bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of GeneChip gene definitions on the microarray study of cancers
Authors: Lu Xuesong , Zhang Xuegong 
Published: July 2006

AbstractThe Affymetrix GeneChip is a popular microarray platform for genome‐wide expression profiling and has been widely used in functional genomics especially in the classification of cancers. Due to the updating of genome data, much of the genome information with which the chips were designed is out‐of‐date and it has been reported that many of the genes/transcripts on the chips differ from their original definition when mapping the probes to the new genome information. Dai et al. have reported that the updated definition can cause as much as 30–50% discrepancy in the genes selected as differentially expressed on a heart tissue expression profiling dataset. Understanding the nature of this difference is therefore very important for the utilization of the data. In this work, with a large cancer dataset as an example, we compared two major definitions and investigated their effects on classification, clustering, discovery of differentially expressed genes and gene‐set‐based analysis. Results show that the two definitions agree well on clustering and classification results but genes and gene sets discovered as differentially expressed or enriched can be very different. Discoveries based on the Affymetrix definition can cover most of those based on the new definition, but tend to have more false positives. BioEssays 28: 739–746, 2006. © 2006 Wiley Periodicals, Inc.
Measuring cooperativity in the formation of a three‐stranded β sheet (double hairpin)
Authors: Hudson F. Michael , Andersen Niels H. 
Published: July 2006

AbstractRecently validated chemical shift measures of hairpin structuring have been applied to a series of turn mutants of the Schenck–Gellman three‐strand β‐sheet model with the aim of measuring the entropic advantage associated with aligning an additional strand onto an existing hairpin versus aligning the same two strands in an initial hairpin formation. In a four‐state analysis (unfolded, 2 single hairpins, and the double hairpin fold in equilibrium) a cooperativity index can be defined as the factor by which the equilibrium constant for hairpin formation is improved when one strand is prestructured. This cooperativity index is 2.7 ± 0.7 for hairpin formation about a stable D‐Pro‐Gly turn locus and increases to 7.6 ± 1.2 for an Asn‐Gly turn locus. The latter corresponds to a cooperativity induced ΔΔG increment of 4.9 kJ/mol for the folding of a hairpin. Although larger than previous experimental measures of folding cooperativity in three‐stranded sheets, the magnitude of this effect (which is considerably less than the TΔΔS expectation for prestructuring three or more β‐strand residue sites) likely reflects the intrinsic preference of these designed sequences for extended conformations. If similar or larger effects apply to protein β‐sheet folding, it is not surprising that particularly favorable hairpin alignments serve as nucleation sites in protein folding pathways. © 2006 Wiley Periodicals, Inc. Biopolymers 83:424–433, 2006This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Fabrication of agar‐gelatin hybrid scaffolds using a novel entrapment method for in vitro tissue engineering applications
Authors: Verma Vipin , Verma Poonam , Kar Santosh , Ray Pratima , Ray Alok R. 
Published: July 2006

AbstractScaffolds of agar and gelatin were developed using a novel entrapment method where agar and gelatin molecules mutually entrapped one another forming stable cell adhesive matrices. Glutaraldehyde was used as a crosslinking agent for gelatin. Three types of hybrid matrices were prepared using agar and gelatin in different proportions in the weight ratio of 1:1, 2:1, and 3:1. Surface characterization of dry scaffolds was carried out by scanning electron microscope. Swelling studies were carried out in phosphate buffer saline (PBS) at physiological pH 7.4. The integral stability of the scaffolds was evaluated by estimating the released disintegrated gelatin from them in PBS at pH 7.4. The attachment kinetics of the cells was evaluated by culturing mouse fibroblast cell line NIH 3T3 on films. The cytocompatibility of these matrices was determined by studying growth kinetics of NIH 3T3 cells on them and morphology of cells was observed through optical photographs taken at various days of culture. It was found that the matrices containing agar and gelatin in 2:1 weight ratio exhibited best growth kinetics. The results obtained from these studies have suggested that the above‐described method is a cheap and easy way to fabricate agar‐gelatin hybrid scaffolds to grow cells which can be used in various in vitro tissue engineering applications like screening of drugs. Biotechnol. Bioeng. 2007;96: 392–400. © 2006 Wiley Periodicals, Inc.
Synthesis and Characterization of Nonconventional Surfactants of Aromatic Amino Acid–Glycerol Ethers: Effect of the Amino Acid Moiety on the Orientation and Surface Properties of These Soap‐Type Amphiphiles
Authors: Varka Evdoxia‐Maria A. , Heli Maria G. , Coutouli‐Argyropoulou Evdoxia , Pegiadou Sofia A. 
Published: July 2006

