bluuebunny/crossref_metadata_2025_split huggingface dataset:
A role for acetylcholine receptors in their own aggregation on muscle cells
Authors: Milholland Rebecca B.R. , Gordon Herman 
Published: March 2007

AbstractBoth neurotrophic factors and activity regulate synaptogenesis. At neuromuscular synapses, the neural factor agrin released from motor neuron terminals stimulates postsynaptic specialization by way of the muscle specific kinase MuSK. In addition, activity through acetylcholine receptors (AChRs) has been implicated in the stabilization of pre‐ and postsynaptic contacts on muscle at various stages of development. We show here that activation of AChRs with specific concentrations of nicotine is sufficient to induce AChR aggregation and that this induction requires the function of L‐type calcium channels (L‐CaChs). Furthermore, AChR function is required for agrin induced AChR aggregation in C2 muscle cells. The same concentrations of nicotine did not induce observable tyrosine phosphorylation on either MuSK or the AChR β subunit, suggesting significant differences between the mechanisms of agrin and activity induced aggregation. The AChR/L‐CaCh pathway provides a mechanism by which neuromuscular signal transmission can act in concert with the agrin‐MuSK signaling cascade to regulate NMJ formation. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2007.
Oxidative stress, nitric oxide, and the mechanisms of cell death in Lurcher Purkinje cells
Authors: McFarland Rebecca , Blokhin Andrei , Sydnor James , Mariani Jean , Vogel Michael W. 
Published: March 2007

AbstractOxidative stress is postulated to play a role in cell death in many neurodegenerative diseases. As a model of neonatal neuronal cell death, we have examined the role of oxidative stress in Purkinje cell death in the heterozygous Lurcher mutant (+/Lc). Lurcher is a gain of function mutation in the δ2 glutamate receptor (GluRδ2) that turns the receptor into a leaky membrane channel, resulting in chronic depolarization of +/Lc Purkinje cells starting around the first week of postnatal development. Virtually, all +/Lc Purkinje cells die by the end of the first postnatal month. To investigate the role of oxidative stress in +/Lc Purkinje cell death, we have examined nitric oxide synthase (NOS) activity and the expression of two markers for oxidative stress, nitrotyrosine and manganese super oxide dismutase (MnSOD), in wild type and +/Lc Purkinje cells at P10, P15, and P25. The results show that NOS activity and immunolabeling for nitrotyrosine and MnSOD are increased in +/Lc Purkinje cells. To determine whether peroxynitrite formation is a prerequisite for +/Lc Purkinje cell death, +/Lc mutants were crossed with an α‐nNOS knockout mutant (nNOSα−/−) to reduce the production of NO. Analysis of the double mutants showed that blocking α‐nNOS expression does not rescue +/Lc Purkinje cells. However, we present evidence for sustained NOS activity and nitrotyrosine formation in the GluRδ2+/Lc:nNOS−/− double mutant Purkinje cells, which suggests that the failure to rescue GluRδ2+/Lc:nNOS−/− Purkinje cells may be explained by the induction of alternative nNOS isoforms. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2007.
Germline transgenesis and insertional mutagenesis in the ascidianCiona intestinalis
Authors: Sasakura Yasunori 
Published: March 2007

AbstractStable transgenesis is a splendid technique that is applicable to the creation of useful marker lines, enhancer/gene traps, and insertional mutagenesis. Recently, transposon‐mediated transformation using a Tc1/marinertransposable elementMinoshas been reported in two ascidians:Ciona intestinalisandC. savignyi. The transposon derived from an insect,Drosophila hydei, has high activity for excision inCionaembryos and transposition in their genome. As much as 37% ofMinos‐injectedC. intestinalistransmitted transposon insertions to the subsequent generation.Minos‐mediated germline transgenesis has also been achieved by means of electroporation method.Minostechniques have been applied to enhancer traps and insertional mutagenesis inCiona. For those reasons,Minosoffers the high potential for use as a powerful tool for future genetic studies. This review specifically addresses recent achievements of transformation techniques inCiona, as exemplified using theMinossystem. Developmental Dynamics 236:1758–1767, 2007. © 2007 Wiley‐Liss, Inc.
The Ditertiary‐Phosphane‐Bridged Heteronuclear Cluster RuOs3(μ‐H)2(CO)9(μ‐CO)2(μ‐dppm): Synthesis and Reactivity with Alkynes
Authors: Tan Yong Leng Kelvin , Leong Weng Kee 
Published: March 2007

