bluuebunny/crossref_metadata_2025 huggingface dataset:
Monitoring of root‐zone water content in the laboratory by 2D geoelectrical tomography
Authors: Werban Ulrike , Attia al Hagrey Said , Rabbel Wolfgang
Published: September 2008

Root water uptake is one of the essential processes within the soil–plant–atmosphere continuum. We present a method for monitoring soil‐water redistributions due to water uptake by roots. Our aim is to image and monitor diurnal soil‐water redistribution during a small‐scale (centimeter‐to‐decimeter range) indoor experiment and to correlate water content determined by applied geoelectrical time‐lapse imaging techniques with values from single‐point time domain reflectometry (TDR) measurements. This includes establishing pedophysical relationships within the root zone and deriving the water‐content distribution from the electrical‐resistivity model. Using DC geoelectrics of high resolution (970 data points for 220 cm2), we monitored significant spatial heterogeneity of soil moisture with time, whereas no irrigation was applied. Thus, we imaged the high heterogeneity of fluid movements within the soil. We found diurnal variations with high spatial variability of soil water content during the morning and afternoon hours. The water content continuously increased from dawn to noon, whereas the increase started in the near‐surface zone from 1 cm to 3 cm above the main root zone. Between 8:00 a.m. and 10:00 a.m., water content decreases along most of the sections. Water content irregularly decreases and increases during the afternoon. During night time, we observed nearly no changes in soil water content due to the absence of transpiration and subsequently soil‐water redistribution. Most of these diurnal variations in soil water content lie within the intensive root zone, as measurements showed on soil samples excavated from these areas after the experiment.

Furthermore, we quantified water content derived from geoelectrical tomography of the monitored area before and after an irrigation event using a geophysical pedotransfer function of Archie, established specifically for the used lupine and the applied physico‐chemical boundary conditions of the experiment. The resulting average water content from 2D geoelectrical tomography agreed well with the values determined by the TDR measurements.
Precipitation of enzymes and organic matter by aluminum—Impacts on carbon mineralization
Authors: Scheel Thorsten , Pritsch Karin , Schloter Michael , Kalbitz Karsten
Published: September 2008

The precipitation of dissolved organic matter (DOM) by aluminum (Al) results in a stable soil organic matter (OM) fraction. Extracellular enzymes can also be removed from soil solution by sorption or precipitation, but whether this affects their activity and their importance for carbon (C) mineralization is largely unknown. We studied the activity of eight extracellular enzymes, precipitated by Al together with DOM, in relation to C mineralization of the precipitated OM. Dissolved OM was obtained from the Oi and Oa horizon of two forest soils and precipitated at different Al : C ratios and pH values to achieve a large variation in composition and C mineralization of precipitated OM. All eight enzymes were present in a functional state in precipitated OM. On average 53% of DOM was precipitated, containing on average 17%–41% of the enzyme activity (EA) involved in C degradation (chitinase, cellobiohydrolase, β‐glucosidase, glucuronidase, lacasse, and xylosidase) previously present in soil solution. In contrast, on average only 4%–7% of leucine‐aminopeptidase and acid‐phosphatase activity was found in precipitated OM. The EA found in precipitates significantly increased the percentage of C mineralized of precipitated OM, with a stronger influence of C‐degrading enzymes than enzymes involved in N and P cycling. However, after 8 weeks of incubation the correlations between EA and C mineralization disappeared, despite substantial EA being still present and only 0.5%–7.7% of C mineralized. Thus, degradation of precipitated OM seems to be governed by EA during the first degradation phase, but the long‐term stability of precipitated OM is probably related to its chemical properties.
Repeated freeze–thaw events affect leaching losses of nitrogen and dissolved organic matter in a forest soil
Authors: Hentschel Kerstin , Borken Werner , Matzner Egbert
Published: September 2008

Freezing and thawing may substantially influence the rates of C and N cycling in soils, and soil frost was proposed to induce NO$ _3^- $ losses with seepage from forest ecosystems. Here, we test the hypothesis that freezing and thawing triggers N and dissolved organic matter (DOM) release from a forest soil after thawing and that low freezing temperatures enhance the effect. Undisturbed soil columns were taken from a soil at a Norway spruce site either comprising only O horizons or O horizons + mineral soil horizons. The columns were subjected to three cycles of freezing and thawing at temperatures of –3°C, –8°C, and –13°C. The control columns were kept at constant +5°C. Following the frost events, the columns were irrigated for 20 d at a rate of 4 mm d–1. Percolates were analyzed for total N, mineral N, and dissolved organic carbon (DOC). The total amount of mineral N extracted from the O horizons in the control amounted to 8.6 g N m–2 during the experimental period of 170 d. Frost reduced the amount of mineral N leached from the soil columns with –8°C and –13°C being most effective. In these treatments, only 3.1 and 4.0 g N m–2 were extracted from the O horizons. Net nitrification was more negatively affected than net ammonification. Severe soil frost increased the release of DOC from the O horizons, but the effect was only observed in the first freeze–thaw cycle. We found no evidence for lysis of microorganisms after soil frost. Our experiment did not confirm the hypothesis that soil frost increases N mineralization after thawing. The total amount of additionally released DOC was rather low in relation to the expected annual fluxes.
Effects of experimental soil frost on the fine‐root system of mature Norway spruce
Authors: Gaul Dirk , Hertel Dietrich , Leuschner Christoph
Published: September 2008

