bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resources for Small Regulatory RNAs
Authors: Bell George W. , Lewitter Fran 
Published: July 2009

AbstractIn the past fifteen years, new classes of regulatory RNAs have been discovered, previously hidden in the transcriptome mostly due to their small size. These small regulatory RNAs include small interfering RNAs (siRNAs), microRNAs (miRNAs), and Piwi‐interacting RNAs (piRNAs). Numerous databases have been developed to store information about these small regulatory RNAs, and many tools have been developed to work with the data. This overview introduces the reader to the many resources available for working with small regulatory RNAs. Curr. Protoc. Mol. Biol. 87:19.8.1‐19.8.13. © 2009 by John Wiley & Sons, Inc.
Fundamentals of Acoustic Cytometry
Authors: Ward Michael , Turner Patrick , DeJohn Marc , Kaduchak Gregory 
Published: July 2009

AbstractAcoustic cytometry is a new technology that replaces or partly replaces hydrodynamic focusing of cells or particles with focusing derived from acoustic radiation pressure forces. It offers new possibilities for improving current flow cytometry assays and creating new ones. To take full advantage of these possibilities, it is necessary to understand the fundamental benefits and limitations of acoustic focusing as employed in flow cytometry analysis, either as a substitute for hydrodynamic focusing or in combination with it. Curr. Protoc. Cytom. 49:1.22.1‐1.22.12. © 2009 by John Wiley & Sons, Inc.
Detection of Extracellular Phosphatase Activity of Heterotrophic Prokaryotes at the Single‐Cell Level by Flow Cytometry
Authors: Duhamel Solange , Gregori Gerald , Wambeke France Van , Nedoma Jiří 
Published: July 2009

AbstractMonitoring cell activity using substrates, which turn fluorescent due to biological activity, allows observing the presence and dynamics of sub‐populations, and provides a very valuable insight in ecological studies. The phosphatase substrate ELF97 phosphate (ELF‐P) is a useful tool to detect and quantify phosphatase activity (PA) of microorganisms at the single‐cell level. Most of the studies dealing with PA at the single‐cell level focus on autotrophic cells and only few concern heterotrophic prokaryotes (referred as bacteria in the text). While flow cytometry is a promising tool to assess the single‐cell analysis, only microscopy tools have been used until now to measure the ELF labeling associated with bacteria expressing PA. Therefore, we have developed a new protocol that enables the detection of ELF alcohol (ELFA), the product of ELF‐P hydrolysis, making possible the specific identification of bacteria showing PA using flow cytometry. Curr. Protoc. Cytom. 49:11.18.1‐11.18.8. © 2009 by John Wiley & Sons, Inc.
Simultaneous Optical Mapping of Intracellular Free Calcium and Action Potentials from Langendorff Perfused Hearts
Authors: Salama Guy , Hwang Seong‐min 
Published: July 2009

AbstractThe cardiac action potential (AP) controls the rise and fall of intracellular free Ca2+(Cai), and thus the amplitude and kinetics of force generation. Besides excitation‐contraction coupling, the reverse process where Caiinfluences the AP through Cai‐dependent ionic currents has been implicated as the mechanism underlying QT alternans and cardiac arrhythmias in heart failure, ischemia/reperfusion, cardiac myopathy, myocardial infarction, congenital and drug‐induced long QT syndrome, and ventricular fibrillation. The development of dual optical mapping at high spatial and temporal resolution provides a powerful tool to investigate the role of Caianomalies in eliciting cardiac arrhythmias. This unit describes experimental protocols to map APs and Caitransients from perfused hearts by labeling the heart with two fluorescent dyes, one to measure transmembrane potential (Vm), the other Caitransients. High spatial and temporal resolution is achieved by selecting Vm and Caiprobes with the same excitation but different emission wavelengths, to avoid cross‐talk and mechanical components.Curr. Protoc. Cytom. 49:12.17.1‐12.17.32. © 2009 by John Wiley & Sons, Inc.
Heterogeneous palladium–cobalt bimetal catalyst for the oxidative carbonylation of bisphenol A to polycarbonate
Authors: Okamoto Masaya , Sugiyama Jun‐ichi 
Published: July 2009

