bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasma‐Immersion‐Ion‐Implantation of Fluorine to Protect TiAl‐Components against High‐Temperature Oxidation
Authors: Donchev Alexander , Kolitsch Andreas , Schütze Michael , Yankov Rossen 
Published: July 2009

AbstractTitanium aluminides are promising light weight materials for several high‐temperature applications, e.g., in aero engines but due to their insufficient oxidation resistance at temperatures above roughly 800 °C they cannot be used yet despite of their good mechanical high‐temperature properties. The oxidation behavior of TiAl‐alloys can be improved significantly by adding small amounts of fluorine into the subsurface zone of the components (microalloying). One possibility to apply fluorine to the surface of complex TiAl‐components is the PI3‐technique (plasma‐immersion‐ion‐implantation). The use of an Ar/CH2F2‐plasma for the F‐PI3 into small coupons led to a positive effect which was as good as the beamline implantation of elemental fluorine gas into samples of the same geometry. Turbine blades, as examples for real TiAl‐components, were implanted with an optimum set of parameters. Post‐exposure investigations like scanning electron microscopy revealed a thin protective alumina scale on the surface of the implanted samples in contrast to a thick mixed oxide scale (TiO2/Al2O3) growing on untreated samples during high‐temperature oxidation in air. The high‐temperature oxidation resistance of several TiAl‐alloys was improved by plasma‐immersion‐ion‐implantation of fluorine. Small coupons showed a much lesser oxidation during high‐temperature exposure after fluorine treatment than untreated samples. The performance of turbine blades for the low pressure compressor of a new generation of jet engines was also improved. Fluorine treated samples are covered with a thin, protective alumina scale after high‐temperature exposure in air instead of a fast growing, nonprotective mixed oxide (TiO2/Al2O3) scale which is found on untreated samples.magnified image
Enhanced AP‐PE‐CVD Process Understanding and Control by Application of Integrated Optical, Electrical and Modelling Diagnostics
Authors: Sawtell David , Martin Philip A. , Sheel David W. 
Published: July 2009

AbstractThis paper reports the use of a multiple thrust methodology to monitor the atmospheric pressure plasma‐enhanced chemical vapour deposition (PE‐CVD) of silica films on glass. Simultaneous spectroscopic analysis: optical emission spectroscopy, FT‐IR spectroscopy and in situ near‐infrared laser diode spectroscopy have been combined with electrical measurements to investigate the plasma during the deposition process. The experimentation has been carried out as a chemometric design so as to derive statistical models tying the affected variables to the measured results. Initial results confirm the viability of this approach for improved process understanding, process control and enhanced design capabilities.
Mapping the local protein interactome of the NuA3 histone acetyltransferase
Authors: Smart Sherri K. , Mackintosh Samuel G. , Edmondson Ricky D. , Taverna Sean D. , Tackett Alan J. 
Published: July 2009

AbstractProtein–protein interactions modulate cellular functions ranging from the activity of enzymes to signal transduction cascades. A technology termed transient isotopic differentiation of interactions as random or targeted (transient I‐DIRT) is described for the identification of stable and transient protein–protein interactions in vivo. The procedure combines mild in vivo chemical cross‐linking and non‐stringent affinity purification to isolate low abundance chromatin‐associated protein complexes. Using isotopic labeling and mass spectrometric readout, purified proteins are categorized with respect to the protein ‘bait’ as stable, transient, or contaminant. Here we characterize the local interactome of the chromatin‐associated NuA3 histone lysine‐acetyltransferase protein complex. We describe transient associations with the yFACT nucleosome assembly complex, RSC chromatin remodeling complex and a nucleosome assembly protein. These novel, physical associations with yFACT, RSC, and Nap1 provide insight into the mechanism of NuA3‐associated transcription and chromatin regulation.
Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust
Authors: Benkert Pascal , Tosatto Silvio C. E. , Schwede Torsten 
Published: July 2009

