bluuebunny/crossref_metadata_2025_split huggingface dataset:
Native state dynamics and mechanical properties of human topoisomerase I within a structure‐based coarse‐grained model
Authors: Szklarczyk Oliwia , Staroń Krzysztof , Cieplak Marek 
Published: April 2009

AbstractA coarse grained molecular dynamics model with an implicit solvent is used to elucidate properties of the human topoisomerase I. The model is defined through the native structure and it allows covering significantly longer time scales than in all atom simulations. Single residue and double residue motional characteristics are studied. The results are consistent with all atom simulations reported in the literature indicating usefulness of the model in further studies of this protein. Novel findings include broadening of the description of the dynamic behavior of the lip and hinge regions and a characterization of the motional properties of the RRM binding site of the enzyme. We also consider mechanical stretching of the protein and identify sources of the force peaks. The elastic properties of topoisomerase I are predicted to be average in comparison to other proteins, yielding a maximum force of resistance to pulling which should be of order 120 pN. The contact unraveling pattern is consistent with the understanding of the structure and function of the protein. We find supporting evidence for the hypothesis that the C‐terminal domain acquires an ordered structure upon binding with the core enzyme even though it forms a molten globule when in isolation. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Control of Fusarium verticillioides, cause of ear rot of maize, by Pseudomonas fluorescens
Authors: Chandra Nayaka Siddaiah , Udaya Shankar Arakere C , Reddy Munagala S , Niranjana Siddapura R , Prakash Harishchandra S , Shetty Hunthrike S , Mortensen Carmen N 
Published: April 2009

AbstractBACKGROUND: Maize is one of the staple food crops grown in India. Fusarium verticillioides (Sacc.) Nirenberg is the most important fungal pathogen of maize, associated with diseases such as ear rot and kernel rot. Apart from the disease, it is capable of producing fumonisins, which have elicited considerable attention over the past decade owing to their association with animal disease syndromes. Hence, the present study was conducted to evaluate ecofriendly approaches by using a maize rhizosphere isolate of Pseudomonas fluorescens (Trev.) Mig. and its formulation to control ear rot disease and fumonisin accumulation, and also to study the capacity to promote growth and yield of maize. In vitro assays were conducted to test the efficacy of P. fluorescens as a seed treatment on seed germination, seedling vigour and also the incidence of F. verticillioides in different maize cultivars. The field trials included both seed treatment and foliar spray. For all the experiments, P. fluorescens was formulated using corn starch, wheat bran and talc powder. In each case there were three different treatments of P. fluorescens, a non‐treated control and chemical control.RESULTS: Pure culture and the formulations, in comparison with the control, increased plant growth and vigour as measured by seed germination, seedling vigour, plant height, 1000 seed weight and yield. P. fluorescens pure culture used as seed treatment and as spray treatment enhanced the growth parameters and reduced the incidence of F. verticillioides and the level of fumonisins to a maximum extent compared with the other treatments.CONCLUSION: The study demonstrates the potential role of P. fluorescens and its formulations in ear rot disease management. The biocontrol potential of this isolate is more suited for fumonisin reduction in maize kernels intended for human and animal feed. Copyright © 2009 Society of Chemical Industry
Endogenous high‐performance liquid chromatography/tandem mass spectrometry interferences and the case of perfluorohexane sulfonate (PFHxS) in human serum; are we overestimating exposure?
Authors: Chan Emily , Sandhu Mandeep , Benskin Jonathan P. , Ralitsch Milan , Thibault Nicole , Birkholz Detlef , Martin Jonathan W. 
Published: April 2009