AbstractPolycarbonates (PCs) were prepared by the oxidative carbonylation of bisphenol A and carbon monoxide with a hydrotalcite‐supported Pd–Co complex, a Pd–Co–poly(4‐vinylpyridine) complex [Pd–Co–(p‐4vpy)], a Pd–Co–polystyrene‐supported triphenylphosphine complex (Pd–Co–PS‐TPP), or a Pd–Co–polyvinylpyrrolidone complex (Pd–Co–pvp) as a heterogeneous Pd–Co bimetal catalyst to separate the PC solution and the Pd–Co bimetal catalyst after the reaction. Propylene carbonate was used as a halogen‐free solvent. Pd–Co–(p‐4vpy) and Pd–Co–PS‐TPP showed recycling potential, whereas Pd–Co–pvp, though not having recycling potential, yielded a high turnover number with a maximum of 1462. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
Improvement of Targeted Gene Delivery to Human Cancer Cells by a Novel Trifunctional Crosslinker
Authors: Shiota Maki , Shamsur Lahman , Kawahara Shun‐ichi , Wadhwa Renu , Ikeda Yutaka 
Published: July 2009

AbstractA facile method for the construction of an immunoconjugate which displays targeting ligands, such as antibody fragments, with a high density is reported. For this purpose, we synthesized a novel trifunctional crosslinking reagent. By the use of this reagent, ligands targeting the specific cell can be displayed on the surface of the drug carrier with a high density. In this study, we display HER2 (human epidermal growth‐factor receptor‐2) binding ligands on branched polyethylenimine (PEI), which can form polyplexes with plasmid DNA. Kinetic analysis of the binding to the extracellular domain of HER2 show the PEI displaying a high density of ligands binds to the target more strongly compared to the PEI displaying ligands at a low density. The increased density of HER2 ligands displayed on the gene carrier contributes to the improved transfection efficiency. This approach can be applied to other drug delivery systems, including liposome, micelle, and so on.
Preparation of C3‐Symmetric Homochiral syn‐Trisnorbornabenzenes through Regioselective Cyclotrimerization of Enantiopure Iodonorbornenes
Authors: Reza A. F. G. Masud , Higashibayashi Shuhei , Sakurai Hidehiro 
Published: July 2009

AbstractC3‐symmetric homochiral (−)‐syn‐trisoxonorbornabenzene 1 possessing a rigid cup‐shaped structure was synthesized through a novel regioselective cyclotrimerization of enantiopure iodonorbornenes catalyzed by palladium nanoclusters. The yield of the cyclotrimerization was dependent on the stability of the palladium clusters, which was ascertained from the appearance and TEM images of the reaction mixtures. The efficient preparation of (−)‐syn‐1 was established in short steps, including the newly developed cyclotrimerization reaction. The thus‐prepared homochiral (−)‐syn‐1 can serve as a key intermediate for the synthesis of C3‐symmetric homochiral cup‐shaped molecules with a helical arrangement of substituents. Introduction of several types of substituents was well demonstrated through palladium‐catalyzed coupling reactions with the corresponding phosphate and triflate of (−)‐syn‐1.
Osmium‐Mediated Oxidative Cyclizations: A Study into the Range of Initiators That Facilitate Cyclization
Authors: Donohoe Timothy J. , Wheelhouse (née Gosby) Katherine M. P. , Lindsay‐Scott Peter J. , Churchill Gwydion H. , Connolly Matthew J. , Butterworth Sam , Glossop Paul A. 
Published: July 2009

AbstractA general route to prepare substituted, saturated five‐membered heterocycles has been developed. The application of a wide range of starting materials to the osmium‐catalyzed oxidative cyclization reaction is described. Diols, hydroxy‐amides, hydroxy‐sulfonamides, and carbamates all cyclize in moderate to excellent yields to give cis‐tetrahydrofurans and pyrrolidines, depending upon the position of the heteroatoms in the starting materials. These cyclizations all proceed with near total selectivity for the cis‐heterocycles, and with stereospecific introduction of a hydroxy group adjacent to the ring. Moreover, routes to enantiopure starting materials are described, which give enantiopure products upon cyclization. Catalyst loadings of as low as one mol percent have been successfully employed for this transformation.
A simple approach to robustD‐stability analysis for uncertain singular delay systems
Authors: Lu Renquan , Su Hongye , Chu Jian , Xue Anke 
Published: July 2009

AbstractThis note presents a simple approach to analyze robustD‐stability for uncertain continuous‐time singular systems with state delay and structured uncertainties. Sufficient conditions, which are computationally simple, and need not calculate the eigenvalues of the system, are proposed to ensure that the uncertain continuous‐time singular delay system is regular, impulse free andD‐stable, that is, all its finite poles are located within a specified disk. Two numerical examples are given to demonstrate the application of the proposed method. Copyright © 2009 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society
Lysozyme‐lysozyme self‐interactions as assessed by the osmotic second virial coefficient: Impact for physical protein stabilization
Authors: Le Brun Virginie , Friess Wolfgang , Schultz‐Fademrecht Torsten , Muehlau Silke , Garidel Patrick 
Published: July 2009

