bluuebunny/crossref_metadata_2025_split huggingface dataset:
Homozygous deletions within the 11q13 cervical cancer tumor‐suppressor locus in radiation‐induced, neoplastically transformed human hybrid cells
Authors: Mendonca Marc S. , Farrington Daphne L. , Mayhugh Brendan M. , Qin Yan , Temples Toni , Comerford Kathleen , Chakrabarti Rita , Zainabadi Kayvan , Redpath J. Leslie , Stanbridge Eric J. , Srivatsan Eri S. 
Published: February 2004

AbstractStudies on nontumorigenic and tumorigenic human cell hybrids derived from the fusion of HeLa (a cervical cancer cell line) with GM00077 (a normal skin fibroblast cell line) have demonstrated “functional” tumor‐suppressor activity on chromosome 11. It has been shown that several of the neoplastically transformed radiation‐induced hybrid cells called GIMs (gamma ray induced mutants), isolated from the nontumorigenic CGL1 cells, have lost one copy of the fibroblast chromosome 11. We hypothesized, therefore, that the remaining copy of the gene might be mutated in the cytogenetically intact copy of fibroblast chromosome 11. Because a cervical cancer tumor suppressor locus has been localized to chromosome band 11q13, we performed deletion‐mapping analysis of eight different GIMs using a total of 32 different polymorphic and microsatellite markers on the long arm (q arm) of chromosome 11. Four irradiated, nontumorigenic hybrid cell lines, called CONs, were also analyzed. Allelic deletion was ascertained by the loss of a fibroblast allele in the hybrid cell lines. The analysis confirmed the loss of a fibroblast chromosome 11 in five of the GIMs. Further, homozygous deletion (complete loss) of chromosome band 11q13 band sequences, including that of D11S913, was observed in two of the GIMs. Detailed mapping with genomic sequences localized the homozygous deletion to a 5.7‐kb interval between EST AW167735 and EST F05086. Southern blot hybridization using genomic DNA probes from the D11S913 locus confirmed the existence of homozygous deletion in the two GIM cell lines. Additionally, PCR analysis showed a reduction in signal intensity for a marker mapped 31 kb centromeric of D11S913 in four other GIMs. Finally, Northern blot hybridization with the genomic probes revealed the presence of a novel >15‐kb transcript in six of the GIMs. These transcripts were not observed in the nontumorigenic hybrid cell lines. Because the chromosome 11q13 band deletions in the tumorigenic hybrid cell lines overlapped with the minimal deletion in cervical cancer, the data suggest that the same gene may be involved in the development of cervical cancer and in radiation‐induced carcinogenesis. We propose that a gene localized in proximity to the homozygous deletion is the candidate tumor‐suppressor gene. © 2004 Wiley‐Liss, Inc.
Amplification of the TOP2A gene does not predict high levels of topoisomerase II alpha protein in human breast tumor samples
Authors: Mueller Rosemary E. , Parkes Robert K. , Andrulis Irene , O'Malley Frances P. 
Published: February 2004

AbstractRecent clinical trials have suggested that patients whose breast tumors overexpress HER2 may derive particular benefit from anthracycline‐containing chemotherapy compared to that without anthracycline. It has been proposed that the HER2 gene amplification reported in these tumors might mask an underlying TOP2A gene amplification that occurs frequently and concurrently with HER2 amplification. Topoisomerase II alpha, encoded by TOP2A, is a direct molecular target of anthracycline drug action and is potentially useful as a predictive marker of response to anthracycline therapy for breast cancer. In this study, we examined whether TOP2A gene amplification is an appropriate marker for identifying breast tumors expressing high levels of topoisomerase II alpha. We determined topoisomerase II alpha protein expression by immunohistochemistry in 81 human breast tumors in relation to HER2 and TOP2A gene copy numbers analyzed by fluorescence in situ hybridization, histologic grade, cell proliferation fraction measured by MIB‐1 expression, and HER2 protein expression determined by immunohistochemistry. The results showed no correlation between TOP2A gene copy number and topoisomerase II alpha protein expression levels in breast tumors, in contrast to the analogous situation for HER2 gene amplification and HER2 immunohistochemistry. Our results suggest that TOP2A gene amplification in breast tumors does not predict high expression of topoisomerase II alpha protein. © 2004 Wiley‐Liss, Inc.
Method for making selective lesions of the hippocampus in macaque monkeys using NMDA and a longitudinal surgical approach
Authors: Hampton Robert R. , Buckmaster Cindy A. , Anuszkiewicz‐Lundgren Dawn , Murray Elisabeth A. 
Published: February 2004

