bluuebunny/crossref_metadata_2025 huggingface dataset:
Soil properties and tree growth along an altitudinal transect in Ecuadorian tropical montane forest
Authors: Wilcke Wolfgang , Oelmann Yvonne , Schmitt Andrea , Valarezo Carlos , Zech Wolfgang , Homeier Jürgen
Published: April 2008

In tropical montane forests, soil properties change with increasing altitude, and tree‐growth decreases. In a tropical montane forest in Ecuador, we determined soil and tree properties along an altitudinal transect between 1960 and 2450 m asl. In different vegetation units, all horizons of three replicate profiles at each of eight sites were sampled and height, basal area, and diameter growth of trees were recorded. We determined pH and total concentrations of Al, C, Ca, K, Mg, Mn, N, Na, P, S, Zn, polyphenols, and lignin in all soil horizons and in the mineral soil additionally the effective cation‐exchange capacity (CEC). The soils were Cambisols, Planosols, and Histosols. The concentrations of Mg, Mn, N, P, and S in the O horizons and of Al, C, and all nutrients except Ca in the A horizons correlated significantly negatively with altitude. The C : N, C : P, and C : S ratios increased, and the lignin concentrations decreased in O and A horizons with increasing altitude. Forest stature, tree basal area, and tree growth decreased with altitude. An ANOVA analysis indicated that macronutrients (e.g., N, P, Ca) and micronutrients (e.g., Mn) in the O layer and in the soil mineral A horizon were correlated with tree growth. Furthermore, lignin concentrations in the O layer and the C : N ratio in soil affected tree growth. These effects were consistent, even if the effect of altitude was accounted for in a hierarchical statistical model. This suggests a contribution of nutrient deficiencies to reduced tree growth possibly caused by reduced organic‐matter turnover at higher altitudes.
Nitrous oxide emissions and dynamics of soil nitrogen under 15N‐labeled cow urine and dung patches on a sandy grassland soil
Authors: Wachendorf Christine , Lampe Carola , Taube Friedhelm , Dittert Klaus
Published: April 2008

Grazing animals highly influence the nutrient cycle by a direct return of 80% of the consumed N in form of dung and urine. In the autumn‐winter period, N uptake by the sward is low and rates of seepage water in sandy soils are high, hence high mineral‐N contents in soil and in seepage water as well as large losses of N2O are expected after cattle grazing in autumn. The objective of this study was the quanitfication of N loss deriving from urine and dung leaching and by N2O emission. Therefore the deposition of urine and dung patches was simulated in maximum rates excreted by cows by application of 15N‐labeled cow urine and dung (equivalent to 1030 kg N ha–1 and 1052 kg N ha–1, respectively) on a sandy pasture soil in N Germany. Leachate was collected in weekly intervals from free‐draining lysimeters, and 15N‐NO$ _3^- $, 15N‐NH$ _4^+ $, and 15N‐DON (dissolved organic N) were monitored over 171 d. Furthermore, the 15N‐N2O emission rates and the dynamics of inorganic 15N in the upper soil layer were monitored in a field trial, adjacent to the lysimeters. After 10 d following the urine application, the urea was completely hydrolyzed, shown by a 100% recovery of urine‐N in the soil NH$ _4^+ $. The following decrease of 15N‐NH$ _4^+ $ in the soil was higher than the increase of 15N‐NO$ _3^- $, and some N loss was explained by leaching. Amounts of 51% and 2.5% of the applied 15N were found in leachate as inorganic N, 2.4% and 0.7% as DON derived from urine and dung, respectively. Release of N2O from urine and dung patches applied to the pasture was low, with losses of 0.05% and 0.33% of the applied 15N, respectively. Overall loss of dung‐derived N was very low, but as the bulk dung N remained in the soil, N loss after mineralization of the dung needs to be investigated.
Classification schemes for the acidity, base saturation, and acidification status of forest soils in Switzerland
Authors: Blaser Peter , Walthert Lorenz , Zimmermann Stephan , Graf Pannatier Elisabeth , Luster Jörg
Published: April 2008

Soil chemical parameters related to soil acidity were determined for 1450 soil samples taken from individual mineral soil horizons in 257 forest soils in Switzerland, 196 developed from carbonate‐containing and 61 from carbonate‐free parent material. The distribution of pH values and exchangeable base cations in corresponding pH ranges were related to the capacity and rate of buffer reactions in the soil. Based on this, five acidity classes for individual soil samples were defined.

To describe and classify the status of soil acidity and base saturation (BS) of an entire soil body, the pH and the BS of the total fine earth in the soil were calculated from the pH and BS, respectively, of the individual soil horizons and the estimated volumetric content of fine earth.

The status of soil acidification of soil profiles was assessed primarily using the total amount of exchangeable acidic cations in percent of the CEC of the fine earth in the entire soil profile. As a second factor, the gradient between the acidity class of the most acidic soil horizon and the estimated acidity class at the beginning of soil formation was used. The application of these classification schemes to our collection of soil profiles revealed the great influence played by the type of parent material. The acidification status of most soils on carbonate‐containing parent material was classified as very weak to weak, whereas soils on carbonate‐free parent material were found to be strongly to very strongly acidified.

