bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the RSL1‐dependent conditional expression system in LNCaP prostate cancer cells and development of a single vector format
Authors: Lessard Julie , Aicha Sonia ben , Fournier Andréa , Calvo Ezequiel , Lavergne Éliane , Pelletier Mélissa , Labrie Claude 
Published: March 2007

AbstractBackgroundConditional expression systems are useful tools for the study of gene function but the use of these systems in prostate cancer cells is limited by the undesired biological effects of the inducing ligands. The RheoSwitch system employs RheoSwitch Ligand 1 (RSL1), a non‐steroidal analog of the insect hormone ecdysone, to activate a modified nuclear receptor heterodimer that controls target gene expression via GAL4 response elements. This system has not been tested in prostate cancer cells.MethodsWe established LNCaP human prostate cancer cell lines that constitutively express RheoSwitch transcription factors to quantify RSL1‐dependent expression and assess the effects of RSL1 on cell proliferation and endogenous gene expression. Potential RSL1‐responsive genes were identified using Affymetrix microarrays and validated by Northern blot hybridization. A single‐vector format was developed to establish cell lines that conditionally produce a recombinant protein.ResultsStable cell lines displayed tight and potent (over several orders of magnitude) RSL1‐dependent regulation of a transiently transfected luciferase reporter gene. RSL1 did not affect basal or androgen‐stimulated cell proliferation and exerted minimal effects on the expression of endogenous genes. Cell lines established using the single‐vector system also displayed strictly RSL1‐dependent production of the recombinant protein encoded by the stably integrated RSL1‐responsive expression cassette.ConclusionsThe RheoSwitch system is well suited for conditional gene expression in prostate cancer cells. The single‐vector format should facilitate the production of stable cell lines. This system should be useful for the study of proteins involved in prostate cancer in both cell and animal models of the disease. Prostate 67: 808–819, 2007. © 2007 Wiley‐Liss, Inc.
The quinoline‐3‐carboxamide anti‐angiogenic agent, tasquinimod, enhances the anti‐prostate cancer efficacy of androgen ablation and taxotere without effecting serum PSA directly in human xenografts
Authors: Dalrymple Susan L. , Becker Robin E. , Isaacs John T. 
Published: March 2007

AbstractPURPOSETasquinimod is a second‐generation orally active quinoline‐3‐carboxamide analog with enhanced potency against prostate cancer via its anti‐angiogenic activity. It is presently undergoing clinical trials. Androgen ablation and taxanes are standard therapies for metastatic prostate cancer. This raises the issue of whether combining tasquinimod with either of these approaches enhances therapeutic efficacy.EXPERIMENTAL DESIGNThe tumor growth of a series of human prostate cancer xenografts (CWR‐22Rv1, CWR‐22R‐H, LAPC‐4, LNCaP, PC‐3 and DU‐145) in male nude mice given nothing versus tasquinimod alone or in combination with androgen ablation or with androgen ablation plus taxotere were evaluated as model systems to resolve these issues.RESULTSThese studies documented that daily oral treatment with tasquinimod consistently, statistically (P < 0.05) inhibited the tumor growth of each of the xenografts in a dose‐dependent manner via an anti‐angiogenic response as monitored by a significant (P < 0.05) decrease in the tumor blood vessel density. Tasquinimod's anti‐prostate cancer efficacy is enhanced when combined with androgen ablation and this enhancement was observed even when androgen ablation was either subsequent to or proceeded by tasquinimod treatment. In addition, tasquinimod also enhanced the tumor growth inhibition and survival when combined with androgen ablation plus taxotere. Companion studies documented that tasquinimod has no direct effect on serum PSA in these xenografts.CONCLUSIONSThese results documented that differences in serum PSA in tasquinimod‐treated hosts are related to inhibition in tumor growth. This suggests that in clinical trials, changes in PSA slope or doubling time are indicative of therapeutic response to tasquinimod. Prostate 67: 790–797, 2007. © 2007 Wiley‐Liss, Inc.
Cation–aromatic database
Authors: Reddy A. Srinivas , Sastry G. Madhavi , Sastry G. Narahari 
Published: March 2007

