bluuebunny/crossref_metadata_2025_split huggingface dataset:
Treatment of disseminated paraganglioma with gemcitabine and docetaxel
Authors: Mora Jaume , Cruz Ofelia , Parareda Andreu , Sola Teresa , de Torres Carmen 
Published: April 2009

AbstractA male with metastatic paraganglioma received different chemotherapy regimens and 14 arterial embolizations with no or short‐lasting clinical benefit. He was started on gemcitabine and docetaxel and, after two cycles, remission of all clinical signs occurred over 2 months. A complete biochemical response was achieved and angiographic signs of portal hypertension disappeared. He received 18 cycles of therapy and no limiting side effects were observed. More than 2 years after gemcitabine and docetaxel treatment, the patient remains symptom free. Gemcitabine and docetaxel could be a potential therapeutic strategy for this patient. Pediatr Blood Cancer 2009;53:663–665. © 2009 Wiley‐Liss, Inc.
Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non‐pathogenic Pseudomonas species
Authors: Ravichandran Ayshwarya , Sugiyama Naoyuki , Tomita Masaru , Swarup Sanjay , Ishihama Yasushi 
Published: April 2009

AbstractProtein phosphorylation on serine, threonine, and tyrosine is well established as a crucial regulatory posttranslational modification in eukaryotes. With the recent whole‐genome sequencing projects reporting the presence of serine/threonine kinases and two‐component proteins both in prokaryotes and eukaryotes, the importance of protein phosphorylation in archaea and bacteria is gaining acceptance. While conventional biochemical methods failed to obtain a snapshot of the bacterial phosphoproteomes, advances in MS methods have paved the way for in‐depth mapping of phosphorylation sites. Here, we present phosphoproteomes of two ecologically diverse non‐enteric Gram‐negative bacteria captured by a nanoLC‐MS‐based approach combined with a novel phosphoenrichment method. While the phosphoproteome data from the two species are not very similar, the results reflect high similarity to the previously published dataset in terms of the pathways the phosphoproteins belong to. This study additionally provides evidence to prior observations that protein phosphorylation is common in bacteria. Notably, phosphoproteins identified in Pseudomonas aeruginosa belong to motility, transport, and pathogenicity pathways that are critical for survival and virulence. We report, for the first time, that motility regulator A, probably acting via the novel secondary messenger cyclic diguanylate monophosphate, significantly affects protein phosphorylation in Pseudomonas putida.
A chimeric mechanism for polyvalent trans‐phosphorylation of PKA by PDK1
Authors: Romano Robert A. , Kannan Natarajan , Kornev Alexandr P. , Allison Craig J. , Taylor Susan S. 
Published: April 2009

AbstractPhosphorylation on the activation loop of AGC kinases is typically mediated by PDK1. The precise mechanism for this in‐trans phosphorylation is unknown; however, docking of a hydrophobic (HF) motif in the C‐tail of the substrate kinase onto the N‐lobe of PDK1 is likely an essential step. Using a peptide array of PKA to identify other PDK1‐interacting sites, we discovered a second AGC‐conserved motif in the C‐tail that interacts with PDK1. Since this motif [FD(X)1‐2Y/F] lies in the active site tether region and in PKA contributes to ATP binding, we call it the Adenosine binding (Ade) motif. The Ade motif is conserved as a PDK1‐interacting site in Akt and PRK2, and we predict it will be a PDK1‐interacting site for most AGC kinases. In PKA, the HF motif is only recognized when the turn motif Ser338 is phosphorylated, possibly serving as a phosphorylation “switch” that regulates how the Ade and HF motifs interact with PDK1. These results demonstrate that the extended AGC C‐tail serves as a polyvalent element that trans‐regulates PDK1 for catalysis. Modeling of the PKA C‐tail onto PDK1 structure creates two chimeric sites; the ATP binding pocket, which is completed by the Ade motif, and the C‐helix, which is positioned by the HF motif. Together, they demonstrate substrate‐assisted catalysis involving two kinases that have co‐evolved as symbiotic partners. The highly regulated turn motifs are the most variable part of the AGC C‐tail. Elucidating the highly regulated cis and trans functions of the AGC tail is a significant future challenge.
Impact of missing data on type 1 error rates in non‐inferiority trials
Authors: Yoo Bongin 
Published: April 2009