In terms of parent rock material, microclimate, and natural vegetation, the results of this study and the proposed classification schemes can be considered appropriate for large parts of Europe.
Do water regimes affect iron‐plaque formation and microbial communities in the rhizosphere of paddy rice?
Authors: Chen Xue‐Ping , Kong Wei‐Dong , He Ji‐Zheng , Liu Wen‐Ju , Smith Sally E. , Smith F. Andrew , Zhu Yong‐Guan
Published: April 2008

Pot experiments were conducted to investigate the effect of soil water regimes on the formation of iron (Fe) plaque on the root surface of rice seedlings (Oryza sativa L.) and on the microbial functional diversity in a paddy soil. The rice seedlings were subjected to three moisture regimes (submergence, 100%, and 60% water‐holding capacity [WHC]), and were grown for 5 and 11 weeks. Aerobic lithotrophic Fe(II)‐oxidizing (FeOB) and acetate‐utilizing Fe(III)‐reducing bacteria (FeRB) in the rhizosphere and non‐rhizosphere soil were determined at 5 weeks using the most probable number (MPN) method. The carbon substrate use patterns of the microbial communities in the rhizosphere and non‐rhizosphere soil samples were determined at 11 weeks using Biolog‐GN2 plates. The amount of Fe plaque (per unit dry root weight) was much higher under submerged conditions than at lower soil moisture contents and decreased with plant age. There was a positive correlation between the amount of Fe plaque and phosphorus accumulated in the Fe plaque at both sampling times (r = 0.98 and 0.92, respectively, n = 12). Numbers of FeOB and FeRB in the submerged soil were lower than in aerobic soil, but by two orders of magnitude higher in the rhizosphere than in the bulk soil. On the other hand, the functional diversity of the rhizosphere microbial communities was much higher than that of the non‐rhizosphere soil, irrespective of soil water regimes. We conclude that soil flooding results in a decreased number and diversity of Fe‐oxidizing/reducing bacteria, while increasing the Fe‐plaque formation.
Plant availability of boron in acid soils as assessed by different extractants
Authors: Sarkar Dibyendu , Mandal Biswapati , Mazumdar Debasis
Published: April 2008

Estimation of available‐boron (B) status through conventional methods in B‐deficient acidic Inceptisols and Entisols is often hampered because of their very low B content. In the present study, the extractability of available B by different extractants was tested in relation to soil properties. Plant availability of B was assessed with mustard (Brassica campestris L.) and wheat (Triticum aestivum L.) in pot experiments. Twelve soils with varying characteristics were extracted for available B with hot water (HW), hot CaCl2 (HCC), KH2PO4 (PDP), tartaric acid (TA), and mannitol‐CaCl2 (MCC). Mustard (cv. B‐9) and wheat (cv. PBW‐343) were grown with four levels of B (0, 0.25, 0.50, and 1.0 mg [kg soil]–1). Dry‐matter accumulation and B concentrations were determined at pre‐flowering and full‐maturity stages for mustard and at panicle‐initiation and maturity stages for wheat. The extraction of B from the soils ranked HCC > HW > PDP > TA > MCC. The higher extractability with HW and HCC was likely due to higher temperature and that of PDP because of its phosphorus content, which facilitated the desorption of B. The low B extraction with MCC resulted from the poor mannitol‐B complex formation in acidic soils. The application of B increased dry‐matter accumulation, plant B concentration, and uptake at all B levels and growth stages in both crops with the responses being more pronounced during the early developmental stage. Based on linear correlations, Mallow's Cp statistics, and principal‐component analyses, HCC and HW were the best extractants for estimating available B in the acidic experimental soils.
Effects of nitrogen supply on water‐use efficiency of higher plants
Authors: Brueck Holger
Published: April 2008

The worldwide increase of food demand and reduced sweet‐water availability in some important food‐producing regions raised interest in more efficient water use, which has become one of the central research topics in agriculture. Improved irrigation management and reduced bare‐soil evaporation have highest priority to increase agronomic water‐use efficiency (WUE). Compared to these technical (irrigation) and basic (crop production) management options, effects of nutrient management on WUE were less frequently considered. Twenty‐nine publications on nitrogen (N) effects on biomass WUE of container‐grown plants are considered in this review. Most of them indicate positive N effects on WUE, and relevance of N effects on intrinsic WUE and unproductive water and carbon loss is discussed. A plot of 90 published data of percent decreases of WUE and dry mass under variable N supply is presented. Extrapolation of biomass WUE from leaf measurements of intrinsic WUE is critically reviewed. The positive correlation between WUE and dry‐mass formation suggests that physiological rather than stomatal effects are more important in order to explain positive N effects on WUE.
Genotypic variation in grain mercury accumulation of lowland rice
Authors: Zhu Cheng , Shen Guoming , Yan Yuping , He Junyu
Published: April 2008

A pot experiment with 38 commonly cultivated rice cultivars from the Yangtze River Delta was conducted in a greenhouse to study the effect of mercury (Hg) contamination of a paddy soil (4.7 mg Hg [kg soil]–1) on crop growth and Hg accumulation in the grains. Mercury contamination differentially affected growth, grain yield, and Hg accumulation in brown rice of the tested cultivars. The average Hg concentration in the grains was significantly higher (p < 0.01) when plants were grown in the Hg‐contaminated compared to the control soil. Averaged over cultivars, the Hg concentration in brown rice exceeded the maximum permissible limit of 20 μg Hg kg–1. Increasing Hg concentrations were associated with grain‐yield declines up to 70%. This yield decline was mainly due to a reduction in the number of panicles. Japonica cultivars tended to be generally less affected by Hg than indica cultivars. The two japonica cultivars Jiahua and Chunjiang 026 showed both low Hg concentrations and no Hg‐induced grain‐yield reduction. These cultivars may be preferred candidates for cultivation in Hg‐contaminated soils or for studies on possible Hg‐exclusion mechanisms.
Effect of crop‐residue management on the production and agronomic nitrogen efficiency in a rice–wheat cropping system
Authors: Sharma S. N. , Prasad Rajendra
Published: April 2008

