bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self‐Assembled Small‐Molecule Microarrays for Protease Screening and Profiling
Authors: Urbina Hugo D. , Debaene François , Jost Bernard , Bole‐Feysot Christine , Mason Daniel E. , Kuzmic Petr , Harris Jennifer L. , Winssinger Nicolas 
Published: September 2006

AbstractSmall‐molecule microarrays are attractive for chemical biology as they permit the analysis of hundreds to thousands of interactions in a highly miniaturized format. Methods to prepare small‐molecule microarrays from combinatorial libraries by a self‐assembly process based on the sequence‐specific hybridization of peptide nucleic acid (PNA) encoded libraries to oligonucleotide arrays are presented. A systematic study of the dynamic range for multiple detection agents, including direct fluorescence of attached fluorescein and cyanine‐3 dyes, antibody‐mediated fluorescence amplification, and biotin–gold nanoparticle detection, demonstrated that individual PNA‐encoded probes can be detected to concentrations of 10 pM on the oligonucleotide microarrays. Furthermore, a new method for parallel processing of biological samples by using gel‐based separation of probes is presented. The methods presented in this report are exemplified through profiling two closely related cysteine proteases, cathepsin K and cathepsin F, across a 625‐member PNA‐encoded tetrapeptide acrylate library. A series of the specific cathepsin K and F inhibitors identified from the library were kinetically characterized and shown to correlate with the observed microarray profile, thus validating the described methods. Importantly, it was shown that this method could be used to obtain orthogonal inhibitors that displayed greater than tenfold selectivity for these closely related cathepsins.
Molecular characterization of the effects of Y‐27632
Authors: Darenfed Hassina , Dayanandan Bama , Zhang Tong , Hsieh Sidney H.‐K. , Fournier Alyson E. , Mandato Craig A. 
Published: September 2006

AbstractMany key cellular functions, such as cell motility and cellular differentiation are mediated by Rho‐associated protein kinases (ROCKs). Numerous studies have been conducted to examine the ROCK signal transduction pathways involved in these motile and contractile events with the aid of pharmacological inhibitors such as Y‐27632. However the molecular mechanism of action of Y‐27632 has not been fully defined. To assess the relative contribution of these Rho effectors to the effects of Y‐27632, we compared the cytoskeletal phenotype, wound healing and neurite outgrowth in cells treated with Y‐27632 or subjected to knockdown with ROCK‐I, ROCK‐II or PRK‐2‐ specific siRNAs. Reduction of ROCK‐I enhances the formation of thin actin‐rich membrane extensions, a phenotype that closely resembles the effect of Y‐27632. Knockdown of ROCK II or PRK‐2, leads to the formation of disc‐like extenstions and thick actin bundles, respectively. The effect of ROCK‐I knockdown also mimicked the effect of Y‐27632 on wound closer rates. ROCK‐I knockdown and Y‐27632 enhanced wound closure rates, while ROCK‐II and PRK‐2 were not appreciably different from control cells. In neurite outgrowth assays, knockdown of ROCK‐I, ROCK‐II or PRK‐2 enhances neurite lengths, however no individual knockdown stimulated neurite outgrowth as robustly as Y‐27632. We conclude that several kinases contribute to the global effect of Y‐27632 on cellular responses. Cell Motil. Cytoskeleton 2006. © 2006 Wiley‐Liss, Inc.
How to determine free Gd and free ligand in solution of Gd chelates. A technical note
Authors: Barge Alessandro , Cravotto Giancarlo , Gianolio Eliana , Fedeli Franco 
Published: September 2006

AbstractGd(III) chelates are often used as reporting probes in magnetic resonance imaging applications. Their use relies on the assumption that their high stability ensures against the release of free ligand and free Gd3+ ions, which are both highly toxic to living systems. The presence of free Gd3+ ions may have a profound effect on the contrast in the MR image as they may form highly hydrated, macromolecular complexes endowed with very high relaxivity thus providing erroneous information on the extent of the contrast effect induced by the given reporting probe. Although the stability of a given complex may be high enough, the complexation step could not have been completed. Therefore any Gd complex preparation has to be carefully checked for the content of free ligand and free metal ions. Herein the currently used procedures that allow an assessment of the amounts of free metal ions and free ligand in a solution of a given Gd complex are described in detail. Copyright © 2006 John Wiley & Sons Ltd.
Topology awareness of overlay P2P networks
Authors: Rostami Habib , Habibi Jafar 
Published: September 2006

