bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhanced laminin binding by α-dystroglycan after enzymatic deglycosylation
Authors: Combs Ariana C. , Ervasti James M.
Published: August 2005

Carbohydrate modifications are clearly important to the function of α-dystroglycan but their composition and structure remain poorly understood. In the present study, we describe experiments aimed at identifying the α-dystroglycan oligosaccharides important for its binding to laminin-1 and carbohydrate-dependent mAbs (monoclonal antibodies) IIH6 and VIA41. We digested highly purified skeletal muscle α-dystroglycan with an array of linkage-specific endo- and exoglycosidases, which were verified for action on α-dystroglycan by loss/gain of reactivity for lectins with defined glyco-epitopes. Notably, digestion with a combination of Arthrobacter ureafaciens sialidase, β(1-4)galactosidase and β-N-acetylglucosaminidase substantially degraded SiaAα2-3Galβ1-4GlcNAcβ1-2Man glycans on highly purified α-dystroglycan that nonetheless exhibited enhanced IIH6, VIA41 and laminin-1 binding activity. Additional results indicate that α-dystroglycan is probably modified with other anionic sugars besides sialic acid and suggest that rare α-linked GlcNAc moieties may block its complete deglycosylation with currently available enzymes.
Density-functional calculation of CeO2 surfaces and prediction of effects of oxygen partial pressure and temperature on stabilities
Authors: Jiang Yong , Adams James B. , van Schilfgaarde Mark
Published: August 2005

We have used density-functional theory to investigate (111), (110), (210), (211), (100), and (310) surfaces of ceria (CeO2). Compared with previous interatomic-potential-based studies, our calculations reported a slightly different relative stability ordering and significantly lower surface energies for the stoichiometric surfaces. Using a defect model, the surface stabilities were evaluated as functions of oxygen partial pressure and temperature. Our investigations were restricted to ideal surface terminations, without considering defect formation on those surfaces. We found that at 300K, the stoichiometric (111) has the lowest free energy for a wide range of oxygen partial pressures up to 1atm, and only at ultrahigh vacuum does the Ce-terminated (111) becomes the most stable one. The transition point for the Ce-terminated (111) surfaces moves to higher oxygen partial pressures when temperature increases. To improve the prediction of electron density of states, we used the local-density approximation plus U(J) correction method to correct the on-site Coulomb correlation and exchange interaction due to the strongly localized Ce-4f electrons. The optimal parameter combination of U=7eV and J=0.7eV was found to improve the O2p–Ce4f gap without much degradation of ground-state bulk properties or the O2p–Ce5d gap. The bulk and surface electronic structures were then analyzed based on the improved density of states.
Smoothening of internal phase boundaries by ion bombardment
Authors: Petersen J. , Mayr S. G.
Published: August 2005

The impact of heavy-ion irradiation on the morphology of bilayers, which are composed of two immiscible metals, is investigated with the help of experiments and molecular-dynamics computer simulations. Using the model system Ag∕Ni, our main focus lies on the interface roughness of the Ag∕Ni phase boundary and its evolution in the course of ion bombardment. The mechanism which underlies these structural changes is identified as radiation-induced viscous flow—in combination with thermodynamic driving forces due to interface stress.
Relativistic dynamics of half-spin particles in a homogeneous magnetic field: An atom with nucleus of spin 1∕2
Authors: Misra Anirban , Datta Sambhu N.
Published: August 2005

An investigation of the relativistic dynamics of N+1 spin-12 particles placed in an external, homogeneous magnetic field is carried out. The system can represent an atom with a fermion nucleus and N electrons. Quantum electrodynamical interactions, namely, projected Briet and magnetic interactions, are chosen to formulate the relativistic Hamiltonian. The quasi-free-particle picture is retained here. The total pseudomomentum is conserved, and its components are distinct when the total charge is zero. Therefore, the center-of-mass motion can be separated from the Hamiltonian for a neutral (N+1)-fermion system, leaving behind a unitarily transformed, effective Hamiltonian H(0) at zero total pseudomomentum. The latter operator represents the complete relativistic dynamics in relative coordinates while interaction is chosen through order α4mc2. Each one-particle part in the effective Hamiltonian can be brought to a separable form for positive- and negative-energy states by replacing the odd operator in it through two successive unitary transformations, one due to Tsai [Phys. Rev. D 7, 1945 (1973)] and the other due to Weaver [J. Math. Phys. 18, 306 (1977)]. Consequently, the projector changes and the interaction that involves the concerned particle also becomes free from the corresponding odd operators. When this maneuver is applied only to the nucleus, and the non-Hermitian part of the transformed interaction is removed by another unitary transformation, a familiar form of the atomic relativistic Hamiltonian Hatom emerges. This operator is equivalent to H(0). A good Hamiltonian for relativistic quantum chemical calculations, HQchem, is obtained by expanding the nuclear part of the atomic Hamiltonian through order α4mc2 for positive-energy states. The operator HQchem is obviously an approximation to Hatom. When the same technique is used for all particles, and subsequently the non-Hermitian terms are removed by suitable unitary transformations, one obtains a Hamiltonian HT that is equivalent to Hatom but is in a completely separable form. As the semidiscrete eigenvalues and eigenfunctions of the one-particle parts are known, the completely separable Hamiltonian can be used in computation. A little more effort leads to the derivation of the correct atomic Hamiltonian in the nonrelativistic limit, Hnonrel. The operator Hnonrel is an approximation to HT. It not only retains the relativistic and radiative effects, but also directly exhibits the phenomena of electron paramagnetic resonance and nuclear magnetic resonance.
Wavelength-dependent effect of ultraviolet irradiation on dielectric constant of boron carbon nitride films
Authors: Zhang Zhengjun , Kimura Chiharu , Sugino Takashi
Published: August 2005