AbstractThe purpose of the presented study is to understand the physicochemical properties of proteins in aqueous solutions in order to identify solution conditions with reduced attractive protein‐protein interactions, to avoid the formation of protein aggregates and to increase protein solubility. This is assessed by measuring the osmotic second virial coefficient (B22), a parameter of solution non‐ideality, which is obtained using self‐interaction chromatography. The model protein is lysozyme. The influence of various solution conditions on B22 was investigated: protonation degree, ionic strength, pharmaceutical relevant excipients and combinations thereof. Under acidic solution conditions B22 is positive, favoring protein repulsion. A similar trend is observed for the variation of the NaCl concentration, showing that with increasing the ionic strength protein attraction is more likely. B22 decreases and becomes negative. Thus, solution conditions are obtained favoring attractive protein‐protein interactions. The B22 parameter also reflects, in general, the influence of the salts of the Hofmeister series with regard to their salting‐in/salting‐out effect. It is also shown that B22 correlates with protein solubility as well as physical protein stability.
Molecular facets of sphingolipids: Mediators of diseases
Authors: Ozbayraktar Fatma Betul Kavun , Ulgen Kutlu O. 
Published: July 2009

AbstractSphingolipids constitute a biologically active lipid class that is significantly important from both structural and regulatory aspects. The manipulation of sphingolipid metabolism is currently being studied as a novel strategy for cancer therapy. The basics of this therapeutic approach lie in the regulation property of sphingolipids on cellular processes, which are important in a cell's fate, such as cell proliferation, apoptosis, cell cycle arrest, senescence, and inflammation. Furthermore, the mutations in the enzymes catalyzing some specific reactions in the sphingolipid metabolism cause mortal lysosomal storage diseases like Fabry, Gaucher, Niemann‐Pick, Farber, Krabbe, and Metachromatic Leukodystrophy. Therefore, the alteration of the sphingolipid metabolic pathway determines the choice between life and death. Understanding the sphingolipid metabolism and regulation is significant for the development of new therapeutic approaches for all sphingolipid‐related diseases, as well as for cancer. An important feature of the sphingolipid metabolic pathway is the compartmentalization into endoplasmic reticulum, the Golgi apparatus, lysosome and plasma membrane, and this compartmentalization makes the transport of sphingolipids critical for proper functioning. This paper focuses on the structures, metabolic pathways, localization, transport mechanisms, and diseases of sphingolipids in Saccharomyces cerevisiae and humans, and provides the latest comprehensive information on sphingolipid research.
Adopting sustainable innovation: what makes consumers sign up to green electricity?
Authors: Ozaki Ritsuko 
Published: July 2009

AbstractThis paper investigates what encourages consumers to adopt a green electricity tariff. When people decide to adopt an innovation, such as green electricity, they consider not only functionality, usability, costs and intended outcomes, but also what the innovation means to them, for example, the way it reflects their identity, image, memberships, values and norms. The study reviews the theoretical frameworks of innovation adoption and consumption, and cognitive and normative behaviour, relevant to consumer adoption of pro‐environmental innovations, and develops a research framework. Through focus group discussions, a questionnaire survey with 103 respondents and an interview with 10 people, the study finds that consumers sympathetic to environmental issues do not necessarily adopt green electricity. This is due to lack of strong social norms and personal relevance, inconvenience of switching, uncertainty about the quality of green electricity and lack of accurate information. The implications of these findings for strategy, policy and future research are explored. Copyright © 2009 John Wiley & Sons, Ltd and ERP Environment.
Empirical analysis of determinants of adoption of proactive environmental strategies in India
Authors: Sangle Shirish 
Published: July 2009

AbstractProactive environmental strategies are beyond extant laws and it is important to understand why companies go beyond compliance. The paper discusses motivations behind their adoption of proactive environmental strategies in India. The research results show that institutional pressure is the most significant determinant of adoption of proactive environmental strategies. Other factors such as managerial attitude, business case of environmental investments and productivity enhancement initiatives are also significant. Based on the research findings, the paper proposes some important managerial implications in connection with adoption of proactive environmental strategies. Copyright © 2009 John Wiley & Sons, Ltd and ERP Environment.
Position‐Dependent Effects of Fluorinated Amino Acids on the Hydrophobic Core Formation of a Heterodimeric Coiled Coil
Authors: Salwiczek Mario , Samsonov Sergey , Vagt Toni , Nyakatura Elisabeth , Fleige Emanuel , Numata Jorge , Cölfen Helmut , Pisabarro M. Teresa , Koksch Beate 
Published: July 2009

