bluuebunny/crossref_metadata_2025_split huggingface dataset:
You save money when you buy in bulk: does volume‐based pricing cause people to buy more beer?
Authors: Bray Jeremy W. , Loomis Brett R. , Engelen Mark 
Published: April 2009

AbstractThis paper uses supermarket scanner data to estimate brand‐ and packaging‐specific own‐ and cross‐price elasticities for beer. We find that brand‐ and packaging‐specific beer sales are highly price elastic. Cross‐price elasticity estimates suggest that individuals are more likely to buy a higher‐volume package of the same brand of beer than they are to switch brands. Policy simulations suggest that regulation of volume‐based price discounts is potentially more effective than a tax increase at reducing beer consumption. Our results suggest that volume‐based price discounting induces people to buy larger‐volume packages of beer and may lead to an increased overall beer consumption. Copyright © 2008 John Wiley & Sons, Ltd.
Contribution of genetic polymorphisms of stromal cell–derived factor‐1 and its receptor, CXCR4, to the susceptibility and clinicopathologic development of oral cancer
Authors: Teng Ying‐Hock , Liu Te‐Hsiung , Tseng Hsien‐Chun , Chung Tsung‐Te , Yeh Chia‐Ming , Li Yu‐Chiung , Ou Yu‐Hsiang , Lin Long‐Yau , Tsai Hsiu‐Ting , Yang Shun‐Fa 
Published: April 2009

AbstractBackground.The aim of this study was to evaluate the relations of SDF‐1 and its receptor, CXCR4, gene variants on oral cancer risk.Methods.PCR‐RFLP was used to measure SDF‐1‐3′A and CXCR4 gene polymorphisms in 284 controls and 113 patients with oral cancer.Results.After being adjusted for age, individuals with A/G heterozygotes of SDF‐1 had a higher risk of 1.86‐fold to develop oral cancer when compared with those with G/G wild type homozygotes. Furthermore, patients with oral cancer with at least 1 mutant T allele of CXCR4 gene had a risk of 2.66‐fold to progress to stage III or IV.Conclusions.SDF‐1‐3′A gene polymorphism may be considered as a factor of increased susceptibility to oral cancer, and at least 1 mutated T allele of CXCR4 gene is associated with the development of stage III or IV and the induction of lymph‐node metastasis of oral cancer disease in Taiwanese. © 2009 Wiley Periodicals, Inc. Head Neck, 2009
Increased APN/CD13 and acid aminopeptidase activities in head and neck squamous cell carcinoma
Authors: Pérez Itxaro , Varona Adolfo , Blanco Lorena , Gil Javier , Santaolalla Francisco , Zabala Aitor , Ibarguen Agustin Martínez , Irazusta Jon , Larrinaga Gorka 
Published: April 2009

AbstractBackground.Involvement of peptidases in carcinogenic processes of several tumor types has been investigated in recent years. Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers worldwide and accounts for more than 90% of all head and neck cancers. Increased understanding of its pathophysiology has led to implication of several proteinases, specially matrix metalloproteinases, in its genesis, growth, and dissemination. However, very little is known about involvement of peptidases in this neoplasm.Methods.Seventeen HNSCC tissue samples were selected for the study. Tumor and normal tissue samples were frozen for enzymatic study. The catalytic activity for a pool of peptidases (PSA, APN/CD13, APB, APA, Asp‐AP, CAP, DPPIV/CD26, NEP/CD10, and PGI) was measured fluorometrically.Results.The activity of 2 cell surface aminopeptidases (APN/CD13 and APA) and a cytosolic aminopeptidase (Asp‐AP) was significantly increased in HNSCC tissues.Conclusions.These data show the involvement of cell surface and cytosolic peptidases in the mechanisms underlying HNSCC. © 2009 Wiley Periodicals, Inc. Head Neck, 2009
Impact of reconstructive microsurgery in patients with advanced oral cavity cancers
Authors: Hanasono Matthew M. , Friel Michael T. , Klem Christopher , Hsu Patrick W. , Robb Geoffrey L. , Weber Randal S. , Roberts Dianna B. , Chang David W. 
Published: April 2009