AbstractThe synthesis, characterization, and surface properties of soap‐type amphiphiles comprising alkyl chains of 10–16 carbon atoms linked through an ether group to a glycerol–amino acid hydrophilic head group is described. The surface properties of members of this series derived from histidine and tyrosine were compared with those of phenylalanine and tryptophan derivatives described previously and with those of conventional soaps. In all cases, the amino acid derivatives showed superior surface properties, and an interesting differentiation was discovered regarding the orientation of tryptophan derivatives.
Homo‐ and Heteropolynuclear Platinum Complexes Stabilized by Dimethylpyrazolato and Alkynyl Bridging Ligands: Synthesis, Structures, and Luminescence
Authors: Forniés Juan , Fuertes Sara , Martín Antonio , Sicilia Violeta , Lalinde Elena , Moreno M. Teresa 
Published: July 2006

AbstractThis work describes the synthesis of cis‐[Pt(CCPh)2(Hdmpz)2] (1) and its use as a precursor for the preparation of homo‐ and heteropolynuclear complexes. Double deprotonation of compound 1 with readily available MI (M = Cu, Ag, Au) or MII (M = Pd, Pt) species affords the discrete hexanuclear clusters [{PtM2(μ‐CCPh)2(μ‐dmpz)2}2] [M = Cu (2), Ag (3), Au (4)], in which both “Pt(CCPh)2(dmpz)2” fragments are connected by four d10 metal centers, and are stabilized by alkynyl and dimethylpyrazolate bridging ligands, or the trinuclear complexes [Pt(μ‐CCPh)2(μ‐dmpz)2{M(C∧P)}2] (M = Pd (5), Pt (6); C∧P = CH2‐C6H4‐P(o‐tolyl)2‐κC,P), respectively. The X‐ray structures of complexes 1–4 and 6 are reported. The X‐ray structure of the platinum–copper derivative 2 shows that all copper centers exhibit similar local geometry being linearly coordinated to a nitrogen atom and η2 to one alkynyl fragment. However in the related platinum–silver (3) and platinum–gold (4) derivatives the silver and gold atoms present three different coordination environments. The complexes have been studied by absorption and emission spectroscopy. The hexanuclear complexes exhibit bright luminescence in the solid state and in fluid solution (except 4 in the solid state at 298 K). Dual long‐lived emission is observed, being clearly resolved in low‐temperature rigid media. The low‐energy emission is ascribed to MLM′CT Pt(d)/π(CCPh)→Pt(pz)/M′(sp)/π*(CCPh) modified by metal–metal interactions whereas the high‐energy emission is tentatively attributed to an emissive state derived from dimethylpyrazolate‐to‐metal (d10) LM′CT transitions π(dmpz)→M′(d10).
Multicomponent Synthesis of Dihydropyrimidines and Thiazines
Authors: Vugts Danielle J. , Koningstein Manoe M. , Schmitz Rob F. , de Kanter Frans J. J. , Groen Marinus B. , Orru Romano V. A. 
Published: July 2006

AbstractA broad range of differently substituted dihydropyrimidines and thiazines can be efficiently prepared by using a four‐component reaction between phosphonates, nitriles, aldehydes, and iso(thio)cyanates. The scope and limitations of this multicomponent reaction are fully described. Variation of all four components has been investigated. The nitrile and aldehyde inputs can be varied extensively, but variation of the phosphonate input remains limited. An interesting rearrangement leading to phosphoramidates has been observed. Furthermore, the multicomponent reaction seems to be restricted to the use of isocyanates with strongly electron‐withdrawing substituents, but an interesting additional exchange reaction under microwave conditions leads to dihydropyrimidines with less electron‐withdrawing substituents at N3. In addition, a diastereoselective formation of dihydropyrimidines has been observed when using a chiral aldehyde as the input. Finally, by changing the isocyanate component to an isothiocyanate, thiazines are efficiently formed instead of the corresponding thio‐dihydropyrimidines.
A Novel Method for the In Situ Determination of Concentration Gradients in the Electrolyte of Li‐Ion Batteries
Authors: Zhou Jiang , Danilov Dmitry , Notten Peter H. L. 
Published: July 2006