AbstractCation–aromatic database (CAD) is a publicly available web‐based database that aims to provide further understanding of interaction between a cation and the π interactions. A tool to identify the interactions in a user‐given protein is also added to the database. CAD is freely accessible via the Internet at http://203.199.182.73/gnsmmg/databases/cad/ Proteins 2007. © 2007 Wiley‐Liss, Inc.
Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model
Authors: Zheng Wenjun , Liao Jung‐Chi , Brooks Bernard R. , Doniach Sebastian 
Published: March 2007

AbstractHepatitis C virus NS3 helicase is an enzyme that unwinds double‐stranded polynucleotides in an ATP‐dependent reaction. It provides a promising target for small molecule therapeutic agents against hepatitis C. Design of such drugs requires a thorough understanding of the dynamical nature of the mechanochemical functioning of the helicase. Despite recent progress, the detailed mechanism of the coupling between ATPase activity and helicase activity remains unclear. Based on an elastic network model (ENM), we apply two computational analysis tools to probe the dynamical mechanism underlying the allosteric coupling between ATP binding and polynucleotide binding in this enzyme. The correlation analysis identifies a network of hot‐spot residues that dynamically couple the ATP‐binding site and the polynucleotide‐binding site. Several of these key residues have been found by mutational experiments as functionally important, while our analysis also reveals previously unexplored hot‐spot residues that are potential targets for future mutational studies. The conformational changes between different crystal structures of NS3 helicase are found to be dominated by the lowest frequency mode solved from the ENM. This mode corresponds to a hinge motion of the highly flexible domain 2. This motion simultaneously modulates the opening/closing of the domains 1–2 cleft where ATP binds, and the domains 2–3 cleft where the polynucleotide binds. Additionally, a small twisting motion of domain 1, observed in both mode 1 and the computed ATP binding induced conformational change, fine‐tunes the binding affinity of the domains 1–3 interface for the polynucleotide. The combination of these motions facilitates the translocation of a single‐stranded polynucleotide in an inchworm‐like manner. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Amino acid sequence autocorrelation vectors and bayesian‐regularized genetic neural networks for modeling protein conformational stability: Gene V protein mutants
Authors: Fernández Leyden , Caballero Julio , Abreu José Ignacio , Fernández Michael 
Published: March 2007

AbstractDevelopment of novel computational approaches for modeling protein properties from their primary structure is the main goal in applied proteomics. In this work, we reported the extension of the autocorrelation vector formalism to amino acid sequences for encoding protein structural information with modeling purposes. Amino acid sequence autocorrelation (AASA) vectors were calculated by measuring the autocorrelations at sequence lags ranging from 1 to 15 on the protein primary structure of 48 amino acid/residue properties selected from the AAindex data base. A total of 720 AASA descriptors were tested for building predictive models of the change of thermal unfolding Gibbs free energy change (ΔΔG) of gene V protein upon mutation. In this sense, ensembles of Bayesian‐regularized genetic neural networks (BRGNNs) were used for obtaining an optimum nonlinear model for the conformational stability. The ensemble predictor described about 88% and 66% variance of the data in training and test sets respectively. Furthermore, the optimum AASA vector subset not only helped to successfully model unfolding stability but also well distributed wild‐type and gene V protein mutants on a stability self‐organized map (SOM), when used for unsupervised training of competitive neurons. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Molecular simulations bring new insights into flavonoid/quercetinase interaction modes
Authors: Fiorucci Sébastien , Golebiowski Jérôme , Cabrol‐Bass Daniel , Antonczak Serge 
Published: March 2007

AbstractMolecular dynamics simulations, using the AMBER force field, were performed to study Quercetin 2,3‐Dioxygenase enzyme (Quercetinase or 2,3QD). We have analyzed the structural modifications of the active site and of the linker region between the native enzyme and the enzyme‐substrate complex. New structural informations, such as an allosteric effect in the presence of the substrate, as well as description of the enzyme‐substrate interactions and values of binding free energies were brought out. All these results confirm the idea that the linker encloses the substrate in the active site and also enlighten the recognition role of the substrate B‐ring by the enzyme. Moreover, a specific interaction scheme has been proposed to explain the relative degradation rate of various flavonoid compounds under the oxygenolysis reaction catalyzed by the Quercetin 2,3‐Dioxygenase enzyme. Proteins 2007. © 2007 Wiley‐Liss, Inc.
The promise of insect genomics
Authors: Grimmelikhuijzen Cornelis JP , Cazzamali Giuseppe , Williamson Michael , Hauser Frank 
Published: March 2007

