bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of candidate genes on chromosome 19 in coeliac disease: an association study of the KIR and LILR gene clusters
Authors: Moodie S. J. , Norman P. J. , King A. L. , Fraser J. S. , Curtis D. , Ellis H. J. , Vaughan R. W. , Ciclitira P. J. 
Published: March 2003

SummaryCoeliac disease is strongly heritable, with more than half of the genetic susceptibility estimated to come from genes outside the HLA region. Several candidate regions have been suggested from genome‐wide linkage studies including chromosome 19q13.4 where linkage has been replicated between populations. The natural killer (NK) cell immunoglobulin‐like receptors (KIRs) and leukocyte immunoglobulin‐like receptor (LILR, also known as ILT and LIR) gene clusters lie within this region in the leukocyte receptor cluster (LRC). KIR molecules are involved in cytotoxic lymphocyte function and expressed by intraepithelial T and NK cells in the duodenum. We studied 132 unrelated UK Caucasian coeliac patients and their parents together with a control group of 171 UK Caucasians. PCR‐SSP for KIR2DL1, KIR2DL2, KIR2DL3, KIR2DL5, LILRA3 (ILT6), LILRA3 deletion and an LILRA3 exon 3 single nucleotide polymorphism (SNP) allowed classification of KIR genotypes into five categories and determination of homozygosity or heterozygosity for the common A and B type KIR haplotypes (as defined in the text) and for the LILRA3 deletion. Case–control analysis found no association of the five KIR genotype categories, the A or B KIR haplotypes, the LILRA3 gene deletion or the LILRA3 exon 3 SNP with coeliac disease. A transmission disequilibrium test also found no association of the A and B KIR haplotypes or the LILRA3 gene deletion with coeliac disease.
Complete characterization of the DQB1 first exon polymorphism
Authors: Pascual M. , López‐Nevot M. A. , Caballero A. , Alonso A. , Zanelli E. , Martín J. 
Published: March 2003

SummaryHere we report an additional source of variation resulting from genetic polymorphism in HLA‐DQβ1 genes, namely, allelic diversity in the first exon of the HLA‐DQB1 locus, which encodes the leader peptide sequence. Six different variants, including a novel polymorphic site, were detected among the DBQ1 haplotypes.
Carbon mineralization, nitrogen immobilization and pH change in soil after adding volatile fatty acids
Authors: SØRENSEN P. 
Published: March 2003

SummaryVolatile fatty acids (VFAs) accumulate in animal manure when it is stored anaerobically, and they quickly decompose when the manure is applied to soil. In this study the influence of VFAs on the immobilization of N and mineralization of C in soil was investigated by incubating mixtures of acetate, propionate and butyrate in soils containing varying amounts of clay. The oxidation of VFAs (300 μg C g−1 soil) caused a significant increase in pH (0.6–2.2 pH units), with the largest increase in the most coarse‐textured soil. The maximum net immobilization of N resulting from decomposition of the VFAs was 33–77 mg N g−1C and was maximal after 1–5 weeks of decomposition. After this time immobilized N was remineralized, and after 12 weeks the VFAs caused no net immobilization of N in the two most sandy soils. Despite this, the concentration of N in the microbial biomass was still greater in the soil amended with VFAs than in the control. After 12 weeks, the mineralization of C from the decomposition of the VFAs was equivalent to 60–113% of the applied C. It seems that mineralization of native soil C and N was stimulated by adding VFAs, except in the most clayey soil. This stimulation was presumably caused by the increase in the soil's pH as the VFAs oxidized.
A new approach for determining effective soil hydraulic functions
Authors: VOGEL H. J. , ROTH K. 
Published: March 2003