AbstractSystematic model investigations of the molecular interactions of fluorinated amino acids within native protein environments substantially improve our understanding of the unique properties of these building blocks. A rationally designed heterodimeric coiled coil peptide (VPE/VPK) and nine variants containing amino acids with variable fluorine content in either position a16 or d19 within the hydrophobic core were synthesized and used to evaluate the impact of fluorinated amino acid substitutions within different hydrophobic protein microenvironments. The structural and thermodynamic stability of the dimers were examined by applying both experimental (CD spectroscopy, FRET, and analytical ultracentrifugation) and theoretical (MD simulations and MM‐PBSA free energy calculations) methods. The coiled coil environment imposes position‐dependent conformations onto the fluorinated side chains and thus affects their packing and relative orientation towards their native interaction partners. We find evidence that such packing effects exert a significant influence on the contribution of fluorine‐induced polarity to coiled coil folding.
Neutral Pentacoordinate Silicon(IV) Complexes with Silicon–Chalcogen (S, Se, Te) Bonds
Authors: Theis Bastian , Metz Stefan , Burschka Christian , Bertermann Rüdiger , Maisch Stefan , Tacke Reinhold 
Published: July 2009

AbstractThe neutral pentacoordinate silicon(IV) complexes 1 (SiS2ONC skeleton), 2 (SiSeSONC), 3 (SiTeSONC), 6/9 (SiSe2O2C), 7 (SiSe2S2C), and 8/10 (SiSe4C) were synthesized and structurally characterized by using single‐crystal X‐ray diffraction and multinuclear solid‐state and solution‐state (except for 6–9) NMR spectroscopy. With the synthesis of compounds 1–3 and 6–10, it has been demonstrated that pentacoordinate silicon compounds with soft chalcogen ligand atoms (S, Se, Te) can be stable in the solid state and in solution.
Helical Chiral Pyridine N‐Oxides: A New Family of Asymmetric Catalysts
Authors: Chen Jinshui , Takenaka Norito 
Published: July 2009

AbstractOptically active chiral alkyl chlorides are valuable compounds because of their bioactivity and versatile synthetic utility. Accordingly, the ring opening of epoxides with a chloride nucleophile stands as an important goal in asymmetric catalysis. We describe herein recent advances in the design and development of chiral pyridine N‐oxide catalysts for the enantioselective synthesis of chlorohydrins.
Is the Backbone Conformation of Cα‐Methyl Proline Restricted to a Single Region?
Authors: De Poli Matteo , Moretto Alessandro , Crisma Marco , Peggion Cristina , Formaggio Fernando , Kaptein Bernard , Broxterman Quirinus B. , Toniolo Claudio 
Published: July 2009

AbstractCα‐Methyl‐L‐proline, or L‐(αMe)Pro, is probably the most conformationally constrained α‐amino acid. In particular, its ω and ϕ torsion angles are restricted to about 180 and −60°, respectively, and only three ranges of values are theoretically available for ψ in mono‐ or longer peptides, namely, about −30° (cis′, 310/α‐helical structure), 60° (inverse γ turn), or 140° (trans′, poly(L‐Pro)n II structure). In this work, we examined the tendency of a number of Nα‐acyl dipeptide N′‐alkylamides of the type RCO‐(αMe)Pro‐Xxx‐NHR′ or RCO‐Xxx‐(αMe)Pro‐NHR′, in which Xxx is L (or D)‐Ala, Aib (α‐aminoisoburyric acid), or L (or D)‐(αMe)Pro, long enough to fold into intramolecularly hydrogen‐bonded γ or β turns. The results are compared with those obtained for the corresponding dipeptides based on Pro, a well‐known turn‐forming residue. For the crystal‐state 3D‐structural analysis we used X‐ray diffraction, whereas our solution conformational analysis was heavily based on the FTIR absorption and 1H and 13C NMR spectroscopy techniques. We conclude that (αMe)Pro is able to explore both trans′ and cis′ ψ areas of the conformational space, but in (αMe)Pro the latter is overwhelmingly more populated, in marked contrast to the Pro preference. This finding is a clear indication that in (αMe)Pro the major 3D‐structural determinant is the Cα‐methyl group. The circular dichroism (CD) signature of a peptide type III′ β‐turn conformation is also proposed.
Dihydroxyacetone Phosphate Aldolase Catalyzed Synthesis of Structurally Diverse Polyhydroxylated Pyrrolidine Derivatives and Evaluation of their Glycosidase Inhibitory Properties
Authors: Calveras Jordi , Egido‐Gabás Meritxell , Gómez Livia , Casas Josefina , Parella Teodor , Joglar Jesús , Bujons Jordi , Clapés Pere 
Published: July 2009