Soil‐frost events may influence the dynamics of fine roots and therefore affect root‐derived C fluxes to the soil. We studied the impact of soil frost on the fine‐root dynamics of Norway spruce (Picea abies [L.] Karst.) by a replicated snow‐removal experiment in a mature forest in SE Germany. Snow removal in the three treatment plots reduced soil temperature significantly with minima <–5.5°C in the O layer while the snow‐covered control plots never reached temperatures below the freezing point. Sequential soil coring in the O layer at the beginning and at the end of the soil‐frost period as well as after thawing revealed that the soil frost treatment increased fine‐root mortality by 29%. However, enhanced fine‐root production in the snow‐removal plots nearly compensated for the fine‐root losses caused by low temperatures. These findings were confirmed by minirhizotron observations in the O layer and the upper 25 cm of the mineral soil showing that relative fine‐root loss was by far higher in the snow‐removal plots than in the control plots. Compensatory fine‐root production in the snow‐removal plots exceeded fine‐root production in the control plots during a period of 8 weeks after the soil frost application by 39% in the O layer while it was similar in both plot types in the mineral soil. Sequential coring and minirhizotron observations led to substantially different fine root–longevity estimates for the soil frost period. However, in both cases, the snow‐removal treatment was characterized by a significant reduction in root longevity indicating a faster fine‐root turnover. As a consequence, experimental soil frost enhanced the C input to the soil via root death at our study site by approx. 42 g m–2 and stimulated the C investment towards the root system of the spruce trees due to a higher sink activity.
Repeated drying–rewetting cycles and their effects on the emission of CO2, N2O, NO, and CH4 in a forest soil
Authors: Muhr Jan , Goldberg Stefanie D. , Borken Werner , Gebauer Gerhard
Published: September 2008

Prolonged summer droughts due to climate change are expected for this century, but little is known about the effects of drying and wetting on biogenic trace‐gas fluxes of forest soils. Here, the response of CO2, N2O, NO, and CH4 fluxes from temperate forest soils towards drying–wetting events has been investigated, using undisturbed soil columns from a Norway spruce forest in the “Fichtelgebirge”, Germany. Two different types of soil columns have been used for this study to quantify the contribution of organic and mineral horizons to the total fluxes: (1) organic horizons (O) and (2) organic and mineral soil horizons (O+M). Three drying–wetting treatments with different rewetting intensities (8, 20, and 50 mm of irrigation d–1) have been compared to a constantly moist control to estimate the influence of rainfall intensity under identical drying conditions and constant temperature (+15°C). Drought significantly reduced CO2, N2O, and NO fluxes in most cycles. Following rewetting, CO2 fluxes quickly recovered back to control level in the O columns but remained significantly reduced in the O+M columns with total CO2 fluxes from the drying–wetting treatment ranging approx. 80% of control fluxes. Fluxes of N2O and NO remained significantly reduced in both O and O+M columns even after rewetting, with cumulative fluxes from drying–wetting treatments ranging between 20% and 90% of the control fluxes, depending on gas and cycle. Fluxes of CH4 were small in all treatments and seem to play no significant role in this soil. No evidence for the release of additional gas fluxes due to drying–wetting was found. The intensity of rewetting had no significant effect on the CO2, N2O, NO, and CH4 fluxes, suggesting that the length of the drought period is more important for the emission of these gases. We can therefore not confirm earlier findings that fluxes of CO2, N2O, and NO during wetting of dry soil exceed the fluxes of constantly moist soil.
Anti‐Biofouling Properties of Polymers with a Carboxybetaine Moiety
Authors: Tada Susumu , Inaba Chika , Mizukami Kazuya , Fujishita Shigeto , Gemmei‐Ide Makoto , Kitano Hiromi , Mochizuki Akira , Tanaka Masaru , Matsunaga Takayuki
Published: September 2008

The resistance of random copolymers of BMA and CMB against biofouling was evaluated. The amount of proteins adsorbed onto the CMB copolymers was smaller than that onto other polymers (non‐ionic polymers and copolymers of ordinary ionic monomers and BMA) and decreased with an increase in the content of CMB residues. Furthermore, there was a dramatic decrease in the number of cells (platelets and fibroblasts) that adhered to the CMB copolymers compared with that to other polymers. In contrast with this, CMB copolymers were slightly perturbative to both complement and coagulation systems. However, the overall results suggest that zwitterionic moieties are effective for making polymer materials biocompatible due to their excellent anti‐biofouling property.

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Synergistic Effect and Hierarchical Nanostructure Formation in Mixing Two Designer Lipid‐Like Peptide Surfactants Ac‐A6D‐OH and Ac‐A6K‐NH2
Authors: Khoe Ulung , Yang Yanlian , Zhang Shuguang
Published: September 2008

We here report the nanostructures from combinational self‐assembly of two designer lipid‐like peptides Ac‐A6D‐OH and Ac‐A6K‐NH2 using dynamic light scattering (DLS) and atomic force microscopy (AFM). The synergistic phenomenon is observed by measuring the critical aggregation concentrations (CACs) of these two mixed peptides, in different molar ratios by DLS. The nanoropes were observed in AFM images at a molar ratio of Ac‐A6D‐OH/Ac‐A6K‐NH2 = 1:1, and the thin film formation with aligned nanoropes is shown at a molar ratio of 2:1. The well aligned nanoropes at the molar ratio of Ac‐A6D‐OH/Ac‐A6K‐NH2 = 2:1 indicated the competition factor between the electrostatic repulsion according to DLVO theory and the hydrophobic interaction arising from the long side chains on lysine residues. This study will further our understanding for designing new nanomaterials based on designer lipid‐like peptide surfactants.