Boron carbon nitride (BCN) films with a low dielectric constant are synthesized by plasma-assisted chemical-vapor deposition. The dielectric constant is measured for the BCN films irradiated with monochromatic ultraviolet lights of 300 and 365 nm in wavelength. It is found that the dielectric constant is decreased due to a 300-nm irradiation while the dielectric constant is enhanced due to a 365-nm irradiation. A reduction in the B–C bond and an increase in the C–N bond occur in the BCN film after the 300-nm irradiation. On the other hand, the 365-nm irradiation leads to an increase in the B–C bond and a reduction in the C–N bond in the film. The 300-nm irradiation is effective in reducing the dielectric constant, suggesting the removal of the molecules with a large polarization.
Deep defects and their electron-capture cross sections in polymorphous silicon-germanium thin films
Authors: Meaudre M. , Gueunier-Farret M. E. , Meaudre R. , Kleider J. P. , Vignoli S. , Canut B.
Published: August 2005

Hydrogenated silicon-germanium alloys (SiGe:H) are deposited by plasma-enhanced chemical vapor deposition in a plasma regime close to that of the formation of powder. It is thus possible to obtain nanostructured materials that we call polymorphous materials, pm-Si1−xGex:H. Studies of space-charge-limited currents and space-charge relaxation allow to get information on midgap states originating from Ge. It is observed that the electron-capture cross section of states at the Fermi level increases linearly with their concentration. This is supported by modulated photocurrent experiments. Finally, it is shown that the variations of both the Ge dangling bond concentration and their electron-capture cross section with Ge content account for the photoresponse in these materials.
Darboux transformations for Schrödinger equations in two variables
Authors: Humi Mayer
Published: August 2005

Darboux transformations in one variable form the basis for the factorization methods and have numerous applications to geometry, nonlinear equations and SUSY quantum mechanics. In spite of this wide range of applications the theory of Darboux transformations in two variables and its elegant relationship to analytic complex functions has not been recognized in the literature. To close this gap we develop in this paper the theory of Darboux transformation in the context of Schrödinger equations in two variables. This yields a constructive algorithm to determine the relationship between potential functions which are related by Darboux transformations.
Strain distribution in arbitrarily shaped quantum dots with nonuniform composition
Authors: Chu H. J. , Wang J.
Published: August 2005

Extensive research over the past several years has revealed graded composition and strong atomistic intermixing between a quantum dot (QD) and its surrounding material. In this paper, the strain and stress fields induced by a QD with an initial misfit strain due to its nonuniform composition are investigated. A general expression of the stress field for an arbitrarily shaped QD structure with a nonuniform composition is presented. It is found that the hydrostatic stress and strain are proportional to the initial misfit strain inside the QD but vanish outside it. The stress field in an arbitrarily shaped QD with a linearly graded composition is studied in detail, and a simple formula containing integrals over the boundary of the QD is derived. It can greatly simplify the numerical calculation of the elastic fields. Based on this formula, a closed-form analytical solution for a cuboidal QD with a linearly graded composition is obtained. It is also demonstrated that the strains inside and around the QD are sensitive to both the composition and the height of the QD in the growth direction.
Stalactite growth as a free-boundary problem
Authors: Short Martin B. , Baygents James C. , Goldstein Raymond E.
Published: August 2005

Stalactites, the most familiar structures found hanging from the ceilings of limestone caves, grow by the precipitation of calcium carbonate from within a thin film of fluid flowing down their surfaces. We have recently shown [M. B. Short, J. C. Baygents, J. W. Beck, D. A. Stone, R. S. Toomey III, and R. E. Goldstein, “Stalactite growth as a free-boundary problem: A geometric law and its Platonic ideal,” Phys. Rev. Lett. 94, 018501 (2005)] that the combination of thin-film fluid dynamics, calcium carbonate chemistry, and carbon dioxide diffusion and outgassing leads to a local geometric growth law for the surface evolution which quantitatively explains the shapes of natural stalactites. Here we provide details of this free-boundary calculation, exploiting a strong separation of time scales among that for diffusion within the layer, contact of a fluid parcel with the growing surface, and growth. When the flow rate, the scale of the stalactite, and the chemistry are in the ranges typically found in nature, the local growth rate is proportional to the local thickness of the fluid layer, itself determined by Stokes flow over the surface. Numerical studies of this law establish that a broad class of initial conditions is attracted to an ideal universal shape, whose mathematical form is found analytically. Statistical analysis of stalactite shapes from Kartchner Caverns (Benson, AZ) shows excellent agreement between the average shape of natural stalactites and the ideal shape. Generalizations of these results to nonaxisymmetric speleothems are discussed.
Charge-trapping memory cell of SiO2∕SiN∕high-k dielectric Al2O3 with TaN metal gate for suppressing backward-tunneling effect
Authors: Lee Chang-Hyun , Park Kyu-Charn , Kim Kinam
Published: August 2005