AbstractInsects are the largest animal group in the world and are ecologically and economically extremely important. This importance of insects is reflected by the existence of currently 24 insect genome projects. Our perspective discusses the state‐of‐the‐art of these genome projects and the impacts that they have on basic insect science and pest control. Copyright © 2007 Society of Chemical Industry
Magnetic ordering of Mn and Ru in (La0.52Ba0.48) (Mn0.51Ru0.49)O3
Authors: Wu S. Y. , Li W.‐H. , Yang C. C. , Lynn J. W. , Liu R. S. 
Published: March 2007

AbstractNeutron diffraction, dc magnetization, and ac magnetic susceptibility measurements have been performed to study the magnetic properties of perovskite (La0.52Ba0.48) (Mn0.51Ru0.49)O3. The compound crystallizes into a cubic Pm$ \bar 3 $m symmetry with a lattice constant of a = 3.9661(4) Å at room temperature. Two anomalies, at around 160 and 60 K, can clearly be seen in the ac susceptibility results, with the peak positions for both anomalies shifting to a higher temperature as a dc magnetic field is applied. Neutron magnetic diffraction measurements show that the anomalies that occur at high and low temperatures are associated, with the ferromagnetic ordering of the Mn and the Ru spins, respectively. The ordering temperatures for the Mn and Ru spins were found to be at TC (Mn) ≈ 195 K and TC (Ru) ≈ 80 K, with a saturated moment of 〈μz–Mn〉 = 2.21(5)μB for the Mn spins and 〈μz–Ru〉 = 1.00(5)μB for the Ru spins. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Order–disorder transitions of t2g‐orbitals of V3+ ions and incommensurate structural deformations in the metallic spinel CuV2S4
Authors: Hidaka M. , Tokiwa N. , Wijesundera R. P. , Awaka J. , Nagata S. , Park Young Jun , Lee Ki Bong 
Published: March 2007

AbstractStructural transitions of the spinel CuV2S4 have been studied by means of X‐ray diffraction using synchrotron radiation. The temperature dependence of reflections forbidden in a cubic spinel structure of Fd3m suggests that there are order–disorder transitions of 3d2 (t2g) orbitals of V3+ ions at about 75 and 210 K. An incommensurate superlattice reflection of (2+3/4, 2, 2+3/4) shows the structural phase transition occurring at about 90 K, in addition to the superlattice structural modulation at about 30–35 and 55 K. A reduced wavevector q = (3/4–δ, 0, 3/4–δ) shows the temperature dependence of the δ value from 0.015 to –0.025. A lock‐in of δ = 0.0 and a crossover of the δ value occur in the region of 40 to 50 K. The incommensurate structural modulation along [110], [011], and [101] directions appearing below about 90 K affects a paramagnetic spin order of V3+ ions at about 30–35 and 55 K, in addition to the 90 K structural transition. The paramagnetic behavior is interpreted mainly by the structural deformation and the (dxy , dyz , dzx ) orbitals in the VS6 octahedral chains sited along [110], [011], and [101] directions. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Temperature dependent dielectric relaxation and electrical conductivity in single‐layer ZnO–Al2O3 nanocomposite thin films
Authors: Das Soumen , Chaudhuri Subhadra 
Published: March 2007

AbstractSingle‐layer ZnO–Al2O3 nanocomposite thin films with thickness approximately 119 nm, containing randomly dispersed nanocrystallites of ZnO in the Al2O3 matrix were prepared by sol gel technique. The relative molar concentration of ZnO was 20% in the matrix. The confined nanoparticles ZnO were investigated through ac impedance spectroscopy in the frequency range of 500 Hz to 5 MHz at 315 K, 325 K, 345 K, 355 K, 395 and 450 K. The dielectric relaxations in each case were found to be of Cole–Cole type. The thermally activated relaxation phenomenon was analysed with the help of an equivalent circuit which is proposed on the basis of the experimentally obtained complex capacitance and impedance spectral studies. The temperature dependent electrical conductivity was analysed on the basis of interstitial Zn ions and free electrons in the system. The defect concentration of the nanocomposite thin film was determined from the complex capacitance measurements. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interaction between edge dislocations and a circular hole with surface stress
Authors: Fang Q. H. , Li B. , Liu Y. W. 
Published: March 2007