AbstractIn overlay networks, the mechanism of a peer randomly joining and leaving a network, causes a topology mismatch between the overlay and the underlying physical topology. This causes a large volume of redundant traffic in the underlying physical network as well as an extra delay in message delivery in the overlay network. Topology mismatch occurs because overlay networks are not aware of their underlying physical networks. In this paper we present a mathematical model for topology awareness of overlay networks (degree of matching between an overlay and its underlying physical network) and the efficiency of message delivery on them. Then we experimentally show that the model is precise in the real world. Also, after determining the computational complexity of the model, we propose an optimization heuristic algorithm to enhance efficiency of message exchange on overlay networks by increasing their topology awareness. Next, we present the results of running the algorithm on different kinds of random graph and show how we can implement the algorithm on peer‐to‐peer networks; we then simulate the implementation on some unstructured peer‐to‐peer overlay networks. Copyright © 2006 John Wiley & Sons, Ltd.
Management of real‐time streaming data Grid services
Authors: Fox Geoffrey , Aydin Galip , Bulut Hasan , Gadgil Harshawardhan , Pallickara Shrideep , Pierce Marlon , Wu Wenjun 
Published: September 2006

AbstractWe discuss our message‐based approach to managing real‐time data streams and building higher level services to produce and consume them. Our messaging system acts as a substrate that can be used to provide qualities of service to various streaming applications ranging from audio–video collaboration systems to sensor Grids. The messaging substrates are composed of distributed, hierarchically arranged message broker networks. Services such as filters are deployed along the edges of the network. We discuss the role of management systems for both broker networks and filter services: broker network topologies must be created and maintained, and distributed filters must be arranged in appropriate sequences. These managed broker networks may be applied to a wide range of problems. We discuss applications to audio–video collaboration in some detail and also describe applications to streaming Global Positioning System data streams. These provide specific application filters that can transform and republish message streams to the broker system. Copyright © 2006 John Wiley & Sons, Ltd.
Networking scientific resources in the Knowledge Grid environment
Authors: Zhuge Hai , Ding Lianhong , Li Xiang 
Published: September 2006

AbstractScientific documents, research instruments, researchers' abilities and co‐operation among researchers are fundamental resources of scientific research. This paper proposes an approach for effectively networking scientific resources by detecting community structures in self‐organized social network, discovering interest in information flow, capturing changes of interests over time and analyzing the relationship between peers. Copyright © 2006 John Wiley & Sons, Ltd.
Distribution of mobile agents in vulnerable networks
Authors: Qu Wenyu , Kitsuregawa Masaru , Shen Hong , Jin Yingwei 
Published: September 2006

AbstractAdvances in the Internet and the computer industry have created many new application areas for network routing such as Grid computing and also brings new challenges to traditional routing techniques. In this paper we propose a mobile agent‐based routing model in vulnerable networks for these applications. To characterize the behaviors of mobile agents and their effects on the network performance, we analyze the population distribution of mobile agents as a measurement of the computational resource consumption. Our analysis reveals theoretical insights into the statistical behaviors of mobile agents and provides useful tools for effectively managing mobile agents in large networks. Copyright © 2006 John Wiley & Sons, Ltd.
Autonomous semantic link networking model for the Knowledge Grid
Authors: Zhuge Hai 
Published: September 2006

AbstractA semantic link network (SLN) consists of nodes (entities, features, concepts, schemas or communities) and semantic links between nodes. This paper proposes an autonomous SLN formalism to support intelligent applications on large‐scale networks. The formalism integrates the SLN logical reasoning with the SLN analogical reasoning and the SLN inductive reasoning, as well as existing techniques to form an autonomous semantic overly. The SLN logical reasoning mechanism derives implicit semantic relations by a semantic matrix and relevant addition and multiplication operations based on semantic link rules. The SLN analogical reasoning mechanism proposes conjectures on semantic relations based on structural mapping between nodes. The SLN inductive reasoning mechanism derives general semantics from special semantics. The cooperation of diverse reasoning mechanisms enhances the reasoning ability of each, therefore providing a powerful semantic ability for the semantic overlay. The self‐organizing diverse scales of the SLN support the intelligent applications of the Knowledge Grid. Copyright © 2006 John Wiley & Sons, Ltd.
Expanding the Diversity of Polycyclic Aromatics Through a Suzuki–Miyaura Cross‐Coupling Strategy
Authors: Kotha Sambasivarao , Lahiri Kakali 
Published: September 2006

