bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dispersion analysis of the meshfree radial point interpolation method for the Helmholtz equation
Authors: Wenterodt Christina , von Estorff Otto 
Published: September 2008

AbstractWhen 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

AbstractPurposeThe 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.MethodsThe 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.ResultsA 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.ConclusionsOur 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

AbstractThree 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

AbstractThe 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

AbstractStreptococcus 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

AbstractAlthough 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

AbstractIn 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

AbstractCell 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

AbstractThe 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

AbstractTo 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

AbstractComprehensive 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

AbstractAlong 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

AbstractA 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

AbstractSo 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

AbstractThe 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.
Grouping of hydrogen‐bond ability of pure solvents and their binary mixtures based on the similarity of their microscopic properties. Part 2
Authors: Pérez Adriana del C. , Mancini Pedro M. 
Published: September 2008

AbstractThe work presents a grouping scheme of some pure solvents (which are able to form hydrogen‐bonded complexes) and their binary mixtures on the basis of the similarity of their molecular‐microscopic properties. The solvatochromic parameters SPP, SA, and SB developed by Catalán et al. are selected as clustering variables. The Ward Method (WM) and the Group Average Method (GA) are applied as clustering procedures. The study pays particular attention to the microscopic solvent feature common to all solvents included in each cluster, describing the relevant solvating properties. It also contributes to a better understanding of the similarities and differences of the explored solvents. Copyright © 2008 John Wiley & Sons, Ltd.
Ab initio and DFT calculations on the gas phase elimination kinetics of 2,2‐diethoxy‐ethylamine and 2,2‐diethoxy‐N,N‐diethyl‐ethylamine
Authors: Mora José Ramón , Tosta María , Cordova Tania , Chuchani Gabriel 
Published: September 2008

AbstractThe mechanisms for the gas phase molecular elimination kinetics of 2,2‐diethoxy‐ethylamine and 2,2‐diethoxy‐N,N‐diethyl‐ethylamine were examined at MP2/6‐31G, B3LYP/6‐31G, B3LYP/6‐31G(d,p), MPW91PW91/6‐31G. MPW91PW91/6‐31G(d,p), PBEPBE/6‐31G, and PBEPBE/6‐31G(d,p) levels of theory. These elimination processes involve two parallel reactions. The first parallel reaction gives ethanol and the corresponding 2‐ethoxyethenamine. The latter compound further decomposes to ethylene, CO, and the corresponding amine. The second parallel reaction produces ethane and the corresponding ethyl ester of an α‐amino acid. Calculated thermodynamic and kinetic parameters from PBEPBE calculations were found to be in good agreement with the experimental values. The transition states of the parallel reactions are best described as four‐membered cyclic structures. The intermediate 2‐ethoxy‐ethenamine undergoes a consecutive elimination through a six‐membered cyclic transition state mechanism. Bond indexes and synchronicity (Sy) parameters are in agreement with concerted semi‐polar transition state structures. Copyright © 2008 John Wiley & Sons, Ltd.
Prediction Method for Specific Impulse Used as Performance Quantity for Explosives
Authors: Keshavarz Mohammad Hossein 
Published: September 2008

AbstractA novel method is presented to estimate the prediction of the specific impulse of mostly ideal and less ideal compositions of explosives. It requires only elemental compositions and some structural parameters of pure and composite explosives. There is no need to use the heat of formation of the explosive, which is an essential input parameter to compute the specific impulse through complicated computer codes. Moreover, there is no need to use any assumed decomposition products to calculate the specific impulse. The new simple method gives good results for any CaHbNcOd explosives, even with complicated molecular structures, and their composite mixtures. The calculated specific impulse can also be used to estimate detonation pressures and velocities of pure and mixed explosives at specified loading densities.