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Polyurethanes Based on Castor Oil: Kinetics, Chemical, Mechanical and Thermal Properties
Authors: Hablot Elodie , Zheng Dan , Bouquey Michel , Avérous Luc
Published: September 2008

Polyurethanes based on vegetable oil were synthesized with castor oil and toluene diisocyanate, isophorone diisocyanate or hexamethylene diisocyanate, using dibutyltin dilaurate as a catalyst. The effects of the nature of the diisocyanate on the evolution of the kinetics, as well as the physical and mechanical properties and the thermal stability, of the different synthesized polyurethanes were investigated, and these complement data from the literature on equivalent systems. The polymerization kinetics, degree of swelling and mechanical properties were greatly affected by the diisocyanate nature, whereas the rheological properties and thermal stability were found to be similar for all polyurethanes.

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Free‐Standing, Thermostable, Micrometer‐Scale Honeycomb Polymer Films and their Properties
Authors: Bormashenko Edward , Schechter Alex , Stanevsky Oleg , Stein Tamir , Balter Sagi , Musin Albina , Bormashenko Yelena , Pogreb Roman , Barkay Zahava , Aurbach Doron
Published: September 2008

A method of manufacturing free‐standing, micrometer‐scale honeycomb polyetherimide films is reported for the first time. Films are manufactured with a dip‐coating technique under water‐assisted self‐assembly. It is shown that the addition of poly(organosilane/siloxane)s and poly(ethylene glycol) allows the formation of regular honeycomb patterns. The films demonstrated the high thermal stability inherent for polyetherimide. The wetting properties of films are reported. The presence of nanopores was revealed with SEM imaging of the films. The makeup of the films allows their use as asymmetric membranes for reverse osmosis and ultrafiltration.

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Crystallization Kinetics and Hydrophilicity Improvement of Biodegradable Poly(butylene succinate) in its Miscible Blends with Poly(ethylene oxide)
Authors: Lu Jiaoming , Qiu Zhaobin , Yang Wantai
Published: September 2008

The spherulitic morphology and growth, overall isothermal crystallization kinetics and hydrophilicity of PBSU were investigated by POM, DSC and WCA measurements in its miscible blends with PEO. The Hoffman‐Lauritzen equation was employed to analyze the spherulitic growth rates of neat and blended PBSU, which show a crystallization regime transition between regime II and III. The overall crystallization rates of PBSU decreased with increasing crystallization temperature, regardless of blend composition, while the crystallization mechanism does not change. A significant improvement in the hydrophilicity of PBSU can be achieved by blending with different weight fractions of PEO, which may be essential for the practical application of PBSU/PEO blends.

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An Improved Rapid Synthesis of Oligo(p‐benzamide) Block Copolymers
Authors: König Hannah M. , Kilbinger Andreas F. M.
Published: September 2008

We describe a new synthesis that allows the preparation of oligo(p‐benzamide)s up to the heptamer on solid support without the need of semi‐temporary amide N‐protective groups. With increase in length, the solubility of oligo(p‐benzamide)s reduces dramatically. Even the tetra(p‐benzamide) is not soluble in common organic solvents. Therefore, solution syntheses of oligomers beyond the tetramer are not feasible. As will be shown in this paper, solid supported synthesis allows the preparation of even longer oligomers (up to the heptamer) in good yields. The high dilution on the solid support is most likely responsible for their pseudo‐solution‐like reactivity and the prevention of aggregation. This procedure is a significant improvement of previous syntheses and an important tool for the rapid exploration of supramolecular rod–coil copolymers based on oligoaramides.

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Molecular Simulation Via Connectivity‐altering Monte Carlo and Scale‐jumping Methods: Application to Amorphous Polystyrene
Authors: Mulder Tim , Harmandaris Vagelis A. , Lyulin Alexey V. , van der Vegt Nico F. A. , Michels M. A. J.
Published: September 2008

Well‐equilibrated atactic‐polystyrene (aPS) samples are obtained through the end‐bridging Monte Carlo (EBMC) algorithm. A coarse‐grained (CG) description of aPS is used; monomers are represented by two CG beads. The algorithm produces correct polymer conformations on all length scales, beyond the size of the CG beads. The code is very efficient, even though the acceptance of 0.001–0.005% is approximately 10–100 times lower than in the original EB code for PE. Systems of aPS of the order of 5000 monomers (50 chains of 100 monomers on average) can be equilibrated on all length scales within a week, in a single‐processor run. The computer code is also adequate for simulations of other polymers that have the same regularity in their sequence of chemical groups and that are modeled at the same or at a coarser level of description.

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Geometries and Electronic Structures of Co‐Oligomers and Co‐Polymers Based on Tricyclic Nonclassical Thiophene: A Theoretical Study
Authors: Fu Yangwu , Shen Wei , Li Ming
Published: September 2008

The geometries and electronic properties of four copolymers based on tricyclic nonclassical thiophene were studied using DFT at the B3LYP/6‐31G(d) level. Bond lengths and their alternation, electron densities at BCPs, NICS, and WBIs were analyzed and correlated with the energy gap. The results show that the degree of conjugation increases upon main chain extension. The energy gap decreased steadily with increasing degree of polymerization. Conjugation is stronger in the central than in the outer section. The results suggest that the narrow HOMO/LUMO separation of tricyclic nonclassical thiophenes can be carried over to their co‐polymers by using them as building blocks for the co‐polymers.