AbstractIn recent years, Pd‐catalyzed Suzuki–Miyaura (SM) cross‐coupling reactions have revolutionized approaches to carbon–carbon bond formation. We have studied the application of SM coupling with several (ca. 16) complex molecular structures of particular relevance to scientists working at the interfaces of chemistry, biology, and materials sciences. In this regard, various structurally or biologically important polycyclic molecules (e.g., benzocrowns,C3‐symmetric molecules, 9,10‐disubstituted anthracenes, and sulfones) and unusual amino acid derivatives have been modified by this reaction, while it has also been shown that allylation of aromatics through the use of a commercially available boronic acid ester by SM coupling under CsF/Pd0conditions is feasible. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Development of Biotechnological Processes by Integrating Genetic and Engineering Methods
Authors: Hempel D. C. 
Published: September 2006

AbstractThe production systems and product lines used in the collaborative research centre (SFB 578) are considered to be an example for the superior goal to develop new tools, methods, data, and models for bioprocess design. Integrating genetic, biologic, biochemical and engineering methods for process design is helpful to reduce the development efforts and costs. Basic parameters describing the whole process have to be found and systems biotechnological models have to be developed. They should enable to synthesize products in biologically active form in high concentration, yield, and purity with as few production steps as possible.
New Approaches to Online Bioprocess Monitoring
Authors: Büttgenbach S. , Michalzik M. , Wilke R. 
Published: September 2006

AbstractAn overview on microfluidic components and microanalysis systems enabling online monitoring of bioprocesses is given in this paper. The design and performance of a capillary electrophoresis microchip and a quartz crystal microbalance, which can be used for measurements of target analytes from a continuous sample flow, are described.
Optimal linear and bilinear algorithms for power control in 3G wireless CDMA networks
Authors: Skataric Dobrila , Gajic Zoran , Qian Lijun 
Published: September 2006

AbstractIn this paper we present two power control algorithms that potentially can be used as efficient techniques for power updates in 3G wireless CDMA communication networks. The algorithms are obtained by optimising the signal‐to‐interference‐ratio (SIR) error. The control laws are distributed, respectively linear and bilinear, and either requires estimation of the channel interference (or the quantity inversely proportional to the signal interference, known as the channel variation) or the development of efficient numerical algorithms for solving a set of obtained algebraic equations. Simulation results show superiority of the proposed algorithm over the distributed constrained power control (DCPC) algorithm. Copyright © 2005 AEIT.
Pannexin1 is expressed by neurons and glia but does not form functional gap junctions
Authors: Huang Yan , Grinspan Judith B. , Abrams Charles K. , Scherer Steven S. 
Published: September 2006

AbstractPannexins are a newly described family of proteins that may form gap junctions. We made antisera against mouse pannexin1 (Panx1). HeLa cells expressing Panx1 have cell surface labeling, but not gap junction plaques, and do not transfer small fluorescent dyes or neurobiotin in a scrape‐loading assay. Neuro2a cells expressing Panx1 are not electrophysiologically coupled. Intracellular Panx1‐immunoreactivity, but not gap junction plaques, is seen in cultured oligodendrocytes, astrocytes, and hippocampal neurons. Thus, at least in these mammalian cells lines, Panx1 does not form morphological or functional gap junctions, and it remains to be demonstrated that Panx1 forms gap junction‐forming protein in the CNS. © 2006 Wiley‐Liss, Inc.
A sensitive and reliable semi‐quantitative real‐time PCR assay to detect JAK2 V617F in blood
Authors: Poodt J , Fijnheer R , Walsh IBB , Hermans MHA 
Published: September 2006