AbstractIdentifying the best candidate model among an ensemble of alternatives is crucial in protein structure prediction. For this purpose, scoring functions have been developed which either calculate a quality estimate on the basis of a single model or derive a score from the information contained in the ensemble of models generated for a given sequence (i.e., consensus methods). At CASP7, consensus methods have performed considerably better than scoring functions operating on single models. However, consensus methods tend to fail if the best models are far from the center of the dominant structural cluster. At CASP8, we investigated whether our hybrid method QMEANclust may overcome this limitation by combining the QMEAN composite scoring function operating on single models with consensus information. We participated with four different scoring functions in the quality assessment category. The QMEANclust consensus scoring function turned out to be a successful method both for the ranking of entire models but especially for the estimation of the per‐residue model quality. In this article, we briefly describe the two scoring functions QMEAN and QMEANclust and discuss their performance in the context of what went right and wrong at CASP8. Both scoring functions are publicly available at http://swissmodel.expasy.org/qmean/. Proteins 2009. © 2009 Wiley‐Liss, Inc.
An inherently mass‐conserving semi‐implicit semi‐Lagrangian discretisation of the shallow‐water equations on the sphere
Authors: Zerroukat M. , Wood N. , Staniforth A. , White A. A. , Thuburn J. 
Published: July 2009

AbstractFor the shallow‐water equations on the sphere, an inherently mass‐conserving semi‐Lagrangian discretisation (SLICE) of the continuity equation is coupled with a semi‐implicit semi‐Lagrangian discretisation of the momentum equations. Various tests from the literature (two with analytical nonlinear solutions) are used to assess the model's performance and also to compare it with that of a variant model that instead employs a standard non‐conserving semi‐implicit semi‐Lagrangian discretisation of the continuity equation. The mass‐conserving version gives results that are overall somewhat better than the non‐conserving one. Copyright © 2009 Royal Meteorological Society and Crown Copyright
Comparative Evaluation of in Silico pKa Prediction Tools on the Gold Standard Dataset
Authors: Balogh György T. , Gyarmati Benjámin , Nagy Balázs , Molnár László , Keserű György M. 
Published: July 2009

AbstractThe predictive performance of five different pKa prediction tools (ACDpKa, Epik, Marvin pKa, Pallas pKa, and VCCpKa) was investigated on the 248‐membered Gold Standard dataset. We found VCC as the most predictive, high throughput pKa predictor. However since VCC calculates pKa for the most acidic or basic group only we concluded that ACD and Marvin are in fact the method of choice for medicinal chemistry applications. Analyzing the common outliers we identified guanidines, enolic hydroxyl groups and weak acidic NHs as most problematic moieties from prediction point of view. Our results obtained on the high quality, homogenous Gold Standard dataset could be useful for end‐users selecting a suitable solution for pKa prediction.
Hair protein and amino acid 13C and 15N abundances take more than 4 weeks to clearly prove influences of animal protein intake in young women with a habitual daily protein consumption of more than 1 g per kg body weight
Authors: Petzke Klaus J. , Lemke Susen 
Published: July 2009