AbstractAn electrochemical method has been developed for the in situ determination of concentration gradients in the electrolyte of sealed Li‐ion batteries by measuring the potential difference between microreference electrodes. Formulas relating the concentration gradient and the potential difference between the microreference electrodes were derived from the Nernst–Planck equation. The concentration gradients in Li‐ion batteries are theoretically and experimentally proven to be linear at steady state under galvanostatic charging and discharging conditions. Based on this finding, both the diffusion coefficient of the lithium ions in the electrolyte and the diffusion overpotential related to the concentration gradient have been calculated. It was found that the concentration gradient is proportional to the applied current over a wide current range and that the obtained diffusion coefficient of lithium ions is almost constant. For the batteries studied in this work, the diffusion overpotential is already noticeable at 0.30 A and the limiting current is estimated to be 1.1 A, corresponding to a C‐rate of 3.7.
Persilylated Phosphoranyl Radicals: The First Persistent Noncyclic Phosphoranyl Radicals
Authors: Berchadsky Yves , Bernard‐Henriet Christiane , Finet Jean‐Pierre , Lauricella Robert , Marque Sylvain R. A. , Tordo Paul 
Published: July 2006

AbstractPersistent noncyclic phosphoranyl radicals have been prepared and observed by electron paramagnetic resonance (EPR) for the first time. They were obtained by UV‐photolysis of a solution containing a bis(trialkylsilyl) peroxide (R = Me, Et) and a tris(trialkylsilyl) phosphite (R = Me, Et, iPr). EPR parameters (aP ≈ 100 mT) are typical of phosphoranyl radicals exhibiting a trigonal‐bipyramidal structure, with the odd electron in an equatorial site. Analysis of the pseudo‐first‐order decay shows that these phosphoranyl radicals decay by SH2 homolytic substitution on the bis(trialkylsilyl) peroxide and by loss of a trialkylsilyloxyl radical (α‐scission reaction). Both the SH2 and α‐scission reactions depend on the steric bulk of the alkyl groups, that is, the bulkier the alkyl group, the slower the SH2 and α‐scission reactions.
Methylazacalixpyridines: Remarkable Bridging Nitrogen‐Tuned Conformations and Cavities with Unique Recognition Properties
Authors: Gong Han‐Yuan , Zhang Xiao‐Hang , Wang De‐Xian , Ma Hong‐Wei , Zheng Qi‐Yu , Wang Mei‐Xiang 
Published: July 2006

AbstractMethylazacalix[n]pyridines (n = 4, 8) and methylazacalix[m]arene[n]pyridines (m = n = 2, 4) have been synthesized by a convenient fragment coupling approach starting from 2,6‐dibromopyridine, 2,6‐diaminopyridine, and benzene‐1,3‐diamine. Thanks to the intrinsic electronic nature of nitrogen, which can adopt mainly sp2 hybridization, allowing it variously to conjugate, partially conjugate, or not conjugate with the adjacent one or two pyridine rings, the resulting nitrogen‐bridged calixpyridine derivatives act as a unique class of macrocyclic host molecules with intriguing conformational structures offering fine‐tunable cavities and versatile recognition properties. Whilst in solution it is fluxional, in the solid state methylazacalix[4]pyridine adopts a 1,3‐alternate conformation with a C2v symmetry in which every two bridging nitrogen atoms conjugate with one pyridine ring. After protonation, the methylazacalix[4]pyridinium species has a different conjugation system of its four bridging nitrogen atoms, yielding the similar twisted 1,3‐alternate conformations with an approximate S4 symmetry. The cavity of each protonated methylazacalix[4]pyridine, however, varies finely to accommodate guest species of different size and geometry, such as planar DMF or HO2CCO2− ion, a twisted HO2CCO2− ion, and a tetrahedral ClO4− ion. As giant macrocyclic hosts, both methylazacalix[8]pyridine and methylazacalix[4]arene[4]pyridine interact efficiently with fullerenes C60 and C70 through van der Waals forces. Their ease of preparation, versatile conformational structures, and recognition properties make these multinitrogen‐containing calixarenes or cyclophanes unique and powerful macrocyclic hosts in supramolecular chemistry.
Gastrodin Interaction with Human Fibrinogen: Anticoagulant Effects and Binding Studies
Authors: Liu Yang , Tang Xiaoling , Pei Jianfeng , Zhang Li , Liu Feng , Li Ke'an 
Published: July 2006