AbstractDiagnosis of the myeloproliferative disorders, polycythemia vera (PV), essential thrombocythemia (ET) and idiopathic myelofibrosis (IMF) is difficult due to lack of diagnostic markers. Recently, the acquisition of a mutation in the Janus kinase 2 (JAK2) gene by hemopoietic cells has been described as a genetic defect underlying myeloproliferative disorders. The mutation leads to constitutive activation of JAK2, a tyrosine kinase involved in cytokine receptor signalling. Because of the clinical importance of this mutation (JAK2 V617F) in diagnosing myeloproliferative disorders and its relevance for disease progression, we developed a semi‐quantitative real‐time PCR test to detect JAK2 V617F. With this assay, quantities down to 0.8% JAK2 V617F amongst wild‐type DNA could reliably be detected. For quantification purposes, low intra‐ and inter‐assay variabilities ensure good reproducibility of the assay. Thus the JAK2 V617F qPCR assay described here is quick, robust, simple and more sensitive than direct sequencing, RFLP, ARMS assay and other methods published so far to detect JAK2 V617F. We therefore believe that the assay will contribute to early diagnosis of myeloproliferative disorders and to disease management, especially when JAK2‐specific inhibitors have become available for therapeutic use. Copyright © 2006 John Wiley & Sons, Ltd.
Osteoblastic response to collagen scaffolds varied in freezing temperature and glutaraldehyde crosslinking
Authors: Chen Dai‐Chian , Lai Yu‐Lin , Lee Shyh‐Yuan , Hung Shan‐Ling , Chen Hen‐Li 
Published: September 2006

AbstractCollagen sponges are widely used scaffolds in bone engineering. To form bone, the osteoblastic cells undergo proliferation, differentiation, and mineralization stages in the scaffold. Crosslinking and freezing temperature are two important variables in fabricating collagen sponges. The purpose of this study was to examine the osteoblastic responses to collagen sponges prepared with or without glutaraldehyde crosslinking at different freezing temperatures (−20°C or −80°C). MC3T3‐E1 osteoblastic cells were cultured in differently prepared sponges. Osteoblastic responses examined included cell numbers, osteocalcin expression, and calcium deposition. Cell numbers were measured by DNA content. Osteocalcin expression was determined by RT‐PCR and real‐time RT‐PCR. Calcium deposition was assayed by ortho‐cresophthalein complexone method and von Kossa stain. The osteoblastic cells grown in all collagen sponges did not show apparent signs of cytotoxicity. Collagen sponges differed in freezing temperatures resulted in similar osteoblastic responses. Glutaraldehyde‐crosslinked sponges demonstrated less cell‐mediated contraction and more cell numbers at day 7 (p < 0.005). However, they showed lower osteocalcin expression at day 7 (p < 0.05) and less calcium deposition at day 21 (p < 0.001). In summary, different freezing temperatures played a minor role in osteoblastic responses. Glutaraldehyde crosslinking process, though improved the dimensional stability of collagen sponges, might compromise the osteoblastic differentiation and mineralization. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res, 2007
Study on the ability of 1,2,3,4‐tetrahydropapaveroline to cause oxidative stress: Mechanisms and potential implications in relation to parkinson's disease
Authors: Soto‐Otero Ramón , Sanmartín‐Suárez Carolina , Sánchez‐Iglesias Sofía , Hermida‐Ameijeiras Álvaro , Sánchez‐Sellero Inés , Méndez‐Álvarez Estefanía 
Published: September 2006