AbstractA high protein or meat intake might be a risk factor for metabolic disorders. Stable isotopic abundances (SIA) of hair can be used as biomarkers for animal protein intake due to characteristic isotopic patterns of food proteins. We investigated if an additional meat intake (M, 200 g pork fillet/day) or an omission of meat and meat products (NOM) can influence the natural 15N and 13C SIA within 4 weeks in hair and plasma of young women. The daily protein intake (means ± SD) was 1.40 ± 0.29, 2.25 ± 0.35, and 1.15 ± 0.26 g/kg at baseline, during M, and during NOM, respectively. At baseline the animal protein intake correlated with bulk SIA of hair (15N: R2 = 0.416; 13C: R2 = 0.664; n = 14). However, isotope ratio mass spectrometry (IRMS) analyses have not shown that hair and plasma SIA were changed significantly after M or NOM. Possible reasons were discussed. Urinary SIA were significantly lower after M than after NOM (15N: p = 0.039; 13C: p = 0.006) and close to those of pork fillet. Characteristic patterns of SIA were measured in individual amino acids (AA) by gas chromatography/combustion isotope ratio mass spectrometry (GC/C/IRMS). The results confirmed considerable differences in SIA between AA (δ15N, up to 22‰; δ13C, up to 31‰). Plots of 15N versus 13C abundances in hair revealed characteristic differences between indispensable and dispensable AA. The intervention‐dependent changes of AA‐specific SIA were not as clear as expected. Although the AA‐specific SIA may reveal more detailed characteristics of physiological conditions, further methodological research is required. We suggest that the SIA of leucine can be potential markers of protein intake. The reliability of SIA as biomarkers of protein intake still have to be tested in longer lasting intervention studies in humans. The results may have implications in the assessment for possible benefits and risks of protein consumption. Copyright © 2009 John Wiley & Sons, Ltd.
Multielement (H, C, N, O, S) stable isotope characteristics of lamb meat from different Italian regions
Authors: Perini Matteo , Camin Federica , Bontempo Luana , Rossmann Andreas , Piasentier Edi 
Published: July 2009

AbstractThe study focuses on the 2H/H, 13C/12C, 15N/14N, 18O/16O and 34S/32S values of defatted dry matter (DFDM) and on the 2H/H, 13C/12C and 18O/16O values of the fat fraction of meat samples from various lamb types reared in seven Italian regions, following different feeding regimes (forage, concentrate, milk). The 13C/12C (r = 0.922), 2H/H (r = 0.577) and 18O/16O (r = 0.449) values of fat and DFDM are significantly correlated, the fat values being significantly lower for C and H and higher for O than for DFDM values and the differences between the two fractions not being constant for different lamb types. The feeding regime significantly affected the 13C/12C, 15N/14N, 18O/16O and 2H/H of fat. The DFDM 2H/H, and 18O/16O values, excluding an outlier, are significantly correlated with the corresponding values in meteoric waters, thus allowing us to trace the variability of geoclimatic factors. 15N/14N is influenced by pedoclimatic conditions, whereas 34S/32S is influenced by the sea spray effect and the surface geology of the provenance area. By applying stepwise linear discriminant analysis only the 2H/H of fat was found not to be significant and 97.7% of the samples were correctly assigned to the lamb type and more than 90% cross‐validated. With the feeding regime, 97.7% of the samples were both correctly assigned and cross‐validated using a predictive model including 13C/12C, 15N/14N, 18O/16O, 34S/32S of DFDM and 18O/16O of fat. Copyright © 2009 John Wiley & Sons, Ltd.
Effects of hydrologic infrastructure on flow regimes of California's Central Valley rivers: Implications for fish populations
Authors: Brown Larry R. , Bauer Marissa L. 
Published: July 2009

AbstractAlteration of natural flow regimes is generally acknowledged to have negative effects on native biota; however, methods for defining ecologically appropriate flow regimes in managed river systems are only beginning to be developed. Understanding how past and present water management has affected rivers is an important part of developing such tools. In this paper, we evaluate how existing hydrologic infrastructure and management affect streamflow characteristics of rivers in the Central Valley, California and discuss those characteristics in the context of habitat requirements of native and alien fishes. We evaluated the effects of water management by comparing observed discharges with estimated discharges assuming no water management (‘full natural runoff’). Rivers in the Sacramento River drainage were characterized by reduced winter–spring discharges and augmented discharges in other months. Rivers in the San Joaquin River drainage were characterized by reduced discharges in all months but particularly in winter and spring. Two largely unaltered streams had hydrographs similar to those based on full natural runoff of the regulated rivers. The reduced discharges in the San Joaquin River drainage streams are favourable for spawning of many alien species, which is consistent with observed patterns of fish distribution and abundance in the Central Valley. However, other factors, such as water temperature, are also important to the relative success of native and alien resident fishes. As water management changes in response to climate change and societal demands, interdisciplinary programs of research and monitoring will be essential for anticipating effects on fishes and to avoid unanticipated ecological outcomes. Published in 2009 by John Wiley & Sons, Ltd.
Characterization of Cassava Starch Attributes of Different Genotypes
Authors: Anggraini Vivi , Sudarmonowati Enny , Hartati N. Sri. , Suurs Luc , Visser Richard G. F. 
Published: July 2009