We present a device structure of SiO2∕SiN∕Al2O3 (SANOS) with tantalum nitride (TaN) metal gate. When TaN metal gate is applied for the SANOS structure instead of commonly used n-type poly-silicon, the unwanted backward Fowler–Nordheim tunneling current of electron through the top oxide is significantly suppressed owing to its higher work function and better compatibility with high-k dielectrics. As a result, the program∕erase speed is significantly improved and the erase threshold voltage (VTH) can be obtained to be negative voltage of −3.5V.
Efficient delivery of small interfering RNA to bone-metastatic tumors by using atelocollagen
in vivo
Authors: Takeshita Fumitaka , Minakuchi Yoshiko , Nagahara Shunji , Honma Kimi , Sasaki Hideo , Hirai Kotaro , Teratani Takumi , Namatame Nachi , Yamamoto Yusuke , Hanai Koji , Kato Takashi , Sano Akihiko , Ochiya Takahiro
Published: August 2005

Silencing of gene expression by small interfering RNAs (siRNAs) is rapidly becoming a powerful tool for genetic analysis and represents a potential strategy for therapeutic product development. However, there are no reports of systemic delivery for siRNAs toward treatment of bone-metastatic cancer. Accordingly, we report here that i.v. injection of GL3 luciferase siRNA complexed with atelocollagen showed effective reduction of luciferase expression from bone-metastatic prostate tumor cells developed in mouse thorax, jaws, and/or legs. We also show that the siRNA/atelocollagen complex can be efficiently delivered to tumors 24 h after injection and can exist intact at least for 3 days. Furthermore, atelocollagen-mediated systemic administration of siRNAs such as enhancer of zeste homolog 2 and phosphoinositide 3′-hydroxykinase p110-α-subunit, which were selected as candidate targets for inhibition of bone metastasis, resulted in an efficient inhibition of metastatic tumor growth in bone tissues. In addition, upregulation of serum IL-12 and IFN-α levels was not associated with the
in vivo
administration of the siRNA/atelocollagen complex. Thus, for treatment of bone metastasis of prostate cancer, an atelocollagen-mediated systemic delivery method could be a reliable and safe approach to the achievement of maximal function of siRNA.
Isolation of a rice regeneration quantitative trait loci gene and its application to transformation systems
Authors: Nishimura Asuka , Ashikari Motoyuki , Lin Shaoyang , Takashi Tomonori , Angeles Enrique R. , Yamamoto Toshio , Matsuoka Makoto
Published: August 2005

Regeneration of plant organs is often the essential step in genetic transformation; however, the regeneration ability of a plant varies depending on the genetic background. By conventional crosses of low-regeneration rice strain Koshihikari with high-regeneration rice strain Kasalath, we identified some quantitative trait loci, which control the regeneration ability in rice. Using a map-based cloning strategy, we isolated a main quantitative trait loci gene encoding ferredoxin-nitrite reductase (NiR) that determines regeneration ability in rice. Molecular analyses revealed that the poor regeneration ability of Koshihikari is caused by lower expression than in Kasalath and the specific activity of NiR. Using theNiRgene as a selection marker, we succeeded in selectively transforming a foreign gene into rice without exogenous marker genes. Our results demonstrate that nitrate assimilation is an important process in rice regeneration and also provide an additional selectable marker for rice transformation.
Kinship-based politics and the optimal size of kin groups
Authors: Hammel E. A.
Published: August 2005

Kin form important political groups, which change in size and relative inequality with demographic shifts. Increases in the rate of population growth increase the size of kin groups but decrease their inequality and vice versa. The optimal size of kin groups may be evaluated from the marginal political product (MPP) of their members. Culture and institutions affect levels and shapes of MPP. Different optimal group sizes, from different perspectives, can be suggested for any MPP schedule. The relative dominance of competing groups is determined by their MPP schedules. Groups driven to extremes of sustainability may react in Malthusian fashion, including fission and fusion, or in Boserupian fashion, altering social technology to accommodate changes in size. The spectrum of alternatives for actors and groups, shaped by existing institutions and natural and cultural selection, is very broad. Nevertheless, selection may result in survival of particular kinds of political structures.
A map of the human genome in linkage disequilibrium units
Authors: Tapper W. , Collins A. , Gibson J. , Maniatis N. , Ennis S. , Morton N. E.
Published: August 2005

Two genetic maps with additive distances contribute information about recombination patterns, recombinogenic sequences, and discovery of genes affecting a particular phenotype. Recombination is measured in morgans (
w
) over a single generation in a linkage map but may cover thousands of generations in a linkage disequilibrium (LD) map measured in LD units (LDU). We used a subset of single nucleotide polymorphisms from the HapMap Project to create a genome-wide map in LDU. Recombination accounts for 96.8% of the LDU variance in chromosome arms and 92.4% in their deciles. However, deeper analysis shows that LDU/
w
, an estimate of the effective bottleneck time (
t
), is significantly variable among chromosome arms because (
i
) the linkage map is approximated from the Haldane function, then adjusted toward the Kosambi function that is more accurate but still exaggerates
w
for all chromosomes, especially shorter ones; (
ii
) the nonpseudoautosomal region of the X chromosome is subject to hemizygous selection; and (
iii
) at resolution less than ≈40,000 markers per
w
, there are indeterminacies (holes) in the LD map reflecting intervals of very high recombination. Selection and stochastic variation in small regions must have effects, which remain to be investigated by comparisons among populations. These considerations suggest an optimal strategy to eliminate holes quickly, greatly enhance the resolution of sex-specific linkage maps, and maximize the gain in association mapping by using LD maps.
The electroosmotic droplet switch: Countering capillarity with electrokinetics
Authors: Vogel Michael J. , Ehrhard Peter , Steen Paul H.
Published: August 2005