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Synthesis and NMR elucidation of novel penta‐cycloundecane amine derivatives as potential antituberculosis agents
Authors: Onajole Oluseye K. , Govender Thavendran , Makatini Maya , Kruger Hendrik G.
Published: September 2008

The synthesis and NMR elucidation of five novel penta‐cycloundecane amine derivatives are reported. These compounds are potential antituberculosis agents. The 1H and 13C spectra showed major overlapping of methine signals of the cage skeleton making it extremely difficult to elucidate these compounds. The overlapping occurs as a result of the additions made to the carbonyl carbon (C‐8/C‐11) of the cage. The two‐dimensional NMR technique proved to be a useful tool in overcoming this problem. All compounds reported are meso compounds thereby not only simplifying the NMR structure elucidation, but also making it indeed possible. Copyright © 2008 John Wiley & Sons, Ltd.
NMR spectroscopic elucidation of the structure and stereochemistry of tricyclic 3‐styrylpyrazolines
Authors: Tóth Gábor , Simon András , Jenei Attila , Jekő József , Lévai Albert
Published: September 2008

Diastereomeric mixtures of tricyclic 3‐styrylpyrazolines have been prepared by the reaction of 3‐cynnamylidenechroman‐4‐ones and their 1‐thio analogs with hydrazine in hot acetic acid or propionic acid solutions. The diastereomeric mixtures were separated by column chromatography to obtain the pure diastereomers. The elucidation of their structure and stereochemistry and complete 1H and 13C assignments have been performed by a combination of various one‐ and two‐dimensional NMR experiments. Copyright © 2008 John Wiley & Sons, Ltd.
Hydrolytic Degradation and Monomer Recovery of Poly(butylene succinate) and Poly(butylene succinate/adipate) in the Melt
Authors: Tsuji Hideto , Yamamura Yoshiko , Ono Tomoyuki , Saeki Takashi , Daimon Hiroyuki , Fujie Koichi
Published: September 2008

Aliphatic dicarboxylic acid/aliphatic diol‐derived polyesters, poly(butylene succinate) and poly(butylene succinate/adipate), have been hydrolytically degraded in the melt in high‐temperature and high‐pressure water over a wide temperature range of 180–300 °C for periods of up to 30 min. The formation/decomposition of succinic acid (SA), adipic acid (AA), and butane‐1,4‐diol (BD), plus the molecular weight change of PBS and PBSA were then investigated. SA and AA were recovered at maximum yields of 65–80%, whereas BD was recovered at a maximum yield of only 30%, probably because of its decomposition. The obtained results were compared with those reported for aliphatic hydroxycarboxylic acid‐derived polyesters and aromatic dicarboxylic acid/aliphatic diol‐derived polyesters.

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Discrete modelling of time‐dependent rockfill behaviour
Authors: Silvani Claire , Désoyer Thierry , Bonelli Stéphane
Published: September 2008

This modelling study deals with the time‐dependent behaviour of rockfill media, which is of particular interest during the life of rockfill dams. Breakage of rock blocks and crack propagation are the main processes responsible for rockfill creep and collapse. The modelling procedure presented here is performed on two scales: on the rock block scale, where the grain is taken to be an assembly of rigid particles initially endowed with cohesive bonds, and on the rockfill scale, which is taken to involve a set of breakable grains interacting via contact and friction processes. The grain breakage process is described in term of a thermodynamically consistent damage interface model, where the damage is a gradual delayed process. This model was implemented in a non‐smooth contact dynamics code. The effects of the main parameters involved were analysed by performing numerical studies. The ability of the model to predict the creep behaviour of rockfill media is confirmed by presenting several simulations. Copyright © 2008 John Wiley & Sons, Ltd.
Fast solvers with block‐diagonal preconditioners for linear FEM–BEM coupling
Authors: Funken Stefan A. , Stephan Ernst P.
Published: September 2008

The purpose of this paper is to present optimal preconditioned iterative methods to solve indefinite linear systems of equations arising from symmetric coupling of finite elements and boundary elements. This is a block‐diagonal preconditioner together with a conjugate residual method and a preconditioned inner–outer iteration. We prove the efficiency of these methods by showing that the number of iterations to preserve a given accuracy is bounded independent of the number of unknowns. Numerical examples underline the efficiency of these methods. Copyright © 2008 John Wiley & Sons, Ltd.
A model for interface cracks in layered orthotropic solids: Convergence of modal decomposition using the interaction integral method
Authors: Merzbacher M. J. , Horst P.
Published: September 2008