The rice–wheat cropping system (RWCS), producing about 5–10 Mg ha–1 y–1 of grain, is the backbone of food‐crop production in South‐East Asia. However, this system shows signs of fatigue as indicated by declining yields, negative nitrogen (N) balances, and reduced responses to applied fertilizer at some research centers. The return of rice and wheat residues can recycle up to 20%–30% of the N absorbed by the crops. However, their wide C : N ratio can temporarily immobilize native and applied N. To overcome this immobilization, wheat‐straw application was supplemented with the incorporation of Sesbania green manure and mungbean residues, and their effects on productivity, agronomic N efficiency, and system's apparent N balances were studied. Combining the application of wheat straw with Sesbania green manure or mungbean residues increased cereal grain yield and agronomic N efficiency and improved the generally negative apparent N balances. The combined use of wheat straw and mungbean produced an additional 0.5–0.6 t ha–1 protein‐rich grain and thus appears to be the most promising residue‐management option for rice–wheat cropping systems in South Asia, provided that the transition cropping season between wheat harvest and rice transplanting is long enough.
Inversion of TDR signals—revisited
Authors: Bänninger Dominik , Wunderli Hans , Nussberger Mathis , Flühler Hannes
Published: April 2008

In this study, we discuss the consistence of measured and calculated TDR traces. The calculated traces are solutions of a time domain reflectometry (TDR) forward solver, an algorithm for computing the TDR trace for a given dielectric profile along a transmission line. An unambiguous and efficient forward solver is a prerequisite for a good solution of the inverse problem, i.e., to extract the spatial distribution of the dielectric properties along the transmission line from a TDR trace. To advance our understanding of TDR inversion, we proceeded in two steps: (1) design of a TDR head section with minimal disturbances on the signal and (2) searching for causes why measured and predicted TDR traces differ. Based on a first experiment with a three‐rod TDR probe of 100 cm length, we demonstrated that our TDR forward solver—like others presented in literature—approximate the measured TDR traces apparently well but not precisely enough for signal inversion. In a second experiment, using a two‐rod TDR probe of 70 cm length, we addressed the problem of non‐parallel transmission lines. We found that the influence of a non‐parallel installation is similar to an increase of the electrical conductivity in soil water but can be distinguished from this property. A third experiment reveals that lateral and longitudinal disturbances in the vicinity of a TDR probe are of minor importance. From the analysis of our experiments, we found that neither lateral disturbances nor non‐parallel rods are responsible for the deviations between calculated and measured traces. This analysis showed us that structure in the sampled medium affects the shape of the TDR traces. Since minor deviations are essential for TDR‐signal inversion, we need new concepts to handle the fuzziness between measurements and calculations.
Phosphorus acquisition and wheat growth are influenced by shoot phosphorus status and soil phosphorus distribution in a split‐root system
Authors: Ma Qifu , Rengel Zed
Published: April 2008

Root proliferation and greater uptake per unit of root in the nutrient‐rich zones are often considered to be compensatory responses. This study aimed to examine the influence of plant phosphorus (P) status and P distribution in the root zone on root P acquisition and root and shoot growth of wheat (Triticum aestivum L.) in a split‐root soil culture. One compartment (A) was supplied with either 4 or 14 mg P (kg soil)–1, whereas the adjoining compartment (B) had 4 mg P kg–1 with a vertical high‐P strip (44 mg kg–1) at 90–110 mm from the plant. Three weeks after growing in the split‐root system, plants with 4 mg P kg–1 (low‐P plants) started to show stimulatory root growth in the high‐P strip. Two weeks later, root dry weight and length density in the high‐P strip were significantly greater for the low‐P plants than for the plants with 14 mg P (kg soil)–1. However, after 8 weeks of growth in the split‐root system, the two P treatments of compartment A had similar root growth in the high‐P strip of compartment B. The study also showed that shoot P concentrations in the low‐P plants were 0.6–0.8 mg g–1 compared with 1.7–1.9 mg g–1 in the 14 mg P kg–1 plants after 3 and 5 weeks of growth, but were similar (1.1–1.4 mg g–1) between the two plants by week 8. The low‐P plants had lower root P concentration in both compartments than those with 14 mg P kg–1 throughout the three harvests. The findings may indicate that root proliferation and P acquisition under heterogeneous conditions are influenced by shoot P status (internal) and soil P distribution (external). There were no differences in the total root and shoot dry weight between the two P treatments at weeks 3 and 5 because enhanced root growth and P uptake in the high‐P strip by the low‐P plants were compensated by reduced root growth elsewhere. In contrast, total plant growth and total root and shoot P contents were greater in the 14 mg P kg–1 soil than in the low‐P soil at week 8. The two P treatments did not affect the ratio of root to shoot dry weight with time. The results suggest that root proliferation and greater P uptake in the P‐enriched zone may meet the demand for P by P‐deficient plants only for a limited period of time.
Crystal and molecular structure of 2‐amino‐5‐chloropyridinium hydrogen selenate—its IR and Raman spectra, DFT calculations and physicochemical properties
Authors: Lorenc J. , Bryndal I. , Marchewka M. , Kucharska E. , Lis T. , Hanuza J.
Published: April 2008