AbstractIn this paper, a simulation study is conducted to systematically investigate the impact of different types of missing data on six different statistical analyses: four different likelihood‐based linear mixed effects models and analysis of covariance (ANCOVA) using two different data sets, in non‐inferiority trial settings for the analysis of longitudinal continuous data. ANCOVA is valid when the missing data are completely at random. Likelihood‐based linear mixed effects model approaches are valid when the missing data are at random. Pattern‐mixture model (PMM) was developed to incorporate non‐random missing mechanism. Our simulations suggest that two linear mixed effects models using unstructured covariance matrix for within‐subject correlation with no random effects or first‐order autoregressive covariance matrix for within‐subject correlation with random coefficient effects provide well control of type 1 error (T1E) rate when the missing data are completely at random or at random. ANCOVA using last observation carried forward imputed data set is the worst method in terms of bias and T1E rate. PMM does not show much improvement on controlling T1E rate compared with other linear mixed effects models when the missing data are not at random but is markedly inferior when the missing data are at random. Copyright © 2009 John Wiley & Sons, Ltd.
Requirements for packaging from an ageing consumer's perspective
Authors: Duizer L. M. , Robertson T. , Han J. 
Published: April 2009

AbstractThe overall objective of this research was to explore ageing consumers' attitudes towards currently available food packaging in New Zealand. Ninety‐nine individuals (over the age of 60) in New Zealand were surveyed to determine packaging attributes of importance when selecting food products. This was followed with a focus group of 13 individuals to discuss improvements to packaging. Frequencies of responses were calculated for the survey data, and cross‐tabulations and chi‐square tests were used to determine the relationships between variables. Price, safety, size of packaging and ability to recycle were of most importance to these individuals. Problems encountered with food packaging included tight lids, small printing and spillage during opening. Of the types of package closures investigated, opening of packages, rather than resealing of packages proved problematic. Fifty percent or more of respondents indicated that peelable induction seals, lug closures and continuous thread closures were problems that occurred ‘very often’ or ‘frequently’. Sixty‐one percent of the participants surveyed had asked for assistance opening some types of packages, and this was particularly prevalent among individuals who had weakness in their arms, hands or wrists. Changes to package closures suggested during the focus groups included increasing the size of twist off caps, larger ring pulls on aluminium cans and including more sliding resealable closures on foil and plastic packaging. Larger printing on labels was also recommended by the participants. Copyright © 2008 John Wiley & Sons, Ltd.This article was published online on 1st December 2008. An error was subsequently identified. This notice is included in the online and print versions to indicate that both were corrected on 19th March 2009.
Beyond QSAR: Lead Hopping to Different Structures
Authors: Martin Yvonne C. , Muchmore Steven 
Published: April 2009

AbstractWe investigated the ability of several computer programs to detect lead hops that had been reported to result from pharmacophore searching. None of the methods identified all of these lead hops and some were not found by any program. The methods that performed the best identified different lead hops. Hence, we have deployed a lead hopping application that uses belief theory to combine the results of ROCS, Daylight, and ECFP_6 similarities.
Calculations of D‐wave bound states and resonance states of the screened helium atom using correlated exponential wave functions
Authors: Kar Sabyasachi , Ho Y. K. 
Published: April 2009

AbstractWe have investigated the effects of screened Coulomb (Yukawa) potentials on the bound 1,3D states and the doubly excited 1,3 De resonance states of helium atom using highly correlated exponential basis functions. The Density of resonance states are calculated using stabilization method. Highly correlated exponential basis functions are used to consider the correlation effect between the charged particles. A total of 18 resonances (nine each for 1 De and 3 De states) below the n = 2 He + threshold has been calculated. For each spin states, this includes four members in the 2pnp series, three members in the 2snd series, and two members in 2pnf series. The resonance energies and widths for various screening parameters ranging from infinity to a small value for these 1,3 De resonance states are reported along with the bound‐excited 1s3d 1,3 D state energies. Overall behavior of the spectral profile of 1s3d 1D state of helium atom due to electron‐electron and electron‐nucleus screening are also presented. Accurate resonance energies and widths are also reported for He in vacuum. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
My association with Frank Harris: An arc of forty‐four years
Authors: Monkhorst Hendrik J. 
Published: April 2009