AbstractWe describe a method for making selective lesions of the hippocampus in macaque monkeys, using a magnetic resonance imaging (MRI)‐guided stereotaxic approach in which the excitotoxin N‐methyl‐D‐aspartic acid (NMDA) is injected at intervals along a single needle track that extends longitudinally through the rostrocaudal extent of the hippocampus. Procedures were conducted on six rhesus monkeys (Macaca mulatta) and were assessed with either in vivo MRI (n = 3) or postmortem microscopic examination of the tissue after standard histological processing of the brains (n = 3). Based on our extensive experience with the standard stereotaxic procedure in which ibotenic acid (IBO) is injected via the dorsal approach, we report that the new method provides a viable and potentially advantageous alternative to the standard procedure. First, the longitudinal approach combined with N‐methyl‐D‐aspartic acid (NMDA) injections increases the reliability and efficacy of hippocampal excitotoxic lesions, probably by limiting the leakage of injectant into the ventricles. Second, the present procedure led to more rapid postoperative recovery compared with that after the standard procedure. Third, because the new method requires fewer needle penetrations than the standard method, it most likely reduces the chances of infarction in extrahippocampal tissue. Finally, the new surgical approach may provide a mechanism for infusing agents into the hippocampus from a single cannula. Published 2003 Wiley‐Liss, Inc.
Expression of different isoforms of protein kinase C in the rat hippocampus after pilocarpine‐induced status epilepticus with special reference to CA1 area and the dentate gyrus
Authors: Tang F.R. , Lee W.L. , Gao H. , Chen Y. , Loh Y.T. , Chia S.C. 
Published: February 2004

AbstractAt 4 h during pilocarpine‐induced status epilepticus (DPISE) in rat, protein kinase C (PKC)β1, PKCβ2, and PKCγ were induced at the border between the stratum oriens and alveus (O/A border) of CA1 in the hippocampus. Induced PKCγ was colocalized with metabotropic glutamate receptor α (mGluRα). By intracerebroventricular injection of mGluR1α antagonists, (RS)‐1‐aminoindan‐1,5‐dicarboxylic acid (AIDA), PKCβ1, PKCβ2, and PKCγ immunoreactive products decreased dramatically; however, intracerebroventricular injection of saline did not change the expression of PKCβ1, PKCβ2, and PKCγ, suggesting that these three PKC isoforms might be involved in mGluR1α‐related excitoneurotoxicity. One day after pilocarpine‐induced status epilepticus (APISE), PKCδ was induced in microglial cells. At this time point, both PKCγ and PKCϵ immunopositive products decreased in the inner molecular layer of upper blade of the stratum granulosum. At 7–31 days APISE, induced PKCβ1, PKCδ, PKCη, and PKCζ positive astrocytes were demonstrated in all parts of hippocampus, suggesting that they may be involved in gliosis. By this time, both PKCγ and PKCϵ immunopositive products in the inner molecular layer had almost disappeared, suggesting that they may be involved in the inhibition of granule cells by controlling neurotransmitter release presynaptically in the dentate gyrus of normal rats. © 2003 Wiley‐Liss, Inc.
Excitotoxic lesions of the pre‐ and parasubiculum disrupt the place fields of hippocampal pyramidal cells
Authors: Liu Ping , Jarrard Leonard E. , Bilkey David K. 
Published: February 2004