The new organic‐inorganic salt, 2‐amino‐5‐chloropyridinium hydrogen selenate, has been synthesised and characterised by means of FT‐IR, FT‐Raman and single crystal X‐ray crystallography. Its vibrational spectra have been discussed on the basis of quantum chemical DFT calculations using the B3LYP/6‐31G(d,p) approach. The crystal and molecular structures have been compared and the role of the intermolecular interactions in this crystal has been analysed. The NHO interactions between the hydrogen atoms of the organic cation and oxygen atoms of hydrogen selenate anion determine the supramolecular arrangement in three‐dimensional space. The possible application of the studied composite material as a Raman laser has been discussed. Copyright © 2008 John Wiley & Sons, Ltd.
Analysis of seized drugs using portable Raman spectroscopy in an airport environment—a proof of principle study
Authors: Hargreaves Michael D. , Page Kristian , Munshi Tasnim , Tomsett Richard , Lynch Gary , Edwards Howell G. M.
Published: April 2008

The rapid identification for drugs‐of‐abuse in airports is of critical importance. In this study we demonstrate the viability of Raman spectroscopy for the rapid identification of illicit substances in their containers in an airport environment.

Raman spectra of drugs‐of‐abuse in situ were collected using portable Raman spectrometers; this technique offers distinct advantages to government agencies, first responders and forensic scientists working in the security field. We have demonstrated that the spectrometers are able to collect the spectra of suspect powders, including cocaine HCl and d‐amphetamine sulphate with unknown constituents rapidly and with a high degree of discrimination. Copyright © 2008 John Wiley & Sons, Ltd.
Macromol. Mater. Eng. 4/2008
Authors: Vilaplana Francisco , Karlsson Sigbritt
Published: April 2008

Cover: Three key research fronts can be considered to improve the mechanical recycling activities and therefore extend the life cycle of polymeric materials: scientific knowledge about the degradation processes during first use and subsequent recycling, development of reliable quality analysis procedures for recycled plastics, and effective upgrading of recyclates. Further details can be found in the article by F. Vilaplana and S. Karlsson* on page 274.
Mouse oocytes derived from fetal germ cells are competent to support the development of embryos by in vitro fertilization
Authors: Shen Wei , Li Lan , Zhang Donghui , Pan Qingjie , Ding Mingxiao , Deng Hongkui
Published: April 2008

Figure 1B in the paper above appeared to be an enlargement of a portion of Figure 1A, while the legend indicated otherwise. This error had been made because the authors labeled the sections by date, but not by source, and because experimental and control sections were similar.

The authors have now confirmed their overall results and have submitted new figures for Figure 1 and Figure 4A presented below.

The original article to which this erratum refers, was published in Molecular Reproduction and Development 2006;73(10):1312–1317. Mol. Reprod. Dev. 75: 1688–1689, 2008. © 2008 Wiley‐Liss, Inc.
Finding the one‐loop soliton solution of the short‐pulse equation by means of the homotopy analysis method
Authors: Parkes E.J. , Abbasbandy S.
Published: April 2008

The homotopy analysis method is applied to the short‐pulse equation in order to find an analytic approximation to the known exact solitary upright‐loop solution. It is demonstrated that the approximate solution agrees well with the exact solution. This provides further evidence that the homotopy analysis method is a powerful tool for finding excellent approximations to nonlinear solitary waves. © 2008 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2009
The effectiveness of NGO self‐regulation: theory and evidence from Africa
Authors: Gugerty Mary Kay
Published: April 2008

Non‐governmental organizations (NGOs) play an increasingly important role in public service provision and policy making in sub‐Saharan Africa, stimulating demand for new forms of regulatory oversight. In response, a number of initiatives in NGO self‐regulation have emerged. Using cross‐national data on 20 African countries, the article shows that self‐regulation in Africa falls into three types: national‐level guilds, NGO‐led clubs and voluntary codes of conduct. Each displays significant weaknesses from a regulatory policy perspective. National guilds have a broad scope, but require high administrative oversight capacity on the part of NGOs. Voluntary clubs have stronger standards but typically have much weaker coverage. Voluntary codes are the most common form of self‐regulation, but have the weakest regulatory strength. This article argues that the weakness of current attempts to improve the accountability and regulatory environment of NGOs stems in part from a mismatch between the goals of regulation and the institutional incentives embedded in the structure of most self‐regulatory regimes. The article uses the logic of collective action to illustrate the nature of this mismatch and the tradeoffs between the potential breadth and strength of various forms of NGO self‐regulation using three detailed case studies. Copyright © 2008 John Wiley & Sons, Ltd.
Polyurethane foam and fire safety
Authors: Hirschler M. M.
Published: April 2008

This paper presents a survey of the fire safety of flexible and rigid polyurethane foam. The principal uses of flexible polyurethane foam are in applications where full resiliency is required, namely in upholstery for furniture, mattresses, and filled bed products. A subcategory of this type of application is the use of the foam in transportation seating, including every type of vehicle: automobiles, buses (and school buses), trains (and subways), ships, and aircraft. The fire safety legally required for these various environments covers a broad range, between virtually nothing for private automobiles and the extreme fire safety associated with airplane seats. Polyurethane foam also forms part of construction products, and in this case the foam is generally not applied exposed (since this is almost never allowed) and is often used as part of composite systems. The fire testing is normally conducted in the composite application, with severe restrictions to general uses. Overall, polyurethane foam can be used safely for applications that require adequate fire safety only if it is appropriately fire‐retarded or if the correct type of fire barriers (or alternate product design) is used. Copyright © 2008 John Wiley & Sons, Ltd.
Prostate stem cells and benign prostatic hyperplasia
Authors: Isaacs John T.
Published: April 2008