AbstractThe genetic variation of starch of Indonesian cassava genotypes with various morphological characteristics of roots and eco‐geographical origin was characterized and compared. The morphological characteristics of the roots of 71 collected cassava genotypes were classified into yellow and white for flesh colors, purple, pink, light brown, yellow, cream and white for cortex colors, dark brown and light brown for external colors, as well as conical and cylindrical for root shapes. Starch samples extracted from 17 genotypes showed that the amylose content varied from 17.1 to 21.3%. The mean particle size was around 7.3 to 9.7 µm, and the gelatinization onset temperature was in the range of 63.5‐66.1°C. Seven genotypes were analyzed in more detail for their physicochemical properties. The granule size distribution was in the range of 3.2 µm to 17.6 µm for d10 and d90 (i.e. 90% of the granules were bigger than 3.2 μm and 90% were smaller than 17.6 μm), respectively, and the median granule size was around 7.7‐10.8 µm. The gelatinization temperatures of the different cassava starches were in the range of 63.5‐66.1°C. The phosphate content varied from 23.5‐25.3 nmol/mg starch. Particle size distribution and gelatinization temperature as well as the phosphate content of the starch of the selected seven genotypes also showed minor differences among the genotypes. The swelling power of all starches showed some differences between genotypes, but the profiles were similar. The opacity of starch of all the tested genotypes increased twofold within six days, but no large differences among the different genotypes could be detected except for the genotype Ketan. Strength of the gels, which are indicated with force, adhesiveness, cohesiveness, and elasticity, also did not show large differences.
Abnormality of synaptic vesicular associated proteins in cerebral cortex and hippocampus after microwave exposure
Authors: Wang Lifeng , Peng Ruiyun , Hu Xiangjun , Gao Yabing , Wang Shuiming , Zhao Li , Dong Ji , Su Zhentao , Xu Xinping , Gao Ronglian , Lei Cuiping 
Published: July 2009

AbstractStudies were performed to determine the effects of microwave on synaptic vesicles and the expression of synaptic vesicular associated proteins including synapsin I, VAMP‐2, syntaxin, and synaptophysin. 25 Wistar rats were exposed to microwave which the average power density was 30 mW/cm2, and whole body average specific absorption rate was 14.1 W/kg for 5 min. Synaptosome preparations in the cerebral cortex and hippocampus were obtained by isotonic Percoll/sucrose discontinuous gradients at 6 h, 1, 3, and 7 days after radiation. The expression of synaptic vesicular associated proteins was measured using Western blots and image analysis. The interaction between VAMP‐2 and syntaxin was examined by coimmunoprecipitation analysis. Synapsin I in the cerebral cortex were decreased at 3 days (P < 0.01) after radiation and in the hippocampus increased at 1 day (P < 0.01), decreased at 3 days (P < 0.01), increased again at 7 days (P < 0.01) after exposure, compared with the sham‐treated controls. Synaptophysin were increased in 1–7 days (P < 0.01) after exposure in the cerebral cortex and hippocampus. VAMP‐2 were decreased at 1 and 3 days (P < 0.01) and syntaxin were decreased in 6 h to 3 days (P < 0.01) after radiation in the cerebral cortex and hippocampus. The interactions between VAMP‐2 and syntaxin were decreased at 3–7 days (P < 0.01) after radiation in the cerebral cortex and hippocampus, compared with the sham‐treated controls. These results suggest that 30 mW/cm2 (SAR 14.1 W/kg) microwave radiation can result in the perturbation of the synaptic vesicles associated proteins: synapsin I, synaptophysin, VAMP‐2, and syntaxin. The perturbation could induce the deposit of synaptic vesicle, which might be relative to the dysfunction of the synaptic transmission, even the cognition deficit. Synapse 63:1010–1016, 2009. © 2009 Wiley‐Liss, Inc.
Genome‐scale metabolic networks
Authors: Terzer Marco , Maynard Nathaniel D. , Covert Markus W. , Stelling Jörg 
Published: July 2009