AbstractTo determine what influence the pre‐ and parasubiculum regions of the hippocampal formation have on neural representations within the dorsal hippocampus, single‐unit recordings were made as rats with bilateral ibotenic acid lesions centered on the former regions (n = 4) or control surgeries (n = 3) foraged freely. Spatial firing specificity was measured using an information content procedure. Cells from lesioned animals (n = 57) provided significantly less spatial information than cells from control animals (n = 44). Whereas some degree of location‐related activity (place fields) was observed in 98% of neurons recorded from control animals, it was observed in only 65% of the neurons from lesioned animals. The spatial resolution of the intact place fields appeared to be compromised in lesioned animals as a result of their having a higher firing rate outside the place field. These findings indicate that the pre‐ and parasubiculum regions have a major role in maintaining the specificity of the place field firing of hippocampal pyramidal cells. Since previous data indicate that these lesioned animals displayed delay‐dependent deficits in spatial tasks, these findings also suggest that a disruption in place field activity may be a causal factor in this spatial memory deficit. © 2003 Wiley‐Liss, Inc.
Neural network‐based prediction of transmembrane β‐strand segments in outer membrane proteins
Authors: Gromiha M. Michael , Ahmad Shandar , Suwa Makiko 
Published: February 2004

AbstractPrediction of transmembrane β‐strands in outer membrane proteins (OMP) is one of the important problems in computational chemistry and biology. In this work, we propose a method based on neural networks for identifying the membrane‐spanning β‐strands. We introduce the concept of “residue probability” for assigning residues in transmembrane β‐strand segments. The performance of our method is evaluated with single‐residue accuracy, correlation, specificity, and sensitivity. Our predicted segments show a good agreement with experimental observations with an accuracy level of 73% solely from amino acid sequence information. Further, the predictive power of N‐ and C‐terminal residues in each segments, number of segments in each protein, and the influence of cutoff probability for identifying membrane‐spanning β‐strands will be discussed. We have developed a Web server for predicting the transmembrane β‐strands from the amino acid sequence, and the prediction results are available at http://psfs.cbrc.jp/tmbeta‐net/. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 762–767, 2004
Enthalpies of formation from B3LYP calculations
Authors: Winget Paul , Clark Timothy 
Published: February 2004

AbstractWe have calculated the geometries, energies, and normal vibrations of 845 compounds containing the elements H, C, N, O, F, Al, Si, P, S, and Cl using hybrid density functional theory in order to investigate the accuracy of atom‐additive schemes for predicting enthalpies of formation at 298 K. The results give a more realistic estimate of the accuracy of density functional calculations than some overoptimistic earlier correlations. We have also calculated atom‐additive schemes for the zero‐point energies and enthalpic corrections to the energies. Remarkably, it is not important to include the vibrational or rotational contributions, which can be estimated well within a purely Born‐Oppenheimer regression model. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 725–733, 2004
Performance of the Harris functional for extended basis sets at the Hartree–Fock and density functional levels
Authors: Cullen John 
Published: February 2004

AbstractThe Harris functional is a noniterative variational procedure that uses an input charge density to produce an energy that is surprisingly accurate compared to the converged Kohn–Sham self‐consistent result. We adapted and generalized this functional for the Hartree–Fock closed‐ and open‐shell cases as well as examined its use for hybrid density functional methods such as B3LYP. Analysis of extended basis set calculations shows that at the B3LYP level an input density formed from a double zeta + polarization orbital basis is accurate enough to reproduce the energy of triple zeta + double polarization + diffuse orbital basis. For large molecules this translates into a computational speed that can be an order of magnitude faster. In the case of Hartree–Fock calculations a “bootstrapping technique” that employs successive applications of the Harris functional can further reduce computational times while retaining sufficient accuracy. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 637–648, 2004
Stochastic search for isomers on a quantum mechanical surface
Authors: Saunders Martin 
Published: February 2004

AbstractIn studying molecules with unusual bonding and structures, it is desirable to be able to find all the isomers that are minima on the energy surface. A stochastic search procedure is described for seeking all the isomers on a surface defined by quantum mechanical calculations involving random kicks followed by optimization. It has been applied to searching for singlet structures for C6 using the restricted Hartree–Fock/6‐311G basis set. In addition to the linear chain and ring previously investigated, 11 additional structures (A–K) were located at this level. These provide a basis for discussing qualitative bonding motifs for this carbon cluster. The application of a similar idea to searching for transition states is discussed. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 621–626, 2004
A multilayered approach to approximating solute polarization
Authors: Maurer Richard I. , Reynolds Christopher A. 
Published: February 2004