AbstractThe problem of the interaction between several parallel edge dislocations and a circular nanosized hole with surface stress is investigated. The explicit solutions of stress fields and image forces exerted on edge dislocations are obtained by the use of the complex variable method. The influence of surface properties and the size of the hole on the glide/climb force is discussed. The results show that different surface properties may cause the glide/climb force to either increase or decrease, which implies that there exists a local softening or hardening at the surface of the hole for considering the surface effects. The effect of a nanosized hole and its surface properties on the image forces between two dislocations is also significant. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Field effect of carbon nanotubes with an ionomeric polymer
Authors: Levitsky Igor A. , Kolobov Igor G. , Euler William B. 
Published: March 2007

AbstractFlexible field effect transistors based on a single walled carbon nanotube (SWNT) network and an ionomeric polymer (nafion) were obtained by spraying nanotubes onto the polymer film. The threshold gate voltage was extremely low, ∼1 V, which was surprising since the nafion layer was so thick, ∼180 μm. This was attributed to the electrolytic nature of nafion, which results in the existence of a screening layer at the polymer‐nanotube interface. FET hysteresis can be rationalized in terms of charge redistribution induced by mobile protons inside nafion clusters in proximity to the nanotube surface. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Homoepitaxy of ZnO: from the substrates to doping
Authors: Neumann C. , Lautenschläger S. , Graubner S. , Sann J. , Volbers N. , Meyer B. K. , Bläsing J. , Krost A. , Bertram F. , Christen J. 
Published: March 2007

AbstractWe report on the homoepitaxial growth of ZnO thin films by chemical vapor deposition techniques. The preparation of the ZnO substrates after mechanical polishing employed a high temperature annealing step which produced atomically flat surfaces and removed all of the surface and subsurface damage. Two dimensional epitaxial growth was achieved without an additional buffer layer. The substrate had a rocking curve with a full width at half maximum of 27″ which can be compared with that of the film of 17″. The films had superior band edge luminescence as compared with the substrate for which the green luminescence band is dominating. The impurity content in the substrates especially Li is reduced by the high temperature annealing step and drops further close to the detection limit in the films. The low substrate temperatures around 660 °C allow for the incorporation of nitrogen on oxygen site as a shallow acceptor. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Non‐uniformity effects in CdZnTe coplanar‐grid detectors
Authors: Carini G. A. , Bolotnikov A. E. , Camarda G. C. , Wright G. W. , James R. B. 
Published: March 2007

AbstractWe discuss the findings from our studies of the performance of commercial coplanar‐grid CdZnTe detectors. The devices were investigated using a highly collimated X‐ray beam available at Brookhaven's National Synchrotron Light Source, and by applying pulse‐shape analysis to measure correlations between the signals read out from the devices. Although the operational principle of coplanar‐grid (CPG) detectors is well known, we found some important new details that help to better clarify the performance limitations of this type of device. The correlation plots we present can also be used as diagnostic tools to characterize the behavior of the CPG devices and to help to improve the designs of electrodes. This work illustrates the typical limitations related to the geometry of the contacts in CPG devices and how material non‐uniformities can amplify these problems. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Metal‐organic vapor phase epitaxy growth and crystallographic study of vanadium‐doped ZnSe
Authors: Tahashi Masahiro , Goto Hideo , Ido Toshiyuki 
Published: March 2007

AbstractAs a new diluted magnetic semiconductor, vanadium‐doped ZnSe is theoretically predicted to induce ferromagnetism above room temperature without carrier doping. Vanadium‐doped ZnSe was epitaxially grown on (100) GaAs substrate by metal‐organic vapor phase epitaxial method in an atmospheric pressure. The local structural of vanadium‐doped ZnSe crystal showed vanadium atoms in ZnSe crystal were substituted by the Se‐site and/or exist in interstitial sites so that ferromagnetism could not found in spite of vanadium doping. The influences of mol supply ratio of dimethyl Se to dimethyl Zn on crystallinity and growth rate were investigated in order to research the optimum vanadium‐doping condition. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrical characterization of ZnO nanorods
Authors: Schlenker E. , Bakin A. , Postels B. , Mofor A. C. , Wehmann H.‐H. , Weimann T. , Hinze P. , Waag A. 
Published: March 2007