AbstractMy collaborations with Frank Harris are reviewed. Besides reminiscing commentary on our long association, I explain the essentials of a recent proposal by Frank and me for a correlated basis set to implement the Molecular Coupled Cluster method I published in 1987. Its use will require the accurate evaluation of integrals over fully correlated Gaussian‐type n body functions. This has been achieved for arbitrary n in a pair of publications. A third paper by Frank shows the way to include angular factors. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
General two‐electron exponential type orbital integrals in polyatomics without orbital translations
Authors: Hoggan Philip E. 
Published: April 2009

AbstractThis article advocates the use of atomic orbitals which have direct physical interpretation, i.e., hydrogen‐like orbitals. They are exponential type orbitals (ETOs). Convenient nodeless linear combinations are used, namely Slater type orbitals (STOs) (with a product of a single power of r and an exponential as radial factor). Until 2008, such orbital products on different atoms were difficult to manipulate for the evaluation of two‐electron integrals. The difficulty was mostly due to cumbersome orbital translations involving slowly convergent infinite sums. These are completely eliminated using Coulomb resolutions. They provide an excellent approximation that reduces these integrals to a sum of one‐electron overlap‐like integral products that each involve orbitals on at most two centers. Such two‐center integrals are separable in prolate spheroidal coordinates. They are thus readily evaluated. Only these integrals need to be re‐evaluated to change basis functions. The above is still valid or three‐center integrals. In four‐center integrals, the resolutions require translating one potential term per product. This is outlined here and detailed elsewhere. Numerical results are reported for the H2 dimer and CH3F molecule. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Bonding in titanocenyl complexes containing O,O′‐cyclic ligands
Authors: Conradie Jeanet 
Published: April 2009

AbstractDensity functional theory calculations show that the formal 16‐electron count of d0 [Cp2TiIV(O,O′‐BID)]0/1 complexes containing a O,O′‐chelated bidentate ligand O,O′‐BID of different ring size, is increased via Ti←O π bonding when both the O donor atoms carry a formal negative charge. The Ti←O π bonding occurs by symmetry lowering of the complex by either symmetrical (Cs) or unsymmetrical (C2) folding of the O,O′‐BID ligand round the O···O axis. An NBO analysis confirms the Ti←O π charge transfer via back‐bonding. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Stueckelberg oscillations in the charge transfer into the n = 2 and n = 3 shells of He2 on collision with H
Authors: Stolterfoht N. , Cabrera‐Trujillo R. , Krstić P. S. , Öhrn Y. , Deumens E. , Sabin J. R. 
Published: April 2009

AbstractProbabilities for charge transfer by He2+ impact on atomic H are calculated at low‐collision energies using an ab initio theory, which solves the time‐dependent Schrödinger equation. The charge transfer is interpreted in terms of radial and rotational couplings of molecular orbitals. Strong Stueckelberg oscillations for the charge transfer probability into the n = 2 shell of helium are observed over nearly the entire impact parameter range. The same oscillations are found for the charge transfer into the n = 3 shell in the impact parameter range from 2.5 a.u. upwards, whereas at impact parameters below 2.5 a.u. the oscillations disappear abruptly. This observation is associated with specific pathways along the potential curves, which are responsible for the charge transfer. Similarities with the interferences in Young's two‐slit experiment are pointed out. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
The highly unsaturated dimetal hexacarbonyls of manganese and rhenium: Alternatives to a formal metal–metal quintuple bond
Authors: Xu Bing , Li Qian‐Shu , Xie Yaoming , King R. Bruce , Schaefer Henry F. 
Published: April 2009