AbstractA hybrid multilayered “ONIOM”‐type approach to solvation is presented in which the basic free energy of hydration is taken from the Poisson Boltzmann method and the contribution to the solute polarization is taken from a quantum mechanical implementation of the Born method. The method has been tested on the 52 neutral molecules used in the AM1–SM2 parameterization, and the polarized continuum method is taken as the standard by which the results are assessed. Regression analysis shows that the method gives a small improvement over the standard Poisson Boltzmann method or a dramatic improvement over the Born method. The system presented here represents one of the more straightforward applications of the multilayered approach to solvation, but other more sophisticated approaches are discussed. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 627–631, 2004
SVMtm: Support vector machines to predict transmembrane segments
Authors: Yuan Zheng , Mattick John S. , Teasdale Rohan D. 
Published: February 2004

AbstractA new method has been developed for prediction of transmembrane helices using support vector machines. Different coding schemes of protein sequences were explored, and their performances were assessed by crossvalidation tests. The best performance method can predict the transmembrane helices with sensitivity of 93.4% and precision of 92.0%. For each predicted transmembrane segment, a score is given to show the strength of transmembrane signal and the prediction reliability. In particular, this method can distinguish transmembrane proteins from soluble proteins with an accuracy of ∼99%. This method can be used to complement current transmembrane helix prediction methods and can be used for consensus analysis of entire proteomes. The predictor is located at http://genet.imb.uq.edu.au/predictors/SVMtm. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 632–636, 2004
Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration, and structural properties
Authors: Patra Michael , Karttunen Mikko 
Published: February 2004

AbstractIn this article we compare different force fields that are widely used (Gromacs, Charmm‐22/x‐Plor, Charmm‐27, Amber‐1999, OPLS‐AA) in biophysical simulations containing aqueous NaCl. We show that the uncertainties of the microscopic parameters of, in particular, sodium, and, to a lesser extent, chloride, translate into large differences in the computed radial‐distribution functions. This uncertainty reflect the incomplete experimental knowledge of the structural properties of ionic aqueous solutions at finite molarity. We discuss possible implications on the computation of potential of mean force and effective potentials. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 678–689, 2004
A generating equation for mixing rules and two new mixing rules for interatomic potential energy parameters
Authors: Al‐Matar Ali Khalaf , Rockstraw David A. 
Published: February 2004

AbstractA generating equation for the mixing rules of interatomic potential energy parameters is proposed. It is demonstrated that this equation can, indeed, reproduce many popular mixing rules. A weighting matrix is used with the generating equation. This weighting matrix approach is superior to the present status of mixing rule development. A systematic framework is given for devising new mixing rules and/or comparing them. Two new mixing rules, which are more accurate than the available rules in the literature, are proposed. These rules are capable of reproducing the collision diameter and well‐depth parameters for the binary values of noble gases to within their experimental uncertainties. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 660–668, 2004
Study of proton adsorption at heterogeneous oxide/electrolyte interface. Prediction of the surface potential using Monte Carlo simulations and 1‐pK approach
Authors: Zarzycki P. , Charmas R. , Szabelski P. 
Published: February 2004

AbstractAdsorption of protons on a heterogeneous solid surface is modeled using the Monte Carlo (MC) simulation method. The surface of an oxide is assumed to consist of adsorption sites with pK assigned according to a quasi‐Gaussian distribution. The influence of the electrostatic interactions combined with the energetic heterogeneity of the surface is examined and the MC results are compared with the predictions of the analytical 1‐pK approach. The surface potential behavior is examined using both “experimental” MC results and “theoretical” results obtained from the application of 1‐pK model. The results are compared qualitatively with experimental determination of the surface potential of metal oxide surfaces. They confirm that the relation between the surface potential and the pH of bulk solution should not be described by the Nernst equation but by the equation with the parameter linearly reducing Nerstian potential. The values of this parameter are examined with respect to degree of surface energetic heterogeneity and site density of the surface. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 704–711, 2004
Importance of solvent accessibility and contact surfaces in modeling side‐chain conformations in proteins
Authors: Eyal Eran , Najmanovich Rafael , Mcconkey Brendan J. , Edelman Marvin , Sobolev Vladimir 
Published: February 2004