AbstractBackground.Our goal was to determine the impact of reconstructive microsurgery on the treatment of advanced oral cavity cancers.Methods.We reviewed 484 patients undergoing resection of T3‐4 oral cavity squamous cell cancers from 1980 to 2004. To examine how reconstructive microsurgery affects outcomes, we compared 135 patients treated prior to the introduction of free tissue transfer and 349 patients treated after the introduction of free tissue transfer.Results.Cancers treated after the introduction of free flaps included a significantly higher proportion of T4 compared to T3 lesions and significantly more advanced N classification lesions. Although cancers were more advanced, survival and recurrence rates were maintained and the rate of positive pathologic margins decreased significantly. In addition, fistula and tracheostomy dependence rates decreased and rates of intelligible speech increased.Conclusion.Reconstructive microsurgery contributes to improved oncologic outcomes in addition to better function and lower morbidity in oral cavity cancer treatment. © 2009 Wiley Periodicals, Inc. Head Neck, 2009
Attention as a cueing function during kindergarten children's dimensional change task performance
Authors: Coldren Jeffrey T. , Colombo John 
Published: April 2009

AbstractThe purpose of this experiment is to test whether shift flexibility in kindergarten children is a joint function of rule‐usage and inhibition of attention. Sixty‐six children were given either a distraction or facilitation condition in a computerized version of the dimensional change card sort task. In the distraction condition, the background of the post‐shift matching stimulus was inconsistent with the relevant matching dimension. In the facilitation condition, the background of the post‐shift matching stimulus was consistent with the relevant matching dimension. Results revealed that children made few errors in the standard version of the shift task, thereby supporting Cognitive complexity and control theory's contention that 5‐year‐old children shift easily across dimensions due to their use of higher‐order setting rules to solve contradictions. The proportion of errors increased however in the distraction condition suggesting that attention to the background interfered with children's ability to shift between dimensions. Therefore, these data provide evidence that refocusing attention to dimensions along with rule‐use processes affect shift flexibility and argue for the inclusion of both factors into theoretical accounts of shift performance. Copyright © 2009 John Wiley & Sons, Ltd.
MILCH SHAKE: An efficient method for constraint dynamics applied to alkanes
Authors: Bailey A. G. , Lowe C. P. 
Published: April 2009

AbstractWe describe a method to impose constraints in a molecular dynamics simulation. A technique developed to solve the special case of a linear topology (MILC SHAKE) is hybridized with the SHAKE algorithm. The methodology, which we term MILC‐hybridized SHAKE (or MILCH SHAKE), applies to more complex topologies. Here we consider the important case of all atom models of alkanes. Exploiting the mass difference between carbon and hydrogen we show that for higher alkanes MILCH SHAKE can be an order of magnitude faster than SHAKE. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
Incorporating support vector machine for identifying protein tyrosine sulfation sites
Authors: Chang Wen‐Chi , Lee Tzong‐Yi , Shien Dray‐Ming , Hsu Justin Bo‐Kai , Horng Jorng‐Tzong , Hsu Po‐Chiang , Wang Ting‐Yuan , Huang Hsien‐Da , Pan Rong‐Long 
Published: April 2009

AbstractTyrosine sulfation is a post‐translational modification of many secreted and membrane‐bound proteins. It governs protein‐protein interactions that are involved in leukocyte adhesion, hemostasis, and chemokine signaling. However, the intrinsic feature of sulfated protein remains elusive and remains to be delineated. This investigation presents SulfoSite, which is a computational method based on a support vector machine (SVM) for predicting protein sulfotyrosine sites. The approach was developed to consider structural information such as concerning the secondary structure and solvent accessibility of amino acids that surround the sulfotyrosine sites. One hundred sixty‐two experimentally verified tyrosine sulfation sites were identified using UniProtKB/SwissProt release 53.0. The results of a five‐fold cross‐validation evaluation suggest that the accessibility of the solvent around the sulfotyrosine sites contributes substantially to predictive accuracy. The SVM classifier can achieve an accuracy of 94.2% in five‐fold cross validation when sequence positional weighted matrix (PWM) is coupled with values of the accessible surface area (ASA). The proposed method significantly outperforms previous methods for accurately predicting the location of tyrosine sulfation sites. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
Characterization of two types of intermolecular interactions on halogen monoxide monohydrates
Authors: Gálvez Oscar , Gómez Pedro C. , Pacios Luis F. 
Published: April 2009