The mode‐partitioning problem for bimaterial interfaces is still not resolved by the classical fracture mechanics approach in a satisfactory manner. Stress oscillations and overlapping crack faces are a direct consequence of the rigorous solution of the elastic boundary value problem, if the constitutive law changes discontinuously across the interface. Conversely, continuously varying material properties, also referred to as functionally graded materials (FGM), avoid these physically not admissible drawbacks. In this case the crack tip fields are of the same nature as those known from homogeneous materials. Therefore, the well‐established stress intensity factor concept can be used without any changes. Following this motivation an FGM‐interface model for delaminated composite beam structures was developed and its characteristics with respect to the modal decomposition of the crack tip fields were investigated. The considered beam structures consisted of two orthotropic layers, each of a different material. The spatial variation of the material properties in the interface region was modeled by a tanh ‐function introducing one transition parameter that controlled the FGM‐gradient. Four load cases were analyzed for each structural configuration: either a unit normal force or a unit bending moment was imposed on each end of the split beam. Thus, any load case can be simply reconstructed from the presented results by means of superposition. The stress intensity factors for modes I and II were then evaluated using an interaction integral method along with the finite element method. The corresponding results are given depending on the mesh density of the interface region, the integration domain and the transition parameter. In this manner, the influence of the transition parameter on the mode ratio and on the convergence behavior of the modal decomposition scheme with respect to its integration domain was identified. Finally, the ability of the FGM‐interface model to represent bimaterial interfaces while still maintaining the advantages of crack analysis in homogeneous materials was highlighted. Copyright © 2008 John Wiley & Sons, Ltd.
Application of the X‐FEM to the fracture of piezoelectric materials
Authors: Béchet E. , Scherzer M. , Kuna M.
Published: September 2008

This paper presents an application of the extended finite element method (X‐FEM) to the analysis of fracture in piezoelectric materials. These materials are increasingly used in actuators and sensors. New applications can be found as constituents of smart composites for adaptive electromechanical structures. Under in service loading, phenomena of crack initiation and propagation may occur due to high electromechanical field concentrations. In the past few years, the X‐FEM has been applied mostly to model cracks in structural materials. The present paper focuses at first on the definition of new enrichment functions suitable for cracks in piezoelectric structures. At second, generalized domain integrals are used for the determination of crack tip parameters. The approach is based on specific asymptotic crack tip solutions, derived for piezoelectric materials. We present convergence results in the energy norm and for the stress intensity factors, in various settings. Copyright © 2008 John Wiley & Sons, Ltd.
SPH with the multiple boundary tangent method
Authors: Yildiz M. , Rook R. A. , Suleman A.
Published: September 2008

In this article, we present an improved solid boundary treatment formulation for the smoothed particle hydrodynamics (SPH) method. Benchmark simulations using previously reported boundary treatments can suffer from particle penetration and may produce results that numerically blow up near solid boundaries. As well, current SPH boundary approaches do not properly treat curved boundaries in complicated flow domains. These drawbacks have been remedied in a new boundary treatment method presented in this article, called the multiple boundary tangent (MBT) approach. In this article we present two important benchmark problems to validate the developed algorithm and show that the multiple boundary tangent treatment produces results that agree with known numerical and experimental solutions. The two benchmark problems chosen are the lid‐driven cavity problem, and flow over a cylinder. The SPH solutions using the MBT approach and the results from literature are in very good agreement. These solutions involved solid boundaries, but the approach presented herein should be extendable to time‐evolving, free‐surface boundaries. Copyright © 2008 John Wiley & Sons, Ltd.
Dispersion analysis of the meshfree radial point interpolation method for the Helmholtz equation
Authors: Wenterodt Christina , von Estorff Otto
Published: September 2008

When numerical methods such as the finite element method (FEM) are used to solve the Helmholtz equation, the solutions suffer from the so‐called pollution effect which leads to inaccurate results, especially for high wave numbers. The main reason for this is that the wave number of the numerical solution disagrees with the wave number of the exact solution, which is known as dispersion. In order to obtain admissible results a very high element resolution is necessary and increased computational time and memory capacity are the consequences.

In this paper a meshfree method, namely the radial point interpolation method (RPIM), is investigated with respect to the pollution effect in the 2D‐case. It is shown that this methodology is able to reduce the dispersion significantly. Two modifications of the RPIM, namely one with polynomial reproduction and another one with a problem‐dependent sine/cosine basis, are also described and tested. Numerical experiments are carried out to demonstrate the advantages of the method compared with the FEM. For identical discretizations, the RPIM yields considerably better results than the FEM. Copyright © 2008 John Wiley & Sons, Ltd.
Detecting signals of opioid analgesic abuse: application of a spatial mixed effect poisson regression model using data from a network of poison control centers
Authors: Smith Meredith Y. , Irish William , Wang Jianmin , Haddox J. David , Dart Richard C.
Published: September 2008

Purpose

The recent rise in the non‐medical use of opioid analgesics in the US has underscored the importance of comprehensive post‐marketing surveillance of these products. To assist pharmacovigilance efforts, we developed a methodology for detecting geo‐specific “signals” of potential outbreaks of prescription drug abuse by 3‐digit ZIP (3DZ) code.

Methods

The number of intentional exposure calls involving nine specific opioid analgesics were obtained from eight regional poison control centers between first quarter 2003 and fourth quarter 2004. The unit of analysis was a combination of drug–quarter/year–3DZ. We fitted an empirical Bayes mixed effects Poisson–Gamma regression model that adjusted for differences across 3DZs in opioid analgesic exposure. A relative report rate (RR) ≥3 at a probability of >0.95 was the signal threshold criterion.

Results

A total of 15 769 valid drug–time–3DZ combinations were identified. Of these, 1.9% (n = 294) met the signal threshold criterion. The number of signals generated per drug–quarter/year–3DZ combination ranged from 0 to 13. The largest number of signals were those involving methadone (n = 71), hydrocodone (n = 57), and branded oxycodone extended‐release (n = 45). Signals for methadone and branded oxycodone extended‐release were predominantly clustered in Appalachia. Hydrocodone‐related signals showed less geographic clustering with approximately 26% reported from California, and the remainder from other regions in the US.