AbstractA high‐yielding alternative synthesis of the dppm‐bridged heteronuclear cluster RuOs3(μ‐H)2(CO)9(μ‐CO)2(μ‐dppm) (1) [dppm = bis(diphenylphosphanyl)methane] has been developed. Thermolysis of 1 resulted in dephenylation of both phosphane groups to afford the butterfly cluster RuOs3(CO)12(μ4,κ2:κ2‐PhPCH2PPh) (2). The reaction of 1 with selected alkynes afforded the products RuOs3(μ‐H)(CO)8(μ‐CO)(μ3,κ2:κ1‐PhPCH2PPh2)(μ3,η1:η2:η1‐L) (3) (L = alkyne) in which the alkyne is aligned parallel to an Os–Os bond(// Os‐Os isomer). The clusters incorporating internal alkynes underwent isomerization to the //Ru‐Os isomer by alkyne and hydride migration. Several other cluster products of these reactions were also identified, including RuOs3(μ‐H)(CO)8(μ‐CO)(μ3,κ2:κ1‐PhPCH2PPh2)(μ3,η1:η2:η1‐tBuC2CHO)(6) in which the methyl group of the alkyne has been oxidized to an aldehyde. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)
Synthesis and Structural Characterization of Novel Ytterbium(III) Complexes with both a μ‐Oxo Group and Bridged Indenyl Ligands, and Ytterbium(II) Complexes with Bridged Indenyl Ligands
Authors: Cheng Lin , Feng Yan , Wang Shaowu , Luo Wei , Yao Wei , Yu Zeyan , Xi Xiaobing , Huang Zixiang 
Published: March 2007

AbstractThe reactivity of the ytterbium(III) amide [(Me3Si)2N]3Yb(μ‐Cl)Li(thf)3 with different bridged indene compounds in the presence of external donor ligands was studied. Reaction of [(Me3Si)2N]3Yb(μ‐Cl)Li(thf)3 with the corresponding 1,2‐bis(indenyl)ethane [(CH2)2(C9H7)2] or Me2Si(C9H7)2, followed by the addition of excess thf, produced a novel tetranuclear ytterbium complex [{η5:η5‐(CH2)2(C9H6)2}Yb(μ‐Cl)(μ3‐O)Yb(Cl)N(SiMe3)2Li(thf)4]2 (1) or a novel dinuclear ytterbium complex [η5:η5‐(CH3)2Si(C9H6)2Yb]2(μ‐Cl)(μ‐O)Li(thf)2 (2), respectively. Treatment of [(Me3Si)2N]3Yb(μ‐Cl)Li(thf)3 with (CH2)2(C9H6SiMe3)2 (3) or Me2Si(C9H7)2 under different conditions produced ytterbium(II) complexes [η5:η5‐(CH2)2(C9H5SiMe3)2]Yb(thf)2·(C6H14)0.5 (4) and [η5:η5‐(CH2)2(C9H5SiMe3)2]Yb·dme (5) or [η5:η5‐(CH3)2Si(C9H6)2]Yb·tmeda (6), respectively. Interaction of the ytterbium(III) amide [η5:η5‐(CH2)2(C9H6)2]YbN(SiMe3)2 with excess tmeda afforded the ytterbium(II) complex [η5:η5‐(CH2)2(C9H6)2]Yb·tmeda (7). All the compounds were fully characterized by spectroscopic methods and elemental analyses. Complexes 1, 2, and 4 were additionally characterized by single‐crystal X‐ray diffraction analyses. The solvents and temperature effects on the reaction are discussed. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)
New Aspects for Modeling Supramolecular Interactions in Vanadium Haloperoxidases: β‐Cyclodextrin Inclusion Compounds of cis‐Dioxovanadium(V) Complexes
Authors: Lippold Ines , Görls Helmar , Plass Winfried 
Published: March 2007

AbstractThe reaction of potassium vanadate and the hydrazone ligand derived from Schiff base condensation of salicylaldehyde and biphenyl‐4‐carboxylic acid hydrazide (H2salhybiph) in the presence of β‐cyclodextrin (β‐CD) in water yields the 1:1 inclusion compound K[VO2(salhybiph)@ β‐CD]. The characterization in solution confirmed the integrity of the inclusion compound in different polar solvents such as DMSO and water. The inclusion compound crystallizes with additional water molecules in the triclinic space group P1. The supramolecular aggregation of the inclusion compound in the solid state is established through hydrogen bonding interactions between adjacent β‐CD hosts and the π–π stacking ability of the ligand side chain of the guest complexes. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)
Quantitative analysis of thiols in consumer products on a microfluidic CE chip with fluorescence detection
Authors: Revermann Tobias , Götz Sebastian , Karst Uwe 
Published: March 2007