SummaryWe investigated the possibility of inferring effective hydraulic properties of soil from the structure of the pore space. The aim was to identify structural properties, which are essential for water flow, so that physical experiments may be replaced by direct morphological measurements. The pore structure was investigated in three dimensions by serial sections through impregnated samples. The complex geometry of pore space was quantified in terms of two characteristics: pore‐size distribution and pore connectivity. Only pores larger than 0.04 mm were considered. The results were used as input parameters for a pore‐scale network model. The main desorption branch of the soil‐water characteristic and the corresponding hydraulic conductivity function of the network model were calculated by numerical simulation. The simulation results, which are exclusively based on morphological investigations, were compared with independently measured results from a multi‐step outflow experiment. This approach was demonstrated for two centrasting soil materials: the A and B horizons of a silty agricultural soil. The simulations were close to the experimental data, except for the absolute values of the hydraulic conductivity. The pore‐size distribution and pore connectivity govern the shape of hydraulic functions and the applied morphometric methods are suitable for predicting essential characteristics of hydraulic soil properties.
Gas diffusion in a silty‐clay soil: experimental study on an undisturbed soil core and simulation in its three‐dimensional reconstruction
Authors: Cousin I. , Porion P. , Renault P. , Levitz P. 
Published: March 2003

SummaryTransport of gas in soil depends on the paths available through the porous system. We determined the rate of diffusion of air through a core of silty‐clay soil experimentally. After the experiment, the core was impregnated with resin and sectioned at 100 μm. From the images of the sections, the porous structure was reconstructed in three dimensions with a 100‐μm resolution and gas diffusion was simulated in it. We computed the self‐diffusion to describe gas diffusion. The experiment and simulation were compared using tortuosity, which is the ratio between the self‐diffusion coefficient calculated in air and the coefficient calculated in the reconstructed sample. The results showed that the experimentally measured tortuosity (2.3) and the numerically calculated tortuosity (1.75) were similar. This suggests that the self‐diffusion propagator is useful for simulating self‐diffusion in a numerical three‐dimensional reconstructed sample and that the scale chosen for the reconstruction of the sample (100 μm) was suitable for this particular soil. Résumé Les propriétés de transfert en phase gazeuse des sols ont étéétudiées sur un sol limono‐argileux. A l’issue de l’expérience, l’échantillon a été imprégné avec une résine polyester puis sectionné en coupes sériées. A l’aide des images numérisées des coupes, l’échantillon a été reconstruit en trois dimensions. Nous avons ensuite simulé le processus de diffusion gazeuse dans l’échantillon reconstruit à l’aide du propagateur de diffusion. Expérience et simulation ont été comparées à l’aide de la tortuosité, rapport entre le coefficient de diffusion gazeuse dans l’air et celui dans le sol. Les résultats montrent que la tortuosité mesurée expérimentalement (2,3) et la tortuosité calculée numériquement (1,75) sont proches. Ceci prouve que l’utilisation du propagateur de diffusion est justifiée pour la simulation du processus de self‐diffusion dans un échantillon tridimensionnel reconstruit et que l’échelle choisie pour la reconstruction (100 μm) s’avère pertinente pour l’étude de la diffusion gazeuse dans ce sol.
Vertical distribution of low molecular weight aliphatic carboxylic acids in some forest soils of Japan
Authors: Tani M. , Higashi T. 
Published: March 2003

SummaryLow molecular weight organic acids are widespread and reactive in soils, but their distribution among mineral horizons is uncertain. We investigated the distribution of low molecular weight aliphatic carboxylic acids (LACAs) in three Japanese forest soils, two Acid Brown Forest soils and one Podzolic soil. The total LACAs ranged from 207.3 to 411.8 μmol kg–1 and were abundant in the lower horizons as well as in the surface horizons of these soils. The illuvial horizons of the Podzolic soil were rich in adsorbed oxalic acid and citric acid. Total LACAs were similar in the two subtypes of Brown Forest soils derived from different parent materials but formed under similar vegetation and climate, and were larger than that in the Podzolic soil. Among the volatile LACAs, formic acid and acetic acid dominated the moist horizons containing much organic material, whereas the non‐volatile LACAs, the most abundant being oxalic acid and citric acid, increased in the subsurface horizons. The distribution of water‐soluble LACAs in the Brown Forest soil profiles was closely correlated with soil acidity.
Simulation of the effect of citrate exudation from roots on the plant availability of phosphate adsorbed on goethite
Authors: Geelhoed J. S. , Van Riemsdijk W. H. , Findenegg G. R. 
Published: March 2003