Conclusions

Our results show marked regional differences in reported abuse of specific opioid analgesics. Additional research is needed to determine the sensitivity and specificity of signals obtained using this spatial mixed effect Poisson regression model. Copyright © 2008 John Wiley & Sons, Ltd.
Catalytic materials manufactured by the polyol process for monolithic dye‐sensitized solar cells
Authors: Skupien Krzysztof , Putyra Piotr , Walter Janusz , Kozłowski Ryszard H. , Khelashvili Guram , Hinsch Andreas , Würfel Uli
Published: September 2008

Three types of screen‐printable catalytic pastes were successfully prepared to be used as counterelectrode for monolithic dye solar cells encapsulated with glass frit. The electroless bottom‐up method or so‐called polyol process has been applied to fabricate thermally stable SnO2:Sb/Pt and carbon black/Pt nanocomposites. The catalytic and electric properties of these materials were compared with a new platinum‐free type of carbon counterelectrode. The layers containing low platinum amounts (less than 5 µg/cm2) exhibit a very low charge transfer resistance of about 0·4 Ω · cm2. Also the conductive carbon layer shows an acceptable charge transfer resistance of 1·6 Ω · cm2. Additionally the catalytic layer containing porous carbon black reveals excellent sheet resistance below 5 Ω/□; this feature has enabled to work out a low cost counterelectrode which combined suitable catalytic and conductive properties. The layers have been characterized using following methods: electrochemical impedance spectroscopy (EIS), field emission scanning electron microscopy (FE‐SEM), energy filter transmission electron microscopy (EF‐TEM) and inductively coupled plasma mass spectroscopy (ICP‐MS). Copyright © 2008 John Wiley & Sons, Ltd.
The effect of Zn1‐xMgxO buffer layer deposition temperature on Cu(In,Ga)Se2 solar cells: A study of the buffer/absorber interface
Authors: Törndahl T. , Coronel E. , Hultqvist A. , Platzer‐Björkman C. , Leifer K. , Edoff M.
Published: September 2008

The effect of atomic layer deposition temperature of Zn1‐xMgxO buffer layers for Cu(In,Ga)Se2 (CIGS) based solar cell devices is evaluated. The Zn1‐xMgxO films are grown using diethyl zinc, bis‐cyclopentadienyl magnesium and water as precursors in a temperature range of 105 to 180°C. High efficiency devices are produced in the region from 105 up to 135°C. At a Zn1‐xMgxO deposition temperature of 120°C, a maximum cell efficiency of 15·5% is reached by using a Zn1‐xMgxO layer with an x‐value of 0·2 and a thickness of 140 nm. A significant drop in cell efficiency due to large losses in open circuit voltage and fill factor is observed for devices grown at temperatures above 150°C. No differences in chemical composition, structure and morphology of the samples are observed, except for the samples prepared at 105 and 120°C that show elemental selenium present at the buffer/absorber interface. The selenium at the interface does not lead to major degradation of the solar cell device efficiency. Instead, a decrease in Zn1‐xMgxO resistivity by more than one order of magnitude at growth temperatures above 150°C may explain the degradation in solar cell performance. From energy filtered transmission electron microscopy, the width of the CIGS/Zn1‐xMgxO chemical interface is found to be thinner than 10 nm without any areas of depletion for Cu, Se, Zn and O. Copyright © 2008 John Wiley & Sons, Ltd.
Physiology of Streptococcus thermophilus during the late stage of milk fermentation with special regard to sulfur amino‐acid metabolism
Authors: Herve‐Jimenez Luciana , Guillouard Isabelle , Guedon Eric , Gautier Céline , Boudebbouze Samira , Hols Pascal , Monnet Véronique , Rul Françoise , Maguin Emmanuelle
Published: September 2008

Streptococcus thermophilus is a thermophilic lactic acid bacterium widely used as starter in the manufacture of dairy products in particular in yoghurt manufacture in combination with Lactobacillus delbrueckii ssp. bulgaricus. However, in spite of its massive use, the physiological state of S. thermophilus in milk has hardly been investigated. We established the first map of the cytosolic proteome of S. thermophilus LMG18311 grown in milk. It comprises 203 identified proteins corresponding to 32% of theoretical proteome. In addition, using proteomic and transcriptomic approaches, we analyzed the physiology of LMG18311 during its late stage of growth in milk (between 2h30 and 5h30). It revealed the up‐regulation of (i) peptides and AA transporters and of specific AA biosynthetic pathways notably for sulfur AA and (ii) genes and proteins involved in the metabolism of various sugars. These two effects were also observed in LMG18311 grown in milk in coculture with L. bulgaricus although the effect on sugar metabolism was less pronounced. It suggests that the stimulatory effect of Lactobacillus on the Streptococcus growth is more complex than AA or peptides supply.
Heat induced changes in protein expression profiles of Norway spruce (Picea abies) ecotypes from different elevations
Authors: Valcu Cristina‐Maria , Lalanne Céline , Plomion Christophe , Schlink Katja
Published: September 2008