Electroosmosis, originating in the double-layer of a small liquid-filled pore (size
R
) and driven by a voltage
V
, is shown to be effective in pumping against the capillary pressure of a larger liquid droplet (size
B
) provided the dimensionless parameter σ
R
2
/ε|ζ|
VB
is small enough. Here σ is surface tension of the droplet liquid/gas interface, ε is the liquid dielectric constant, and ζ is the zeta potential of the solid/liquid pair. As droplet size diminishes, the voltage required to pump eletroosmotically scales as
V
∼
R
2
/
B
. Accordingly, the voltage needed to pump against smaller higher-pressure droplets can actually decrease provided the pump poresize scales down with droplet size appropriately. The technological implication of this favorable scaling is that electromechanical transducers made of moving droplets, so-called “droplet transducers,” become feasible. To illustrate, we demonstrate a switch whose bistable energy landscape derives from the surface energy of a droplet–droplet system and whose triggering derives from the electroosmosis effect. The switch is an electromechanical transducer characterized by individual addressability, fast switching time with low voltage, and no moving solid parts. We report experimental results for millimeter-scale droplets to verify key predictions of a mathematical model of the switch. With millimeter-size water droplets and micrometer-size pores, 5 V can yield switching times of 1 s. Switching time scales as
B
3
/
VR
2
. Two possible “grab-and-release” applications of arrays of switches are described. One mimics the controlled adhesion of an insect, the palm beetle; the other uses wettability to move a particle along a trajectory.
Monitoring disease progression in transgenic mouse models of Alzheimer's disease with proton magnetic resonance spectroscopy
Authors: Marjanska Malgorzata , Curran Geoffrey L. , Wengenack Thomas M. , Henry Pierre-Gilles , Bliss Robin L. , Poduslo Joseph F. , Jack Clifford R. , Uğurbil Kâmil , Garwood Michael
Published: August 2005

Currently no definitive biomarker of Alzheimer's disease (AD) is available, and this impedes both clinical diagnosis in humans and drug discovery in transgenic animal models. Proton magnetic resonance spectroscopy (
1
H MRS) provides a noninvasive way to investigate
in vivo
neurochemical abnormalities. Each observable metabolite can potentially provide information about unique
in vivo
pathological processes at the molecular or cellular level. In this study, the age-dependent
1
H MRS profile of transgenic AD mice was compared to that of wild-type mice. Twenty-seven APP-PS1 mice (which coexpress mutated human presenilin 1 and amyloid-β precursor protein) and 30 wild-type mice age 66-904 days were examined, some repeatedly. A reduction in the levels of
N
-acetylaspartate and glutamate, compared with total creatine levels, was found in APP-PS1 mice with advancing age. The most striking finding was a dramatic increase in the concentration of
myo
-inositol with age in APP-PS1 mice, which was not observed in wild-type mice. The age-dependent neurochemical changes observed in APP-PS1 mice agree with results obtained from
in vivo
human MRS studies. Among the different transgenic mouse models of AD that have been studied with
1
H MRS, APP-PS1 mice seem to best match the neurochemical profile exhibited in human AD.
1
H MRS could serve as a sensitive
in vivo
surrogate indicator of therapeutic efficacy in trials of agents designed to reduce neurotoxicity due to microglial activation. Because of its noninvasive and repeatable nature, MRS in transgenic models of AD could substantially accelerate drug discovery for this disease.
Observation of the skin-depth effect on the Casimir force between metallic surfaces
Authors: Lisanti Mariangela , Iannuzzi Davide , Capasso Federico
Published: August 2005

We have performed measurements of the Casimir force between a metallic plate and a transparent sphere coated with metallic films of different thicknesses. We have observed that, if the thickness of the coating is less than the skin-depth of the electromagnetic modes that mostly contribute to the interaction, the force is significantly smaller than that measured with a thick bulk-like film. Our results provide direct evidence of the skin-depth effect on the Casimir force between metallic surfaces.
Decoding the Interactions of SM Proteins with SNAREs
Authors: Peng Ren-Wang
Published: August 2005

The success and efficiency of fusion of transport vesicles to target membranes depend upon sets of proteins that are functionally and evolutionarily conserved. The solubleN-ethylmaleimide-sensitive fusion (NSF)-attachment protein receptor (SNARE) family and the Sec1/Munc18 family, also termed SM proteins, are central players in this process. SM proteins interact with syntaxins of SNARE family, which has been regarded intrinsic for function. By exploring the bi-molecular interactions of SM proteins with syntaxins and their functional implicationsin vivoin several eukaryotes, which has been enormously facilitated by the availability of the three-dimensional structures of members of both protein families, the long-standing assumption that SM proteins fulfill their regulatory role by binding to syntaxins has to be reconsidered.
Jejunal Perforation During Percutaneous Nephrolithotrypsy
Authors: Al-Assiri M. , Binsaleh S. , Libman J. , Anidjar M.
Published: August 2005