Pharmacological approaches are available to medically‐managed patients with symptomatic BPH before surgical intervention is required. These include daily treatment with alpha‐blockers and 5‐alpha‐reductase inhibitors alone or in combination. These medical approaches have two major problems. First, treatments are chronic and must be taken daily. Second, there are significant financial costs and quality of life issues for such chronic treatments. Is it possible to develop effective acute therapy for symptomatic BPH without the long‐term androgen deprivation‐induced side effects? Two seminal but rarely cited studies of Walsh [Peters, Walsh: N Engl J Med 317:599–604, 1987] and Coffey et al. [Sufrin et al.: Invest Urol 13:418–423, 1976], combined with the growing understanding of the stem cell organization of the prostate stromal (S) and epithelial (E) compartments and their reciprocal paracrine and autocrine interactions provides the rationale for an acute approach.

The Walsh study documents that: (1) androgen deprivation disrupts the reciprocal interaction between the prostate S and E thereby decreasing the weight of both compartments and (2) once BPH develops, androgen deprivation does not decrease the number of stem cell units in either the S or E compartments since subsequent androgen restoration fully restores the enlarged gland. The Coffey study documents that acute androgen deprivation sensitizes S–E interactions to radiation induced disruptions so that following radiation, androgen restoration does not induce full gland regrowth. Therefore, effective therapy for symptomatic BPH should be achievable by acute treatment with reversible androgen deprivation for a limited period followed by a single dose of conformal external beam radiation before allowing the man to recovery his normal serum testosterone. Prostate 68:1025–1034, 2008. © 2008 Wiley‐Liss, Inc.
Crystal structure of archaeal tRNA(m1G37)methyltransferase aTrm5
Authors: Goto‐Ito Sakurako , Ito Takuhiro , Ishii Ryohei , Muto Yutaka , Bessho Yoshitaka , Yokoyama Shigeyuki
Published: April 2008

Methylation of the N1 atom of guanosine at position 37 in tRNA, the position 3′‐adjacent to the anticodon, generates the modified nucleoside m1G37. In archaea and eukaryotes, m1G37 synthesis is catalyzed by tRNA(m1G37)methyltransferase (archaeal or eukaryotic Trm5, a/eTrm5). Here we report the crystal structure of archaeal Trm5 (aTrm5) from Methanocaldococcus jannaschii (formerly known as Methanococcus jannaschii) in complex with the methyl donor analogue at 2.2 Å resolution. The crystal structure revealed that the entire protein is composed of three structural domains, D1, D2, and D3. In the a/eTrm5 primary structures, D2 and D3 are highly conserved, while D1 is not conserved. The D3 structure is the Rossmann fold, which is the hallmark of the canonical class‐I methyltransferases. The a/eTrm5‐defining domain, D2, exhibits structural similarity to some class‐I methyltransferases. In contrast, a DALI search with the D1 structure yielded no structural homologues. In the crystal structure, D3 contacts both D1 and D2. The residues involved in the D1:D3 interactions are not conserved, while those participating in the D2:D3 interactions are well conserved. D1 and D2 do not contact each other, and the linker between them is disordered. aTrm5 fragments corresponding to the D1 and D2‐D3 regions were prepared in a soluble form. The NMR analysis of the D1 fragment revealed that D1 is well folded by itself, and it did not interact with either the D2‐D3 fragment or the tRNA. The NMR analysis of the D2‐D3 fragment revealed that it is well folded, independently of D1, and that it interacts with tRNA. Furthermore, the D2‐D3 fragment was as active as the full‐length enzyme for tRNA methylation. The positive charges on the surface of D2‐D3 may be involved in tRNA binding. Therefore, these findings suggest that the interaction between D1 and D3 is not persistent, and that the D2‐D3 region plays the major role in tRNA methylation. © 2008 Wiley‐Liss, Inc.
Structure‐based mutagenesis of Penicillium griseofulvum xylanase using computational design
Authors: André‐Leroux Gwénaëlle , Berrin Jean‐Guy , Georis Jacques , Arnaut Filip , Juge Nathalie
Published: April 2008

Penicillium griseofulvum xylanase (PgXynA) belongs to family 11 glycoside hydrolase. It exhibits unique amino acid features but its three‐dimensional structure is not known. Based upon the X‐ray structure of Penicillium funiculosum xylanase (PfXynC), we generated a three‐dimensional model of PgXynA by homology modeling. The native structure of PgXynA displayed the overall β‐jelly roll folding common to family 11 xylanases with two large β‐pleated sheets and a single α‐helix that form a structure resembling a partially closed right hand. Although many features of PgXynA were very similar to previously described enzymes from this family, crucial differences were observed in the loop forming the “thumb” and at the edge of the binding cleft. The robustness of the xylanase was challenged by extensive in silico‐based mutagenesis analysis targeting mutations retaining stereochemical and energetical control of the protein folding. On the basis of structural alignments, modeled three‐dimensional structure, in silico mutations and docking analysis, we targeted several positions for the replacement of amino acids by site‐directed mutagenesis to change substrate and inhibitor specificity, alter pH profile and improve overall catalytic activity. We demonstrated the crucial role played by Ser44PgXynA and Ser129PgXynA, two residues unique to PgXynA, in conferring distinct specificity to P. griseofulvum xylanase. We showed that the pH optimum of PgXynA could be shifted by −1 to +0.5 units by mutating Ser44PgXynA to Asp and Asn, respectively. The S44D and S44N mutants showed only slight alteration in Km and Vmax whereas a S44A mutant lost both pH‐dependence profile and activity. We were able to produce PgXynA S129G mutants with acquired sensitivity to the Xylanase Inhibitor Protein, XIP‐I. The replacement of Gln121PgXynA, located at the start of the thumb, into an Arg residue resulted in an enzyme that possessed a higher catalytic activity. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Sorption of sulfuryl fluoride by food commodities
Authors: Sriranjini Venkata‐rao , Rajendran Somiahnadar
Published: April 2008