AbstractA microchip CE‐based method for the quantification of the thiols mercaptoethanoic acid (MAA) and 2‐mercaptopropionic acid (2‐MPA) in depilatory cream and cold wave lotions was developed. The thiols were first derivatized with the fluorogenic reagent ammonium‐7‐fluorobenzo‐2‐oxa‐1,3‐diazole‐4‐sulfonate (SBD‐F). The derivatives were separated within only 20 s by microchip CE and detected by their fluorescence. Conventional CE with diode array detection and LC with fluorescence detection were used for validation. The internal standard 3‐mercaptopropionic acid (3‐MPA) provided RSDs of multiple injections of only 4% or less for the MCE approach. LOD is 2 μM, LOQ 6 μM, and the linear range comprises nearly three decades of concentration starting at the LOQ.
Experimental verification of a wireless sensing and control system for structural control using MR dampers
Authors: Loh Chin‐Hsiung , Lynch Jerome P. , Lu Kung‐Chun , Wang Yang , Chang Chia‐Ming , Lin Pei‐Yang , Yeh Ting‐Hei 
Published: March 2007

AbstractThe performance aspects of a wireless ‘active’ sensor, including the reliability of the wireless communication channel for real‐time data delivery and its application to feedback structural control, are explored in this study. First, the control of magnetorheological (MR) dampers using wireless sensors is examined. Second, the application of the MR‐damper to actively control a half‐scale three‐storey steel building excited at its base by shaking table is studied using a wireless control system assembled from wireless active sensors. With an MR damper installed on each floor (three dampers total), structural responses during seismic excitation are measured by the system's wireless active sensors and wirelessly communicated to each other; upon receipt of response data, the wireless sensor interfaced to each MR damper calculates a desired control action using an LQG controller implemented in the wireless sensor's computational core. In this system, the wireless active sensor is responsible for the reception of response data, determination of optimal control forces, and the issuing of command signals to the MR damper. Various control solutions are formulated in this study and embedded in the wireless control system including centralized and decentralized control algorithms. Copyright © 2007 John Wiley & Sons, Ltd.
Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates
Authors: Gront Dominik , Kmiecik Sebastian , Kolinski Andrzej 
Published: March 2007

AbstractIn this contribution, we present an algorithm for protein backbone reconstruction that comprises very high computational efficiency with high accuracy. Reconstruction of the main chain atomic coordinates from the α carbon trace is a common task in protein modeling, including de novo structure prediction, comparative modeling, and processing experimental data. The method employed in this work follows the main idea of some earlier approaches to the problem. The details and careful design of the present approach are new and lead to the algorithm that outperforms all commonly used earlier applications. BBQ (Backbone Building from Quadrilaterals) program has been extensively tested both on native structures as well as on near‐native decoy models and compared with the different available existing methods. Obtained results provide a comprehensive benchmark of existing tools and evaluate their applicability to a large scale modeling using a reduced representation of protein conformational space. The BBQ package is available for downloading from our website at http://biocomp.chem.uw.edu.pl/services/BBQ/. This webpage also provides a user manual that describes BBQ functions in detail. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Can an OH radical form a strong hydrogen bond? A theoretical comparison with H2O
Authors: Lai Chin‐Hung , Chou Pi‐Tai 
Published: March 2007

AbstractIn this study, we apply UCCSD/6‐31++G** to investigate the ability of an OH radical acting as a hydrogen bond acceptor with HF, HCl, and H2O (HO…HX; XF, Cl, OH) or as a hydrogen bond donor with H2O and H2S (OH…XH2; XO and S). We also replace OH with H2O and make a fair comparison between them. Additionally, the counterpoise method (CP) has been used to examine the effect of basis set superposition error (BSSE). Our results reveal that OH is a stronger hydrogen bond donor but a weaker hydrogen bond acceptor than H2O. This conclusion is independent of the correction for BSSE and can be rationalized by the NBO analysis, the results of which indicate that OH radical has a lowernOand σ*O–Hin energy than that of H2O. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007
Energy landscapes of nucleophilic substitution reactions: A comparison of density functional theory and coupled cluster methods
Authors: Swart Marcel , Solà Miquel , Bickelhaupt F. Matthias 
Published: March 2007