AbstractIn an effort to identify the anticoagulant activity of gastrodin (GAS) and to investigate the possibility of its use as a novel anticoagulant drug, the binding characteristics of GAS to human fibrinogen (Fg) were studied by using a quartz crystal microbalance (QCM) biosensor, anticoagulant animal experiments, and a molecular docking simulation. Real‐time kinetic analysis with the QCM biosensor revealed that the in vitro binding of GAS to Fg was strong under physiological ionic conditions as the determined equilibrium dissociation constant (KD) was 1.94×10−6 M. To check whether this strong binding may influence the natural coagulation function of Fg, the in vivo effect of GAS on the coagulation system of rats was examined. The results showed that GAS can significantly prolong the coagulation time (CT) and decrease the Fg content, while it had no effect on the activated kaolin partial thromboplastin time (KPTT) or prothrombin time (PT) in rats. To clarify the mechanism of the specific interaction, a molecular docking simulation was also performed to provide reasonable binding models for the interaction of GAS with Fg at the atomic level. GAS binds strongly to the inherent polymerization sites “a” and “b” (holes) on the Fg molecule with similar binding free energies of about −34 kJ mol−1. Altogether, these findings confirmed first that GAS possesses anticoagulant activity and that the possible anticoagulation mechanism of GAS mainly involves its interference with the knob‐to‐hole interactions between fibrin molecules, thereby effectively inhibiting the formation of clots and decreasing the risk of thrombosis. The study has also shown the potential usefulness of QCM biosensor technology for the rapid screening of drug–protein interactions.
Visualizing neurons one‐by‐one in vivo: Optical dissection and reconstruction of neural networks with reversible fluorescent proteins
Authors: Aramaki Shinsuke , Hatta Kohei 
Published: July 2006

AbstractA great many axons and dendrites intermingle to fasciculate, creating synapses as well as glomeruli. During live imaging in particular, it is often impossible to distinguish between individual neurons when they are contiguous spatially and labeled in the same fluorescent color. In an attempt to solve this problem, we have taken advantage of Dronpa, a green fluorescent protein whose fluorescence can be erased with strong blue light, and reversibly highlighted with violet or ultraviolet light. We first visualized a neural network with fluorescent Dronpa using the Gal4‐UAS system. During the time‐lapse imaging of axonal navigation, we erased the Dronpa fluorescence entirely; re‐highlighted it in a single neuron anterogradely from the soma or retrogradely from the axon; then repeated this procedure for other single neurons. After collecting images of several individual neurons, we then recombined them in multiple pseudo‐colors to reconstruct the network. We have also successfully re‐highlighted Dronpa using two‐photon excitation microscopy to label individual cells located inside of tissues and were able to demonstrate visualization of a Mauthner neuron extending an axon. These “optical dissection” techniques have the potential to be automated in the future and may provide an effective means to identify gene function in morphogenesis and network formation at the single cell level. Developmental Dynamics, 2006. © 2006 Wiley‐Liss, Inc.
Tamoxifen‐inducible NaV1.8‐CreERT2 recombinase activity in nociceptive neurons of dorsal root ganglia
Authors: Zhao Jing , Nassar Mohammed A. , Gavazzi Isabella , Wood John N. 
Published: July 2006

AbstractTo explore the function of genes expressed in adult mouse nociceptive neurons, we generated heterozygous knock‐in mice expressing the tamoxifen‐inducible Cre recombinase construct CreERT2 downstream of the NaV1.8 promoter. CreERT2 encodes a Cre recombinase (Cre) fused to a mutant estrogen ligand‐binding domain (ERT2) that requires the presence of tamoxifen for activity. We have previously shown that heterozygous NaV1.8‐Cre mice will delete loxP flanked genes specifically in nociceptive sensory neurons from embryonic day 14. We therefore used the same strategy of homologous recombination and mouse generation, substituting the Cre cassette with CreERT2. No functional Cre recombinase activity was found in CreERT2 mice crossed with reporter mice in the absence of tamoxifen. We found that, as with NaV1.8‐Cre mice, functional Cre recombinase was present in nociceptive sensory neurons after tamoxifen induction in vivo. However, the percentage of dorsal root ganglion (DRG) neurons expressing functional Cre activity was much reduced (<10% of the number found in the NaV1.8‐Cre mouse). We also examined Cre recombinase activity in sensory neurons in culture. After treatment with 1 μM tamoxifen for 48 h, 15% of DRG neurons showed Cre activity. NaV1.8‐CreERT2 animals may thus be useful for single cell studies of the functional consequences of gene ablation in culture, but are unlikely to be useful for behavioral studies. genesis 44:364–371, 2006. © 2006 Wiley‐Liss, Inc.
Rx‐Cre, a tool for inactivation of gene expression in the developing retina
Authors: Swindell Eric C. , Bailey Travis J. , Loosli Felix , Liu Chaomei , Amaya‐Manzanares Felipe , Mahon Kathleen A. , Wittbrodt Joachim , Jamrich Milan 
Published: July 2006