AbstractZinc oxide (ZnO) nanorods were grown by a wet chemical approach and by vapor phase transport. To explore the electrical properties of individual nanostructures current–voltage (I –V) characteristics were obtained by using an atomic force microscope (AFM) with a conductive tip or by detaching the nanorods from the growth substrate, transferring them to an isolating substrate and contacting them with evaporated Ti/Au electrodes patterned by electron‐beam lithography. The AFM‐approach only yields a Schottky diode behavior, while the Ti/Au forms ohmic contacts to the ZnO. For the latter method the obtained I –V curves reveal a resistivity of the nanorods in the order of 10–5 Ω cm which is unusually low for undoped ZnO. We therefore assume the existence of a highly conductive surface channel. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effects of growth temperature and oxygen pressure on the properties of heteroepitaxial ZnO thin films on sapphire (0001) substrates by pulsed laser deposition
Authors: Liu Chunli , Chang S. H. , Noh T. W. , Song J.‐H. , Xie J. 
Published: March 2007

AbstractWe report a systematic study on the effect of growth temperature and O2 pressure on the structural, optical, and electrical properties of heteroepitaxial ZnO thin films prepared by pulsed laser deposition on sapphire (0001) substrates. The combination of high growth temperature and low O2 pressure was found to improve the crystalline quality of initial heteroepitaxial ZnO films, which can be attributed to the enhanced surface migration of adatoms and thermal energy. The low‐temperature photoluminescence spectra from ZnO films were dominated by donor‐bound exciton emission with very weak deep level emission. The temperature dependent Hall measurement showed that the films are highly degenerated, mainly due to the high defect density near the interface region. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Strong anharmonicity and phonon confinement on the lowest‐frequency Raman mode of nanocrystalline anatase TiO2
Authors: Gao Kun 
Published: March 2007

AbstractWe calculated and analyzed the effects of temperature and crystallite size on the Raman properties of nanocrystalline anatase TiO2 by using the related models mentioned previously [Tang and Herman, Phys. Rev. B 43, 2299 (1991); Richter et al., Solid State Commun. 39, 625 (1981)]. The temperature dependence of the Raman spectra of two different crystallite sizes of anatase TiO2 were obtained. Careful measurements of the frequency shifts of Raman modes were carried out at different temperatures. Through fitting the experimental data, pure‐volume and the pure‐temperature contributions to the frequency shifts of the lowest‐ and highest‐frequency Eg modes, respectively, have been calculated. The results indicated that strongly intrinsic anharmonicity arising from optical‐phonon couplings was the origin of hardening upon increasing temperature for the lowest‐frequency Raman mode. The phonon‐confinement effect on this mode was analyzed and anharmonic shifts of optical phonons with two different kinds of crystallite sizes were also compared. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Weibull prediction of event times in clinical trials
Authors: Ying Gui‐shuang , Heitjan Daniel F. 
Published: March 2007

AbstractIn clinical trials with interim analyses planned at pre‐specified event counts, one may wish to predict the times of these landmark events as a tool for logistical planning. Currently available methods use either a parametric approach based on an exponential model for survival (Bagiella and Heitjan, Statistics in Medicine 2001; 20:2055) or a non‐parametric approach based on the Kaplan–Meier estimate (Ying et al., Clinical Trials 2004; 1:352). Ying et al. (2004) demonstrated the trade‐off between bias and variance in these models; the exponential method is highly efficient when its assumptions hold but potentially biased when they do not, whereas the non‐parametric method has minimal bias and is well calibrated under a range of survival models but typically gives wider prediction intervals and may fail to produce useful predictions early in the trial. As a potential compromise, we propose here to make predictions under a Weibull survival model. Computations are somewhat more difficult than with the simpler exponential model, but Monte Carlo studies show that predictions are robust under a broader range of assumptions. We demonstrate the method using data from a trial of immunotherapy for chronic granulomatous disease. Copyright © 2007 John Wiley & Sons, Ltd.