabetes aetiology. The polymorphisms responsible for the effect are yet not defined, and the findings reported for the known markers have been discrepant in various populations. We analysed 15 markers around the CTLA4 gene in 138 Finnish affected sib‐pair families. A maximum multipoint LOD score (MMLS) of 0.83 at the CTLA4‐(AT)n microsatellite was obtained for the whole data set. When stratified, the MMLS increased to 2.61 in the IBS2 (identical by state 2) dataset. In a transmission/disequilibrium test (TDT), some sex‐specific effects were observed in transmissions of alleles of CTLA4‐(AT)n and D2S105 in siblings. The transmission of the CTLA4 +49 A/G single nucleotide polymorphism (SNP) did not deviate from the expected frequency in this study. In conclusion, our study confirms the linkage of the CTLA4 region to T1D in the Finnish population. In addition, the observations suggest that the polymorphism actually involved in the disease is not the CTLA4 +49 A/G SNP but a polymorphism in linkage disequilibrium with CTLA4 markers and probably closer to CTLA4‐(AT)n than to the CTLA4 +49 A/G SNP.
The application of double‐layer theory to drainage, drying and wetting, and the Gapon Exchange constant in a soil with mono‐ and divalent cations
Authors: Collis‐George N. 
Published: December 2004

SummaryClassical double‐layer theory is adapted to consider drainage under gravity, air‐drying, rewetting with distilled water or with solution, and cation exchange when the double‐layer is under a very small retaining pressure or matric potential. In this study, the solid system retains its geometry and the double‐layers are either bounded by an air–water interface or are restricted by the solid geometry. The model as presented is suitable for PCs but is restricted to mono‐ and divalent cations in the presence of a monovalent anion. Representative results for three surface charge densities, three ionic strengths and three ratios of mono‐ to divalent cations are presented. During drainage, the proportion of monovalent cations increases slightly, the ambient anion concentration decreases, whereas the ionic ratio is relatively constant. During drying by evaporation, the proportion of monovalent cations decreases markedly, whereas the anion concentration and the ionic ratio both increase in the ambient solution. These patterns affect the behaviour of roots and organisms in the soil.The Gapon Exchange constant is found to vary with the initial composition of the double‐layer and with the composition of the added solution, but for each combination it tends to an equilibrium value as the volume of the added solution increases. The value of the constant is sensitive to the charge density of the clay surface; the greater the charge density the smaller is the Gapon Exchange constant, suggesting that it should be referred to as the Gapon parameter rather than the Gapon constant. The limitations of the classical theory are discussed in relation to the results obtained.
Concentrations of 60 elements in the soil solution as related to the soil acidity
Authors: Tyler G. , Olsson T. 
Published: December 2004

SummaryLittle is known about solubility and soil solution concentrations of most elements occurring in the solid phase of soils. This study reports changes in solution concentrations of 60 mineral elements following CaCO3 addition to a moderately acid semi‐natural soil, and possible mechanisms accounting for the differing solubility patterns as related to soil acidity are discussed. Soil solutions were obtained by high‐speed centrifuging and ultrafiltration (0.2 μm) of samples at 60% water‐holding capacity of the A horizon of a Cambisol developed from a shale–gneiss moraine and supplied with CaCO3 at 20 rates to yield a soil solution pH range of 5.2–7.8. Concentrations of elements were determined in the solutions by ICP‐AES or (for most elements) ICP‐MS. Several distinct patterns of soil solution concentrations as a function of soil solution pH were demonstrated. Positively related to pH and CaCO3 supply were soil solution concentrations of As, Br, Mo, S, Sb, Se, U, and W, and to a lesser degree, Co, Cr, Hg, Mg, and Sr. Inversely related to pH were concentrations of Al, B, Ba, Bi, Cs, Ce, Eu, Ga, Ge, Fe, Li, K, Rb, Na, Th, and Ti; less distinctly inversely rated were Dy, Er, Gd, Hf, La, Lu, Mn, Nd, Pr, Sm, Sc, Si, Tl, Tm, and Yb. ‘U‐shaped’ relationships to pH were demonstrated for the concentrations of Ag, Cd, Nb, Ni, P, V, and Zr. There were no or irregular relations between pH and concentrations of Be, Cu, Ho, Pb, Ta, and Tb. Differences between elements in their soil solution concentrations as related to total (HNO3‐digestible) concentrations and the solubility of organic C were also treated. Increasing the pH of a soil by adding CaCO3 changes the solubility of most mineral elements substantially, the several distinct patterns observed being governed by, for example, ionic properties and charge, affinity for organic compounds, and pH‐dependent formation and solubility of complexes.
Losses of carbon and nitrogen with prolonged arable cropping from sandy soils of the South African Highveld
Authors: Lobe I. , Amelung W. , Du Preez C. C. 
Published: December 2004