SummaryRhizosphere processes strongly influence the availability of phosphorus (P) to plants. Organic ligands that are exuded from the root surface mobilize phosphorus by dissolution of P minerals or by desorption of adsorbed phosphate. We developed a mechanistic model to study the mobilization of phosphate sorbed on goethite by the exudation of citrate and consequent uptake of phosphate by the root. The use of a model allows the effects of the organic anion and pH on P desorption to be separated. The model is also used to predict concentration profiles developing around the root for phosphate, citrate (with or without accounting for degradation) and pH, providing insight into the processes that occur in the rhizosphere. Results of model calculations show that with larger rates of citrate exudation, greater P availability is predicted. Exudation at a rate of 0.5 μmol citrate m–1 root day–1, which is in the range found for P‐deficient plants, increased P availability almost 2‐fold at fairly large phosphate loading of goethite (1.9 μmol m–2) and almost 30‐fold at small phosphate loading (1.3 μmol m–2). Competitive adsorption causes a much greater relative increase in the phosphate concentration in solution at small than at large phosphate loading, which explains this result. Simultaneous acidification of the rhizosphere results in a smaller P mobilization than at a fixed pH of 5, as a result of the pH dependence of phosphate adsorption in the presence of citrate. Sorption of citrate increases its persistence against microbial decay, and hence has a positive effect on the mobilization of adsorbed phosphate.
A numerical experiment on pore size, pore connectivity, water retention, permeability, and solute transport using network models
Authors: Vogel H. J. 
Published: March 2003

SummaryNetwork models are idealized geometrical representations of porous media. They allow the simulation of effective hydraulic properties and of solute transport for well‐defined porous structures. In this paper, the relation between pore structure and effective properties is studied using a network model which can be adjusted to predefined pore‐size distributions and pore topologies. I show that pore topology can be adjusted such that quite different pore‐size distributions lead to essentially identical water retention curves. This puts into question the common interpretation of the retention curve as being indicative of the pore‐size distribution. However, I also found that both the hydraulic conductivity and the dispersion of a solute depend on the water retention curve and not on the particular combination of pore‐size distribution and topology which make it up. This corroborates the widely used approach of inferring relative permeabilities from water retention data.
The effect of iron concentration, hindered settling, saturating cation and aggregate density of clays on the size distribution determined by gravitation X‐ray sedimentometry
Authors: Watts C. W. , Whalley W. R. , Bird N. R. A. , Ashman M. R. 
Published: March 2003

SummaryX‐ray sedimentation is potentially attractive for estimating the particle‐size distribution of soil, but has been thought to overestimate clay fractions because of the iron they contain. We have examined X‐ray sedimentation for estimating the particle‐size distribution of fully dispersed and of aggregated clay. We obtained good agreement between the pipette and X‐ray sedimentation methods using two different kaolinite samples with a small iron concentration. We also studied montmorillonite saturated with Li, Na, K, Mg or Ca to investigate possible effects of hindered settling. For the Ca montmorillonite, we obtained good agreement between X‐ray sedimentation and the pipette method at concentrations up to 40 g l−1. We also found that X‐ray sedimentation could be used at concentrations less than those recommended by the manufacturer. Hindered settling was observed at concentrations > 20 g l−1 for Li‐ and Na‐saturated montmorillonite. Our data suggest that conducting experiments at different mass concentrations is a sensitive test to detect such problems. Finally we used a fractal model to investigate the possible errors that might result from the size dependence of aggregate density and show that the error caused by assuming a single value for particle density of solids is small.
Reactions of zinc with iron‐oxide coated calcite surfaces at alkaline pH
Authors: Uygur V. , Rimmer D. L. 
Published: March 2003