AbstractThe chemoenzymatic synthesis of a collection of pyrrolidine‐type iminosugars generated by the aldol addition of dihydroxyacetone phosphate (DHAP) to C‐α‐substituted N‐Cbz‐2‐aminoaldehydes derivatives, catalyzed by DHAP aldolases is reported. L‐Fuculose‐1‐phosphate aldolase (FucA) and L‐rhamnulose‐1‐phosphate aldolase (RhuA) from E. coli were used as biocatalysts to generate configurational diversity on the iminosugars. Alkyl linear substitutions at C‐α were well tolerated by FucA catalyst (i.e., 40–70 % conversions to aldol adduct), whereas no product was observed with C‐α‐alkyl branched substitutions, except for dimethyl and benzyl substitutions (20 %). RhuA was the most versatile biocatalyst: C‐α‐alkyl linear groups gave the highest conversions to aldol adducts (60–99 %), while the C‐α‐alkyl branched ones gave moderate to good conversions (50–80 %), with the exception of dimethyl and benzyl substituents (20 %). FucA was the most stereoselective biocatalyst (90–100 % anti (3R,4R) adduct). RhuA was highly stereoselective with (S)‐N‐Cbz‐2‐aminoaldehydes (90–100 % syn (i.e., 3R,4S) adduct), whereas those with R configuration gave mixtures of anti/syn adducts. For iPr and iBu substituents, RhuA furnished the anti adduct (i.e., FucA stereochemistry) with high stereoselectivity. Molecular models of aldol products with iPr and iBu substituents and as complexes with the RhuA active site suggest that the anti adducts could be kinetically preferred, while the syn adducts would be the equilibrium products. The polyhydroxylated pyrrolidines generated were tested as inhibitors against seven glycosidases. Among them, good inhibitors of α‐L‐fucosidase (IC50=1–20 μM), moderate of α‐L‐rhamnosidase (IC50=7–150 μM), and weak of α‐D‐mannosidase (IC50=80–400 μM) were identified. The apparent inhibition constant values (Ki) were calculated for the most relevant inhibitors and computational docking studies were performed to understand both their binding capacity and the mode of interaction with the glycosidases.
Adaptive workflow processing and execution in Pegasus
Authors: Lee Kevin , Paton Norman W. , Sakellariou Rizos , Deelman Ewa , Fernandes Alvaro A. A. , Mehta Gaurang 
Published: July 2009

AbstractWorkflows are widely used in applications that require coordinated use of computational resources. Workflow definition languages typically abstract over some aspects of the way in which a workflow is to be executed, such as the level of parallelism to be used or the physical resources to be deployed. As a result, a workflow management system has the responsibility of establishing how best to execute a workflow given the available resources. The Pegasus workflow management system compiles abstract workflows into concrete execution plans, and has been widely used in large‐scale e‐Science applications. This paper describes an extension to Pegasus whereby resource allocation decisions are revised during workflow evaluation, in the light of feedback on the performance of jobs at runtime. The contributions of this paper include: (i) a description of how adaptive processing has been retrofitted to an existing workflow management system; (ii) a scheduling algorithm that allocates resources based on runtime performance; and (iii) an experimental evaluation of the resulting infrastructure using grid middleware over clusters. Copyright © 2009 John Wiley & Sons, Ltd.
A Vibrational Raman Optical Activity Study of 1,1′‐Binaphthyl Derivatives
Authors: Liégeois Vincent 
Published: July 2009

AbstractThe Raman polarized and vibrational Raman optical activity (VROA) backward spectra are simulated for a series of 2,2′‐substituted 1,1′‐binaphthyl compounds presenting a variety of torsion angles between the two naphthalene rings. The substitution prevents free rotation along this torsion angle and the chirality of these compounds is thus called atropisomerism. However, the rotation is not completely frozen so that two different conformations, namely cisoid and transoid, are found and their Raman and VROA signatures are studied. As expected, the Raman spectra are not very sensitive whereas the VROA spectra present more complex patterns, which evolve as a function of the torsion angle between the two naphthalene groups. In particular, our analysis shows that some modes can be used as a probe for the determination of the torsion angle of these molecules in solution. The contributions of both invariants to the VROA backward intensity are also assessed.