SummaryA knowledge of the kinetics of organic matter transformations in arable soils is important for managing them sustainably. Our aim in this study was to elucidate the effects of cropping period on pools of C and N in coarse‐textured savanna soils of the South African Highveld. Composite samples were taken from the top 20 cm of soils (Plinthustalfs) that have been cropped for lengths of time varying from 0 to 98 years in each of three different agro‐ecosystems in the Free State Province of South Africa. Thereafter, soil organic C and N concentrations were determined in the bulk soil (< 2 mm) as well as in the clay (< 2 μm), silt (2–20 μm), fine sand (20–250 μm), and coarse sand (250–2000 μm) separates. Long‐term cultivation of native grassland reduced soil C and N concentrations by 65 and 55%, respectively. Losses of soil organic matter occurred from all particle‐size separates, although rate loss constants increased as particle size increased. The concentrations of organic C reached equilibrium after 34 years for the bulk soil and after 55 years for clay‐size separates. Nevertheless, organic matter attached to silt continued to be lost as the cropping continued, probably due to wind erosion. Changes in soil properties thereby continued even after almost 100 years of cultivation.
Regolith and soils in Bhutan, Eastern Himalayas
Authors: Baillie I. C. , Tshering Kado , Dorji Tshering , Tamang H. B. , Dorji Tsheten , Norbu Chencho , Hutcheon A. A. , Bäumler R. 
Published: December 2004

SummaryBhutan lies at altitudes of 100–7500 m on the steep, long and complex southern slopes of the Eastern Himalayas. Soil surveys show that, despite steep gradients, there are many moderately or deeply weathered soils. Many slopes are mantled with polycyclic, layered drift materials, so soil horizons owe as much to regolith heterogeneity as to pedogenesis. In the limited arable areas soil profiles are further complicated by rice cultivation and the construction, maintenance and irrigation of flat terraces on steep slopes. Some natural pedogenic horizonation is apparent, and there is an altitudinal zonation of soil types. Although the climate is warm and seasonally wet, most soils on the subtropical southern foothills are not particularly weathered and leached. The foothills are seismically active, and many soils are formed in unstable landslide debris. Elsewhere the regoliths are more stable. The main soils up to about 3000 m in the inner valleys are moderately weathered and leached, and have bright subsoil colours and thin dark topsoils. Above these there is a zone of bright orange‐coloured non‐volcanic andosolic soils. Further upslope there are acid soils with thick surface litter, stagnogleyic topsoils, and drab brown subsoils with organic cutans. These grade to weak podzols, which extend from about 3500 m up to the treeline, around 4000 m. Above this, alpine turf soils, with deep, dark, and friable topsoils and yellowish friable subsoils, are intermixed with unweathered glacial deposits. The interactions between pedogenesis and the deposition of the varied and layered drift materials complicate mapping and classification of the soils.
Immobilization of the heavy metals Cd, Cu and Pb in an acid soil amended with gypsum‐ and lime‐rich industrial by‐products
Authors: Illera V. , Garrido F. , Serrano S. , García‐González M. T. 
Published: December 2004

SummaryIn situstabilization of heavy metals in contaminated soils by the addition of various types of soil amendment is an attractive technique for remediation. We investigated the potential of three industrial by‐products (phosphogypsum, red gypsum and dolomitic residue) for boosting the heavy metal sorption capacity of an acid soil (patents pending, Spanish applications no 200201704 and 200201375) by using sorption isotherm experiments. The three by‐products were found substantially to increase the retention of lead, cadmium and copper on the solid components of the soil. The increase in lead retention of the soil horizons upon the addition of both phosphogypsum and red gypsum was dominated by the formation of anglesite minerals. The dolomitic residue increased the metal retention capacity of the soil horizons through the precipitation of laurionite‐type minerals as well as cadmium and copper hydroxy‐chlorides. In addition to the batch sorption study, we used scanning electron microscopy to investigate the metal sorption processes in the soil by the effect of the treatments. Lead was frequently found to be linked to the edge charges of kaolinite minerals. The three metals were found to be associated with organic matter in the Ap horizon treated with the three by‐products. Finally, the three metals were found to be associated with undissolved dolomitic residue particles.
Influence of soil composition on adsorption of glyphosate and phosphate by contrasting Danish surface soils
Authors: Gimsing A. L. , Borggaard O. K. , Bang M. 
Published: December 2004

SummaryThe herbicide glyphosate and inorganic phosphate are strongly adsorbed by inorganic soil components, especially aluminium and iron oxides, where they seem to compete for the same adsorption sites. Consequently, heavy phosphate application may exhaust soil's capacity to bind glyphosate, which may lead to pollution of drain‐ and groundwater. Adsorption of phosphate and glyphosate to five contrasting Danish surface soils was investigated by batch adsorption experiments. The different soils adsorbed different amounts of glyphosate and phosphate, and there was some competition between glyphosate and phosphate for adsorption sites, but the adsorption of glyphosate and phosphate seemed to be both competitive and additive. The competition was, however, less pronounced than found for goethite and gibbsite in an earlier study. The soil's pH seemed to be the only important factor in determining the amount of glyphosate and phosphate that could be adsorbed by the soils; consequently, glyphosate and phosphate adsorption by the soils was well predicted by pH, though predictions were somewhat improved by incorporation of oxalate‐extractable iron. Other soil factors such as organic carbon, the clay content and the mineralogy of the clay fraction had no effect on glyphosate and phosphate adsorption. The effect of pH on the adsorption of glyphosate and phosphate in one of the soils was further investigated by batch experiments with pH adjusted to 6, 7 and 8. These experiments showed that pH strongly influenced the adsorption of glyphosate. A decrease in pH resulted in increasing glyphosate adsorption, while pH had only a small effect on phosphate adsorption.