SummaryBoth iron oxides and carbonate minerals, such as calcite, can sorb zinc (Zn), and therefore are important in controlling the solution concentration and availability of Zn to plants growing in calcareous soil. When present together, interactions between these components affect their sorption behaviour. We investigated changes in the reactions of Zn with calcite at alkaline pH, as the calcite surface was progressively coated by iron oxide. Coated calcite surfaces were prepared that had from 0.05 to 1.45% iron oxide. The initial concentration of Zn and the amount of iron oxide on the calcite were the most critical factors affecting adsorption, precipitation of solid phases, and the desorbability of sorbed Zn. For pure calcite at small initial Zn concentrations (< 2.5 × 10−5 m) adsorption was dominant; with increasing concentration, precipitation of hydrozincite (ZHC) became more important. With increasing amounts of iron oxide the amount of Zn adsorbed increased, the desorbability of the Zn decreased, and precipitation became progressively less evident, and at 1.45% iron oxide content there was no evidence of any precipitation of ZHC. The calculated maximum adsorption attributable to the iron oxide coating was inversely proportional to the thickness of the oxides on the calcite, and greatly exceeded that of iron oxide as a separate phase. The common occurrence of iron‐coated carbonates in calcareous soils and their capacity to adsorb Zn contributes to the problems of Zn deficiency, for which these soils are noted.
Aluminium solubility mechanisms in moderately acid Bs horizons of podzolized soils
Authors: Gustafsson J. P. , Berggren D. , Simonsson M. , Zysset M. , Mulder J. 
Published: March 2003

SummaryThe processes controlling the retention and release of aluminium in acid forest soils are still subject to controversy, and therefore a universal hypothesis as to what mechanisms are operating has not been firmly established. By studying the Bs horizons of Swedish and Swiss podzolized soils, and by analysing data in the literature, we have found that aluminium hydroxide, and in some cases also poorly ordered imogolite, may control Al solubility in moderately acid (pH > 4.2–4.3) Bs horizons. The strongest evidence in support of the presence of a quickly reacting Al(OH)3 pool came from the temperature dependence of Al solubility in a Bs horizon, which was consistent with the reaction enthalpy of an Al(OH)3 phase such as gibbsite, and from the observation that the ion activity product for Al(OH)3 was the same regardless of whether equilibrium was reached from over‐ or undersaturation. The pool of Al(OH)3 is commonly small and may be completely dissolved after large additions of acid. This may be explained by the continuing redissolution of reactive Al(OH)3 to form less soluble imogolite‐type phases. By using the same methods it was found that soil suspensions did not reach equilibrium with poorly ordered imogolite even after 17 days. Thus, imogolite probably does not control Al solubility in the short term in many soils despite the common occurrence of this mineral. This is due to the relatively slow kinetics of imogolite formation and dissolution, especially at low temperatures and at small solution H4SiO4 concentrations.
Effect of termites on clay minerals in tropical soils: fungus‐growing termites as weathering agents
Authors: Jouquet P. , Mamou L. , Lepage M. , Velde B. 
Published: March 2003

SummaryTermites of the subfamily Macrotermitinae play an important role in tropical ecosystems: they modify the soil's physical properties and thereby make food available for other organisms. Clay is important in the architecture of Macrotermitinae termite nests, and it has been postulated that termites could modify the mineralogical properties of some clays. We have tested this hypothesis of clay transformation by termites in the laboratory under controlled conditions, using Odontotermes nr. pauperans termite species, one of the main fungus‐growing species at Lamto Research Station (Côte d'Ivoire). Soil handled by termites in nest building was saturated with SrCl2, glycol or KCl and afterwards heated at 250°C for X‐ray diffraction analyses. Termite handling led to an increase in the expandable layers of the component clay minerals. Heating and saturation by potassium of modified clays did not close the newly formed expandable clay layers. However, differences occurred between parts of the constructions built by termites, and the clays can be ranked according to their degree of alteration in the following order: unhandled soils < galleries < chamber walls. Consequently, termites can be seen as weathering agents of clay minerals, as previously shown for micro‐organisms and plants.
The use of brushwood bundles as fish spawning media
Authors: Nash K. T. , Hendry K. , Cragg‐Hine D. 
Published: March 2003