AbstractContact surface area and chemical properties of atoms are used to concurrently predict conformations of multiple amino acid side chains on a fixed protein backbone. The combination of surface complementarity and solvent‐accessible surface accounts for van der Waals forces and solvation free energy. The scoring function is particularly suitable for modeling partially buried side chains. Both iterative and stochastic searching approaches are used. Our programs (Sccomp‐I and Sccomp‐S), with relatively fast execution times, correctly predict χ1 angles for 92–93% of buried residues and 82–84% for all residues, with an RMSD of ∼1.7 Å for side chain heavy atoms. We find that the differential between the atomic solvation parameters and the contact surface parameters (including those between noncomplementary atoms) is positive; i.e., most protein atoms prefer surface contact with other protein atoms rather than with the solvent. This might correspond to the driving force for maximizing packing of the protein. The influence of the crystal packing, completeness of rotamer library and precise positioning of Cβ atoms on the accuracy of side‐chain prediction are examined. The Sccomp‐S and Sccomp‐I programs can be accessed through the Web (http://sgedg.weizmann.ac.il/sccomp.html) and are available for several platforms. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 712–724, 2004
Numerical examination of performance of some exchange‐correlation functionals for molecules containing heavy elements
Authors: Wang Fan , Li Lemin 
Published: February 2004

AbstractThe performance of 17 exchange‐correlation functionals for molecules containing heavy elements are numerically examined through four‐component relativistic density DFT calculations. The examined functionals show the similar accuracy as they do for the molecules containing light elements only except for bond lengths. LDA and OP86 produce good results for bond lengths and frequencies but bad bond energies. Different functionals do not show much different performance for bond energies except LDA. BP86 and GP86 produce results with average accuracy while LYP does not perform well. Although encouraging results are obtained with functional B97GGA‐1, other heavily parameterized and meta‐GGA functionals do not produce impressive results. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 669–677, 2004
Solvent effects on glycine II. Water‐assisted tautomerization
Authors: Balta Bülent , Aviyente Viktorya 
Published: February 2004

AbstractThe water‐assisted tautomerization of glycine has been investigated at the B3LYP/6‐31+G** level using supermolecules containing up to six water molecules as well as considering a 1:1 glycine–water complex embedded in a continuum. The conformations of the tautomers in this mechanism do not display an intramolecular H bond, instead the functional groups are bridged by a water molecule. The replacement of the intramolecular H bond by the bridging water reduces the polarity of the NH bond in the zwitterion and increases that of the OH bond in the neutral, stabilizing the zwitterion. Both the charge transfer effects and electrostatic interactions stabilize the nonintramolecularly H‐bonded zwitterion conformer over the intramolecularly hydrogen bonded one. The nonintramolecularly H‐bonded neutral is favored only by charge transfer effects. Although there is no strong evidence whether the intramolecularly hydrogen bonded or non hydrogen bonded structures are favored in the bulk solution represented as a dielectric continuum, it is likely that the latter species are more stable. The free energy of activation of the water‐assisted mechanism is higher than the intramolecular proton transfer channel. However, when the presumably higher conformational energy of the zwitterion reacting in the intramolecular mechanism is taken into account, both mechanisms are observed to compete. The various conformers of the neutral glycine may form via multiple proton transfer reactions through several water molecules instead of a conformational rearrangement. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 690–703, 2004
Simple algorithm for isothermal–isobaric molecular dynamics
Authors: Stern Harry A. 
Published: February 2004

AbstractWe review principles of non‐Hamiltonian statistical mechanics and present a new set of equations and integration algorithm for isothermal–isobaric dynamics. The chief advantage of the present scheme is that it is somewhat simpler than previous methods. We perform numerical simulations to test the accuracy of the algorithm and compare its stability to that of a “gold standard,” a symplectic integrator for Hamiltonian dynamics of the same system. The stability of the isothermal–isobaric algorithm is comparable to the stability of the symplectic integrator. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 749–761, 2004