AbstractPerfluorinated acids have received increasing scientific attention due to their widespread global distribution, environmental persistence and bioaccumulation in wildlife and humans. For perfluorohexane sulfonate (PFHxS, C6F13SO, m/z 399), all existing human data have been generated using high‐performance liquid chromatography (HPLC) and its most sensitive tandem mass spectrometric (MS/MS) transitions (m/z 399/80 [SO3]− or m/z 399/99 [SO3F]−), but this may be problematic because of co‐eluting endogenous steroid sulfates that share common fragmentation pathways. We examined the magnitude of over‐reporting for PFHxS in pregnant women (n = 29), and in pooled serum of males, non‐pregnant and pregnant females (n = 3, 100 samples per pool), by comparing m/z 399/80 and 399/99 data with an interference‐free transition, m/z 399/119. PFHxS concentrations in pregnant women determined using m/z 399/80 and 399/99 (p < 0.05), but not m/z 399/119, were positively correlated to the response of the steroid sulfates. This led to an average overestimation of PFHxS by 1.5‐ and 4.7‐fold, using m/z 399/80 and 399/99, respectively, and validated the use of m/z 399/119 for the first time. The interferences were a problem in all human serum samples, and analysis of pooled serum revealed statistically significant over‐reporting by m/z 399/80 and 399/99 for pregnant women > non‐pregnant women > men. The magnitude of over‐reporting here represents a worst‐case scenario, but the extent to which the published literature values are biased is unknown due to limited details of methods in existing reports. Instead of using the less sensitive m/z 399/119 transition, we showed that an alternative selection of column and mobile phase can allow for sufficient chromatographic separation of the interferences. In conclusion, it was shown that routine analytical methods are prone to systematically overestimating PFHxS concentrations in serum of men or women, but that this can be avoided by alternative chromatographic steps or MS/MS transitions. Copyright © 2009 John Wiley & Sons, Ltd.
High‐resolution extracted ion chromatography, a new tool for metabolomics and lipidomics using a second‐generation orbitrap mass spectrometer
Authors: Koulman Albert , Woffendin Gary , Narayana Vinod K. , Welchman Helen , Crone Catharina , Volmer Dietrich A. 
Published: April 2009

AbstractMost analytical methods in metabolomics are based on one of two strategies. The first strategy is aimed at specifically analysing a limited number of known metabolites or compound classes. Alternatively, an unbiased approach can be used for profiling as many features as possible in a given metabolome without prior knowledge of the identity of these features. Using high‐resolution mass spectrometry with instruments capable of measuring m/z ratios with sufficiently low mass measurement uncertainties and simultaneous high scan speeds, it is possible to combine these two strategies, allowing unbiased profiling of biological samples and targeted analysis of specific compounds at the same time without compromises. Such high mass accuracy and mass resolving power reduces the number of candidate metabolites occupying the same retention time and m/z ratio space to a minimum. In this study, we demonstrate how targeted analysis of phospholipids as well as unbiased profiling is achievable using a benchtop orbitrap instrument after high‐speed reversed‐phase chromatography. The ability to apply both strategies in one experiment is an important step forward in comprehensive analysis of the metabolome. Copyright © 2009 John Wiley & Sons, Ltd.
The quantification of carbon dioxide in humid air and exhaled breath by selected ion flow tube mass spectrometry
Authors: Smith David , Pysanenko Andriy , Španěl Patrik 
Published: April 2009

AbstractThe reactions of carbon dioxide, CO2, with the precursor ions used for selected ion flow tube mass spectrometry, SIFT‐MS, analyses, viz. H3O+, NO+ and O, are so slow that the presence of CO2 in exhaled breath has, until recently, not had to be accounted for in SIFT‐MS analyses of breath. This has, however, to be accounted for in the analysis of acetaldehyde in breath, because an overlap occurs of the monohydrate of protonated acetaldehyde and the weakly bound adduct ion, H3O+CO2, formed by the slow association reaction of the precursor ion H3O+ with CO2 molecules. The understanding of the kinetics of formation and the loss rates of the relevant ions gained from experimentation using the new generation of more sensitive SIFT‐MS instruments now allows accurate quantification of CO2 in breath using the level of the H3O+CO2 adduct ion. However, this is complicated by the rapid reaction of H3O+CO2 with water vapour molecules, H2O, that are in abundance in exhaled breath. Thus, a study has been carried out of the formation of this adduct ion by the slow three‐body association reaction of H3O+ with CO2 and its rapid loss in the two‐body reaction with H2O molecules. It is seen that the signal level of the H3O+CO2 adduct ion is sensitively dependent on the humidity (H2O concentration) of the sample to be analysed and a functional form of this dependence has been obtained. This has resulted in an appropriate extension of the SIFT‐MS software and kinetics library that allows accurate measurement of CO2 levels in air samples, ranging from very low percentage levels (0.03% typical of tropospheric air) to the 6% level that is about the upper limit in exhaled breath. Thus, the level of CO2 can be traced through single time exhalation cycles along with that of water vapour, also close to the 6% level, and of trace gas metabolites that are present at only a few parts‐per‐billion. This has added a further dimension to the analysis of major and trace compounds in breath using SIFT‐MS. Copyright © 2009 John Wiley & Sons, Ltd.
Precolumn derivatization reagents for high‐speed analysis of amines and amino acids in biological fluid using liquid chromatography/electrospray ionization tandem mass spectrometry
Authors: Shimbo Kazutaka , Oonuki Takashi , Yahashi Akihisa , Hirayama Kazuo , Miyano Hiroshi 
Published: April 2009