AbstractThe structures of M2(CO)6 (M = Mn, Re) are of interest since a formal metal–metal quintuple bond is required to give each metal atom the favored 18‐electron configuration, assuming that all six carbonyl groups are the usual two‐electron donors. However, density functional theory studies on these systems provide no evidence for such structures having the very short metal–metal distances required for formal metal–metal quintuple bonds. Instead, the lowest energy structures predicted for Mn2(CO)6 have geometries consistent with a formal MnMn triple bond and two four‐electron donor bridging carbonyl groups, which also lead to the favored 18‐electron configuration for each manganese atom. For Mn2(CO)6, there is a higher‐lying structure (6–9 kcal/mol above the global minimum) with a MnMn quadruple bond distance of ∼2.18 Å. Four‐electron donor bridging carbonyl groups appear to be less favorable in the low‐energy Re2(CO)6 structures. Thus, the lowest energy Re2(CO)6 structure by ∼12 kcal/mol has all terminal carbonyl groups and a ReRe distance of 2.55 Å thereby suggesting a formal triple bond and a 16‐electron configuration for both rhenium atoms. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Spectrum‐like graphical representation of RNA secondary structure
Authors: Randić Milan , Vračko Marjan , Novič Marjana , Plavšić Dejan 
Published: April 2009

AbstractWe consider graphical representation for RNA secondary structure by assigning four horizontal lines to the unpaired bases A, C, G, U and four horizontal lines to paired bases A′, C′, G′, U′. The RNA graphical representation based on eight equidistant horizontal lines can be viewed as natural extension of the earlier four‐line graphical representation of DNA (Randić et al., Chem Phys Lett, 2003, 371, 202) to RNA. Numerical characterization of RNA is based on 8 × 8 matrices recording the adjacency of the nucleotide bases in the primary sequence of RNA when RNA is read from 5′ to 3′. The approach is illustrated on a set of nine viral RNAs, reported in the literature. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
On the Brillouin‐zone integrations in second‐order many‐body perturbation calculations for extended systems of one‐dimensional periodicity
Authors: Shimazaki Tomomi , Hirata So 
Published: April 2009

AbstractThe validity and accuracy of various ways of drastically reducing the number of k‐points in the Brillouin zone integrations occurring in second‐order many‐body perturbation calculations of one‐dimensional solids has been investigated. The most promising approximation can recover correlation energies of polyethylene and polyacetylene within 1% of converged values at less than a tenth of usual computational cost. The quasi‐particle energy bands have also been reproduced quantitatively with the same approximation. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Polarizabilities and second hyperpolarizabilities of hydrogen chains using the spin‐component‐scaled Møller–Plesset second‐order method
Authors: Champagne Benoît , Kirtman Bernard 
Published: April 2009

AbstractStatic longitudinal polarizabilities (α) and second hyperpolarizabilities (γ) of model H2 chains have been calculated at different ab initio levels to address the performance of the recently proposed spin‐component‐scaled MP2 (SCS‐MP2) method (Grimme, J. Chem Phys 2003, 118, 9095). For both α and γ, the SCS‐MP2 method improves over the MP2 results in comparison with reference values evaluated at the CCSD(T) level. Differences from the reference are in the range of 4–6% for α and 1–4% for γ. In the case of γ, the SCS‐MP2 scheme improves not only over MP2 but also MP4 and CCSD. Further studies are needed on π‐conjugated systems to evaluate the generality of these results. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Dynamics for the dynamic Frank Harris: Exploring H+ + CF4 at Elab = 20 and 30 eV
Authors: Maiti Buddhadev , McLaurin Patrick M. , Sadeghi Raymond , Ajith Perera S. , Morales Jorge A. 
Published: April 2009

AbstractThe H+ + CF4 reaction at collision energies ELab = 20 and 30 eV is investigated with the electron nuclear dynamics (END) theory. The level of END herein employed prescribes a classical‐mechanics description for the nuclei and a single‐determinantal representation for the electrons. The results include visualizations of the simulated collisions, and calculations of various scattering properties. The present simulations always predict noncharge‐transfer scattering (NCTS) for H+ + CF4 and exclude charge‐transfer, dissociation, and rearrangement reactions. The predicted rainbow angles and the total NCTS differential cross sections agree satisfactorily with the available experimental results. The present results are compared with those of the previously simulated H+ + CH4. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
An SO(4) invariant Hamiltonian and the two‐body bound state. I: Coulomb interaction between two spinless particles
Authors: Huntington Lee M. J. , Nooijen Marcel 
Published: April 2009