Colonic and duodenal perforations, albeit rare, are known complications of PCNL; however, to our knowledge, jejunal perforation has never been reported. We report a case of an 83-year-old man, underwent left PCNL for a 2cm stone in the renal pelvis, confirmed to have a jejunal perforation. He was successfully managed conservatively. His diagnostic work up and management will be discussed.
CAMM Techniques for the Prediction of the Mechanical Properties of Tendons and Ligaments Nanostructures
Authors: Vesentini Simone , Montevecchi Franco M. , Redaelli Alberto
Published: August 2005

Theoretical prediction of the mechanical properties of soft tissues usually relies on a top-down approach; that is analysis is gradually refined to observe smaller structures and properties until technical limits are reached. Computer-Assisted Molecular Modeling (CAMM) allows for the reversal of this approach and the performance of bottom-up modeling instead. The wealth of available sequences and structures provides an enormous database for computational efforts to predict structures, simulate docking and folding processes, simulate molecular interactions, and understand them in quantitative energetic terms. Tendons and ligaments can be considered an ideal arena due to their well defined and highly organized architecture which involves not only the main structural constituent, the collagen molecule, but also other important molecular “actors” such as proteoglycans and glycosaminoglycans. In this ideal arena each structure is well organized and recognizable, and using the molecular modeling tool it is possible to evaluate their mutual interactions and to characterize their mechanical function. Knowledge of these relationships can be useful in understanding connective tissue performance as a result of the cooperation and mutual interaction between different biological structures at the nanoscale.
Identification of differentially expressed genes in psoriasis using expression profiling approaches
Authors: Itoh K. , Kawasaki S. , Kawamoto S. , Seishima M. , Chiba H. , Michibata H. , Wakimoto K. , Imai Y. , Minesaki Y. , Otsuji M. , Okubo K.
Published: August 2005

Abstract:  To identify differentially expressed genes which play causal roles in pathogenesis and maintenance for psoriasis, we used BodyMapping and introduced amplified fragment length polymorphism approaches. From the BodyMap database, we selected 2007 genes which specifically expressed in epithelial tissues. Among 2007 genes, we surveyed genes which differentially expressed in involved or uninvolved psoriatic lesional skin samples compared with atopic dermatitis, mycosis fungoides, and normal skin samples. As a result of surveying 2007 genes, 241 genes were differentially expressed only in involved psoriatic skin but not in the other samples. Hierarchical cluster analysis of gene expression profiles showed that 13 independent psoriatic‐involved skin samples clustered tightly together, reflecting highly similar expression profiles. Using the same 2007 gene set, we examined gene expression levels in five serial lesions from distal uninvolved psoriatic skin to involved psoriatic plaque. We identified seven genes such as alpha‐1‐microglobulin/bikunin precursor, calnexin, claudin 1, leucine zipper down‐regulated in cancer 1, tyrosinase‐related protein 1, Yes‐associated protein 1, and unc‐13‐like protein (Coleonyx elegans) which show high‐expression levels only in uninvolved psoriatic lesions. These seven genes, which were reported to be related to apoptosis or antiproliferation, might have causal roles in pathophysiology in psoriasis.
CD44, but not l‐selectin, is critically involved in leucocyte migration into the skin in a murine model of allergic dermatitis
Authors: Gonda Andrea , Gál István , Szántó Sándor , Sarraj Bara , Glant Tibor T. , Hunyadi János , Mikecz Katalin
Published: August 2005

Abstract:  CD44 and l‐selectin (CD62L) are major adhesion receptors that mediate leucocyte recruitment at inflammatory sites and lymph nodes, by supporting cell rolling under blood flow. Both CD44 and CD62L have been implicated in inflammatory skin disorders, but their specific involvement in an immediate‐type allergic reaction remains uncertain. We used mice deficient in CD44 or CED62L or both in order to determine whether one or both of these molecules were required for leucocyte extravasation in an atopic dermatitis‐like allergic response. Wild‐type (WT) mice and mice deficient in CD44, CD62L or both were immunized with ovalbumin (OVA). Inflammatory reaction in the ear was elicited once by means of intradermal injection of OVA. Effective sensitization of CD62L knockout (KO) mice required intraperitoneal antigen injection; however, OVA‐specific T helper 2 (Th2)‐type immune responses and IgE production in mice lacking CD44, CD62L or both were comparable to those in WT mice following intraperitoneal immunization. We employed intravital videomicroscopy to monitor the recruitment of fluorescence‐labelled leucocytes to the ear tissue following challenge with OVA. The number of adherent leucocytes was significantly reduced in CD44 KO and CD44/CD62L double KO mice, indicating that CD44 was involved in firm adhesion, the committed step of leucocyte extravasation. Histology of the OVA‐challenged ears showed a diminished leucocyte infiltration in the ears of CD44 KO and double KO mice. The results of our study demonstrate that CD44, but not CD62L, is required for leucocyte extravasation during a Th2‐type inflammatory response.
MEL4B3, a novel mRNA is induced in skin tumors and regulated by TGF‐β and pro‐inflammatory cytokines
Authors: Anderegg Ulf , Breitschwerdt Kerstin , Köhler Martin J. , Sticherling Michael , Haustein Uwe‐Frithjof , Simon Jan C. , Saalbach Anja
Published: August 2005