AbstractA rapid analytical method for amines and amino acids was developed, involving derivatization with the novel reagent 3‐aminopyridyl‐N‐hydroxysuccinimidyl carbamate (APDS), followed by reversed‐phase high‐performance liquid chromatography and electrospray ionization tandem mass spectrometry (HPLC/ESI‐MS/MS). More than 100 different analytes with amino groups, including amino acids in biological fluids such as mammalian plasma, could be measured within 10 min. The analytes were easily derivatized with APDS under the mild conditions. Selective reaction monitoring of ESI‐MS/MS in positive mode was carried out to include the transitions of all of the protonated molecular ions of analytes derivatized with APDS to the common fragment at m/z 121, which was derived from the amino pyridyl moiety of the reagent. We evaluated the retention time precision, the quantification limits, the linearity, the intra‐ and inter‐day precisions and the accuracy of 22 typical amino acids found in biological fluids, by analyzing a standard amino acid mixture and rat plasma. The intra‐day relative standard deviations (RSDs) of the retention times of the 22 amino acids and their internal standards were within 0.9% and the inter‐day RSDs were less than 1.1%, except for asparagines, with an RSD of 1.9%. The intra‐day and inter‐day RSDs of amino acid analyses in rat plasma were within 8.0% and 4.5%, respectively. The method, which facilitates the amino acid analysis of more than 100 samples in a day, represents an alternative to traditional amino acid analysis techniques, such as chromatography using postcolumn derivatization by ninhydrin. Copyright © 2009 John Wiley & Sons, Ltd.
Nonlinear Laguerre–Volterra observer‐controller and its application to process control
Authors: Zhang Hai‐Tao , Chen Michael Z. Q. , Chen Zhiyong 
Published: April 2009

AbstractBy expanding each kernel using the orthonormal Laguerre series, a Volterra functional series is used to represent the input/output relation of a nonlinear dynamic system. With the feedback of the modeling error, we design a novel nonlinear state observer, based on which an output feedback controller is derived for both the stabilization and tracking problems. The stability of the closed‐loop system is analyzed theoretically. The algorithm is effectively applied on the continuous stirring tank reactor and chemical reactor temperature control system. Copyright © 2009 John Wiley & Sons, Ltd.
Exploring a school–aquarium collaboration: An intersection of communities of practice
Authors: Kisiel James F. 
Published: April 2009

AbstractThis study examines the development and ongoing activities of a collaboration between an urban elementary school and a nearby aquarium. Although the benefits of such collaborations in support of science education are touted by numerous national organizations, the pathway to creating a successful relationship between these two different institutions, with inherently different cultures, is less well documented. Using the theoretical framework of communities of practice (E. Wenger, 1998), a better understanding of the challenges and successes of this collaboration is presented. In particular, the analysis suggests that participant engagement in both communities (school and aquarium) led to the development of an overlap in these communities of practice. This resulted when common forms of mutual engagement, joint enterprise, and shared repertoire emerged over the course of the project. Consistent with Wenger's framework, boundary objects and brokers could be identified that helped secure such overlap in this particular case. Implications of this theoretical perspective for facilitating the development of such institutional collaborations are also discussed. © 2009 Wiley Periodicals, Inc. Sci Ed 94:95–121, 2010
Extracardiac lesions and chromosomal abnormalities associated with major fetal heart defects: comparison of intrauterine, postnatal and postmortem diagnoses
Authors: Song M. S. , Hu A. , Dyhamenahali U. , Chitayat D. , Winsor E. J. T. , Ryan G. , Smallhorn J. , Barrett J. , Yoo S.‐J. , Hornberger L. K. 
Published: April 2009