AbstractDuring the last decade, models have been developed to characterize cellular metabolism at the level of an entire metabolic network. The main concept that underlies whole‐network metabolic modeling is the identification and mathematical definition of constraints. Here, we review large‐scale metabolic network modeling, in particular, stoichiometric‐ and constraint‐based approaches. Although many such models have been reconstructed, few networks have been extensively validated and tested experimentally, and we focus on these. We describe how metabolic networks can be represented using stoichiometric matrices and well‐defined constraints on metabolic fluxes. We then discuss relatively successful approaches, including flux balance analysis (FBA), pathway analysis, and common extensions or modifications to these approaches. Finally, we describe techniques for integrating these approaches with models of other biological processes Copyright © 2009 John Wiley & Sons, Inc.This article is categorized under:

Models of Systems Properties and Processes > Cellular Models
From StPowla processes to SRML models
Authors: Bocchi Laura , Gorton Stephen , Reiff-Marganiec Stephan 
Published: July 2009

AbstractService Oriented Computing is a paradigm for developing software systems as the composition of a number of services. Services are loosely coupled entities, that can be dynamically published, discovered and invoked over a network. The engineering of such systems presents novel challenges, mostly due to the dynamicity and distributed nature of service-based applications. In this paper, we focus on the modelling of service orchestrations. We discuss the relationship between two languages developed under theSensoriaproject: SRML as a high level modelling language for Service Oriented Architectures, andStPowlaas a process-oriented orchestration approach that separates core business processes from system variability at the end-user’s level, where the focus is towards achieving business goals. A fundamental challenge of software engineering is to correctly align business goals with IT strategy, and as such we present an encoding ofStPowlato SRML. This provides a formal framework forStPowlaand also a separated view of policies representing system variability that is not present in SRML.
Lessons Learned from the First 109 Laparoscopic Cholecystectomies Performed in a Single Pediatric Surgery Center
Authors: Esposito Ciro , Alicchio Francesca , Giurin Ida , Perricone Flavio , Ascione Giuseppe , Settimi Alessandro 
Published: July 2009

AbstractBackgroundLaparoscopic cholecystectomy (LC) is a frequent operation in adults but is seldom performed in children. A retrospective review of 109 consecutive patients who underwent LC over an 11‐year period was performed to see what lessons were learned from this experience.MethodsFrom January 1996 to January 2007, a total of 109 patients were referred to our unit to undergo LC. Nine adult patients were excluded from the analysis. The remaining 100 pediatric patients form the basis of this report. Isolated cholecystectomies were performed using a four‐trocar technique, with a fifth trocar added for cases in which splenectomy was required. One patient with main bile duct dilatation at preoperative echography underwent peroperative cholangiography.ResultsWe recorded three anatomic anomalies (3%), two involving the bile duct and one the cystic artery. We recorded four minor problems during surgery: In one case there was failure of the tip of reusable scissors, and in three cases there was a small perforation of the gallbladder during the dissection step. We recorded four (4%) postoperative complications, which required redo surgery: one patient with bleeding from the cystic artery; one case of dislocation of clips positioned on the cystic duct; and two patients with lesions of the main bile duct that had not been detected during surgery. The treatment consisted in choledojejunostomy on postoperative day 7 in one case and suture of the choledocus on a stent positioned using endoscopic retrograde cholangiopancreatography on postoperative day 5 in the second case. Both biliary complications occurred in patients more than 14 years of age. We also recorded one umbilical granuloma.ConclusionsLC is an effective procedure in children. On the basis of our experience, it seems that major complications can occur even with experienced surgeons, and they are more frequent in teenagers. Biliary or vascular anomalies of the gallbladder are encountered in about 3% of patients.