Abstract:  Tumor–stroma interactions play a decisive role in the growth and metastasis of solid tumors, and involve signalling either by soluble mediators or direct cell–cell interaction. Here, we report the isolation and characterisation of a novel cDNA (MEL4B3), which is induced in cultured dermal fibroblasts exposed to supernatants of melanoma cell lines. MEL4B3 shares high homology with two predicted cDNA sequences for which no activity has so far been described. In situ hybridisation revealed the expression of MEL4B3 in malignant melanoma increasing with tumor depth; in basal cell carcinoma and in squamous cell carcinoma. MEL4B3 was barely detectable in normal skin or non‐malignant melanocytic naevi. Furthermore, MEL4B3 was expressed at high level in the epidermis of psoriatic skin. In vitro, the expression of MEL4B3 was found to be induced by the exposure of human dermal fibroblasts to melanoma cell culture supernatants or to transforming growth factor‐β, interleukin‐1 and tumor necrosis factor‐α. The expression MEL4B3 therefore reflects closely cell activation occurring during tumor growth, metastasis and inflammation.
Integrating soil map information in modelling the spatial variation of continuous soil properties
Authors: GOOVAERTS P. , JOURNEL A.G.
Published: August 2005

This paper presents two indicator algorithms that integrate soil map information into modelling the spatial variation of continuous soil properties: these are simple indicator kriging with varying means and the Markov–Bayes algorithm. Both methods are used to evaluate probabilities for copper and cobalt deficiencies in the Borders Region of Scotland. Results are compared with maps obtained by the polygonal method (Thiessen polygons) and an indicator kriging algorithm that does not use soil map information. Accounting for soil map information is shown to improve delineation of the deficient areas, especially where the sampling is sparse.

Test locations are classified as deficient or not so as to minimize an expected cost of mis‐classification that is derived from local probability distributions of copper or cobalt and functions measuring the cost of overestimating or underestimating metal concentrations. The comparison of classification results with actual copper and cobalt concentrations at test locations shows that the two proposed algorithms can decrease substantially the economic loss attached to misclassification.
Molecular phylogenetic analysis of a soil microbial community in a soybean field
Authors: UEDA T. , SUGA Y. , MATSUGUCHI T.
Published: August 2005

We report here the phylogenetic characterization of small subunit rRNA gene sequences obtained by polymerase chain reaction (PCR) amplification of mixed population DNA extracted directly from soil in a soybean field without culturing the organisms. The phylogenetic analysis of 17 soil clones by the neighbour‐joining method shows that the soil sample contained broadly diverse prokaryotes; a clone related to archaea, a clone to gram‐positive bacteria with high G+C contents, two clones to green sulphur bacteria, four clones to proteobacteria, and nine clones were not in clusters of any previously reported bacterial groups, which suggests they belong to members of novel groups in Bacteria. In addition, the archaeal sequence, FIE16, is phylogenetically similar to ANTARCTIC 12, a clone obtained from surface waters of Antarctica by PCR. Their occurrence in both the ocean and soil suggests a global distribution of this archaeal group. In conclusion, rRNA gene sequences recovered from soil biomass document the occurrence of many more bacterial lingeages than have been recognized previously through cultivation‐based techniques.
Adsorption mechanisms of thiazafluron in mineral soil clay components
Authors: COX L. , HERMOSIN M.C. , CORNEJO J.
Published: August 2005

The adsorption of the herbicide thiazafluron, 1,3‐dimethyl‐1‐(5‐trifluoromethyl‐1,3,4‐thiadiazol‐2‐yl)urea, by three smectites, illite, kaolinite, ferrihydrite and the clay fraction of an illitic soil (54.9% illite, 17.0% montmorillonite and 24.9% kaolinite) and a montmorillonitic soil (33.9% illite, 55.0% montmorillonite and 11.1% kaolinite) has been determined. Thiazafluron adsorbed on neither kaolinite nor iron oxide. The adsorption isotherms on smectites and illite conformed to the Freundlich equation. Values of Kf‐obtained for smectites were larger than for the illite and increased as the layer charge of the smectite decreased. Desorption of thiazafluron on smectites was shown to be highly irreversible. Adsorption isotherms of thiazafluron on different homoionic montmorillonite samples suggest an important role of the exchangeable cations in the adsorption. Infrared spectra and X‐ray diffraction analysis of the complexes of thiazafluron with homoionic montmorillonites indicated that thiazafluron adsorbs in the interlamellar space of the smectites, mainly by substitution of water molecules associated with the exchangeable cations through the carbonyl‐amide group and formation of H‐bonds or waterbridge between the NH group of the amide and the basal oxygens of the montmorillonite. The illitic soil clay adsorbed more of the herbicide than the montmorillonitic one did, suggesting that illite and montmorillonite may be present in soils in altered forms giving rise to different adsorption capacities from those of the pure minerals.
Total and young organic matter distributions in aggregates of silty cultivated soils
Authors: PUGET P. , CHENU C. , BALESDENT J.
Published: August 2005

The distribution of organic matter in soil aggregates was investigated by fractionating aggregates and measuring carbon contents. The distribution of recently incorporated organic carbon was analyzed using 13C natural abundance. The soils of the experiment, which previously only had C3 vegetation, were cropped to maize, aC4 plant, for 6 or 23 years.