BACKGROUND: The use of sulfuryl fluoride, a structural fumigant for termite and woodborer control, has recently been expanded to treating stored food commodities and food facilities. There is, however, a lack of data on the sorption of sulfuryl fluoride by food commodities. Knowledge about sorption is important in the context of effective treatment and residues.

RESULTS: When sulfuryl fluoride was applied at a dose of 50 g m−3 to various food commodities (total 68) with 300 g per replicate in 0.75 L gas wash bottles (fumigation chambers) at 25 ± 1 °C, in most cases (81%) the gas concentrations in the free space of the commodities exceeded 50 g m−3 (range 51–80 g m−3) at the end of 24 h exposure. In chambers without the substrate, an average concentration of 49.7 g m−3 was recorded. About 54% of the commodities showed low‐level ( ≤ 25%) sorption of sulfuryl fluoride, 34% showed medium‐level (26–50%) sorption and only 12% were highly sorptive (>50%). The latter include white oats (terminal gas concentration 17.8 g m−3), some of the decorticated split pulses (24.0–29.3 g m−3), chickpea flour (26.3 g m−3), dried ginger (29.0 g m−3), refined wheat flour (30.3 g m−3) and coriander powder (40.5 g m−3). In unfumigated control commodities, owing to interfering volatiles, Fumiscope® readings in the range 0–13 were noted.

CONCLUSION: Sulfuryl fluoride has the advantage of a low or moderate level of sorption with the majority of the food commodities. Copyright © 2008 Society of Chemical Industry
Dielectric function and optical transitions of silicon nanocrystals between 0.6 eV and 6.5 eV
Authors: Mansour M. , En Naciri A. , Johann L. , Grob J. J. , Stchakovsky M.
Published: April 2008

In this work, we report on the study of the dielectric function of nanocrystal silicon (nc‐Si) implanted in a SiO2 matrix on a silicon substrate by spectroscopic ellipsometry (SE). The formed nc‐Si have an average size around 4 nm. The SE measurements are performed at an angle of incidence of 70° in air at room temperature and in the spectral range of 0.6 eV to 6.5 eV. Two models are used to extract the optical responses of nc‐Si: Forouhi–Bloomer formalism and wavelength‐by‐wavelength inversion. The nc‐Si exhibits a significant reduction in the dielectric functions in comparison with the bulk Si. We have observed a reduction of the amplitude of the E1 transition with a very weak shift of its energy position. The transition E2 is characterized by a rather broad peak with an amplitude greater than that of E1. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Conventional and generalized ellipsometric investigation of isotropic spherical and anisotropic ellipsoidal cobalt nanoparticles
Authors: Gilliot M. , Naciri A. En , Johann L. , Stoquert J. P. , Grob J. J. , Muller D.
Published: April 2008

We propose an optical characterization of complex nanostructured thin layers by spectroscopic ellipsometry. These layers are either made of spherical or ellipsoidal‐shaped cobalt particles buried in a silica thin layer on a silicon substrate. Conventional ellipsometry is used to characterize the optically isotropic layers. It is shown that these implanted layers can be represented by a stack of three sublayers: a Maxwell‐Garnett homogeneous mixture of silica and cobalt clusters sandwiched between two silica sublayers. Ellipsoidal particles are obtained after irradiation of spherical nanostructures by swift heavy ions. In this case, generalized ellipsometry is used to study the uniaxial anisotropic optical effects of these particles. A correlation between the shape anisotropy of the particles and the optical anisotropy of the sample is shown and discussed using generalized Maxwell‐Garnett theory. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Imaging ellipsometry: quantitative analysis
Authors: Asinovski L. , Beaglehole D. , Clarkson M. T.
Published: April 2008

Imaging ellipsometry (IE) combines spatial resolution of optical microscopy with thin‐film measurement capabilities of ellipsometry. It has gained significant interest in recent years and is been used for a wide range of applications from biotechnology to semiconductor metrology. Traditionally, IE is used either as a qualitative technique – not unlike polarized microscopy or Surface Plasmon Resonance (SPR) – with “ellipsometry images” showing surface topology variation, or as a quasi‐quantitative technique where the change in “ellipsometry images” is used to deduce the change in film thickness. In this paper we give a brief critical review of different measurement systems configurations from the point of view of their fitness to quantitative IE measurement. We discuss the methods of calibration and correction that enable to achieve a truly quantitative IE measurement. We show that a fast and reliable quantitative IE can be practically implemented. It is consistent and can be used in lieu of a classical single point ellipsometry in many applications. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Comparison of surface layers on copper, titanium and tantalum created by methane plasma‐based ion implantation
Authors: Kraft G. , Flege S. , Baba K. , Hatada R. , Ensinger W.
Published: April 2008