AbstractMonohydrates of halogen monoxides ClO·H2O and BrO·H2O have been studied by means of DFT (B3LYP) andab initio(MP2) correlated calculations with aug‐cc‐pVnZ basis sets ranging from triple‐ up to quintuple‐ζ. These complexes might be formed in the troposphere and stratosphere and participate in chemical reactions involved in ozone depletion. Two stable structures are found that differ in the intermolecular interaction which takes place, namely: conventional XO…HOH hydrogen bond and OX…OH2halogen bond. We demonstrate that both types of interactions participate in the formation of these complexes yet all the computational methods tested predict a slightly greater stability for the latter OX…O link. Both intermolecular interactions are characterized upon analyzing electron density distribution, charge transfer effects, and electron localization domains. These analyses reveal the central role played by electron redistribution. Because of this, the greater spatial extent of the electron density in Cl or Br as compared to H could be the main cause to yield a slightly greater stability for the OX…O halogen bond with respect to the O…HO hydrogen bond. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
Relativistic and electron‐correlation effects on magnetizabilities investigated by the Douglas‐Kroll‐Hess method and the second‐order Møller‐Plesset perturbation theory
Authors: Yoshizawa Terutaka , Hada Masahiko 
Published: April 2009

AbstractIsotropic and anisotropic magnetizabilities for noble gas atoms and a series of singlet and triplet molecules were calculated using the second‐order Douglas‐Kroll‐Hess (DKH2) Hamiltonian containing the vector potential A and in part using second‐order generalized unrestricted Møller‐Plesset (GUMP2) theory. The DKH2 Hamiltonian was resolved into three parts (spin‐free terms, spin‐dependent terms, and magnetic perturbation terms), and the magnetizabilities were decomposed into diamagnetic and paramagnetic terms to investigate the relativistic and electron‐correlation effects in detail. For Ne, Kr, and Xe, the calculated magnetizabilities approached the experimental values, once relativistic and electron‐correlation effects were included. For the IF molecule, the magnetizability was strongly affected by the spin‐orbit interaction, and the total relativistic contribution amounted to 22%. For group 17, 16, 15, and 14 hydrides, the calculated relativistic effects were small (less than 3%), and trends were observed in relativistic and electron‐correlation effects across groups and periods. The magnetizability anisotropies of triplet molecules were generally larger than those of similar singlet molecules. The so‐called relativistic‐correlation interference for the magnetizabilities computed using the relativistic GUMP2 method can be neglected for the molecules evaluated, with exception of triplet SbH. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
Modified regional self‐interaction corrected time‐dependent density functional theory for core excited‐state calculations
Authors: Nakata Ayako , Tsuneda Takao , Hirao Kimihiko 
Published: April 2009

AbstractA modified regional self‐interaction correction (mRSIC) method is proposed for obtaining accurate core‐excitation energies in time‐dependent density functional theory (TDDFT) calculations. The mRSIC method is an improvement of the RSIC method (Tsuneda et al. J Comput Chem 2003, 24, 1592). It takes into account the energy contributions from 2s and higher atomic orbitals that the RSIC method neglects. Furthermore, mRSIC improves the poor description for the nuclear‐electron cusp of Gaussian basis functions. The mRSIC method was combined with a long‐range correction (LC) scheme, which has been proved to give accurate valence‐, Rydberg‐, and charge transfer (CT)‐excitation energies. In so doing, it dramatically improved the accuracy of the calculated core‐excitation energies and did not affect the already accurate values of valence‐, Rydberg‐, and CT‐excitation energies produced by the LC functionals. These results mean that the combined scheme is accurate for all excitation energy forms. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009
An analytic potential energy function for the amide–amide and amide–water intermolecular hydrogen bonds in peptides
Authors: Sun Chang‐Liang , Jiang Xiao‐Nan , Wang Chang‐Sheng 
Published: April 2009

AbstractAn analytic potential energy function is proposed and applied to evaluate the amide–amide and amide–water hydrogen‐bonding interaction energies in peptides. The parameters in the analytic function are derived from fitting to the potential energy curves of 10 hydrogen‐bonded training dimers. The analytic potential energy function is then employed to calculate the NH…OC, CH…OC, NH…OH2, and CO…HOH hydrogen‐bonding interaction energies in amide–amide and amide–water dimers containing N‐methylacetamide, acetamide, glycine dipeptide, alanine dipeptide, N‐methylformamide, N‐methylpropanamide, N‐ethylacetamide and/or water molecules. The potential energy curves of these systems are therefore obtained, including the equilibrium hydrogen bond distances R(O…H) and the hydrogen‐bonding energies. The function is also applied to calculate the binding energies in models of β‐sheets. The calculation results show that the potential energy curves obtained from the analytic function are in good agreement with those obtained from MP2/6‐31+G** calculations by including the BSSE correction, which demonstrate that the analytic function proposed in this work can be used to predict the hydrogen‐bonding interaction energies in peptides quickly and accurately. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
The performance of computational techniques in locating the charge separated intermediates in organocatalytic transformations
Authors: Wei Yin , Sateesh Bandaru , Maryasin Boris , Sastry G. N. , Zipse Hendrik 
Published: April 2009