Aggregate size distributions were determined for silty soils with different organic matter contents. Slaking‐resistant macroaggregates were enriched in C as compared to dry‐sieved macroaggregates or to microaggregates, and the C content increased with the size of aggregates. The δ13C value was used to calculate the amount of C3‐derived and C4‐derived organic carbon in the fractions. The larger carbon contents in stable macroaggregates were due to young C4‐derived organic carbon (<6 or 23 years), and we concluded that young organic matter was responsible for macroaggregate stability.
Medium‐term transformations of organic N in a cultivated soil
Authors: BALABANE M. , BALESDENT J.
Published: August 2005

We followed in situ the evolution of nitrogen recently incorporated into a soil under maize culture for 4 years. Each year, a different pair of plots treated by removal or return of maize crop residues received a single pulse of 15N‐labelled fertilizer. Unlabelled fertilizer was otherwise supplied. In parallel, plots supplied with unlabelled fertilizer received a single pulse of 15N‐labelled maize crop residues.

Varying weather affected total and fertilizer‐derived N in the crop and residual inorganic N in the topsoil, but it did not affect fertilizer‐N immobilization and remineralization. There was no consistent effect of crop residue return on total soil N, immobilization of fertilizer N, or the decay kinetics of recently immobilized N.

Recently incorporated organic N from crop residues and microbial immobilization of inorganic N displayed similar mid‐term decay kinetics. Crop residue N and immobilized N enter a labile compartment with an average residence time of a few months. A proportion, estimated at 28%, enters a more stable compartment from which the mineralization was imperceptible in 4 years. Particle‐size fractions >50 um, which receive most of the crop residue N, retained it for only a short time. The mid‐term stabilization of N was mainly in soil fractions <50 um.
Nitrous oxide fluxes from grassland in the Netherlands: II. Effects of soil type, nitrogen fertilizer application and grazing
Authors: VELTHOF G.L. , OENEMA O.
Published: August 2005

Intensively managed grasslands are potentially a large source of nitrous oxide (N2O) in the Netherlands because of the large nitrogen (N) input and the fairly wet soil conditions. To quantify the effects of soil type, N‐fertilizer application and grazing on total N2O losses from grassland, fluxes of N2O were measured weekly from unfertilized and mown, N fertilized and mown, and N fertilized and predominantly grazed grassland on a sand soil, a clay soil, and two peat soils during the growing season of 1992.

Total N2O losses from unfertilized grassland were 2.5–13.5 times more from the peat soils than from the sand and clay soils. Application of calcium ammonium nitrate fertilizer significantly increased N2O flux on all sites, especially when the soil was wet. The percentage of fertilizer N applied lost to the atmosphere as N2O during the season ranged from 0.5 on the sand soil to 3.9 on one of the peat soils. Total N2O losses were 1.5–2.5 times more from grazed grassland than from mown grassland, probably because of the extra N input from urine and dung. From 1.0 to 7.7% of the calculated total amount of N excreted in urine and dung was emitted as N2O on grazed grassland. The large N2O losses measured from the peat soils, combined with the large proportion of grassland on peat in the Netherlands, mean that these grasslands contribute significantly to the total emission from the country.
Fertilization effects on organic matter in physically fractionated soils as studied by 13C NMR: Results from two long‐term field experiments
Authors: RANDALL E.W. , MAHIEU N. , POWLSON D.S. , CHRISTENSEN B.T.
Published: August 2005

l3C–nuclear magnetic resonance (NMR) spectra taken using magic–angle spinning (MAS), cross polarization (CP) and with total suppression of side bands (TOSS) are reported for soils from two long–term field experiments. One set of soils was from the Broadbalk Experiment at Rothamsted, UK (monoculture of winter wheat since 1843) and the other was from the Lermarken site of the Askov Long–Term Experiment on Animal Manure and Mineral Fertilizers (arable rotation since 1894). At both sites soil samples were taken from three fertilizer treatments: nil, inorganic fertilizers, animal manure. Spectra were obtained from whole soil samples and from the size fractions clay (<2 μrn), silt (2–20 μm) and, in some cases, sand (20–2000 μm).

Comparison of the total strengths of the 13C–NMR signal for each size separate in relation to its total organic C content shows that clay, particularly, contains large percentages of C not detected by NMR because of the large magnetic susceptibilities of the soil minerals. It is proposed that the observed signals come from the more labile pools of soil organic matter (SOM), on the presumption that these pools are less closely associated with soil minerals and iron oxides and are likely to be less protected from microbial or enzymic decomposition.

For both Rothamsted and Askov, functional groups in the 45–110 ppm region (N– and O–alkyls) dominate in the spectra for whole soils, with aromatics (110–160 ppm) and alkyls (0–45 ppm) signals being the next prominent. In the Askov whole soil samples 13C–NMR revealed no differences between nil, inorganic fertilizer and animal manure treatments but in the Rothamsted whole soil there were some small differences.

Clay and silt fractions from Askov contain more alkyls and less aromatics than those from Rothamsted. For both sites clay in enriched in alkyls and depleted in aromatics relative to silt. Clay from Askov, but not Rothamsted, contains more N–alkyls (45–65 ppm) and less acetals (90–110 ppm) than silt. O–alkyls (65–90 ppm) account for more than 20% of the total signal in clay and silt from both sites. Fertilization regimes have not significantly affected the chemical composition of SOM associated with clay– and silt–sized fractions in the soils at either site. We conclude that the chemical composition of SOM is determined primarily by the interaction between the organisms responsible for decomposition and the mineral soil matrix rather than the nature of substrate input.
Dynamic programming analysis of pore space
Authors: EGGLESTON J.R. , PEIRCE J.J.
Published: August 2005