AbstractWe have carried out a detailed evaluation of the performance of all classes of density functional theory (DFT) for describing the potential energy surface (PES) of a wide range of nucleophilic substitution (SN2) reactions involving, amongst others, nucleophilic attack at carbon, nitrogen, silicon, and sulfur. In particular, we investigate the ability of the local density approximation (LDA), generalized gradient approximation (GGA), meta‐GGA as well as hybrid DFT to reproduce high‐level coupled cluster (CCSD(T)) benchmarks that are close to the basis set limit. The most accurate GGA, meta‐GGA, and hybrid functionals yield mean absolute deviations of about 2 kcal/mol relative to the coupled cluster data, for reactant complexation, central barriers, overall barriers as well as reaction energies. For the three nonlocal DFT classes, the best functionals are found to be OPBE (GGA), OLAP3 (meta‐GGA), and mPBE0KCIS (hybrid DFT). The popular B3LYP functional is not bad but performs significantly worse than the best GGA functionals. Furthermore, we have compared the geometries from several density functionals with the reference CCSD(T) data. The same GGA functionals that perform best for the energies (OPBE, OLYP), also perform best for the geometries with average absolute deviations in bond lengths of 0.06 Å and 0.6°, even better than the best meta‐GGA and hybrid functionals. In view of the reduced computational effort of GGAs with respect to meta‐GGAs and hybrid functionals, let alone coupled cluster, we recommend the use of accurate GGAs such as OPBE or OLYP for the study of SN2 reactions. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Quantum mechanical charge field molecular dynamics simulation of the TiO2+ ion in aqueous solution
Authors: Fatmi M. Qaiser , Hofer Thomas S. , Randolf Bernhard R. , Rode Bernd M. 
Published: March 2007

AbstractStructural and dynamical properties of the TiO2+ ion in aqueous solution have been investigated by using the new ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) formalism, which does not require any other potential functions except those for solvent–solvent interactions. Both first and second hydration shell have been treated at Hartree‐Fock (HF) quantum mechanical level. A TiO bond distance of 1.5 Å was observed for the [TiO]2+ ion. The first hydration shell of the ion shows a varying coordination number ranging from 5 to 7, five being the dominant one and representing one axial and four equatorial water molecules directly coordinated to Ti, which are located at 2.3 Å and 2.1 Å, respectively. The flexibility in the coordination number reflects the fast exchange processes, which occur only at the oxo atom, where water ligands are weakly bound through hydrogen bonds. Considering the first shell hydration, the composition of the TiO2+ hydrate can be characterized as [(H2O)0.7(H2O)(H2O)ax]2+. The second shell consists in average of 12 water molecules located at a mean distance of 4.4 Å. Several other structural parameters such as radial and angular distribution functions and coordination number distributions were analyzed to fully characterize the hydration structure of the TiO2+ ion in aqueous solution. For the dynamics of the TiO2+ ion, different sets of dynamical parameters such as Ti=O, TiOeq, and TiOax stretching frequencies and ligands' mean residence times were evaluated. During the simulation time of 15 ps, 3 water exchange processes in the first shell were observed at the oxo atom, corresponding to a mean residence time of 3.6 ps. The ligands' mean residence time for the second shell was determined as 3.5 ps. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Finding the transition state without initial guess: The growing string method for Newton trajectory to isomerization and enantiomerization reaction of alanine dipeptide and poly(15)alanine
Authors: Quapp Wolfgang 
Published: March 2007

AbstractWe report a new, high‐dimensional application of a method for finding a transition state (TS) between a reactant and a product on the potential energy surface: the search of a growing string along a reaction path defined by any Newton trajectory in combination with the Berny method (Quapp, J Chem Phys (2005), 122, 174106; we have provided this algorithm on a web page). Two given minima are connected by a one‐dimensional, but usually curvilinear reaction coordinate. It leads to the TS region. The application of the method to alanine dipeptide finds the TS of the isomerisation C7 ax → C5, some TSs of the enantiomerisation of C7 ax from L‐form to quasi‐D‐form, and it finds the TS region of a transition of a partly unfolded, bent structure which turns back into a mainly α‐helix in the Ac(Ala)15NHMe polyalanine (all at the quantum mechanical level B3LYP/6‐31G: the growing string calculation is interfaced with the Gaussian03 package). The formation or dissolvation of some α‐ or 310‐hydrogen bonds of the helix are discussed along the TS pathway, as well as the case of an enantiomer at the central residue of the helix. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Vertical excitation energies for ribose and deoxyribose nucleosides
Authors: So Remmick , Alavi Saman 
Published: March 2007