Two carbide forming metals, titanium and tantalum, and a typical non carbide former, copper, were treated by methane plasma immersion ion implantation. The polished metal samples were exposed to high voltage pulses at –20 kV in an atmosphere of methane. The lateral distribution of the carbon was investigated via electron probe microanalysis, the depth distribution of the respective metal, carbon and hydrogen was determined by secondary ion mass spectrometry. X‐ray photoelectron spectroscopy in conjunction with argon sputtering showed the evolution of the binding conditions with depth. The phase composition of the samples was also analyzed by glancing incidence X‐ray diffraction. The generated carbon layers exhibited considerable differences depending on the respective substrate. Although there was no carbide formation with the copper samples, some carbon was incorporated into the surfaces. On copper the lateral carbon distributions showed inhomogeneities whereas the appearances of the ones on titanium and tantalum were uniform. The resulting thickness of the carbon layer was not only dependent on the substrate material, but also on the process parameters. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A comparative ab initio study of Cu overlayers on BaTiO3(001) and MgO(001) substrates
Authors: Zhukovskii Yu. F. , Kotomin E. A. , Ellis D. E.
Published: April 2008

In order to compare Cu adhesion upon two kinds of perfect cubic (001) oxide surfaces: (i) TiO2‐ and BaO‐terminated substrates of partly covalent BaTiO3 and (ii) highly ionic MgO substrate, we have performed DFT‐LCAO calculations using a hybrid B3PW Hamiltonian. 2D symmetrical slabs used here contain seven BaTiO3 and five MgO substrate layers covered on both sides by submonolayers of ordered Cu atoms. The Cu periodic coverage density atop the surface oxygen anions was varied from 1/8 to 1/2 monolayer. Copper bonding on the BaTiO3(001) surface has been found to be noticeably stronger than that on ionic MgO(001). Cu adatoms attract the electron density from BaO‐terminated and donate it towards TiO2‐terminated BaTiO3(001) substrates, respectively, by an amount that is about threefold larger than for a Cu/MgO(001) interface. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrical and topographical characterization of aluminum implanted layers in 4H silicon carbide
Authors: Rambach M. , Bauer A. J. , Ryssel H.
Published: April 2008

Electrical parameters and surface topography of aluminum (Al) implanted layers in 4H silicon carbide (SiC) are analyzed. The implantation is conducted for temperatures from room temperature up to 1000 °C. The impact of the post implantation annealing step on the Al implanted layers is investigated for two different annealing systems, a furnace system and a lamp system. The implanted layers are characterized in detail by atomic force microscopy and resistivity measurements. A model based on resistivity data is developed for the determination of activation and compensation and is discussed in order to get a better insight into the influence of the annealing step on the electrical parameters (e.g., hole mobility). In particular, the effect of elevated implantation temperatures on resistivity is identified. Additionally, the surface topography is examined regarding the annealing gas atmosphere. For that, a silicon carbide coated graphite crucible is used to achieve a silicon overpressure during annealing. The effectiveness of this crucible is identified by modeling. Measurements confirm the modeling results, that such a crucible prevents surface degradation only in the lamp system with heating rates of several 1000 K/min, and not in the furnace with heating rates in the range of some 10 K/min. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Femtosecond THz studies of intra‐excitonic transitions
Authors: Huber R. , Schmid B. A. , Kaindl R. A. , Chemla D. S.
Published: April 2008

Few‐cycle THz pulses are employed to resonantly access the internal fine structure of photogenerated excitons in semiconductors, on the femtosecond time scale. This technique allows us to gain novel insight into many‐body effects of excitons and reveal key quantum optical processes. We discuss experiments that monitor the density‐dependent renormalization of the binding energy of a high‐density exciton gas in GaAs/Al0.3Ga0.7As quantum wells close to the Mott transition. In a dilute ensemble of 3p excitons in Cu2O, stimulated THz emission from internal transitions to the energetically lower 2s state is observed at a photon energy of 6.6 meV, with a cross section of 10–14 cm2. Simultaneous interband excitation of both exciton levels drives quantum beats, which cause efficient THz emission at the difference frequency. By extending this principle to various other exciton resonances, we develop a novel way of mapping the fine structure by two‐dimensional THz emission spectroscopy. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Spin‐polarized excitonic emission from quantum dots after electrical injection
Authors: Löffler W. , Hetterich M. , Mauser C. , Li S. , Leuthold J. , Kalt H.
Published: April 2008

The spin of a single electron confined in a semiconductor quantum dot is a possible candidate for a qubit to realize quantum information processing. Here we discuss the initialization of the electron spins in single quantum dots using a semi‐magnetic spin aligner layer. We have succeeded in the concurrent initialization of five quantum dots with near‐unity fidelity. The electron spin is read‐out by observing the polarization of the emitted photons. These originate from excitonic recombination of the electron with an unpolarized hole in the dot. We find dots emitting highly polarized photons over the whole inhomogeneously broadened quantum‐dot ensemble emission spectrum. However, a pronounced dependency between the statistical average of the polarization degree and the quantum‐dot ground‐state energy is found. The influence of charged‐exciton recombination due to donors and defects is discussed. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
First‐principles study of the (001) surface of cubic Ba0.5Sr0.5TiO3
Authors: Wang Yuan Xu
Published: April 2008