AbstractObjectivesThe clinical outcome of prenatally diagnosed congenital heart defects (CHD) continues to be affected significantly by associated extracardiac and chromosomal abnormalities. We sought to: determine the frequency and type of major extracardiac abnormalities (with impact on quality of life) and chromosomal abnormalities associated with fetal CHD; and compare the extracardiac abnormalities detected prenatally to the postnatal and autopsy findings in affected fetuses, to find the incidence of extracardiac abnormalities missed on prenatal ultrasound.MethodsWe reviewed the computerized database of the Division of Cardiology of the Hospital for Sick Children in Toronto to identify all cases of major CHD detected prenatally from 1990 to 2002. Medical records, fetal echocardiograms and ultrasound, cytogenetic and autopsy reports were reviewed. The types of CHD detected were grouped into categories and the frequencies of major extracardiac and chromosomal abnormalities in these categories were noted. Prenatal ultrasound findings were compared with those at autopsy or postnatal examination.ResultsOf 491 fetuses with major structural CHD, complete data were obtained for 382. Of these, there were 141 (36.9%) with major extracardiac abnormalities at autopsy or postnatal exam, of which 46 had chromosomal abnormalities and 95 did not. In the absence of chromosomal abnormalities, the organ systems most affected were urogenital (12.2%) and gastrointestinal (11.6%). CHDs with the highest incidence of extracardiac abnormalities (>25%) included: heterotaxy, single left ventricle and tricuspid atresia, hypoplastic left heart syndrome and tetralogy of Fallot. Ninety‐four of 334 (28.1%) fetuses tested had chromosomal abnormalities. The most common chromosomal abnormalities were trisomies 21 (43.6%), 18 (19.1%) and 13 (9.6%), monosomy X (7.4%) and 22q11.2 deletion (7.4%). Of 289 extracardiac abnormalities from the complete series, 134 (46.4%) were not identified prenatally. Of the missed extracardiac abnormalities, 65 were considered not detectable at prenatal ultrasound, so 23.9% (69/289) of detectable extracardiac abnormalities were missed prenatally.ConclusionsMajor extracardiac and chromosomal abnormalities are common in fetuses with major fetal CHD. Many important associated extracardiac abnormalities may be missed prenatally, which should be taken into consideration in the prenatal counseling for fetal CHD. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Fetal aortic isthmus blood flow and the fraction of cardiac output distributed to the upper body and brain at 11– 20 weeks of gestation
Authors: Vimpeli T. , Huhtala H. , Wilsgaard T. , Acharya G. 
Published: April 2009

AbstractObjectiveTo measure serial changes in fetal aortic isthmus (AI) blood flow and estimate the fraction of fetal cardiac output distributed to the upper body, including the brain, at 11–20 weeks of gestation.MethodsUsing pulsed‐wave Doppler and two‐dimensional ultrasound, blood flow velocities and inner diameter of the AI, aortic valve (AV) and pulmonary valve (PV) were measured longitudinally in 143 fetuses and volume blood flows (Q) were calculated for each site using the formula: Q (mL/min) = π× (diameter/2)2 × velocity time integral × heart rate × 60. The sum of Qav and Qpv constituted the combined cardiac output (CCO) and the fraction (%) of the upper body (including brain) blood flow was calculated as: (Qav−Qai)×100/CCO.ResultsAI blood velocities as well as the vessel diameter increased with advancing gestation, resulting in a significant increase in Qai from 1.9 to 40.5 mL/min during weeks 11 to 20. The AI peak systolic velocity increased from 29 to 63 cm/s, end‐diastolic velocity from 1.2 to 5.2 cm/s, and the time‐averaged maximum velocity from 11 to 22 cm/s, resulting in a fairly stable pulsatility index (PI) of 2.4–2.6 and resistance index (RI) of 0.91–0.94. On average, 75% of blood ejected by the left ventricle (which represented about 35% of the CCO) passed through the AI to the descending aorta. The fraction of CCO distributed to the upper body, including the brain, was estimated as approximately 13%.ConclusionWe have established longitudinal reference ranges for fetal AI diameter, blood flow velocities, PI, RI and volume blood flow at 11–20 weeks of gestation. The human fetus appears to direct a relatively small fraction (13%) of its CCO to the upper body, including the brain, during this period of pregnancy. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Sequence of the yeast protein expression plasmid pEG(KT)
Authors: Pierce B. Daniel , Wendland Beverly 
Published: April 2009