Although tree species typically exhibit low genetic differentiation between populations, ecotypes adapted to different environmental conditions can vary in their capacity to withstand and recover from environmental stresses like heat stress. Two month old seedlings of a Picea abies ecotype adapted to high elevation showed lower level of thermotolerance and higher level of tolerance to oxidative stress relative to a low elevation ecotype. Protein expression patterns following exposure to severe heat stress of the two ecotypes were compared by means of 2‐DE. Several proteins exhibiting ecotype and tissue specific expression were identified by MS/MS. Among them, small heat shock proteins of the HSP 20 family and proteins involved in protection from oxidative stress displayed qualitative and quantitative differences in expression between the ecotypes correlated with the observed phenotypic differences. On the basis of these results, it can be speculated that the observed interpopulation polymorphism of protein regulation in response to heat stress could underlie their different capacities to withstand and recover from heat stress. These local adaptations are potentially relevant for the species adaptation to the conditions predicted by the current models for climate change.
Peptide enrichment and protein fractionation using selective electrophoresis
Authors: Ly Linda , Wasinger Valerie C.
Published: September 2008

In recent times, the analysis of the peptidome has become increasingly valuable to gain a better understanding of the critical roles native peptides play in biological processes. Here, we show a technique using a novel electrophoretic device named MF10, for the fractionation of proteins and peptides based on size and also pH in low volume liquid phase under an electric field. A 1 μM, 7‐protein and peptide standard mix ranging from 1 to 25 kDa has been used to show peptide migration into a fraction contained by 1–5 kDa membranes. Simultaneous fractionation of the higher mass protein standards to the correct fraction also occurred. To assess the MF10's ability to fractionate more complex samples, human plasma was used to enrich for the peptidome below 5 kDa in the presence of the proteome. Peptide enrichment was achieved while simultaneously fractionating higher mass proteins to three other mass restricted fractions. The utility of this approach is demonstrated with the identification (with at least 2 ppm mass accuracy) of 76 unique peptides, equating to 22 proteins enriched to the 1–5 kDa fraction of the MF10.
Comparative analysis of proteome differential regulation during cell dedifferentiation in Arabidopsis
Authors: Chitteti Brahmananda Reddy , Tan Feng , Mujahid Hana , Magee Bryce G. , Bridges Susan M. , Peng Zhaohua
Published: September 2008

Cell dedifferentiation is a cell fate switching process in which differentiated cells undergo genome reprogramming to regain the competency of cell division and organ regeneration. The molecular mechanism underlying the cell dedifferentiation process remains obscure. In this report, we investigate the cell dedifferentiation process in Arabidopsis using a shotgun proteomics approach. A total of 758 proteins are identified by two or more matched peptides. Comparative analyses at four time points using two label‐free methods reveal that 193 proteins display up‐regulation and 183 proteins display down‐regulation within 48 h. While the results of the two label‐free quantification methods match well with each other, comparison with previously published 2‐DE gel results reveal that label‐free quantification results differ substantially from those of the 2‐DE method for proteins with peptides common to multiple proteins, suggesting a limitation of the label‐free methods in quantifying proteins with closely related family members in complex samples. Our results show that the shotgun approach and the traditional 2‐DE gel approach complement each other in both protein identification and quantification. An interesting observation is that core histones and histone variants are subjected to extensive down‐regulation, indicating that there is a dramatic change in the chromatin during cell differentiation.
Phosphoproteomics, oncogenic signaling and cancer research
Authors: Chong Poh‐Kuan , Lee Huiyin , Kong Jacklyn Wai‐Fun , Loh Marie Chiew‐Shia , Wong Chee‐Hong , Lim Yoon‐Pin
Published: September 2008

The past 5 years have seen an explosion of phosphoproteomics methods development. In this review, using epidermal growth‐factor signaling as a model, we will discuss how phosphoproteomics, along with bioinformatics and computational modeling, have impacted key aspects of oncogenic signaling such as in the temporal fine mapping of phosphorylation events, and the identification of novel tyrosine kinase substrates and phosphorylation sites. We submit that the next decade will see considerable exploitation of phosphoproteomics in cancer research. Such a phenomenon is already happening as exemplified by its use in promoting the understanding of the molecular etiology of cancer and target‐directed therapeutics.
Hemocyte‐lineage marker proteins in a crustacean, the freshwater crayfish, Pacifastacus leniusculus
Authors: Wu Chenglin , Söderhäll Irene , Kim Young‐A , Liu Haipeng , Söderhäll Kenneth
Published: September 2008

To identify proteins associated with development of different hemocyte types in the freshwater crayfish Pacifastacus leniusculus, 2‐DE followed by MS analysis was carried out with hematopoietic tissue (Hpt) cells, semigranular cells (SGC) and granular cells (GC). Within the hemocyte lineages one two‐domain Kazal proteinase inhibitor (KPI) was found to be specific for SGC, while a superoxide dismutase (SOD) was specific for GC at protein as well as at mRNA level. The proliferation cell nuclear antigen (PCNA) was detected at the mRNA level in Hpt cells only. We also provide evidence that SGC and GC most likely differentiate to maturation as separate lineages. We found that after laminarin or lipopolysaccharide (LPS) injection into crayfish, the transcript levels of PCNA and SOD increased in the Hpt cells, whereas the KPI transcript never was present in Hpt regardless of any challenge. RNA interference of PCNA in the Hpt cells led to that most of the cells did not spread or attach to the tissue culture dish. These results suggest that PCNA, KPI and SOD can be used as markers for Hpt cells, SGC and GC, respectively, and in conjunction with these results, a model is proposed how the Hpt responds to a microbial challenge by proliferation and release of Hpt cells.
Subproteomic tools to increase genome annotation complexity
Authors: Wei Candong , Peng Junping , Xiong Zhaohui , Yang Jian , Wang Jing , Jin Qi
Published: September 2008