We have theoretically investigated basic properties of the (001) surface of cubic Ba0.5Sr0.5TiO3 (BST) by the plane‐wave pseudopotential method within the local‐density approximation. For the BaSrO2‐terminated surface, the surface‐layer Sr atoms move inward and the surface‐layer Ba atoms move outward. Moreover, the displacement of the surface‐layer Sr atoms is much larger than the surface‐layer Ba atoms. The rumpling of the BaSrO2‐terminated surface is much larger than that of the Ti2O4‐terminated one. The surface state appears in the band structure of the Ti2O4‐terminated surface of BST. Based on the results of the calculated grand thermodynamic potential, only the BaSrO2‐terminated surface can exist in the (001) surface of cubic BST. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Contextual shifting: Teachers emphasizing students' academic identity to promote scientific literacy
Authors: Reveles John M. , Brown Bryan A.
Published: April 2008

This research presents a case study of two teachers' emphasis on students' academic identity as a means of facilitating their science literacy development. These cases support a theoretical position that deconstructs the notion of normative science literacy into its constitutive components: (a) being scientific and (b) appropriating its literate practices. Such a perspective views language as a substantive resource for academic identity construction. As such, we utilize a theoretical metaphor of “contextual shifting” to underscore teachers' central role in facilitating student understanding of literate practices associated with school science. Through a cross‐case analysis of two elementary science classrooms, we identified ways that students' academic identities were connected to their affiliation with specific scientific literate practices. Our findings reveal that the teachers in both research classrooms utilized teaching practices designed to afford students opportunities to develop academic identities commensurate with science learning. © 2008 Wiley Periodicals, Inc.Sci Ed92:1015–1041, 2008
Surface initiated‐atom transfer radical polymerization of a sugar methacrylate on gold nanoparticles
Authors: Yoon Kuk Ro , Lee Soo Min , Ramaraj B. , Kim Dong‐Pyo
Published: April 2008

For development of surface‐functionalized gold nanoparticles (GNPs) as cellular probes, we report herein the synthesis of glycoconjugates of GNPs with cyclic sugar methacrylate, 2‐lactobionamidoethyl methacrylate (LAMA). The strategy involves the attachment of an initiator on the nanoparticle surface followed by surface initiated‐atom transfer radical polymerization (SI‐ATRP) of LAMA. SI‐ATRP of LAMA was achieved by reacting a mixture of copper (I) bromide (CuBr), 2,2′‐bipyridine (bpy) and initiator‐bound GNPs in methanol at 20 °C for 12 h. The resultant GNP glycoconjugates were characterized using Fourier‐transform infrared (FT‐IR) spectroscopy, X‐ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). The FT‐IR spectra of GNP glycoconjugates show IR peaks characteristic of LAMA demonstrating the formation of a LAMA layer on the GNPs' surface. The XPS spectrum of glycoconjugates shows signals due to the presence of carbon (C1s, 288 eV) and oxygen (O1s, 536 eV) along with gold (Au 4f, 100 eV; Au 4p, 743 eV). The increase in diameter of GNPs from 13 to 25 nm measured by SEM further confirms the presence of a LAMA layer on the surface of the GNPs. Considering the biological importance of glycoconjugates, such as cell recognition, cell adhesion and cell growth regulation, the method described herein would be beneficial in many areas such as pathogen detection and biosensors. Copyright © 2008 John Wiley & Sons, Ltd.
Intensive research activity alters short‐term seedling dynamics in a tropical forest
Authors: Comita Liza S. , Goldsmith Gregory R. , Hubbell Stephen P.
Published: April 2008

Researchers can have unintentional, yet significant effects on their study systems. We tested for the effects of an intensive tree census on seedling dynamics in a 50‐ha permanent forest plot on Barro Colorado Island, Panama. At the community level, and for different shade‐tolerance guilds, we found no significant differences in seedling recruitment or survival inside compared to controls outside the plot. However, among growth forms, canopy trees and lianas exhibited significantly lower seedling survival inside the plot. Results suggest that intense researcher activity impacts short‐term vegetation dynamics, but effects do not accumulate over time.
Seasonal change in the gut clearance rate of three stonefly species in a Japanese stream
Authors: Miyasaka Hitoshi , Genkai‐Kato Motomi
Published: April 2008

We measured seasonal changes in the gut clearance rate of three stonefly species in a stream. The rate declined with water temperature. Based on the gut clearance rate obtained here, we estimated the half‐reduction time of gut contents and consumption rate of stoneflies on algae. Irrespective of stonefly species, the half‐reduction time in winter (2 days) was twice as long as that in summer (1 day). The areal consumption rates of stoneflies varied depending on species and season. These results imply that the seasonal consumption impact of aquatic insects can be different, despite their daily ration being similar among species.
The Breastfeeding Surgical Patient
Authors: Dumphy Deborah
Published: April 2008

IN THE UNITED STATES, more than 10 million women are either pregnant or breastfeeding at any given time. Of the women currently pregnant, over 70% will initially choose to breastfeed.

THE NEEDS OF A BREASTFEEDING surgical patient are unique and are best met by a supportive surgical team using evidenced‐based practice. The outcomes of such care will have long‐term effects on both the breastfeeding surgical patient and her infant.

EVIDENCED‐BASED PRACTICE resources for care of the breastfeeding surgical patient are scarce. This article applies available resources to the perioperative care of the breastfeeding surgical patient. AORN J 87 (April 2008) 759–766. © AORN, Inc, 2008.