AbstractThe formation of zwitterionic adducts between neutral nucleophiles such as NMe3 and PMe3 with neutral electrophiles such as methyl vinyl ketone (MVK) has been studied with a wide variety of theoretical methods. It has been found that hybrid density functional methods such as B3LYP are not capable of describing these zwitterionic structures as minima on the potential energy surface. This is also true for combinations of MP2 theory with basis sets lacking diffuse basis functions. The mPW1K hybrid functional, in contrast, correctly describes zwitterionic adducts as true intermediates on the PES. On the basis of this insight, a new version of the G3 compound energy scheme has been developed for the accurate description of zwitterionic structures. It has also been verified that modifications of the B2‐PLYP double‐hybrid functional are equally capable of the proper description of zwitterionic adducts. The applicability of this latter class of methods to a larger dataset involving combinations of different nucleophiles and electrophiles has been documented. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
Roles of K151 and D180 in L‐2‐haloacid dehalogenase from Pseudomonas sp. YL: Analysis by molecular dynamics and ab initio fragment molecular orbital calculations
Authors: Nakamura Takashi , Yamaguchi Azusa , Kondo Hirotaka , Watanabe Hirofumi , Kurihara Tatsuo , Esaki Nobuyoshi , Hirono Shuichi , Tanaka Shigenori 
Published: April 2009

AbstractL‐2‐haloacid dehalogenase (L‐DEX) catalyzes the hydrolytic dehalogenation of L‐2‐haloalkanoic acids to produce the corresponding D‐2‐hydroxyalkanoic acids. This enzyme is expected to be applicable to the bioremediation of environments contaminated with halogenated organic compounds. We analyzed the reaction mechanism of L‐DEX from Pseudomonas sp. YL (L‐DEX YL) by using molecular modeling. The complexes of wild‐type L‐DEX YL and its K151A and D180A mutants with its typical substrate, L‐2‐chloropropionate, were constructed by docking simulation. Subsequently, molecular dynamics (MD) and ab initio fragment molecular orbital (FMO) calculations of the complexes were performed. The ab initio FMO method was applied at the MP2/6‐31G level to estimate interfragment interaction energies. K151 and D180, which are experimentally shown to be important for enzyme activity, interact particularly strongly with L‐2‐chloropropionate, catalytic water, nucleophile (D10), and with each other. Our calculations suggest that K151 stabilizes substrate orientation and balances the charge around the active site, while D180 stabilizes the rotation of the nucleophile D10, fixes catalytic water around D10, and prevents K151 from approaching D10. Further, D180 may activate catalytic water on its own or with K151, S175, and N177. These roles are consistent with the previous results. Thus, MD and ab initio FMO calculations are powerful tools for the elucidation of the mechanism of enzymatic reaction at the molecular level and can be applied to other catalytically important residues. The results obtained here will play an important role in elucidating the reaction mechanism and rational design of L‐DEX YL with improved enzymatic activity or substrate specificity. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
Survival responses of human embryonic stem cells to DNA damage
Authors: Filion Tera M. , Qiao Meng , Ghule Prachi N. , Mandeville Matthew , van Wijnen Andre J. , Stein Janet L. , Lian Jane B. , Altieri Dario C. , Stein Gary S. 
Published: April 2009

AbstractPluripotent human embryonic stem (hES) cells require mechanisms to maintain genomic integrity in response to DNA damage that could compromise competency for lineage‐commitment, development, and tissue‐renewal. The mechanisms that protect the genome in rapidly proliferating hES cells are minimally understood. Human ES cells have an abbreviated cell cycle with a very brief G1 period suggesting that mechanisms mediating responsiveness to DNA damage may deviate from those in somatic cells. Here, we investigated how hES cells react to DNA damage induced by ionizing radiation (IR) and whether genomic insult evokes DNA repair pathways and/or cell death. We find that hES cells respond to DNA damage by rapidly inducing Caspase‐3 and ‐8, phospho‐H2AX foci, phosphorylation of p53 on Ser15 and p21 mRNA levels, as well as concomitant cell cycle arrest in G2 based on Ki67 staining and FACS analysis. Unlike normal somatic cells, hES cells and cancer cells robustly express the anti‐apoptotic protein Survivin, consistent with the immortal growth phenotype. SiRNA depletion of Survivin diminishes hES survival post‐irradiation. Thus, our findings provide insight into pathways and processes that are activated in human embryonic stem cells upon DNA insult to support development and tissue regeneration. J. Cell. Physiol. 220: 586–592, 2009. © 2009 Wiley‐Liss, Inc.
Mercury(II) removal using polymer inclusion membranes containing Cyanex 471X
Authors: Mercader‐Trejo Flora E , Rodríguez de San Miguel Eduardo , de Gyves Josefina 
Published: April 2009