Comprehensive and precise annotations of short protein‐coding genes are always a challenging task. Here we propose a new design to facilitate the characterization of previously overlooked short protein‐coding genes by integrating a shotgun proteomics method and oligonucleotide array analysis. Using Shigella flexneri as a model, we validate 163 annotated ORFs and 51 hypothetical or putative transcripts at the protein level, and discover four novel short ORFs. This strategy will contribute significantly to comprehensive and accurate genome‐wide annotation, and to our understanding of prokaryotic genome structure.
Simplified validation of borderline hits of database searches
Authors: Thomas Henrik , Shevchenko Andrej
Published: September 2008

Along with unequivocal hits produced by matching multiple MS/MS spectra to database sequences, LC‐MS/MS analysis often yields a large number of hits of borderline statistical confidence. To simplify their validation, we propose to use rapid de novo interpretation of all acquired MS/MS spectra and, with the help of a simple software tool, display the candidate sequences together with each database search hit. We demonstrate that comparing hit database sequences and independent de novo interpretations of the same MS/MS spectra assists in rapid examination of ambiguous matches.
Proteomic analysis of alterations in the secretome of Arabidopsis thaliana suspension cells subjected to nutritional phosphate deficiency
Authors: Tran Hue T. , Plaxton William C.
Published: September 2008

A proteomic approach was applied to compare the secretome (culture filtrate proteome) of phosphate‐sufficient (+Pi) and Pi‐deficient (−Pi) Arabidopsis thaliana suspension cell cultures. Secretomes harvested from the +Pi and −Pi cells yielded dissimilar 2‐DE maps. PMF via MALDI‐TOF MS resulted in the identification of 50 protein spots representing 37 discrete proteins having unique gene identities. A total of 24 Pi‐starvation responsive proteins were identified, with 18 of these being up‐regulated and six down‐regulated. Secreted proteins up‐regulated by the −Pi cells included a ribonuclease involved in Pi scavenging from extracellular nucleic acids, as well as enzymes of cell wall modification, proteolysis, pathogen responses, and ROS metabolism. Enzyme activity assays and immunoblotting demonstrated that a pair of purple acid phosphatase isoforms having subunit Mrs of 65 and 55 kDa was also secreted by the −Pi cells. Semiquantitative RT‐PCR was used to assess the relationship between mRNA levels and relative amounts of selected secretome proteins. The results indicate that transcriptional control is but one of many factors contributing to Arabidopsis Pi starvation responses, and highlight the importance of parallel biochemical/proteomic studies of −Pi plants.
Cerebrospinal fluid‐optimized two‐dimensional difference gel electrophoresis (2‐D DIGE) facilitates the differential diagnosis of Creutzfeldt–Jakob disease
Authors: Brechlin Peter , Jahn Olaf , Steinacker Petra , Cepek Lukas , Kratzin Hartmut , Lehnert Stefan , Jesse Sarah , Mollenhauer Brit , Kretzschmar Hans A. , Wiltfang Jens , Otto Markus
Published: September 2008

So far only the detection of 14‐3‐3 proteins in cerebrospinal fluid (CSF) is included in the diagnostic criteria for sporadic Creutzfeldt–Jakob disease (sCJD). However, this assay cannot be used for screening because of the high rate of false positive results in sCJD, and often negative results in variant CJD. To facilitate the differential diagnosis of CJD, we applied 2‐D differential gel‐electrophoresis (2‐D DIGE) as a quantitative proteomic screening system for CSF proteins. We compared 36 patients suffering from sCJD with 30 patients suffering from other neurodegenerative diseases. Sample preparation was optimized in consideration of the fact that CSF is composed of blood‐ and brain‐derived proteins, and an improved 2‐D DIGE protocol was established. Using this method in combination with protein identification by MALDI‐TOF‐MS, several known surrogate markers of sCJD like 14‐3‐3 protein, neuron‐specific enolase, and lactate dehydrogenase were readily identified. Moreover, a not yet identified protein with an approximate molecular mass of 85 kDa was found as marker for sCJD with high diagnostic specificity and sensitivity. We conclude that our proteomic approach is useful to differentiate CJD from other neurodegenerative diseases and expect that CSF‐optimized 2‐D DIGE will find broad application in the search for other brain derived proteins in CSF.
Annual Spring Meeting of the Proteomics Standards Initiative 23–25 April 2008, Toledo, Spain
Authors: Orchard Sandra , Albar Juan‐Pablo , Deutsch Eric W. , Binz Pierre‐Alain , Jones Andrew R. , Creasy David , Hermjakob Henning
Published: September 2008

The role of the Human Proteome Organisation Proteomics Standards Initiative (HUPO‐PSI) is to produce and release community‐accepted reporting requirements, interchange formats and controlled vocabularies for mass spectrometry proteomics and related technologies such as gel electrophoresis, column chromatography and molecular interactions. A number of significant advances were made at this workshop, with the new MS standard, mzML, being finalised prior to release on 1st June 2008 and analysisXML, which will allow protein and peptide identifications and post‐translational modifications to be captured, being prepared to enter the review process this summer. The accompanying controlled vocabularies are continuing to evolve and a number of standards papers are now being finalised prior to publication.