AbstractSalford Quays is a redeveloped freshwater dockland, which initially constituted part of the grossly polluted Manchester Docks, Manchester, UK. Such water bodies are characterized by a lack of suitable spawning sites and littoral refuges, and this will act to reduce fish recruitment. To redress this, a variety of artificial spawning substrates were introduced to these waters. Spawning structures were made from bundles of different types of thin brushwood suspended from the dock walls. Roach, Rutilus rutilus (L.), spawned on bundles of willow, Salix alba (L.), and spruce, Pilea abies (L.), branches, whilst perch, Perca fluviatilis L., spawned on bundles of willow, sycamore, Acer pseudoplatanus (L.), spruce and plastic netting. Unused bundles were made up of lime, Tilia platyphyloss (Scop.), pear willow, Pyrus salicitolia (Pall.), and laurel, Laurus nobilis (L.). Perch spawning began around 20 May and showed a preference for open structures (between one and three ribbons per bundle). Roach spawning began about 10 days after perch and showed a preference for dense bundles of spruce (geometric mean egg density 1.5 cm− 2 spruce). The use of such structures in fisheries management is discussed.
Comparison of mortality of wild and released reared 0‐group turbot, Scophthalmus maximus, on an exposed beach (Ría de Vigo, NW Spain) and a study of the population dynamics and ecology of the natural population
Authors: Iglesias J. , Ojea G. , Otero J. J. , Fuentes L. , Ellis T. 
Published: March 2003

Abstract
Marked reared turbot,
Scophthalmus maximus (L.) (594) were released onto an exposed beach nursery ground together with marked wild fish (438) of approximately the same size (4–6 cm TL) and were sampled at intervals for 38 days. A consistent ratio of marked wild: unmarked wild indicated that marking did not increase mortality. The wild 0‐group turbot population size was estimated at 1540 at the time of release, indicating that hatchery‐reared individuals could theoretically make a significant contribution to the local population size. However, the absolute and relative catches of the marked, reared fish were lower than those of the marked wild fish, and no reared fish were caught after 23 days. The higher mortality rate was attributed to both a smaller size and their hatchery‐reared origin. The population dynamics of the 1994–1995 year‐classes of wild turbot were also studied. Recruitment of post‐larvae (3 cm) to the beach started in March and continued until October. Population size peaked over the August–October period. Juvenile turbot remained on the nursery beach until June of the following year when they presumably emigrated to deeper water. During this 15‐month period their length increased from 3 to 12–15 cm.
Uncertainty about estimating total returns of Atlantic salmon, Salmo salar to the Gander River, Newfoundland, Canada, evaluated using a fish counting fence
Authors: O'Connell M. F. 
Published: March 2003

Abstract
For a number of rivers in Newfoundland, Atlantic salmon,
Salmo salar L., is managed in relation to river‐specific conservation spawning requirements. One such river is the Gander River, where between 1989 and 1999, the escapement of Atlantic salmon, a major factor in assessing the status of stock, was determined using a fish counting fence. In 2000, the counting fence was discontinued and alternative means of calculating total returns were explored. Regression and simulation methods, using relationships between total returns and salmon counts at an upstream tributary during 1989–99, formed the basis for estimates of returns for 2000, and the uncertainty around estimates. The accuracy of methods is evaluated by retrospective comparisons with actual total returns between 1989 and 1999. Estimates of total returns deviated from the actual by as much as 50–60%, depending on the method. Management implications of the approach are discussed.
Return migration of adult Atlantic salmon, Salmo salar, in relation to water diverted through a power station
Authors: Thorstad E. B. , Økland F. , Johnsen B. O. , Næsje T. F. 
Published: March 2003

Abstract
The migration of Atlantic salmon,
Salmo salar L., returning to the River Suldalslågen, Norway, was studied in relation to redirection of freshwater flow through a power station. The outlet of the power station is situated in the Hylsfjord, a fjord adjacent to the river mouth. Seventy‐two salmon were tagged with acoustic transmitters, released in the outer part of the fjord system and automatically recorded when entering the Hylsfjord or the river. Data were collected during one period when the power station was running and two periods when the power station was closed. The release of water from the power station did not greatly attract the salmon during their return migration. Proportions of salmon entering the river or time from release to entering the river did not differ among salmon tagged in the different periods. The salmon were recorded in the Hylsfjord both when the power station was running and closed and there were no differences in number of times, number of days or hours recorded in the Hylsfjord among salmon tagged in the three periods. The only significant difference found among periods was duration of continuous stays in the inner part of the Hylsfjord. This may indicate a slight attraction to the freshwater release, but the difference seems small (1.8 vs. 0.7 h) compared with the time the fish stayed in the fjord system before entering the river (16–85 days).