A method based on the principles of dynamic programming is developed and applied to digital soil images to determine tortuosity, effective porosity, and the shortest paths available for flow. Pathways for flow are determined by minimizing a resistance factor. Analysis of two numerically simulated soils finds that a platy soil has greater effective porosity and smaller tortuosity than a layered soil. The ability of the dynamic programming model to analyse large digital images with complex pore structure is subsequently demonstrated by the analysis of a digital image of an agricultural soil. The results from the agricultural soil point to the need for digital soil image analysis to be three–dimensional if convective and diffusive soil properties are to be examined. It is demonstrated that, because determination of flow paths can be treated as a routing problem solved by applying a few simple rules, dynamic programming analysis is not limited by complexity of pore structures.
A fuzzy allocation scheme for the Australian Great Soil Groups Classification system
Authors: MAZAHERI S.A. , KOPPI A.J. , McBRATNEY A.B.
Published: August 2005

Conventional methods of soil classification are based largely on hierarchies and treat soil attribute value ranges as exactly specifiable quantities. Misclassification may result from ignoring the continuous complex nature of soil variation, and the inability to sample and measure every aspect of soil. The Australian Great Soil Groups (GSG) system of classification is essentially a fuzzy classification, and for the most part central concepts have not been defined explicitly.

Centroids were generated, together with fuzzy group membership, using data from the 147 soil profile descriptions in The Handbook of Australian Soils. Some of the GSG, such as Siliceous Sands and Red and Brown Hardpan Soils, were divided into their component parts for better and easier quantification and allocation. The centroids of GSG were examined, and the method of fuzzy κ‐means was then used to allocate unknown profiles to the GSG. The results show that the system is intuitively reasonable.
Aluminium chemistry of the soil solution in an acid forest soil as influenced by percolation rate and soil structure
Authors: FRANKEN G. , PIJPERS M. , MATZNER E.
Published: August 2005

The predicted activity of Al in the soil solutions of acid forest soils often differs from that observed in the field. We have investigated the influence of soil structure and flow rate of the soil solution on the aluminum release to explain this divergence. Disturbed and undisturbed samples of soil were collected from the A and B horizons of a dystric cambisol at Waldstein (Fichtelgebirge, Germany). The samples were irrigated with solutions mixed according to field data on throughfall or soil solution composition with pH 3.5 with flow rates of 4 mm d−1, 12 mm d−1 and 36 mm d−1. The percolates were analysed for major ions. Resulting relations between pH and pAl were compared with batch experiments. In neither the A horizon nor in the B horizon did soil structure influence the relation between pH and pAl. The apparent equilibrium between pH and pAl was described as the pKapp value with pKapp= pAl—a pH (where a is an empirical constant). It was found that the pKapp values for the column percolates were in the range of variation of those found in batch experiments.

Flow rate had no influence on pKapp at 4 and 12 mm d−1. At 36 mm d−1 a significant increase of pKapp was observed. This relative undersaturation of Al was more pronounced in the A horizon than in the B horizon. When flow is fast Al release into the percolating soil solution might be limited by diffusion.
Characterizing heavy‐metal adsorption on oxides and oxyhydroxides
Authors: SPARK K.M. , JOHNSON B.B. , WELLS J.D.
Published: August 2005

Adsorption of Cu(II), Zn(II), Co(II) and Cd(II) on three different substrates: goethite, alumina and silica, was investigated over the pH range from 3.5 to 10. The consistent variation in the pH at which 50% of the metal is adsorbed (pH50) indicates that the identity of the adsorbing ion is the principal factor determining the pH range over which adsorption occurs. However, the nature of the substrate does play a lesser role. The proton coefficient, χ, ranged from about 0.5 to 1.8, and was correlated with the difference between pH50 and the pH for 50% precipitation. It is suggested that for most metal‐substrate systems, for which χ is about 1, MOH+ plays a dominant role in adsorption. Increasing the substrate concentration decreased pH50 for adsorption of metals on goethite, but there was little change in χ. The change in pH50 was inversely related to χ. While the effect of the nature and concentration of the background electrolyte on Cu(II), Zn(II) and Co(II) adsorption depended on the substrate, increased ionic strength was found to decrease Cd(II) adsorption on all substrates.
Effect of temperature and flooding duration on phosphate sorption in an acid sulphate soil from Vietnam
Authors: VO QUANG DINH , DUFEY J.E.
Published: August 2005

Phosphate sorption in soil is controlled largely by Fe‐oxihydroxides, and so important changes in P dynamics are expected when the redox potential is modified. Such changes in P sorption when acid soil is flooded, as for rice cultivation, have been evaluated. Samples from an acid sulphate soil in the Mekong Delta of Vietnam were flooded for up to 56 d at 20°C and 30°C. Some of the samples incubated at 30°C were dried in open air for 30 d after flooding. Small redox potential (Eh<0) and pH>6 were rapidly reached in soil flooded at 30°C; less drastic reducing conditions (Eh ≅0.2 V) and pH 4–5 occurred at 20°C. Phosphate sorption increased during flooding. The increase was twofold at 20°C, and 10‐fold at 30°C. Phosphate sorption index decreased in the soil that was air dried after flooding at 30°C, but still remained two to three times greater than before flooding. These results were compared to the changes in oxalate‐extractable Fe, i.e. poorly crystalline or amorphous Fe‐oxihydroxides. The increase of P sorption per unit increase of oxalate‐Fe was seven to eight fold larger at 30°C than at 20°C.