AbstractVertical excitation energies for DNA and RNA nucleosides are determined with electron structure calculations using the time‐dependent density functional theory (TDDFT) method at the B3LYP/6‐311++G(d,p) level for nucleoside structures optimized at the same level of theory. The excitation energies and state assignments are verified using B3LYP/aug‐cc‐pVDZ level calculations. The nature of the first four excited states of the nucleosides are studied and compared with those of isolated bases. The lowest nπ* and ππ* transitions in the nucleoside remain localized on the aromatic rings of the base moiety. New low‐energy nπ* and πσ* transitions are introduced in the nucleosides as a result of bonding to the ribose and deoxyribose molecules. The effect on the low‐lying excited state transitions of the binding to phosphate groups at the 5′‐ and 3′,5′‐hydroxyl sites of the uracil ribose nucleoside are also studied. Some implications of these calculations on the de‐excitation dynamics of nucleic acids are discussed. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007.
Clinical MR imaging of degenerative spinal disease: Pulse sequences, gradient‐echo techniques, and contrast agents
Authors: Ross Jeffrey S. , Tkach Jean , VanDyke Carolyn , Modic Michael T. 
Published: March 2007

AbstractDEGENERATION OF THE INTERVERTEBRAL disk is a ubiquitous process, seen at autopsy in 97% of adults by age 49 years (1). Low back pain is the most expensive health care problem in patients 20–50 years old, with $14 billion spent yearly on treatment and compensation (2). The greatest costs connected with low back pain occur in patients who have pain longer than 3 months and in those with recurrent pain episodes (3). Approximately 5.2 million people are disabled by back pain (3–5).These statistics indicate that the accurate diagnosis of back pain disease is obviously of great importance. In the diagnosis of disk degeneration and its sequelae, magnetic resonance (MR) imaging has become a key ingredient. The utility of conventional two‐dimensional spin‐echo MR imaging of the spine has been firmly established for extradural disease (6–8). Gradient‐echo techniques have more recently been used to enhance the cerebrospinal fluid (CSF)‐extradural interface in the evaluation of degenerative disease (9–13). Some of the new imaging findings and concepts regarding the use of contrast material and three‐dimensional techniques in the evaluation of degenerative disease of the spine are reviewed.
MR imaging of the vocal tract during vowel production
Authors: Lakshminarayanan A. V. , Lee Sungbok , McCutcheon Martin J. 
Published: March 2007

AbstractModeling of vocal tract behavior during speech production requires accurate measurements of the entire vocal tract. To accomplish this, magnetic resonance (MR) imaging was performed on a 0.5‐T system with a custom‐made, double‐loop, wraparound coil. A midsagittal section of the region from the glottis to the lips was imaged during sustained production of five American English vowels. A gradient‐spoiled gradient‐echo sequence was used to achieve a 4‐second imaging time. Images showed clear profiles of the entire vocal tract and exhibited essential articulatory features of vowel production. It was possible to measure midsagittal widths at various points along the vocal tract with 1‐mm resolution. The measurements were used to construct a tube model for prediction of the acoustic output of the vocal tract. It is concluded that risk‐free MR imaging promises to be an important means of acquiring data for vocal tract modeling, with applications to speech pathology, linguistics, and artificial speech.
Modified iterative model based on data extrapolation method to reduce Gibbs ringing
Authors: Amartur Sundar , Haacke E. Mark 
Published: March 2007

AbstractAn iterative algorithm that involves image filtering and data replacement (as suggested by Constable and Henkelman) is investigated for reducing the Gibbs artifact in magnetic resonance imaging. The image is processed with an edge‐preserving filter to estimate the height and location of a set of model elements (ó functions or boxes) for generating the missing high‐frequency information. Filtering was performed in the complex image domain to account for discontinuities in phase as well as magnitude. The process is repeated after each data replacement to handle varying degrees of contrast. The convergence and signal‐to‐noise characteristics of the algorithm are investigated by means of simulated and clinical examples. The results indicate that the algorithm performs reasonably well in reducing ringing artifacts due to nearby edge contrast seen in most of the homogeneous, isointense regions. Nevertheless, it may generate some spurious thickening of structures that do not match the assumed step‐edge models.