AbstractWe consider the nonrelativistic treatment of a hydrogenic atom in a four‐dimensional Euclidean space. The focus of this work is on the angular part of the problem, as this is potentially more generally applicable. Using a suitable coordinate system, the su(2)×su(2) structure of the so(4) Lie algebra is exploited. The hyperspherical harmonic solutions of the angular part of the problem are obtained in two ways: as solutions of a partial differential equation and by means of a ladder operator approach. The solutions of the radial equation and energy spectrum are determined and possible implications of the model are briefly discussed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Chemical reactions in the gas phase and in condensed matter: From wavefunctions to density operators
Authors: Micha David A. 
Published: April 2009

AbstractThis contribution generalizes the treatment of chemical reactions in the gas phase based on the reaction channel decomposition of the wavefunction, by introducing a similar channel decomposition of the statistical density operator valid also for condensed phases such as liquid solutions and solid surfaces. Coupled equations for the channel components of the density operator are derived and a brief presentation is given of their partial Wigner transform, which leads to a general treatment for coupling quantum and classical variables. This provides a general approach for reactions involving electronically excited states in many‐atom systems. It is pointed out that reactions involving coupled quantal and classical variables can be correctly described provided (a) initial conditions for trajectories are generated from quantal distributions and (b) the bundle of trajectories for the whole initial classical phase space is propagated coupled to the quantal elements of the density matrix and used in the calculation of reaction flux averages. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Infinite‐order functional for nonlinear parameters optimization in explicitly correlated coupled cluster theory
Authors: Przybytek Michal , Jeziorski Bogumil , Szalewicz Krzysztof 
Published: April 2009

AbstractCoupled cluster (CC) calculations with Gaussian geminals rely heavily on extensive optimizations of nonlinear parameters (exponents and positions) defining the geminal basis functions. As the CC method is not a variational theory, it provides no functional for such an optimization. The nonlinear parameters must therefore be supplied by some other theory, giving pair functions that can be expected to be close to those of the CC method. The conventional approach thus far was to use the second‐order many‐body perturbation theory with Møller–Plesset partition of the Hamiltonian (MP2) for this purpose and to minimize the corresponding Hylleraas‐type functional. We present a new functional, which goes beyond the second order, and can be applied in situations when the Møller–Plesset theory converges slowly. This functional does take a partial account of infinite‐order terms in the MP theory, but neglects the interpair coupling in the spirit of the independent electron pair approximation approach. The pair functions minimizing this new functional include the most important infinite‐order contributions from the point of view of the MP theory and are much closer to the CC pair functions than the first‐order ones. The nonlinear parameters obtained using this infinite‐order functional are then better suited for coupled cluster calculations than those obtained using the MP2 functional. The effectiveness of the new functional is demonstrated by performing coupled cluster doubles (CCD) calculations for the Be atom and Li− ion. The obtained energies are much better than those based on the MP2 optimizations and represent the most accurate CCD energies for these systems obtained thus far. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
An accurate few‐parameter ground state wave function for the lithium atom
Authors: Guevara Nicolais L. , Harris Frank E. , Turbiner Alexander V. 
Published: April 2009

AbstractA simple, seven‐parameter trial function is proposed for a description of the ground state of the Lithium atom. It includes both spin functions. Inter‐electronic distances appear in exponential form as well as in a pre‐exponential factor, and the necessary energy matrix elements are evaluated by numerical integration in the space of the relative coordinates. Encouragingly accurate values of the energy and the cusp parameters as well as for some expectation values are obtained. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Quantum potential for diffraction and exchange effects
Authors: Dufty James , Dutta Sandipan , Bonitz Michael , Filinov Alexei 
Published: April 2009

AbstractSemiclassical methods of statistical mechanics can incorporate essential quantum effects by using effective quantum potentials. An ideal Fermi gas interacting with an impurity is represented by a classical fluid with effective electron–electron and electron‐impurity quantum potentials. The electron‐impurity quantum potential is evaluated at weak coupling, leading to a generalization of the Kelbg potential to include both diffraction and degeneracy effects. The electron–electron quantum potential for exchange effects only is the same as that discussed earlier by others. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009