AbstractRx is a homeobox‐containing gene that is critical for vertebrate eye development. Its expression domain delineates a field of cells from which the retina and the ventral hypothalamus develop. The 5′ upstream regulatory sequences of the medaka fish Rx gene are functionally conserved during evolution to a degree that they direct gene expression into the Rx‐expressing field of cells in mice. Using these sequences, we made a Cre line that can be used for inactivation of gene expression in the developing retina. genesis 44:361–363, 2006. Published 2006 Wiley‐Liss, Inc.
Power and emotion in negotiation: power moderates the interpersonal effects of anger and happiness on concession making
Authors: Van Kleef Gerben A. , De Dreu Carsten K.W. , Pietroni Davide , Manstead Antony S. R. 
Published: July 2006

AbstractThis paper focuses on the interactive effects of power and emotion in negotiation. Previous research has shown that negotiators concede more to angry opponents than to happy ones, and that power influences the amount of attention that is devoted to the social environment. Integrating these two lines of inquiry, we predicted that low‐power negotiators would be influenced by their opponent's emotions (conceding more to an angry opponent than to a happy one), whereas high‐power negotiators would not. Five studies using different methods (an experiment, a field simulation, and three scenario studies), different samples (students, general population, managers), and different operationalisations of power (BATNA, number of alternatives, legitimacy, support) support this hypothesis. The results are discussed in terms of a motivated information processing model of the interpersonal effects of emotions in negotiations. Copyright © 2006 John Wiley & Sons, Ltd.
20q11.1 amplification in giant‐cell tumor of bone: Array CGH, FISH, and association with outcome
Authors: Smith Laura T. , Mayerson Joel , Nowak Norma J. , Suster David , Mohammed Nehad , Long Susan , Auer Herbert , Jones Susie , McKeegan Christina , Young Gregory , Bos Gary , Plass Christoph , Morrison Carl 
Published: July 2006

AbstractThe goal of this study was to identify recurrent regions of genomic gain or loss in giant‐cell tumor of bone (GCTb). Array comparative genomic hybridization (aCGH) was performed for 20 frozen tumor samples of GCTb. A separate subset of 59 GCTb with outcome data was used for validation. The most frequent region of change identified by aCGH was gain of a 1‐Mbp region at 20q11.1. In the validation arm of 59 cases the minimal common region of copy number gain at 20q11.1, seen in 54% of the samples, was BAC clone RP11‐4O9, which contained the genes TPX2 and BCL2L1. For most cases, amplification was restricted to the mononuclear component and was not present in the multinucleated giant cells. Southern blot for TPX2 and BCL2L1 identified the former as the gene with the highest level of amplification for these two proposed candidate genes of importance. Immunohistochemistry for TPX2 expression correlated with amplification, while BCL2L1 expression was not identified. Kaplan–Meier curves for progression‐free survival showed a statistically significant difference for cases with 20q11.1 amplification (P = 0.0001). Univariate analysis involving Cox proportional hazards models did not show a significant difference for initial treatment type (curettage versus resection) (P = 0.575), age (≤50 vs. >50) (P = 0.543), or sex (P = 0.268), but did correlate with 20q11.1 amplification (P = 0.001). By multivariate analysis, it was found that 20q11.1 amplification (P = 0.001) was the only factor to reach statistical significance. 20q11.1 amplification can be used as a marker of prognostic importance in GCTb. We propose TPX2 as a candidate oncogene in the core‐amplified region at 20q11.1. © 2006 Wiley‐Liss, Inc.