AbstractThe plasmid pEG(KT) is a widely used plasmid for expressing high levels of GST fusion proteins in the yeast Saccharomyces cerevisiae. Unfortunately, a complete sequence file has been lacking, thus complicating efforts to design cloning projects or to modify the plasmid for other uses (e.g. exchanging selection markers, epitope tags or protease cleavage sites to remove the epitope tag). Here, the complete sequence of the pEG(KT) plasmid is reported, thus facilitating its use. Additionally, its use as a vector backbone for high‐level expression of a TAP‐tagged protein is shown. Copyright © 2009 John Wiley & Sons, Ltd.
Sdo1p, the yeast orthologue of Shwachman–Bodian–Diamond syndrome protein, binds RNA and interacts with nuclear rRNA‐processing factors
Authors: Luz Juliana S. , Georg Raphaela C. , Gomes Carlos H. , Machado‐Santelli Gláucia M. , Oliveira Carla C. 
Published: April 2009

AbstractThe Shwachman–Bodian–Diamond syndrome protein (SBDS) is a member of a highly conserved protein family of not well understood function, with putative orthologues found in different organisms ranging from Archaea, yeast and plants to vertebrate animals. The yeast orthologue of SBDS, Sdo1p, has been previously identified in association with the 60S ribosomal subunit and is proposed to participate in ribosomal recycling. Here we show that Sdo1p interacts with nucleolar rRNA processing factors and ribosomal proteins, indicating that it might bind the pre‐60S complex and remain associated with it during processing and transport to the cytoplasm. Corroborating the protein interaction data, Sdo1p localizes to the nucleus and cytoplasm and co‐immunoprecipitates precursors of 60S and 40S subunits, as well as the mature rRNAs. Sdo1p binds RNA directly, suggesting that it may associate with the ribosomal subunits also through RNA interaction. Copyright © 2009 John Wiley & Sons, Ltd.
Large bending deformations of a cylindrical membrane with internal pressure
Authors: Kolesnikov A.M. , Zubov L.M. 
Published: April 2009

AbstractWe consider the large bending of a thin‐walled cylinder made of a rubberlike material. It is loaded by internal pressure and bending moments at the ends. The exact formulation of the problem is given within the framework of the nonlinear membrane theory taking into account large strains of the cylinder. Using the special substitution describing the pure bending of the cylinder, the problem is reduced to the system of nonlinear ordinary differential equations. The latter is solved numerically. We establish that there exists the limit value of the bending moment, which depends essentially upon the internal pressure. As an example, the Mooney–Rivlin material is considered. On the base of the calculations we propose the approximate formulae describing the bending moment dependence on the axis curvature of the cylinder and the ultimate bending moment dependence on the internal pressure.
On the linear theory of micropolar plates
Authors: Altenbach H. , Eremeyev V.A. 
Published: April 2009

AbstractWe discuss the general linear six‐parametric theory of plates based on the direct approach. We consider the plate as a deformable surface. Each material point of the surface can be regarded as an infinitesimal small rigid body with six degrees of freedom. The kinematics of the plate is described by using the vector of translation and the vector of rotation as the independent variables. The relations between the equilibrium conditions of a three‐dimensional micropolar plate‐like body and the two‐dimensional equilibrium equations of the deformable surface are established. Using the three‐dimensional constitutive equations of a micropolar material we discuss the determination of the effective stiffness tensors appearing in the two‐dimensional constitutive equations.
Generalized self‐consistent homogenization using the Finite Element Method
Authors: Lefik M. , Boso D.P. , Schrefler B.A. 
Published: April 2009

AbstractThis paper presents a development of the usual generalized self‐consistent method for homogenization of composite materials. The classical self‐consistent scheme is appropriate for phases that are “disordered”, i.e. what is called “random texture”. In the case of both linear and non linear components, the self‐consistent homogenization can be used to identify expressions for bounds of effective mechanical characteristics. In this paper we formulate a coupled thermo‐mechanical problem for non linear composites having properties depending on temperature. The solution is found in a non‐classical way, as we use the Finite Element Method to solve the elastic‐plastic problem at hand. In this sense we propose a “problem‐oriented” technique of solution. The method is finally applied to the real case of superconducting strands used for the coils of the future ITER experimental reactor.