AbstractTetrahydropapaveroline (THP) is a compound derived from dopamine monoamine oxidase–mediated metabolism, particularly present in the brain of parkinsonian patients receiving L‐dopa therapy, and is capable of causing dopaminergic neurodegeneration. The aim of this work was to evaluate the potential of THP to cause oxidative stress on mitochondrial preparations and to gain insight into the molecular mechanisms responsible for its neurotoxicity. Our data show that THP autoxidation occurs with a continuous generation of hydroxyl radicals (•OH) and without the involvement of the Fenton reaction. The presence of ascorbate enhances this process by establishing a redox cycle, which regenerates THP from its quinolic forms. It has been shown that the production of •OH is not affected by the presence of either ferrous or ferric iron. Although THP does not affect lipid peroxidation, it is capable of reducing the high levels of thiobarbituric acid–reactive substances obtained in the presence of ascorbate and/or iron. However, THP autoxidation in the presence of ascorbate causes both an increase in protein carbonyl content and a reduction in protein‐free thiol content. THP also increases protein carbonyl content when the autoxidation occurs in the presence of iron. The remarkable role played by ascorbate in the production of oxidative stress by THP autoxidation is of particular interest. © 2006 Wiley Periodicals, Inc. J Biochem Mol Toxicol 20:209–220, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20138
Metabolic effects of carbenoxolone in rat liver
Authors: Pivato Leandro Silva , Constantin Rodrigo Polimeni , Ishii‐Iwamoto Emy L. , Kelmer‐Bracht Ana Maria , Yamamoto Nair Seiko , Constantin Jorgete , Bracht Adelar 
Published: September 2006

AbstractThe action of carbenoxolone on hepatic energy metabolism was investigated in the perfused rat liver and isolated mitochondria. In perfused livers, carbenoxolone (200–300 μM) increased oxygen consumption, glucose production and glycolysis from endogenous glycogen. Gluconeogenesis from lactate or fructose, an energy‐dependent process, was inhibited. This effect was already evident at a concentration of 25 μM. The cellular ATP levels and the adenine nucleotide content were decreased by carbenoxolone, whereas the AMP levels were increased. In isolated mitochondria, carbenoxolone stimulated state IV respiration and decreased the respiratory coefficient with the substrates β‐hydroxybutyrate and succinate. The ATPase of intact mitochondria was stimulated, the ATPase of uncoupled mitochondria was inhibited, and the ATPase of disrupted mitochondria was not altered by carbenoxolone. These results indicate that carbenoxolone acts as an uncoupler of oxidative phosphorylation and, possibly, as an inhibitor of the ATP/ADP exchange system. The inhibitory action of carbenoxolone on mitochondrial energy metabolism could be contributing to induce the mitochondrial permeability transition (MPT), a key phenomenon in apoptosis. The results of the present study can explain, partly at least, the in vivo hepatotoxic actions of carbenoxolone that were found in a previous clinical evaluation. © 2006 Wiley Periodicals, Inc. J Biochem Mol Toxicol 20:230–240, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20139
Heterogeneity of the coumarin anticoagulant targeted vitamin K epoxide reduction system. Study of kinetic parameters in susceptible and resistant mice (Mus musculus domesticus)
Authors: Lasseur Romain , Grandemange Agnès , Longin‐Sauvageon Christiane , Berny Philippe , Benoit Etienne 
Published: September 2006

AbstractVitamin K epoxide reductase (VKOR) activity in liver microsomes from a susceptible and a genetically warfarin‐resistant strain of mice (Mus Musculus domesticus) was analyzed to determine the mechanism of resistance to this 4‐hydroxycoumarin derivative. Kinetic parameters for VKOR were calculated for each strain by incubating liver microsomes with vitamin K epoxide ± warfarin. In susceptible mice, an Eadie–Hofstee plot of the data was not linear and suggested the involvement of at least two different components. Apparent kinetic parameters were obtained by nonlinear regression using a Michaelis‐‐Menten model, which takes into account two enzymatic components. Component A presents a high Km and a high Vm, and as a consequence only an enzymatic efficiency Vm/Km was obtained (0.0024 mL/min/mg). Estimated warfarin Ki was 0.17 μM. Component B presented an apparent Km of 12.73 μM, an apparent Vm of 0.32 nmol/min/mg, and an apparent Ki for warfarin of 6.0 μM. In resistant mice, the enzymatic efficiency corresponding to component A was highly decreased (0.0003–0.00066 mL/min/mg) while the Ki for warfarin was not modified. The apparent Vm of component B was poorly modified between susceptible and resistant mice. The apparent Km of component B observed in resistant mice was similar to the Km observed in susceptible mice. These modifications of the catalytic properties are associated with a single nucleotide polymorphism (T175G) in the VKOR‐C1 gene, which corresponds to a Trp59Gly mutation in the protein. © 2006 Wiley Periodicals, Inc. J Biochem Mol Toxicol 20:221–229, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20144