AbstractBACKGROUND: Regulatory controls to limit mercury emissions in waters have impacted on the development of membrane extraction‐based methodologies for its separation. The specific advantages (effective carrier immobilization, easy preparation, versatility, and good mechanical properties) of polymer inclusion membranes (PIMs) make them suitable for this purpose. In this work a novel procedure using PIMs for mercury separation with a commercial available extractant (Cyanex 471X) is described and evaluated through the determination of the efficiency parameters (permeability, selectivity, stability) and membrane characterization.RESULTS: Using a membrane composed of 30% cellulose triacetate (CTA), 60% 2‐nitrophenyl octyl ether (NPOE), and 10% w/w Cyanex 471X a 0.1 mmol dm−3 Hg(II) solution prepared in 0.01 mol dm−3 HCl was transported to a 0.05 mol dm−3 NaCl solution at pH 12.3 with permeability values in the feed and strip phases of 0.25 and 0.15 cm min−1, respectively. A diffusive Fickian‐type mechanism was inferred from the results. High separation factors ranging between 2 and 5900, less than 11% of competing metal ions transported, active transport of the metal ion and a successful reuse of the PIM were achieved.CONCLUSION: Optimized PIMs using Cyanex 471X represent an interesting alternative for Hg(II) removal from waters showing high efficiency factors and easy implementation. Copyright © 2009 Society of Chemical Industry
Organization of the vitelline envelope in ovarian follicles of Torpedo marmorata Risso, 1810 (Elasmobranchii: Torpediniformes)
Authors: Prisco Marina , Del Giudice Giuseppina , Agnese Marisa , Ricchiari Loredana , Campanella Chiara , Andreuccetti Piero 
Published: April 2009

AbstractIn Torpedo marmorata, the vitelline envelope (VE), an extracellular envelope surrounding the growing oocyte, consists of fibrils and amorphous materials that are deposited in the perivitelline space starting from the initial steps of oocyte growth. SDS‐PAGE analysis of the isolated and purified VE reveals that it consists of different glycoproteins. Furthermore, our investigations showed that the 120 and 66 kDa glycoproteins are positive to an antibody directed against gp69/64 of the Xenopus laevis VE and are synthesized under the control of 17β‐estradiol in the liver, that, together follicle cells and the oocyte, is the biosynthetic site of VE components. J. Exp. Zool. (Mol. Dev. Evol.) 312B:714–721, 2009. © 2009 Wiley‐Liss, Inc.
Grünbaum colorings of toroidal triangulations
Authors: Albertson Michael O. , Alpert Hannah , belcastro sarah‐marie , Haas Ruth 
Published: April 2009

AbstractWe prove that if G is a triangulation of the torus and χ(G)≠5, then there is a 3‐coloring of the edges of G so that the edges bounding every face are assigned three different colors. © 2009 Wiley Periodicals, Inc. J Graph Theory 63: 68–81, 2010
On the conjecture for certain Laplacian integral spectrum of graphs
Authors: Das Kinkar Ch. , Lee Sang‐Gu , Cheon Gi‐Sang 
Published: April 2009

AbstractLet G be a simple graph of order n with Laplacian spectrum {λn, λn−1, …, λ1} where 0=λn≤λn−1≤⋅≤λ1. If there exists a graph whose Laplacian spectrum is S={0, 1, …, n−1}, then we say that S is Laplacian realizable. In 6, Fallat et al. posed a conjecture that S is not Laplacian realizable for any n≥2 and showed that the conjecture holds for n≤11, n is prime, or n=2, 3(mod4). In this article, we have proved that (i) if G is connected and λ1=n−1 then G has diameter either 2 or 3, and (ii) if λ1=n−1 and λn−1=1 then both G and Ḡ, the complement of G, have diameter 3. © 2009 Wiley Periodicals, Inc. J Graph Theory 63: 106–113, 2010